From 54f24930180861cf649c0f05669e9e9dc1a7bb7d Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Tue, 28 Nov 2017 14:53:44 -0700 Subject: [PATCH 001/302] Added ReductionView to Kokkos ReaxFF --- src/KOKKOS/fix_qeq_reax_kokkos.cpp | 74 ++++++------- src/KOKKOS/fix_qeq_reax_kokkos.h | 3 + src/KOKKOS/pair_kokkos.h | 15 ++- src/KOKKOS/pair_reaxc_kokkos.cpp | 169 +++++++++++++++++++++++------ src/KOKKOS/pair_reaxc_kokkos.h | 11 ++ 5 files changed, 199 insertions(+), 73 deletions(-) diff --git a/src/KOKKOS/fix_qeq_reax_kokkos.cpp b/src/KOKKOS/fix_qeq_reax_kokkos.cpp index 5d2f6a0438..764b2f9191 100644 --- a/src/KOKKOS/fix_qeq_reax_kokkos.cpp +++ b/src/KOKKOS/fix_qeq_reax_kokkos.cpp @@ -254,12 +254,18 @@ void FixQEqReaxKokkos::pre_force(int vflag) k_t.template modify(); k_t.template sync(); + if (neighflag != FULL) + red_o = Kokkos::Experimental::create_reduction_view<> (k_o.d_view); // allocate duplicated memory + // 1st cg solve over b_s, s cg_solve1(); // 2nd cg solve over b_t, t cg_solve2(); + if (neighflag != FULL) + red_o = decltype(red_o)(); // free duplicated memory + // calculate_Q(); calculate_q(); @@ -494,13 +500,9 @@ void FixQEqReaxKokkos::cg_solve1() Kokkos::parallel_for(inum,sparse12_functor); if (neighflag != FULL) { Kokkos::parallel_for(Kokkos::RangePolicy(nlocal,nlocal+atom->nghost),*this); - if (neighflag == HALF) { - FixQEqReaxKokkosSparse13Functor sparse13_functor(this); - Kokkos::parallel_for(inum,sparse13_functor); - } else { - FixQEqReaxKokkosSparse13Functor sparse13_functor(this); - Kokkos::parallel_for(inum,sparse13_functor); - } + FixQEqReaxKokkosSparse13Functor sparse13_functor(this); + Kokkos::parallel_for(inum,sparse13_functor); + Kokkos::Experimental::contribute(k_o.d_view, red_o); } else { Kokkos::parallel_for(Kokkos::TeamPolicy (inum, teamsize), *this); } @@ -548,18 +550,14 @@ void FixQEqReaxKokkos::cg_solve1() Kokkos::parallel_for(inum,sparse22_functor); if (neighflag != FULL) { Kokkos::parallel_for(Kokkos::RangePolicy(nlocal,nlocal+atom->nghost),*this); - if (neighflag == HALF) { - FixQEqReaxKokkosSparse23Functor sparse23_functor(this); - Kokkos::parallel_for(inum,sparse23_functor); - } else { - FixQEqReaxKokkosSparse23Functor sparse23_functor(this); - Kokkos::parallel_for(inum,sparse23_functor); - } + red_o.reset_except(d_o); + FixQEqReaxKokkosSparse23Functor sparse23_functor(this); + Kokkos::parallel_for(inum,sparse23_functor); + Kokkos::Experimental::contribute(k_o.d_view, red_o); } else { Kokkos::parallel_for(Kokkos::TeamPolicy (inum, teamsize), *this); } - if (neighflag != FULL) { k_o.template modify(); k_o.template sync(); @@ -625,13 +623,10 @@ void FixQEqReaxKokkos::cg_solve2() Kokkos::parallel_for(inum,sparse32_functor); if (neighflag != FULL) { Kokkos::parallel_for(Kokkos::RangePolicy(nlocal,nlocal+atom->nghost),*this); - if (neighflag == HALF) { - FixQEqReaxKokkosSparse33Functor sparse33_functor(this); - Kokkos::parallel_for(inum,sparse33_functor); - } else { - FixQEqReaxKokkosSparse33Functor sparse33_functor(this); - Kokkos::parallel_for(inum,sparse33_functor); - } + red_o.reset_except(d_o); + FixQEqReaxKokkosSparse33Functor sparse33_functor(this); + Kokkos::parallel_for(inum,sparse33_functor); + Kokkos::Experimental::contribute(k_o.d_view, red_o); } else { Kokkos::parallel_for(Kokkos::TeamPolicy (inum, teamsize), *this); } @@ -679,13 +674,10 @@ void FixQEqReaxKokkos::cg_solve2() Kokkos::parallel_for(inum,sparse22_functor); if (neighflag != FULL) { Kokkos::parallel_for(Kokkos::RangePolicy(nlocal,nlocal+atom->nghost),*this); - if (neighflag == HALF) { - FixQEqReaxKokkosSparse23Functor sparse23_functor(this); - Kokkos::parallel_for(inum,sparse23_functor); - } else { - FixQEqReaxKokkosSparse23Functor sparse23_functor(this); - Kokkos::parallel_for(inum,sparse23_functor); - } + red_o.reset_except(d_o); + FixQEqReaxKokkosSparse23Functor sparse23_functor(this); + Kokkos::parallel_for(inum,sparse23_functor); + Kokkos::Experimental::contribute(k_o.d_view, red_o); } else { Kokkos::parallel_for(Kokkos::TeamPolicy (inum, teamsize), *this); } @@ -797,8 +789,8 @@ template KOKKOS_INLINE_FUNCTION void FixQEqReaxKokkos::sparse13_item(int ii) const { - // The q array is atomic for Half/Thread neighbor style - Kokkos::View::value> > a_o = d_o; + // The q array is duplicated for OpenMP, atomic for CUDA, and neither for Serial + auto a_o = red_o.access(); const int i = d_ilist[ii]; if (mask[i] & groupbit) { @@ -806,9 +798,9 @@ void FixQEqReaxKokkos::sparse13_item(int ii) const for(int jj = d_firstnbr[i]; jj < d_firstnbr[i] + d_numnbrs[i]; jj++) { const int j = d_jlist(jj); tmp += d_val(jj) * d_s[j]; - a_o[j] += d_val(jj) * d_s[i]; + a_o(j) += d_val(jj) * d_s[i]; } - a_o[i] += tmp; + a_o(i) += tmp; } } @@ -849,8 +841,8 @@ template KOKKOS_INLINE_FUNCTION void FixQEqReaxKokkos::sparse23_item(int ii) const { - // The q array is atomic for Half/Thread neighbor style - Kokkos::View::value> > a_o = d_o; + // The q array is duplicated for OpenMP, atomic for CUDA, and neither for Serial + auto a_o = red_o.access(); const int i = d_ilist[ii]; if (mask[i] & groupbit) { @@ -858,9 +850,9 @@ void FixQEqReaxKokkos::sparse23_item(int ii) const for(int jj = d_firstnbr[i]; jj < d_firstnbr[i] + d_numnbrs[i]; jj++) { const int j = d_jlist(jj); tmp += d_val(jj) * d_d[j]; - a_o[j] += d_val(jj) * d_d[i]; + a_o(j) += d_val(jj) * d_d[i]; } - a_o[i] += tmp; + a_o(i) += tmp; } } @@ -908,8 +900,8 @@ template KOKKOS_INLINE_FUNCTION void FixQEqReaxKokkos::sparse33_item(int ii) const { - // The q array is atomic for Half/Thread neighbor style - Kokkos::View::value> > a_o = d_o; + // The q array is duplicated for OpenMP, atomic for CUDA, and neither for Serial + auto a_o = red_o.access(); const int i = d_ilist[ii]; if (mask[i] & groupbit) { @@ -917,9 +909,9 @@ void FixQEqReaxKokkos::sparse33_item(int ii) const for(int jj = d_firstnbr[i]; jj < d_firstnbr[i] + d_numnbrs[i]; jj++) { const int j = d_jlist(jj); tmp += d_val(jj) * d_t[j]; - a_o[j] += d_val(jj) * d_t[i]; + a_o(j) += d_val(jj) * d_t[i]; } - a_o[i] += tmp; + a_o(i) += tmp; } } diff --git a/src/KOKKOS/fix_qeq_reax_kokkos.h b/src/KOKKOS/fix_qeq_reax_kokkos.h index 9014e20b8e..dd7b4073c2 100644 --- a/src/KOKKOS/fix_qeq_reax_kokkos.h +++ b/src/KOKKOS/fix_qeq_reax_kokkos.h @@ -22,6 +22,7 @@ FixStyle(qeq/reax/kk/host,FixQEqReaxKokkos) #ifndef LMP_FIX_QEQ_REAX_KOKKOS_H #define LMP_FIX_QEQ_REAX_KOKKOS_H +#include #include "fix_qeq_reax.h" #include "kokkos_type.h" #include "neigh_list.h" @@ -192,6 +193,8 @@ class FixQEqReaxKokkos : public FixQEqReax { HAT::t_ffloat_2d h_s_hist, h_t_hist; typename AT::t_ffloat_2d_randomread r_s_hist, r_t_hist; + Kokkos::Experimental::ReductionView red_o; + void init_shielding_k(); void init_hist(); void allocate_matrix(); diff --git a/src/KOKKOS/pair_kokkos.h b/src/KOKKOS/pair_kokkos.h index f0e357270c..c8e926a721 100644 --- a/src/KOKKOS/pair_kokkos.h +++ b/src/KOKKOS/pair_kokkos.h @@ -19,9 +19,10 @@ #define LMP_PAIR_KOKKOS_H #include "Kokkos_Macros.hpp" +#include "Kokkos_Vectorization.hpp" +#include "Kokkos_ReductionView.hpp" #include "pair.h" #include "neigh_list_kokkos.h" -#include "Kokkos_Vectorization.hpp" namespace LAMMPS_NS { @@ -58,6 +59,18 @@ struct AtomicF { enum {value = Kokkos::Atomic|Kokkos::Unmanaged}; }; +// Determine memory traits for force array +// Do atomic trait when running HALFTHREAD neighbor list style +template +struct AtomicDup { + enum {value = Kokkos::Experimental::ReductionNonAtomic}; +}; + +template<> +struct AtomicDup { + enum {value = Kokkos::Experimental::ReductionAtomic}; +}; + //Specialisation for Neighborlist types Half, HalfThread, Full template struct PairComputeFunctor { diff --git a/src/KOKKOS/pair_reaxc_kokkos.cpp b/src/KOKKOS/pair_reaxc_kokkos.cpp index d5f83f4537..79d9241ea4 100644 --- a/src/KOKKOS/pair_reaxc_kokkos.cpp +++ b/src/KOKKOS/pair_reaxc_kokkos.cpp @@ -711,6 +711,15 @@ void PairReaxCKokkos::compute(int eflag_in, int vflag_in) d_neighbors = k_list->d_neighbors; d_ilist = k_list->d_ilist; + // allocate duplicated memory + if (neighflag != FULL) { + dup_f = Kokkos::Experimental::create_reduction_view<>(f); + dup_eatom = Kokkos::Experimental::create_reduction_view<>(v_eatom); + dup_vatom = Kokkos::Experimental::create_reduction_view<>(v_vatom); + dup_dDeltap_self = Kokkos::Experimental::create_reduction_view<>(d_dDeltap_self); + dup_total_bo = Kokkos::Experimental::create_reduction_view<>(d_total_bo); + } + if (eflag_global) { for (int i = 0; i < 14; i++) pvector[i] = 0.0; @@ -802,7 +811,7 @@ void PairReaxCKokkos::compute(int eflag_in, int vflag_in) if (neighflag == HALF) Kokkos::parallel_for(Kokkos::RangePolicy >(0,ignum),*this); else if (neighflag == HALFTHREAD) - Kokkos::parallel_for(Kokkos::RangePolicy >(0,ignum),*this); + Kokkos::parallel_for(Kokkos::RangePolicy >(0,ignum),*this); else //(neighflag == FULL) Kokkos::parallel_for(Kokkos::RangePolicy(0,ignum),*this); @@ -817,14 +826,32 @@ void PairReaxCKokkos::compute(int eflag_in, int vflag_in) if (resize_hb) maxhb++; resize = resize_bo || resize_hb; - if (resize) allocate_array(); + if (resize) { + allocate_array(); + if (neighflag != FULL) { + dup_dDeltap_self = Kokkos::Experimental::create_reduction_view<>(d_dDeltap_self); + dup_total_bo = Kokkos::Experimental::create_reduction_view<>(d_total_bo); + } + } } + // allocate duplicated memory + if (neighflag != FULL) { + dup_CdDelta = Kokkos::Experimental::create_reduction_view<>(d_CdDelta); + dup_Cdbo = Kokkos::Experimental::create_reduction_view<>(d_Cdbo); + dup_Cdbopi = Kokkos::Experimental::create_reduction_view<>(d_Cdbopi); + dup_Cdbopi2 = Kokkos::Experimental::create_reduction_view<>(d_Cdbopi2); + } + + // reduction over duplicated memory + if (neighflag != FULL) + Kokkos::Experimental::contribute(d_total_bo, dup_total_bo); // needed in BondOrder1 + // Bond order if (neighflag == HALF) { Kokkos::parallel_for(Kokkos::RangePolicy(0,ignum),*this); } else if (neighflag == HALFTHREAD) { - Kokkos::parallel_for(Kokkos::RangePolicy(0,ignum),*this); + Kokkos::parallel_for(Kokkos::RangePolicy(0,ignum),*this); } Kokkos::parallel_for(Kokkos::RangePolicy(0,ignum),*this); Kokkos::parallel_for(Kokkos::RangePolicy(0,ignum),*this); @@ -923,9 +950,29 @@ void PairReaxCKokkos::compute(int eflag_in, int vflag_in) pvector[7] = ev.ereax[8]; ev_all.evdwl += ev.ereax[8]; + // reduction over duplicated memory + if (neighflag != FULL) { + Kokkos::Experimental::contribute(d_dDeltap_self, dup_dDeltap_self); // needed in ComputeBond2 + Kokkos::Experimental::contribute(d_CdDelta, dup_CdDelta); // needed in ComputeBond2 + + Kokkos::Experimental::contribute(d_Cdbo, dup_Cdbo); // needed in UpdateBond, but also used in UpdateBond + Kokkos::Experimental::contribute(d_Cdbopi, dup_Cdbopi); // needed in UpdateBond, but also used in UpdateBond + Kokkos::Experimental::contribute(d_Cdbopi2, dup_Cdbopi2); // needed in UpdateBond, but also used in UpdateBond + dup_Cdbo.reset_except(d_Cdbo); + dup_Cdbopi.reset_except(d_Cdbopi); + dup_Cdbopi2.reset_except(d_Cdbopi2); + } + // Bond force if (neighflag == HALF) { Kokkos::parallel_for(Kokkos::RangePolicy >(0,ignum),*this); + + // reduction over duplicated memory + if (neighflag != FULL) { + Kokkos::Experimental::contribute(d_Cdbo, dup_Cdbo); // needed in ComputeBond2 + Kokkos::Experimental::contribute(d_Cdbopi, dup_Cdbopi); // needed in ComputeBond2 + Kokkos::Experimental::contribute(d_Cdbopi2, dup_Cdbopi2); // needed in ComputeBond2 + } if (evflag) Kokkos::parallel_reduce(Kokkos::RangePolicy >(0,ignum),*this,ev); else @@ -934,6 +981,13 @@ void PairReaxCKokkos::compute(int eflag_in, int vflag_in) pvector[0] += ev.evdwl; } else { //if (neighflag == HALFTHREAD) { Kokkos::parallel_for(Kokkos::RangePolicy >(0,ignum),*this); + + // reduction over duplicated memory + if (neighflag != FULL) { + Kokkos::Experimental::contribute(d_Cdbo, dup_Cdbo); // needed in ComputeBond2 + Kokkos::Experimental::contribute(d_Cdbopi, dup_Cdbopi); // needed in ComputeBond2 + Kokkos::Experimental::contribute(d_Cdbopi2, dup_Cdbopi2); // needed in ComputeBond2 + } if (evflag) Kokkos::parallel_reduce(Kokkos::RangePolicy >(0,ignum),*this,ev); else @@ -942,6 +996,10 @@ void PairReaxCKokkos::compute(int eflag_in, int vflag_in) pvector[0] += ev.evdwl; } + // reduction over duplicated memory + if (neighflag != FULL) + Kokkos::Experimental::contribute(f, dup_f); + if (eflag_global) { eng_vdwl += ev_all.evdwl; eng_coul += ev_all.ecoul; @@ -958,11 +1016,15 @@ void PairReaxCKokkos::compute(int eflag_in, int vflag_in) if (vflag_fdotr) pair_virial_fdotr_compute(this); if (eflag_atom) { + if (neighflag != FULL) + Kokkos::Experimental::contribute(v_eatom, dup_eatom); k_eatom.template modify(); k_eatom.template sync(); } if (vflag_atom) { + if (neighflag != FULL) + Kokkos::Experimental::contribute(v_vatom, dup_vatom); k_vatom.template modify(); k_vatom.template sync(); } @@ -970,6 +1032,19 @@ void PairReaxCKokkos::compute(int eflag_in, int vflag_in) if (fixspecies_flag) FindBondSpecies(); + // free duplicated memory + if (neighflag != FULL) { + dup_f = decltype(f)(); + dup_dDeltap_self = decltype(d_dDeltap_self)(); + dup_total_bo = decltype(d_total_bo)(); + dup_CdDelta = decltype(d_CdDelta)(); + dup_Cdbo = decltype(d_Cdbo)(); + dup_Cdbopi = decltype(d_Cdbopi)(); + dup_Cdbopi2 = decltype(d_Cdbopi2)(); + dup_eatom = decltype(v_eatom)(); + dup_vatom = decltype(v_vatom)(); + } + copymode = 0; } @@ -1010,7 +1085,8 @@ KOKKOS_INLINE_FUNCTION void PairReaxCKokkos::operator()(PairReaxComputeLJCoulomb, const int &ii, EV_FLOAT_REAX& ev) const { // The f array is atomic for Half/Thread neighbor style - Kokkos::View::value> > a_f = f; + //Kokkos::View::value> > a_f = f; + auto a_f = dup_f.access(); F_FLOAT powr_vdw, powgi_vdw, fn13, dfn13, exp1, exp2, etmp; F_FLOAT evdwl, fvdwl; @@ -1169,7 +1245,8 @@ KOKKOS_INLINE_FUNCTION void PairReaxCKokkos::operator()(PairReaxComputeTabulatedLJCoulomb, const int &ii, EV_FLOAT_REAX& ev) const { // The f array is atomic for Half/Thread neighbor style - Kokkos::View::value> > a_f = f; + //Kokkos::View::value> > a_f = f; + auto a_f = dup_f.access(); const int i = d_ilist[ii]; const X_FLOAT xtmp = x(i,0); @@ -1548,8 +1625,10 @@ void PairReaxCKokkos::operator()(PairReaxBuildListsHalf, if (d_resize_bo() || d_resize_hb()) return; - Kokkos::View::value> > a_dDeltap_self = d_dDeltap_self; - Kokkos::View::value> > a_total_bo = d_total_bo; + //Kokkos::View::value> > a_dDeltap_self = d_dDeltap_self; + //Kokkos::View::value> > a_total_bo = d_total_bo; + auto a_dDeltap_self = dup_dDeltap_self.access(); + auto a_total_bo = dup_total_bo.access(); const int i = d_ilist[ii]; const X_FLOAT xtmp = x(i,0); @@ -2236,10 +2315,14 @@ template KOKKOS_INLINE_FUNCTION void PairReaxCKokkos::operator()(PairReaxComputeMulti2, const int &ii, EV_FLOAT_REAX& ev) const { - Kokkos::View::value> > a_CdDelta = d_CdDelta; - Kokkos::View::value> > a_Cdbo = d_Cdbo; - Kokkos::View::value> > a_Cdbopi = d_Cdbopi; - Kokkos::View::value> > a_Cdbopi2 = d_Cdbopi2; + //Kokkos::View::value> > a_CdDelta = d_CdDelta; + //Kokkos::View::value> > a_Cdbo = d_Cdbo; + //Kokkos::View::value> > a_Cdbopi = d_Cdbopi; + //Kokkos::View::value> > a_Cdbopi2 = d_Cdbopi2; + auto a_CdDelta = dup_CdDelta.access(); + auto a_Cdbo = dup_Cdbo.access(); + auto a_Cdbopi = dup_Cdbopi.access(); + auto a_Cdbopi2 = dup_Cdbopi2.access(); const int i = d_ilist[ii]; const int itype = type(i); @@ -2390,9 +2473,13 @@ template KOKKOS_INLINE_FUNCTION void PairReaxCKokkos::operator()(PairReaxComputeAngular, const int &ii, EV_FLOAT_REAX& ev) const { - Kokkos::View::value> > a_f = f; - Kokkos::View::value> > a_Cdbo = d_Cdbo; - Kokkos::View::value> > a_CdDelta = d_CdDelta; + //Kokkos::View::value> > a_f = f; + //Kokkos::View::value> > a_Cdbo = d_Cdbo; + //Kokkos::View::value> > a_CdDelta = d_CdDelta; + auto a_f = dup_f.access(); + auto a_Cdbo = dup_Cdbo.access(); + auto a_CdDelta = dup_CdDelta.access(); + const int i = d_ilist[ii]; const int itype = type(i); @@ -2699,9 +2786,12 @@ template KOKKOS_INLINE_FUNCTION void PairReaxCKokkos::operator()(PairReaxComputeTorsion, const int &ii, EV_FLOAT_REAX& ev) const { - Kokkos::View::value> > a_f = f; - Kokkos::View::value> > a_CdDelta = d_CdDelta; - Kokkos::View::value> > a_Cdbo = d_Cdbo; + //Kokkos::View::value> > a_f = f; + //Kokkos::View::value> > a_CdDelta = d_CdDelta; + //Kokkos::View::value> > a_Cdbo = d_Cdbo; + auto a_f = dup_f.access(); + auto a_CdDelta = dup_CdDelta.access(); + auto a_Cdbo = dup_Cdbo.access(); // in reaxc_torsion_angles: j = i, k = j, i = k; @@ -3071,7 +3161,8 @@ template KOKKOS_INLINE_FUNCTION void PairReaxCKokkos::operator()(PairReaxComputeHydrogen, const int &ii, EV_FLOAT_REAX& ev) const { - Kokkos::View::value> > a_f = f; + //Kokkos::View::value> > a_f = f; + auto a_f = dup_f.access(); int hblist[MAX_BONDS]; F_FLOAT theta, cos_theta, sin_xhz4, cos_xhz1, sin_theta2; @@ -3218,9 +3309,12 @@ template KOKKOS_INLINE_FUNCTION void PairReaxCKokkos::operator()(PairReaxUpdateBond, const int &ii) const { - Kokkos::View::value> > a_Cdbo = d_Cdbo; - Kokkos::View::value> > a_Cdbopi = d_Cdbopi; - Kokkos::View::value> > a_Cdbopi2 = d_Cdbopi2; + //Kokkos::View::value> > a_Cdbo = d_Cdbo; + //Kokkos::View::value> > a_Cdbopi = d_Cdbopi; + //Kokkos::View::value> > a_Cdbopi2 = d_Cdbopi2; + auto a_Cdbo = dup_Cdbo.access(); + auto a_Cdbopi = dup_Cdbopi.access(); + auto a_Cdbopi2 = dup_Cdbopi2.access(); const int i = d_ilist[ii]; const tagint itag = tag(i); @@ -3267,8 +3361,10 @@ template KOKKOS_INLINE_FUNCTION void PairReaxCKokkos::operator()(PairReaxComputeBond1, const int &ii, EV_FLOAT_REAX& ev) const { - Kokkos::View::value> > a_f = f; - Kokkos::View::value> > a_CdDelta = d_CdDelta; + //Kokkos::View::value> > a_f = f; + //Kokkos::View::value> > a_CdDelta = d_CdDelta; + auto a_f = dup_f.access(); + auto a_CdDelta = dup_CdDelta.access(); F_FLOAT delij[3]; F_FLOAT p_be1, p_be2, De_s, De_p, De_pp, pow_BOs_be2, exp_be12, CEbo, ebond; @@ -3405,7 +3501,8 @@ template KOKKOS_INLINE_FUNCTION void PairReaxCKokkos::operator()(PairReaxComputeBond2, const int &ii, EV_FLOAT_REAX& ev) const { - Kokkos::View::value> > a_f = f; + //Kokkos::View::value> > a_f = f; + auto a_f = dup_f.access(); F_FLOAT delij[3], delik[3], deljk[3], tmpvec[3]; F_FLOAT dBOp_i[3], dBOp_k[3], dln_BOp_pi[3], dln_BOp_pi2[3]; @@ -3618,8 +3715,10 @@ void PairReaxCKokkos::ev_tally(EV_FLOAT_REAX &ev, const int &i, cons const int VFLAG = vflag_either; // The eatom and vatom arrays are atomic for Half/Thread neighbor style - Kokkos::View::value> > a_eatom = v_eatom; - Kokkos::View::value> > a_vatom = v_vatom; + //Kokkos::View::value> > a_eatom = v_eatom; + //Kokkos::View::value> > a_vatom = v_vatom; + auto a_eatom = dup_eatom.access(); + auto a_vatom = dup_vatom.access(); if (eflag_atom) { const E_FLOAT epairhalf = 0.5 * epair; @@ -3685,7 +3784,9 @@ void PairReaxCKokkos::e_tally(EV_FLOAT_REAX &ev, const int &i, const // The eatom array is atomic for Half/Thread neighbor style if (eflag_atom) { - Kokkos::View::value> > a_eatom = v_eatom; + //Kokkos::View::value> > a_eatom = v_eatom; + auto a_eatom = dup_eatom.access(); + const E_FLOAT epairhalf = 0.5 * epair; a_eatom[i] += epairhalf; a_eatom[j] += epairhalf; @@ -3701,7 +3802,8 @@ void PairReaxCKokkos::e_tally_single(EV_FLOAT_REAX &ev, const int &i const F_FLOAT &epair) const { // The eatom array is atomic for Half/Thread neighbor style - Kokkos::View::value> > a_eatom = v_eatom; + //Kokkos::View::value> > a_eatom = v_eatom; + auto a_eatom = dup_eatom.access(); a_eatom[i] += epair; } @@ -3734,7 +3836,9 @@ void PairReaxCKokkos::v_tally(EV_FLOAT_REAX &ev, const int &i, } if (vflag_atom) { - Kokkos::View::value> > a_vatom = v_vatom; + //Kokkos::View::value> > a_vatom = v_vatom; + auto a_vatom = dup_vatom.access(); + a_vatom(i,0) += v[0]; a_vatom(i,1) += v[1]; a_vatom(i,2) += v[2]; a_vatom(i,3) += v[3]; a_vatom(i,4) += v[4]; a_vatom(i,5) += v[5]; } @@ -3750,7 +3854,8 @@ void PairReaxCKokkos::v_tally3(EV_FLOAT_REAX &ev, const int &i, cons { // The eatom and vatom arrays are atomic for Half/Thread neighbor style - Kokkos::View::value> > a_vatom = v_vatom; + //Kokkos::View::value> > a_vatom = v_vatom; + auto a_vatom = dup_vatom.access(); F_FLOAT v[6]; @@ -3810,7 +3915,9 @@ void PairReaxCKokkos::v_tally4(EV_FLOAT_REAX &ev, const int &i, cons } if (vflag_atom) { - Kokkos::View::value> > a_vatom = v_vatom; + //Kokkos::View::value> > a_vatom = v_vatom; + auto a_vatom = dup_vatom.access(); + a_vatom(i,0) += 0.25 * v[0]; a_vatom(i,1) += 0.25 * v[1]; a_vatom(i,2) += 0.25 * v[2]; a_vatom(i,3) += 0.25 * v[3]; a_vatom(i,4) += 0.25 * v[4]; a_vatom(i,5) += 0.25 * v[5]; a_vatom(j,0) += 0.25 * v[0]; a_vatom(j,1) += 0.25 * v[1]; a_vatom(j,2) += 0.25 * v[2]; diff --git a/src/KOKKOS/pair_reaxc_kokkos.h b/src/KOKKOS/pair_reaxc_kokkos.h index 95fd7ced38..e25077f2cf 100644 --- a/src/KOKKOS/pair_reaxc_kokkos.h +++ b/src/KOKKOS/pair_reaxc_kokkos.h @@ -24,6 +24,7 @@ PairStyle(reax/c/kk/host,PairReaxCKokkos) #define LMP_PAIR_REAXC_KOKKOS_H #include +#include #include "pair_kokkos.h" #include "pair_reaxc.h" #include "neigh_list_kokkos.h" @@ -411,6 +412,16 @@ class PairReaxCKokkos : public PairReaxC { typename AT::t_ffloat_2d_dl d_C1dbopi2, d_C2dbopi2, d_C3dbopi2, d_C4dbopi2; typename AT::t_ffloat_2d_dl d_Cdbo, d_Cdbopi, d_Cdbopi2, d_dDeltap_self; + Kokkos::Experimental::ReductionView dup_total_bo; + Kokkos::Experimental::ReductionView dup_CdDelta; + Kokkos::Experimental::ReductionView dup_eatom; + Kokkos::Experimental::ReductionView dup_f; + Kokkos::Experimental::ReductionView dup_vatom; + Kokkos::Experimental::ReductionView dup_dDeltap_self; + Kokkos::Experimental::ReductionView dup_Cdbo; + Kokkos::Experimental::ReductionView dup_Cdbopi; + Kokkos::Experimental::ReductionView dup_Cdbopi2; + typedef Kokkos::DualView tdual_ffloat_2d_n7; typedef typename tdual_ffloat_2d_n7::t_dev_const_randomread t_ffloat_2d_n7_randomread; typedef typename tdual_ffloat_2d_n7::t_host t_host_ffloat_2d_n7; From 41202c3627bb2ea5a4a8bf725b679484edc58ed5 Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Tue, 28 Nov 2017 16:28:17 -0700 Subject: [PATCH 002/302] Turn atomics back on for some views in pair_reaxc_kokkos --- src/KOKKOS/pair_reaxc_kokkos.cpp | 80 ++++++++++++++++---------------- 1 file changed, 40 insertions(+), 40 deletions(-) diff --git a/src/KOKKOS/pair_reaxc_kokkos.cpp b/src/KOKKOS/pair_reaxc_kokkos.cpp index 79d9241ea4..8a1f1291e5 100644 --- a/src/KOKKOS/pair_reaxc_kokkos.cpp +++ b/src/KOKKOS/pair_reaxc_kokkos.cpp @@ -811,7 +811,7 @@ void PairReaxCKokkos::compute(int eflag_in, int vflag_in) if (neighflag == HALF) Kokkos::parallel_for(Kokkos::RangePolicy >(0,ignum),*this); else if (neighflag == HALFTHREAD) - Kokkos::parallel_for(Kokkos::RangePolicy >(0,ignum),*this); + Kokkos::parallel_for(Kokkos::RangePolicy >(0,ignum),*this); else //(neighflag == FULL) Kokkos::parallel_for(Kokkos::RangePolicy(0,ignum),*this); @@ -838,9 +838,9 @@ void PairReaxCKokkos::compute(int eflag_in, int vflag_in) // allocate duplicated memory if (neighflag != FULL) { dup_CdDelta = Kokkos::Experimental::create_reduction_view<>(d_CdDelta); - dup_Cdbo = Kokkos::Experimental::create_reduction_view<>(d_Cdbo); - dup_Cdbopi = Kokkos::Experimental::create_reduction_view<>(d_Cdbopi); - dup_Cdbopi2 = Kokkos::Experimental::create_reduction_view<>(d_Cdbopi2); + //dup_Cdbo = Kokkos::Experimental::create_reduction_view<>(d_Cdbo); + //dup_Cdbopi = Kokkos::Experimental::create_reduction_view<>(d_Cdbopi); + //dup_Cdbopi2 = Kokkos::Experimental::create_reduction_view<>(d_Cdbopi2); } // reduction over duplicated memory @@ -851,7 +851,7 @@ void PairReaxCKokkos::compute(int eflag_in, int vflag_in) if (neighflag == HALF) { Kokkos::parallel_for(Kokkos::RangePolicy(0,ignum),*this); } else if (neighflag == HALFTHREAD) { - Kokkos::parallel_for(Kokkos::RangePolicy(0,ignum),*this); + Kokkos::parallel_for(Kokkos::RangePolicy(0,ignum),*this); } Kokkos::parallel_for(Kokkos::RangePolicy(0,ignum),*this); Kokkos::parallel_for(Kokkos::RangePolicy(0,ignum),*this); @@ -955,12 +955,12 @@ void PairReaxCKokkos::compute(int eflag_in, int vflag_in) Kokkos::Experimental::contribute(d_dDeltap_self, dup_dDeltap_self); // needed in ComputeBond2 Kokkos::Experimental::contribute(d_CdDelta, dup_CdDelta); // needed in ComputeBond2 - Kokkos::Experimental::contribute(d_Cdbo, dup_Cdbo); // needed in UpdateBond, but also used in UpdateBond - Kokkos::Experimental::contribute(d_Cdbopi, dup_Cdbopi); // needed in UpdateBond, but also used in UpdateBond - Kokkos::Experimental::contribute(d_Cdbopi2, dup_Cdbopi2); // needed in UpdateBond, but also used in UpdateBond - dup_Cdbo.reset_except(d_Cdbo); - dup_Cdbopi.reset_except(d_Cdbopi); - dup_Cdbopi2.reset_except(d_Cdbopi2); + //Kokkos::Experimental::contribute(d_Cdbo, dup_Cdbo); // needed in UpdateBond, but also used in UpdateBond + //Kokkos::Experimental::contribute(d_Cdbopi, dup_Cdbopi); // needed in UpdateBond, but also used in UpdateBond + //Kokkos::Experimental::contribute(d_Cdbopi2, dup_Cdbopi2); // needed in UpdateBond, but also used in UpdateBond + //dup_Cdbo.reset_except(d_Cdbo); + //dup_Cdbopi.reset_except(d_Cdbopi); + //dup_Cdbopi2.reset_except(d_Cdbopi2); } // Bond force @@ -968,11 +968,11 @@ void PairReaxCKokkos::compute(int eflag_in, int vflag_in) Kokkos::parallel_for(Kokkos::RangePolicy >(0,ignum),*this); // reduction over duplicated memory - if (neighflag != FULL) { - Kokkos::Experimental::contribute(d_Cdbo, dup_Cdbo); // needed in ComputeBond2 - Kokkos::Experimental::contribute(d_Cdbopi, dup_Cdbopi); // needed in ComputeBond2 - Kokkos::Experimental::contribute(d_Cdbopi2, dup_Cdbopi2); // needed in ComputeBond2 - } + //if (neighflag != FULL) { + // Kokkos::Experimental::contribute(d_Cdbo, dup_Cdbo); // needed in ComputeBond2 + // Kokkos::Experimental::contribute(d_Cdbopi, dup_Cdbopi); // needed in ComputeBond2 + // Kokkos::Experimental::contribute(d_Cdbopi2, dup_Cdbopi2); // needed in ComputeBond2 + //} if (evflag) Kokkos::parallel_reduce(Kokkos::RangePolicy >(0,ignum),*this,ev); else @@ -983,11 +983,11 @@ void PairReaxCKokkos::compute(int eflag_in, int vflag_in) Kokkos::parallel_for(Kokkos::RangePolicy >(0,ignum),*this); // reduction over duplicated memory - if (neighflag != FULL) { - Kokkos::Experimental::contribute(d_Cdbo, dup_Cdbo); // needed in ComputeBond2 - Kokkos::Experimental::contribute(d_Cdbopi, dup_Cdbopi); // needed in ComputeBond2 - Kokkos::Experimental::contribute(d_Cdbopi2, dup_Cdbopi2); // needed in ComputeBond2 - } + //if (neighflag != FULL) { + // Kokkos::Experimental::contribute(d_Cdbo, dup_Cdbo); // needed in ComputeBond2 + // Kokkos::Experimental::contribute(d_Cdbopi, dup_Cdbopi); // needed in ComputeBond2 + // Kokkos::Experimental::contribute(d_Cdbopi2, dup_Cdbopi2); // needed in ComputeBond2 + //} if (evflag) Kokkos::parallel_reduce(Kokkos::RangePolicy >(0,ignum),*this,ev); else @@ -1038,9 +1038,9 @@ void PairReaxCKokkos::compute(int eflag_in, int vflag_in) dup_dDeltap_self = decltype(d_dDeltap_self)(); dup_total_bo = decltype(d_total_bo)(); dup_CdDelta = decltype(d_CdDelta)(); - dup_Cdbo = decltype(d_Cdbo)(); - dup_Cdbopi = decltype(d_Cdbopi)(); - dup_Cdbopi2 = decltype(d_Cdbopi2)(); + //dup_Cdbo = decltype(d_Cdbo)(); + //dup_Cdbopi = decltype(d_Cdbopi)(); + //dup_Cdbopi2 = decltype(d_Cdbopi2)(); dup_eatom = decltype(v_eatom)(); dup_vatom = decltype(v_vatom)(); } @@ -2316,13 +2316,13 @@ KOKKOS_INLINE_FUNCTION void PairReaxCKokkos::operator()(PairReaxComputeMulti2, const int &ii, EV_FLOAT_REAX& ev) const { //Kokkos::View::value> > a_CdDelta = d_CdDelta; - //Kokkos::View::value> > a_Cdbo = d_Cdbo; - //Kokkos::View::value> > a_Cdbopi = d_Cdbopi; - //Kokkos::View::value> > a_Cdbopi2 = d_Cdbopi2; + Kokkos::View::value> > a_Cdbo = d_Cdbo; + Kokkos::View::value> > a_Cdbopi = d_Cdbopi; + Kokkos::View::value> > a_Cdbopi2 = d_Cdbopi2; auto a_CdDelta = dup_CdDelta.access(); - auto a_Cdbo = dup_Cdbo.access(); - auto a_Cdbopi = dup_Cdbopi.access(); - auto a_Cdbopi2 = dup_Cdbopi2.access(); + //auto a_Cdbo = dup_Cdbo.access(); + //auto a_Cdbopi = dup_Cdbopi.access(); + //auto a_Cdbopi2 = dup_Cdbopi2.access(); const int i = d_ilist[ii]; const int itype = type(i); @@ -2474,10 +2474,10 @@ KOKKOS_INLINE_FUNCTION void PairReaxCKokkos::operator()(PairReaxComputeAngular, const int &ii, EV_FLOAT_REAX& ev) const { //Kokkos::View::value> > a_f = f; - //Kokkos::View::value> > a_Cdbo = d_Cdbo; + Kokkos::View::value> > a_Cdbo = d_Cdbo; //Kokkos::View::value> > a_CdDelta = d_CdDelta; auto a_f = dup_f.access(); - auto a_Cdbo = dup_Cdbo.access(); + //auto a_Cdbo = dup_Cdbo.access(); auto a_CdDelta = dup_CdDelta.access(); @@ -2788,10 +2788,10 @@ void PairReaxCKokkos::operator()(PairReaxComputeTorsion::value> > a_f = f; //Kokkos::View::value> > a_CdDelta = d_CdDelta; - //Kokkos::View::value> > a_Cdbo = d_Cdbo; + Kokkos::View::value> > a_Cdbo = d_Cdbo; auto a_f = dup_f.access(); auto a_CdDelta = dup_CdDelta.access(); - auto a_Cdbo = dup_Cdbo.access(); + //auto a_Cdbo = dup_Cdbo.access(); // in reaxc_torsion_angles: j = i, k = j, i = k; @@ -3309,12 +3309,12 @@ template KOKKOS_INLINE_FUNCTION void PairReaxCKokkos::operator()(PairReaxUpdateBond, const int &ii) const { - //Kokkos::View::value> > a_Cdbo = d_Cdbo; - //Kokkos::View::value> > a_Cdbopi = d_Cdbopi; - //Kokkos::View::value> > a_Cdbopi2 = d_Cdbopi2; - auto a_Cdbo = dup_Cdbo.access(); - auto a_Cdbopi = dup_Cdbopi.access(); - auto a_Cdbopi2 = dup_Cdbopi2.access(); + Kokkos::View::value> > a_Cdbo = d_Cdbo; + Kokkos::View::value> > a_Cdbopi = d_Cdbopi; + Kokkos::View::value> > a_Cdbopi2 = d_Cdbopi2; + //auto a_Cdbo = dup_Cdbo.access(); + //auto a_Cdbopi = dup_Cdbopi.access(); + //auto a_Cdbopi2 = dup_Cdbopi2.access(); const int i = d_ilist[ii]; const tagint itag = tag(i); From ee9ba99cde572c5146cfa8569cc3626219ff41dd Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Wed, 29 Nov 2017 11:11:20 -0700 Subject: [PATCH 003/302] Fix some bugs in pair_reaxc_kokkos --- src/KOKKOS/pair_reaxc_kokkos.cpp | 30 +++++++++++++++++------------- 1 file changed, 17 insertions(+), 13 deletions(-) diff --git a/src/KOKKOS/pair_reaxc_kokkos.cpp b/src/KOKKOS/pair_reaxc_kokkos.cpp index 8a1f1291e5..6791690cf0 100644 --- a/src/KOKKOS/pair_reaxc_kokkos.cpp +++ b/src/KOKKOS/pair_reaxc_kokkos.cpp @@ -716,8 +716,6 @@ void PairReaxCKokkos::compute(int eflag_in, int vflag_in) dup_f = Kokkos::Experimental::create_reduction_view<>(f); dup_eatom = Kokkos::Experimental::create_reduction_view<>(v_eatom); dup_vatom = Kokkos::Experimental::create_reduction_view<>(v_vatom); - dup_dDeltap_self = Kokkos::Experimental::create_reduction_view<>(d_dDeltap_self); - dup_total_bo = Kokkos::Experimental::create_reduction_view<>(d_total_bo); } if (eflag_global) { @@ -789,6 +787,12 @@ void PairReaxCKokkos::compute(int eflag_in, int vflag_in) allocate_array(); } + // allocate duplicated memory + if (neighflag != FULL) { + dup_dDeltap_self = Kokkos::Experimental::create_reduction_view<>(d_dDeltap_self); + dup_total_bo = Kokkos::Experimental::create_reduction_view<>(d_total_bo); + } + // Neighbor lists for bond and hbond // try, resize if necessary @@ -811,7 +815,7 @@ void PairReaxCKokkos::compute(int eflag_in, int vflag_in) if (neighflag == HALF) Kokkos::parallel_for(Kokkos::RangePolicy >(0,ignum),*this); else if (neighflag == HALFTHREAD) - Kokkos::parallel_for(Kokkos::RangePolicy >(0,ignum),*this); + Kokkos::parallel_for(Kokkos::RangePolicy >(0,ignum),*this); else //(neighflag == FULL) Kokkos::parallel_for(Kokkos::RangePolicy(0,ignum),*this); @@ -851,7 +855,7 @@ void PairReaxCKokkos::compute(int eflag_in, int vflag_in) if (neighflag == HALF) { Kokkos::parallel_for(Kokkos::RangePolicy(0,ignum),*this); } else if (neighflag == HALFTHREAD) { - Kokkos::parallel_for(Kokkos::RangePolicy(0,ignum),*this); + Kokkos::parallel_for(Kokkos::RangePolicy(0,ignum),*this); } Kokkos::parallel_for(Kokkos::RangePolicy(0,ignum),*this); Kokkos::parallel_for(Kokkos::RangePolicy(0,ignum),*this); @@ -1034,15 +1038,15 @@ void PairReaxCKokkos::compute(int eflag_in, int vflag_in) // free duplicated memory if (neighflag != FULL) { - dup_f = decltype(f)(); - dup_dDeltap_self = decltype(d_dDeltap_self)(); - dup_total_bo = decltype(d_total_bo)(); - dup_CdDelta = decltype(d_CdDelta)(); - //dup_Cdbo = decltype(d_Cdbo)(); - //dup_Cdbopi = decltype(d_Cdbopi)(); - //dup_Cdbopi2 = decltype(d_Cdbopi2)(); - dup_eatom = decltype(v_eatom)(); - dup_vatom = decltype(v_vatom)(); + dup_f = decltype(dup_f)(); + dup_dDeltap_self = decltype(dup_dDeltap_self)(); + dup_total_bo = decltype(dup_total_bo)(); + dup_CdDelta = decltype(dup_CdDelta)(); + //dup_Cdbo = decltype(dup_Cdbo)(); + //dup_Cdbopi = decltype(dup_Cdbopi)(); + //dup_Cdbopi2 = decltype(dup_Cdbopi2)(); + dup_eatom = decltype(dup_eatom)(); + dup_vatom = decltype(dup_vatom)(); } copymode = 0; From d2da1f5797faa0b752b7408822f361e565ea8d64 Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Wed, 6 Dec 2017 09:41:29 -0700 Subject: [PATCH 004/302] Template out atomics for full neighbor list --- src/KOKKOS/fix_qeq_reax_kokkos.cpp | 6 ++-- src/KOKKOS/pair_reaxc_kokkos.cpp | 56 +++++++++++++++--------------- 2 files changed, 31 insertions(+), 31 deletions(-) diff --git a/src/KOKKOS/fix_qeq_reax_kokkos.cpp b/src/KOKKOS/fix_qeq_reax_kokkos.cpp index 764b2f9191..e5f1901c1b 100644 --- a/src/KOKKOS/fix_qeq_reax_kokkos.cpp +++ b/src/KOKKOS/fix_qeq_reax_kokkos.cpp @@ -790,7 +790,7 @@ KOKKOS_INLINE_FUNCTION void FixQEqReaxKokkos::sparse13_item(int ii) const { // The q array is duplicated for OpenMP, atomic for CUDA, and neither for Serial - auto a_o = red_o.access(); + auto a_o = red_o.template access::value>(); const int i = d_ilist[ii]; if (mask[i] & groupbit) { @@ -842,7 +842,7 @@ KOKKOS_INLINE_FUNCTION void FixQEqReaxKokkos::sparse23_item(int ii) const { // The q array is duplicated for OpenMP, atomic for CUDA, and neither for Serial - auto a_o = red_o.access(); + auto a_o = red_o.template access::value>(); const int i = d_ilist[ii]; if (mask[i] & groupbit) { @@ -901,7 +901,7 @@ KOKKOS_INLINE_FUNCTION void FixQEqReaxKokkos::sparse33_item(int ii) const { // The q array is duplicated for OpenMP, atomic for CUDA, and neither for Serial - auto a_o = red_o.access(); + auto a_o = red_o.template access::value>(); const int i = d_ilist[ii]; if (mask[i] & groupbit) { diff --git a/src/KOKKOS/pair_reaxc_kokkos.cpp b/src/KOKKOS/pair_reaxc_kokkos.cpp index 27cf18b02e..07d17408ca 100644 --- a/src/KOKKOS/pair_reaxc_kokkos.cpp +++ b/src/KOKKOS/pair_reaxc_kokkos.cpp @@ -1090,7 +1090,7 @@ void PairReaxCKokkos::operator()(PairReaxComputeLJCoulomb::value> > a_f = f; - auto a_f = dup_f.access(); + auto a_f = dup_f.template access::value>(); F_FLOAT powr_vdw, powgi_vdw, fn13, dfn13, exp1, exp2, etmp; F_FLOAT evdwl, fvdwl; @@ -1250,7 +1250,7 @@ void PairReaxCKokkos::operator()(PairReaxComputeTabulatedLJCoulomb::value> > a_f = f; - auto a_f = dup_f.access(); + auto a_f = dup_f.template access::value>(); const int i = d_ilist[ii]; const X_FLOAT xtmp = x(i,0); @@ -1633,8 +1633,8 @@ void PairReaxCKokkos::operator()(PairReaxBuildListsHalf, //Kokkos::View::value> > a_dDeltap_self = d_dDeltap_self; //Kokkos::View::value> > a_total_bo = d_total_bo; - auto a_dDeltap_self = dup_dDeltap_self.access(); - auto a_total_bo = dup_total_bo.access(); + auto a_dDeltap_self = dup_dDeltap_self.template access::value>(); + auto a_total_bo = dup_total_bo.template access::value>(); const int i = d_ilist[ii]; const X_FLOAT xtmp = x(i,0); @@ -2329,10 +2329,10 @@ void PairReaxCKokkos::operator()(PairReaxComputeMulti2::value> > a_Cdbo = d_Cdbo; Kokkos::View::value> > a_Cdbopi = d_Cdbopi; Kokkos::View::value> > a_Cdbopi2 = d_Cdbopi2; - auto a_CdDelta = dup_CdDelta.access(); - //auto a_Cdbo = dup_Cdbo.access(); - //auto a_Cdbopi = dup_Cdbopi.access(); - //auto a_Cdbopi2 = dup_Cdbopi2.access(); + auto a_CdDelta = dup_CdDelta.template access::value>(); + //auto a_Cdbo = dup_Cdbo.template access::value>(); + //auto a_Cdbopi = dup_Cdbopi.template access::value>(); + //auto a_Cdbopi2 = dup_Cdbopi2.template access::value>(); const int i = d_ilist[ii]; const int itype = type(i); @@ -2486,9 +2486,9 @@ void PairReaxCKokkos::operator()(PairReaxComputeAngular::value> > a_f = f; Kokkos::View::value> > a_Cdbo = d_Cdbo; //Kokkos::View::value> > a_CdDelta = d_CdDelta; - auto a_f = dup_f.access(); - //auto a_Cdbo = dup_Cdbo.access(); - auto a_CdDelta = dup_CdDelta.access(); + auto a_f = dup_f.template access::value>(); + //auto a_Cdbo = dup_Cdbo.template access::value>(); + auto a_CdDelta = dup_CdDelta.template access::value>(); const int i = d_ilist[ii]; @@ -2799,9 +2799,9 @@ void PairReaxCKokkos::operator()(PairReaxComputeTorsion::value> > a_f = f; //Kokkos::View::value> > a_CdDelta = d_CdDelta; Kokkos::View::value> > a_Cdbo = d_Cdbo; - auto a_f = dup_f.access(); - auto a_CdDelta = dup_CdDelta.access(); - //auto a_Cdbo = dup_Cdbo.access(); + auto a_f = dup_f.template access::value>(); + auto a_CdDelta = dup_CdDelta.template access::value>(); + //auto a_Cdbo = dup_Cdbo.template access::value>(); // in reaxc_torsion_angles: j = i, k = j, i = k; @@ -3172,7 +3172,7 @@ KOKKOS_INLINE_FUNCTION void PairReaxCKokkos::operator()(PairReaxComputeHydrogen, const int &ii, EV_FLOAT_REAX& ev) const { //Kokkos::View::value> > a_f = f; - auto a_f = dup_f.access(); + auto a_f = dup_f.template access::value>(); int hblist[MAX_BONDS]; F_FLOAT theta, cos_theta, sin_xhz4, cos_xhz1, sin_theta2; @@ -3322,9 +3322,9 @@ void PairReaxCKokkos::operator()(PairReaxUpdateBond, cons Kokkos::View::value> > a_Cdbo = d_Cdbo; Kokkos::View::value> > a_Cdbopi = d_Cdbopi; Kokkos::View::value> > a_Cdbopi2 = d_Cdbopi2; - //auto a_Cdbo = dup_Cdbo.access(); - //auto a_Cdbopi = dup_Cdbopi.access(); - //auto a_Cdbopi2 = dup_Cdbopi2.access(); + //auto a_Cdbo = dup_Cdbo.template access::value>(); + //auto a_Cdbopi = dup_Cdbopi.template access::value>(); + //auto a_Cdbopi2 = dup_Cdbopi2.template access::value>(); const int i = d_ilist[ii]; const tagint itag = tag(i); @@ -3373,8 +3373,8 @@ void PairReaxCKokkos::operator()(PairReaxComputeBond1::value> > a_f = f; //Kokkos::View::value> > a_CdDelta = d_CdDelta; - auto a_f = dup_f.access(); - auto a_CdDelta = dup_CdDelta.access(); + auto a_f = dup_f.template access::value>(); + auto a_CdDelta = dup_CdDelta.template access::value>(); F_FLOAT delij[3]; F_FLOAT p_be1, p_be2, De_s, De_p, De_pp, pow_BOs_be2, exp_be12, CEbo, ebond; @@ -3512,7 +3512,7 @@ KOKKOS_INLINE_FUNCTION void PairReaxCKokkos::operator()(PairReaxComputeBond2, const int &ii, EV_FLOAT_REAX& ev) const { //Kokkos::View::value> > a_f = f; - auto a_f = dup_f.access(); + auto a_f = dup_f.template access::value>(); F_FLOAT delij[3], delik[3], deljk[3], tmpvec[3]; F_FLOAT dBOp_i[3], dBOp_k[3], dln_BOp_pi[3], dln_BOp_pi2[3]; @@ -3727,8 +3727,8 @@ void PairReaxCKokkos::ev_tally(EV_FLOAT_REAX &ev, const int &i, cons // The eatom and vatom arrays are atomic for Half/Thread neighbor style //Kokkos::View::value> > a_eatom = v_eatom; //Kokkos::View::value> > a_vatom = v_vatom; - auto a_eatom = dup_eatom.access(); - auto a_vatom = dup_vatom.access(); + auto a_eatom = dup_eatom.template access::value>(); + auto a_vatom = dup_vatom.template access::value>(); if (eflag_atom) { const E_FLOAT epairhalf = 0.5 * epair; @@ -3795,7 +3795,7 @@ void PairReaxCKokkos::e_tally(EV_FLOAT_REAX &ev, const int &i, const if (eflag_atom) { //Kokkos::View::value> > a_eatom = v_eatom; - auto a_eatom = dup_eatom.access(); + auto a_eatom = dup_eatom.template access::value>(); const E_FLOAT epairhalf = 0.5 * epair; a_eatom[i] += epairhalf; @@ -3813,7 +3813,7 @@ void PairReaxCKokkos::e_tally_single(EV_FLOAT_REAX &ev, const int &i { // The eatom array is atomic for Half/Thread neighbor style //Kokkos::View::value> > a_eatom = v_eatom; - auto a_eatom = dup_eatom.access(); + auto a_eatom = dup_eatom.template access::value>(); a_eatom[i] += epair; } @@ -3847,7 +3847,7 @@ void PairReaxCKokkos::v_tally(EV_FLOAT_REAX &ev, const int &i, if (vflag_atom) { //Kokkos::View::value> > a_vatom = v_vatom; - auto a_vatom = dup_vatom.access(); + auto a_vatom = dup_vatom.template access::value>(); a_vatom(i,0) += v[0]; a_vatom(i,1) += v[1]; a_vatom(i,2) += v[2]; a_vatom(i,3) += v[3]; a_vatom(i,4) += v[4]; a_vatom(i,5) += v[5]; @@ -3865,7 +3865,7 @@ void PairReaxCKokkos::v_tally3(EV_FLOAT_REAX &ev, const int &i, cons // The eatom and vatom arrays are atomic for Half/Thread neighbor style //Kokkos::View::value> > a_vatom = v_vatom; - auto a_vatom = dup_vatom.access(); + auto a_vatom = dup_vatom.template access::value>(); F_FLOAT v[6]; @@ -3926,7 +3926,7 @@ void PairReaxCKokkos::v_tally4(EV_FLOAT_REAX &ev, const int &i, cons if (vflag_atom) { //Kokkos::View::value> > a_vatom = v_vatom; - auto a_vatom = dup_vatom.access(); + auto a_vatom = dup_vatom.template access::value>(); a_vatom(i,0) += 0.25 * v[0]; a_vatom(i,1) += 0.25 * v[1]; a_vatom(i,2) += 0.25 * v[2]; a_vatom(i,3) += 0.25 * v[3]; a_vatom(i,4) += 0.25 * v[4]; a_vatom(i,5) += 0.25 * v[5]; From 8a9a7f4e504ef6b59536cba3e48297d29222ea14 Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Wed, 6 Dec 2017 14:06:35 -0700 Subject: [PATCH 005/302] Fix issues --- src/KOKKOS/fix_qeq_reax_kokkos.cpp | 10 +-- src/KOKKOS/pair_kokkos.h | 4 +- src/KOKKOS/pair_reaxc_kokkos.cpp | 98 ++++++++++++------------------ 3 files changed, 47 insertions(+), 65 deletions(-) diff --git a/src/KOKKOS/fix_qeq_reax_kokkos.cpp b/src/KOKKOS/fix_qeq_reax_kokkos.cpp index e5f1901c1b..638837e265 100644 --- a/src/KOKKOS/fix_qeq_reax_kokkos.cpp +++ b/src/KOKKOS/fix_qeq_reax_kokkos.cpp @@ -255,7 +255,7 @@ void FixQEqReaxKokkos::pre_force(int vflag) k_t.template sync(); if (neighflag != FULL) - red_o = Kokkos::Experimental::create_reduction_view<> (k_o.d_view); // allocate duplicated memory + red_o = Kokkos::Experimental::create_reduction_view<> (d_o); // allocate duplicated memory // 1st cg solve over b_s, s cg_solve1(); @@ -502,7 +502,7 @@ void FixQEqReaxKokkos::cg_solve1() Kokkos::parallel_for(Kokkos::RangePolicy(nlocal,nlocal+atom->nghost),*this); FixQEqReaxKokkosSparse13Functor sparse13_functor(this); Kokkos::parallel_for(inum,sparse13_functor); - Kokkos::Experimental::contribute(k_o.d_view, red_o); + Kokkos::Experimental::contribute(d_o, red_o); } else { Kokkos::parallel_for(Kokkos::TeamPolicy (inum, teamsize), *this); } @@ -553,7 +553,7 @@ void FixQEqReaxKokkos::cg_solve1() red_o.reset_except(d_o); FixQEqReaxKokkosSparse23Functor sparse23_functor(this); Kokkos::parallel_for(inum,sparse23_functor); - Kokkos::Experimental::contribute(k_o.d_view, red_o); + Kokkos::Experimental::contribute(d_o, red_o); } else { Kokkos::parallel_for(Kokkos::TeamPolicy (inum, teamsize), *this); } @@ -626,7 +626,7 @@ void FixQEqReaxKokkos::cg_solve2() red_o.reset_except(d_o); FixQEqReaxKokkosSparse33Functor sparse33_functor(this); Kokkos::parallel_for(inum,sparse33_functor); - Kokkos::Experimental::contribute(k_o.d_view, red_o); + Kokkos::Experimental::contribute(d_o, red_o); } else { Kokkos::parallel_for(Kokkos::TeamPolicy (inum, teamsize), *this); } @@ -677,7 +677,7 @@ void FixQEqReaxKokkos::cg_solve2() red_o.reset_except(d_o); FixQEqReaxKokkosSparse23Functor sparse23_functor(this); Kokkos::parallel_for(inum,sparse23_functor); - Kokkos::Experimental::contribute(k_o.d_view, red_o); + Kokkos::Experimental::contribute(d_o, red_o); } else { Kokkos::parallel_for(Kokkos::TeamPolicy (inum, teamsize), *this); } diff --git a/src/KOKKOS/pair_kokkos.h b/src/KOKKOS/pair_kokkos.h index c8e926a721..04c56d0aa7 100644 --- a/src/KOKKOS/pair_kokkos.h +++ b/src/KOKKOS/pair_kokkos.h @@ -19,10 +19,10 @@ #define LMP_PAIR_KOKKOS_H #include "Kokkos_Macros.hpp" -#include "Kokkos_Vectorization.hpp" -#include "Kokkos_ReductionView.hpp" #include "pair.h" #include "neigh_list_kokkos.h" +#include "Kokkos_Vectorization.hpp" +#include "Kokkos_ReductionView.hpp" namespace LAMMPS_NS { diff --git a/src/KOKKOS/pair_reaxc_kokkos.cpp b/src/KOKKOS/pair_reaxc_kokkos.cpp index 07d17408ca..7a45c068be 100644 --- a/src/KOKKOS/pair_reaxc_kokkos.cpp +++ b/src/KOKKOS/pair_reaxc_kokkos.cpp @@ -712,11 +712,9 @@ void PairReaxCKokkos::compute(int eflag_in, int vflag_in) d_ilist = k_list->d_ilist; // allocate duplicated memory - if (neighflag != FULL) { - dup_f = Kokkos::Experimental::create_reduction_view<>(f); - dup_eatom = Kokkos::Experimental::create_reduction_view<>(v_eatom); - dup_vatom = Kokkos::Experimental::create_reduction_view<>(v_vatom); - } + dup_f = Kokkos::Experimental::create_reduction_view<>(f); + dup_eatom = Kokkos::Experimental::create_reduction_view<>(v_eatom); + dup_vatom = Kokkos::Experimental::create_reduction_view<>(v_vatom); if (eflag_global) { for (int i = 0; i < 14; i++) @@ -788,10 +786,8 @@ void PairReaxCKokkos::compute(int eflag_in, int vflag_in) } // allocate duplicated memory - if (neighflag != FULL) { - dup_dDeltap_self = Kokkos::Experimental::create_reduction_view<>(d_dDeltap_self); - dup_total_bo = Kokkos::Experimental::create_reduction_view<>(d_total_bo); - } + dup_dDeltap_self = Kokkos::Experimental::create_reduction_view<>(d_dDeltap_self); + dup_total_bo = Kokkos::Experimental::create_reduction_view<>(d_total_bo); // Neighbor lists for bond and hbond @@ -832,24 +828,19 @@ void PairReaxCKokkos::compute(int eflag_in, int vflag_in) resize = resize_bo || resize_hb; if (resize) { allocate_array(); - if (neighflag != FULL) { - dup_dDeltap_self = Kokkos::Experimental::create_reduction_view<>(d_dDeltap_self); - dup_total_bo = Kokkos::Experimental::create_reduction_view<>(d_total_bo); - } + dup_dDeltap_self = Kokkos::Experimental::create_reduction_view<>(d_dDeltap_self); + dup_total_bo = Kokkos::Experimental::create_reduction_view<>(d_total_bo); } } // allocate duplicated memory - if (neighflag != FULL) { - dup_CdDelta = Kokkos::Experimental::create_reduction_view<>(d_CdDelta); - //dup_Cdbo = Kokkos::Experimental::create_reduction_view<>(d_Cdbo); - //dup_Cdbopi = Kokkos::Experimental::create_reduction_view<>(d_Cdbopi); - //dup_Cdbopi2 = Kokkos::Experimental::create_reduction_view<>(d_Cdbopi2); - } + dup_CdDelta = Kokkos::Experimental::create_reduction_view<>(d_CdDelta); + //dup_Cdbo = Kokkos::Experimental::create_reduction_view<>(d_Cdbo); + //dup_Cdbopi = Kokkos::Experimental::create_reduction_view<>(d_Cdbopi); + //dup_Cdbopi2 = Kokkos::Experimental::create_reduction_view<>(d_Cdbopi2); // reduction over duplicated memory - if (neighflag != FULL) - Kokkos::Experimental::contribute(d_total_bo, dup_total_bo); // needed in BondOrder1 + Kokkos::Experimental::contribute(d_total_bo, dup_total_bo); // needed in BondOrder1 // Bond order if (neighflag == HALF) { @@ -955,28 +946,25 @@ void PairReaxCKokkos::compute(int eflag_in, int vflag_in) ev_all.evdwl += ev.ereax[8]; // reduction over duplicated memory - if (neighflag != FULL) { - Kokkos::Experimental::contribute(d_dDeltap_self, dup_dDeltap_self); // needed in ComputeBond2 - Kokkos::Experimental::contribute(d_CdDelta, dup_CdDelta); // needed in ComputeBond2 + Kokkos::Experimental::contribute(d_dDeltap_self, dup_dDeltap_self); // needed in ComputeBond2 + Kokkos::Experimental::contribute(d_CdDelta, dup_CdDelta); // needed in ComputeBond2 - //Kokkos::Experimental::contribute(d_Cdbo, dup_Cdbo); // needed in UpdateBond, but also used in UpdateBond - //Kokkos::Experimental::contribute(d_Cdbopi, dup_Cdbopi); // needed in UpdateBond, but also used in UpdateBond - //Kokkos::Experimental::contribute(d_Cdbopi2, dup_Cdbopi2); // needed in UpdateBond, but also used in UpdateBond - //dup_Cdbo.reset_except(d_Cdbo); - //dup_Cdbopi.reset_except(d_Cdbopi); - //dup_Cdbopi2.reset_except(d_Cdbopi2); - } + //Kokkos::Experimental::contribute(d_Cdbo, dup_Cdbo); // needed in UpdateBond, but also used in UpdateBond + //Kokkos::Experimental::contribute(d_Cdbopi, dup_Cdbopi); // needed in UpdateBond, but also used in UpdateBond + //Kokkos::Experimental::contribute(d_Cdbopi2, dup_Cdbopi2); // needed in UpdateBond, but also used in UpdateBond + //dup_Cdbo.reset_except(d_Cdbo); + //dup_Cdbopi.reset_except(d_Cdbopi); + //dup_Cdbopi2.reset_except(d_Cdbopi2); // Bond force if (neighflag == HALF) { Kokkos::parallel_for(Kokkos::RangePolicy >(0,ignum),*this); // reduction over duplicated memory - //if (neighflag != FULL) { - // Kokkos::Experimental::contribute(d_Cdbo, dup_Cdbo); // needed in ComputeBond2 - // Kokkos::Experimental::contribute(d_Cdbopi, dup_Cdbopi); // needed in ComputeBond2 - // Kokkos::Experimental::contribute(d_Cdbopi2, dup_Cdbopi2); // needed in ComputeBond2 - //} + //Kokkos::Experimental::contribute(d_Cdbo, dup_Cdbo); // needed in ComputeBond2 + //Kokkos::Experimental::contribute(d_Cdbopi, dup_Cdbopi); // needed in ComputeBond2 + //Kokkos::Experimental::contribute(d_Cdbopi2, dup_Cdbopi2); // needed in ComputeBond2 + if (evflag) Kokkos::parallel_reduce(Kokkos::RangePolicy >(0,ignum),*this,ev); else @@ -987,11 +975,10 @@ void PairReaxCKokkos::compute(int eflag_in, int vflag_in) Kokkos::parallel_for(Kokkos::RangePolicy >(0,ignum),*this); // reduction over duplicated memory - //if (neighflag != FULL) { - // Kokkos::Experimental::contribute(d_Cdbo, dup_Cdbo); // needed in ComputeBond2 - // Kokkos::Experimental::contribute(d_Cdbopi, dup_Cdbopi); // needed in ComputeBond2 - // Kokkos::Experimental::contribute(d_Cdbopi2, dup_Cdbopi2); // needed in ComputeBond2 - //} + //Kokkos::Experimental::contribute(d_Cdbo, dup_Cdbo); // needed in ComputeBond2 + //Kokkos::Experimental::contribute(d_Cdbopi, dup_Cdbopi); // needed in ComputeBond2 + //Kokkos::Experimental::contribute(d_Cdbopi2, dup_Cdbopi2); // needed in ComputeBond2 + if (evflag) Kokkos::parallel_reduce(Kokkos::RangePolicy >(0,ignum),*this,ev); else @@ -1001,8 +988,7 @@ void PairReaxCKokkos::compute(int eflag_in, int vflag_in) } // reduction over duplicated memory - if (neighflag != FULL) - Kokkos::Experimental::contribute(f, dup_f); + Kokkos::Experimental::contribute(f, dup_f); if (eflag_global) { eng_vdwl += ev_all.evdwl; @@ -1020,15 +1006,13 @@ void PairReaxCKokkos::compute(int eflag_in, int vflag_in) if (vflag_fdotr) pair_virial_fdotr_compute(this); if (eflag_atom) { - if (neighflag != FULL) - Kokkos::Experimental::contribute(v_eatom, dup_eatom); + Kokkos::Experimental::contribute(v_eatom, dup_eatom); k_eatom.template modify(); k_eatom.template sync(); } if (vflag_atom) { - if (neighflag != FULL) - Kokkos::Experimental::contribute(v_vatom, dup_vatom); + Kokkos::Experimental::contribute(v_vatom, dup_vatom); k_vatom.template modify(); k_vatom.template sync(); } @@ -1037,17 +1021,15 @@ void PairReaxCKokkos::compute(int eflag_in, int vflag_in) FindBondSpecies(); // free duplicated memory - if (neighflag != FULL) { - dup_f = decltype(dup_f)(); - dup_dDeltap_self = decltype(dup_dDeltap_self)(); - dup_total_bo = decltype(dup_total_bo)(); - dup_CdDelta = decltype(dup_CdDelta)(); - //dup_Cdbo = decltype(dup_Cdbo)(); - //dup_Cdbopi = decltype(dup_Cdbopi)(); - //dup_Cdbopi2 = decltype(dup_Cdbopi2)(); - dup_eatom = decltype(dup_eatom)(); - dup_vatom = decltype(dup_vatom)(); - } + dup_f = decltype(dup_f)(); + dup_dDeltap_self = decltype(dup_dDeltap_self)(); + dup_total_bo = decltype(dup_total_bo)(); + dup_CdDelta = decltype(dup_CdDelta)(); + //dup_Cdbo = decltype(dup_Cdbo)(); + //dup_Cdbopi = decltype(dup_Cdbopi)(); + //dup_Cdbopi2 = decltype(dup_Cdbopi2)(); + dup_eatom = decltype(dup_eatom)(); + dup_vatom = decltype(dup_vatom)(); copymode = 0; } From a5790ef68f564b3b6fc3c120fd4e530213944ca1 Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Mon, 11 Dec 2017 08:38:54 -0700 Subject: [PATCH 006/302] Rename to ScatterView --- src/KOKKOS/fix_qeq_reax_kokkos.cpp | 2 +- src/KOKKOS/fix_qeq_reax_kokkos.h | 4 ++-- src/KOKKOS/pair_kokkos.h | 6 +++--- src/KOKKOS/pair_reaxc_kokkos.cpp | 22 +++++++++++----------- src/KOKKOS/pair_reaxc_kokkos.h | 20 ++++++++++---------- 5 files changed, 27 insertions(+), 27 deletions(-) diff --git a/src/KOKKOS/fix_qeq_reax_kokkos.cpp b/src/KOKKOS/fix_qeq_reax_kokkos.cpp index d8723339ad..aefc2ea130 100644 --- a/src/KOKKOS/fix_qeq_reax_kokkos.cpp +++ b/src/KOKKOS/fix_qeq_reax_kokkos.cpp @@ -255,7 +255,7 @@ void FixQEqReaxKokkos::pre_force(int vflag) k_t.template sync(); if (neighflag != FULL) - red_o = Kokkos::Experimental::create_reduction_view<> (d_o); // allocate duplicated memory + red_o = Kokkos::Experimental::create_scatter_view<> (d_o); // allocate duplicated memory // 1st cg solve over b_s, s cg_solve1(); diff --git a/src/KOKKOS/fix_qeq_reax_kokkos.h b/src/KOKKOS/fix_qeq_reax_kokkos.h index dd7b4073c2..64f81b9141 100644 --- a/src/KOKKOS/fix_qeq_reax_kokkos.h +++ b/src/KOKKOS/fix_qeq_reax_kokkos.h @@ -22,7 +22,7 @@ FixStyle(qeq/reax/kk/host,FixQEqReaxKokkos) #ifndef LMP_FIX_QEQ_REAX_KOKKOS_H #define LMP_FIX_QEQ_REAX_KOKKOS_H -#include +#include #include "fix_qeq_reax.h" #include "kokkos_type.h" #include "neigh_list.h" @@ -193,7 +193,7 @@ class FixQEqReaxKokkos : public FixQEqReax { HAT::t_ffloat_2d h_s_hist, h_t_hist; typename AT::t_ffloat_2d_randomread r_s_hist, r_t_hist; - Kokkos::Experimental::ReductionView red_o; + Kokkos::Experimental::ScatterView red_o; void init_shielding_k(); void init_hist(); diff --git a/src/KOKKOS/pair_kokkos.h b/src/KOKKOS/pair_kokkos.h index 3243af26e7..a409035dc6 100644 --- a/src/KOKKOS/pair_kokkos.h +++ b/src/KOKKOS/pair_kokkos.h @@ -23,7 +23,7 @@ #include "neighbor_kokkos.h" #include "neigh_list_kokkos.h" #include "Kokkos_Vectorization.hpp" -#include "Kokkos_ReductionView.hpp" +#include "Kokkos_ScatterView.hpp" namespace LAMMPS_NS { @@ -64,12 +64,12 @@ struct AtomicF { // Do atomic trait when running HALFTHREAD neighbor list style template struct AtomicDup { - enum {value = Kokkos::Experimental::ReductionNonAtomic}; + enum {value = Kokkos::Experimental::ScatterNonAtomic}; }; template<> struct AtomicDup { - enum {value = Kokkos::Experimental::ReductionAtomic}; + enum {value = Kokkos::Experimental::ScatterAtomic}; }; //Specialisation for Neighborlist types Half, HalfThread, Full diff --git a/src/KOKKOS/pair_reaxc_kokkos.cpp b/src/KOKKOS/pair_reaxc_kokkos.cpp index c3197e222f..3a3faefc24 100644 --- a/src/KOKKOS/pair_reaxc_kokkos.cpp +++ b/src/KOKKOS/pair_reaxc_kokkos.cpp @@ -713,9 +713,9 @@ void PairReaxCKokkos::compute(int eflag_in, int vflag_in) d_ilist = k_list->d_ilist; // allocate duplicated memory - dup_f = Kokkos::Experimental::create_reduction_view<>(f); - dup_eatom = Kokkos::Experimental::create_reduction_view<>(v_eatom); - dup_vatom = Kokkos::Experimental::create_reduction_view<>(v_vatom); + dup_f = Kokkos::Experimental::create_scatter_view<>(f); + dup_eatom = Kokkos::Experimental::create_scatter_view<>(v_eatom); + dup_vatom = Kokkos::Experimental::create_scatter_view<>(v_vatom); if (eflag_global) { for (int i = 0; i < 14; i++) @@ -787,8 +787,8 @@ void PairReaxCKokkos::compute(int eflag_in, int vflag_in) } // allocate duplicated memory - dup_dDeltap_self = Kokkos::Experimental::create_reduction_view<>(d_dDeltap_self); - dup_total_bo = Kokkos::Experimental::create_reduction_view<>(d_total_bo); + dup_dDeltap_self = Kokkos::Experimental::create_scatter_view<>(d_dDeltap_self); + dup_total_bo = Kokkos::Experimental::create_scatter_view<>(d_total_bo); // Neighbor lists for bond and hbond @@ -829,16 +829,16 @@ void PairReaxCKokkos::compute(int eflag_in, int vflag_in) resize = resize_bo || resize_hb; if (resize) { allocate_array(); - dup_dDeltap_self = Kokkos::Experimental::create_reduction_view<>(d_dDeltap_self); - dup_total_bo = Kokkos::Experimental::create_reduction_view<>(d_total_bo); + dup_dDeltap_self = Kokkos::Experimental::create_scatter_view<>(d_dDeltap_self); + dup_total_bo = Kokkos::Experimental::create_scatter_view<>(d_total_bo); } } // allocate duplicated memory - dup_CdDelta = Kokkos::Experimental::create_reduction_view<>(d_CdDelta); - //dup_Cdbo = Kokkos::Experimental::create_reduction_view<>(d_Cdbo); - //dup_Cdbopi = Kokkos::Experimental::create_reduction_view<>(d_Cdbopi); - //dup_Cdbopi2 = Kokkos::Experimental::create_reduction_view<>(d_Cdbopi2); + dup_CdDelta = Kokkos::Experimental::create_scatter_view<>(d_CdDelta); + //dup_Cdbo = Kokkos::Experimental::create_scatter_view<>(d_Cdbo); + //dup_Cdbopi = Kokkos::Experimental::create_scatter_view<>(d_Cdbopi); + //dup_Cdbopi2 = Kokkos::Experimental::create_scatter_view<>(d_Cdbopi2); // reduction over duplicated memory Kokkos::Experimental::contribute(d_total_bo, dup_total_bo); // needed in BondOrder1 diff --git a/src/KOKKOS/pair_reaxc_kokkos.h b/src/KOKKOS/pair_reaxc_kokkos.h index e25077f2cf..70aef2d608 100644 --- a/src/KOKKOS/pair_reaxc_kokkos.h +++ b/src/KOKKOS/pair_reaxc_kokkos.h @@ -24,7 +24,7 @@ PairStyle(reax/c/kk/host,PairReaxCKokkos) #define LMP_PAIR_REAXC_KOKKOS_H #include -#include +#include #include "pair_kokkos.h" #include "pair_reaxc.h" #include "neigh_list_kokkos.h" @@ -412,15 +412,15 @@ class PairReaxCKokkos : public PairReaxC { typename AT::t_ffloat_2d_dl d_C1dbopi2, d_C2dbopi2, d_C3dbopi2, d_C4dbopi2; typename AT::t_ffloat_2d_dl d_Cdbo, d_Cdbopi, d_Cdbopi2, d_dDeltap_self; - Kokkos::Experimental::ReductionView dup_total_bo; - Kokkos::Experimental::ReductionView dup_CdDelta; - Kokkos::Experimental::ReductionView dup_eatom; - Kokkos::Experimental::ReductionView dup_f; - Kokkos::Experimental::ReductionView dup_vatom; - Kokkos::Experimental::ReductionView dup_dDeltap_self; - Kokkos::Experimental::ReductionView dup_Cdbo; - Kokkos::Experimental::ReductionView dup_Cdbopi; - Kokkos::Experimental::ReductionView dup_Cdbopi2; + Kokkos::Experimental::ScatterView dup_total_bo; + Kokkos::Experimental::ScatterView dup_CdDelta; + Kokkos::Experimental::ScatterView dup_eatom; + Kokkos::Experimental::ScatterView dup_f; + Kokkos::Experimental::ScatterView dup_vatom; + Kokkos::Experimental::ScatterView dup_dDeltap_self; + Kokkos::Experimental::ScatterView dup_Cdbo; + Kokkos::Experimental::ScatterView dup_Cdbopi; + Kokkos::Experimental::ScatterView dup_Cdbopi2; typedef Kokkos::DualView tdual_ffloat_2d_n7; typedef typename tdual_ffloat_2d_n7::t_dev_const_randomread t_ffloat_2d_n7_randomread; From 2b99a26b47781bd59bdff63a10f0be0e9d7ad0dc Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Mon, 18 Dec 2017 13:57:56 -0700 Subject: [PATCH 007/302] Fix issue in fix_qeq_reax_kokkos, can't call child function from base constructor --- src/KOKKOS/fix_qeq_reax_kokkos.cpp | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/src/KOKKOS/fix_qeq_reax_kokkos.cpp b/src/KOKKOS/fix_qeq_reax_kokkos.cpp index b251c634b6..ca14159b55 100644 --- a/src/KOKKOS/fix_qeq_reax_kokkos.cpp +++ b/src/KOKKOS/fix_qeq_reax_kokkos.cpp @@ -64,6 +64,10 @@ FixQEqReaxKokkos(LAMMPS *lmp, int narg, char **arg) : nmax = nmax = m_cap = 0; allocated_flag = 0; nprev = 4; + + memory->destroy(s_hist); + memory->destroy(t_hist); + grow_arrays(atom->nmax); } /* ---------------------------------------------------------------------- */ From 5886cadeef893d114570e50cd33b51f9b7f82198 Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Mon, 18 Dec 2017 14:09:39 -0700 Subject: [PATCH 008/302] Fix compiler warnings in atom_vec_hybrid_kokkos --- src/KOKKOS/atom_vec_hybrid_kokkos.cpp | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/src/KOKKOS/atom_vec_hybrid_kokkos.cpp b/src/KOKKOS/atom_vec_hybrid_kokkos.cpp index b5aadb18d6..67dce07b80 100644 --- a/src/KOKKOS/atom_vec_hybrid_kokkos.cpp +++ b/src/KOKKOS/atom_vec_hybrid_kokkos.cpp @@ -255,6 +255,7 @@ int AtomVecHybridKokkos::pack_comm_kokkos(const int &n, const DAT::tdual_int_2d const int &pbc_flag, const int pbc[]) { error->all(FLERR,"AtomVecHybridKokkos doesn't yet support threaded comm"); + return 0; } void AtomVecHybridKokkos::unpack_comm_kokkos(const int &n, const int &nfirst, const DAT::tdual_xfloat_2d &buf) @@ -266,12 +267,14 @@ int AtomVecHybridKokkos::pack_comm_self(const int &n, const DAT::tdual_int_2d &l const int &pbc_flag, const int pbc[]) { error->all(FLERR,"AtomVecHybridKokkos doesn't yet support threaded comm"); + return 0; } int AtomVecHybridKokkos::pack_border_kokkos(int n, DAT::tdual_int_2d k_sendlist, DAT::tdual_xfloat_2d buf,int iswap, int pbc_flag, int *pbc, ExecutionSpace space) { error->all(FLERR,"AtomVecHybridKokkos doesn't yet support threaded comm"); + return 0; } void AtomVecHybridKokkos::unpack_border_kokkos(const int &n, const int &nfirst, const DAT::tdual_xfloat_2d &buf, @@ -286,12 +289,14 @@ int AtomVecHybridKokkos::pack_exchange_kokkos(const int &nsend,DAT::tdual_xfloat X_FLOAT lo, X_FLOAT hi) { error->all(FLERR,"AtomVecHybridKokkos doesn't yet support threaded comm"); + return 0; } int AtomVecHybridKokkos::unpack_exchange_kokkos(DAT::tdual_xfloat_2d &k_buf, int nrecv, int nlocal, int dim, X_FLOAT lo, X_FLOAT hi, ExecutionSpace space) { error->all(FLERR,"AtomVecHybridKokkos doesn't yet support threaded comm"); + return 0; } /* ---------------------------------------------------------------------- */ From dbbfacc5985b1b8bb19c126bc9d997a7f92adc99 Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Wed, 20 Dec 2017 16:13:28 -0700 Subject: [PATCH 009/302] Fix atomic issues --- src/KOKKOS/fix_qeq_reax_kokkos.cpp | 18 +++++----- src/KOKKOS/pair_kokkos.h | 6 ++-- src/KOKKOS/pair_reaxc_kokkos.cpp | 56 +++++++++++++++--------------- 3 files changed, 41 insertions(+), 39 deletions(-) diff --git a/src/KOKKOS/fix_qeq_reax_kokkos.cpp b/src/KOKKOS/fix_qeq_reax_kokkos.cpp index 0f578707a4..d7632fe793 100644 --- a/src/KOKKOS/fix_qeq_reax_kokkos.cpp +++ b/src/KOKKOS/fix_qeq_reax_kokkos.cpp @@ -777,7 +777,7 @@ KOKKOS_INLINE_FUNCTION void FixQEqReaxKokkos::sparse13_item(int ii) const { // The q array is duplicated for OpenMP, atomic for CUDA, and neither for Serial - auto a_o = red_o.template access::value>(); + auto a_o = red_o.template access::value>(); const int i = d_ilist[ii]; if (mask[i] & groupbit) { @@ -785,9 +785,9 @@ void FixQEqReaxKokkos::sparse13_item(int ii) const for(int jj = d_firstnbr[i]; jj < d_firstnbr[i] + d_numnbrs[i]; jj++) { const int j = d_jlist(jj); tmp += d_val(jj) * d_s[j]; - a_o(j) += d_val(jj) * d_s[i]; + a_o[j] += d_val(jj) * d_s[i]; } - a_o(i) += tmp; + a_o[i] += tmp; } } @@ -829,7 +829,7 @@ KOKKOS_INLINE_FUNCTION void FixQEqReaxKokkos::sparse23_item(int ii) const { // The q array is duplicated for OpenMP, atomic for CUDA, and neither for Serial - auto a_o = red_o.template access::value>(); + auto a_o = red_o.template access::value>(); const int i = d_ilist[ii]; if (mask[i] & groupbit) { @@ -837,9 +837,9 @@ void FixQEqReaxKokkos::sparse23_item(int ii) const for(int jj = d_firstnbr[i]; jj < d_firstnbr[i] + d_numnbrs[i]; jj++) { const int j = d_jlist(jj); tmp += d_val(jj) * d_d[j]; - a_o(j) += d_val(jj) * d_d[i]; + a_o[j] += d_val(jj) * d_d[i]; } - a_o(i) += tmp; + a_o[i] += tmp; } } @@ -888,7 +888,7 @@ KOKKOS_INLINE_FUNCTION void FixQEqReaxKokkos::sparse33_item(int ii) const { // The q array is duplicated for OpenMP, atomic for CUDA, and neither for Serial - auto a_o = red_o.template access::value>(); + auto a_o = red_o.template access::value>(); const int i = d_ilist[ii]; if (mask[i] & groupbit) { @@ -896,9 +896,9 @@ void FixQEqReaxKokkos::sparse33_item(int ii) const for(int jj = d_firstnbr[i]; jj < d_firstnbr[i] + d_numnbrs[i]; jj++) { const int j = d_jlist(jj); tmp += d_val(jj) * d_t[j]; - a_o(j) += d_val(jj) * d_t[i]; + a_o[j] += d_val(jj) * d_t[i]; } - a_o(i) += tmp; + a_o[i] += tmp; } } diff --git a/src/KOKKOS/pair_kokkos.h b/src/KOKKOS/pair_kokkos.h index a409035dc6..445583c455 100644 --- a/src/KOKKOS/pair_kokkos.h +++ b/src/KOKKOS/pair_kokkos.h @@ -62,15 +62,17 @@ struct AtomicF { // Determine memory traits for force array // Do atomic trait when running HALFTHREAD neighbor list style -template +template struct AtomicDup { enum {value = Kokkos::Experimental::ScatterNonAtomic}; }; +#ifdef KOKKOS_ENABLE_CUDA template<> -struct AtomicDup { +struct AtomicDup { enum {value = Kokkos::Experimental::ScatterAtomic}; }; +#endif //Specialisation for Neighborlist types Half, HalfThread, Full template diff --git a/src/KOKKOS/pair_reaxc_kokkos.cpp b/src/KOKKOS/pair_reaxc_kokkos.cpp index 3a3faefc24..1cbe8933e9 100644 --- a/src/KOKKOS/pair_reaxc_kokkos.cpp +++ b/src/KOKKOS/pair_reaxc_kokkos.cpp @@ -1073,7 +1073,7 @@ void PairReaxCKokkos::operator()(PairReaxComputeLJCoulomb::value> > a_f = f; - auto a_f = dup_f.template access::value>(); + auto a_f = dup_f.template access::value>(); F_FLOAT powr_vdw, powgi_vdw, fn13, dfn13, exp1, exp2, etmp; F_FLOAT evdwl, fvdwl; @@ -1233,7 +1233,7 @@ void PairReaxCKokkos::operator()(PairReaxComputeTabulatedLJCoulomb::value> > a_f = f; - auto a_f = dup_f.template access::value>(); + auto a_f = dup_f.template access::value>(); const int i = d_ilist[ii]; const X_FLOAT xtmp = x(i,0); @@ -1616,8 +1616,8 @@ void PairReaxCKokkos::operator()(PairReaxBuildListsHalf, //Kokkos::View::value> > a_dDeltap_self = d_dDeltap_self; //Kokkos::View::value> > a_total_bo = d_total_bo; - auto a_dDeltap_self = dup_dDeltap_self.template access::value>(); - auto a_total_bo = dup_total_bo.template access::value>(); + auto a_dDeltap_self = dup_dDeltap_self.template access::value>(); + auto a_total_bo = dup_total_bo.template access::value>(); const int i = d_ilist[ii]; const X_FLOAT xtmp = x(i,0); @@ -2312,10 +2312,10 @@ void PairReaxCKokkos::operator()(PairReaxComputeMulti2::value> > a_Cdbo = d_Cdbo; Kokkos::View::value> > a_Cdbopi = d_Cdbopi; Kokkos::View::value> > a_Cdbopi2 = d_Cdbopi2; - auto a_CdDelta = dup_CdDelta.template access::value>(); - //auto a_Cdbo = dup_Cdbo.template access::value>(); - //auto a_Cdbopi = dup_Cdbopi.template access::value>(); - //auto a_Cdbopi2 = dup_Cdbopi2.template access::value>(); + auto a_CdDelta = dup_CdDelta.template access::value>(); + //auto a_Cdbo = dup_Cdbo.template access::value>(); + //auto a_Cdbopi = dup_Cdbopi.template access::value>(); + //auto a_Cdbopi2 = dup_Cdbopi2.template access::value>(); const int i = d_ilist[ii]; const int itype = type(i); @@ -2469,9 +2469,9 @@ void PairReaxCKokkos::operator()(PairReaxComputeAngular::value> > a_f = f; Kokkos::View::value> > a_Cdbo = d_Cdbo; //Kokkos::View::value> > a_CdDelta = d_CdDelta; - auto a_f = dup_f.template access::value>(); - //auto a_Cdbo = dup_Cdbo.template access::value>(); - auto a_CdDelta = dup_CdDelta.template access::value>(); + auto a_f = dup_f.template access::value>(); + //auto a_Cdbo = dup_Cdbo.template access::value>(); + auto a_CdDelta = dup_CdDelta.template access::value>(); const int i = d_ilist[ii]; @@ -2782,9 +2782,9 @@ void PairReaxCKokkos::operator()(PairReaxComputeTorsion::value> > a_f = f; //Kokkos::View::value> > a_CdDelta = d_CdDelta; Kokkos::View::value> > a_Cdbo = d_Cdbo; - auto a_f = dup_f.template access::value>(); - auto a_CdDelta = dup_CdDelta.template access::value>(); - //auto a_Cdbo = dup_Cdbo.template access::value>(); + auto a_f = dup_f.template access::value>(); + auto a_CdDelta = dup_CdDelta.template access::value>(); + //auto a_Cdbo = dup_Cdbo.template access::value>(); // in reaxc_torsion_angles: j = i, k = j, i = k; @@ -3155,7 +3155,7 @@ KOKKOS_INLINE_FUNCTION void PairReaxCKokkos::operator()(PairReaxComputeHydrogen, const int &ii, EV_FLOAT_REAX& ev) const { //Kokkos::View::value> > a_f = f; - auto a_f = dup_f.template access::value>(); + auto a_f = dup_f.template access::value>(); int hblist[MAX_BONDS]; F_FLOAT theta, cos_theta, sin_xhz4, cos_xhz1, sin_theta2; @@ -3305,9 +3305,9 @@ void PairReaxCKokkos::operator()(PairReaxUpdateBond, cons Kokkos::View::value> > a_Cdbo = d_Cdbo; Kokkos::View::value> > a_Cdbopi = d_Cdbopi; Kokkos::View::value> > a_Cdbopi2 = d_Cdbopi2; - //auto a_Cdbo = dup_Cdbo.template access::value>(); - //auto a_Cdbopi = dup_Cdbopi.template access::value>(); - //auto a_Cdbopi2 = dup_Cdbopi2.template access::value>(); + //auto a_Cdbo = dup_Cdbo.template access::value>(); + //auto a_Cdbopi = dup_Cdbopi.template access::value>(); + //auto a_Cdbopi2 = dup_Cdbopi2.template access::value>(); const int i = d_ilist[ii]; const tagint itag = tag(i); @@ -3356,8 +3356,8 @@ void PairReaxCKokkos::operator()(PairReaxComputeBond1::value> > a_f = f; //Kokkos::View::value> > a_CdDelta = d_CdDelta; - auto a_f = dup_f.template access::value>(); - auto a_CdDelta = dup_CdDelta.template access::value>(); + auto a_f = dup_f.template access::value>(); + auto a_CdDelta = dup_CdDelta.template access::value>(); F_FLOAT delij[3]; F_FLOAT p_be1, p_be2, De_s, De_p, De_pp, pow_BOs_be2, exp_be12, CEbo, ebond; @@ -3495,7 +3495,7 @@ KOKKOS_INLINE_FUNCTION void PairReaxCKokkos::operator()(PairReaxComputeBond2, const int &ii, EV_FLOAT_REAX& ev) const { //Kokkos::View::value> > a_f = f; - auto a_f = dup_f.template access::value>(); + auto a_f = dup_f.template access::value>(); F_FLOAT delij[3], delik[3], deljk[3], tmpvec[3]; F_FLOAT dBOp_i[3], dBOp_k[3], dln_BOp_pi[3], dln_BOp_pi2[3]; @@ -3710,8 +3710,8 @@ void PairReaxCKokkos::ev_tally(EV_FLOAT_REAX &ev, const int &i, cons // The eatom and vatom arrays are atomic for Half/Thread neighbor style //Kokkos::View::value> > a_eatom = v_eatom; //Kokkos::View::value> > a_vatom = v_vatom; - auto a_eatom = dup_eatom.template access::value>(); - auto a_vatom = dup_vatom.template access::value>(); + auto a_eatom = dup_eatom.template access::value>(); + auto a_vatom = dup_vatom.template access::value>(); if (eflag_atom) { const E_FLOAT epairhalf = 0.5 * epair; @@ -3778,7 +3778,7 @@ void PairReaxCKokkos::e_tally(EV_FLOAT_REAX &ev, const int &i, const if (eflag_atom) { //Kokkos::View::value> > a_eatom = v_eatom; - auto a_eatom = dup_eatom.template access::value>(); + auto a_eatom = dup_eatom.template access::value>(); const E_FLOAT epairhalf = 0.5 * epair; a_eatom[i] += epairhalf; @@ -3796,7 +3796,7 @@ void PairReaxCKokkos::e_tally_single(EV_FLOAT_REAX &ev, const int &i { // The eatom array is atomic for Half/Thread neighbor style //Kokkos::View::value> > a_eatom = v_eatom; - auto a_eatom = dup_eatom.template access::value>(); + auto a_eatom = dup_eatom.template access::value>(); a_eatom[i] += epair; } @@ -3830,7 +3830,7 @@ void PairReaxCKokkos::v_tally(EV_FLOAT_REAX &ev, const int &i, if (vflag_atom) { //Kokkos::View::value> > a_vatom = v_vatom; - auto a_vatom = dup_vatom.template access::value>(); + auto a_vatom = dup_vatom.template access::value>(); a_vatom(i,0) += v[0]; a_vatom(i,1) += v[1]; a_vatom(i,2) += v[2]; a_vatom(i,3) += v[3]; a_vatom(i,4) += v[4]; a_vatom(i,5) += v[5]; @@ -3848,7 +3848,7 @@ void PairReaxCKokkos::v_tally3(EV_FLOAT_REAX &ev, const int &i, cons // The eatom and vatom arrays are atomic for Half/Thread neighbor style //Kokkos::View::value> > a_vatom = v_vatom; - auto a_vatom = dup_vatom.template access::value>(); + auto a_vatom = dup_vatom.template access::value>(); F_FLOAT v[6]; @@ -3909,7 +3909,7 @@ void PairReaxCKokkos::v_tally4(EV_FLOAT_REAX &ev, const int &i, cons if (vflag_atom) { //Kokkos::View::value> > a_vatom = v_vatom; - auto a_vatom = dup_vatom.template access::value>(); + auto a_vatom = dup_vatom.template access::value>(); a_vatom(i,0) += 0.25 * v[0]; a_vatom(i,1) += 0.25 * v[1]; a_vatom(i,2) += 0.25 * v[2]; a_vatom(i,3) += 0.25 * v[3]; a_vatom(i,4) += 0.25 * v[4]; a_vatom(i,5) += 0.25 * v[5]; From 81331e2a34fb79dbc15cf00f5e17c1d90821163b Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Thu, 21 Dec 2017 11:07:06 -0700 Subject: [PATCH 010/302] Better load balance fix_qeq_reax_kokkos for half neigh list --- src/KOKKOS/fix_qeq_reax_kokkos.cpp | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/src/KOKKOS/fix_qeq_reax_kokkos.cpp b/src/KOKKOS/fix_qeq_reax_kokkos.cpp index d7632fe793..28838f27b6 100644 --- a/src/KOKKOS/fix_qeq_reax_kokkos.cpp +++ b/src/KOKKOS/fix_qeq_reax_kokkos.cpp @@ -398,19 +398,19 @@ void FixQEqReaxKokkos::compute_h_item(int ii, int &m_fill, const boo const X_FLOAT delz = x(j,2) - ztmp; if (neighflag != FULL) { + // skip half of the interactions const tagint jtag = tag(j); - flag = 0; - if (j < nlocal) flag = 1; - else if (itag < jtag) flag = 1; - else if (itag == jtag) { - if (delz > SMALL) flag = 1; - else if (fabs(delz) < SMALL) { - if (dely > SMALL) flag = 1; - else if (fabs(dely) < SMALL && delx > SMALL) - flag = 1; + if (j >= nlocal) { + if (itag > jtag) { + if ((itag+jtag) % 2 == 0) continue; + } else if (itag < jtag) { + if ((itag+jtag) % 2 == 1) continue; + } else { + if (x(j,2) < ztmp) continue; + if (x(j,2) == ztmp && x(j,1) < ytmp) continue; + if (x(j,2) == ztmp && x(j,1) == ytmp && x(j,0) < xtmp) continue; } } - if (!flag) continue; } const F_FLOAT rsq = delx*delx + dely*dely + delz*delz; From dbc308f35233d1a88ae6dbeb6b3330280d29fc0c Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Thu, 1 Mar 2018 10:06:43 -0700 Subject: [PATCH 011/302] Add warning --- src/KOKKOS/kokkos.cpp | 6 ++++ src/KOKKOS/pair_kokkos.h | 47 +++++++++++++++++++++++++++++++- src/KOKKOS/pair_reaxc_kokkos.cpp | 39 ++++++++++++++------------ src/KOKKOS/pair_reaxc_kokkos.h | 18 ++++++------ 4 files changed, 83 insertions(+), 27 deletions(-) diff --git a/src/KOKKOS/kokkos.cpp b/src/KOKKOS/kokkos.cpp index 5a74223353..2f9fbdb28b 100644 --- a/src/KOKKOS/kokkos.cpp +++ b/src/KOKKOS/kokkos.cpp @@ -119,6 +119,12 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) Kokkos::Cuda::initialize(select_device); #else LMPHostType::initialize(num_threads,numa); + +#ifndef KOKKOS_HAVE_SERIAL + if (num_threads == 1) + error->warning(FLERR,"Using Kokkos Serial backend (i.e. Makefile.kokkos_mpi_only) performs better with 1 thread"); +#endif + #endif // default settings for package kokkos command diff --git a/src/KOKKOS/pair_kokkos.h b/src/KOKKOS/pair_kokkos.h index d9288cb7e8..4f10a4eb2f 100644 --- a/src/KOKKOS/pair_kokkos.h +++ b/src/KOKKOS/pair_kokkos.h @@ -61,7 +61,7 @@ struct AtomicF { }; // Determine memory traits for force array -// Do atomic trait when running HALFTHREAD neighbor list style +// Do atomic trait when running HALFTHREAD neighbor list style with CUDA template struct AtomicDup { enum {value = Kokkos::Experimental::ScatterNonAtomic}; @@ -74,6 +74,51 @@ struct AtomicDup { }; #endif +#ifdef LMP_KOKKOS_USE_ATOMICS + +#ifdef KOKKOS_ENABLE_OPENMP +template<> +struct AtomicDup { + enum {value = Kokkos::Experimental::ScatterAtomic}; +}; +#endif + +#ifdef KOKKOS_ENABLE_THREADS +template<> +struct AtomicDup { + enum {value = Kokkos::Experimental::ScatterAtomic}; +}; +#endif + +#endif + + +// Determine duplication traits for force array +// Use duplication when running threaded and not using atomics +template +struct DupF { + enum {value = Kokkos::Experimental::ScatterNonDuplicated}; +}; + +#ifndef LMP_KOKKOS_USE_ATOMICS + +#ifdef KOKKOS_ENABLE_OPENMP +template<> +struct DupF { + enum {value = Kokkos::Experimental::ScatterDuplicated}; +}; +#endif + +#ifdef KOKKOS_ENABLE_THREADS +template<> +struct DupF { + enum {value = Kokkos::Experimental::ScatterDuplicated}; +}; +#endif + +#endif + + //Specialisation for Neighborlist types Half, HalfThread, Full template struct PairComputeFunctor { diff --git a/src/KOKKOS/pair_reaxc_kokkos.cpp b/src/KOKKOS/pair_reaxc_kokkos.cpp index 1cbe8933e9..f34549bc8c 100644 --- a/src/KOKKOS/pair_reaxc_kokkos.cpp +++ b/src/KOKKOS/pair_reaxc_kokkos.cpp @@ -73,6 +73,14 @@ PairReaxCKokkos::PairReaxCKokkos(LAMMPS *lmp) : PairReaxC(lmp) k_error_flag = DAT::tdual_int_scalar("pair:error_flag"); k_nbuf_local = DAT::tdual_int_scalar("pair:nbuf_local"); + + static double t1 = 0.0; + static double t2 = 0.0; + static double t3 = 0.0; + static double t4 = 0.0; + static double t5 = 0.0; + static double t6 = 0.0; + static double t7 = 0.0; } /* ---------------------------------------------------------------------- */ @@ -674,6 +682,8 @@ void PairReaxCKokkos::LR_vdW_Coulomb( int i, int j, double r_ij, LR_ template void PairReaxCKokkos::compute(int eflag_in, int vflag_in) { + Kokkos::Timer timer; + copymode = 1; bocnt = hbcnt = 0; @@ -809,6 +819,7 @@ void PairReaxCKokkos::compute(int eflag_in, int vflag_in) // zero Kokkos::parallel_for(Kokkos::RangePolicy(0,nmax),*this); + if (neighflag == HALF) Kokkos::parallel_for(Kokkos::RangePolicy >(0,ignum),*this); else if (neighflag == HALFTHREAD) @@ -2309,13 +2320,7 @@ KOKKOS_INLINE_FUNCTION void PairReaxCKokkos::operator()(PairReaxComputeMulti2, const int &ii, EV_FLOAT_REAX& ev) const { //Kokkos::View::value> > a_CdDelta = d_CdDelta; - Kokkos::View::value> > a_Cdbo = d_Cdbo; - Kokkos::View::value> > a_Cdbopi = d_Cdbopi; - Kokkos::View::value> > a_Cdbopi2 = d_Cdbopi2; auto a_CdDelta = dup_CdDelta.template access::value>(); - //auto a_Cdbo = dup_Cdbo.template access::value>(); - //auto a_Cdbopi = dup_Cdbopi.template access::value>(); - //auto a_Cdbopi2 = dup_Cdbopi2.template access::value>(); const int i = d_ilist[ii]; const int itype = type(i); @@ -2714,10 +2719,10 @@ void PairReaxCKokkos::operator()(PairReaxComputeAngular::operator()(PairReaxComputeAngular::operator()(PairReaxComputeTorsion::operator()(PairReaxUpdateBond, cons } if (flag) { - a_Cdbo(j,k_index) += Cdbo_i; - a_Cdbopi(j,k_index) += Cdbopi_i; - a_Cdbopi2(j,k_index) += Cdbopi2_i; + d_Cdbo(j,k_index) += Cdbo_i; + d_Cdbopi(j,k_index) += Cdbopi_i; + d_Cdbopi2(j,k_index) += Cdbopi2_i; } } } diff --git a/src/KOKKOS/pair_reaxc_kokkos.h b/src/KOKKOS/pair_reaxc_kokkos.h index 70aef2d608..f341da84c4 100644 --- a/src/KOKKOS/pair_reaxc_kokkos.h +++ b/src/KOKKOS/pair_reaxc_kokkos.h @@ -412,15 +412,15 @@ class PairReaxCKokkos : public PairReaxC { typename AT::t_ffloat_2d_dl d_C1dbopi2, d_C2dbopi2, d_C3dbopi2, d_C4dbopi2; typename AT::t_ffloat_2d_dl d_Cdbo, d_Cdbopi, d_Cdbopi2, d_dDeltap_self; - Kokkos::Experimental::ScatterView dup_total_bo; - Kokkos::Experimental::ScatterView dup_CdDelta; - Kokkos::Experimental::ScatterView dup_eatom; - Kokkos::Experimental::ScatterView dup_f; - Kokkos::Experimental::ScatterView dup_vatom; - Kokkos::Experimental::ScatterView dup_dDeltap_self; - Kokkos::Experimental::ScatterView dup_Cdbo; - Kokkos::Experimental::ScatterView dup_Cdbopi; - Kokkos::Experimental::ScatterView dup_Cdbopi2; + Kokkos::Experimental::ScatterView::value> dup_total_bo; + Kokkos::Experimental::ScatterView::value> dup_CdDelta; + Kokkos::Experimental::ScatterView::value> dup_eatom; + Kokkos::Experimental::ScatterView::value> dup_f; + Kokkos::Experimental::ScatterView::value> dup_vatom; + Kokkos::Experimental::ScatterView::value> dup_dDeltap_self; + Kokkos::Experimental::ScatterView::value> dup_Cdbo; + Kokkos::Experimental::ScatterView::value> dup_Cdbopi; + Kokkos::Experimental::ScatterView::value> dup_Cdbopi2; typedef Kokkos::DualView tdual_ffloat_2d_n7; typedef typename tdual_ffloat_2d_n7::t_dev_const_randomread t_ffloat_2d_n7_randomread; From ed494b295fab613fbc83d49e8236105a337f574d Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Thu, 1 Mar 2018 11:52:39 -0700 Subject: [PATCH 012/302] WIP --- src/KOKKOS/fix_qeq_reax_kokkos.cpp | 2 +- src/KOKKOS/fix_qeq_reax_kokkos.h | 3 +- src/KOKKOS/kokkos_type.h | 74 ++++++++++++++++++++++++++++++ src/KOKKOS/neigh_list_kokkos.h | 2 +- src/KOKKOS/pair_kokkos.h | 70 ---------------------------- src/KOKKOS/pair_reaxc_kokkos.cpp | 22 ++++----- src/KOKKOS/pair_reaxc_kokkos.h | 1 - 7 files changed, 88 insertions(+), 86 deletions(-) diff --git a/src/KOKKOS/fix_qeq_reax_kokkos.cpp b/src/KOKKOS/fix_qeq_reax_kokkos.cpp index 28838f27b6..7fa7f7f05a 100644 --- a/src/KOKKOS/fix_qeq_reax_kokkos.cpp +++ b/src/KOKKOS/fix_qeq_reax_kokkos.cpp @@ -250,7 +250,7 @@ void FixQEqReaxKokkos::pre_force(int vflag) k_t.template sync(); if (neighflag != FULL) - red_o = Kokkos::Experimental::create_scatter_view<> (d_o); // allocate duplicated memory + red_o = Kokkos::Experimental::create_scatter_view::value> (d_o); // allocate duplicated memory // 1st cg solve over b_s, s cg_solve1(); diff --git a/src/KOKKOS/fix_qeq_reax_kokkos.h b/src/KOKKOS/fix_qeq_reax_kokkos.h index 27be712ad8..9920325cf1 100644 --- a/src/KOKKOS/fix_qeq_reax_kokkos.h +++ b/src/KOKKOS/fix_qeq_reax_kokkos.h @@ -22,7 +22,6 @@ FixStyle(qeq/reax/kk/host,FixQEqReaxKokkos) #ifndef LMP_FIX_QEQ_REAX_KOKKOS_H #define LMP_FIX_QEQ_REAX_KOKKOS_H -#include #include "fix_qeq_reax.h" #include "kokkos_type.h" #include "neigh_list.h" @@ -193,7 +192,7 @@ class FixQEqReaxKokkos : public FixQEqReax { HAT::t_ffloat_2d h_s_hist, h_t_hist; typename AT::t_ffloat_2d_randomread r_s_hist, r_t_hist; - Kokkos::Experimental::ScatterView red_o; + Kokkos::Experimental::ScatterView::value> red_o; void init_shielding_k(); void init_hist(); diff --git a/src/KOKKOS/kokkos_type.h b/src/KOKKOS/kokkos_type.h index 6b6fc8610a..de0dab8eb1 100644 --- a/src/KOKKOS/kokkos_type.h +++ b/src/KOKKOS/kokkos_type.h @@ -20,6 +20,9 @@ #include #include #include +#include + +enum{FULL=1u,HALFTHREAD=2u,HALF=4u,N2=8u}; // same as in neigh_list_kokkos.h #if defined(KOKKOS_HAVE_CXX11) #undef ISFINITE @@ -205,6 +208,77 @@ struct ExecutionSpaceFromDevice { }; #endif + +// Determine memory traits for force array +// Do atomic trait when running HALFTHREAD neighbor list style +template +struct AtomicF { + enum {value = Kokkos::Unmanaged}; +}; + +template<> +struct AtomicF { + enum {value = Kokkos::Atomic|Kokkos::Unmanaged}; +}; + +// Determine memory traits for force array +// Do atomic trait when running HALFTHREAD neighbor list style with CUDA +template +struct AtomicDup { + enum {value = Kokkos::Experimental::ScatterNonAtomic}; +}; + +#ifdef KOKKOS_ENABLE_CUDA +template<> +struct AtomicDup { + enum {value = Kokkos::Experimental::ScatterAtomic}; +}; +#endif + +#ifdef LMP_KOKKOS_USE_ATOMICS + +#ifdef KOKKOS_ENABLE_OPENMP +template<> +struct AtomicDup { + enum {value = Kokkos::Experimental::ScatterAtomic}; +}; +#endif + +#ifdef KOKKOS_ENABLE_THREADS +template<> +struct AtomicDup { + enum {value = Kokkos::Experimental::ScatterAtomic}; +}; +#endif + +#endif + + +// Determine duplication traits for force array +// Use duplication when running threaded and not using atomics +template +struct DupF { + enum {value = Kokkos::Experimental::ScatterNonDuplicated}; +}; + +#ifndef LMP_KOKKOS_USE_ATOMICS + +#ifdef KOKKOS_ENABLE_OPENMP +template<> +struct DupF { + enum {value = Kokkos::Experimental::ScatterDuplicated}; +}; +#endif + +#ifdef KOKKOS_ENABLE_THREADS +template<> +struct DupF { + enum {value = Kokkos::Experimental::ScatterDuplicated}; +}; +#endif + +#endif + // define precision // handle global precision, force, energy, positions, kspace separately diff --git a/src/KOKKOS/neigh_list_kokkos.h b/src/KOKKOS/neigh_list_kokkos.h index 1c433f321c..993543157b 100644 --- a/src/KOKKOS/neigh_list_kokkos.h +++ b/src/KOKKOS/neigh_list_kokkos.h @@ -20,7 +20,7 @@ namespace LAMMPS_NS { -enum{FULL=1u,HALFTHREAD=2u,HALF=4u,N2=8u}; +enum{FULL=1u,HALFTHREAD=2u,HALF=4u,N2=8u}; // same as in kokkos_type.h class AtomNeighbors { diff --git a/src/KOKKOS/pair_kokkos.h b/src/KOKKOS/pair_kokkos.h index 4f10a4eb2f..be4eb574e2 100644 --- a/src/KOKKOS/pair_kokkos.h +++ b/src/KOKKOS/pair_kokkos.h @@ -48,76 +48,6 @@ struct DoCoul<1> { typedef CoulTag type; }; -// Determine memory traits for force array -// Do atomic trait when running HALFTHREAD neighbor list style -template -struct AtomicF { - enum {value = Kokkos::Unmanaged}; -}; - -template<> -struct AtomicF { - enum {value = Kokkos::Atomic|Kokkos::Unmanaged}; -}; - -// Determine memory traits for force array -// Do atomic trait when running HALFTHREAD neighbor list style with CUDA -template -struct AtomicDup { - enum {value = Kokkos::Experimental::ScatterNonAtomic}; -}; - -#ifdef KOKKOS_ENABLE_CUDA -template<> -struct AtomicDup { - enum {value = Kokkos::Experimental::ScatterAtomic}; -}; -#endif - -#ifdef LMP_KOKKOS_USE_ATOMICS - -#ifdef KOKKOS_ENABLE_OPENMP -template<> -struct AtomicDup { - enum {value = Kokkos::Experimental::ScatterAtomic}; -}; -#endif - -#ifdef KOKKOS_ENABLE_THREADS -template<> -struct AtomicDup { - enum {value = Kokkos::Experimental::ScatterAtomic}; -}; -#endif - -#endif - - -// Determine duplication traits for force array -// Use duplication when running threaded and not using atomics -template -struct DupF { - enum {value = Kokkos::Experimental::ScatterNonDuplicated}; -}; - -#ifndef LMP_KOKKOS_USE_ATOMICS - -#ifdef KOKKOS_ENABLE_OPENMP -template<> -struct DupF { - enum {value = Kokkos::Experimental::ScatterDuplicated}; -}; -#endif - -#ifdef KOKKOS_ENABLE_THREADS -template<> -struct DupF { - enum {value = Kokkos::Experimental::ScatterDuplicated}; -}; -#endif - -#endif - //Specialisation for Neighborlist types Half, HalfThread, Full template diff --git a/src/KOKKOS/pair_reaxc_kokkos.cpp b/src/KOKKOS/pair_reaxc_kokkos.cpp index f34549bc8c..55354f7c93 100644 --- a/src/KOKKOS/pair_reaxc_kokkos.cpp +++ b/src/KOKKOS/pair_reaxc_kokkos.cpp @@ -723,9 +723,9 @@ void PairReaxCKokkos::compute(int eflag_in, int vflag_in) d_ilist = k_list->d_ilist; // allocate duplicated memory - dup_f = Kokkos::Experimental::create_scatter_view<>(f); - dup_eatom = Kokkos::Experimental::create_scatter_view<>(v_eatom); - dup_vatom = Kokkos::Experimental::create_scatter_view<>(v_vatom); + dup_f = Kokkos::Experimental::create_scatter_view::value>(f); + dup_eatom = Kokkos::Experimental::create_scatter_view::value>(v_eatom); + dup_vatom = Kokkos::Experimental::create_scatter_view::value>(v_vatom); if (eflag_global) { for (int i = 0; i < 14; i++) @@ -797,8 +797,8 @@ void PairReaxCKokkos::compute(int eflag_in, int vflag_in) } // allocate duplicated memory - dup_dDeltap_self = Kokkos::Experimental::create_scatter_view<>(d_dDeltap_self); - dup_total_bo = Kokkos::Experimental::create_scatter_view<>(d_total_bo); + dup_dDeltap_self = Kokkos::Experimental::create_scatter_view::value>(d_dDeltap_self); + dup_total_bo = Kokkos::Experimental::create_scatter_view::value>(d_total_bo); // Neighbor lists for bond and hbond @@ -840,16 +840,16 @@ void PairReaxCKokkos::compute(int eflag_in, int vflag_in) resize = resize_bo || resize_hb; if (resize) { allocate_array(); - dup_dDeltap_self = Kokkos::Experimental::create_scatter_view<>(d_dDeltap_self); - dup_total_bo = Kokkos::Experimental::create_scatter_view<>(d_total_bo); + dup_dDeltap_self = Kokkos::Experimental::create_scatter_view::value>(d_dDeltap_self); + dup_total_bo = Kokkos::Experimental::create_scatter_view::value>(d_total_bo); } } // allocate duplicated memory - dup_CdDelta = Kokkos::Experimental::create_scatter_view<>(d_CdDelta); - //dup_Cdbo = Kokkos::Experimental::create_scatter_view<>(d_Cdbo); - //dup_Cdbopi = Kokkos::Experimental::create_scatter_view<>(d_Cdbopi); - //dup_Cdbopi2 = Kokkos::Experimental::create_scatter_view<>(d_Cdbopi2); + dup_CdDelta = Kokkos::Experimental::create_scatter_view::value>(d_CdDelta); + //dup_Cdbo = Kokkos::Experimental::create_scatter_view::value>(d_Cdbo); + //dup_Cdbopi = Kokkos::Experimental::create_scatter_view::value>(d_Cdbopi); + //dup_Cdbopi2 = Kokkos::Experimental::create_scatter_view::value>(d_Cdbopi2); // reduction over duplicated memory Kokkos::Experimental::contribute(d_total_bo, dup_total_bo); // needed in BondOrder1 diff --git a/src/KOKKOS/pair_reaxc_kokkos.h b/src/KOKKOS/pair_reaxc_kokkos.h index f341da84c4..23a5c79b24 100644 --- a/src/KOKKOS/pair_reaxc_kokkos.h +++ b/src/KOKKOS/pair_reaxc_kokkos.h @@ -24,7 +24,6 @@ PairStyle(reax/c/kk/host,PairReaxCKokkos) #define LMP_PAIR_REAXC_KOKKOS_H #include -#include #include "pair_kokkos.h" #include "pair_reaxc.h" #include "neigh_list_kokkos.h" From 6dd8efd0b479ba3648798765fe1d8a294b3000e4 Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Wed, 21 Mar 2018 17:20:45 -0600 Subject: [PATCH 013/302] Add if statements --- src/KOKKOS/fix_qeq_reax_kokkos.cpp | 46 +++++-- src/KOKKOS/fix_qeq_reax_kokkos.h | 4 +- src/KOKKOS/kokkos.h | 13 ++ src/KOKKOS/pair_kokkos.h | 29 +++- src/KOKKOS/pair_reaxc_kokkos.cpp | 210 ++++++++++++++++++----------- src/KOKKOS/pair_reaxc_kokkos.h | 35 +++-- 6 files changed, 229 insertions(+), 108 deletions(-) diff --git a/src/KOKKOS/fix_qeq_reax_kokkos.cpp b/src/KOKKOS/fix_qeq_reax_kokkos.cpp index 28838f27b6..be04d305cb 100644 --- a/src/KOKKOS/fix_qeq_reax_kokkos.cpp +++ b/src/KOKKOS/fix_qeq_reax_kokkos.cpp @@ -249,8 +249,12 @@ void FixQEqReaxKokkos::pre_force(int vflag) k_t.template modify(); k_t.template sync(); - if (neighflag != FULL) - red_o = Kokkos::Experimental::create_scatter_view<> (d_o); // allocate duplicated memory + need_dup = lmp->kokkos->need_dup(); + + if (need_dup) + dup_o = Kokkos::Experimental::create_scatter_view (d_o); // allocate duplicated memory + else + ndup_o = Kokkos::Experimental::create_scatter_view (d_o); // 1st cg solve over b_s, s cg_solve1(); @@ -258,8 +262,8 @@ void FixQEqReaxKokkos::pre_force(int vflag) // 2nd cg solve over b_t, t cg_solve2(); - if (neighflag != FULL) - red_o = decltype(red_o)(); // free duplicated memory + if (need_dup) + dup_o = decltype(dup_o)(); // free duplicated memory // calculate_Q(); calculate_q(); @@ -489,7 +493,9 @@ void FixQEqReaxKokkos::cg_solve1() Kokkos::parallel_for(Kokkos::RangePolicy(nlocal,nlocal+atom->nghost),*this); FixQEqReaxKokkosSparse13Functor sparse13_functor(this); Kokkos::parallel_for(inum,sparse13_functor); - Kokkos::Experimental::contribute(d_o, red_o); + if (need_dup) + if (need_dup) + Kokkos::Experimental::contribute(d_o, dup_o); } else { Kokkos::parallel_for(Kokkos::TeamPolicy (inum, teamsize), *this); } @@ -537,10 +543,13 @@ void FixQEqReaxKokkos::cg_solve1() Kokkos::parallel_for(inum,sparse22_functor); if (neighflag != FULL) { Kokkos::parallel_for(Kokkos::RangePolicy(nlocal,nlocal+atom->nghost),*this); - red_o.reset_except(d_o); + if (need_dup) + dup_o.reset_except(d_o); FixQEqReaxKokkosSparse23Functor sparse23_functor(this); Kokkos::parallel_for(inum,sparse23_functor); - Kokkos::Experimental::contribute(d_o, red_o); + if (need_dup) + if (need_dup) + Kokkos::Experimental::contribute(d_o, dup_o); } else { Kokkos::parallel_for(Kokkos::TeamPolicy (inum, teamsize), *this); } @@ -610,10 +619,13 @@ void FixQEqReaxKokkos::cg_solve2() Kokkos::parallel_for(inum,sparse32_functor); if (neighflag != FULL) { Kokkos::parallel_for(Kokkos::RangePolicy(nlocal,nlocal+atom->nghost),*this); - red_o.reset_except(d_o); + if (need_dup) + dup_o.reset_except(d_o); FixQEqReaxKokkosSparse33Functor sparse33_functor(this); Kokkos::parallel_for(inum,sparse33_functor); - Kokkos::Experimental::contribute(d_o, red_o); + if (need_dup) + if (need_dup) + Kokkos::Experimental::contribute(d_o, dup_o); } else { Kokkos::parallel_for(Kokkos::TeamPolicy (inum, teamsize), *this); } @@ -661,10 +673,13 @@ void FixQEqReaxKokkos::cg_solve2() Kokkos::parallel_for(inum,sparse22_functor); if (neighflag != FULL) { Kokkos::parallel_for(Kokkos::RangePolicy(nlocal,nlocal+atom->nghost),*this); - red_o.reset_except(d_o); + if (need_dup) + dup_o.reset_except(d_o); FixQEqReaxKokkosSparse23Functor sparse23_functor(this); Kokkos::parallel_for(inum,sparse23_functor); - Kokkos::Experimental::contribute(d_o, red_o); + if (need_dup) + if (need_dup) + Kokkos::Experimental::contribute(d_o, dup_o); } else { Kokkos::parallel_for(Kokkos::TeamPolicy (inum, teamsize), *this); } @@ -777,7 +792,8 @@ KOKKOS_INLINE_FUNCTION void FixQEqReaxKokkos::sparse13_item(int ii) const { // The q array is duplicated for OpenMP, atomic for CUDA, and neither for Serial - auto a_o = red_o.template access::value>(); + auto v_o = ScatterViewHelper::value,decltype(dup_o),decltype(ndup_o)>::get(dup_o,ndup_o); + auto a_o = v_o.template access::value>(); const int i = d_ilist[ii]; if (mask[i] & groupbit) { @@ -829,7 +845,8 @@ KOKKOS_INLINE_FUNCTION void FixQEqReaxKokkos::sparse23_item(int ii) const { // The q array is duplicated for OpenMP, atomic for CUDA, and neither for Serial - auto a_o = red_o.template access::value>(); + auto v_o = ScatterViewHelper::value,decltype(dup_o),decltype(ndup_o)>::get(dup_o,ndup_o); + auto a_o = v_o.template access::value>(); const int i = d_ilist[ii]; if (mask[i] & groupbit) { @@ -888,7 +905,8 @@ KOKKOS_INLINE_FUNCTION void FixQEqReaxKokkos::sparse33_item(int ii) const { // The q array is duplicated for OpenMP, atomic for CUDA, and neither for Serial - auto a_o = red_o.template access::value>(); + auto v_o = ScatterViewHelper::value,decltype(dup_o),decltype(ndup_o)>::get(dup_o,ndup_o); + auto a_o = v_o.template access::value>(); const int i = d_ilist[ii]; if (mask[i] & groupbit) { diff --git a/src/KOKKOS/fix_qeq_reax_kokkos.h b/src/KOKKOS/fix_qeq_reax_kokkos.h index 27be712ad8..4caacdf8a8 100644 --- a/src/KOKKOS/fix_qeq_reax_kokkos.h +++ b/src/KOKKOS/fix_qeq_reax_kokkos.h @@ -149,6 +149,7 @@ class FixQEqReaxKokkos : public FixQEqReax { private: int inum; int allocated_flag; + int need_dup; typedef Kokkos::DualView tdual_int_1d; Kokkos::DualView k_params; @@ -193,7 +194,8 @@ class FixQEqReaxKokkos : public FixQEqReax { HAT::t_ffloat_2d h_s_hist, h_t_hist; typename AT::t_ffloat_2d_randomread r_s_hist, r_t_hist; - Kokkos::Experimental::ScatterView red_o; + Kokkos::Experimental::ScatterView dup_o; + Kokkos::Experimental::ScatterView ndup_o; void init_shielding_k(); void init_hist(); diff --git a/src/KOKKOS/kokkos.h b/src/KOKKOS/kokkos.h index 7b7848f1f0..6ecb27eb32 100644 --- a/src/KOKKOS/kokkos.h +++ b/src/KOKKOS/kokkos.h @@ -16,6 +16,7 @@ #include "pointers.h" #include "kokkos_type.h" +#include "pair_kokkos.h" namespace LAMMPS_NS { @@ -39,6 +40,18 @@ class KokkosLMP : protected Pointers { ~KokkosLMP(); void accelerator(int, char **); int neigh_count(int); + + template + int need_dup() + { + int value = 0; + + if (neighflag == HALFTHREAD) + value = NeedDup::value; + + return value; + }; + private: static void my_signal_handler(int); }; diff --git a/src/KOKKOS/pair_kokkos.h b/src/KOKKOS/pair_kokkos.h index 4f10a4eb2f..1ec5dff0c8 100644 --- a/src/KOKKOS/pair_kokkos.h +++ b/src/KOKKOS/pair_kokkos.h @@ -95,8 +95,8 @@ struct AtomicDup { // Determine duplication traits for force array // Use duplication when running threaded and not using atomics -template -struct DupF { +template +struct NeedDup { enum {value = Kokkos::Experimental::ScatterNonDuplicated}; }; @@ -104,20 +104,41 @@ struct DupF { #ifdef KOKKOS_ENABLE_OPENMP template<> -struct DupF { +struct NeedDup { enum {value = Kokkos::Experimental::ScatterDuplicated}; }; #endif #ifdef KOKKOS_ENABLE_THREADS template<> -struct DupF { +struct NeedDup { enum {value = Kokkos::Experimental::ScatterDuplicated}; }; #endif #endif +template +class ScatterViewHelper {}; + +template +class ScatterViewHelper { +public: + KOKKOS_INLINE_FUNCTION + static T1 get(const T1 &dup, const T2 &nondup) { + return dup; + } +}; + +template +class ScatterViewHelper { +public: + KOKKOS_INLINE_FUNCTION + static T2 get(const T1 &dup, const T2 &nondup) { + return nondup; + } +}; + //Specialisation for Neighborlist types Half, HalfThread, Full template diff --git a/src/KOKKOS/pair_reaxc_kokkos.cpp b/src/KOKKOS/pair_reaxc_kokkos.cpp index f34549bc8c..842aeeea43 100644 --- a/src/KOKKOS/pair_reaxc_kokkos.cpp +++ b/src/KOKKOS/pair_reaxc_kokkos.cpp @@ -722,10 +722,18 @@ void PairReaxCKokkos::compute(int eflag_in, int vflag_in) d_neighbors = k_list->d_neighbors; d_ilist = k_list->d_ilist; + need_dup = lmp->kokkos->need_dup(); + // allocate duplicated memory - dup_f = Kokkos::Experimental::create_scatter_view<>(f); - dup_eatom = Kokkos::Experimental::create_scatter_view<>(v_eatom); - dup_vatom = Kokkos::Experimental::create_scatter_view<>(v_vatom); + if (need_dup) { + dup_f = Kokkos::Experimental::create_scatter_view(f); + dup_eatom = Kokkos::Experimental::create_scatter_view(d_eatom); + dup_vatom = Kokkos::Experimental::create_scatter_view(d_vatom); + } else { + ndup_f = Kokkos::Experimental::create_scatter_view(f); + ndup_eatom = Kokkos::Experimental::create_scatter_view(d_eatom); + ndup_vatom = Kokkos::Experimental::create_scatter_view(d_vatom); + } if (eflag_global) { for (int i = 0; i < 14; i++) @@ -797,9 +805,13 @@ void PairReaxCKokkos::compute(int eflag_in, int vflag_in) } // allocate duplicated memory - dup_dDeltap_self = Kokkos::Experimental::create_scatter_view<>(d_dDeltap_self); - dup_total_bo = Kokkos::Experimental::create_scatter_view<>(d_total_bo); - + if (need_dup) { + dup_dDeltap_self = Kokkos::Experimental::create_scatter_view(d_dDeltap_self); + dup_total_bo = Kokkos::Experimental::create_scatter_view(d_total_bo); + } else { + ndup_dDeltap_self = Kokkos::Experimental::create_scatter_view(d_dDeltap_self); + ndup_total_bo = Kokkos::Experimental::create_scatter_view(d_total_bo); + } // Neighbor lists for bond and hbond // try, resize if necessary @@ -840,19 +852,32 @@ void PairReaxCKokkos::compute(int eflag_in, int vflag_in) resize = resize_bo || resize_hb; if (resize) { allocate_array(); - dup_dDeltap_self = Kokkos::Experimental::create_scatter_view<>(d_dDeltap_self); - dup_total_bo = Kokkos::Experimental::create_scatter_view<>(d_total_bo); + if (need_dup) { + dup_dDeltap_self = Kokkos::Experimental::create_scatter_view(d_dDeltap_self); + dup_total_bo = Kokkos::Experimental::create_scatter_view(d_total_bo); + } else { + ndup_dDeltap_self = Kokkos::Experimental::create_scatter_view(d_dDeltap_self); + ndup_total_bo = Kokkos::Experimental::create_scatter_view(d_total_bo); + } } } // allocate duplicated memory - dup_CdDelta = Kokkos::Experimental::create_scatter_view<>(d_CdDelta); - //dup_Cdbo = Kokkos::Experimental::create_scatter_view<>(d_Cdbo); - //dup_Cdbopi = Kokkos::Experimental::create_scatter_view<>(d_Cdbopi); - //dup_Cdbopi2 = Kokkos::Experimental::create_scatter_view<>(d_Cdbopi2); + if (need_dup) { + dup_CdDelta = Kokkos::Experimental::create_scatter_view(d_CdDelta); + //dup_Cdbo = Kokkos::Experimental::create_scatter_view(d_Cdbo); + //dup_Cdbopi = Kokkos::Experimental::create_scatter_view(d_Cdbopi); + //dup_Cdbopi2 = Kokkos::Experimental::create_scatter_view(d_Cdbopi2); + } else { + ndup_CdDelta = Kokkos::Experimental::create_scatter_view(d_CdDelta); + //ndup_Cdbo = Kokkos::Experimental::create_scatter_view(d_Cdbo); + //ndup_Cdbopi = Kokkos::Experimental::create_scatter_view(d_Cdbopi); + //ndup_Cdbopi2 = Kokkos::Experimental::create_scatter_view(d_Cdbopi2); + } // reduction over duplicated memory - Kokkos::Experimental::contribute(d_total_bo, dup_total_bo); // needed in BondOrder1 + if (need_dup) + Kokkos::Experimental::contribute(d_total_bo, dup_total_bo); // needed in BondOrder1 // Bond order if (neighflag == HALF) { @@ -958,24 +983,28 @@ void PairReaxCKokkos::compute(int eflag_in, int vflag_in) ev_all.evdwl += ev.ereax[8]; // reduction over duplicated memory - Kokkos::Experimental::contribute(d_dDeltap_self, dup_dDeltap_self); // needed in ComputeBond2 - Kokkos::Experimental::contribute(d_CdDelta, dup_CdDelta); // needed in ComputeBond2 + if (need_dup) { + Kokkos::Experimental::contribute(d_dDeltap_self, dup_dDeltap_self); // needed in ComputeBond2 + Kokkos::Experimental::contribute(d_CdDelta, dup_CdDelta); // needed in ComputeBond2 - //Kokkos::Experimental::contribute(d_Cdbo, dup_Cdbo); // needed in UpdateBond, but also used in UpdateBond - //Kokkos::Experimental::contribute(d_Cdbopi, dup_Cdbopi); // needed in UpdateBond, but also used in UpdateBond - //Kokkos::Experimental::contribute(d_Cdbopi2, dup_Cdbopi2); // needed in UpdateBond, but also used in UpdateBond - //dup_Cdbo.reset_except(d_Cdbo); - //dup_Cdbopi.reset_except(d_Cdbopi); - //dup_Cdbopi2.reset_except(d_Cdbopi2); + //Kokkos::Experimental::contribute(d_Cdbo, dup_Cdbo); // needed in UpdateBond, but also used in UpdateBond + //Kokkos::Experimental::contribute(d_Cdbopi, dup_Cdbopi); // needed in UpdateBond, but also used in UpdateBond + //Kokkos::Experimental::contribute(d_Cdbopi2, dup_Cdbopi2); // needed in UpdateBond, but also used in UpdateBond + //dup_Cdbo.reset_except(d_Cdbo); + //dup_Cdbopi.reset_except(d_Cdbopi); + //dup_Cdbopi2.reset_except(d_Cdbopi2); + } // Bond force if (neighflag == HALF) { Kokkos::parallel_for(Kokkos::RangePolicy >(0,ignum),*this); // reduction over duplicated memory - //Kokkos::Experimental::contribute(d_Cdbo, dup_Cdbo); // needed in ComputeBond2 - //Kokkos::Experimental::contribute(d_Cdbopi, dup_Cdbopi); // needed in ComputeBond2 - //Kokkos::Experimental::contribute(d_Cdbopi2, dup_Cdbopi2); // needed in ComputeBond2 + //if (need_dup) { + // Kokkos::Experimental::contribute(d_Cdbo, dup_Cdbo); // needed in ComputeBond2 + // Kokkos::Experimental::contribute(d_Cdbopi, dup_Cdbopi); // needed in ComputeBond2 + // Kokkos::Experimental::contribute(d_Cdbopi2, dup_Cdbopi2); // needed in ComputeBond2 + //} if (evflag) Kokkos::parallel_reduce(Kokkos::RangePolicy >(0,ignum),*this,ev); @@ -987,9 +1016,11 @@ void PairReaxCKokkos::compute(int eflag_in, int vflag_in) Kokkos::parallel_for(Kokkos::RangePolicy >(0,ignum),*this); // reduction over duplicated memory - //Kokkos::Experimental::contribute(d_Cdbo, dup_Cdbo); // needed in ComputeBond2 - //Kokkos::Experimental::contribute(d_Cdbopi, dup_Cdbopi); // needed in ComputeBond2 - //Kokkos::Experimental::contribute(d_Cdbopi2, dup_Cdbopi2); // needed in ComputeBond2 + //if (need_dup) { + // Kokkos::Experimental::contribute(d_Cdbo, dup_Cdbo); // needed in ComputeBond2 + // Kokkos::Experimental::contribute(d_Cdbopi, dup_Cdbopi); // needed in ComputeBond2 + // Kokkos::Experimental::contribute(d_Cdbopi2, dup_Cdbopi2); // needed in ComputeBond2 + //} if (evflag) Kokkos::parallel_reduce(Kokkos::RangePolicy >(0,ignum),*this,ev); @@ -1000,7 +1031,8 @@ void PairReaxCKokkos::compute(int eflag_in, int vflag_in) } // reduction over duplicated memory - Kokkos::Experimental::contribute(f, dup_f); + if (need_dup) + Kokkos::Experimental::contribute(f, dup_f); if (eflag_global) { eng_vdwl += ev_all.evdwl; @@ -1018,13 +1050,15 @@ void PairReaxCKokkos::compute(int eflag_in, int vflag_in) if (vflag_fdotr) pair_virial_fdotr_compute(this); if (eflag_atom) { - Kokkos::Experimental::contribute(v_eatom, dup_eatom); + if (need_dup) + Kokkos::Experimental::contribute(d_eatom, dup_eatom); k_eatom.template modify(); k_eatom.template sync(); } if (vflag_atom) { - Kokkos::Experimental::contribute(v_vatom, dup_vatom); + if (need_dup) + Kokkos::Experimental::contribute(d_vatom, dup_vatom); k_vatom.template modify(); k_vatom.template sync(); } @@ -1033,15 +1067,17 @@ void PairReaxCKokkos::compute(int eflag_in, int vflag_in) FindBondSpecies(); // free duplicated memory - dup_f = decltype(dup_f)(); - dup_dDeltap_self = decltype(dup_dDeltap_self)(); - dup_total_bo = decltype(dup_total_bo)(); - dup_CdDelta = decltype(dup_CdDelta)(); - //dup_Cdbo = decltype(dup_Cdbo)(); - //dup_Cdbopi = decltype(dup_Cdbopi)(); - //dup_Cdbopi2 = decltype(dup_Cdbopi2)(); - dup_eatom = decltype(dup_eatom)(); - dup_vatom = decltype(dup_vatom)(); + if (need_dup) { + dup_f = decltype(dup_f)(); + dup_dDeltap_self = decltype(dup_dDeltap_self)(); + dup_total_bo = decltype(dup_total_bo)(); + dup_CdDelta = decltype(dup_CdDelta)(); + //dup_Cdbo = decltype(dup_Cdbo)(); + //dup_Cdbopi = decltype(dup_Cdbopi)(); + //dup_Cdbopi2 = decltype(dup_Cdbopi2)(); + dup_eatom = decltype(dup_eatom)(); + dup_vatom = decltype(dup_vatom)(); + } copymode = 0; } @@ -1084,7 +1120,8 @@ void PairReaxCKokkos::operator()(PairReaxComputeLJCoulomb::value> > a_f = f; - auto a_f = dup_f.template access::value>(); + auto v_f = ScatterViewHelper::value,decltype(dup_f),decltype(ndup_f)>::get(dup_f,ndup_f); + auto a_f = v_f.template access::value>(); F_FLOAT powr_vdw, powgi_vdw, fn13, dfn13, exp1, exp2, etmp; F_FLOAT evdwl, fvdwl; @@ -1244,7 +1281,8 @@ void PairReaxCKokkos::operator()(PairReaxComputeTabulatedLJCoulomb::value> > a_f = f; - auto a_f = dup_f.template access::value>(); + auto v_f = ScatterViewHelper::value,decltype(dup_f),decltype(ndup_f)>::get(dup_f,ndup_f); + auto a_f = v_f.template access::value>(); const int i = d_ilist[ii]; const X_FLOAT xtmp = x(i,0); @@ -1444,18 +1482,18 @@ void PairReaxCKokkos::operator()(PairReaxZero, const int &n) const { template KOKKOS_INLINE_FUNCTION void PairReaxCKokkos::operator()(PairReaxZeroEAtom, const int &i) const { - v_eatom(i) = 0.0; + d_eatom(i) = 0.0; } template KOKKOS_INLINE_FUNCTION void PairReaxCKokkos::operator()(PairReaxZeroVAtom, const int &i) const { - v_vatom(i,0) = 0.0; - v_vatom(i,1) = 0.0; - v_vatom(i,2) = 0.0; - v_vatom(i,3) = 0.0; - v_vatom(i,4) = 0.0; - v_vatom(i,5) = 0.0; + d_vatom(i,0) = 0.0; + d_vatom(i,1) = 0.0; + d_vatom(i,2) = 0.0; + d_vatom(i,3) = 0.0; + d_vatom(i,4) = 0.0; + d_vatom(i,5) = 0.0; } /* ---------------------------------------------------------------------- */ @@ -1626,9 +1664,11 @@ void PairReaxCKokkos::operator()(PairReaxBuildListsHalf, return; //Kokkos::View::value> > a_dDeltap_self = d_dDeltap_self; + auto v_dDeltap_self = ScatterViewHelper::value,decltype(dup_dDeltap_self),decltype(ndup_dDeltap_self)>::get(dup_dDeltap_self,ndup_dDeltap_self); + auto a_dDeltap_self = v_dDeltap_self.template access::value>(); //Kokkos::View::value> > a_total_bo = d_total_bo; - auto a_dDeltap_self = dup_dDeltap_self.template access::value>(); - auto a_total_bo = dup_total_bo.template access::value>(); + auto v_total_bo = ScatterViewHelper::value,decltype(dup_total_bo),decltype(ndup_total_bo)>::get(dup_total_bo,ndup_total_bo); + auto a_total_bo = v_total_bo.template access::value>(); const int i = d_ilist[ii]; const X_FLOAT xtmp = x(i,0); @@ -2320,7 +2360,8 @@ KOKKOS_INLINE_FUNCTION void PairReaxCKokkos::operator()(PairReaxComputeMulti2, const int &ii, EV_FLOAT_REAX& ev) const { //Kokkos::View::value> > a_CdDelta = d_CdDelta; - auto a_CdDelta = dup_CdDelta.template access::value>(); + auto v_CdDelta = ScatterViewHelper::value,decltype(dup_CdDelta),decltype(ndup_CdDelta)>::get(dup_CdDelta,ndup_CdDelta); + auto a_CdDelta = v_CdDelta.template access::value>(); const int i = d_ilist[ii]; const int itype = type(i); @@ -2472,12 +2513,13 @@ KOKKOS_INLINE_FUNCTION void PairReaxCKokkos::operator()(PairReaxComputeAngular, const int &ii, EV_FLOAT_REAX& ev) const { //Kokkos::View::value> > a_f = f; + auto v_f = ScatterViewHelper::value,decltype(dup_f),decltype(ndup_f)>::get(dup_f,ndup_f); + auto a_f = v_f.template access::value>(); Kokkos::View::value> > a_Cdbo = d_Cdbo; - //Kokkos::View::value> > a_CdDelta = d_CdDelta; - auto a_f = dup_f.template access::value>(); //auto a_Cdbo = dup_Cdbo.template access::value>(); - auto a_CdDelta = dup_CdDelta.template access::value>(); - + //Kokkos::View::value> > a_CdDelta = d_CdDelta; + auto v_CdDelta = ScatterViewHelper::value,decltype(dup_CdDelta),decltype(ndup_CdDelta)>::get(dup_CdDelta,ndup_CdDelta); + auto a_CdDelta = v_CdDelta.template access::value>(); const int i = d_ilist[ii]; const int itype = type(i); @@ -2785,10 +2827,12 @@ KOKKOS_INLINE_FUNCTION void PairReaxCKokkos::operator()(PairReaxComputeTorsion, const int &ii, EV_FLOAT_REAX& ev) const { //Kokkos::View::value> > a_f = f; + auto v_f = ScatterViewHelper::value,decltype(dup_f),decltype(ndup_f)>::get(dup_f,ndup_f); + auto a_f = v_f.template access::value>(); //Kokkos::View::value> > a_CdDelta = d_CdDelta; + auto v_CdDelta = ScatterViewHelper::value,decltype(dup_CdDelta),decltype(ndup_CdDelta)>::get(dup_CdDelta,ndup_CdDelta); + auto a_CdDelta = v_CdDelta.template access::value>(); Kokkos::View::value> > a_Cdbo = d_Cdbo; - auto a_f = dup_f.template access::value>(); - auto a_CdDelta = dup_CdDelta.template access::value>(); //auto a_Cdbo = dup_Cdbo.template access::value>(); // in reaxc_torsion_angles: j = i, k = j, i = k; @@ -3160,7 +3204,8 @@ KOKKOS_INLINE_FUNCTION void PairReaxCKokkos::operator()(PairReaxComputeHydrogen, const int &ii, EV_FLOAT_REAX& ev) const { //Kokkos::View::value> > a_f = f; - auto a_f = dup_f.template access::value>(); + auto v_f = ScatterViewHelper::value,decltype(dup_f),decltype(ndup_f)>::get(dup_f,ndup_f); + auto a_f = v_f.template access::value>(); int hblist[MAX_BONDS]; F_FLOAT theta, cos_theta, sin_xhz4, cos_xhz1, sin_theta2; @@ -3360,9 +3405,12 @@ KOKKOS_INLINE_FUNCTION void PairReaxCKokkos::operator()(PairReaxComputeBond1, const int &ii, EV_FLOAT_REAX& ev) const { //Kokkos::View::value> > a_f = f; + auto v_f = ScatterViewHelper::value,decltype(dup_f),decltype(ndup_f)>::get(dup_f,ndup_f); + auto a_f = v_f.template access::value>(); //Kokkos::View::value> > a_CdDelta = d_CdDelta; - auto a_f = dup_f.template access::value>(); - auto a_CdDelta = dup_CdDelta.template access::value>(); + auto v_CdDelta = ScatterViewHelper::value,decltype(dup_CdDelta),decltype(ndup_CdDelta)>::get(dup_CdDelta,ndup_CdDelta); + auto a_CdDelta = v_CdDelta.template access::value>(); + F_FLOAT delij[3]; F_FLOAT p_be1, p_be2, De_s, De_p, De_pp, pow_BOs_be2, exp_be12, CEbo, ebond; @@ -3500,7 +3548,8 @@ KOKKOS_INLINE_FUNCTION void PairReaxCKokkos::operator()(PairReaxComputeBond2, const int &ii, EV_FLOAT_REAX& ev) const { //Kokkos::View::value> > a_f = f; - auto a_f = dup_f.template access::value>(); + auto v_f = ScatterViewHelper::value,decltype(dup_f),decltype(ndup_f)>::get(dup_f,ndup_f); + auto a_f = v_f.template access::value>(); F_FLOAT delij[3], delik[3], deljk[3], tmpvec[3]; F_FLOAT dBOp_i[3], dBOp_k[3], dln_BOp_pi[3], dln_BOp_pi2[3]; @@ -3713,10 +3762,12 @@ void PairReaxCKokkos::ev_tally(EV_FLOAT_REAX &ev, const int &i, cons const int VFLAG = vflag_either; // The eatom and vatom arrays are atomic for Half/Thread neighbor style - //Kokkos::View::value> > a_eatom = v_eatom; - //Kokkos::View::value> > a_vatom = v_vatom; - auto a_eatom = dup_eatom.template access::value>(); - auto a_vatom = dup_vatom.template access::value>(); + //Kokkos::View::value> > a_eatom = d_eatom; + auto v_eatom = ScatterViewHelper::value,decltype(dup_eatom),decltype(ndup_eatom)>::get(dup_eatom,ndup_eatom); + auto a_eatom = v_eatom.template access::value>(); + //Kokkos::View::value> > a_vatom = d_vatom; + auto v_vatom = ScatterViewHelper::value,decltype(dup_vatom),decltype(ndup_vatom)>::get(dup_vatom,ndup_vatom); + auto a_vatom = v_vatom.template access::value>(); if (eflag_atom) { const E_FLOAT epairhalf = 0.5 * epair; @@ -3782,8 +3833,9 @@ void PairReaxCKokkos::e_tally(EV_FLOAT_REAX &ev, const int &i, const // The eatom array is atomic for Half/Thread neighbor style if (eflag_atom) { - //Kokkos::View::value> > a_eatom = v_eatom; - auto a_eatom = dup_eatom.template access::value>(); + //Kokkos::View::value> > a_eatom = d_eatom; + auto v_eatom = ScatterViewHelper::value,decltype(dup_eatom),decltype(ndup_eatom)>::get(dup_eatom,ndup_eatom); + auto a_eatom = v_eatom.template access::value>(); const E_FLOAT epairhalf = 0.5 * epair; a_eatom[i] += epairhalf; @@ -3800,8 +3852,9 @@ void PairReaxCKokkos::e_tally_single(EV_FLOAT_REAX &ev, const int &i const F_FLOAT &epair) const { // The eatom array is atomic for Half/Thread neighbor style - //Kokkos::View::value> > a_eatom = v_eatom; - auto a_eatom = dup_eatom.template access::value>(); + //Kokkos::View::value> > a_eatom = d_eatom; + auto v_eatom = ScatterViewHelper::value,decltype(dup_eatom),decltype(ndup_eatom)>::get(dup_eatom,ndup_eatom); + auto a_eatom = v_eatom.template access::value>(); a_eatom[i] += epair; } @@ -3834,8 +3887,9 @@ void PairReaxCKokkos::v_tally(EV_FLOAT_REAX &ev, const int &i, } if (vflag_atom) { - //Kokkos::View::value> > a_vatom = v_vatom; - auto a_vatom = dup_vatom.template access::value>(); + //Kokkos::View::value> > a_vatom = d_vatom; + auto v_vatom = ScatterViewHelper::value,decltype(dup_vatom),decltype(ndup_vatom)>::get(dup_vatom,ndup_vatom); + auto a_vatom = v_vatom.template access::value>(); a_vatom(i,0) += v[0]; a_vatom(i,1) += v[1]; a_vatom(i,2) += v[2]; a_vatom(i,3) += v[3]; a_vatom(i,4) += v[4]; a_vatom(i,5) += v[5]; @@ -3852,8 +3906,9 @@ void PairReaxCKokkos::v_tally3(EV_FLOAT_REAX &ev, const int &i, cons { // The eatom and vatom arrays are atomic for Half/Thread neighbor style - //Kokkos::View::value> > a_vatom = v_vatom; - auto a_vatom = dup_vatom.template access::value>(); + //Kokkos::View::value> > a_vatom = d_vatom; + auto v_vatom = ScatterViewHelper::value,decltype(dup_vatom),decltype(ndup_vatom)>::get(dup_vatom,ndup_vatom); + auto a_vatom = v_vatom.template access::value>(); F_FLOAT v[6]; @@ -3913,8 +3968,9 @@ void PairReaxCKokkos::v_tally4(EV_FLOAT_REAX &ev, const int &i, cons } if (vflag_atom) { - //Kokkos::View::value> > a_vatom = v_vatom; - auto a_vatom = dup_vatom.template access::value>(); + //Kokkos::View::value> > a_vatom = d_vatom; + auto v_vatom = ScatterViewHelper::value,decltype(dup_vatom),decltype(ndup_vatom)>::get(dup_vatom,ndup_vatom); + auto a_vatom = v_vatom.template access::value>(); a_vatom(i,0) += 0.25 * v[0]; a_vatom(i,1) += 0.25 * v[1]; a_vatom(i,2) += 0.25 * v[2]; a_vatom(i,3) += 0.25 * v[3]; a_vatom(i,4) += 0.25 * v[4]; a_vatom(i,5) += 0.25 * v[5]; @@ -4012,13 +4068,13 @@ void PairReaxCKokkos::ev_setup(int eflag, int vflag) maxeatom = atom->nmax; memoryKK->destroy_kokkos(k_eatom,eatom); memoryKK->create_kokkos(k_eatom,eatom,maxeatom,"pair:eatom"); - v_eatom = k_eatom.view(); + d_eatom = k_eatom.view(); } if (vflag_atom && atom->nmax > maxvatom) { maxvatom = atom->nmax; memoryKK->destroy_kokkos(k_vatom,vatom); memoryKK->create_kokkos(k_vatom,vatom,maxvatom,6,"pair:vatom"); - v_vatom = k_vatom.view(); + d_vatom = k_vatom.view(); } // zero accumulators diff --git a/src/KOKKOS/pair_reaxc_kokkos.h b/src/KOKKOS/pair_reaxc_kokkos.h index f341da84c4..aefa63a03d 100644 --- a/src/KOKKOS/pair_reaxc_kokkos.h +++ b/src/KOKKOS/pair_reaxc_kokkos.h @@ -391,11 +391,10 @@ class PairReaxCKokkos : public PairReaxC { typename AT::t_tagint_1d_randomread molecule; DAT::tdual_efloat_1d k_eatom; - typename AT::t_efloat_1d v_eatom; + typename AT::t_efloat_1d d_eatom; DAT::tdual_virial_array k_vatom; - typename ArrayTypes::t_virial_array d_vatom; - typename AT::t_virial_array v_vatom; + typename AT::t_virial_array d_vatom; HAT::t_virial_array h_vatom; DAT::tdual_float_1d k_tap; @@ -412,15 +411,27 @@ class PairReaxCKokkos : public PairReaxC { typename AT::t_ffloat_2d_dl d_C1dbopi2, d_C2dbopi2, d_C3dbopi2, d_C4dbopi2; typename AT::t_ffloat_2d_dl d_Cdbo, d_Cdbopi, d_Cdbopi2, d_dDeltap_self; - Kokkos::Experimental::ScatterView::value> dup_total_bo; - Kokkos::Experimental::ScatterView::value> dup_CdDelta; - Kokkos::Experimental::ScatterView::value> dup_eatom; - Kokkos::Experimental::ScatterView::value> dup_f; - Kokkos::Experimental::ScatterView::value> dup_vatom; - Kokkos::Experimental::ScatterView::value> dup_dDeltap_self; - Kokkos::Experimental::ScatterView::value> dup_Cdbo; - Kokkos::Experimental::ScatterView::value> dup_Cdbopi; - Kokkos::Experimental::ScatterView::value> dup_Cdbopi2; + Kokkos::Experimental::ScatterView dup_total_bo; + Kokkos::Experimental::ScatterView dup_CdDelta; + Kokkos::Experimental::ScatterView dup_eatom; + Kokkos::Experimental::ScatterView dup_f; + Kokkos::Experimental::ScatterView dup_vatom; + Kokkos::Experimental::ScatterView dup_dDeltap_self; + Kokkos::Experimental::ScatterView dup_Cdbo; + Kokkos::Experimental::ScatterView dup_Cdbopi; + Kokkos::Experimental::ScatterView dup_Cdbopi2; + + Kokkos::Experimental::ScatterView ndup_total_bo; + Kokkos::Experimental::ScatterView ndup_CdDelta; + Kokkos::Experimental::ScatterView ndup_eatom; + Kokkos::Experimental::ScatterView ndup_f; + Kokkos::Experimental::ScatterView ndup_vatom; + Kokkos::Experimental::ScatterView ndup_dDeltap_self; + Kokkos::Experimental::ScatterView ndup_Cdbo; + Kokkos::Experimental::ScatterView ndup_Cdbopi; + Kokkos::Experimental::ScatterView ndup_Cdbopi2; + + int need_dup; typedef Kokkos::DualView tdual_ffloat_2d_n7; typedef typename tdual_ffloat_2d_n7::t_dev_const_randomread t_ffloat_2d_n7_randomread; From 2dcee75ae4deb58117cddcc65adbd1091fd544c4 Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Thu, 22 Mar 2018 10:01:50 -0600 Subject: [PATCH 014/302] Add data duplication to pair_kokkos.h --- src/KOKKOS/kokkos_type.h | 31 +++++- src/KOKKOS/pair_kokkos.h | 197 ++++++++++++++------------------------- 2 files changed, 99 insertions(+), 129 deletions(-) diff --git a/src/KOKKOS/kokkos_type.h b/src/KOKKOS/kokkos_type.h index de0dab8eb1..c870bac31c 100644 --- a/src/KOKKOS/kokkos_type.h +++ b/src/KOKKOS/kokkos_type.h @@ -221,6 +221,7 @@ struct AtomicF { enum {value = Kokkos::Atomic|Kokkos::Unmanaged}; }; + // Determine memory traits for force array // Do atomic trait when running HALFTHREAD neighbor list style with CUDA template @@ -256,8 +257,8 @@ struct AtomicDup { // Determine duplication traits for force array // Use duplication when running threaded and not using atomics -template -struct DupF { +template +struct NeedDup { enum {value = Kokkos::Experimental::ScatterNonDuplicated}; }; @@ -265,20 +266,42 @@ struct DupF { #ifdef KOKKOS_ENABLE_OPENMP template<> -struct DupF { +struct NeedDup { enum {value = Kokkos::Experimental::ScatterDuplicated}; }; #endif #ifdef KOKKOS_ENABLE_THREADS template<> -struct DupF { +struct NeedDup { enum {value = Kokkos::Experimental::ScatterDuplicated}; }; #endif #endif +template +class ScatterViewHelper {}; + +template +class ScatterViewHelper { +public: + KOKKOS_INLINE_FUNCTION + static T1 get(const T1 &dup, const T2 &nondup) { + return dup; + } +}; + +template +class ScatterViewHelper { +public: + KOKKOS_INLINE_FUNCTION + static T2 get(const T1 &dup, const T2 &nondup) { + return nondup; + } +}; + + // define precision // handle global precision, force, energy, positions, kspace separately diff --git a/src/KOKKOS/pair_kokkos.h b/src/KOKKOS/pair_kokkos.h index 1ec5dff0c8..ab616d2c07 100644 --- a/src/KOKKOS/pair_kokkos.h +++ b/src/KOKKOS/pair_kokkos.h @@ -48,125 +48,48 @@ struct DoCoul<1> { typedef CoulTag type; }; -// Determine memory traits for force array -// Do atomic trait when running HALFTHREAD neighbor list style -template -struct AtomicF { - enum {value = Kokkos::Unmanaged}; -}; - -template<> -struct AtomicF { - enum {value = Kokkos::Atomic|Kokkos::Unmanaged}; -}; - -// Determine memory traits for force array -// Do atomic trait when running HALFTHREAD neighbor list style with CUDA -template -struct AtomicDup { - enum {value = Kokkos::Experimental::ScatterNonAtomic}; -}; - -#ifdef KOKKOS_ENABLE_CUDA -template<> -struct AtomicDup { - enum {value = Kokkos::Experimental::ScatterAtomic}; -}; -#endif - -#ifdef LMP_KOKKOS_USE_ATOMICS - -#ifdef KOKKOS_ENABLE_OPENMP -template<> -struct AtomicDup { - enum {value = Kokkos::Experimental::ScatterAtomic}; -}; -#endif - -#ifdef KOKKOS_ENABLE_THREADS -template<> -struct AtomicDup { - enum {value = Kokkos::Experimental::ScatterAtomic}; -}; -#endif - -#endif - - -// Determine duplication traits for force array -// Use duplication when running threaded and not using atomics -template -struct NeedDup { - enum {value = Kokkos::Experimental::ScatterNonDuplicated}; -}; - -#ifndef LMP_KOKKOS_USE_ATOMICS - -#ifdef KOKKOS_ENABLE_OPENMP -template<> -struct NeedDup { - enum {value = Kokkos::Experimental::ScatterDuplicated}; -}; -#endif - -#ifdef KOKKOS_ENABLE_THREADS -template<> -struct NeedDup { - enum {value = Kokkos::Experimental::ScatterDuplicated}; -}; -#endif - -#endif - -template -class ScatterViewHelper {}; - -template -class ScatterViewHelper { -public: - KOKKOS_INLINE_FUNCTION - static T1 get(const T1 &dup, const T2 &nondup) { - return dup; - } -}; - -template -class ScatterViewHelper { -public: - KOKKOS_INLINE_FUNCTION - static T2 get(const T1 &dup, const T2 &nondup) { - return nondup; - } -}; - //Specialisation for Neighborlist types Half, HalfThread, Full template struct PairComputeFunctor { typedef typename PairStyle::device_type device_type ; + typedef ArrayTypes AT; // Reduction type, contains evdwl, ecoul and virial[6] typedef EV_FLOAT value_type; // The copy of the pair style PairStyle c; + typename AT::t_f_array f; + typename AT::t_efloat_1d d_eatom; + typename AT::t_virial_array d_vatom; // The force array is atomic for Half/Thread neighbor style - Kokkos::View::value> > f; + //Kokkos::View::value> > f; + Kokkos::Experimental::ScatterView::value > dup_f; // The eatom and vatom arrays are atomic for Half/Thread neighbor style - Kokkos::View::value> > eatom; - Kokkos::View::value> > vatom; + //Kokkos::View::value> > eatom; + Kokkos::Experimental::ScatterView::value > dup_eatom; + + //Kokkos::View::value> > vatom; + Kokkos::Experimental::ScatterView::value > dup_vatom; + + NeighListKokkos list; PairComputeFunctor(PairStyle* c_ptr, NeighListKokkos* list_ptr): - c(*c_ptr),f(c.f),eatom(c.d_eatom), - vatom(c.d_vatom),list(*list_ptr) {}; + c(*c_ptr),list(*list_ptr) { + // allocate duplicated memory + dup_f = Kokkos::Experimental::create_scatter_view::value >(c.f); + dup_eatom = Kokkos::Experimental::create_scatter_view::value >(c.d_eatom); + dup_vatom = Kokkos::Experimental::create_scatter_view::value >(c.d_vatom); + }; // Call cleanup_copy which sets allocations NULL which are destructed by the PairStyle ~PairComputeFunctor() {c.cleanup_copy();list.copymode = 1;}; @@ -175,12 +98,25 @@ struct PairComputeFunctor { return j >> SBBITS & 3; } + void contribute() { + Kokkos::Experimental::contribute(c.f, dup_f); + + if (c.eflag_atom) + Kokkos::Experimental::contribute(c.d_eatom, dup_eatom); + + if (c.vflag_atom) + Kokkos::Experimental::contribute(c.d_vatom, dup_vatom); + } + // Loop over neighbors of one atom without coulomb interaction // This function is called in parallel template KOKKOS_FUNCTION EV_FLOAT compute_item(const int& ii, const NeighListKokkos &list, const NoCoulTag&) const { + + auto a_f = dup_f.template access::value>(); + EV_FLOAT ev; const int i = list.d_ilist[ii]; const X_FLOAT xtmp = c.x(i,0); @@ -214,9 +150,9 @@ struct PairComputeFunctor { fztmp += delz*fpair; if ((NEIGHFLAG==HALF || NEIGHFLAG==HALFTHREAD) && (NEWTON_PAIR || j < c.nlocal)) { - f(j,0) -= delx*fpair; - f(j,1) -= dely*fpair; - f(j,2) -= delz*fpair; + a_f(j,0) -= delx*fpair; + a_f(j,1) -= dely*fpair; + a_f(j,2) -= delz*fpair; } if (EVFLAG) { @@ -232,9 +168,9 @@ struct PairComputeFunctor { } - f(i,0) += fxtmp; - f(i,1) += fytmp; - f(i,2) += fztmp; + a_f(i,0) += fxtmp; + a_f(i,1) += fytmp; + a_f(i,2) += fztmp; return ev; } @@ -245,6 +181,9 @@ struct PairComputeFunctor { KOKKOS_FUNCTION EV_FLOAT compute_item(const int& ii, const NeighListKokkos &list, const CoulTag& ) const { + + auto a_f = dup_f.template access::value>(); + EV_FLOAT ev; const int i = list.d_ilist[ii]; const X_FLOAT xtmp = c.x(i,0); @@ -285,9 +224,9 @@ struct PairComputeFunctor { fztmp += delz*fpair; if ((NEIGHFLAG==HALF || NEIGHFLAG==HALFTHREAD) && (NEWTON_PAIR || j < c.nlocal)) { - f(j,0) -= delx*fpair; - f(j,1) -= dely*fpair; - f(j,2) -= delz*fpair; + a_f(j,0) -= delx*fpair; + a_f(j,1) -= dely*fpair; + a_f(j,2) -= delz*fpair; } if (EVFLAG) { @@ -309,9 +248,9 @@ struct PairComputeFunctor { } } - f(i,0) += fxtmp; - f(i,1) += fytmp; - f(i,2) += fztmp; + a_f(i,0) += fxtmp; + a_f(i,1) += fytmp; + a_f(i,2) += fztmp; return ev; } @@ -321,6 +260,9 @@ struct PairComputeFunctor { const F_FLOAT &epair, const F_FLOAT &fpair, const F_FLOAT &delx, const F_FLOAT &dely, const F_FLOAT &delz) const { + auto a_eatom = dup_eatom.template access::value>(); + auto a_vatom = dup_vatom.template access::value>(); + const int EFLAG = c.eflag; const int NEWTON_PAIR = c.newton_pair; const int VFLAG = c.vflag_either; @@ -328,8 +270,8 @@ struct PairComputeFunctor { if (EFLAG) { if (c.eflag_atom) { const E_FLOAT epairhalf = 0.5 * epair; - if (NEWTON_PAIR || i < c.nlocal) eatom[i] += epairhalf; - if ((NEWTON_PAIR || j < c.nlocal) && NEIGHFLAG != FULL) eatom[j] += epairhalf; + if (NEWTON_PAIR || i < c.nlocal) a_eatom[i] += epairhalf; + if ((NEWTON_PAIR || j < c.nlocal) && NEIGHFLAG != FULL) a_eatom[j] += epairhalf; } } @@ -380,20 +322,20 @@ struct PairComputeFunctor { if (c.vflag_atom) { if (NEWTON_PAIR || i < c.nlocal) { - vatom(i,0) += 0.5*v0; - vatom(i,1) += 0.5*v1; - vatom(i,2) += 0.5*v2; - vatom(i,3) += 0.5*v3; - vatom(i,4) += 0.5*v4; - vatom(i,5) += 0.5*v5; + a_vatom(i,0) += 0.5*v0; + a_vatom(i,1) += 0.5*v1; + a_vatom(i,2) += 0.5*v2; + a_vatom(i,3) += 0.5*v3; + a_vatom(i,4) += 0.5*v4; + a_vatom(i,5) += 0.5*v5; } if ((NEWTON_PAIR || j < c.nlocal) && NEIGHFLAG != FULL) { - vatom(j,0) += 0.5*v0; - vatom(j,1) += 0.5*v1; - vatom(j,2) += 0.5*v2; - vatom(j,3) += 0.5*v3; - vatom(j,4) += 0.5*v4; - vatom(j,5) += 0.5*v5; + a_vatom(j,0) += 0.5*v0; + a_vatom(j,1) += 0.5*v1; + a_vatom(j,2) += 0.5*v2; + a_vatom(j,3) += 0.5*v3; + a_vatom(j,4) += 0.5*v4; + a_vatom(j,5) += 0.5*v5; } } } @@ -432,6 +374,9 @@ struct PairComputeFunctor { return j >> SBBITS & 3; } + + void contribute() {} + template KOKKOS_FUNCTION EV_FLOAT compute_item(const int& ii, @@ -570,10 +515,12 @@ EV_FLOAT pair_compute_neighlist (PairStyle* fpair, typename Kokkos::Impl::enable PairComputeFunctor ff(fpair,list); if (fpair->eflag || fpair->vflag) Kokkos::parallel_reduce(list->inum,ff,ev); else Kokkos::parallel_for(list->inum,ff); + ff.contribute(); } else { PairComputeFunctor ff(fpair,list); if (fpair->eflag || fpair->vflag) Kokkos::parallel_reduce(list->inum,ff,ev); else Kokkos::parallel_for(list->inum,ff); + ff.contribute(); } return ev; } From 28b894a1d76ce7b4038d2a8bd0e4d00aa3cbb40e Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Thu, 22 Mar 2018 12:09:04 -0600 Subject: [PATCH 015/302] Remove unnecessary semicolon --- src/KOKKOS/kokkos.h | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/KOKKOS/kokkos.h b/src/KOKKOS/kokkos.h index 6ecb27eb32..c955bec600 100644 --- a/src/KOKKOS/kokkos.h +++ b/src/KOKKOS/kokkos.h @@ -50,7 +50,7 @@ class KokkosLMP : protected Pointers { value = NeedDup::value; return value; - }; + } private: static void my_signal_handler(int); From 385e1e5adf38668ddb4077a42eec22ada11576b7 Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Thu, 22 Mar 2018 12:28:21 -0600 Subject: [PATCH 016/302] Fix compile error with CUDA --- src/KOKKOS/kokkos_type.h | 2 +- src/KOKKOS/neigh_list_kokkos.h | 2 -- 2 files changed, 1 insertion(+), 3 deletions(-) diff --git a/src/KOKKOS/kokkos_type.h b/src/KOKKOS/kokkos_type.h index 21430455ba..665e53ac34 100644 --- a/src/KOKKOS/kokkos_type.h +++ b/src/KOKKOS/kokkos_type.h @@ -22,7 +22,7 @@ #include #include -enum{FULL=1u,HALFTHREAD=2u,HALF=4u,N2=8u}; // same as in neigh_list_kokkos.h +enum{FULL=1u,HALFTHREAD=2u,HALF=4u,N2=8u}; #if defined(KOKKOS_HAVE_CXX11) #undef ISFINITE diff --git a/src/KOKKOS/neigh_list_kokkos.h b/src/KOKKOS/neigh_list_kokkos.h index 993543157b..585422c54f 100644 --- a/src/KOKKOS/neigh_list_kokkos.h +++ b/src/KOKKOS/neigh_list_kokkos.h @@ -20,8 +20,6 @@ namespace LAMMPS_NS { -enum{FULL=1u,HALFTHREAD=2u,HALF=4u,N2=8u}; // same as in kokkos_type.h - class AtomNeighbors { public: From 52254fe155e7cd5e4678c0b729305ba12850c8b4 Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Mon, 2 Apr 2018 12:10:30 -0600 Subject: [PATCH 017/302] Fix issue in fix_qeq_reax_kokkos --- src/KOKKOS/fix_qeq_reax_kokkos.cpp | 36 +++++++++++++++++++++++------- 1 file changed, 28 insertions(+), 8 deletions(-) diff --git a/src/KOKKOS/fix_qeq_reax_kokkos.cpp b/src/KOKKOS/fix_qeq_reax_kokkos.cpp index 4d2ff8b1e5..b9fd49dd4e 100644 --- a/src/KOKKOS/fix_qeq_reax_kokkos.cpp +++ b/src/KOKKOS/fix_qeq_reax_kokkos.cpp @@ -487,8 +487,13 @@ void FixQEqReaxKokkos::cg_solve1() Kokkos::parallel_for(inum,sparse12_functor); if (neighflag != FULL) { Kokkos::parallel_for(Kokkos::RangePolicy(nlocal,nlocal+atom->nghost),*this); - FixQEqReaxKokkosSparse13Functor sparse13_functor(this); - Kokkos::parallel_for(inum,sparse13_functor); + if (neighflag == HALF) { + FixQEqReaxKokkosSparse13Functor sparse13_functor(this); + Kokkos::parallel_for(inum,sparse13_functor); + } else if (neighflag == HALFTHREAD) { + FixQEqReaxKokkosSparse13Functor sparse13_functor(this); + Kokkos::parallel_for(inum,sparse13_functor); + } if (need_dup) if (need_dup) Kokkos::Experimental::contribute(d_o, dup_o); @@ -541,8 +546,13 @@ void FixQEqReaxKokkos::cg_solve1() Kokkos::parallel_for(Kokkos::RangePolicy(nlocal,nlocal+atom->nghost),*this); if (need_dup) dup_o.reset_except(d_o); - FixQEqReaxKokkosSparse23Functor sparse23_functor(this); - Kokkos::parallel_for(inum,sparse23_functor); + if (neighflag == HALF) { + FixQEqReaxKokkosSparse23Functor sparse23_functor(this); + Kokkos::parallel_for(inum,sparse23_functor); + } else if (neighflag == HALFTHREAD) { + FixQEqReaxKokkosSparse23Functor sparse23_functor(this); + Kokkos::parallel_for(inum,sparse23_functor); + } if (need_dup) if (need_dup) Kokkos::Experimental::contribute(d_o, dup_o); @@ -616,8 +626,13 @@ void FixQEqReaxKokkos::cg_solve2() Kokkos::parallel_for(Kokkos::RangePolicy(nlocal,nlocal+atom->nghost),*this); if (need_dup) dup_o.reset_except(d_o); - FixQEqReaxKokkosSparse33Functor sparse33_functor(this); - Kokkos::parallel_for(inum,sparse33_functor); + if (neighflag == HALF) { + FixQEqReaxKokkosSparse33Functor sparse33_functor(this); + Kokkos::parallel_for(inum,sparse33_functor); + } else if (neighflag == HALFTHREAD) { + FixQEqReaxKokkosSparse33Functor sparse33_functor(this); + Kokkos::parallel_for(inum,sparse33_functor); + } if (need_dup) if (need_dup) Kokkos::Experimental::contribute(d_o, dup_o); @@ -670,8 +685,13 @@ void FixQEqReaxKokkos::cg_solve2() Kokkos::parallel_for(Kokkos::RangePolicy(nlocal,nlocal+atom->nghost),*this); if (need_dup) dup_o.reset_except(d_o); - FixQEqReaxKokkosSparse23Functor sparse23_functor(this); - Kokkos::parallel_for(inum,sparse23_functor); + if (neighflag == HALF) { + FixQEqReaxKokkosSparse23Functor sparse23_functor(this); + Kokkos::parallel_for(inum,sparse23_functor); + } else if (neighflag == HALFTHREAD) { + FixQEqReaxKokkosSparse23Functor sparse23_functor(this); + Kokkos::parallel_for(inum,sparse23_functor); + } if (need_dup) if (need_dup) Kokkos::Experimental::contribute(d_o, dup_o); From 0a5b027bac7a6f4c1eceed5735f4e44e2a59f18c Mon Sep 17 00:00:00 2001 From: Denis Taniguchi Date: Tue, 3 Jul 2018 11:10:27 -0400 Subject: [PATCH 018/302] Porting pair gran/hooke/history to Kokkos. --- src/GRANULAR/pair_gran_hooke_history.cpp | 2 + src/KOKKOS/Install.sh | 6 + src/KOKKOS/atom_vec_sphere_kokkos.cpp | 2155 +++++++++++++++++ src/KOKKOS/atom_vec_sphere_kokkos.h | 155 ++ src/KOKKOS/fix_neigh_history_kokkos.cpp | 346 +++ src/KOKKOS/fix_neigh_history_kokkos.h | 107 + src/KOKKOS/npair_kokkos.cpp | 382 ++- src/KOKKOS/npair_kokkos.h | 105 +- src/KOKKOS/pair_gran_hooke_history_kokkos.cpp | 440 ++++ src/KOKKOS/pair_gran_hooke_history_kokkos.h | 127 + src/KOKKOS/verlet_kokkos.cpp | 74 +- src/comm_brick.cpp | 2 +- src/fix_neigh_history.cpp | 2 + 13 files changed, 3814 insertions(+), 89 deletions(-) create mode 100644 src/KOKKOS/atom_vec_sphere_kokkos.cpp create mode 100644 src/KOKKOS/atom_vec_sphere_kokkos.h create mode 100644 src/KOKKOS/fix_neigh_history_kokkos.cpp create mode 100644 src/KOKKOS/fix_neigh_history_kokkos.h create mode 100644 src/KOKKOS/pair_gran_hooke_history_kokkos.cpp create mode 100644 src/KOKKOS/pair_gran_hooke_history_kokkos.h diff --git a/src/GRANULAR/pair_gran_hooke_history.cpp b/src/GRANULAR/pair_gran_hooke_history.cpp index d70c7391e2..df6db8ddfa 100644 --- a/src/GRANULAR/pair_gran_hooke_history.cpp +++ b/src/GRANULAR/pair_gran_hooke_history.cpp @@ -63,6 +63,8 @@ PairGranHookeHistory::PairGranHookeHistory(LAMMPS *lmp) : Pair(lmp) PairGranHookeHistory::~PairGranHookeHistory() { + if (copymode) return; + delete [] svector; if (fix_history) modify->delete_fix("NEIGH_HISTORY"); diff --git a/src/KOKKOS/Install.sh b/src/KOKKOS/Install.sh index c6fab2a1b1..73fa21cb41 100755 --- a/src/KOKKOS/Install.sh +++ b/src/KOKKOS/Install.sh @@ -71,6 +71,8 @@ action atom_vec_kokkos.cpp action atom_vec_kokkos.h action atom_vec_molecular_kokkos.cpp atom_vec_molecular.cpp action atom_vec_molecular_kokkos.h atom_vec_molecular.h +action atom_vec_sphere_kokkos.cpp atom_vec_sphere.cpp +action atom_vec_sphere_kokkos.h atom_vec_sphere.h action bond_class2_kokkos.cpp bond_class2.cpp action bond_class2_kokkos.h bond_class2.h action bond_fene_kokkos.cpp bond_fene.cpp @@ -97,6 +99,8 @@ action fix_eos_table_rx_kokkos.cpp fix_eos_table_rx.cpp action fix_eos_table_rx_kokkos.h fix_eos_table_rx.h action fix_langevin_kokkos.cpp action fix_langevin_kokkos.h +action fix_neigh_history_kokkos.cpp +action fix_neigh_history_kokkos.h action fix_nh_kokkos.cpp action fix_nh_kokkos.h action fix_nph_kokkos.cpp @@ -191,6 +195,8 @@ action pair_eam_fs_kokkos.cpp pair_eam_fs.cpp action pair_eam_fs_kokkos.h pair_eam_fs.h action pair_exp6_rx_kokkos.cpp pair_exp6_rx.cpp action pair_exp6_rx_kokkos.h pair_exp6_rx.h +action pair_gran_hooke_history_kokkos.h +action pair_gran_hooke_history_kokkos.cpp action pair_hybrid_kokkos.cpp action pair_hybrid_kokkos.h action pair_hybrid_overlay_kokkos.cpp diff --git a/src/KOKKOS/atom_vec_sphere_kokkos.cpp b/src/KOKKOS/atom_vec_sphere_kokkos.cpp new file mode 100644 index 0000000000..c2788526d7 --- /dev/null +++ b/src/KOKKOS/atom_vec_sphere_kokkos.cpp @@ -0,0 +1,2155 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include +#include +#include +#include "atom_vec_sphere_kokkos.h" +#include "atom_kokkos.h" +#include "atom_masks.h" +#include "comm_kokkos.h" +#include "domain.h" +#include "modify.h" +#include "force.h" +#include "fix.h" +#include "fix_adapt.h" +#include "math_const.h" +#include "memory.h" +#include "error.h" +#include "memory_kokkos.h" + +using namespace LAMMPS_NS; + +#define DELTA 10000 + +static const double MY_PI = 3.14159265358979323846; // pi + +/* ---------------------------------------------------------------------- */ + +AtomVecSphereKokkos::AtomVecSphereKokkos(LAMMPS *lmp) : AtomVecKokkos(lmp) +{ + molecular = 0; + + comm_x_only = 1; + comm_f_only = 0; + size_forward = 3; + size_reverse = 6; + size_border = 8; + size_velocity = 6; + size_data_atom = 7; + size_data_vel = 7; + xcol_data = 5; + + atom->sphere_flag = 1; + atom->radius_flag = atom->rmass_flag = atom->omega_flag = + atom->torque_flag = 1; + + k_count = DAT::tdual_int_1d("atom::k_count",1); + atomKK = (AtomKokkos *) atom; + commKK = (CommKokkos *) comm; +} + +/* ---------------------------------------------------------------------- */ + +void AtomVecSphereKokkos::init() +{ + AtomVec::init(); + + // set radvary if particle diameters are time-varying due to fix adapt + + radvary = 0; + comm_x_only = 1; + size_forward = 3; + + for (int i = 0; i < modify->nfix; i++) { + if (strcmp(modify->fix[i]->style,"adapt") == 0) { + FixAdapt *fix = (FixAdapt *) modify->fix[i]; + if (fix->diamflag) { + radvary = 1; + comm_x_only = 0; + size_forward = 5; + } + } + } +} + +/* ---------------------------------------------------------------------- + grow atom arrays + n = 0 grows arrays by a chunk + n > 0 allocates arrays to size n +------------------------------------------------------------------------- */ + +void AtomVecSphereKokkos::grow(int n) +{ + if (n == 0) nmax += DELTA; + else nmax = n; + atom->nmax = nmax; + if (nmax < 0 || nmax > MAXSMALLINT) + error->one(FLERR,"Per-processor system is too big"); + + sync(Device,ALL_MASK); + modified(Device,ALL_MASK); + + memoryKK->grow_kokkos(atomKK->k_tag,atomKK->tag,nmax,"atom:tag"); + memoryKK->grow_kokkos(atomKK->k_type,atomKK->type,nmax,"atom:type"); + memoryKK->grow_kokkos(atomKK->k_mask,atomKK->mask,nmax,"atom:mask"); + memoryKK->grow_kokkos(atomKK->k_image,atomKK->image,nmax,"atom:image"); + + memoryKK->grow_kokkos(atomKK->k_x,atomKK->x,nmax,3,"atom:x"); + memoryKK->grow_kokkos(atomKK->k_v,atomKK->v,nmax,3,"atom:v"); + memoryKK->grow_kokkos(atomKK->k_f,atomKK->f,nmax,3,"atom:f"); + memoryKK->grow_kokkos(atomKK->k_radius,atomKK->radius,nmax,"atom:radius"); + memoryKK->grow_kokkos(atomKK->k_rmass,atomKK->rmass,nmax,"atom:rmass"); + memoryKK->grow_kokkos(atomKK->k_omega,atomKK->omega,nmax,3,"atom:omega"); + memoryKK->grow_kokkos(atomKK->k_torque,atomKK->torque,nmax,3,"atom:torque"); + + if (atom->nextra_grow) + for (int iextra = 0; iextra < atom->nextra_grow; iextra++) + modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax); + + grow_reset(); + sync(Host,ALL_MASK); +} + +/* ---------------------------------------------------------------------- + reset local array ptrs +------------------------------------------------------------------------- */ + +void AtomVecSphereKokkos::grow_reset() +{ + tag = atomKK->tag; + d_tag = atomKK->k_tag.d_view; + h_tag = atomKK->k_tag.h_view; + + type = atomKK->type; + d_type = atomKK->k_type.d_view; + h_type = atomKK->k_type.h_view; + mask = atomKK->mask; + d_mask = atomKK->k_mask.d_view; + h_mask = atomKK->k_mask.h_view; + image = atomKK->image; + d_image = atomKK->k_image.d_view; + h_image = atomKK->k_image.h_view; + + x = atomKK->x; + d_x = atomKK->k_x.d_view; + h_x = atomKK->k_x.h_view; + v = atomKK->v; + d_v = atomKK->k_v.d_view; + h_v = atomKK->k_v.h_view; + f = atomKK->f; + d_f = atomKK->k_f.d_view; + h_f = atomKK->k_f.h_view; + radius = atomKK->radius; + d_radius = atomKK->k_radius.d_view; + h_radius = atomKK->k_radius.h_view; + rmass = atomKK->rmass; + d_rmass = atomKK->k_rmass.d_view; + h_rmass = atomKK->k_rmass.h_view; + omega = atomKK->omega; + d_omega = atomKK->k_omega.d_view; + h_omega = atomKK->k_omega.h_view; + torque = atomKK->torque; + d_torque = atomKK->k_torque.d_view; + h_torque = atomKK->k_torque.h_view; +} + +/* ---------------------------------------------------------------------- + copy atom I info to atom J +------------------------------------------------------------------------- */ + +void AtomVecSphereKokkos::copy(int i, int j, int delflag) +{ + sync(Host,X_MASK | V_MASK | TAG_MASK | TYPE_MASK | + MASK_MASK | IMAGE_MASK | RADIUS_MASK | + RMASS_MASK | OMEGA_MASK); + + h_tag[j] = h_tag[i]; + h_type[j] = h_type[i]; + h_mask[j] = h_mask[i]; + h_image[j] = h_image[i]; + h_x(j,0) = h_x(i,0); + h_x(j,1) = h_x(i,1); + h_x(j,2) = h_x(i,2); + h_v(j,0) = h_v(i,0); + h_v(j,1) = h_v(i,1); + h_v(j,2) = h_v(i,2); + + h_radius[j] = h_radius[i]; + h_rmass[j] = h_rmass[i]; + h_omega(j,0) = h_omega(i,0); + h_omega(j,1) = h_omega(i,1); + h_omega(j,2) = h_omega(i,2); + + if (atom->nextra_grow) + for (int iextra = 0; iextra < atom->nextra_grow; iextra++) + modify->fix[atom->extra_grow[iextra]]->copy_arrays(i,j,delflag); + + modified(Host,X_MASK | V_MASK | TAG_MASK | TYPE_MASK | + MASK_MASK | IMAGE_MASK | RADIUS_MASK | + RMASS_MASK | OMEGA_MASK); +} + +/* ---------------------------------------------------------------------- */ + +template +struct AtomVecSphereKokkos_PackComm { + typedef DeviceType device_type; + + typename ArrayTypes::t_x_array_randomread _x; + typename ArrayTypes::t_float_1d _radius,_rmass; + typename ArrayTypes::t_xfloat_2d_um _buf; + typename ArrayTypes::t_int_2d_const _list; + const int _iswap; + X_FLOAT _xprd,_yprd,_zprd,_xy,_xz,_yz; + X_FLOAT _pbc[6]; + + AtomVecSphereKokkos_PackComm( + const typename DAT::tdual_x_array &x, + const typename DAT::tdual_float_1d &radius, + const typename DAT::tdual_float_1d &rmass, + const typename DAT::tdual_xfloat_2d &buf, + const typename DAT::tdual_int_2d &list, + const int & iswap, + const X_FLOAT &xprd, const X_FLOAT &yprd, const X_FLOAT &zprd, + const X_FLOAT &xy, const X_FLOAT &xz, const X_FLOAT &yz, const int* const pbc): + _x(x.view()), + _radius(radius.view()), + _rmass(rmass.view()), + _list(list.view()),_iswap(iswap), + _xprd(xprd),_yprd(yprd),_zprd(zprd), + _xy(xy),_xz(xz),_yz(yz) { + const size_t maxsend = (buf.view().extent(0)*buf.view().extent(1))/3; + const size_t elements = 5; + buffer_view(_buf,buf,maxsend,elements); + _pbc[0] = pbc[0]; _pbc[1] = pbc[1]; _pbc[2] = pbc[2]; + _pbc[3] = pbc[3]; _pbc[4] = pbc[4]; _pbc[5] = pbc[5]; + } + + KOKKOS_INLINE_FUNCTION + void operator() (const int& i) const { + const int j = _list(_iswap,i); + if (PBC_FLAG == 0) { + _buf(i,0) = _x(j,0); + _buf(i,1) = _x(j,1); + _buf(i,2) = _x(j,2); + } else { + if (TRICLINIC == 0) { + _buf(i,0) = _x(j,0) + _pbc[0]*_xprd; + _buf(i,1) = _x(j,1) + _pbc[1]*_yprd; + _buf(i,2) = _x(j,2) + _pbc[2]*_zprd; + } else { + _buf(i,0) = _x(j,0) + _pbc[0]*_xprd + _pbc[5]*_xy + _pbc[4]*_xz; + _buf(i,1) = _x(j,1) + _pbc[1]*_yprd + _pbc[3]*_yz; + _buf(i,2) = _x(j,2) + _pbc[2]*_zprd; + } + } + _buf(i,3) = _radius(j); + _buf(i,4) = _rmass(j); + } +}; + +/* ---------------------------------------------------------------------- */ + +int AtomVecSphereKokkos::pack_comm_kokkos( + const int &n, + const DAT::tdual_int_2d &list, + const int & iswap, + const DAT::tdual_xfloat_2d &buf, + const int &pbc_flag, + const int* const pbc) +{ + // Fallback to AtomVecKokkos if radvary == 0 + if (radvary == 0) + return AtomVecKokkos::pack_comm_kokkos(n,list,iswap,buf,pbc_flag,pbc); + // Check whether to always run forward communication on the host + // Choose correct forward PackComm kernel + if(commKK->forward_comm_on_host) { + sync(Host,X_MASK|RADIUS_MASK|RMASS_MASK); + if(pbc_flag) { + if(domain->triclinic) { + struct AtomVecSphereKokkos_PackComm f( + atomKK->k_x, + atomKK->k_radius,atomKK->k_rmass, + buf,list,iswap, + domain->xprd,domain->yprd,domain->zprd, + domain->xy,domain->xz,domain->yz,pbc); + Kokkos::parallel_for(n,f); + } else { + struct AtomVecSphereKokkos_PackComm f( + atomKK->k_x, + atomKK->k_radius,atomKK->k_rmass, + buf,list,iswap, + domain->xprd,domain->yprd,domain->zprd, + domain->xy,domain->xz,domain->yz,pbc); + Kokkos::parallel_for(n,f); + } + } else { + if(domain->triclinic) { + struct AtomVecSphereKokkos_PackComm f( + atomKK->k_x, + atomKK->k_radius,atomKK->k_rmass, + buf,list,iswap, + domain->xprd,domain->yprd,domain->zprd, + domain->xy,domain->xz,domain->yz,pbc); + Kokkos::parallel_for(n,f); + } else { + struct AtomVecSphereKokkos_PackComm f( + atomKK->k_x, + atomKK->k_radius,atomKK->k_rmass, + buf,list,iswap, + domain->xprd,domain->yprd,domain->zprd, + domain->xy,domain->xz,domain->yz,pbc); + Kokkos::parallel_for(n,f); + } + } + } else { + sync(Device,X_MASK|RADIUS_MASK|RMASS_MASK); + if(pbc_flag) { + if(domain->triclinic) { + struct AtomVecSphereKokkos_PackComm f( + atomKK->k_x, + atomKK->k_radius,atomKK->k_rmass, + buf,list,iswap, + domain->xprd,domain->yprd,domain->zprd, + domain->xy,domain->xz,domain->yz,pbc); + Kokkos::parallel_for(n,f); + } else { + struct AtomVecSphereKokkos_PackComm f( + atomKK->k_x, + atomKK->k_radius,atomKK->k_rmass, + buf,list,iswap, + domain->xprd,domain->yprd,domain->zprd, + domain->xy,domain->xz,domain->yz,pbc); + Kokkos::parallel_for(n,f); + } + } else { + if(domain->triclinic) { + struct AtomVecSphereKokkos_PackComm f( + atomKK->k_x, + atomKK->k_radius,atomKK->k_rmass, + buf,list,iswap, + domain->xprd,domain->yprd,domain->zprd, + domain->xy,domain->xz,domain->yz,pbc); + Kokkos::parallel_for(n,f); + } else { + struct AtomVecSphereKokkos_PackComm f( + atomKK->k_x, + atomKK->k_radius,atomKK->k_rmass, + buf,list,iswap, + domain->xprd,domain->yprd,domain->zprd, + domain->xy,domain->xz,domain->yz,pbc); + Kokkos::parallel_for(n,f); + } + } + } + return n*size_forward; +} + +/* ---------------------------------------------------------------------- */ + +template +struct AtomVecSphereKokkos_PackCommSelf { + typedef DeviceType device_type; + + typename ArrayTypes::t_x_array_randomread _x; + typename ArrayTypes::t_x_array _xw; + typename ArrayTypes::t_float_1d _radius,_rmass; + int _nfirst; + typename ArrayTypes::t_int_2d_const _list; + const int _iswap; + X_FLOAT _xprd,_yprd,_zprd,_xy,_xz,_yz; + X_FLOAT _pbc[6]; + + AtomVecSphereKokkos_PackCommSelf( + const typename DAT::tdual_x_array &x, + const typename DAT::tdual_float_1d &radius, + const typename DAT::tdual_float_1d &rmass, + const int &nfirst, + const typename DAT::tdual_int_2d &list, + const int & iswap, + const X_FLOAT &xprd, const X_FLOAT &yprd, const X_FLOAT &zprd, + const X_FLOAT &xy, const X_FLOAT &xz, const X_FLOAT &yz, const int* const pbc): + _x(x.view()),_xw(x.view()), + _radius(radius.view()), + _rmass(rmass.view()), + _nfirst(nfirst),_list(list.view()),_iswap(iswap), + _xprd(xprd),_yprd(yprd),_zprd(zprd), + _xy(xy),_xz(xz),_yz(yz) { + _pbc[0] = pbc[0]; _pbc[1] = pbc[1]; _pbc[2] = pbc[2]; + _pbc[3] = pbc[3]; _pbc[4] = pbc[4]; _pbc[5] = pbc[5]; + }; + + KOKKOS_INLINE_FUNCTION + void operator() (const int& i) const { + const int j = _list(_iswap,i); + if (PBC_FLAG == 0) { + _xw(i+_nfirst,0) = _x(j,0); + _xw(i+_nfirst,1) = _x(j,1); + _xw(i+_nfirst,2) = _x(j,2); + } else { + if (TRICLINIC == 0) { + _xw(i+_nfirst,0) = _x(j,0) + _pbc[0]*_xprd; + _xw(i+_nfirst,1) = _x(j,1) + _pbc[1]*_yprd; + _xw(i+_nfirst,2) = _x(j,2) + _pbc[2]*_zprd; + } else { + _xw(i+_nfirst,0) = _x(j,0) + _pbc[0]*_xprd + _pbc[5]*_xy + _pbc[4]*_xz; + _xw(i+_nfirst,1) = _x(j,1) + _pbc[1]*_yprd + _pbc[3]*_yz; + _xw(i+_nfirst,2) = _x(j,2) + _pbc[2]*_zprd; + } + } + _radius(i+_nfirst) = _radius(j); + _rmass(i+_nfirst) = _rmass(j); + } +}; + +/* ---------------------------------------------------------------------- */ + +int AtomVecSphereKokkos::pack_comm_self( + const int &n, const DAT::tdual_int_2d &list, const int & iswap, + const int nfirst, const int &pbc_flag, const int* const pbc) { + // Fallback to AtomVecKokkos if radvary == 0 + if (radvary == 0) + return AtomVecKokkos::pack_comm_self(n,list,iswap,nfirst,pbc_flag,pbc); + if(commKK->forward_comm_on_host) { + sync(Host,X_MASK|RADIUS_MASK|RMASS_MASK); + modified(Host,X_MASK|RADIUS_MASK|RMASS_MASK); + if(pbc_flag) { + if(domain->triclinic) { + struct AtomVecSphereKokkos_PackCommSelf f( + atomKK->k_x, + atomKK->k_radius,atomKK->k_rmass, + nfirst,list,iswap, + domain->xprd,domain->yprd,domain->zprd, + domain->xy,domain->xz,domain->yz,pbc); + Kokkos::parallel_for(n,f); + } else { + struct AtomVecSphereKokkos_PackCommSelf f( + atomKK->k_x, + atomKK->k_radius,atomKK->k_rmass, + nfirst,list,iswap, + domain->xprd,domain->yprd,domain->zprd, + domain->xy,domain->xz,domain->yz,pbc); + Kokkos::parallel_for(n,f); + } + } else { + if(domain->triclinic) { + struct AtomVecSphereKokkos_PackCommSelf f( + atomKK->k_x, + atomKK->k_radius,atomKK->k_rmass, + nfirst,list,iswap, + domain->xprd,domain->yprd,domain->zprd, + domain->xy,domain->xz,domain->yz,pbc); + Kokkos::parallel_for(n,f); + } else { + struct AtomVecSphereKokkos_PackCommSelf f( + atomKK->k_x, + atomKK->k_radius,atomKK->k_rmass, + nfirst,list,iswap, + domain->xprd,domain->yprd,domain->zprd, + domain->xy,domain->xz,domain->yz,pbc); + Kokkos::parallel_for(n,f); + } + } + } else { + sync(Device,X_MASK|RADIUS_MASK|RMASS_MASK); + modified(Device,X_MASK|RADIUS_MASK|RMASS_MASK); + if(pbc_flag) { + if(domain->triclinic) { + struct AtomVecSphereKokkos_PackCommSelf f( + atomKK->k_x, + atomKK->k_radius,atomKK->k_rmass, + nfirst,list,iswap, + domain->xprd,domain->yprd,domain->zprd, + domain->xy,domain->xz,domain->yz,pbc); + Kokkos::parallel_for(n,f); + } else { + struct AtomVecSphereKokkos_PackCommSelf f( + atomKK->k_x, + atomKK->k_radius,atomKK->k_rmass, + nfirst,list,iswap, + domain->xprd,domain->yprd,domain->zprd, + domain->xy,domain->xz,domain->yz,pbc); + Kokkos::parallel_for(n,f); + } + } else { + if(domain->triclinic) { + struct AtomVecSphereKokkos_PackCommSelf f( + atomKK->k_x, + atomKK->k_radius,atomKK->k_rmass, + nfirst,list,iswap, + domain->xprd,domain->yprd,domain->zprd, + domain->xy,domain->xz,domain->yz,pbc); + Kokkos::parallel_for(n,f); + } else { + struct AtomVecSphereKokkos_PackCommSelf f( + atomKK->k_x, + atomKK->k_radius,atomKK->k_rmass, + nfirst,list,iswap, + domain->xprd,domain->yprd,domain->zprd, + domain->xy,domain->xz,domain->yz,pbc); + Kokkos::parallel_for(n,f); + } + } + } + return n*3; +} + +/* ---------------------------------------------------------------------- */ + +template +struct AtomVecSphereKokkos_UnpackComm { + typedef DeviceType device_type; + + typename ArrayTypes::t_x_array _x; + typename ArrayTypes::t_float_1d _radius,_rmass; + typename ArrayTypes::t_xfloat_2d_const _buf; + int _first; + + AtomVecSphereKokkos_UnpackComm( + const typename DAT::tdual_x_array &x, + const typename DAT::tdual_float_1d &radius, + const typename DAT::tdual_float_1d &rmass, + const typename DAT::tdual_xfloat_2d &buf, + const int& first): + _x(x.view()), + _radius(radius.view()), + _rmass(rmass.view()), + _buf(buf.view()), + _first(first) {}; + + KOKKOS_INLINE_FUNCTION + void operator() (const int& i) const { + _x(i+_first,0) = _buf(i,0); + _x(i+_first,1) = _buf(i,1); + _x(i+_first,2) = _buf(i,2); + _radius(i+_first) = _buf(i,3); + _rmass(i+_first) = _buf(i,4); + } +}; + +/* ---------------------------------------------------------------------- */ + +void AtomVecSphereKokkos::unpack_comm_kokkos( + const int &n, const int &first, + const DAT::tdual_xfloat_2d &buf ) { + // Fallback to AtomVecKokkos if radvary == 0 + if (radvary == 0) { + AtomVecKokkos::unpack_comm_kokkos(n,first,buf); + return; + } + if(commKK->forward_comm_on_host) { + sync(Host,X_MASK|RADIUS_MASK|RMASS_MASK); + modified(Host,X_MASK|RADIUS_MASK|RMASS_MASK); + struct AtomVecSphereKokkos_UnpackComm f( + atomKK->k_x, + atomKK->k_radius,atomKK->k_rmass, + buf,first); + Kokkos::parallel_for(n,f); + } else { + sync(Device,X_MASK|RADIUS_MASK|RMASS_MASK); + modified(Device,X_MASK|RADIUS_MASK|RMASS_MASK); + struct AtomVecSphereKokkos_UnpackComm f( + atomKK->k_x, + atomKK->k_radius,atomKK->k_rmass, + buf,first); + Kokkos::parallel_for(n,f); + } +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecSphereKokkos::pack_comm(int n, int *list, double *buf, + int pbc_flag, int *pbc) +{ + int i,j,m; + double dx,dy,dz; + + if (radvary == 0) { + // Not sure if we need to call sync for X here + sync(Host,X_MASK); + m = 0; + if (pbc_flag == 0) { + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = h_x(j,0); + buf[m++] = h_x(j,1); + buf[m++] = h_x(j,2); + } + } else { + if (domain->triclinic == 0) { + dx = pbc[0]*domain->xprd; + dy = pbc[1]*domain->yprd; + dz = pbc[2]*domain->zprd; + } else { + dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz; + dy = pbc[1]*domain->yprd + pbc[3]*domain->yz; + dz = pbc[2]*domain->zprd; + } + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = h_x(j,0) + dx; + buf[m++] = h_x(j,1) + dy; + buf[m++] = h_x(j,2) + dz; + } + } + } else { + sync(Host,X_MASK|RADIUS_MASK|RMASS_MASK); + m = 0; + if (pbc_flag == 0) { + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = h_x(j,0); + buf[m++] = h_x(j,1); + buf[m++] = h_x(j,2); + buf[m++] = h_radius[j]; + buf[m++] = h_rmass[j]; + } + } else { + if (domain->triclinic == 0) { + dx = pbc[0]*domain->xprd; + dy = pbc[1]*domain->yprd; + dz = pbc[2]*domain->zprd; + } else { + dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz; + dy = pbc[1]*domain->yprd + pbc[3]*domain->yz; + dz = pbc[2]*domain->zprd; + } + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = h_x(j,0) + dx; + buf[m++] = h_x(j,1) + dy; + buf[m++] = h_x(j,2) + dz; + buf[m++] = h_radius[j]; + buf[m++] = h_rmass[j]; + } + } + } + + return m; +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecSphereKokkos::pack_comm_vel(int n, int *list, double *buf, + int pbc_flag, int *pbc) +{ + int i,j,m; + double dx,dy,dz,dvx,dvy,dvz; + + if (radvary == 0) { + sync(Host,X_MASK|V_MASK|OMEGA_MASK); + m = 0; + if (pbc_flag == 0) { + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = h_x(j,0); + buf[m++] = h_x(j,1); + buf[m++] = h_x(j,2); + buf[m++] = h_v(j,0); + buf[m++] = h_v(j,1); + buf[m++] = h_v(j,2); + buf[m++] = h_omega(j,0); + buf[m++] = h_omega(j,1); + buf[m++] = h_omega(j,2); + } + } else { + if (domain->triclinic == 0) { + dx = pbc[0]*domain->xprd; + dy = pbc[1]*domain->yprd; + dz = pbc[2]*domain->zprd; + } else { + dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz; + dy = pbc[1]*domain->yprd + pbc[3]*domain->yz; + dz = pbc[2]*domain->zprd; + } + if (!deform_vremap) { + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = h_x(j,0) + dx; + buf[m++] = h_x(j,1) + dy; + buf[m++] = h_x(j,2) + dz; + buf[m++] = h_v(j,0); + buf[m++] = h_v(j,1); + buf[m++] = h_v(j,2); + buf[m++] = h_omega(j,0); + buf[m++] = h_omega(j,1); + buf[m++] = h_omega(j,2); + } + } else { + dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4]; + dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3]; + dvz = pbc[2]*h_rate[2]; + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = h_x(j,0) + dx; + buf[m++] = h_x(j,1) + dy; + buf[m++] = h_x(j,2) + dz; + if (mask[i] & deform_groupbit) { + buf[m++] = h_v(j,0) + dvx; + buf[m++] = h_v(j,1) + dvy; + buf[m++] = h_v(j,2) + dvz; + } else { + buf[m++] = h_v(j,0); + buf[m++] = h_v(j,1); + buf[m++] = h_v(j,2); + } + buf[m++] = h_omega(j,0); + buf[m++] = h_omega(j,1); + buf[m++] = h_omega(j,2); + } + } + } + + } else { + sync(Host,X_MASK|RADIUS_MASK|RMASS_MASK|V_MASK|OMEGA_MASK); + m = 0; + if (pbc_flag == 0) { + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = h_x(j,0); + buf[m++] = h_x(j,1); + buf[m++] = h_x(j,2); + buf[m++] = h_radius[j]; + buf[m++] = h_rmass[j]; + buf[m++] = h_v(j,0); + buf[m++] = h_v(j,1); + buf[m++] = h_v(j,2); + buf[m++] = h_omega(j,0); + buf[m++] = h_omega(j,1); + buf[m++] = h_omega(j,2); + } + } else { + if (domain->triclinic == 0) { + dx = pbc[0]*domain->xprd; + dy = pbc[1]*domain->yprd; + dz = pbc[2]*domain->zprd; + } else { + dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz; + dy = pbc[1]*domain->yprd + pbc[3]*domain->yz; + dz = pbc[2]*domain->zprd; + } + if (!deform_vremap) { + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = h_x(j,0) + dx; + buf[m++] = h_x(j,1) + dy; + buf[m++] = h_x(j,2) + dz; + buf[m++] = h_radius[j]; + buf[m++] = h_rmass[j]; + buf[m++] = h_v(j,0); + buf[m++] = h_v(j,1); + buf[m++] = h_v(j,2); + buf[m++] = h_omega(j,0); + buf[m++] = h_omega(j,1); + buf[m++] = h_omega(j,2); + } + } else { + dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4]; + dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3]; + dvz = pbc[2]*h_rate[2]; + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = h_x(j,0) + dx; + buf[m++] = h_x(j,1) + dy; + buf[m++] = h_x(j,2) + dz; + buf[m++] = h_radius[j]; + buf[m++] = h_rmass[j]; + if (mask[i] & deform_groupbit) { + buf[m++] = h_v(j,0) + dvx; + buf[m++] = h_v(j,1) + dvy; + buf[m++] = h_v(j,2) + dvz; + } else { + buf[m++] = h_v(j,0); + buf[m++] = h_v(j,1); + buf[m++] = h_v(j,2); + } + buf[m++] = h_omega(j,0); + buf[m++] = h_omega(j,1); + buf[m++] = h_omega(j,2); + } + } + } + } + + return m; +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecSphereKokkos::pack_comm_hybrid(int n, int *list, double *buf) +{ + if (radvary == 0) return 0; + + sync(Host,RADIUS_MASK|RMASS_MASK); + + int m = 0; + for (int i = 0; i < n; i++) { + const int j = list[i]; + buf[m++] = h_radius[j]; + buf[m++] = h_rmass[j]; + } + return m; +} + +/* ---------------------------------------------------------------------- */ + +void AtomVecSphereKokkos::unpack_comm(int n, int first, double *buf) +{ + if (radvary == 0) { + int m = 0; + const int last = first + n; + for (int i = first; i < last; i++) { + h_x(i,0) = buf[m++]; + h_x(i,1) = buf[m++]; + h_x(i,2) = buf[m++]; + } + modified(Host,X_MASK); + } else { + int m = 0; + const int last = first + n; + for (int i = first; i < last; i++) { + h_x(i,0) = buf[m++]; + h_x(i,1) = buf[m++]; + h_x(i,2) = buf[m++]; + h_radius[i] = buf[m++]; + h_rmass[i] = buf[m++]; + } + modified(Host,X_MASK|RADIUS_MASK|RMASS_MASK); + } +} + +/* ---------------------------------------------------------------------- */ + +void AtomVecSphereKokkos::unpack_comm_vel(int n, int first, double *buf) +{ + if (radvary == 0) { + int m = 0; + const int last = first + n; + for (int i = first; i < last; i++) { + h_x(i,0) = buf[m++]; + h_x(i,1) = buf[m++]; + h_x(i,2) = buf[m++]; + h_v(i,0) = buf[m++]; + h_v(i,1) = buf[m++]; + h_v(i,2) = buf[m++]; + h_omega(i,0) = buf[m++]; + h_omega(i,1) = buf[m++]; + h_omega(i,2) = buf[m++]; + } + modified(Host,X_MASK|V_MASK|OMEGA_MASK); + } else { + int m = 0; + const int last = first + n; + for (int i = first; i < last; i++) { + h_x(i,0) = buf[m++]; + h_x(i,1) = buf[m++]; + h_x(i,2) = buf[m++]; + h_radius[i] = buf[m++]; + h_rmass[i] = buf[m++]; + h_v(i,0) = buf[m++]; + h_v(i,1) = buf[m++]; + h_v(i,2) = buf[m++]; + h_omega(i,0) = buf[m++]; + h_omega(i,1) = buf[m++]; + h_omega(i,2) = buf[m++]; + } + modified(Host,X_MASK|RADIUS_MASK|RMASS_MASK|V_MASK|OMEGA_MASK); + } +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecSphereKokkos::unpack_comm_hybrid(int n, int first, double *buf) +{ + if (radvary == 0) return 0; + + int m = 0; + const int last = first + n; + for (int i = first; i < last; i++) { + h_radius[i] = buf[m++]; + h_rmass[i] = buf[m++]; + } + modified(Host,RADIUS_MASK|RMASS_MASK); + return m; +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecSphereKokkos::pack_reverse(int n, int first, double *buf) +{ + if(n > 0) + sync(Host,F_MASK|TORQUE_MASK); + + int m = 0; + const int last = first + n; + for (int i = first; i < last; i++) { + buf[m++] = h_f(i,0); + buf[m++] = h_f(i,1); + buf[m++] = h_f(i,2); + buf[m++] = h_torque(i,0); + buf[m++] = h_torque(i,1); + buf[m++] = h_torque(i,2); + } + return m; +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecSphereKokkos::pack_reverse_hybrid(int n, int first, double *buf) +{ + if(n > 0) + sync(Host,TORQUE_MASK); + + int m = 0; + const int last = first + n; + for (int i = first; i < last; i++) { + buf[m++] = h_torque(i,0); + buf[m++] = h_torque(i,1); + buf[m++] = h_torque(i,2); + } + return m; +} + +/* ---------------------------------------------------------------------- */ + +void AtomVecSphereKokkos::unpack_reverse(int n, int *list, double *buf) +{ + if(n > 0) { + sync(Host,F_MASK|TORQUE_MASK); + modified(Host,F_MASK|TORQUE_MASK); + } + + int m = 0; + for (int i = 0; i < n; i++) { + const int j = list[i]; + h_f(j,0) += buf[m++]; + h_f(j,1) += buf[m++]; + h_f(j,2) += buf[m++]; + h_torque(j,0) += buf[m++]; + h_torque(j,1) += buf[m++]; + h_torque(j,2) += buf[m++]; + } +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecSphereKokkos::unpack_reverse_hybrid(int n, int *list, double *buf) +{ + if(n > 0) { + sync(Host,TORQUE_MASK); + modified(Host,TORQUE_MASK); + } + + int m = 0; + for (int i = 0; i < n; i++) { + const int j = list[i]; + h_torque(j,0) += buf[m++]; + h_torque(j,1) += buf[m++]; + h_torque(j,2) += buf[m++]; + } + return m; +} + +/* ---------------------------------------------------------------------- */ + +template +struct AtomVecSphereKokkos_PackBorder { + typedef DeviceType device_type; + + typename ArrayTypes::t_xfloat_2d _buf; + const typename ArrayTypes::t_int_2d_const _list; + const int _iswap; + const typename ArrayTypes::t_x_array_randomread _x; + const typename ArrayTypes::t_tagint_1d _tag; + const typename ArrayTypes::t_int_1d _type; + const typename ArrayTypes::t_int_1d _mask; + typename ArrayTypes::t_float_1d _radius,_rmass; + X_FLOAT _dx,_dy,_dz; + + AtomVecSphereKokkos_PackBorder(const typename ArrayTypes::t_xfloat_2d &buf, + const typename ArrayTypes::t_int_2d_const &list, + const int & iswap, + const typename ArrayTypes::t_x_array &x, + const typename ArrayTypes::t_tagint_1d &tag, + const typename ArrayTypes::t_int_1d &type, + const typename ArrayTypes::t_int_1d &mask, + const typename ArrayTypes::t_float_1d &radius, + const typename ArrayTypes::t_float_1d &rmass, + const X_FLOAT &dx, const X_FLOAT &dy, const X_FLOAT &dz): + _buf(buf),_list(list),_iswap(iswap), + _x(x),_tag(tag),_type(type),_mask(mask), + _radius(radius), + _rmass(rmass), + _dx(dx),_dy(dy),_dz(dz) {} + + KOKKOS_INLINE_FUNCTION + void operator() (const int& i) const { + const int j = _list(_iswap,i); + if (PBC_FLAG == 0) { + _buf(i,0) = _x(j,0); + _buf(i,1) = _x(j,1); + _buf(i,2) = _x(j,2); + } else { + _buf(i,0) = _x(j,0) + _dx; + _buf(i,1) = _x(j,1) + _dy; + _buf(i,2) = _x(j,2) + _dz; + } + _buf(i,3) = _tag(j); + _buf(i,4) = _type(j); + _buf(i,5) = _mask(j); + _buf(i,6) = _radius(j); + _buf(i,7) = _rmass(j); + } +}; + +/* ---------------------------------------------------------------------- */ + +int AtomVecSphereKokkos::pack_border_kokkos(int n, DAT::tdual_int_2d k_sendlist, DAT::tdual_xfloat_2d buf,int iswap, + int pbc_flag, int *pbc, ExecutionSpace space) +{ + X_FLOAT dx,dy,dz; + + // This was in atom_vec_dpd_kokkos but doesn't appear in any other atom_vec + sync(space,ALL_MASK); + + if (pbc_flag != 0) { + if (domain->triclinic == 0) { + dx = pbc[0]*domain->xprd; + dy = pbc[1]*domain->yprd; + dz = pbc[2]*domain->zprd; + } else { + dx = pbc[0]; + dy = pbc[1]; + dz = pbc[2]; + } + if(space==Host) { + AtomVecSphereKokkos_PackBorder f( + buf.view(), k_sendlist.view(), + iswap,h_x,h_tag,h_type,h_mask, + h_radius,h_rmass, + dx,dy,dz); + Kokkos::parallel_for(n,f); + } else { + AtomVecSphereKokkos_PackBorder f( + buf.view(), k_sendlist.view(), + iswap,d_x,d_tag,d_type,d_mask, + d_radius,d_rmass, + dx,dy,dz); + Kokkos::parallel_for(n,f); + } + } else { + dx = dy = dz = 0; + if(space==Host) { + AtomVecSphereKokkos_PackBorder f( + buf.view(), k_sendlist.view(), + iswap,h_x,h_tag,h_type,h_mask, + h_radius,h_rmass, + dx,dy,dz); + Kokkos::parallel_for(n,f); + } else { + AtomVecSphereKokkos_PackBorder f( + buf.view(), k_sendlist.view(), + iswap,d_x,d_tag,d_type,d_mask, + d_radius,d_rmass, + dx,dy,dz); + Kokkos::parallel_for(n,f); + } + } + return n*6; +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecSphereKokkos::pack_border(int n, int *list, double *buf, + int pbc_flag, int *pbc) +{ + int i,j,m; + double dx,dy,dz; + + sync(Host,ALL_MASK); + + m = 0; + if (pbc_flag == 0) { + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = h_x(j,0); + buf[m++] = h_x(j,1); + buf[m++] = h_x(j,2); + buf[m++] = ubuf(h_tag[j]).d; + buf[m++] = ubuf(h_type[j]).d; + buf[m++] = ubuf(h_mask[j]).d; + buf[m++] = h_radius[j]; + buf[m++] = h_rmass[j]; + } + } else { + if (domain->triclinic == 0) { + dx = pbc[0]*domain->xprd; + dy = pbc[1]*domain->yprd; + dz = pbc[2]*domain->zprd; + } else { + dx = pbc[0]; + dy = pbc[1]; + dz = pbc[2]; + } + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = h_x(j,0) + dx; + buf[m++] = h_x(j,1) + dy; + buf[m++] = h_x(j,2) + dz; + buf[m++] = ubuf(h_tag[j]).d; + buf[m++] = ubuf(h_type[j]).d; + buf[m++] = ubuf(h_mask[j]).d; + buf[m++] = h_radius[j]; + buf[m++] = h_rmass[j]; + } + } + + if (atom->nextra_border) + for (int iextra = 0; iextra < atom->nextra_border; iextra++) + m += modify->fix[atom->extra_border[iextra]]->pack_border(n,list,&buf[m]); + + return m; +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecSphereKokkos::pack_border_vel(int n, int *list, double *buf, + int pbc_flag, int *pbc) +{ + int i,j,m; + double dx,dy,dz,dvx,dvy,dvz; + + sync(Host,ALL_MASK); + + m = 0; + if (pbc_flag == 0) { + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = h_x(j,0); + buf[m++] = h_x(j,1); + buf[m++] = h_x(j,2); + buf[m++] = ubuf(h_tag[j]).d; + buf[m++] = ubuf(h_type[j]).d; + buf[m++] = ubuf(h_mask[j]).d; + buf[m++] = h_radius[j]; + buf[m++] = h_rmass[j]; + buf[m++] = h_v(j,0); + buf[m++] = h_v(j,1); + buf[m++] = h_v(j,2); + buf[m++] = h_omega(j,0); + buf[m++] = h_omega(j,1); + buf[m++] = h_omega(j,2); + } + } else { + if (domain->triclinic == 0) { + dx = pbc[0]*domain->xprd; + dy = pbc[1]*domain->yprd; + dz = pbc[2]*domain->zprd; + } else { + dx = pbc[0]; + dy = pbc[1]; + dz = pbc[2]; + } + if (!deform_vremap) { + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = h_x(j,0) + dx; + buf[m++] = h_x(j,1) + dy; + buf[m++] = h_x(j,2) + dz; + buf[m++] = ubuf(h_tag[j]).d; + buf[m++] = ubuf(h_type[j]).d; + buf[m++] = ubuf(h_mask[j]).d; + buf[m++] = h_radius[j]; + buf[m++] = h_rmass[j]; + buf[m++] = h_v(j,0); + buf[m++] = h_v(j,1); + buf[m++] = h_v(j,2); + buf[m++] = h_omega(j,0); + buf[m++] = h_omega(j,1); + buf[m++] = h_omega(j,2); + } + } else { + dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4]; + dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3]; + dvz = pbc[2]*h_rate[2]; + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = h_x(j,0) + dx; + buf[m++] = h_x(j,1) + dy; + buf[m++] = h_x(j,2) + dz; + buf[m++] = ubuf(h_tag[j]).d; + buf[m++] = ubuf(h_type[j]).d; + buf[m++] = ubuf(h_mask[j]).d; + buf[m++] = h_radius[j]; + buf[m++] = h_rmass[j]; + if (mask[i] & deform_groupbit) { + buf[m++] = h_v(j,0) + dvx; + buf[m++] = h_v(j,1) + dvy; + buf[m++] = h_v(j,2) + dvz; + } else { + buf[m++] = h_v(j,0); + buf[m++] = h_v(j,1); + buf[m++] = h_v(j,2); + } + buf[m++] = h_omega(j,0); + buf[m++] = h_omega(j,1); + buf[m++] = h_omega(j,2); + } + } + } + + if (atom->nextra_border) + for (int iextra = 0; iextra < atom->nextra_border; iextra++) + m += modify->fix[atom->extra_border[iextra]]->pack_border(n,list,&buf[m]); + + return m; +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecSphereKokkos::pack_border_hybrid(int n, int *list, double *buf) +{ + sync(Host,RADIUS_MASK|RMASS_MASK); + + int m = 0; + for (int i = 0; i < n; i++) { + const int j = list[i]; + buf[m++] = h_radius[j]; + buf[m++] = h_rmass[j]; + } + return m; +} + +/* ---------------------------------------------------------------------- */ + +template +struct AtomVecSphereKokkos_UnpackBorder { + typedef DeviceType device_type; + + const typename ArrayTypes::t_xfloat_2d_const _buf; + typename ArrayTypes::t_x_array _x; + typename ArrayTypes::t_tagint_1d _tag; + typename ArrayTypes::t_int_1d _type; + typename ArrayTypes::t_int_1d _mask; + typename ArrayTypes::t_float_1d _radius,_rmass; + int _first; + + AtomVecSphereKokkos_UnpackBorder( + const typename ArrayTypes::t_xfloat_2d_const &buf, + typename ArrayTypes::t_x_array &x, + typename ArrayTypes::t_tagint_1d &tag, + typename ArrayTypes::t_int_1d &type, + typename ArrayTypes::t_int_1d &mask, + const typename ArrayTypes::t_float_1d &radius, + const typename ArrayTypes::t_float_1d &rmass, + const int& first): + _buf(buf),_x(x),_tag(tag),_type(type),_mask(mask), + _radius(radius), + _rmass(rmass), + _first(first) {}; + + KOKKOS_INLINE_FUNCTION + void operator() (const int& i) const { + _x(i+_first,0) = _buf(i,0); + _x(i+_first,1) = _buf(i,1); + _x(i+_first,2) = _buf(i,2); + _tag(i+_first) = static_cast (_buf(i,3)); + _type(i+_first) = static_cast (_buf(i,4)); + _mask(i+_first) = static_cast (_buf(i,5)); + _radius(i+_first) = _buf(i,6); + _rmass(i+_first) = _buf(i,7); + } +}; + +/* ---------------------------------------------------------------------- */ + +void AtomVecSphereKokkos::unpack_border_kokkos(const int &n, const int &first, + const DAT::tdual_xfloat_2d &buf,ExecutionSpace space) { + modified(space,X_MASK|TAG_MASK|TYPE_MASK|MASK_MASK| + RADIUS_MASK|RMASS_MASK); + while (first+n >= nmax) grow(0); + modified(space,X_MASK|TAG_MASK|TYPE_MASK|MASK_MASK| + RADIUS_MASK|RMASS_MASK); + if(space==Host) { + struct AtomVecSphereKokkos_UnpackBorder f(buf.view(), + h_x,h_tag,h_type,h_mask, + h_radius,h_rmass, + first); + Kokkos::parallel_for(n,f); + } else { + struct AtomVecSphereKokkos_UnpackBorder f(buf.view(), + d_x,d_tag,d_type,d_mask, + d_radius,d_rmass, + first); + Kokkos::parallel_for(n,f); + } +} + +/* ---------------------------------------------------------------------- */ + +void AtomVecSphereKokkos::unpack_border(int n, int first, double *buf) +{ + int m = 0; + const int last = first + n; + for (int i = first; i < last; i++) { + if (i == nmax) grow(0); + h_x(i,0) = buf[m++]; + h_x(i,1) = buf[m++]; + h_x(i,2) = buf[m++]; + h_tag[i] = (tagint) ubuf(buf[m++]).i; + h_type[i] = (int) ubuf(buf[m++]).i; + h_mask[i] = (int) ubuf(buf[m++]).i; + h_radius[i] = buf[m++]; + h_rmass[i] = buf[m++]; + } + + if (atom->nextra_border) + for (int iextra = 0; iextra < atom->nextra_border; iextra++) + m += modify->fix[atom->extra_border[iextra]]-> + unpack_border(n,first,&buf[m]); + + modified(Host,X_MASK|TAG_MASK|TYPE_MASK|MASK_MASK|RADIUS_MASK|RMASS_MASK); +} + + +/* ---------------------------------------------------------------------- */ + +void AtomVecSphereKokkos::unpack_border_vel(int n, int first, double *buf) +{ + int m = 0; + const int last = first + n; + for (int i = first; i < last; i++) { + if (i == nmax) grow(0); + h_x(i,0) = buf[m++]; + h_x(i,1) = buf[m++]; + h_x(i,2) = buf[m++]; + h_tag[i] = (tagint) ubuf(buf[m++]).i; + h_type[i] = (int) ubuf(buf[m++]).i; + h_mask[i] = (int) ubuf(buf[m++]).i; + h_radius[i] = buf[m++]; + h_rmass[i] = buf[m++]; + h_v(i,0) = buf[m++]; + h_v(i,1) = buf[m++]; + h_v(i,2) = buf[m++]; + h_omega(i,0) = buf[m++]; + h_omega(i,1) = buf[m++]; + h_omega(i,2) = buf[m++]; + } + + if (atom->nextra_border) + for (int iextra = 0; iextra < atom->nextra_border; iextra++) + m += modify->fix[atom->extra_border[iextra]]-> + unpack_border(n,first,&buf[m]); + + modified(Host,X_MASK|TAG_MASK|TYPE_MASK|MASK_MASK|RADIUS_MASK|RMASS_MASK|V_MASK|OMEGA_MASK); +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecSphereKokkos::unpack_border_hybrid(int n, int first, double *buf) +{ + int m = 0; + const int last = first + n; + for (int i = first; i < last; i++) { + h_radius[i] = buf[m++]; + h_rmass[i] = buf[m++]; + } + modified(Host,RADIUS_MASK|RMASS_MASK); + return m; +} + +/* ---------------------------------------------------------------------- */ + +template +struct AtomVecSphereKokkos_PackExchangeFunctor { + typedef DeviceType device_type; + typedef ArrayTypes AT; + typename AT::t_x_array_randomread _x; + typename AT::t_v_array_randomread _v; + typename AT::t_tagint_1d_randomread _tag; + typename AT::t_int_1d_randomread _type; + typename AT::t_int_1d_randomread _mask; + typename AT::t_imageint_1d_randomread _image; + typename AT::t_float_1d_randomread _radius,_rmass; + typename AT::t_v_array_randomread _omega; + typename AT::t_x_array _xw; + typename AT::t_v_array _vw; + typename AT::t_tagint_1d _tagw; + typename AT::t_int_1d _typew; + typename AT::t_int_1d _maskw; + typename AT::t_imageint_1d _imagew; + typename AT::t_float_1d _radiusw,_rmassw; + typename AT::t_v_array _omegaw; + typename AT::t_xfloat_2d_um _buf; + typename AT::t_int_1d_const _sendlist; + typename AT::t_int_1d_const _copylist; + int _nlocal,_dim; + X_FLOAT _lo,_hi; + + AtomVecSphereKokkos_PackExchangeFunctor( + const AtomKokkos* atom, + const typename AT::tdual_xfloat_2d buf, + typename AT::tdual_int_1d sendlist, + typename AT::tdual_int_1d copylist,int nlocal, int dim,X_FLOAT lo, X_FLOAT hi): + _x(atom->k_x.view()), + _v(atom->k_v.view()), + _tag(atom->k_tag.view()), + _type(atom->k_type.view()), + _mask(atom->k_mask.view()), + _image(atom->k_image.view()), + _radius(atom->k_radius.view()), + _rmass(atom->k_rmass.view()), + _omega(atom->k_omega.view()), + _xw(atom->k_x.view()), + _vw(atom->k_v.view()), + _tagw(atom->k_tag.view()), + _typew(atom->k_type.view()), + _maskw(atom->k_mask.view()), + _imagew(atom->k_image.view()), + _radiusw(atom->k_radius.view()), + _rmassw(atom->k_rmass.view()), + _omegaw(atom->k_omega.view()), + _sendlist(sendlist.template view()), + _copylist(copylist.template view()), + _nlocal(nlocal),_dim(dim), + _lo(lo),_hi(hi){ + const size_t elements = 16; + const int maxsendlist = (buf.template view().extent(0)*buf.template view().extent(1))/elements; + + buffer_view(_buf,buf,maxsendlist,elements); + } + + KOKKOS_INLINE_FUNCTION + void operator() (const int &mysend) const { + const int i = _sendlist(mysend); + _buf(mysend,0) = 16; + _buf(mysend,1) = _x(i,0); + _buf(mysend,2) = _x(i,1); + _buf(mysend,3) = _x(i,2); + _buf(mysend,4) = _v(i,0); + _buf(mysend,5) = _v(i,1); + _buf(mysend,6) = _v(i,2); + _buf(mysend,7) = _tag[i]; + _buf(mysend,8) = _type[i]; + _buf(mysend,9) = _mask[i]; + _buf(mysend,10) = _image[i]; + _buf(mysend,11) = _radius[i]; + _buf(mysend,12) = _rmass[i]; + _buf(mysend,13) = _omega(i,0); + _buf(mysend,14) = _omega(i,1); + _buf(mysend,15) = _omega(i,2); + const int j = _copylist(mysend); + + if (j>-1) { + _xw(i,0) = _x(j,0); + _xw(i,1) = _x(j,1); + _xw(i,2) = _x(j,2); + _vw(i,0) = _v(j,0); + _vw(i,1) = _v(j,1); + _vw(i,2) = _v(j,2); + _tagw[i] = _tag(j); + _typew[i] = _type(j); + _maskw[i] = _mask(j); + _imagew[i] = _image(j); + _radiusw[i] = _radius(j); + _rmassw[i] = _rmass(j); + _omegaw(i,0) = _omega(j,0); + _omegaw(i,1) = _omega(j,1); + _omegaw(i,2) = _omega(j,2); + } + } +}; + +/* ---------------------------------------------------------------------- */ + +int AtomVecSphereKokkos::pack_exchange_kokkos(const int &nsend,DAT::tdual_xfloat_2d &k_buf, DAT::tdual_int_1d k_sendlist,DAT::tdual_int_1d k_copylist,ExecutionSpace space,int dim,X_FLOAT lo,X_FLOAT hi ) +{ + if(nsend > (int) (k_buf.view().extent(0)*k_buf.view().extent(1))/16) { + int newsize = nsend*17/k_buf.view().extent(1)+1; + k_buf.resize(newsize,k_buf.view().extent(1)); + } + sync(space,X_MASK | V_MASK | TAG_MASK | TYPE_MASK | + MASK_MASK | IMAGE_MASK| RADIUS_MASK | RMASS_MASK | + OMEGA_MASK); + + if(space == Host) { + AtomVecSphereKokkos_PackExchangeFunctor f(atomKK,k_buf,k_sendlist,k_copylist,atom->nlocal,dim,lo,hi); + Kokkos::parallel_for(nsend,f); + } else { + AtomVecSphereKokkos_PackExchangeFunctor f(atomKK,k_buf,k_sendlist,k_copylist,atom->nlocal,dim,lo,hi); + Kokkos::parallel_for(nsend,f); + } + return nsend*16; +} + +/* ---------------------------------------------------------------------- + pack data for atom I for sending to another proc + xyz must be 1st 3 values, so comm::exchange() can test on them +------------------------------------------------------------------------- */ + +int AtomVecSphereKokkos::pack_exchange(int i, double *buf) +{ + sync(Host,X_MASK | V_MASK | TAG_MASK | TYPE_MASK | + MASK_MASK | IMAGE_MASK| RADIUS_MASK | RMASS_MASK | + OMEGA_MASK); + + + int m = 1; + buf[m++] = h_x(i,0); + buf[m++] = h_x(i,1); + buf[m++] = h_x(i,2); + buf[m++] = h_v(i,0); + buf[m++] = h_v(i,1); + buf[m++] = h_v(i,2); + buf[m++] = ubuf(h_tag[i]).d; + buf[m++] = ubuf(h_type[i]).d; + buf[m++] = ubuf(h_mask[i]).d; + buf[m++] = ubuf(h_image[i]).d; + + buf[m++] = h_radius[i]; + buf[m++] = h_rmass[i]; + buf[m++] = h_omega(i,0); + buf[m++] = h_omega(i,1); + buf[m++] = h_omega(i,2); + + if (atom->nextra_grow) + for (int iextra = 0; iextra < atom->nextra_grow; iextra++) + m += modify->fix[atom->extra_grow[iextra]]->pack_exchange(i,&buf[m]); + + buf[0] = m; + return m; +} + +/* ---------------------------------------------------------------------- */ + +template +struct AtomVecSphereKokkos_UnpackExchangeFunctor { + typedef DeviceType device_type; + typedef ArrayTypes AT; + typename AT::t_x_array _x; + typename AT::t_v_array _v; + typename AT::t_tagint_1d _tag; + typename AT::t_int_1d _type; + typename AT::t_int_1d _mask; + typename AT::t_imageint_1d _image; + typename AT::t_float_1d _radius; + typename AT::t_float_1d _rmass; + typename AT::t_v_array _omega; + typename AT::t_xfloat_2d_um _buf; + typename AT::t_int_1d _nlocal; + int _dim; + X_FLOAT _lo,_hi; + + AtomVecSphereKokkos_UnpackExchangeFunctor( + const AtomKokkos* atom, + const typename AT::tdual_xfloat_2d buf, + typename AT::tdual_int_1d nlocal, + int dim, X_FLOAT lo, X_FLOAT hi): + _x(atom->k_x.view()), + _v(atom->k_v.view()), + _tag(atom->k_tag.view()), + _type(atom->k_type.view()), + _mask(atom->k_mask.view()), + _image(atom->k_image.view()), + _nlocal(nlocal.template view()),_dim(dim), + _lo(lo),_hi(hi){ + const size_t elements = 16; + const int maxsendlist = (buf.template view().extent(0)*buf.template view().extent(1))/elements; + + buffer_view(_buf,buf,maxsendlist,elements); + } + + KOKKOS_INLINE_FUNCTION + void operator() (const int &myrecv) const { + X_FLOAT x = _buf(myrecv,_dim+1); + if (x >= _lo && x < _hi) { + int i = Kokkos::atomic_fetch_add(&_nlocal(0),1); + _x(i,0) = _buf(myrecv,1); + _x(i,1) = _buf(myrecv,2); + _x(i,2) = _buf(myrecv,3); + _v(i,0) = _buf(myrecv,4); + _v(i,1) = _buf(myrecv,5); + _v(i,2) = _buf(myrecv,6); + _tag[i] = _buf(myrecv,7); + _type[i] = _buf(myrecv,8); + _mask[i] = _buf(myrecv,9); + _image[i] = _buf(myrecv,10); + _radius[i] = _buf(myrecv,11); + _rmass[i] = _buf(myrecv,12); + _omega(i,0) = _buf(myrecv,13); + _omega(i,1) = _buf(myrecv,14); + _omega(i,2) = _buf(myrecv,15); + } + } +}; + +/* ---------------------------------------------------------------------- */ + +int AtomVecSphereKokkos::unpack_exchange_kokkos(DAT::tdual_xfloat_2d &k_buf,int nrecv,int nlocal,int dim,X_FLOAT lo,X_FLOAT hi,ExecutionSpace space) { + if(space == Host) { + k_count.h_view(0) = nlocal; + AtomVecSphereKokkos_UnpackExchangeFunctor f(atomKK,k_buf,k_count,dim,lo,hi); + Kokkos::parallel_for(nrecv/16,f); + } else { + k_count.h_view(0) = nlocal; + k_count.modify(); + k_count.sync(); + AtomVecSphereKokkos_UnpackExchangeFunctor f(atomKK,k_buf,k_count,dim,lo,hi); + Kokkos::parallel_for(nrecv/16,f); + k_count.modify(); + k_count.sync(); + } + + modified(space,X_MASK | V_MASK | TAG_MASK | TYPE_MASK | + MASK_MASK | IMAGE_MASK| RADIUS_MASK | RMASS_MASK | + OMEGA_MASK); + + return k_count.h_view(0); +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecSphereKokkos::unpack_exchange(double *buf) +{ + int nlocal = atom->nlocal; + if (nlocal == nmax) grow(0); + + int m = 1; + h_x(nlocal,0) = buf[m++]; + h_x(nlocal,1) = buf[m++]; + h_x(nlocal,2) = buf[m++]; + h_v(nlocal,0) = buf[m++]; + h_v(nlocal,1) = buf[m++]; + h_v(nlocal,2) = buf[m++]; + h_tag[nlocal] = (tagint) ubuf(buf[m++]).i; + h_type[nlocal] = (int) ubuf(buf[m++]).i; + h_mask[nlocal] = (int) ubuf(buf[m++]).i; + h_image[nlocal] = (imageint) ubuf(buf[m++]).i; + + h_radius[nlocal] = buf[m++]; + h_rmass[nlocal] = buf[m++]; + h_omega(nlocal,0) = buf[m++]; + h_omega(nlocal,1) = buf[m++]; + h_omega(nlocal,2) = buf[m++]; + + if (atom->nextra_grow) + for (int iextra = 0; iextra < atom->nextra_grow; iextra++) + m += modify->fix[atom->extra_grow[iextra]]-> + unpack_exchange(nlocal,&buf[m]); + + modified(Host,X_MASK | V_MASK | TAG_MASK | TYPE_MASK | + MASK_MASK | IMAGE_MASK | RADIUS_MASK | RMASS_MASK | + OMEGA_MASK); + + atom->nlocal++; + return m; +} + +/* ---------------------------------------------------------------------- + size of restart data for all atoms owned by this proc + include extra data stored by fixes +------------------------------------------------------------------------- */ + +int AtomVecSphereKokkos::size_restart() +{ + int i; + + int nlocal = atom->nlocal; + int n = 16 * nlocal; + + if (atom->nextra_restart) + for (int iextra = 0; iextra < atom->nextra_restart; iextra++) + for (i = 0; i < nlocal; i++) + n += modify->fix[atom->extra_restart[iextra]]->size_restart(i); + + return n; +} + +/* ---------------------------------------------------------------------- + pack atom I's data for restart file including extra quantities + xyz must be 1st 3 values, so that read_restart can test on them + molecular types may be negative, but write as positive +------------------------------------------------------------------------- */ + +int AtomVecSphereKokkos::pack_restart(int i, double *buf) +{ + sync(Host,X_MASK | TAG_MASK | TYPE_MASK | + MASK_MASK | IMAGE_MASK | V_MASK | + RADIUS_MASK | RMASS_MASK | OMEGA_MASK); + + int m = 1; + buf[m++] = h_x(i,0); + buf[m++] = h_x(i,1); + buf[m++] = h_x(i,2); + buf[m++] = ubuf(h_tag[i]).d; + buf[m++] = ubuf(h_type[i]).d; + buf[m++] = ubuf(h_mask[i]).d; + buf[m++] = ubuf(h_image[i]).d; + buf[m++] = h_v(i,0); + buf[m++] = h_v(i,1); + buf[m++] = h_v(i,2); + + buf[m++] = h_radius[i]; + buf[m++] = h_rmass[i]; + buf[m++] = h_omega(i,0); + buf[m++] = h_omega(i,1); + buf[m++] = h_omega(i,2); + + if (atom->nextra_restart) + for (int iextra = 0; iextra < atom->nextra_restart; iextra++) + m += modify->fix[atom->extra_restart[iextra]]->pack_restart(i,&buf[m]); + + buf[0] = m; + return m; +} + +/* ---------------------------------------------------------------------- + unpack data for one atom from restart file including extra quantities +------------------------------------------------------------------------- */ + +int AtomVecSphereKokkos::unpack_restart(double *buf) +{ + int nlocal = atom->nlocal; + if (nlocal == nmax) { + grow(0); + if (atom->nextra_store) + memory->grow(atom->extra,nmax,atom->nextra_store,"atom:extra"); + } + + int m = 1; + h_x(nlocal,0) = buf[m++]; + h_x(nlocal,1) = buf[m++]; + h_x(nlocal,2) = buf[m++]; + h_tag[nlocal] = (tagint) ubuf(buf[m++]).i; + h_type[nlocal] = (int) ubuf(buf[m++]).i; + h_mask[nlocal] = (int) ubuf(buf[m++]).i; + h_image[nlocal] = (imageint) ubuf(buf[m++]).i; + h_v(nlocal,0) = buf[m++]; + h_v(nlocal,1) = buf[m++]; + h_v(nlocal,2) = buf[m++]; + + h_radius[nlocal] = buf[m++]; + h_rmass[nlocal] = buf[m++]; + h_omega(nlocal,0) = buf[m++]; + h_omega(nlocal,1) = buf[m++]; + h_omega(nlocal,2) = buf[m++]; + + double **extra = atom->extra; + if (atom->nextra_store) { + int size = static_cast (buf[0]) - m; + for (int i = 0; i < size; i++) extra[nlocal][i] = buf[m++]; + } + + modified(Host,X_MASK | TAG_MASK | TYPE_MASK | + MASK_MASK | IMAGE_MASK | V_MASK | + RADIUS_MASK | RMASS_MASK | OMEGA_MASK); + + atom->nlocal++; + return m; +} + +/* ---------------------------------------------------------------------- + create one atom of itype at coord + set other values to defaults +------------------------------------------------------------------------- */ + +void AtomVecSphereKokkos::create_atom(int itype, double *coord) +{ + int nlocal = atom->nlocal; + if (nlocal == nmax) { + atomKK->modified(Host,ALL_MASK); + grow(0); + } + atomKK->modified(Host,ALL_MASK); + + h_tag[nlocal] = 0; + h_type[nlocal] = itype; + h_x(nlocal,0) = coord[0]; + h_x(nlocal,1) = coord[1]; + h_x(nlocal,2) = coord[2]; + h_mask[nlocal] = 1; + h_image[nlocal] = ((imageint) IMGMAX << IMG2BITS) | + ((imageint) IMGMAX << IMGBITS) | IMGMAX; + h_v(nlocal,0) = 0.0; + h_v(nlocal,1) = 0.0; + h_v(nlocal,2) = 0.0; + + h_radius[nlocal] = 0.5; + h_rmass[nlocal] = 4.0*MY_PI/3.0 * h_radius[nlocal]*h_radius[nlocal]*h_radius[nlocal]; + h_omega(nlocal,0) = 0.0; + h_omega(nlocal,1) = 0.0; + h_omega(nlocal,2) = 0.0; + + atom->nlocal++; +} + +/* ---------------------------------------------------------------------- + unpack one line from Atoms section of data file + initialize other atom quantities +------------------------------------------------------------------------- */ + +void AtomVecSphereKokkos::data_atom(double *coord, imageint imagetmp, char **values) +{ + int nlocal = atom->nlocal; + if (nlocal == nmax) grow(0); + + tag[nlocal] = ATOTAGINT(values[0]); + type[nlocal] = atoi(values[1]); + if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) + error->one(FLERR,"Invalid atom type in Atoms section of data file"); + + radius[nlocal] = 0.5 * atof(values[2]); + if (radius[nlocal] < 0.0) + error->one(FLERR,"Invalid radius in Atoms section of data file"); + + double density = atof(values[3]); + if (density <= 0.0) + error->one(FLERR,"Invalid density in Atoms section of data file"); + + if (radius[nlocal] == 0.0) rmass[nlocal] = density; + else + rmass[nlocal] = 4.0*MY_PI/3.0 * + radius[nlocal]*radius[nlocal]*radius[nlocal] * density; + + x[nlocal][0] = coord[0]; + x[nlocal][1] = coord[1]; + x[nlocal][2] = coord[2]; + + image[nlocal] = imagetmp; + + mask[nlocal] = 1; + v[nlocal][0] = 0.0; + v[nlocal][1] = 0.0; + v[nlocal][2] = 0.0; + omega[nlocal][0] = 0.0; + omega[nlocal][1] = 0.0; + omega[nlocal][2] = 0.0; + + atom->nlocal++; +} + +/* ---------------------------------------------------------------------- + unpack hybrid quantities from one line in Atoms section of data file + initialize other atom quantities for this sub-style +------------------------------------------------------------------------- */ + +int AtomVecSphereKokkos::data_atom_hybrid(int nlocal, char **values) +{ + radius[nlocal] = 0.5 * atof(values[0]); + if (radius[nlocal] < 0.0) + error->one(FLERR,"Invalid radius in Atoms section of data file"); + + double density = atof(values[1]); + if (density <= 0.0) + error->one(FLERR,"Invalid density in Atoms section of data file"); + + if (radius[nlocal] == 0.0) rmass[nlocal] = density; + else + rmass[nlocal] = 4.0*MY_PI/3.0 * + radius[nlocal]*radius[nlocal]*radius[nlocal] * density; + + return 2; +} + +/* ---------------------------------------------------------------------- + unpack one line from Velocities section of data file +------------------------------------------------------------------------- */ + +void AtomVecSphereKokkos::data_vel(int m, char **values) +{ + sync(Host,V_MASK|OMEGA_MASK); + h_v(m,0) = atof(values[0]); + h_v(m,1) = atof(values[1]); + h_v(m,2) = atof(values[2]); + h_omega(m,0) = atof(values[3]); + h_omega(m,1) = atof(values[4]); + h_omega(m,2) = atof(values[5]); + modified(Host,V_MASK|OMEGA_MASK); +} + +/* ---------------------------------------------------------------------- + unpack hybrid quantities from one line in Velocities section of data file +------------------------------------------------------------------------- */ + +int AtomVecSphereKokkos::data_vel_hybrid(int m, char **values) +{ + sync(Host,OMEGA_MASK); + omega[m][0] = atof(values[0]); + omega[m][1] = atof(values[1]); + omega[m][2] = atof(values[2]); + modified(Host,OMEGA_MASK); + return 3; +} + +/* ---------------------------------------------------------------------- + pack atom info for data file including 3 image flags +------------------------------------------------------------------------- */ + +void AtomVecSphereKokkos::pack_data(double **buf) +{ + atomKK->sync(Host,TAG_MASK|TYPE_MASK|RADIUS_MASK|RMASS_MASK|X_MASK|IMAGE_MASK); + + int nlocal = atom->nlocal; + for (int i = 0; i < nlocal; i++) { + buf[i][0] = ubuf(h_tag[i]).d; + buf[i][1] = ubuf(h_type[i]).d; + buf[i][2] = 2.0*h_radius[i]; + if (h_radius[i] == 0.0) buf[i][3] = h_rmass[i]; + else + buf[i][3] = h_rmass[i] / (4.0*MY_PI/3.0 * h_radius[i]*h_radius[i]*h_radius[i]); + buf[i][4] = h_x(i,0); + buf[i][5] = h_x(i,1); + buf[i][6] = h_x(i,2); + buf[i][7] = ubuf((h_image[i] & IMGMASK) - IMGMAX).d; + buf[i][8] = ubuf((h_image[i] >> IMGBITS & IMGMASK) - IMGMAX).d; + buf[i][9] = ubuf((h_image[i] >> IMG2BITS) - IMGMAX).d; + } +} + +/* ---------------------------------------------------------------------- + pack hybrid atom info for data file +------------------------------------------------------------------------- */ + +int AtomVecSphereKokkos::pack_data_hybrid(int i, double *buf) +{ + atomKK->sync(Host,RADIUS_MASK|RMASS_MASK); + + buf[0] = 2.0*h_radius[i]; + if (h_radius[i] == 0.0) buf[1] = h_rmass[i]; + else buf[1] = h_rmass[i] / (4.0*MY_PI/3.0 * h_radius[i]*h_radius[i]*h_radius[i]); + return 2; +} + +/* ---------------------------------------------------------------------- + write atom info to data file including 3 image flags +------------------------------------------------------------------------- */ + +void AtomVecSphereKokkos::write_data(FILE *fp, int n, double **buf) +{ + for (int i = 0; i < n; i++) + fprintf(fp,TAGINT_FORMAT + " %d %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %d %d %d\n", + (tagint) ubuf(buf[i][0]).i,(int) ubuf(buf[i][1]).i, + buf[i][2],buf[i][3], + buf[i][4],buf[i][5],buf[i][6], + (int) ubuf(buf[i][7]).i,(int) ubuf(buf[i][8]).i, + (int) ubuf(buf[i][9]).i); +} + +/* ---------------------------------------------------------------------- + write hybrid atom info to data file +------------------------------------------------------------------------- */ + +int AtomVecSphereKokkos::write_data_hybrid(FILE *fp, double *buf) +{ + fprintf(fp," %-1.16e %-1.16e",buf[0],buf[1]); + return 2; +} + +/* ---------------------------------------------------------------------- + pack velocity info for data file +------------------------------------------------------------------------- */ + +void AtomVecSphereKokkos::pack_vel(double **buf) +{ + sync(Host,TAG_MASK|V_MASK|OMEGA_MASK); + + int nlocal = atom->nlocal; + for (int i = 0; i < nlocal; i++) { + buf[i][0] = ubuf(h_tag[i]).d; + buf[i][1] = h_v(i,0); + buf[i][2] = h_v(i,1); + buf[i][3] = h_v(i,2); + buf[i][4] = h_omega(i,0); + buf[i][5] = h_omega(i,1); + buf[i][6] = h_omega(i,2); + } +} + +/* ---------------------------------------------------------------------- + pack hybrid velocity info for data file +------------------------------------------------------------------------- */ + +int AtomVecSphereKokkos::pack_vel_hybrid(int i, double *buf) +{ + sync(Host,OMEGA_MASK); + + buf[0] = h_omega(i,0); + buf[1] = h_omega(i,1); + buf[2] = h_omega(i,2); + return 3; +} + +/* ---------------------------------------------------------------------- + write velocity info to data file +------------------------------------------------------------------------- */ + +void AtomVecSphereKokkos::write_vel(FILE *fp, int n, double **buf) +{ + for (int i = 0; i < n; i++) + fprintf(fp,TAGINT_FORMAT + " %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e\n", + (tagint) ubuf(buf[i][0]).i,buf[i][1],buf[i][2],buf[i][3], + buf[i][4],buf[i][5],buf[i][6]); +} + +/* ---------------------------------------------------------------------- + write hybrid velocity info to data file +------------------------------------------------------------------------- */ + +int AtomVecSphereKokkos::write_vel_hybrid(FILE *fp, double *buf) +{ + fprintf(fp," %-1.16e %-1.16e %-1.16e",buf[0],buf[1],buf[2]); + return 3; +} + +/* ---------------------------------------------------------------------- + return # of bytes of allocated memory +------------------------------------------------------------------------- */ + +bigint AtomVecSphereKokkos::memory_usage() +{ + bigint bytes = 0; + + if (atom->memcheck("tag")) bytes += memory->usage(tag,nmax); + if (atom->memcheck("type")) bytes += memory->usage(type,nmax); + if (atom->memcheck("mask")) bytes += memory->usage(mask,nmax); + if (atom->memcheck("image")) bytes += memory->usage(image,nmax); + if (atom->memcheck("x")) bytes += memory->usage(x,nmax,3); + if (atom->memcheck("v")) bytes += memory->usage(v,nmax,3); + if (atom->memcheck("f")) bytes += memory->usage(f,nmax*comm->nthreads,3); + + if (atom->memcheck("radius")) bytes += memory->usage(radius,nmax); + if (atom->memcheck("rmass")) bytes += memory->usage(rmass,nmax); + if (atom->memcheck("omega")) bytes += memory->usage(omega,nmax,3); + if (atom->memcheck("torque")) + bytes += memory->usage(torque,nmax*comm->nthreads,3); + + return bytes; +} + +/* ---------------------------------------------------------------------- */ + +void AtomVecSphereKokkos::sync(ExecutionSpace space, unsigned int mask) +{ + if (space == Device) { + if (mask & X_MASK) atomKK->k_x.sync(); + if (mask & V_MASK) atomKK->k_v.sync(); + if (mask & F_MASK) atomKK->k_f.sync(); + if (mask & TAG_MASK) atomKK->k_tag.sync(); + if (mask & TYPE_MASK) atomKK->k_type.sync(); + if (mask & MASK_MASK) atomKK->k_mask.sync(); + if (mask & IMAGE_MASK) atomKK->k_image.sync(); + if (mask & RADIUS_MASK) atomKK->k_radius.sync(); + if (mask & RMASS_MASK) atomKK->k_rmass.sync(); + if (mask & OMEGA_MASK) atomKK->k_omega.sync(); + if (mask & TORQUE_MASK) atomKK->k_torque.sync(); + } else { + if (mask & X_MASK) atomKK->k_x.sync(); + if (mask & V_MASK) atomKK->k_v.sync(); + if (mask & F_MASK) atomKK->k_f.sync(); + if (mask & TAG_MASK) atomKK->k_tag.sync(); + if (mask & TYPE_MASK) atomKK->k_type.sync(); + if (mask & MASK_MASK) atomKK->k_mask.sync(); + if (mask & IMAGE_MASK) atomKK->k_image.sync(); + if (mask & RADIUS_MASK) atomKK->k_radius.sync(); + if (mask & RMASS_MASK) atomKK->k_rmass.sync(); + if (mask & OMEGA_MASK) atomKK->k_omega.sync(); + if (mask & TORQUE_MASK) atomKK->k_torque.sync(); + } +} + +/* ---------------------------------------------------------------------- */ + +void AtomVecSphereKokkos::sync_overlapping_device(ExecutionSpace space, unsigned int mask) +{ + if (space == Device) { + if ((mask & X_MASK) && atomKK->k_x.need_sync()) + perform_async_copy(atomKK->k_x,space); + if ((mask & V_MASK) && atomKK->k_v.need_sync()) + perform_async_copy(atomKK->k_v,space); + if ((mask & F_MASK) && atomKK->k_f.need_sync()) + perform_async_copy(atomKK->k_f,space); + if ((mask & TAG_MASK) && atomKK->k_tag.need_sync()) + perform_async_copy(atomKK->k_tag,space); + if ((mask & TYPE_MASK) && atomKK->k_type.need_sync()) + perform_async_copy(atomKK->k_type,space); + if ((mask & MASK_MASK) && atomKK->k_mask.need_sync()) + perform_async_copy(atomKK->k_mask,space); + if ((mask & IMAGE_MASK) && atomKK->k_image.need_sync()) + perform_async_copy(atomKK->k_image,space); + if ((mask & RADIUS_MASK) && atomKK->k_radius.need_sync()) + perform_async_copy(atomKK->k_radius,space); + if ((mask & RMASS_MASK) && atomKK->k_rmass.need_sync()) + perform_async_copy(atomKK->k_rmass,space); + if ((mask & OMEGA_MASK) && atomKK->k_omega.need_sync()) + perform_async_copy(atomKK->k_omega,space); + if ((mask & TORQUE_MASK) && atomKK->k_torque.need_sync()) + perform_async_copy(atomKK->k_torque,space); + } else { + if ((mask & X_MASK) && atomKK->k_x.need_sync()) + perform_async_copy(atomKK->k_x,space); + if ((mask & V_MASK) && atomKK->k_v.need_sync()) + perform_async_copy(atomKK->k_v,space); + if ((mask & F_MASK) && atomKK->k_f.need_sync()) + perform_async_copy(atomKK->k_f,space); + if ((mask & TAG_MASK) && atomKK->k_tag.need_sync()) + perform_async_copy(atomKK->k_tag,space); + if ((mask & TYPE_MASK) && atomKK->k_type.need_sync()) + perform_async_copy(atomKK->k_type,space); + if ((mask & MASK_MASK) && atomKK->k_mask.need_sync()) + perform_async_copy(atomKK->k_mask,space); + if ((mask & IMAGE_MASK) && atomKK->k_image.need_sync()) + perform_async_copy(atomKK->k_image,space); + if ((mask & RADIUS_MASK) && atomKK->k_radius.need_sync()) + perform_async_copy(atomKK->k_radius,space); + if ((mask & RMASS_MASK) && atomKK->k_rmass.need_sync()) + perform_async_copy(atomKK->k_rmass,space); + if ((mask & OMEGA_MASK) && atomKK->k_omega.need_sync()) + perform_async_copy(atomKK->k_omega,space); + if ((mask & TORQUE_MASK) && atomKK->k_torque.need_sync()) + perform_async_copy(atomKK->k_torque,space); + } +} + +/* ---------------------------------------------------------------------- */ + +void AtomVecSphereKokkos::modified(ExecutionSpace space, unsigned int mask) +{ + if (space == Device) { + if (mask & X_MASK) atomKK->k_x.modify(); + if (mask & V_MASK) atomKK->k_v.modify(); + if (mask & F_MASK) atomKK->k_f.modify(); + if (mask & TAG_MASK) atomKK->k_tag.modify(); + if (mask & TYPE_MASK) atomKK->k_type.modify(); + if (mask & MASK_MASK) atomKK->k_mask.modify(); + if (mask & IMAGE_MASK) atomKK->k_image.modify(); + if (mask & RADIUS_MASK) atomKK->k_radius.modify(); + if (mask & RMASS_MASK) atomKK->k_rmass.modify(); + if (mask & OMEGA_MASK) atomKK->k_omega.modify(); + if (mask & TORQUE_MASK) atomKK->k_torque.modify(); + } else { + if (mask & X_MASK) atomKK->k_x.modify(); + if (mask & V_MASK) atomKK->k_v.modify(); + if (mask & F_MASK) atomKK->k_f.modify(); + if (mask & TAG_MASK) atomKK->k_tag.modify(); + if (mask & TYPE_MASK) atomKK->k_type.modify(); + if (mask & MASK_MASK) atomKK->k_mask.modify(); + if (mask & IMAGE_MASK) atomKK->k_image.modify(); + if (mask & RADIUS_MASK) atomKK->k_radius.modify(); + if (mask & RMASS_MASK) atomKK->k_rmass.modify(); + if (mask & OMEGA_MASK) atomKK->k_omega.modify(); + if (mask & TORQUE_MASK) atomKK->k_torque.modify(); + } +} diff --git a/src/KOKKOS/atom_vec_sphere_kokkos.h b/src/KOKKOS/atom_vec_sphere_kokkos.h new file mode 100644 index 0000000000..d6739cb714 --- /dev/null +++ b/src/KOKKOS/atom_vec_sphere_kokkos.h @@ -0,0 +1,155 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef ATOM_CLASS + +AtomStyle(sphere/kk,AtomVecSphereKokkos) + +#else + +#ifndef LMP_ATOM_VEC_SPHERE_KOKKOS_H +#define LMP_ATOM_VEC_SPHERE_KOKKOS_H + +#include "atom_vec_kokkos.h" +#include "kokkos_type.h" + +namespace LAMMPS_NS { + +class AtomVecSphereKokkos : public AtomVecKokkos { + public: + AtomVecSphereKokkos(class LAMMPS *); + ~AtomVecSphereKokkos() {} + void init(); + void grow(int); + void grow_reset(); + void copy(int, int, int); + int pack_comm(int, int *, double *, int, int *); + int pack_comm_vel(int, int *, double *, int, int *); + int pack_comm_hybrid(int, int *, double *); + void unpack_comm(int, int, double *); + void unpack_comm_vel(int, int, double *); + int unpack_comm_hybrid(int, int, double *); + int pack_reverse(int, int, double *); + int pack_reverse_hybrid(int, int, double *); + void unpack_reverse(int, int *, double *); + int unpack_reverse_hybrid(int, int *, double *); + int pack_border(int, int *, double *, int, int *); + int pack_border_vel(int, int *, double *, int, int *); + int pack_border_hybrid(int, int *, double *); + void unpack_border(int, int, double *); + void unpack_border_vel(int, int, double *); + int unpack_border_hybrid(int, int, double *); + int pack_exchange(int, double *); + int unpack_exchange(double *); + int size_restart(); + int pack_restart(int, double *); + int unpack_restart(double *); + void create_atom(int, double *); + void data_atom(double *, imageint, char **); + int data_atom_hybrid(int, char **); + void data_vel(int, char **); + int data_vel_hybrid(int, char **); + void pack_data(double **); + int pack_data_hybrid(int, double *); + void write_data(FILE *, int, double **); + int write_data_hybrid(FILE *, double *); + void pack_vel(double **); + int pack_vel_hybrid(int, double *); + void write_vel(FILE *, int, double **); + int write_vel_hybrid(FILE *, double *); + bigint memory_usage(); + + int pack_comm_kokkos(const int &n, const DAT::tdual_int_2d &k_sendlist, + const int & iswap, + const DAT::tdual_xfloat_2d &buf, + const int &pbc_flag, const int pbc[]); + void unpack_comm_kokkos(const int &n, const int &nfirst, + const DAT::tdual_xfloat_2d &buf); + int pack_comm_self(const int &n, const DAT::tdual_int_2d &list, + const int & iswap, const int nfirst, + const int &pbc_flag, const int pbc[]); + int pack_border_kokkos(int n, DAT::tdual_int_2d k_sendlist, + DAT::tdual_xfloat_2d buf,int iswap, + int pbc_flag, int *pbc, ExecutionSpace space); + void unpack_border_kokkos(const int &n, const int &nfirst, + const DAT::tdual_xfloat_2d &buf, + ExecutionSpace space); + int pack_exchange_kokkos(const int &nsend,DAT::tdual_xfloat_2d &buf, + DAT::tdual_int_1d k_sendlist, + DAT::tdual_int_1d k_copylist, + ExecutionSpace space, int dim, + X_FLOAT lo, X_FLOAT hi); + int unpack_exchange_kokkos(DAT::tdual_xfloat_2d &k_buf, int nrecv, + int nlocal, int dim, X_FLOAT lo, X_FLOAT hi, + ExecutionSpace space); + + void sync(ExecutionSpace space, unsigned int mask); + void modified(ExecutionSpace space, unsigned int mask); + void sync_overlapping_device(ExecutionSpace space, unsigned int mask); + + private: + tagint *tag; + int *type,*mask; + imageint *image; + double **x,**v,**f; + double *radius,*rmass; + double **omega,**torque; + int radvary; + + DAT::t_tagint_1d d_tag; + HAT::t_tagint_1d h_tag; + DAT::t_imageint_1d d_image; + HAT::t_imageint_1d h_image; + DAT::t_int_1d d_type, d_mask; + HAT::t_int_1d h_type, h_mask; + + DAT::t_x_array d_x; + DAT::t_v_array d_v; + DAT::t_f_array d_f; + DAT::t_float_1d d_radius; + HAT::t_float_1d h_radius; + DAT::t_float_1d d_rmass; + HAT::t_float_1d h_rmass; + DAT::t_v_array d_omega; + HAT::t_v_array h_omega; + DAT::t_f_array d_torque; + HAT::t_f_array h_torque; + + DAT::tdual_int_1d k_count; +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Per-processor system is too big + +The number of owned atoms plus ghost atoms on a single +processor must fit in 32-bit integer. + +E: Invalid atom type in Atoms section of data file + +Atom types must range from 1 to specified # of types. + +E: Invalid radius in Atoms section of data file + +Radius must be >= 0.0. + +E: Invalid density in Atoms section of data file + +Density value cannot be <= 0.0. + +*/ diff --git a/src/KOKKOS/fix_neigh_history_kokkos.cpp b/src/KOKKOS/fix_neigh_history_kokkos.cpp new file mode 100644 index 0000000000..d5277c0188 --- /dev/null +++ b/src/KOKKOS/fix_neigh_history_kokkos.cpp @@ -0,0 +1,346 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "fix_neigh_history_kokkos.h" +#include "atom_kokkos.h" +#include "error.h" +#include "memory_kokkos.h" +#include "neigh_list_kokkos.h" +#include "pair_kokkos.h" +#include "comm.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +template +FixNeighHistoryKokkos::FixNeighHistoryKokkos(LAMMPS *lmp, int narg, char **arg) : + FixNeighHistory(lmp, narg, arg) +{ + kokkosable = 1; + atomKK = (AtomKokkos *)atom; + execution_space = ExecutionSpaceFromDevice::space; + + memory->destroy(npartner); + memory->destroy(partner); + memory->destroy(valuepartner); + + maxpartner = 8; + grow_arrays(atom->nmax); + + d_resize = typename ArrayTypes::t_int_scalar("FixNeighHistoryKokkos::resize"); +#ifndef KOKKOS_USE_CUDA_UVM + h_resize = Kokkos::create_mirror_view(d_resize); +#else + h_resize = d_resize; +#endif + h_resize() = 1; +} + +/* ---------------------------------------------------------------------- */ + +template +FixNeighHistoryKokkos::~FixNeighHistoryKokkos() +{ + if (copymode) return; + + memoryKK->destroy_kokkos(k_npartner, npartner); + memoryKK->destroy_kokkos(k_partner, partner); + memoryKK->destroy_kokkos(k_valuepartner, valuepartner); +} + +/* ---------------------------------------------------------------------- */ + +template +void FixNeighHistoryKokkos::init() +{ + if (atomKK->tag_enable == 0) + error->all(FLERR,"Neighbor history requires atoms have IDs"); +} + +/* ---------------------------------------------------------------------- */ + +template +void FixNeighHistoryKokkos::pre_exchange() +{ + copymode = 1; + + h_resize() = 1; + while (h_resize() > 0) { + FixNeighHistoryKokkosZeroPartnerCountFunctor zero(this); + Kokkos::parallel_for(nlocal_neigh,zero); + + h_resize() = 0; + deep_copy(d_resize, h_resize); + + FixNeighHistoryKokkosPreExchangeFunctor f(this); + Kokkos::parallel_for(nlocal_neigh,f); + + deep_copy(h_resize, d_resize); + if (h_resize() > 0) { + maxpartner += 8; + memoryKK->grow_kokkos(k_partner,partner,atom->nmax,maxpartner,"neighbor_history:partner"); + memoryKK->grow_kokkos(k_valuepartner,valuepartner,atom->nmax,dnum*maxpartner,"neighbor_history:valuepartner"); + } + } + + copymode = 0; + + comm->maxexchange_fix = MAX(comm->maxexchange_fix,(dnum+1)*maxpartner+1); +} + +/* ---------------------------------------------------------------------- */ + +template +void FixNeighHistoryKokkos::zero_partner_count_item(const int &i) const +{ + d_npartner[i] = 0; +} + +template +void FixNeighHistoryKokkos::pre_exchange_item(const int &ii) const +{ + const int i = d_ilist[ii]; + const int jnum = d_numneigh[i]; + + for (int jj = 0; jj < jnum; jj++) { + if (d_firstflag(i,jj)) { + int j = d_neighbors(i,jj); + j &= NEIGHMASK; + int m = Kokkos::atomic_fetch_add(&d_npartner[i],1); + if (m < maxpartner) { + d_partner(i,m) = tag[j]; + for (int k = 0; k < dnum; k++) + d_valuepartner(i,dnum*m+k) = d_firstvalue(i,dnum*jj+k); + } else { + d_resize() = 1; + } + if (j < nlocal_neigh) { + m = Kokkos::atomic_fetch_add(&d_npartner[j],1); + if (m < maxpartner) { + d_partner(j,m) = tag[i]; + for (int k = 0; k < dnum; k++) + d_valuepartner(j,dnum*m+k) = d_firstvalue(i,dnum*jj+k); + } else { + d_resize() = 1; + } + } + } + } +} + +/* ---------------------------------------------------------------------- */ + +template +void FixNeighHistoryKokkos::setup_post_neighbor() +{ + post_neighbor(); +} + +/* ---------------------------------------------------------------------- */ + +template +void FixNeighHistoryKokkos::post_neighbor() +{ + tag = atomKK->k_tag.view(); + + int inum = pair->list->inum; + NeighListKokkos* k_list = static_cast*>(pair->list); + d_numneigh = k_list->d_numneigh; + d_neighbors = k_list->d_neighbors; + d_ilist = k_list->d_ilist; + + // store atom counts used for new neighbor list which was just built + + int nlocal = atom->nlocal; + int nall = nlocal + atom->nghost; + nlocal_neigh = nlocal; + nall_neigh = nall; + + // realloc firstflag and firstvalue if needed + + if (maxatom < nlocal || k_list->maxneighs > d_firstflag.extent(1)) { + maxatom = nall; + d_firstflag = typename ArrayTypes::t_int_2d("neighbor_history:firstflag",maxatom,k_list->maxneighs); + d_firstvalue = typename ArrayTypes::t_float_2d("neighbor_history:firstvalue",maxatom,k_list->maxneighs*dnum); + } + + copymode = 1; + + FixNeighHistoryKokkosPostNeighborFunctor f(this); + Kokkos::parallel_for(inum,f); + + copymode = 0; + +#ifdef LMP_KOKKOS_DEBUG + typename ArrayTypes::t_neighbors_2d h_neighbors("neighbor_history:h_neighbor",k_list->d_neighbors.extent(0), k_list->d_neighbors.extent(1)); + deep_copy(h_neighbors, d_neighbors); + + typename ArrayTypes::t_int_1d h_numneigh("neighbor_history:h_numneigh",k_list->d_numneigh.extent(0)); + deep_copy(h_numneigh, d_numneigh); + + typename ArrayTypes::t_int_2d h_firstflag("neighbor_history:h_firstflag",maxatom,k_list->maxneighs); + deep_copy(h_firstflag, d_firstflag); + + typename ArrayTypes::t_float_2d h_firstvalue("neighbor_history:h_firstvalue",maxatom,k_list->maxneighs*dnum); + deep_copy(h_firstvalue, d_firstvalue); +#endif +} + +/* ---------------------------------------------------------------------- */ + +template +KOKKOS_INLINE_FUNCTION +void FixNeighHistoryKokkos::post_neighbor_item(const int &ii) const +{ + const int i = d_ilist[ii]; + const int jnum = d_numneigh[i]; + const int np = d_npartner[i]; + + for (int jj = 0; jj < jnum; jj++) { + int j = d_neighbors(i,jj); + const int rflag = j >> SBBITS & 3; + j &= NEIGHMASK; + + int m; + if (rflag) { + int jtag = tag(j); + for (m = 0; m < np; m++) + if (d_partner(i, m) == jtag) break; + if (m < np) { + d_firstflag(i,jj) = 1; + for (int k = 0; k < dnum; k++) { + d_firstvalue(i, dnum*jj+k) = d_valuepartner(i, dnum*m+k); + } + } else { + d_firstflag(i,jj) = 0; + for (int k = 0; k < dnum; k++) { + d_firstvalue(i, dnum*jj+k) = 0; + } + } + } else { + d_firstflag(i,jj) = 0; + for (int k = 0; k < dnum; k++) { + d_firstvalue(i, dnum*jj+k) = 0; + } + } + } +} + +/* ---------------------------------------------------------------------- + memory usage of local atom-based arrays +------------------------------------------------------------------------- */ + +template +double FixNeighHistoryKokkos::memory_usage() +{ + double bytes = d_firstflag.extent(0)*d_firstflag.extent(1)*sizeof(int); + bytes += d_firstvalue.extent(0)*d_firstvalue.extent(1)*sizeof(double); + bytes += 2*k_npartner.extent(0)*sizeof(int); + bytes += 2*k_partner.extent(0)*k_partner.extent(1)*sizeof(int); + bytes += 2*k_valuepartner.extent(0)*k_valuepartner.extent(1)*sizeof(double); + return bytes; +} + +/* ---------------------------------------------------------------------- + allocate fictitious charge arrays +------------------------------------------------------------------------- */ + +template +void FixNeighHistoryKokkos::grow_arrays(int nmax) +{ + k_npartner.template sync(); // force reallocation on host + k_partner.template sync(); + k_valuepartner.template sync(); + + memoryKK->grow_kokkos(k_npartner,npartner,nmax,"neighbor_history:npartner"); + memoryKK->grow_kokkos(k_partner,partner,nmax,maxpartner,"neighbor_history:partner"); + memoryKK->grow_kokkos(k_valuepartner,valuepartner,nmax,dnum*maxpartner,"neighbor_history:valuepartner"); + + d_npartner = k_npartner.template view(); + d_partner = k_partner.template view(); + d_valuepartner = k_valuepartner.template view(); + + k_npartner.template modify(); + k_partner.template modify(); + k_valuepartner.template modify(); +} + +/* ---------------------------------------------------------------------- + copy values within fictitious charge arrays +------------------------------------------------------------------------- */ + +template +void FixNeighHistoryKokkos::copy_arrays(int i, int j, int delflag) +{ + k_npartner.template sync(); + k_partner.template sync(); + k_valuepartner.template sync(); + + npartner[j] = npartner[i]; + for (int m = 0; m < npartner[i]; m++) { + partner[j][m] = partner[i][m]; + valuepartner[j][m] = valuepartner[i][m]; + } + + k_npartner.template modify(); + k_partner.template modify(); + k_valuepartner.template modify(); +} + +/* ---------------------------------------------------------------------- + pack values in local atom-based array for exchange with another proc +------------------------------------------------------------------------- */ + +template +int FixNeighHistoryKokkos::pack_exchange(int i, double *buf) +{ + k_npartner.template sync(); + k_partner.template sync(); + k_valuepartner.template sync(); + + int n = 0; + buf[n++] = npartner[i]; + for (int m = 0; m < npartner[i]; m++) buf[n++] = partner[i][m]; + for (int m = 0; m < dnum*npartner[i]; m++) buf[n++] = valuepartner[i][m]; + + return n; +} + +/* ---------------------------------------------------------------------- + unpack values in local atom-based array from exchange with another proc +------------------------------------------------------------------------- */ + +template +int FixNeighHistoryKokkos::unpack_exchange(int nlocal, double *buf) +{ + int n = 0; + npartner[nlocal] = static_cast(buf[n++]); + for (int m = 0; m < npartner[nlocal]; m++) partner[nlocal][m] = static_cast(buf[n++]); + for (int m = 0; m < dnum*npartner[nlocal]; m++) valuepartner[nlocal][m] = buf[n++]; + + k_npartner.template modify(); + k_partner.template modify(); + k_valuepartner.template modify(); + + return n; +} + +/* ---------------------------------------------------------------------- */ + +namespace LAMMPS_NS { +template class FixNeighHistoryKokkos; +#ifdef KOKKOS_HAVE_CUDA +template class FixNeighHistoryKokkos; +#endif +} diff --git a/src/KOKKOS/fix_neigh_history_kokkos.h b/src/KOKKOS/fix_neigh_history_kokkos.h new file mode 100644 index 0000000000..68bd59722f --- /dev/null +++ b/src/KOKKOS/fix_neigh_history_kokkos.h @@ -0,0 +1,107 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef FIX_CLASS + +FixStyle(NEIGH_HISTORY/KK,FixNeighHistoryKokkos) +FixStyle(NEIGH_HISTORY/KK/DEVICE,FixNeighHistoryKokkos) +FixStyle(NEIGH_HISTORY/KK/HOST,FixNeighHistoryKokkos) + +#else + +#ifndef LMP_FIX_NEIGH_HISTORY_KOKKOS_H +#define LMP_FIX_NEIGH_HISTORY_KOKKOS_H + +#include "fix_neigh_history.h" +#include "kokkos_type.h" + +namespace LAMMPS_NS { +template +class FixNeighHistoryKokkos : public FixNeighHistory { + public: + FixNeighHistoryKokkos(class LAMMPS *, int, char **); + ~FixNeighHistoryKokkos(); + + void init(); + void pre_exchange(); + void setup_post_neighbor(); + virtual void post_neighbor(); + double memory_usage(); + void grow_arrays(int); + void copy_arrays(int, int, int); + int pack_exchange(int, double *); + int unpack_exchange(int, double *); + + KOKKOS_INLINE_FUNCTION + void zero_partner_count_item(const int &i) const; + KOKKOS_INLINE_FUNCTION + void pre_exchange_item(const int &ii) const; + KOKKOS_INLINE_FUNCTION + void post_neighbor_item(const int &ii) const; + + typename ArrayTypes::t_int_2d d_firstflag; + typename ArrayTypes::t_float_2d d_firstvalue; + + private: + typename ArrayTypes::tdual_int_1d k_npartner; + typename ArrayTypes::tdual_int_2d k_partner; + typename ArrayTypes::tdual_float_2d k_valuepartner; + + // for neighbor list lookup + typename ArrayTypes::t_neighbors_2d d_neighbors; + typename ArrayTypes::t_int_1d_randomread d_ilist; + typename ArrayTypes::t_int_1d_randomread d_numneigh; + + typename ArrayTypes::t_tagint_1d tag; + typename ArrayTypes::t_int_1d d_npartner; + typename ArrayTypes::t_int_2d d_partner; + typename ArrayTypes::t_float_2d d_valuepartner; + + typename ArrayTypes::t_int_scalar d_resize; + typename ArrayTypes::t_int_scalar h_resize; +}; + +template +struct FixNeighHistoryKokkosZeroPartnerCountFunctor { + FixNeighHistoryKokkos c; + FixNeighHistoryKokkosZeroPartnerCountFunctor(FixNeighHistoryKokkos *c_ptr): c(*c_ptr) {} + KOKKOS_INLINE_FUNCTION + void operator()(const int &i) const { + c.zero_partner_count_item(i); + } +}; + +template +struct FixNeighHistoryKokkosPreExchangeFunctor { + FixNeighHistoryKokkos c; + FixNeighHistoryKokkosPreExchangeFunctor(FixNeighHistoryKokkos *c_ptr): c(*c_ptr) {} + KOKKOS_INLINE_FUNCTION + void operator() (const int &i) const { + c.pre_exchange_item(i); + } +}; + +template +struct FixNeighHistoryKokkosPostNeighborFunctor { + FixNeighHistoryKokkos c; + FixNeighHistoryKokkosPostNeighborFunctor(FixNeighHistoryKokkos *c_ptr): c(*c_ptr) {} + KOKKOS_INLINE_FUNCTION + void operator() (const int &i) const { + c.post_neighbor_item(i); + } +}; + +} // namespace LAMMPS_NS + +#endif // LMP_FIX_NEIGH_HISTORY_KOKKOS_H +#endif // FIX_CLASS diff --git a/src/KOKKOS/npair_kokkos.cpp b/src/KOKKOS/npair_kokkos.cpp index 4411627a78..c50d6305e7 100644 --- a/src/KOKKOS/npair_kokkos.cpp +++ b/src/KOKKOS/npair_kokkos.cpp @@ -24,8 +24,8 @@ namespace LAMMPS_NS { /* ---------------------------------------------------------------------- */ -template -NPairKokkos::NPairKokkos(LAMMPS *lmp) : NPair(lmp) { +template +NPairKokkos::NPairKokkos(LAMMPS *lmp) : NPair(lmp) { } @@ -33,8 +33,8 @@ NPairKokkos::NPairKokkos(LAMMPS *lmp) : NPair(l copy needed info from Neighbor class to this build class ------------------------------------------------------------------------- */ -template -void NPairKokkos::copy_neighbor_info() +template +void NPairKokkos::copy_neighbor_info() { NPair::copy_neighbor_info(); @@ -63,8 +63,8 @@ void NPairKokkos::copy_neighbor_info() copy per-atom and per-bin vectors from NBin class to this build class ------------------------------------------------------------------------- */ -template -void NPairKokkos::copy_bin_info() +template +void NPairKokkos::copy_bin_info() { NPair::copy_bin_info(); @@ -80,8 +80,8 @@ void NPairKokkos::copy_bin_info() copy needed info from NStencil class to this build class ------------------------------------------------------------------------- */ -template -void NPairKokkos::copy_stencil_info() +template +void NPairKokkos::copy_stencil_info() { NPair::copy_stencil_info(); @@ -110,8 +110,8 @@ void NPairKokkos::copy_stencil_info() /* ---------------------------------------------------------------------- */ -template -void NPairKokkos::build(NeighList *list_) +template +void NPairKokkos::build(NeighList *list_) { NeighListKokkos* list = (NeighListKokkos*) list_; const int nlocal = includegroup?atom->nfirst:atom->nlocal; @@ -131,6 +131,7 @@ void NPairKokkos::build(NeighList *list_) k_stencilxyz.view(), nlocal, atomKK->k_x.view(), + atomKK->k_radius.view(), atomKK->k_type.view(), atomKK->k_mask.view(), atomKK->k_molecule.view(), @@ -155,7 +156,8 @@ void NPairKokkos::build(NeighList *list_) k_ex_mol_intra.view(), bboxhi,bboxlo, domain->xperiodic,domain->yperiodic,domain->zperiodic, - domain->xprd_half,domain->yprd_half,domain->zprd_half); + domain->xprd_half,domain->yprd_half,domain->zprd_half, + skin); k_cutneighsq.sync(); k_ex1_type.sync(); @@ -171,7 +173,7 @@ void NPairKokkos::build(NeighList *list_) k_bincount.sync(); k_bins.sync(); k_atom2bin.sync(); - atomKK->sync(Device,X_MASK|TYPE_MASK|MASK_MASK|MOLECULE_MASK|TAG_MASK|SPECIAL_MASK); + atomKK->sync(Device,X_MASK|RADIUS_MASK|TYPE_MASK|MASK_MASK|MOLECULE_MASK|TAG_MASK|SPECIAL_MASK); data.special_flag[0] = special_flag[0]; data.special_flag[1] = special_flag[1]; @@ -198,25 +200,49 @@ void NPairKokkos::build(NeighList *list_) Kokkos::parallel_for(nall, f); } else { if (newton_pair) { - NPairKokkosBuildFunctor f(data,atoms_per_bin * 5 * sizeof(X_FLOAT) * factor); + if (SIZE) { + NPairKokkosBuildFunctorSize f(data,atoms_per_bin * 5 * sizeof(X_FLOAT) * factor); #ifdef KOKKOS_HAVE_CUDA - if (ExecutionSpaceFromDevice::space == Device) - Kokkos::parallel_for(config, f); - else - Kokkos::parallel_for(nall, f); + if (ExecutionSpaceFromDevice::space == Device) + Kokkos::parallel_for(config, f); + else + Kokkos::parallel_for(nall, f); #else - Kokkos::parallel_for(nall, f); + Kokkos::parallel_for(nall, f); #endif + } else { + NPairKokkosBuildFunctor f(data,atoms_per_bin * 5 * sizeof(X_FLOAT) * factor); +#ifdef KOKKOS_HAVE_CUDA + if (ExecutionSpaceFromDevice::space == Device) + Kokkos::parallel_for(config, f); + else + Kokkos::parallel_for(nall, f); +#else + Kokkos::parallel_for(nall, f); +#endif + } } else { - NPairKokkosBuildFunctor f(data,atoms_per_bin * 5 * sizeof(X_FLOAT) * factor); + if (SIZE) { + NPairKokkosBuildFunctorSize f(data,atoms_per_bin * 5 * sizeof(X_FLOAT) * factor); #ifdef KOKKOS_HAVE_CUDA - if (ExecutionSpaceFromDevice::space == Device) - Kokkos::parallel_for(config, f); - else - Kokkos::parallel_for(nall, f); + if (ExecutionSpaceFromDevice::space == Device) + Kokkos::parallel_for(config, f); + else + Kokkos::parallel_for(nall, f); #else - Kokkos::parallel_for(nall, f); + Kokkos::parallel_for(nall, f); #endif + } else { + NPairKokkosBuildFunctor f(data,atoms_per_bin * 5 * sizeof(X_FLOAT) * factor); +#ifdef KOKKOS_HAVE_CUDA + if (ExecutionSpaceFromDevice::space == Device) + Kokkos::parallel_for(config, f); + else + Kokkos::parallel_for(nall, f); +#else + Kokkos::parallel_for(nall, f); +#endif + } } } deep_copy(data.h_resize, data.resize); @@ -774,19 +800,307 @@ void NeighborKokkosExecute:: neigh_list.d_ilist(i) = i; } +/* ---------------------------------------------------------------------- */ + +template template +void NeighborKokkosExecute:: + build_ItemSize(const int &i) const +{ + /* if necessary, goto next page and add pages */ + int n = 0; + int which = 0; + + // get subview of neighbors of i + + const AtomNeighbors neighbors_i = neigh_list.get_neighbors(i); + const X_FLOAT xtmp = x(i, 0); + const X_FLOAT ytmp = x(i, 1); + const X_FLOAT ztmp = x(i, 2); + const X_FLOAT radi = radius(i); + const int itype = type(i); + + const int ibin = c_atom2bin(i); + + const typename ArrayTypes::t_int_1d_const_um stencil + = d_stencil; + + const int mask_history = 3 << SBBITS; + + // loop over all bins in neighborhood (includes ibin) + if(HalfNeigh) + for(int m = 0; m < c_bincount(ibin); m++) { + const int j = c_bins(ibin,m); + const int jtype = type(j); + + //for same bin as atom i skip j if i==j and skip atoms "below and to the left" if using HalfNeighborlists + if((j == i) || (HalfNeigh && !Newton && (j < i)) || + (HalfNeigh && Newton && ((j < i) || ((j >= nlocal) && + ((x(j, 2) < ztmp) || (x(j, 2) == ztmp && x(j, 1) < ytmp) || + (x(j, 2) == ztmp && x(j, 1) == ytmp && x(j, 0) < xtmp))))) + ) continue; + if(exclude && exclusion(i,j,itype,jtype)) continue; + + const X_FLOAT delx = xtmp - x(j, 0); + const X_FLOAT dely = ytmp - x(j, 1); + const X_FLOAT delz = ztmp - x(j, 2); + const X_FLOAT rsq = delx * delx + dely * dely + delz * delz; + const X_FLOAT radsum = radi + radius(j); + const X_FLOAT cutsq = (radsum + skin) * (radsum + skin); + + if(rsq <= cutsq) { + if(n::t_int_1d_const_um =Kokkos::subview(bins,jbin,ALL); + for(int m = 0; m < c_bincount(jbin); m++) { + + const int j = c_bins(jbin,m); + const int jtype = type(j); + + if(HalfNeigh && !Newton && (j < i)) continue; + if(!HalfNeigh && j==i) continue; + if(Tri) { + if (x(j,2) < ztmp) continue; + if (x(j,2) == ztmp) { + if (x(j,1) < ytmp) continue; + if (x(j,1) == ytmp) { + if (x(j,0) < xtmp) continue; + if (x(j,0) == xtmp && j <= i) continue; + } + } + } + if(exclude && exclusion(i,j,itype,jtype)) continue; + + const X_FLOAT delx = xtmp - x(j, 0); + const X_FLOAT dely = ytmp - x(j, 1); + const X_FLOAT delz = ztmp - x(j, 2); + const X_FLOAT rsq = delx * delx + dely * dely + delz * delz; + const X_FLOAT radsum = radi + radius(j); + const X_FLOAT cutsq = (radsum + skin) * (radsum + skin); + + if(rsq <= cutsq) { + if(n neigh_list.maxneighs) { + resize() = 1; + + if(n > new_maxneighs()) new_maxneighs() = n; // avoid atomics, safe because in while loop + } + + neigh_list.d_ilist(i) = i; +} + +/* ---------------------------------------------------------------------- */ + +#ifdef KOKKOS_HAVE_CUDA +template template +__device__ inline +void NeighborKokkosExecute::build_ItemSizeCuda(typename Kokkos::TeamPolicy::member_type dev) const +{ + /* loop over atoms in i's bin, + */ + const int atoms_per_bin = c_bins.extent(1); + const int BINS_PER_TEAM = dev.team_size()/atoms_per_bin<1?1:dev.team_size()/atoms_per_bin; + const int TEAMS_PER_BIN = atoms_per_bin/dev.team_size()<1?1:atoms_per_bin/dev.team_size(); + const int MY_BIN = dev.team_rank()/atoms_per_bin; + + const int ibin = dev.league_rank()*BINS_PER_TEAM+MY_BIN; + + if(ibin >=c_bincount.extent(0)) return; + X_FLOAT* other_x = sharedmem; + other_x = other_x + 6*atoms_per_bin*MY_BIN; + + int* other_id = (int*) &other_x[5 * atoms_per_bin]; + + int bincount_current = c_bincount[ibin]; + + for(int kk = 0; kk < TEAMS_PER_BIN; kk++) { + const int MY_II = dev.team_rank()%atoms_per_bin+kk*dev.team_size(); + const int i = MY_II < bincount_current ? c_bins(ibin, MY_II) : -1; + /* if necessary, goto next page and add pages */ + + int n = 0; + + X_FLOAT xtmp; + X_FLOAT ytmp; + X_FLOAT ztmp; + X_FLOAT radi; + int itype; + const AtomNeighbors neighbors_i = neigh_list.get_neighbors((i>=0&&i= 0) { + xtmp = x(i, 0); + ytmp = x(i, 1); + ztmp = x(i, 2); + radi = radius(i); + itype = type(i); + other_x[MY_II] = xtmp; + other_x[MY_II + atoms_per_bin] = ytmp; + other_x[MY_II + 2 * atoms_per_bin] = ztmp; + other_x[MY_II + 3 * atoms_per_bin] = itype; + other_x[MY_II + 4 * atoms_per_bin] = radi; + } + other_id[MY_II] = i; + int test = (__syncthreads_count(i >= 0 && i <= nlocal) == 0); + + if(test) return; + + if(i >= 0 && i < nlocal) { + #pragma unroll 4 + for(int m = 0; m < bincount_current; m++) { + int j = other_id[m]; + const int jtype = other_x[m + 3 * atoms_per_bin]; + + //for same bin as atom i skip j if i==j and skip atoms "below and to the left" if using halfneighborlists + if((j == i) || + (HalfNeigh && !Newton && (j < i)) || + (HalfNeigh && Newton && + ((j < i) || + ((j >= nlocal) && ((x(j, 2) < ztmp) || (x(j, 2) == ztmp && x(j, 1) < ytmp) || + (x(j, 2) == ztmp && x(j, 1) == ytmp && x(j, 0) < xtmp))))) + ) continue; + if(Tri) { + if (x(j,2) < ztmp) continue; + if (x(j,2) == ztmp) { + if (x(j,1) < ytmp) continue; + if (x(j,1) == ytmp) { + if (x(j,0) < xtmp) continue; + if (x(j,0) == xtmp && j <= i) continue; + } + } + } + if(exclude && exclusion(i,j,itype,jtype)) continue; + const X_FLOAT delx = xtmp - other_x[m]; + const X_FLOAT dely = ytmp - other_x[m + atoms_per_bin]; + const X_FLOAT delz = ztmp - other_x[m + 2 * atoms_per_bin]; + const X_FLOAT rsq = delx * delx + dely * dely + delz * delz; + const X_FLOAT radsum = radi + other_x[m + 4 * atoms_per_bin]; + const X_FLOAT cutsq = (radsum + skin) * (radsum + skin); + + if(rsq <= cutsq) { + if(n::t_int_1d_const_um stencil + = d_stencil; + for(int k = 0; k < nstencil; k++) { + const int jbin = ibin + stencil[k]; + + if(ibin == jbin) continue; + + bincount_current = c_bincount[jbin]; + int j = MY_II < bincount_current ? c_bins(jbin, MY_II) : -1; + + if(j >= 0) { + other_x[MY_II] = x(j, 0); + other_x[MY_II + atoms_per_bin] = x(j, 1); + other_x[MY_II + 2 * atoms_per_bin] = x(j, 2); + other_x[MY_II + 3 * atoms_per_bin] = type(j); + other_x[MY_II + 4 * atoms_per_bin] = radius(j); + } + + other_id[MY_II] = j; + + __syncthreads(); + + if(i >= 0 && i < nlocal) { + #pragma unroll 8 + for(int m = 0; m < bincount_current; m++) { + const int j = other_id[m]; + const int jtype = other_x[m + 3 * atoms_per_bin]; + + if(HalfNeigh && (j < i)) continue; + if(HalfNeigh && !Newton && (j < i)) continue; + if(!HalfNeigh && j==i) continue; + if(Tri) { + if (x(j,2) < ztmp) continue; + if (x(j,2) == ztmp) { + if (x(j,1) < ytmp) continue; + if (x(j,1) == ytmp) { + if (x(j,0) < xtmp) continue; + if (x(j,0) == xtmp && j <= i) continue; + } + } + } + if(exclude && exclusion(i,j,itype,jtype)) continue; + + const X_FLOAT delx = xtmp - other_x[m]; + const X_FLOAT dely = ytmp - other_x[m + atoms_per_bin]; + const X_FLOAT delz = ztmp - other_x[m + 2 * atoms_per_bin]; + const X_FLOAT rsq = delx * delx + dely * dely + delz * delz; + const X_FLOAT radsum = radi + other_x[m + 4 * atoms_per_bin]; + const X_FLOAT cutsq = (radsum + skin) * (radsum + skin); + + if(rsq <= cutsq) { + if(n= 0 && i < nlocal) { + neigh_list.d_numneigh(i) = n; + neigh_list.d_ilist(i) = i; + } + + if(n > neigh_list.maxneighs) { + resize() = 1; + + if(n > new_maxneighs()) new_maxneighs() = n; // avoid atomics, safe because in while loop + } + } +} +#endif + } namespace LAMMPS_NS { -template class NPairKokkos; -template class NPairKokkos; -template class NPairKokkos; -template class NPairKokkos; -template class NPairKokkos; +template class NPairKokkos; +template class NPairKokkos; +template class NPairKokkos; +template class NPairKokkos; +template class NPairKokkos; +template class NPairKokkos; +template class NPairKokkos; #ifdef KOKKOS_HAVE_CUDA -template class NPairKokkos; -template class NPairKokkos; -template class NPairKokkos; -template class NPairKokkos; -template class NPairKokkos; +template class NPairKokkos; +template class NPairKokkos; +template class NPairKokkos; +template class NPairKokkos; +template class NPairKokkos; +template class NPairKokkos; +template class NPairKokkos; #endif } diff --git a/src/KOKKOS/npair_kokkos.h b/src/KOKKOS/npair_kokkos.h index 6c1c0e958b..a8837fa9f3 100644 --- a/src/KOKKOS/npair_kokkos.h +++ b/src/KOKKOS/npair_kokkos.h @@ -13,56 +13,76 @@ #ifdef NPAIR_CLASS -typedef NPairKokkos NPairKokkosFullBinHost; +typedef NPairKokkos NPairKokkosFullBinHost; NPairStyle(full/bin/kk/host, NPairKokkosFullBinHost, NP_FULL | NP_BIN | NP_KOKKOS_HOST | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI) -typedef NPairKokkos NPairKokkosFullBinDevice; +typedef NPairKokkos NPairKokkosFullBinDevice; NPairStyle(full/bin/kk/device, NPairKokkosFullBinDevice, NP_FULL | NP_BIN | NP_KOKKOS_DEVICE | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI) -typedef NPairKokkos NPairKokkosFullBinGhostHost; +typedef NPairKokkos NPairKokkosFullBinGhostHost; NPairStyle(full/bin/ghost/kk/host, NPairKokkosFullBinGhostHost, NP_FULL | NP_BIN | NP_KOKKOS_HOST | NP_NEWTON | NP_NEWTOFF | NP_GHOST | NP_ORTHO | NP_TRI) -typedef NPairKokkos NPairKokkosFullBinGhostDevice; +typedef NPairKokkos NPairKokkosFullBinGhostDevice; NPairStyle(full/bin/ghost/kk/device, NPairKokkosFullBinGhostDevice, NP_FULL | NP_BIN | NP_KOKKOS_DEVICE | NP_NEWTON | NP_NEWTOFF | NP_GHOST | NP_ORTHO | NP_TRI) -typedef NPairKokkos NPairKokkosHalfBinHost; +typedef NPairKokkos NPairKokkosHalfBinHost; NPairStyle(half/bin/kk/host, NPairKokkosHalfBinHost, NP_HALF | NP_BIN | NP_KOKKOS_HOST | NP_NEWTON | NP_NEWTOFF | NP_ORTHO) -typedef NPairKokkos NPairKokkosHalfBinDevice; +typedef NPairKokkos NPairKokkosHalfBinDevice; NPairStyle(half/bin/kk/device, NPairKokkosHalfBinDevice, NP_HALF | NP_BIN | NP_KOKKOS_DEVICE | NP_NEWTON | NP_NEWTOFF | NP_ORTHO) -typedef NPairKokkos NPairKokkosHalfBinHostTri; +typedef NPairKokkos NPairKokkosHalfBinHostTri; NPairStyle(half/bin/kk/host, NPairKokkosHalfBinHostTri, NP_HALF | NP_BIN | NP_KOKKOS_HOST | NP_NEWTON | NP_NEWTOFF | NP_TRI) -typedef NPairKokkos NPairKokkosHalfBinDeviceTri; +typedef NPairKokkos NPairKokkosHalfBinDeviceTri; NPairStyle(half/bin/kk/device, NPairKokkosHalfBinDeviceTri, NP_HALF | NP_BIN | NP_KOKKOS_DEVICE | NP_NEWTON | NP_NEWTOFF | NP_TRI) -typedef NPairKokkos NPairKokkosHalfBinGhostHost; +typedef NPairKokkos NPairKokkosHalfBinGhostHost; NPairStyle(half/bin/ghost/kk/host, NPairKokkosHalfBinGhostHost, NP_HALF | NP_BIN | NP_KOKKOS_HOST | NP_NEWTON | NP_NEWTOFF | NP_GHOST | NP_ORTHO | NP_TRI) -typedef NPairKokkos NPairKokkosHalfBinGhostDevice; +typedef NPairKokkos NPairKokkosHalfBinGhostDevice; NPairStyle(half/bin/ghost/kk/device, NPairKokkosHalfBinGhostDevice, NP_HALF | NP_BIN | NP_KOKKOS_DEVICE | NP_NEWTON | NP_NEWTOFF | NP_GHOST | NP_ORTHO | NP_TRI) +typedef NPairKokkos NPairKokkosHalfSizeBinHost; +NPairStyle(half/size/bin/kk/host, + NPairKokkosHalfSizeBinHost, + NP_HALF | NP_SIZE | NP_BIN | NP_KOKKOS_HOST | NP_NEWTON | NP_NEWTOFF | NP_ORTHO) + +typedef NPairKokkos NPairKokkosHalfSizeBinDevice; +NPairStyle(half/size/bin/kk/device, + NPairKokkosHalfSizeBinDevice, + NP_HALF | NP_SIZE | NP_BIN | NP_KOKKOS_DEVICE | NP_NEWTON | NP_NEWTOFF | NP_ORTHO) + +typedef NPairKokkos NPairKokkosHalfSizeBinHostTri; +NPairStyle(half/size/bin/kk/host, + NPairKokkosHalfSizeBinHostTri, + NP_HALF | NP_SIZE | NP_BIN | NP_KOKKOS_HOST | NP_NEWTON | NP_NEWTOFF | NP_TRI) + +typedef NPairKokkos NPairKokkosHalfSizeBinDeviceTri; +NPairStyle(half/size/bin/kk/device, + NPairKokkosHalfSizeBinDeviceTri, + NP_HALF | NP_SIZE | NP_BIN | NP_KOKKOS_DEVICE | NP_NEWTON | NP_NEWTOFF | NP_TRI) + #else #ifndef LMP_NPAIR_KOKKOS_H @@ -73,7 +93,7 @@ NPairStyle(half/bin/ghost/kk/device, namespace LAMMPS_NS { -template +template class NPairKokkos : public NPair { public: NPairKokkos(class LAMMPS *); @@ -162,6 +182,7 @@ class NeighborKokkosExecute // data from Atom class const typename AT::t_x_array_randomread x; + const typename AT::t_float_1d_randomread radius; const typename AT::t_int_1d_const type,mask; const typename AT::t_tagint_1d_const molecule; const typename AT::t_tagint_1d_const tag; @@ -188,6 +209,9 @@ class NeighborKokkosExecute const int xperiodic, yperiodic, zperiodic; const int xprd_half, yprd_half, zprd_half; + // GRANULAR required member variables + const X_FLOAT skin; + NeighborKokkosExecute( const NeighListKokkos &_neigh_list, const typename AT::t_xfloat_2d_randomread &_cutneighsq, @@ -199,6 +223,7 @@ class NeighborKokkosExecute const typename AT::t_int_1d_3 &_d_stencilxyz, const int _nlocal, const typename AT::t_x_array_randomread &_x, + const typename AT::t_float_1d_randomread &_radius, const typename AT::t_int_1d_const &_type, const typename AT::t_int_1d_const &_mask, const typename AT::t_tagint_1d_const &_molecule, @@ -225,13 +250,14 @@ class NeighborKokkosExecute const typename AT::t_int_1d_const & _ex_mol_intra, const X_FLOAT *_bboxhi, const X_FLOAT* _bboxlo, const int & _xperiodic, const int & _yperiodic, const int & _zperiodic, - const int & _xprd_half, const int & _yprd_half, const int & _zprd_half): + const int & _xprd_half, const int & _yprd_half, const int & _zprd_half, + const X_FLOAT _skin): neigh_list(_neigh_list), cutneighsq(_cutneighsq), bincount(_bincount),c_bincount(_bincount),bins(_bins),c_bins(_bins), atom2bin(_atom2bin),c_atom2bin(_atom2bin), nstencil(_nstencil),d_stencil(_d_stencil),d_stencilxyz(_d_stencilxyz), nlocal(_nlocal), - x(_x),type(_type),mask(_mask),molecule(_molecule), + x(_x),radius(_radius),type(_type),mask(_mask),molecule(_molecule), tag(_tag),special(_special),nspecial(_nspecial),molecular(_molecular), nbinx(_nbinx),nbiny(_nbiny),nbinz(_nbinz), mbinx(_mbinx),mbiny(_mbiny),mbinz(_mbinz), @@ -245,7 +271,8 @@ class NeighborKokkosExecute ex_mol_group(_ex_mol_group),ex_mol_bit(_ex_mol_bit), ex_mol_intra(_ex_mol_intra), xperiodic(_xperiodic),yperiodic(_yperiodic),zperiodic(_zperiodic), - xprd_half(_xprd_half),yprd_half(_yprd_half),zprd_half(_zprd_half) { + xprd_half(_xprd_half),yprd_half(_yprd_half),zprd_half(_zprd_half), + skin(_skin) { if (molecular == 2) moltemplate = 1; else moltemplate = 0; @@ -280,10 +307,18 @@ class NeighborKokkosExecute KOKKOS_FUNCTION void build_Item_Ghost(const int &i) const; + template + KOKKOS_FUNCTION + void build_ItemSize(const int &i) const; + #ifdef KOKKOS_HAVE_CUDA template __device__ inline void build_ItemCuda(typename Kokkos::TeamPolicy::member_type dev) const; + + template + __device__ inline + void build_ItemSizeCuda(typename Kokkos::TeamPolicy::member_type dev) const; #endif KOKKOS_INLINE_FUNCTION @@ -399,6 +434,48 @@ struct NPairKokkosBuildFunctorGhost { } }; +template +struct NPairKokkosBuildFunctorSize { + typedef DeviceType device_type; + + const NeighborKokkosExecute c; + const size_t sharedsize; + + NPairKokkosBuildFunctorSize(const NeighborKokkosExecute &_c, + const size_t _sharedsize): c(_c), sharedsize(_sharedsize) {}; + + KOKKOS_INLINE_FUNCTION + void operator() (const int & i) const { + c.template build_ItemSize(i); + } + +#ifdef KOKKOS_HAVE_CUDA + __device__ inline + void operator() (typename Kokkos::TeamPolicy::member_type dev) const { + c.template build_ItemSizeCuda(dev); + } + size_t shmem_size(const int team_size) const { (void) team_size; return sharedsize; } +#endif +}; + +template +struct NPairKokkosBuildFunctorSize { + typedef LMPHostType device_type; + + const NeighborKokkosExecute c; + const size_t sharedsize; + + NPairKokkosBuildFunctorSize(const NeighborKokkosExecute &_c, + const size_t _sharedsize): c(_c), sharedsize(_sharedsize) {}; + + KOKKOS_INLINE_FUNCTION + void operator() (const int & i) const { + c.template build_ItemSize(i); + } + + void operator() (typename Kokkos::TeamPolicy::member_type dev) const {} // Should error out +}; + } #endif diff --git a/src/KOKKOS/pair_gran_hooke_history_kokkos.cpp b/src/KOKKOS/pair_gran_hooke_history_kokkos.cpp new file mode 100644 index 0000000000..d7c8f8a99e --- /dev/null +++ b/src/KOKKOS/pair_gran_hooke_history_kokkos.cpp @@ -0,0 +1,440 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "pair_gran_hooke_history_kokkos.h" +#include "kokkos.h" +#include "atom_kokkos.h" +#include "atom_masks.h" +#include "memory_kokkos.h" +#include "force.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "error.h" +#include "modify.h" +#include "fix_neigh_history_kokkos.h" +#include "update.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +template +PairGranHookeHistoryKokkos::PairGranHookeHistoryKokkos(LAMMPS *lmp) : PairGranHookeHistory(lmp) +{ + atomKK = (AtomKokkos *) atom; + execution_space = ExecutionSpaceFromDevice::space; + datamask_read = X_MASK | V_MASK | OMEGA_MASK | F_MASK | TORQUE_MASK | TYPE_MASK | MASK_MASK | ENERGY_MASK | VIRIAL_MASK | RMASS_MASK | RADIUS_MASK; + datamask_modify = F_MASK | TORQUE_MASK | ENERGY_MASK | VIRIAL_MASK; +} + +/* ---------------------------------------------------------------------- */ + +template +PairGranHookeHistoryKokkos::~PairGranHookeHistoryKokkos() +{ + if (copymode) return; + + if (allocated) { + memoryKK->destroy_kokkos(k_eatom,eatom); + memoryKK->destroy_kokkos(k_vatom,vatom); + eatom = NULL; + vatom = NULL; + } +} + +/* ---------------------------------------------------------------------- + init specific to this pair style +------------------------------------------------------------------------- */ + +template +void PairGranHookeHistoryKokkos::init_style() +{ + if (history && fix_history == NULL) { + char dnumstr[16]; + sprintf(dnumstr,"%d",3); + char **fixarg = new char*[4]; + fixarg[0] = (char *) "NEIGH_HISTORY"; + fixarg[1] = (char *) "all"; + if (execution_space == Device) + fixarg[2] = (char *) "NEIGH_HISTORY/KK/DEVICE"; + else + fixarg[2] = (char *) "NEIGH_HISTORY/KK/HOST"; + fixarg[3] = dnumstr; + modify->add_fix(4,fixarg,1); + delete [] fixarg; + fix_history = (FixNeighHistory *) modify->fix[modify->nfix-1]; + fix_history->pair = this; + fix_historyKK = (FixNeighHistoryKokkos *)fix_history; + } + + PairGranHookeHistory::init_style(); + + // irequest = neigh request made by parent class + + neighflag = lmp->kokkos->neighflag; + int irequest = neighbor->nrequest - 1; + + neighbor->requests[irequest]-> + kokkos_host = Kokkos::Impl::is_same::value && + !Kokkos::Impl::is_same::value; + neighbor->requests[irequest]-> + kokkos_device = Kokkos::Impl::is_same::value; + + if (neighflag == HALF || neighflag == HALFTHREAD) { + neighbor->requests[irequest]->full = 0; + neighbor->requests[irequest]->half = 1; + } else { + error->all(FLERR,"Cannot use chosen neighbor list style with gran/hooke/history/kk"); + } +} + +/* ---------------------------------------------------------------------- */ + +template +void PairGranHookeHistoryKokkos::compute(int eflag_in, int vflag_in) +{ + copymode = 1; + + eflag = eflag_in; + vflag = vflag_in; + + if (neighflag == FULL) no_virial_fdotr_compute = 1; + + if (eflag || vflag) ev_setup(eflag,vflag,0); + else evflag = vflag_fdotr = 0; + + int shearupdate = 1; + if (update->setupflag) shearupdate = 0; + + // reallocate per-atom arrays if necessary + + if (eflag_atom) { + memoryKK->destroy_kokkos(k_eatom,eatom); + memoryKK->create_kokkos(k_eatom,eatom,maxeatom,"pair:eatom"); + d_eatom = k_eatom.view(); + } + if (vflag_atom) { + memoryKK->destroy_kokkos(k_vatom,vatom); + memoryKK->create_kokkos(k_vatom,vatom,maxvatom,6,"pair:vatom"); + d_vatom = k_vatom.view(); + } + + atomKK->sync(execution_space,datamask_read); + if (eflag || vflag) atomKK->modified(execution_space,datamask_modify); + else atomKK->modified(execution_space,F_MASK | TORQUE_MASK); + + x = atomKK->k_x.view(); + v = atomKK->k_v.view(); + omega = atomKK->k_omega.view(); + c_x = atomKK->k_x.view(); + f = atomKK->k_f.view(); + torque = atomKK->k_torque.view(); + type = atomKK->k_type.view(); + mask = atomKK->k_mask.view(); + tag = atomKK->k_tag.view(); + rmass = atomKK->k_rmass.view(); + radius = atomKK->k_radius.view(); + nlocal = atom->nlocal; + nall = atom->nlocal + atom->nghost; + newton_pair = force->newton_pair; + special_lj[0] = force->special_lj[0]; + special_lj[1] = force->special_lj[1]; + special_lj[2] = force->special_lj[2]; + special_lj[3] = force->special_lj[3]; + + int inum = list->inum; + NeighListKokkos* k_list = static_cast*>(list); + d_numneigh = k_list->d_numneigh; + d_neighbors = k_list->d_neighbors; + d_ilist = k_list->d_ilist; + + d_firsttouch = fix_historyKK->d_firstflag; + d_firstshear = fix_historyKK->d_firstvalue; + + EV_FLOAT ev; + + if (lmp->kokkos->neighflag == HALF) { + if (force->newton_pair) { + if (evflag) { + if (shearupdate) { + Kokkos::parallel_for(Kokkos::RangePolicy>(0,inum),*this); + } else { + Kokkos::parallel_for(Kokkos::RangePolicy>(0,inum),*this); + } + } else { + if (shearupdate) { + Kokkos::parallel_for(Kokkos::RangePolicy>(0,inum),*this); + } else { + Kokkos::parallel_for(Kokkos::RangePolicy>(0,inum),*this); + } + } + } else { + if (evflag) { + if (shearupdate) { + Kokkos::parallel_for(Kokkos::RangePolicy>(0,inum),*this); + } else { + Kokkos::parallel_for(Kokkos::RangePolicy>(0,inum),*this); + } + } else { + if (shearupdate) { + Kokkos::parallel_for(Kokkos::RangePolicy>(0,inum),*this); + } else { + Kokkos::parallel_for(Kokkos::RangePolicy>(0,inum),*this); + } + } + } + } else { // HALFTHREAD + if (force->newton_pair) { + if (evflag) { + if (shearupdate) { + Kokkos::parallel_for(Kokkos::RangePolicy>(0,inum),*this); + } else { + Kokkos::parallel_for(Kokkos::RangePolicy>(0,inum),*this); + } + } else { + if (shearupdate) { + Kokkos::parallel_for(Kokkos::RangePolicy>(0,inum),*this); + } else { + Kokkos::parallel_for(Kokkos::RangePolicy>(0,inum),*this); + } + } + } else { + if (evflag) { + if (shearupdate) { + Kokkos::parallel_for(Kokkos::RangePolicy>(0,inum),*this); + } else { + Kokkos::parallel_for(Kokkos::RangePolicy>(0,inum),*this); + } + } else { + if (shearupdate) { + Kokkos::parallel_for(Kokkos::RangePolicy>(0,inum),*this); + } else { + Kokkos::parallel_for(Kokkos::RangePolicy>(0,inum),*this); + } + } + } + } + + if (eflag_global) eng_vdwl += ev.evdwl; + if (vflag_global) { + virial[0] += ev.v[0]; + virial[1] += ev.v[1]; + virial[2] += ev.v[2]; + virial[3] += ev.v[3]; + virial[4] += ev.v[4]; + virial[5] += ev.v[5]; + } + + if (eflag_atom) { + k_eatom.template modify(); + k_eatom.template sync(); + } + + if (vflag_atom) { + k_vatom.template modify(); + k_vatom.template sync(); + } + + if (vflag_fdotr) pair_virial_fdotr_compute(this); + + copymode = 0; +} + +template +template +KOKKOS_INLINE_FUNCTION +void PairGranHookeHistoryKokkos::operator()(TagPairGranHookeHistoryCompute, const int &ii) const { + + // The f and torque arrays are atomic for Half/Thread neighbor style + Kokkos::View::value> > a_f = f; + Kokkos::View::value> > a_torque = torque; + + int i = d_ilist[ii]; + double xtmp = x(i,0); + double ytmp = x(i,1); + double ztmp = x(i,2); + int itype = type[i]; + double imass = rmass[i]; + double irad = radius[i]; + int jnum = d_numneigh[i]; + + double fx_i = 0.0; + double fy_i = 0.0; + double fz_i = 0.0; + + double torquex_i = 0.0; + double torquey_i = 0.0; + double torquez_i = 0.0; + + for (int jj = 0; jj < jnum; jj++) { + int j = d_neighbors(i,jj); + j &= NEIGHMASK; + + double delx = xtmp - x(j,0); + double dely = ytmp - x(j,1); + double delz = ztmp - x(j,2); + double rsq = delx*delx + dely*dely + delz*delz; + int jtype = type[j]; + double jmass = rmass[j]; + double jrad = radius[j]; + double radsum = irad + jrad; + + // check for touching neighbors + + if (rsq >= radsum * radsum) { + d_firsttouch(i,jj) = 0; + d_firstshear(i,3*jj) = 0; + d_firstshear(i,3*jj+1) = 0; + d_firstshear(i,3*jj+2) = 0; + } else { + double r = sqrt(rsq); + double rinv = 1.0/r; + double rsqinv = 1/rsq; + + // relative translational velocity + + double vr1 = v(i,0) - v(j,0); + double vr2 = v(i,1) - v(j,1); + double vr3 = v(i,2) - v(j,2); + + // normal component + + double vnnr = vr1*delx + vr2*dely + vr3*delz; + double vn1 = delx*vnnr * rsqinv; + double vn2 = dely*vnnr * rsqinv; + double vn3 = delz*vnnr * rsqinv; + + // tangential component + + double vt1 = vr1 - vn1; + double vt2 = vr2 - vn2; + double vt3 = vr3 - vn3; + + // relative rotational velocity + + double wr1 = (irad*omega(i,0) + jrad*omega(j,0)) * rinv; + double wr2 = (irad*omega(i,1) + jrad*omega(j,1)) * rinv; + double wr3 = (irad*omega(i,2) + jrad*omega(j,2)) * rinv; + + double meff = imass*jmass / (imass+jmass); + if (mask[i] & freeze_group_bit) meff = jmass; + if (mask[j] & freeze_group_bit) meff = imass; + + double damp = meff*gamman*vnnr*rsqinv; + double ccel = kn*(radsum-r)*rinv - damp; + + // relative velocities + + double vtr1 = vt1 - (delz*wr2-dely*wr3); + double vtr2 = vt2 - (delx*wr3-delz*wr1); + double vtr3 = vt3 - (dely*wr1-delx*wr2); + double vrel = vtr1*vtr1 + vtr2*vtr2 + vtr3*vtr3; + vrel = sqrt(vrel); + + // shear history effects + + d_firsttouch(i,jj) = 1; + double shear1 = d_firstshear(i,3*jj); + double shear2 = d_firstshear(i,3*jj+1); + double shear3 = d_firstshear(i,3*jj+2); + if (SHEARUPDATE) { + shear1 += vtr1*dt; + shear2 += vtr2*dt; + shear3 += vtr3*dt; + } + double shrmag = sqrt(shear1*shear1 + shear2*shear2 + + shear3*shear3); + + // rotate shear displacements + + double rsht = shear1*delx + shear2*dely + shear3*delz; + rsht *= rsqinv; + if (SHEARUPDATE) { + shear1 -= rsht*delx; + shear2 -= rsht*dely; + shear3 -= rsht*delz; + } + + // tangential forces = shear + tangential velocity damping + + double fs1 = - (kt*shear1 + meff*gammat*vtr1); + double fs2 = - (kt*shear2 + meff*gammat*vtr2); + double fs3 = - (kt*shear3 + meff*gammat*vtr3); + + // rescale frictional displacements and forces if needed + + double fs = sqrt(fs1*fs1 + fs2*fs2 + fs3*fs3); + double fn = xmu * fabs(ccel*r); + + if (fs > fn) { + if (shrmag != 0.0) { + shear1 = (fn/fs) * (shear1 + meff*gammat*vtr1/kt) - + meff*gammat*vtr1/kt; + shear2 = (fn/fs) * (shear2 + meff*gammat*vtr2/kt) - + meff*gammat*vtr2/kt; + shear3 = (fn/fs) * (shear3 + meff*gammat*vtr3/kt) - + meff*gammat*vtr3/kt; + fs1 *= fn/fs; + fs2 *= fn/fs; + fs3 *= fn/fs; + } else fs1 = fs2 = fs3 = 0.0; + } + + if (SHEARUPDATE) { + d_firstshear(i,3*jj) = shear1; + d_firstshear(i,3*jj+1) = shear2; + d_firstshear(i,3*jj+2) = shear3; + } + + // forces & torques + + double fx = delx*ccel + fs1; + double fy = dely*ccel + fs2; + double fz = delz*ccel + fs3; + fx_i += fx; + fy_i += fy; + fz_i += fz; + + double tor1 = rinv * (dely*fs3 - delz*fs2); + double tor2 = rinv * (delz*fs1 - delx*fs3); + double tor3 = rinv * (delx*fs2 - dely*fs1); + torquex_i -= irad*tor1; + torquey_i -= irad*tor2; + torquez_i -= irad*tor3; + + if (NEWTON_PAIR || j < nlocal) { + a_f(j,0) -= fx; + a_f(j,1) -= fy; + a_f(j,2) -= fz; + a_torque(j,0) -= jrad*tor1; + a_torque(j,1) -= jrad*tor2; + a_torque(j,2) -= jrad*tor3; + } + } + } + + a_f(i,0) += fx_i; + a_f(i,1) += fy_i; + a_f(i,2) += fz_i; + a_torque(i,0) += torquex_i; + a_torque(i,1) += torquey_i; + a_torque(i,2) += torquez_i; +} + +namespace LAMMPS_NS { +template class PairGranHookeHistoryKokkos; +#ifdef KOKKOS_HAVE_CUDA +template class PairGranHookeHistoryKokkos; +#endif +} diff --git a/src/KOKKOS/pair_gran_hooke_history_kokkos.h b/src/KOKKOS/pair_gran_hooke_history_kokkos.h new file mode 100644 index 0000000000..84dc412078 --- /dev/null +++ b/src/KOKKOS/pair_gran_hooke_history_kokkos.h @@ -0,0 +1,127 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS + +PairStyle(gran/hooke/history/kk,PairGranHookeHistoryKokkos) +PairStyle(gran/hooke/history/kk/device,PairGranHookeHistoryKokkos) +PairStyle(gran/hooke/history/kk/host,PairGranHookeHistoryKokkos) + +#else + +#ifndef LMP_PAIR_GRAN_HOOKE_HISTORY_KOKKOS_H +#define LMP_PAIR_GRAN_HOOKE_HISTORY_KOKKOS_H + +#include "pair_gran_hooke_history.h" +#include "pair_kokkos.h" +#include "kokkos_type.h" + +namespace LAMMPS_NS { + +template +class FixNeighHistoryKokkos; + +template +struct TagPairGranHookeHistoryCompute{}; + +template +class PairGranHookeHistoryKokkos : public PairGranHookeHistory { + public: + typedef DeviceType device_type; + typedef ArrayTypes AT; + + PairGranHookeHistoryKokkos(class LAMMPS *); + virtual ~PairGranHookeHistoryKokkos(); + virtual void compute(int, int); + void init_style(); + + template + KOKKOS_INLINE_FUNCTION + void operator()(TagPairGranHookeHistoryCompute, const int&) const; + + protected: + typename AT::t_x_array_randomread x; + typename AT::t_x_array c_x; + typename AT::t_v_array_randomread v; + typename AT::t_v_array_randomread omega; + typename AT::t_f_array f; + typename AT::t_f_array torque; + typename AT::t_int_1d_randomread type; + typename AT::t_int_1d_randomread mask; + typename AT::t_float_1d_randomread rmass; + typename AT::t_float_1d_randomread radius; + + DAT::tdual_efloat_1d k_eatom; + DAT::tdual_virial_array k_vatom; + typename AT::t_efloat_1d d_eatom; + typename AT::t_virial_array d_vatom; + typename AT::t_tagint_1d tag; + + typename AT::t_neighbors_2d d_neighbors; + typename AT::t_int_1d_randomread d_ilist; + typename AT::t_int_1d_randomread d_numneigh; + + typename AT::t_int_2d d_firsttouch; + typename AT::t_float_2d d_firstshear; + + int newton_pair; + double special_lj[4]; + + int neighflag; + int nlocal,nall,eflag,vflag; + + FixNeighHistoryKokkos *fix_historyKK; + + friend void pair_virial_fdotr_compute(PairGranHookeHistoryKokkos*); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: Incorrect args for pair coefficients + +Self-explanatory. Check the input script or data file. + +E: Pair granular requires atom attributes radius, rmass + +The atom style defined does not have these attributes. + +E: Pair granular requires ghost atoms store velocity + +Use the comm_modify vel yes command to enable this. + +E: Could not find pair fix neigh history ID + +UNDOCUMENTED + +U: Pair granular with shear history requires newton pair off + +This is a current restriction of the implementation of pair +granular styles with history. + +U: Could not find pair fix ID + +A fix is created internally by the pair style to store shear +history information. You cannot delete it. + +*/ diff --git a/src/KOKKOS/verlet_kokkos.cpp b/src/KOKKOS/verlet_kokkos.cpp index 136e543a2c..417de2d94a 100644 --- a/src/KOKKOS/verlet_kokkos.cpp +++ b/src/KOKKOS/verlet_kokkos.cpp @@ -55,6 +55,20 @@ struct ForceAdder { /* ---------------------------------------------------------------------- */ +template +struct Zero { + View v; + Zero(const View &v_):v(v_) {} + KOKKOS_INLINE_FUNCTION + void operator()(const int &i) const { + v(i,0) = 0; + v(i,1) = 0; + v(i,2) = 0; + } +}; + +/* ---------------------------------------------------------------------- */ + VerletKokkos::VerletKokkos(LAMMPS *lmp, int narg, char **arg) : Verlet(lmp, narg, arg) { @@ -120,6 +134,7 @@ void VerletKokkos::setup(int flag) atomKK->modified(Host,ALL_MASK); neighbor->build(1); + modify->setup_post_neighbor(); neighbor->ncalls = 0; // compute all forces @@ -175,7 +190,7 @@ void VerletKokkos::setup(int flag) modify->setup(vflag); output->setup(flag); lmp->kokkos->auto_sync = 1; - update->setupflag = 1; + update->setupflag = 0; } /* ---------------------------------------------------------------------- @@ -223,6 +238,7 @@ void VerletKokkos::setup_minimal(int flag) atomKK->modified(Host,ALL_MASK); neighbor->build(1); + modify->setup_post_neighbor(); neighbor->ncalls = 0; } @@ -567,8 +583,6 @@ void VerletKokkos::run(int n) void VerletKokkos::force_clear() { - int i; - if (external_force_clear) return; // clear force on all particles @@ -576,23 +590,15 @@ void VerletKokkos::force_clear() // when using threads always clear all forces. if (neighbor->includegroup == 0) { - int nall; - if (force->newton) nall = atomKK->nlocal + atomKK->nghost; - else nall = atomKK->nlocal; + int nall = atomKK->nlocal; + if (force->newton) nall += atomKK->nghost; - size_t nbytes = sizeof(double) * nall; - - if (nbytes) { - if (atomKK->k_f.modified_host() > atomKK->k_f.modified_device()) { - memset_kokkos(atomKK->k_f.view()); - atomKK->modified(Host,F_MASK); - atomKK->sync(Device,F_MASK); - } else { - memset_kokkos(atomKK->k_f.view()); - atomKK->modified(Device,F_MASK); - } - if (torqueflag) memset(&(atomKK->torque[0][0]),0,3*nbytes); + Kokkos::parallel_for(nall, Zero::t_f_array>(atomKK->k_f.view())); + atomKK->modified(Device,F_MASK); + if (torqueflag) { + Kokkos::parallel_for(nall, Zero::t_f_array>(atomKK->k_torque.view())); + atomKK->modified(Device,TORQUE_MASK); } // neighbor includegroup flag is set @@ -600,35 +606,23 @@ void VerletKokkos::force_clear() // if either newton flag is set, also include ghosts } else { - int nall = atomKK->nfirst; - if (atomKK->k_f.modified_host() > atomKK->k_f.modified_device()) { - memset_kokkos(atomKK->k_f.view()); - atomKK->modified(Host,F_MASK); - } else { - memset_kokkos(atomKK->k_f.view()); - atomKK->modified(Device,F_MASK); - } + Kokkos::parallel_for(atomKK->nfirst, Zero::t_f_array>(atomKK->k_f.view())); + atomKK->modified(Device,F_MASK); + if (torqueflag) { - double **torque = atomKK->torque; - for (i = 0; i < nall; i++) { - torque[i][0] = 0.0; - torque[i][1] = 0.0; - torque[i][2] = 0.0; - } + Kokkos::parallel_for(atomKK->nfirst, Zero::t_f_array>(atomKK->k_torque.view())); + atomKK->modified(Device,TORQUE_MASK); } if (force->newton) { - nall = atomKK->nlocal + atomKK->nghost; + auto range = Kokkos::RangePolicy(atomKK->nlocal, atomKK->nlocal + atomKK->nghost); + Kokkos::parallel_for(range, Zero::t_f_array>(atomKK->k_f.view())); + atomKK->modified(Device,F_MASK); if (torqueflag) { - double **torque = atomKK->torque; - for (i = atomKK->nlocal; i < nall; i++) { - torque[i][0] = 0.0; - torque[i][1] = 0.0; - torque[i][2] = 0.0; - } + Kokkos::parallel_for(range, Zero::t_f_array>(atomKK->k_torque.view())); + atomKK->modified(Device,TORQUE_MASK); } - } } } diff --git a/src/comm_brick.cpp b/src/comm_brick.cpp index 3aa6d7748c..f4e733a5ac 100644 --- a/src/comm_brick.cpp +++ b/src/comm_brick.cpp @@ -609,7 +609,7 @@ void CommBrick::exchange() maxexchange = maxexchange_atom + maxexchange_fix; bufextra = maxexchange + BUFEXTRA; if (bufextra > bufextra_old) - memory->grow(buf_send,maxsend+bufextra,"comm:buf_send"); + grow_send(maxsend+bufextra,1); // subbox bounds for orthogonal or triclinic diff --git a/src/fix_neigh_history.cpp b/src/fix_neigh_history.cpp index 3329b604ef..90b77821e6 100644 --- a/src/fix_neigh_history.cpp +++ b/src/fix_neigh_history.cpp @@ -95,6 +95,8 @@ FixNeighHistory::FixNeighHistory(LAMMPS *lmp, int narg, char **arg) : FixNeighHistory::~FixNeighHistory() { + if (copymode) return; + // unregister this fix so atom class doesn't invoke it any more atom->delete_callback(id,0); From 8ebe38474d71a777391d22b34d80625f3502b66e Mon Sep 17 00:00:00 2001 From: Denis Taniguchi Date: Tue, 3 Jul 2018 11:13:27 -0400 Subject: [PATCH 019/302] Porting fix nve/sphere to Kokkos. --- src/KOKKOS/Install.sh | 2 + src/KOKKOS/fix_nve_sphere_kokkos.cpp | 155 +++++++++++++++++++++++++++ src/KOKKOS/fix_nve_sphere_kokkos.h | 79 ++++++++++++++ 3 files changed, 236 insertions(+) create mode 100644 src/KOKKOS/fix_nve_sphere_kokkos.cpp create mode 100644 src/KOKKOS/fix_nve_sphere_kokkos.h diff --git a/src/KOKKOS/Install.sh b/src/KOKKOS/Install.sh index 73fa21cb41..a713aff8d7 100755 --- a/src/KOKKOS/Install.sh +++ b/src/KOKKOS/Install.sh @@ -109,6 +109,8 @@ action fix_npt_kokkos.cpp action fix_npt_kokkos.h action fix_nve_kokkos.cpp action fix_nve_kokkos.h +action fix_nve_sphere_kokkos.cpp +action fix_nve_sphere_kokkos.h action fix_nvt_kokkos.cpp action fix_nvt_kokkos.h action fix_property_atom_kokkos.cpp diff --git a/src/KOKKOS/fix_nve_sphere_kokkos.cpp b/src/KOKKOS/fix_nve_sphere_kokkos.cpp new file mode 100644 index 0000000000..d636f56b20 --- /dev/null +++ b/src/KOKKOS/fix_nve_sphere_kokkos.cpp @@ -0,0 +1,155 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "fix_nve_sphere_kokkos.h" +#include "atom_masks.h" +#include "atom_kokkos.h" +#include "error.h" + +using namespace LAMMPS_NS; + +enum{NONE,DIPOLE}; + +/* ---------------------------------------------------------------------- */ + +template +FixNVESphereKokkos::FixNVESphereKokkos(LAMMPS *lmp, int narg, char **arg) : + FixNVESphere(lmp, narg, arg) +{ + kokkosable = 1; + atomKK = (AtomKokkos *)atom; + execution_space = ExecutionSpaceFromDevice::space; + + datamask_read = F_MASK | TORQUE_MASK | RMASS_MASK | RADIUS_MASK | MASK_MASK; + datamask_modify = X_MASK | V_MASK | OMEGA_MASK; +} + +/* ---------------------------------------------------------------------- */ + +template +void FixNVESphereKokkos::cleanup_copy() +{ + id = style = NULL; + vatom = NULL; +} + +/* ---------------------------------------------------------------------- */ + +template +void FixNVESphereKokkos::init() +{ + FixNVESphere::init(); + + if (extra == DIPOLE) { + error->all(FLERR,"Fix nve/sphere/kk doesn't yet support dipole"); + } +} + +/* ---------------------------------------------------------------------- */ + +template +void FixNVESphereKokkos::initial_integrate(int vflag) +{ + atomKK->sync(execution_space,datamask_read); + atomKK->modified(execution_space,datamask_modify); + + x = atomKK->k_x.view(); + v = atomKK->k_v.view(); + omega = atomKK->k_omega.view(); + f = atomKK->k_f.view(); + torque = atomKK->k_torque.view(); + mask = atomKK->k_mask.view(); + rmass = atomKK->k_rmass.view(); + radius = atomKK->k_radius.view(); + + int nlocal = atom->nlocal; + if (igroup == atom->firstgroup) nlocal = atom->nfirst; + + FixNVESphereKokkosInitialIntegrateFunctor f(this); + Kokkos::parallel_for(nlocal,f); +} + +/* ---------------------------------------------------------------------- */ + +template +KOKKOS_INLINE_FUNCTION +void FixNVESphereKokkos::initial_integrate_item(const int i) const +{ + const double dtfrotate = dtf / inertia; + + if (mask(i) & groupbit) { + const double dtfm = dtf / rmass(i); + v(i,0) += dtfm * f(i,0); + v(i,1) += dtfm * f(i,1); + v(i,2) += dtfm * f(i,2); + x(i,0) += dtv * v(i,0); + x(i,1) += dtv * v(i,1); + x(i,2) += dtv * v(i,2); + + const double dtirotate = dtfrotate / (radius(i)*radius(i)*rmass(i)); + omega(i,0) += dtirotate * torque(i,0); + omega(i,1) += dtirotate * torque(i,1); + omega(i,2) += dtirotate * torque(i,2); + } +} + +/* ---------------------------------------------------------------------- */ + +template +void FixNVESphereKokkos::final_integrate() +{ + atomKK->sync(execution_space,datamask_read); + atomKK->modified(execution_space,datamask_modify); + + v = atomKK->k_v.view(); + omega = atomKK->k_omega.view(); + f = atomKK->k_f.view(); + torque = atomKK->k_torque.view(); + mask = atomKK->k_mask.view(); + rmass = atomKK->k_rmass.view(); + radius = atomKK->k_radius.view(); + + int nlocal = atom->nlocal; + if (igroup == atom->firstgroup) nlocal = atom->nfirst; + + FixNVESphereKokkosFinalIntegrateFunctor f(this); + Kokkos::parallel_for(nlocal,f); +} + +/* ---------------------------------------------------------------------- */ + +template +KOKKOS_INLINE_FUNCTION +void FixNVESphereKokkos::final_integrate_item(const int i) const +{ + const double dtfrotate = dtf / inertia; + + if (mask(i) & groupbit) { + const double dtfm = dtf / rmass(i); + v(i,0) += dtfm * f(i,0); + v(i,1) += dtfm * f(i,1); + v(i,2) += dtfm * f(i,2); + + const double dtirotate = dtfrotate / (radius(i)*radius(i)*rmass(i)); + omega(i,0) += dtirotate * torque(i,0); + omega(i,1) += dtirotate * torque(i,1); + omega(i,2) += dtirotate * torque(i,2); + } +} + +namespace LAMMPS_NS { +template class FixNVESphereKokkos; +#ifdef KOKKOS_HAVE_CUDA +template class FixNVESphereKokkos; +#endif +} diff --git a/src/KOKKOS/fix_nve_sphere_kokkos.h b/src/KOKKOS/fix_nve_sphere_kokkos.h new file mode 100644 index 0000000000..382e530319 --- /dev/null +++ b/src/KOKKOS/fix_nve_sphere_kokkos.h @@ -0,0 +1,79 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef FIX_CLASS + +FixStyle(nve/sphere/kk,FixNVESphereKokkos) +FixStyle(nve/sphere/kk/device,FixNVESphereKokkos) +FixStyle(nve/sphere/kk/host,FixNVESphereKokkos) + +#else + +#ifndef LMP_FIX_NVE_SPHERE_KOKKOS_H +#define LMP_FIX_NVE_SPHERE_KOKKOS_H + +#include "fix_nve_sphere.h" +#include "kokkos_type.h" + +namespace LAMMPS_NS { + +template +class FixNVESphereKokkos : public FixNVESphere { + public: + FixNVESphereKokkos(class LAMMPS *, int, char **); + virtual ~FixNVESphereKokkos() {} + void cleanup_copy(); + void init(); + void initial_integrate(int); + void final_integrate(); + + KOKKOS_INLINE_FUNCTION + void initial_integrate_item(const int i) const; + KOKKOS_INLINE_FUNCTION + void final_integrate_item(const int i) const; + + private: + typename ArrayTypes::t_x_array x; + typename ArrayTypes::t_v_array v; + typename ArrayTypes::t_v_array omega; + typename ArrayTypes::t_f_array f; + typename ArrayTypes::t_f_array torque; + typename ArrayTypes::t_float_1d rmass; + typename ArrayTypes::t_float_1d radius; + typename ArrayTypes::t_int_1d mask; +}; + +template +struct FixNVESphereKokkosInitialIntegrateFunctor { + FixNVESphereKokkos c; + FixNVESphereKokkosInitialIntegrateFunctor(FixNVESphereKokkos *c_ptr): c(*c_ptr) { c.cleanup_copy(); } + KOKKOS_INLINE_FUNCTION + void operator()(const int i) const { + c.initial_integrate_item(i); + } +}; + +template +struct FixNVESphereKokkosFinalIntegrateFunctor { + FixNVESphereKokkos c; + FixNVESphereKokkosFinalIntegrateFunctor(FixNVESphereKokkos *c_ptr): c(*c_ptr) { c.cleanup_copy(); } + KOKKOS_INLINE_FUNCTION + void operator()(const int i) const { + c.final_integrate_item(i); + } +}; + +} // namespace LAMMPS_NS + +#endif // LMP_FIX_NVE_SPHERE_KOKKOS_H +#endif // FIX_CLASS From a365246e3a9769290d0125dcd520fa52694519a6 Mon Sep 17 00:00:00 2001 From: Denis Taniguchi Date: Tue, 3 Jul 2018 11:21:54 -0400 Subject: [PATCH 020/302] Porting fix gravity to Kokkos. --- src/KOKKOS/Install.sh | 2 + src/KOKKOS/fix_gravity_kokkos.cpp | 121 ++++++++++++++++++++++++++++++ src/KOKKOS/fix_gravity_kokkos.h | 57 ++++++++++++++ src/fix_gravity.cpp | 2 + src/fix_gravity.h | 2 +- 5 files changed, 183 insertions(+), 1 deletion(-) create mode 100644 src/KOKKOS/fix_gravity_kokkos.cpp create mode 100644 src/KOKKOS/fix_gravity_kokkos.h diff --git a/src/KOKKOS/Install.sh b/src/KOKKOS/Install.sh index a713aff8d7..58a17833c8 100755 --- a/src/KOKKOS/Install.sh +++ b/src/KOKKOS/Install.sh @@ -97,6 +97,8 @@ action fix_deform_kokkos.cpp action fix_deform_kokkos.h action fix_eos_table_rx_kokkos.cpp fix_eos_table_rx.cpp action fix_eos_table_rx_kokkos.h fix_eos_table_rx.h +action fix_gravity_kokkos.cpp +action fix_gravity_kokkos.h action fix_langevin_kokkos.cpp action fix_langevin_kokkos.h action fix_neigh_history_kokkos.cpp diff --git a/src/KOKKOS/fix_gravity_kokkos.cpp b/src/KOKKOS/fix_gravity_kokkos.cpp new file mode 100644 index 0000000000..2aff7af56c --- /dev/null +++ b/src/KOKKOS/fix_gravity_kokkos.cpp @@ -0,0 +1,121 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "fix_gravity_kokkos.h" +#include "atom_masks.h" +#include "modify.h" +#include "input.h" +#include "variable.h" +#include "update.h" +#include "atom_kokkos.h" +#include "atom_vec.h" + +using namespace LAMMPS_NS; + +enum{CONSTANT,EQUAL}; + +/* ---------------------------------------------------------------------- */ + +template +FixGravityKokkos::FixGravityKokkos(LAMMPS *lmp, int narg, char **arg) : + FixGravity(lmp, narg, arg) +{ + kokkosable = 1; + atomKK = (AtomKokkos *)atom; + execution_space = ExecutionSpaceFromDevice::space; + + datamask_read = X_MASK | F_MASK | RMASS_MASK | MASK_MASK | TYPE_MASK; + datamask_modify = F_MASK; +} + +/* ---------------------------------------------------------------------- */ + +template +void FixGravityKokkos::post_force(int vflag) +{ + // update gravity due to variables + + if (varflag != CONSTANT) { + modify->clearstep_compute(); + if (mstyle == EQUAL) magnitude = input->variable->compute_equal(mvar); + if (vstyle == EQUAL) vert = input->variable->compute_equal(vvar); + if (pstyle == EQUAL) phi = input->variable->compute_equal(pvar); + if (tstyle == EQUAL) theta = input->variable->compute_equal(tvar); + if (xstyle == EQUAL) xdir = input->variable->compute_equal(xvar); + if (ystyle == EQUAL) ydir = input->variable->compute_equal(yvar); + if (zstyle == EQUAL) zdir = input->variable->compute_equal(zvar); + modify->addstep_compute(update->ntimestep + 1); + + set_acceleration(); + } + + atomKK->sync(execution_space,datamask_read); + atomKK->modified(execution_space,datamask_modify); + + x = atomKK->k_x.view(); + f = atomKK->k_f.view(); + if (atomKK->rmass) + rmass = atomKK->k_rmass.view(); + else + mass = atomKK->k_mass.view(); + type = atomKK->k_type.view(); + mask = atomKK->k_mask.view(); + int nlocal = atomKK->nlocal; + if (igroup == atomKK->firstgroup) nlocal = atomKK->nfirst; + + copymode = 1; + + eflag = 0; + egrav = 0.0; + + if (atomKK->rmass) { + Kokkos::parallel_reduce(Kokkos::RangePolicy(0,nlocal), *this, egrav); + } + else { + Kokkos::parallel_reduce(Kokkos::RangePolicy(0,nlocal), *this, egrav); + } + copymode = 0; +} + +template +KOKKOS_INLINE_FUNCTION +void FixGravityKokkos::operator()(TagFixGravityRMass, const int i, double &eg) const +{ + if (mask[i] & groupbit) { + double massone = rmass[i]; + f(i,0) += massone*xacc; + f(i,1) += massone*yacc; + f(i,2) += massone*zacc; + eg -= massone * (xacc*x(i,0) + yacc*x(i,1) + zacc*x(i,2)); + } +} + +template +KOKKOS_INLINE_FUNCTION +void FixGravityKokkos::operator()(TagFixGravityMass, const int i, double &eg) const +{ + if (mask[i] & groupbit) { + double massone = mass[type[i]]; + f(i,0) += massone*xacc; + f(i,1) += massone*yacc; + f(i,2) += massone*zacc; + eg -= massone * (xacc*x(i,0) + yacc*x(i,1) + zacc*x(i,2)); + } +} + +namespace LAMMPS_NS { +template class FixGravityKokkos; +#ifdef KOKKOS_HAVE_CUDA +template class FixGravityKokkos; +#endif +} diff --git a/src/KOKKOS/fix_gravity_kokkos.h b/src/KOKKOS/fix_gravity_kokkos.h new file mode 100644 index 0000000000..cc487a0e2d --- /dev/null +++ b/src/KOKKOS/fix_gravity_kokkos.h @@ -0,0 +1,57 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef FIX_CLASS + +FixStyle(gravity/kk,FixGravityKokkos) +FixStyle(gravity/kk/device,FixGravityKokkos) +FixStyle(gravity/kk/host,FixGravityKokkos) + +#else + +#ifndef LMP_FIX_GRAVITY_KOKKOS_H +#define LMP_FIX_GRAVITY_KOKKOS_H + +#include "fix_gravity.h" +#include "kokkos_type.h" + +namespace LAMMPS_NS { + +struct TagFixGravityRMass {}; +struct TagFixGravityMass {}; + +template +class FixGravityKokkos : public FixGravity { + public: + FixGravityKokkos(class LAMMPS *, int, char **); + virtual ~FixGravityKokkos() {} + void post_force(int); + + KOKKOS_INLINE_FUNCTION + void operator()(TagFixGravityRMass, const int, double &) const; + KOKKOS_INLINE_FUNCTION + void operator()(TagFixGravityMass, const int, double &) const; + + private: + typename ArrayTypes::t_x_array x; + typename ArrayTypes::t_f_array f; + typename ArrayTypes::t_float_1d_randomread rmass; + typename ArrayTypes::t_float_1d_randomread mass; + typename ArrayTypes::t_int_1d type; + typename ArrayTypes::t_int_1d mask; +}; + +} // namespace LAMMPS_NS + +#endif // LMP_FIX_GRAVITY_KOKKOS_H +#endif // FIX_CLASS diff --git a/src/fix_gravity.cpp b/src/fix_gravity.cpp index 9ace9d45ff..2baf3ff24d 100644 --- a/src/fix_gravity.cpp +++ b/src/fix_gravity.cpp @@ -141,6 +141,8 @@ FixGravity::FixGravity(LAMMPS *lmp, int narg, char **arg) : FixGravity::~FixGravity() { + if (copymode) return; + delete [] mstr; delete [] vstr; delete [] pstr; diff --git a/src/fix_gravity.h b/src/fix_gravity.h index 35be23a40a..1f18ee274b 100644 --- a/src/fix_gravity.h +++ b/src/fix_gravity.h @@ -29,7 +29,7 @@ class FixGravity : public Fix { public: FixGravity(class LAMMPS *, int, char **); - ~FixGravity(); + virtual ~FixGravity(); int setmask(); void init(); void setup(int); From 11a5ed0e030b52f439300d43a77961e484d7f737 Mon Sep 17 00:00:00 2001 From: Denis Taniguchi Date: Tue, 3 Jul 2018 11:29:13 -0400 Subject: [PATCH 021/302] Porting fix freeze to Kokkos. --- src/GRANULAR/fix_freeze.h | 2 +- src/KOKKOS/Install.sh | 2 + src/KOKKOS/fix_freeze_kokkos.cpp | 124 +++++++++++++++++++++++++++++++ src/KOKKOS/fix_freeze_kokkos.h | 80 ++++++++++++++++++++ 4 files changed, 207 insertions(+), 1 deletion(-) create mode 100644 src/KOKKOS/fix_freeze_kokkos.cpp create mode 100644 src/KOKKOS/fix_freeze_kokkos.h diff --git a/src/GRANULAR/fix_freeze.h b/src/GRANULAR/fix_freeze.h index 52badc3e1b..a249226aa7 100644 --- a/src/GRANULAR/fix_freeze.h +++ b/src/GRANULAR/fix_freeze.h @@ -34,7 +34,7 @@ class FixFreeze : public Fix { void post_force_respa(int, int, int); double compute_vector(int); - private: + protected: int force_flag; double foriginal[3],foriginal_all[3]; }; diff --git a/src/KOKKOS/Install.sh b/src/KOKKOS/Install.sh index 58a17833c8..a75281cd20 100755 --- a/src/KOKKOS/Install.sh +++ b/src/KOKKOS/Install.sh @@ -97,6 +97,8 @@ action fix_deform_kokkos.cpp action fix_deform_kokkos.h action fix_eos_table_rx_kokkos.cpp fix_eos_table_rx.cpp action fix_eos_table_rx_kokkos.h fix_eos_table_rx.h +action fix_freeze_kokkos.cpp +action fix_freeze_kokkos.h action fix_gravity_kokkos.cpp action fix_gravity_kokkos.h action fix_langevin_kokkos.cpp diff --git a/src/KOKKOS/fix_freeze_kokkos.cpp b/src/KOKKOS/fix_freeze_kokkos.cpp new file mode 100644 index 0000000000..b87ec86f8f --- /dev/null +++ b/src/KOKKOS/fix_freeze_kokkos.cpp @@ -0,0 +1,124 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "fix_freeze_kokkos.h" +#include "atom_masks.h" +#include "atom_kokkos.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +template +FixFreezeKokkos::FixFreezeKokkos(LAMMPS *lmp, int narg, char **arg) : + FixFreeze(lmp, narg, arg) +{ + kokkosable = 1; + atomKK = (AtomKokkos *)atom; + execution_space = ExecutionSpaceFromDevice::space; + + datamask_read = F_MASK | MASK_MASK; + datamask_modify = F_MASK | TORQUE_MASK; +} + +/* ---------------------------------------------------------------------- */ + +template +int FixFreezeKokkos::setmask() +{ + return FixFreeze::setmask(); +} + +/* ---------------------------------------------------------------------- */ + +template +void FixFreezeKokkos::init() +{ + FixFreeze::init(); +} + +/* ---------------------------------------------------------------------- */ + +template +void FixFreezeKokkos::setup(int vflag) +{ + FixFreeze::setup(vflag); +} + +/* ---------------------------------------------------------------------- */ + +template +void FixFreezeKokkos::post_force(int vflag) +{ + atomKK->sync(execution_space,datamask_read); + atomKK->modified(execution_space,datamask_modify); + + f = atomKK->k_f.view(); + torque = atomKK->k_torque.view(); + mask = atomKK->k_mask.view(); + + int nlocal = atom->nlocal; + if (igroup == atom->firstgroup) nlocal = atom->nfirst; + + force_flag = 0; + copymode = 1; + OriginalForce original; + Kokkos::parallel_reduce(nlocal, *this, original); + copymode = 0; + + foriginal[0] = original.values[0]; + foriginal[1] = original.values[1]; + foriginal[2] = original.values[2]; +} + +/* ---------------------------------------------------------------------- */ + +template +void FixFreezeKokkos::post_force_respa(int vflag, int ilevel, int iloop) +{ + post_force(vflag); +} + +/* ---------------------------------------------------------------------- + return components of total force on fix group before force was changed +------------------------------------------------------------------------- */ + +template +double FixFreezeKokkos::compute_vector(int n) +{ + return FixFreeze::compute_vector(n); +} + +/* ---------------------------------------------------------------------- */ + +template +void FixFreezeKokkos::operator()(const int i, OriginalForce &original) const { + if (mask[i] & groupbit) { + original.values[0] += f(i,0); + original.values[1] += f(i,1); + original.values[2] += f(i,2); + f(i,0) = 0.0; + f(i,1) = 0.0; + f(i,2) = 0.0; + torque(i,0) = 0.0; + torque(i,1) = 0.0; + torque(i,2) = 0.0; + } +} + +namespace LAMMPS_NS { +template class FixFreezeKokkos; +#ifdef KOKKOS_HAVE_CUDA +template class FixFreezeKokkos; +#endif +} diff --git a/src/KOKKOS/fix_freeze_kokkos.h b/src/KOKKOS/fix_freeze_kokkos.h new file mode 100644 index 0000000000..3ad341d087 --- /dev/null +++ b/src/KOKKOS/fix_freeze_kokkos.h @@ -0,0 +1,80 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef FIX_CLASS + +FixStyle(freeze/kk,FixFreezeKokkos) +FixStyle(freeze/kk/device,FixFreezeKokkos) +FixStyle(freeze/kk/host,FixFreezeKokkos) + +#else + +#ifndef LMP_FIX_FREEZE_KOKKOS_H +#define LMP_FIX_FREEZE_KOKKOS_H + +#include "fix_freeze.h" +#include "kokkos_type.h" + +namespace LAMMPS_NS { + +template +class FixFreezeKokkos : public FixFreeze { + public: + struct OriginalForce { + double values[3]; + + KOKKOS_INLINE_FUNCTION + OriginalForce() { + values[0] = 0; + values[1] = 0; + values[2] = 0; + } + + KOKKOS_INLINE_FUNCTION + OriginalForce &operator+=(const OriginalForce &rhs) { + values[0] += rhs.values[0]; + values[1] += rhs.values[1]; + values[2] += rhs.values[2]; + return *this; + } + + KOKKOS_INLINE_FUNCTION + volatile OriginalForce &operator+=(const volatile OriginalForce &rhs) volatile { + values[0] += rhs.values[0]; + values[1] += rhs.values[1]; + values[2] += rhs.values[2]; + return *this; + } + }; + + FixFreezeKokkos(class LAMMPS *, int, char **); + int setmask(); + void init(); + void setup(int); + void post_force(int); + void post_force_respa(int, int, int); + double compute_vector(int); + + KOKKOS_INLINE_FUNCTION + void operator()(const int i, OriginalForce &original) const; + + private: + typename ArrayTypes::t_f_array f; + typename ArrayTypes::t_f_array torque; + typename ArrayTypes::t_int_1d mask; +}; + +} // namespace LAMMPS_NS + +#endif // LMP_FIX_FREEZE_KOKKOS_H +#endif // FIX_CLASS From f394ed94f307b6c7a0fe874bc7c696d23ec511c2 Mon Sep 17 00:00:00 2001 From: Denis Taniguchi Date: Tue, 3 Jul 2018 11:33:55 -0400 Subject: [PATCH 022/302] dump vtk also works with VTK version 8. --- src/USER-VTK/dump_vtk.cpp | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/USER-VTK/dump_vtk.cpp b/src/USER-VTK/dump_vtk.cpp index 5f2e3d62ec..edbc647a81 100644 --- a/src/USER-VTK/dump_vtk.cpp +++ b/src/USER-VTK/dump_vtk.cpp @@ -93,10 +93,10 @@ enum{VTK,VTP,VTU,PVTP,PVTU}; // file formats #define ONEFIELD 32 #define DELTA 1048576 -#if VTK_MAJOR_VERSION == 7 +#if VTK_MAJOR_VERSION >= 7 #define InsertNextTupleValue InsertNextTypedTuple -#elif VTK_MAJOR_VERSION > 7 -#error This code has only been tested with VTK 5, 6, and 7 +#elif VTK_MAJOR_VERSION > 8 +#error This code has only been tested with VTK 5, 6, 7, and 8 #endif /* ---------------------------------------------------------------------- */ From a6df61a63712765f328acb8ef9b48ff6263bd2c5 Mon Sep 17 00:00:00 2001 From: Denis Taniguchi Date: Tue, 3 Jul 2018 12:05:21 -0400 Subject: [PATCH 023/302] Making ComputeTempKokkos compatible with rmass in device memory. --- src/KOKKOS/compute_temp_kokkos.cpp | 16 ++++++++++------ src/KOKKOS/compute_temp_kokkos.h | 2 +- 2 files changed, 11 insertions(+), 7 deletions(-) diff --git a/src/KOKKOS/compute_temp_kokkos.cpp b/src/KOKKOS/compute_temp_kokkos.cpp index fec3d89fff..d94c6e76b5 100644 --- a/src/KOKKOS/compute_temp_kokkos.cpp +++ b/src/KOKKOS/compute_temp_kokkos.cpp @@ -49,8 +49,10 @@ double ComputeTempKokkos::compute_scalar() invoked_scalar = update->ntimestep; v = atomKK->k_v.view(); - rmass = atomKK->rmass; - mass = atomKK->k_mass.view(); + if (atomKK->rmass) + rmass = atomKK->k_rmass.view(); + else + mass = atomKK->k_mass.view(); type = atomKK->k_type.view(); mask = atomKK->k_mask.view(); int nlocal = atom->nlocal; @@ -59,7 +61,7 @@ double ComputeTempKokkos::compute_scalar() CTEMP t_kk; copymode = 1; - if (rmass) + if (atomKK->rmass) Kokkos::parallel_reduce(Kokkos::RangePolicy >(0,nlocal),*this,t_kk); else Kokkos::parallel_reduce(Kokkos::RangePolicy >(0,nlocal),*this,t_kk); @@ -102,8 +104,10 @@ void ComputeTempKokkos::compute_vector() invoked_vector = update->ntimestep; v = atomKK->k_v.view(); - rmass = atomKK->rmass; - mass = atomKK->k_mass.view(); + if (atomKK->rmass) + rmass = atomKK->k_rmass.view(); + else + mass = atomKK->k_mass.view(); type = atomKK->k_type.view(); mask = atomKK->k_mask.view(); int nlocal = atom->nlocal; @@ -113,7 +117,7 @@ void ComputeTempKokkos::compute_vector() CTEMP t_kk; copymode = 1; - if (rmass) + if (atomKK->rmass) Kokkos::parallel_reduce(Kokkos::RangePolicy >(0,nlocal),*this,t_kk); else Kokkos::parallel_reduce(Kokkos::RangePolicy >(0,nlocal),*this,t_kk); diff --git a/src/KOKKOS/compute_temp_kokkos.h b/src/KOKKOS/compute_temp_kokkos.h index a01bb42f8c..7f116f7120 100644 --- a/src/KOKKOS/compute_temp_kokkos.h +++ b/src/KOKKOS/compute_temp_kokkos.h @@ -84,7 +84,7 @@ class ComputeTempKokkos : public ComputeTemp { protected: typename ArrayTypes::t_v_array_randomread v; - double *rmass; + typename ArrayTypes::t_float_1d_randomread rmass; typename ArrayTypes::t_float_1d_randomread mass; typename ArrayTypes::t_int_1d_randomread type; typename ArrayTypes::t_int_1d_randomread mask; From dc93d4ceea7df758e2ddad975ef04f3758c63c16 Mon Sep 17 00:00:00 2001 From: Denis Taniguchi Date: Thu, 5 Jul 2018 06:03:27 -0400 Subject: [PATCH 024/302] Added virial computation to PairGranHookeHistoryKokkos. --- src/KOKKOS/pair_gran_hooke_history_kokkos.cpp | 263 +++++++++++++----- src/KOKKOS/pair_gran_hooke_history_kokkos.h | 17 +- 2 files changed, 203 insertions(+), 77 deletions(-) diff --git a/src/KOKKOS/pair_gran_hooke_history_kokkos.cpp b/src/KOKKOS/pair_gran_hooke_history_kokkos.cpp index d7c8f8a99e..b245896be5 100644 --- a/src/KOKKOS/pair_gran_hooke_history_kokkos.cpp +++ b/src/KOKKOS/pair_gran_hooke_history_kokkos.cpp @@ -166,11 +166,17 @@ void PairGranHookeHistoryKokkos::compute(int eflag_in, int vflag_in) if (lmp->kokkos->neighflag == HALF) { if (force->newton_pair) { - if (evflag) { + if (vflag_atom) { if (shearupdate) { - Kokkos::parallel_for(Kokkos::RangePolicy>(0,inum),*this); + Kokkos::parallel_for(Kokkos::RangePolicy>(0,inum),*this); } else { - Kokkos::parallel_for(Kokkos::RangePolicy>(0,inum),*this); + Kokkos::parallel_for(Kokkos::RangePolicy>(0,inum),*this); + } + } else if (vflag_global) { + if (shearupdate) { + Kokkos::parallel_reduce(Kokkos::RangePolicy>(0,inum),*this, ev); + } else { + Kokkos::parallel_reduce(Kokkos::RangePolicy>(0,inum),*this, ev); } } else { if (shearupdate) { @@ -180,11 +186,17 @@ void PairGranHookeHistoryKokkos::compute(int eflag_in, int vflag_in) } } } else { - if (evflag) { + if (vflag_atom) { if (shearupdate) { - Kokkos::parallel_for(Kokkos::RangePolicy>(0,inum),*this); + Kokkos::parallel_for(Kokkos::RangePolicy>(0,inum),*this); } else { - Kokkos::parallel_for(Kokkos::RangePolicy>(0,inum),*this); + Kokkos::parallel_for(Kokkos::RangePolicy>(0,inum),*this); + } + } else if (vflag_global) { + if (shearupdate) { + Kokkos::parallel_reduce(Kokkos::RangePolicy>(0,inum),*this, ev); + } else { + Kokkos::parallel_reduce(Kokkos::RangePolicy>(0,inum),*this, ev); } } else { if (shearupdate) { @@ -196,11 +208,17 @@ void PairGranHookeHistoryKokkos::compute(int eflag_in, int vflag_in) } } else { // HALFTHREAD if (force->newton_pair) { - if (evflag) { + if (vflag_atom) { if (shearupdate) { - Kokkos::parallel_for(Kokkos::RangePolicy>(0,inum),*this); + Kokkos::parallel_for(Kokkos::RangePolicy>(0,inum),*this); } else { - Kokkos::parallel_for(Kokkos::RangePolicy>(0,inum),*this); + Kokkos::parallel_for(Kokkos::RangePolicy>(0,inum),*this); + } + } else if (vflag_global) { + if (shearupdate) { + Kokkos::parallel_reduce(Kokkos::RangePolicy>(0,inum),*this, ev); + } else { + Kokkos::parallel_reduce(Kokkos::RangePolicy>(0,inum),*this, ev); } } else { if (shearupdate) { @@ -210,11 +228,17 @@ void PairGranHookeHistoryKokkos::compute(int eflag_in, int vflag_in) } } } else { - if (evflag) { + if (vflag_atom) { if (shearupdate) { - Kokkos::parallel_for(Kokkos::RangePolicy>(0,inum),*this); + Kokkos::parallel_for(Kokkos::RangePolicy>(0,inum),*this); } else { - Kokkos::parallel_for(Kokkos::RangePolicy>(0,inum),*this); + Kokkos::parallel_for(Kokkos::RangePolicy>(0,inum),*this); + } + } else if (vflag_global) { + if (shearupdate) { + Kokkos::parallel_reduce(Kokkos::RangePolicy>(0,inum),*this, ev); + } else { + Kokkos::parallel_reduce(Kokkos::RangePolicy>(0,inum),*this, ev); } } else { if (shearupdate) { @@ -226,7 +250,6 @@ void PairGranHookeHistoryKokkos::compute(int eflag_in, int vflag_in) } } - if (eflag_global) eng_vdwl += ev.evdwl; if (vflag_global) { virial[0] += ev.v[0]; virial[1] += ev.v[1]; @@ -236,11 +259,6 @@ void PairGranHookeHistoryKokkos::compute(int eflag_in, int vflag_in) virial[5] += ev.v[5]; } - if (eflag_atom) { - k_eatom.template modify(); - k_eatom.template sync(); - } - if (vflag_atom) { k_vatom.template modify(); k_vatom.template sync(); @@ -254,41 +272,41 @@ void PairGranHookeHistoryKokkos::compute(int eflag_in, int vflag_in) template template KOKKOS_INLINE_FUNCTION -void PairGranHookeHistoryKokkos::operator()(TagPairGranHookeHistoryCompute, const int &ii) const { +void PairGranHookeHistoryKokkos::operator()(TagPairGranHookeHistoryCompute, const int ii, EV_FLOAT &ev) const { // The f and torque arrays are atomic for Half/Thread neighbor style Kokkos::View::value> > a_f = f; Kokkos::View::value> > a_torque = torque; int i = d_ilist[ii]; - double xtmp = x(i,0); - double ytmp = x(i,1); - double ztmp = x(i,2); + X_FLOAT xtmp = x(i,0); + X_FLOAT ytmp = x(i,1); + X_FLOAT ztmp = x(i,2); int itype = type[i]; - double imass = rmass[i]; - double irad = radius[i]; + LMP_FLOAT imass = rmass[i]; + LMP_FLOAT irad = radius[i]; int jnum = d_numneigh[i]; - double fx_i = 0.0; - double fy_i = 0.0; - double fz_i = 0.0; + F_FLOAT fx_i = 0.0; + F_FLOAT fy_i = 0.0; + F_FLOAT fz_i = 0.0; - double torquex_i = 0.0; - double torquey_i = 0.0; - double torquez_i = 0.0; + F_FLOAT torquex_i = 0.0; + F_FLOAT torquey_i = 0.0; + F_FLOAT torquez_i = 0.0; for (int jj = 0; jj < jnum; jj++) { int j = d_neighbors(i,jj); j &= NEIGHMASK; - double delx = xtmp - x(j,0); - double dely = ytmp - x(j,1); - double delz = ztmp - x(j,2); - double rsq = delx*delx + dely*dely + delz*delz; + X_FLOAT delx = xtmp - x(j,0); + X_FLOAT dely = ytmp - x(j,1); + X_FLOAT delz = ztmp - x(j,2); + X_FLOAT rsq = delx*delx + dely*dely + delz*delz; int jtype = type[j]; - double jmass = rmass[j]; - double jrad = radius[j]; - double radsum = irad + jrad; + LMP_FLOAT jmass = rmass[j]; + LMP_FLOAT jrad = radius[j]; + LMP_FLOAT radsum = irad + jrad; // check for touching neighbors @@ -298,67 +316,67 @@ void PairGranHookeHistoryKokkos::operator()(TagPairGranHookeHistoryC d_firstshear(i,3*jj+1) = 0; d_firstshear(i,3*jj+2) = 0; } else { - double r = sqrt(rsq); - double rinv = 1.0/r; - double rsqinv = 1/rsq; + LMP_FLOAT r = sqrt(rsq); + LMP_FLOAT rinv = 1.0/r; + LMP_FLOAT rsqinv = 1/rsq; // relative translational velocity - double vr1 = v(i,0) - v(j,0); - double vr2 = v(i,1) - v(j,1); - double vr3 = v(i,2) - v(j,2); + V_FLOAT vr1 = v(i,0) - v(j,0); + V_FLOAT vr2 = v(i,1) - v(j,1); + V_FLOAT vr3 = v(i,2) - v(j,2); // normal component - double vnnr = vr1*delx + vr2*dely + vr3*delz; - double vn1 = delx*vnnr * rsqinv; - double vn2 = dely*vnnr * rsqinv; - double vn3 = delz*vnnr * rsqinv; + V_FLOAT vnnr = vr1*delx + vr2*dely + vr3*delz; + V_FLOAT vn1 = delx*vnnr * rsqinv; + V_FLOAT vn2 = dely*vnnr * rsqinv; + V_FLOAT vn3 = delz*vnnr * rsqinv; // tangential component - double vt1 = vr1 - vn1; - double vt2 = vr2 - vn2; - double vt3 = vr3 - vn3; + V_FLOAT vt1 = vr1 - vn1; + V_FLOAT vt2 = vr2 - vn2; + V_FLOAT vt3 = vr3 - vn3; // relative rotational velocity - double wr1 = (irad*omega(i,0) + jrad*omega(j,0)) * rinv; - double wr2 = (irad*omega(i,1) + jrad*omega(j,1)) * rinv; - double wr3 = (irad*omega(i,2) + jrad*omega(j,2)) * rinv; + V_FLOAT wr1 = (irad*omega(i,0) + jrad*omega(j,0)) * rinv; + V_FLOAT wr2 = (irad*omega(i,1) + jrad*omega(j,1)) * rinv; + V_FLOAT wr3 = (irad*omega(i,2) + jrad*omega(j,2)) * rinv; - double meff = imass*jmass / (imass+jmass); + LMP_FLOAT meff = imass*jmass / (imass+jmass); if (mask[i] & freeze_group_bit) meff = jmass; if (mask[j] & freeze_group_bit) meff = imass; - double damp = meff*gamman*vnnr*rsqinv; - double ccel = kn*(radsum-r)*rinv - damp; + F_FLOAT damp = meff*gamman*vnnr*rsqinv; + F_FLOAT ccel = kn*(radsum-r)*rinv - damp; // relative velocities - double vtr1 = vt1 - (delz*wr2-dely*wr3); - double vtr2 = vt2 - (delx*wr3-delz*wr1); - double vtr3 = vt3 - (dely*wr1-delx*wr2); - double vrel = vtr1*vtr1 + vtr2*vtr2 + vtr3*vtr3; + V_FLOAT vtr1 = vt1 - (delz*wr2-dely*wr3); + V_FLOAT vtr2 = vt2 - (delx*wr3-delz*wr1); + V_FLOAT vtr3 = vt3 - (dely*wr1-delx*wr2); + V_FLOAT vrel = vtr1*vtr1 + vtr2*vtr2 + vtr3*vtr3; vrel = sqrt(vrel); // shear history effects d_firsttouch(i,jj) = 1; - double shear1 = d_firstshear(i,3*jj); - double shear2 = d_firstshear(i,3*jj+1); - double shear3 = d_firstshear(i,3*jj+2); + X_FLOAT shear1 = d_firstshear(i,3*jj); + X_FLOAT shear2 = d_firstshear(i,3*jj+1); + X_FLOAT shear3 = d_firstshear(i,3*jj+2); if (SHEARUPDATE) { shear1 += vtr1*dt; shear2 += vtr2*dt; shear3 += vtr3*dt; } - double shrmag = sqrt(shear1*shear1 + shear2*shear2 + + X_FLOAT shrmag = sqrt(shear1*shear1 + shear2*shear2 + shear3*shear3); // rotate shear displacements - double rsht = shear1*delx + shear2*dely + shear3*delz; + X_FLOAT rsht = shear1*delx + shear2*dely + shear3*delz; rsht *= rsqinv; if (SHEARUPDATE) { shear1 -= rsht*delx; @@ -368,14 +386,14 @@ void PairGranHookeHistoryKokkos::operator()(TagPairGranHookeHistoryC // tangential forces = shear + tangential velocity damping - double fs1 = - (kt*shear1 + meff*gammat*vtr1); - double fs2 = - (kt*shear2 + meff*gammat*vtr2); - double fs3 = - (kt*shear3 + meff*gammat*vtr3); + F_FLOAT fs1 = - (kt*shear1 + meff*gammat*vtr1); + F_FLOAT fs2 = - (kt*shear2 + meff*gammat*vtr2); + F_FLOAT fs3 = - (kt*shear3 + meff*gammat*vtr3); // rescale frictional displacements and forces if needed - double fs = sqrt(fs1*fs1 + fs2*fs2 + fs3*fs3); - double fn = xmu * fabs(ccel*r); + F_FLOAT fs = sqrt(fs1*fs1 + fs2*fs2 + fs3*fs3); + F_FLOAT fn = xmu * fabs(ccel*r); if (fs > fn) { if (shrmag != 0.0) { @@ -399,16 +417,16 @@ void PairGranHookeHistoryKokkos::operator()(TagPairGranHookeHistoryC // forces & torques - double fx = delx*ccel + fs1; - double fy = dely*ccel + fs2; - double fz = delz*ccel + fs3; + F_FLOAT fx = delx*ccel + fs1; + F_FLOAT fy = dely*ccel + fs2; + F_FLOAT fz = delz*ccel + fs3; fx_i += fx; fy_i += fy; fz_i += fz; - double tor1 = rinv * (dely*fs3 - delz*fs2); - double tor2 = rinv * (delz*fs1 - delx*fs3); - double tor3 = rinv * (delx*fs2 - dely*fs1); + F_FLOAT tor1 = rinv * (dely*fs3 - delz*fs2); + F_FLOAT tor2 = rinv * (delz*fs1 - delx*fs3); + F_FLOAT tor3 = rinv * (delx*fs2 - dely*fs1); torquex_i -= irad*tor1; torquey_i -= irad*tor2; torquez_i -= irad*tor3; @@ -421,6 +439,11 @@ void PairGranHookeHistoryKokkos::operator()(TagPairGranHookeHistoryC a_torque(j,1) -= jrad*tor2; a_torque(j,2) -= jrad*tor3; } + + if (EVFLAG == 2) + ev_tally_xyz_atom(ev, i, j, fx_i, fy_i, fz_i, delx, dely, delz); + if (EVFLAG == 1) + ev_tally_xyz(ev, i, j, fx_i, fy_i, fz_i, delx, dely, delz); } } @@ -432,6 +455,94 @@ void PairGranHookeHistoryKokkos::operator()(TagPairGranHookeHistoryC a_torque(i,2) += torquez_i; } + +template +template +KOKKOS_INLINE_FUNCTION +void PairGranHookeHistoryKokkos::operator()(TagPairGranHookeHistoryCompute, const int ii) const { + EV_FLOAT ev; + this->template operator()(TagPairGranHookeHistoryCompute(), ii, ev); +} + +template +template +KOKKOS_INLINE_FUNCTION +void PairGranHookeHistoryKokkos::ev_tally_xyz(EV_FLOAT &ev, int i, int j, + F_FLOAT fx, F_FLOAT fy, F_FLOAT fz, + X_FLOAT delx, X_FLOAT dely, X_FLOAT delz) const +{ + F_FLOAT v[6]; + + v[0] = delx*fx; + v[1] = dely*fy; + v[2] = delz*fz; + v[3] = delx*fy; + v[4] = delx*fz; + v[5] = dely*fz; + + if (NEWTON_PAIR) { + ev.v[0] += v[0]; + ev.v[1] += v[1]; + ev.v[2] += v[2]; + ev.v[3] += v[3]; + ev.v[4] += v[4]; + ev.v[5] += v[5]; + } else { + if (i < nlocal) { + ev.v[0] += 0.5*v[0]; + ev.v[1] += 0.5*v[1]; + ev.v[2] += 0.5*v[2]; + ev.v[3] += 0.5*v[3]; + ev.v[4] += 0.5*v[4]; + ev.v[5] += 0.5*v[5]; + } + if (j < nlocal) { + ev.v[0] += 0.5*v[0]; + ev.v[1] += 0.5*v[1]; + ev.v[2] += 0.5*v[2]; + ev.v[3] += 0.5*v[3]; + ev.v[4] += 0.5*v[4]; + ev.v[5] += 0.5*v[5]; + } + } +} + +template +template +KOKKOS_INLINE_FUNCTION +void PairGranHookeHistoryKokkos::ev_tally_xyz_atom(EV_FLOAT &ev, int i, int j, + F_FLOAT fx, F_FLOAT fy, F_FLOAT fz, + X_FLOAT delx, X_FLOAT dely, X_FLOAT delz) const +{ + Kokkos::View::value> > v_vatom = k_vatom.view(); + + F_FLOAT v[6]; + + v[0] = delx*fx; + v[1] = dely*fy; + v[2] = delz*fz; + v[3] = delx*fy; + v[4] = delx*fz; + v[5] = dely*fz; + + if (NEWTON_PAIR || i < nlocal) { + v_vatom(i,0) += 0.5*v[0]; + v_vatom(i,1) += 0.5*v[1]; + v_vatom(i,2) += 0.5*v[2]; + v_vatom(i,3) += 0.5*v[3]; + v_vatom(i,4) += 0.5*v[4]; + v_vatom(i,5) += 0.5*v[5]; + } + if (NEWTON_PAIR || j < nlocal) { + v_vatom(j,0) += 0.5*v[0]; + v_vatom(j,1) += 0.5*v[1]; + v_vatom(j,2) += 0.5*v[2]; + v_vatom(j,3) += 0.5*v[3]; + v_vatom(j,4) += 0.5*v[4]; + v_vatom(j,5) += 0.5*v[5]; + } +} + namespace LAMMPS_NS { template class PairGranHookeHistoryKokkos; #ifdef KOKKOS_HAVE_CUDA diff --git a/src/KOKKOS/pair_gran_hooke_history_kokkos.h b/src/KOKKOS/pair_gran_hooke_history_kokkos.h index 84dc412078..dd5aac96d3 100644 --- a/src/KOKKOS/pair_gran_hooke_history_kokkos.h +++ b/src/KOKKOS/pair_gran_hooke_history_kokkos.h @@ -39,6 +39,7 @@ class PairGranHookeHistoryKokkos : public PairGranHookeHistory { public: typedef DeviceType device_type; typedef ArrayTypes AT; + typedef EV_FLOAT value_type; PairGranHookeHistoryKokkos(class LAMMPS *); virtual ~PairGranHookeHistoryKokkos(); @@ -47,8 +48,22 @@ class PairGranHookeHistoryKokkos : public PairGranHookeHistory { template KOKKOS_INLINE_FUNCTION - void operator()(TagPairGranHookeHistoryCompute, const int&) const; + void operator()(TagPairGranHookeHistoryCompute, const int, EV_FLOAT &ev) const; + template + KOKKOS_INLINE_FUNCTION + void operator()(TagPairGranHookeHistoryCompute, const int) const; + template + KOKKOS_INLINE_FUNCTION + void ev_tally_xyz(EV_FLOAT &ev, int i, int j, + F_FLOAT fx, F_FLOAT fy, F_FLOAT fz, + X_FLOAT delx, X_FLOAT dely, X_FLOAT delz) const; + template + KOKKOS_INLINE_FUNCTION + void ev_tally_xyz_atom(EV_FLOAT &ev, int i, int j, + F_FLOAT fx, F_FLOAT fy, F_FLOAT fz, + X_FLOAT delx, X_FLOAT dely, X_FLOAT delz) const; + protected: typename AT::t_x_array_randomread x; typename AT::t_x_array c_x; From 13efc1b76d6a643912eb1891a080c6a64169a281 Mon Sep 17 00:00:00 2001 From: Denis Taniguchi Date: Thu, 5 Jul 2018 18:03:00 -0400 Subject: [PATCH 025/302] Attempt to fix compilation issue with kokkos_omp. --- src/KOKKOS/fix_neigh_history_kokkos.cpp | 14 -------------- src/KOKKOS/fix_neigh_history_kokkos.h | 4 ++-- 2 files changed, 2 insertions(+), 16 deletions(-) diff --git a/src/KOKKOS/fix_neigh_history_kokkos.cpp b/src/KOKKOS/fix_neigh_history_kokkos.cpp index d5277c0188..0b58a68f13 100644 --- a/src/KOKKOS/fix_neigh_history_kokkos.cpp +++ b/src/KOKKOS/fix_neigh_history_kokkos.cpp @@ -181,20 +181,6 @@ void FixNeighHistoryKokkos::post_neighbor() Kokkos::parallel_for(inum,f); copymode = 0; - -#ifdef LMP_KOKKOS_DEBUG - typename ArrayTypes::t_neighbors_2d h_neighbors("neighbor_history:h_neighbor",k_list->d_neighbors.extent(0), k_list->d_neighbors.extent(1)); - deep_copy(h_neighbors, d_neighbors); - - typename ArrayTypes::t_int_1d h_numneigh("neighbor_history:h_numneigh",k_list->d_numneigh.extent(0)); - deep_copy(h_numneigh, d_numneigh); - - typename ArrayTypes::t_int_2d h_firstflag("neighbor_history:h_firstflag",maxatom,k_list->maxneighs); - deep_copy(h_firstflag, d_firstflag); - - typename ArrayTypes::t_float_2d h_firstvalue("neighbor_history:h_firstvalue",maxatom,k_list->maxneighs*dnum); - deep_copy(h_firstvalue, d_firstvalue); -#endif } /* ---------------------------------------------------------------------- */ diff --git a/src/KOKKOS/fix_neigh_history_kokkos.h b/src/KOKKOS/fix_neigh_history_kokkos.h index 68bd59722f..4e2ca05e54 100644 --- a/src/KOKKOS/fix_neigh_history_kokkos.h +++ b/src/KOKKOS/fix_neigh_history_kokkos.h @@ -54,7 +54,7 @@ class FixNeighHistoryKokkos : public FixNeighHistory { private: typename ArrayTypes::tdual_int_1d k_npartner; - typename ArrayTypes::tdual_int_2d k_partner; + typename ArrayTypes::tdual_tagint_2d k_partner; typename ArrayTypes::tdual_float_2d k_valuepartner; // for neighbor list lookup @@ -64,7 +64,7 @@ class FixNeighHistoryKokkos : public FixNeighHistory { typename ArrayTypes::t_tagint_1d tag; typename ArrayTypes::t_int_1d d_npartner; - typename ArrayTypes::t_int_2d d_partner; + typename ArrayTypes::t_tagint_2d d_partner; typename ArrayTypes::t_float_2d d_valuepartner; typename ArrayTypes::t_int_scalar d_resize; From 2f3343b7edeb353f8b5d225799d910b120af953c Mon Sep 17 00:00:00 2001 From: Denis Taniguchi Date: Fri, 6 Jul 2018 05:24:26 -0400 Subject: [PATCH 026/302] Fixing dependencies with GRANULAR. --- src/KOKKOS/Install.sh | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/KOKKOS/Install.sh b/src/KOKKOS/Install.sh index a75281cd20..4926a288c4 100755 --- a/src/KOKKOS/Install.sh +++ b/src/KOKKOS/Install.sh @@ -97,8 +97,8 @@ action fix_deform_kokkos.cpp action fix_deform_kokkos.h action fix_eos_table_rx_kokkos.cpp fix_eos_table_rx.cpp action fix_eos_table_rx_kokkos.h fix_eos_table_rx.h -action fix_freeze_kokkos.cpp -action fix_freeze_kokkos.h +action fix_freeze_kokkos.cpp fix_freeze.cpp +action fix_freeze_kokkos.h fix_freeze.h action fix_gravity_kokkos.cpp action fix_gravity_kokkos.h action fix_langevin_kokkos.cpp @@ -201,8 +201,8 @@ action pair_eam_fs_kokkos.cpp pair_eam_fs.cpp action pair_eam_fs_kokkos.h pair_eam_fs.h action pair_exp6_rx_kokkos.cpp pair_exp6_rx.cpp action pair_exp6_rx_kokkos.h pair_exp6_rx.h -action pair_gran_hooke_history_kokkos.h -action pair_gran_hooke_history_kokkos.cpp +action pair_gran_hooke_history_kokkos.h pair_gran_hooke_history.h +action pair_gran_hooke_history_kokkos.cpp pair_gran_hooke_history.cpp action pair_hybrid_kokkos.cpp action pair_hybrid_kokkos.h action pair_hybrid_overlay_kokkos.cpp From acb043605783b71af5d26e361f7867a49f832990 Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Fri, 6 Jul 2018 09:31:48 -0600 Subject: [PATCH 027/302] Allow Kokkos version of fix gravity in fix pour --- src/GRANULAR/fix_pour.cpp | 1 + 1 file changed, 1 insertion(+) diff --git a/src/GRANULAR/fix_pour.cpp b/src/GRANULAR/fix_pour.cpp index 318c54c99a..5090112ec4 100644 --- a/src/GRANULAR/fix_pour.cpp +++ b/src/GRANULAR/fix_pour.cpp @@ -181,6 +181,7 @@ FixPour::FixPour(LAMMPS *lmp, int narg, char **arg) : for (ifix = 0; ifix < modify->nfix; ifix++) { if (strcmp(modify->fix[ifix]->style,"gravity") == 0) break; if (strcmp(modify->fix[ifix]->style,"gravity/omp") == 0) break; + if (strcmp(modify->fix[ifix]->style,"gravity/kk") == 0) break; } if (ifix == modify->nfix) error->all(FLERR,"No fix gravity defined for fix pour"); From 67ed11a9601c3f31f4317825acd5c05d445365b3 Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Fri, 6 Jul 2018 09:52:41 -0600 Subject: [PATCH 028/302] Allow Kokkos version of fix gravity in fix pour, including kk/device and kk/host suffixes --- src/GRANULAR/fix_pour.cpp | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/GRANULAR/fix_pour.cpp b/src/GRANULAR/fix_pour.cpp index 5090112ec4..95ed79ffc0 100644 --- a/src/GRANULAR/fix_pour.cpp +++ b/src/GRANULAR/fix_pour.cpp @@ -181,7 +181,7 @@ FixPour::FixPour(LAMMPS *lmp, int narg, char **arg) : for (ifix = 0; ifix < modify->nfix; ifix++) { if (strcmp(modify->fix[ifix]->style,"gravity") == 0) break; if (strcmp(modify->fix[ifix]->style,"gravity/omp") == 0) break; - if (strcmp(modify->fix[ifix]->style,"gravity/kk") == 0) break; + if (strstr(modify->fix[ifix]->style,"gravity/kk") != NULL) break; } if (ifix == modify->nfix) error->all(FLERR,"No fix gravity defined for fix pour"); @@ -316,6 +316,7 @@ void FixPour::init() for (ifix = 0; ifix < modify->nfix; ifix++) { if (strcmp(modify->fix[ifix]->style,"gravity") == 0) break; if (strcmp(modify->fix[ifix]->style,"gravity/omp") == 0) break; + if (strstr(modify->fix[ifix]->style,"gravity/kk") != NULL) break; } if (ifix == modify->nfix) error->all(FLERR,"No fix gravity defined for fix pour"); From cce0755ee93339e5cc458e3671ad2ebcbb388b38 Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Fri, 6 Jul 2018 10:08:21 -0600 Subject: [PATCH 029/302] Fix memory free issue in fix_neigh_history_kokkos --- src/KOKKOS/fix_neigh_history_kokkos.cpp | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/src/KOKKOS/fix_neigh_history_kokkos.cpp b/src/KOKKOS/fix_neigh_history_kokkos.cpp index 0b58a68f13..8320d72545 100644 --- a/src/KOKKOS/fix_neigh_history_kokkos.cpp +++ b/src/KOKKOS/fix_neigh_history_kokkos.cpp @@ -32,8 +32,11 @@ FixNeighHistoryKokkos::FixNeighHistoryKokkos(LAMMPS *lmp, int narg, execution_space = ExecutionSpaceFromDevice::space; memory->destroy(npartner); - memory->destroy(partner); - memory->destroy(valuepartner); + memory->sfree(partner); + memory->sfree(valuepartner); + npartner = NULL; + partner = NULL; + valuepartner = NULL; maxpartner = 8; grow_arrays(atom->nmax); From 64fb7674b1e53a8a37739c6abbc50947bf44c70f Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Fri, 6 Jul 2018 11:58:42 -0600 Subject: [PATCH 030/302] Fix compile warning in fix_freeze_kokkos --- src/KOKKOS/fix_freeze_kokkos.h | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/src/KOKKOS/fix_freeze_kokkos.h b/src/KOKKOS/fix_freeze_kokkos.h index 3ad341d087..193e011995 100644 --- a/src/KOKKOS/fix_freeze_kokkos.h +++ b/src/KOKKOS/fix_freeze_kokkos.h @@ -49,11 +49,10 @@ class FixFreezeKokkos : public FixFreeze { } KOKKOS_INLINE_FUNCTION - volatile OriginalForce &operator+=(const volatile OriginalForce &rhs) volatile { + void operator+=(const volatile OriginalForce &rhs) volatile { values[0] += rhs.values[0]; values[1] += rhs.values[1]; values[2] += rhs.values[2]; - return *this; } }; From 228caa3fabe8755bb673ba9d05db1ec6eee1260e Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Fri, 6 Jul 2018 11:59:25 -0600 Subject: [PATCH 031/302] Remove randomread from radius to prevent Kokkos runtime error when radius isn't defined --- src/KOKKOS/npair_kokkos.cpp | 1 - src/KOKKOS/npair_kokkos.h | 6 +++--- 2 files changed, 3 insertions(+), 4 deletions(-) diff --git a/src/KOKKOS/npair_kokkos.cpp b/src/KOKKOS/npair_kokkos.cpp index c50d6305e7..6ea2cebefc 100644 --- a/src/KOKKOS/npair_kokkos.cpp +++ b/src/KOKKOS/npair_kokkos.cpp @@ -686,7 +686,6 @@ void NeighborKokkosExecute:: { /* if necessary, goto next page and add pages */ int n = 0; - int which = 0; int moltemplate; if (molecular == 2) moltemplate = 1; else moltemplate = 0; diff --git a/src/KOKKOS/npair_kokkos.h b/src/KOKKOS/npair_kokkos.h index a8837fa9f3..970e40c9fc 100644 --- a/src/KOKKOS/npair_kokkos.h +++ b/src/KOKKOS/npair_kokkos.h @@ -182,7 +182,7 @@ class NeighborKokkosExecute // data from Atom class const typename AT::t_x_array_randomread x; - const typename AT::t_float_1d_randomread radius; + const typename AT::t_float_1d radius; const typename AT::t_int_1d_const type,mask; const typename AT::t_tagint_1d_const molecule; const typename AT::t_tagint_1d_const tag; @@ -223,7 +223,7 @@ class NeighborKokkosExecute const typename AT::t_int_1d_3 &_d_stencilxyz, const int _nlocal, const typename AT::t_x_array_randomread &_x, - const typename AT::t_float_1d_randomread &_radius, + const typename AT::t_float_1d &_radius, const typename AT::t_int_1d_const &_type, const typename AT::t_int_1d_const &_mask, const typename AT::t_tagint_1d_const &_molecule, @@ -251,7 +251,7 @@ class NeighborKokkosExecute const X_FLOAT *_bboxhi, const X_FLOAT* _bboxlo, const int & _xperiodic, const int & _yperiodic, const int & _zperiodic, const int & _xprd_half, const int & _yprd_half, const int & _zprd_half, - const X_FLOAT _skin): + const X_FLOAT _skin): neigh_list(_neigh_list), cutneighsq(_cutneighsq), bincount(_bincount),c_bincount(_bincount),bins(_bins),c_bins(_bins), atom2bin(_atom2bin),c_atom2bin(_atom2bin), From 13d562e969aa31aa524e4b8ea7ff9b55c83dd153 Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Fri, 6 Jul 2018 12:06:09 -0600 Subject: [PATCH 032/302] Removed wrong which variable --- src/KOKKOS/npair_kokkos.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/KOKKOS/npair_kokkos.cpp b/src/KOKKOS/npair_kokkos.cpp index 6ea2cebefc..6f75e6cabc 100644 --- a/src/KOKKOS/npair_kokkos.cpp +++ b/src/KOKKOS/npair_kokkos.cpp @@ -686,6 +686,7 @@ void NeighborKokkosExecute:: { /* if necessary, goto next page and add pages */ int n = 0; + int which = 0; int moltemplate; if (molecular == 2) moltemplate = 1; else moltemplate = 0; @@ -807,7 +808,6 @@ void NeighborKokkosExecute:: { /* if necessary, goto next page and add pages */ int n = 0; - int which = 0; // get subview of neighbors of i From 2cd95d1a99d63d8ab109a3b6cd8df76b271d709e Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Fri, 6 Jul 2018 15:47:14 -0600 Subject: [PATCH 033/302] Fix misnamed variable in comm_kokkos --- src/KOKKOS/comm_kokkos.cpp | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/src/KOKKOS/comm_kokkos.cpp b/src/KOKKOS/comm_kokkos.cpp index 96d1c64d0d..d00d766318 100644 --- a/src/KOKKOS/comm_kokkos.cpp +++ b/src/KOKKOS/comm_kokkos.cpp @@ -707,7 +707,7 @@ void CommKokkos::borders() if (!exchange_comm_classic) { static int print = 1; - if (style != Comm::SINGLE || bordergroup || ghost_velocity) { + if (mode != Comm::SINGLE || bordergroup || ghost_velocity) { if (print && comm->me==0) { error->warning(FLERR,"Required border comm not yet implemented in Kokkos communication, " "switching to classic communication"); @@ -815,7 +815,7 @@ void CommKokkos::borders_device() { // store sent atom indices in list for use in future timesteps x = atom->x; - if (style == Comm::SINGLE) { + if (mode == Comm::SINGLE) { lo = slablo[iswap]; hi = slabhi[iswap]; } else { @@ -844,7 +844,7 @@ void CommKokkos::borders_device() { if (sendflag) { if (!bordergroup || ineed >= 2) { - if (style == Comm::SINGLE) { + if (mode == Comm::SINGLE) { k_total_send.h_view() = 0; k_total_send.template modify(); k_total_send.template sync(); @@ -892,7 +892,7 @@ void CommKokkos::borders_device() { } else { error->all(FLERR,"Required border comm not yet " "implemented with Kokkos"); - if (style == Comm::SINGLE) { + if (mode == Comm::SINGLE) { ngroup = atom->nfirst; for (i = 0; i < ngroup; i++) if (x[i][dim] >= lo && x[i][dim] <= hi) { @@ -1097,7 +1097,7 @@ void CommKokkos::grow_swap(int n) { free_swap(); allocate_swap(n); - if (style == Comm::MULTI) { + if (mode == Comm::MULTI) { free_multi(); allocate_multi(n); } From ee98daeba5aa6d43ec63f7a2f08c1b43f1a97044 Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Fri, 6 Jul 2018 16:47:55 -0600 Subject: [PATCH 034/302] Fix bug in atom_vec_sphere_kokkos --- src/KOKKOS/atom_vec_sphere_kokkos.cpp | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/src/KOKKOS/atom_vec_sphere_kokkos.cpp b/src/KOKKOS/atom_vec_sphere_kokkos.cpp index c2788526d7..d34e2f9c61 100644 --- a/src/KOKKOS/atom_vec_sphere_kokkos.cpp +++ b/src/KOKKOS/atom_vec_sphere_kokkos.cpp @@ -1562,6 +1562,9 @@ struct AtomVecSphereKokkos_UnpackExchangeFunctor { _type(atom->k_type.view()), _mask(atom->k_mask.view()), _image(atom->k_image.view()), + _radius(atom->k_radius.view()), + _rmass(atom->k_rmass.view()), + _omega(atom->k_omega.view()), _nlocal(nlocal.template view()),_dim(dim), _lo(lo),_hi(hi){ const size_t elements = 16; @@ -1613,7 +1616,7 @@ int AtomVecSphereKokkos::unpack_exchange_kokkos(DAT::tdual_xfloat_2d &k_buf,int modified(space,X_MASK | V_MASK | TAG_MASK | TYPE_MASK | MASK_MASK | IMAGE_MASK| RADIUS_MASK | RMASS_MASK | - OMEGA_MASK); + OMEGA_MASK); return k_count.h_view(0); } From b259de95d27d1b5828379351a995bfb77aa098b5 Mon Sep 17 00:00:00 2001 From: Rene Halver Date: Mon, 9 Jul 2018 13:00:52 -0600 Subject: [PATCH 035/302] fix for ScaFaCoS library --- cmake/CMakeLists.txt | 13 +- examples/scafacos/data.NaCl | 25 ++ examples/scafacos/in.scafacos | 22 ++ src/SCAFACOS/Install.sh | 67 +++++ src/SCAFACOS/fix_scafacos.cpp | 488 ++++++++++++++++++++++++++++++++++ src/SCAFACOS/fix_scafacos.h | 164 ++++++++++++ 6 files changed, 776 insertions(+), 3 deletions(-) create mode 100644 examples/scafacos/data.NaCl create mode 100644 examples/scafacos/in.scafacos create mode 100755 src/SCAFACOS/Install.sh create mode 100644 src/SCAFACOS/fix_scafacos.cpp create mode 100644 src/SCAFACOS/fix_scafacos.h diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index 8bc079fd85..a335a441da 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -119,7 +119,7 @@ option(ENABLE_ALL "Build all default packages" OFF) set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GRANULAR KSPACE MANYBODY MC MEAM MISC MOLECULE PERI QEQ REAX REPLICA RIGID SHOCK SNAP SRD) -set(OTHER_PACKAGES KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE +set(OTHER_PACKAGES KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE SCAFACOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-MESO USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD USER-LB USER-MANIFOLD USER-MEAMC USER-MGPT USER-MISC @@ -150,11 +150,11 @@ pkg_depends(CORESHELL KSPACE) ###################################################### # packages with special compiler needs or external libs ###################################################### -if(PKG_REAX OR PKG_MEAM OR PKG_USER-QUIP OR PKG_USER-QMMM OR PKG_LATTE) +if(PKG_REAX OR PKG_MEAM OR PKG_USER-QUIP OR PKG_USER-QMMM OR PKG_LATTE OR PKG_SCAFACOS) enable_language(Fortran) endif() -if(PKG_MEAM OR PKG_USER-H5MD OR PKG_USER-QMMM) +if(PKG_MEAM OR PKG_USER-H5MD OR PKG_USER-QMMM OR PKG_SCAFACOS) enable_language(C) endif() @@ -313,6 +313,13 @@ if(PKG_LATTE) list(APPEND LAMMPS_LINK_LIBS ${LATTE_LIBRARIES} ${LAPACK_LIBRARIES}) endif() +if(PKG_SCAFACOS) + FIND_PACKAGE(PkgConfig) + PKG_CHECK_MODULES(SCAFACOS scafacos) + include_directories(${SCAFACOS_INCLUDE_DIRS}) + list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_LDFLAGS}) +endif() + if(PKG_USER-MOLFILE) add_library(molfile INTERFACE) target_include_directories(molfile INTERFACE ${LAMMPS_LIB_SOURCE_DIR}/molfile) diff --git a/examples/scafacos/data.NaCl b/examples/scafacos/data.NaCl new file mode 100644 index 0000000000..1a599b957d --- /dev/null +++ b/examples/scafacos/data.NaCl @@ -0,0 +1,25 @@ + LAMMPS Description + + 8 atoms + + 2 atom types + + 0.0000000000000000 2.000000000000000 xlo xhi + 0.0000000000000000 2.000000000000000 ylo yhi + 0.0000000000000000 2.000000000000000 zlo zhi + + Masses + + 1 22.98976928 + 2 35.45 + + Atoms + + 1 1 1 1.0 0.0 0.0 0.0 + 2 1 2 -1.0 1.0 0.0 0.0 + 3 1 2 -1.0 0.0 1.0 0.0 + 4 1 1 1.0 1.0 1.0 0.0 + 5 1 2 -1.0 0.0 0.0 1.0 + 6 1 1 1.0 1.0 0.0 1.0 + 7 1 1 1.0 0.0 1.0 1.0 + 8 1 2 -1.0 1.0 1.0 1.0 diff --git a/examples/scafacos/in.scafacos b/examples/scafacos/in.scafacos new file mode 100644 index 0000000000..a2849583f5 --- /dev/null +++ b/examples/scafacos/in.scafacos @@ -0,0 +1,22 @@ +# Point dipoles in a 2d box + +units lj +atom_style full + +read_data data.NaCl + +# need both mass settings due to hybrid atom style + +velocity all set 0.0 0.0 0.0 mom no + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all scafacos fmm + +timestep 0.005 + +run 100 diff --git a/src/SCAFACOS/Install.sh b/src/SCAFACOS/Install.sh new file mode 100755 index 0000000000..ace610050b --- /dev/null +++ b/src/SCAFACOS/Install.sh @@ -0,0 +1,67 @@ +# Install/unInstall package files in LAMMPS +# mode = 0/1/2 for uninstall/install/update + +mode=$1 + +# enforce using portable C locale +LC_ALL=C +export LC_ALL + +# arg1 = file, arg2 = file it depends on + +action () { + if (test $mode = 0) then + rm -f ../$1 + elif (! cmp -s $1 ../$1) then + if (test -z "$2" || test -e ../$2) then + cp $1 .. + if (test $mode = 2) then + echo " updating src/$1" + fi + fi + elif (test -n "$2") then + if (test ! -e ../$2) then + rm -f ../$1 + fi + fi +} + +# all package files with no dependencies + +for file in *.cpp *.h; do + test -f ${file} && action $file +done + +# edit 2 Makefile.package files to include/exclude package info + +if (test $1 = 1) then + + if (test -e ../Makefile.package) then + sed -i -e 's/[^ \t]*scafacos[^ \t]* //' ../Makefile.package + sed -i -e 's|^PKG_INC =[ \t]*|&-I../../lib/scafacos/includelink |' ../Makefile.package + sed -i -e 's|^PKG_PATH =[ \t]*|&-L../../lib/scafacos/liblink |' ../Makefile.package + #sed -i -e 's|^PKG_LIB =[ \t]*|&-lscafacos |' ../Makefile.package + sed -i -e 's|^PKG_SYSINC =[ \t]*|&$(scafacos_SYSINC) |' ../Makefile.package + sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(scafacos_SYSLIB) |' ../Makefile.package + sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(scafacos_SYSPATH) |' ../Makefile.package + fi + + if (test -e ../Makefile.package.settings) then + sed -i -e '/^include.*scafacos.*$/d' ../Makefile.package.settings + # multiline form needed for BSD sed on Macs + sed -i -e '4 i \ +include ..\/..\/lib\/scafacos\/Makefile.lammps +' ../Makefile.package.settings + fi + +elif (test $1 = 0) then + + if (test -e ../Makefile.package) then + sed -i -e 's/[^ \t]*scafacos[^ \t]* //' ../Makefile.package + fi + + if (test -e ../Makefile.package.settings) then + sed -i -e '/^include.*scafacos.*$/d' ../Makefile.package.settings + fi + +fi diff --git a/src/SCAFACOS/fix_scafacos.cpp b/src/SCAFACOS/fix_scafacos.cpp new file mode 100644 index 0000000000..f888747047 --- /dev/null +++ b/src/SCAFACOS/fix_scafacos.cpp @@ -0,0 +1,488 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Rene Halver (JSC) +------------------------------------------------------------------------- */ + +#include +#include +#include "fix_scafacos.h" +#include "atom.h" +#include "comm.h" +#include "update.h" +#include "neighbor.h" +#include "domain.h" +#include "force.h" +#include "pair.h" +#include "modify.h" +#include "compute.h" +#include "memory.h" +#include "error.h" + +// ScaFaCoS library +#include +#include +#include +#include "fcs.h" +#include "universe.h" + +using namespace LAMMPS_NS; +using namespace FixConst; + +#define INVOKED_PERATOM 8 + +/* ---------------------------------------------------------------------- */ + +FixScafacos::FixScafacos(LAMMPS *lmp, int narg, char **arg) : + Fix(lmp, narg, arg) +{ + // form of fix string: + // fix <#> scafacos [ tolerance ] + + + if (narg < 4) error->all(FLERR,"Illegal fix scafacos command"); + + // read method from fix input + method = arg[3]; + // check if fmm method was chosen + fmm_chosen = !strcmp(method.c_str(),"fmm"); + + int arg_index = 4; + + tolerance_set = false; + + while(arg_index < narg) + { + // check if tolerance option is set + if (strcmp(arg[arg_index],"tolerance") == 0) + { + tolerance_set = true; + ++arg_index; + if (strcmp(arg[arg_index],"energy") == 0) + tolerance_type = FCS_TOLERANCE_TYPE_ENERGY; + else if (strcmp(arg[arg_index],"energy_rel") == 0) + tolerance_type = FCS_TOLERANCE_TYPE_ENERGY_REL; + else if (strcmp(arg[arg_index],"field") == 0) + tolerance_type = FCS_TOLERANCE_TYPE_FIELD; + else if (strcmp(arg[arg_index],"field_rel") == 0) + tolerance_type = FCS_TOLERANCE_TYPE_FIELD_REL; + else if (strcmp(arg[arg_index],"potential") == 0) + tolerance_type = FCS_TOLERANCE_TYPE_POTENTIAL; + else if (strcmp(arg[arg_index],"potential_rel") == 0) + tolerance_type = FCS_TOLERANCE_TYPE_POTENTIAL_REL; + else + error->all(FLERR,"Illegal fix scafacos command"); + ++arg_index; + tolerance_value = atof(arg[arg_index]); + ++arg_index; + } + else + error->all(FLERR,"Illegal fix scafacos command"); + } +} + +/* ---------------------------------------------------------------------- */ + +FixScafacos::~FixScafacos() +{ + memory->destroy(pot); + memory->destroy(field); +} + +/* ---------------------------------------------------------------------- */ + +int FixScafacos::setmask() +{ + int mask = 0; + //mask |= INITIAL_INTEGRATE; + //mask |= FINAL_INTEGRATE; + mask |= PRE_REVERSE; + mask |= POST_FORCE; + mask |= MIN_POST_FORCE; + mask |= THERMO_ENERGY; + return mask; +} + +/* ---------------------------------------------------------------------- */ + +void FixScafacos::init() +{ + // error checks + + if (domain->dimension == 2) + error->all(FLERR,"Fix scafacos requires 3d problem"); + + rank = comm->me; + + int nlocal = 0; + int proc_grid[3] = {comm->procgrid[0], comm->procgrid[1], comm->procgrid[2]}; + int myloc[3] = {comm->myloc[0], comm->myloc[1], comm->myloc[2]}; + + // call ScaFaCoS init + // TODO: check if universe->uworld is a good idea for computations + result = fcs_init(&fcs,method.c_str(),universe->uworld); + if (!check_result(result, rank)) return; + + setup_handle(); + + nlocal = atom -> nlocal; + // get particle data + x = &atom->x[0][0]; + q = atom->q; + + if (tolerance_set) + { + result = fcs_set_tolerance(fcs,tolerance_type,tolerance_value); + if (!check_result(result, rank)) return; + } + + // print out parameters within handle + if (rank == 0) fcs_print_parameters(fcs); + + // call the tuning routine (needs to be redone, if critical system parameters should change) + result = fcs_tune(fcs,nlocal,x,q); + if (!check_result(result, rank)) return; + + // allocate arrays larger in order to avoid fast reallocation due to fluctuations + local_array_size = (int)(1.25 * (double)nlocal); + + // allocate new result arrays + memory->create(pot,local_array_size,"scafacos:potential"); + memory->create(field,local_array_size*3,"scafacos:field"); + + // set result vectors to zero + for ( int i = 0; i < local_array_size; ++i) + { + pot[i] = 0.0; + field[3*i] = field[3*i+1] = field[3*i+2] = 0.0; + } +} + +/* ---------------------------------------------------------------------- */ + +void FixScafacos::init_list(int id, NeighList *ptr) +{ +} + +/* ---------------------------------------------------------------------- */ + +void FixScafacos::setup(int vflag) +{ + post_force(vflag); +} + +/* ---------------------------------------------------------------------- */ + +void FixScafacos::min_setup(int vflag) +{ + post_force(vflag); +} + +/* ---------------------------------------------------------------------- */ + +void FixScafacos::setup_pre_reverse(int eflag, int vflag) +{ + pre_reverse(eflag,vflag); +} + +/* ---------------------------------------------------------------------- + integrate electronic degrees of freedom +------------------------------------------------------------------------- */ + +void FixScafacos::initial_integrate(int vflag) {} + +/* ---------------------------------------------------------------------- + store eflag, so can use it in post_force to tally per-atom energies +------------------------------------------------------------------------- */ + +void FixScafacos::pre_reverse(int eflag, int vflag) +{ + int eflag_caller = eflag; +} + +/* ---------------------------------------------------------------------- */ + +void FixScafacos::post_force(int vflag) +{ + + int nlocal; + + nlocal = atom->nlocal; + x = &atom->x[0][0]; + q = atom->q; + + // check if box has changed since the last call of fcs_tune, if yes, call fcs_tune + if (box_has_changed()) + { + setup_handle(); + // print out parameters within handle + if (rank == 0) + { + std::cout << " updated ScaFaCoS handle: " << std::endl; + fcs_print_parameters(fcs); + } + // call the tuning routine (needs to be redone, if critical system parameters should change) + result = fcs_tune(fcs,nlocal,x,q); + if (!check_result(result, rank)) return; + } + + /* + if (fmm_chosen && phantom_particle) + for (int i = 0; i < nlocal; ++i) + { + std::cout << rank << " " << i << " " << x[3*i] << " " << x[3*i+1] << " " << x[3*i+2] << " " << q[i] << std::endl; + } + */ + + // check if arrays for potentials and field are still large enough for the number of particles on process + if (nlocal > local_array_size) + { + // allocate arrays larger in order to avoid fast reallocation due to fluctuations + local_array_size = (int)(1.25 * (double)nlocal); + + // destroy old result arrays + memory->destroy(pot); + memory->destroy(field); + + // allocate result arrays + memory->create(pot,local_array_size,"scafacos:potential"); + memory->create(field,3*local_array_size,"scafacos:field"); + + } + + // set result vectors to zero + for ( int i = 0; i < nlocal; ++i) + { + pot[i] = 0.0; + field[3*i] = field[3*i+1] = field[3*i+2] = 0.0; + } + + // compute Coulomb + fcs_run(fcs, nlocal, x, q, field, pot); + if(!check_result(result,rank)) return; + + double E_coul_loc = 0.0; + // no reduction required (?) + //double E_coul = 0.0; + + for (int i = 0; i < atom->nlocal; ++i) + { + //std::cout << atom->f[i][0] << " " << field[3*i] << " " << q[i] << std::endl; + atom->f[i][0] += field[3*i] * q[i]; + atom->f[i][1] += field[3*i+1] * q[i]; + atom->f[i][2] += field[3*i+2] * q[i]; + E_coul_loc += 0.5 * q[i] * pot[i]; + } + + // not required (?) + // MPI_ALLREDUCE(&E_coul_loc, &E_coul, 1, MPI_DOUBLE, MPI_SUM, universe->uworld); + + force->pair->eng_coul += E_coul_loc; + +} + +/* ---------------------------------------------------------------------- */ + +void FixScafacos::min_post_force(int vflag) +{ + post_force(vflag); +} + +/* ---------------------------------------------------------------------- + integrate electronic degrees of freedom +------------------------------------------------------------------------- */ + +void FixScafacos::final_integrate() {} + +/* ---------------------------------------------------------------------- */ + +void FixScafacos::reset_dt() +{ + //dtv = update->dt; + //dtf = 0.5 * update->dt * force->ftm2v; +} + +/* ---------------------------------------------------------------------- + DFTB energy from LATTE +------------------------------------------------------------------------- */ + +double FixScafacos::compute_scalar() +{ +} + +/* ---------------------------------------------------------------------- + memory usage of local arrays +------------------------------------------------------------------------- */ + +double FixScafacos::memory_usage() +{ + double bytes = 0.0; + bytes += local_array_size * sizeof(double); + bytes += local_array_size * 3 * sizeof(double); + return bytes; +} + +/* ---------------------------------------------------------------------- + setup of ScaFaCoS handle with common parameters +------------------------------------------------------------------------- */ +void FixScafacos::setup_handle() +{ + // store periodicity + periodicity[0] = domain->xperiodic; + periodicity[1] = domain->yperiodic; + periodicity[2] = domain->zperiodic; + + // store offset of the system + offset[0] = domain->boundary[0][0]; + offset[1] = domain->boundary[1][0]; + offset[2] = domain->boundary[2][0]; + + // calculate box vectors + box_x[0] = domain->prd[0]; + box_x[1] = box_x[2] = 0.0; + + box_y[1] = domain->prd[1]; + box_y[0] = box_y[2] = 0.0; + + box_z[2] = domain->prd[2]; + box_z[1] = box_z[0] = 0.0; + + total_particles = atom->natoms; + + // TODO: for now disable short-range calculations within LAMMPS + near_field_flag = 0; + + // enter all parameters required to ScaFaCoS handle + result = fcs_set_box_a(fcs, box_x); + if (!check_result(result, rank)) return; + + result = fcs_set_box_b(fcs, box_y); + if (!check_result(result, rank)) return; + + result = fcs_set_box_c(fcs, box_z); + if (!check_result(result, rank)) return; + + result = fcs_set_box_origin(fcs, offset); + if (!check_result(result, rank)) return; + + result = fcs_set_periodicity(fcs, periodicity); + if (!check_result(result, rank)) return; + + result = fcs_set_near_field_flag(fcs, near_field_flag); + if (!check_result(result, rank)) return; + + result = fcs_set_total_particles(fcs, atom->natoms); + if (!check_result(result, rank)) return; +} + +/* ---------------------------------------------------------------------- + check if box parameters changed, requiring a new call to fcs_tune +------------------------------------------------------------------------- */ +bool FixScafacos::box_has_changed() +{ + bool changed = false; + + double n_periodicity[3]; + double n_offset[3]; + double n_box_x[3]; + double n_box_y[3]; + double n_box_z[3]; + + int n_total_particles; + + // store periodicity + n_periodicity[0] = domain->xperiodic; + n_periodicity[1] = domain->yperiodic; + n_periodicity[2] = domain->zperiodic; + + // store offset of the system + n_offset[0] = domain->boundary[0][0]; + n_offset[1] = domain->boundary[1][0]; + n_offset[2] = domain->boundary[2][0]; + + // calculate box vectors + n_box_x[0] = domain->prd[0]; + n_box_x[1] = n_box_x[2] = 0.0; + + n_box_y[1] = domain->prd[1]; + n_box_y[0] = n_box_y[2] = 0.0; + + n_box_z[2] = domain->prd[2]; + n_box_z[1] = n_box_z[0] = 0.0; + + n_total_particles = atom->natoms; + + changed = changed || + ( n_periodicity[0] != periodicity[0] ) || + ( n_periodicity[1] != periodicity[1] ) || + ( n_periodicity[2] != periodicity[2] ) || + ( n_offset[0] != offset[0] ) || + ( n_offset[1] != offset[1] ) || + ( n_offset[2] != offset[2] ) || + ( n_box_x[0] != box_x[0] ) || + ( n_box_x[1] != box_x[1] ) || + ( n_box_x[2] != box_x[2] ) || + ( n_box_y[0] != box_y[0] ) || + ( n_box_y[1] != box_y[1] ) || + ( n_box_y[2] != box_y[2] ) || + ( n_box_z[0] != box_z[0] ) || + ( n_box_z[1] != box_z[1] ) || + ( n_box_z[2] != box_z[2] ) || + ( n_total_particles != total_particles ); +/* + if (changed) + { + std::cout << rank << " " << "n_per_x : per_x" << n_periodicity[0] << " " << periodicity[0] << std::endl; + std::cout << rank << " " << "n_per_y : per_y" << n_periodicity[1] << " " << periodicity[1] << std::endl; + std::cout << rank << " " << "n_per_z : per_z" << n_periodicity[2] << " " << periodicity[2] << std::endl; + std::cout << rank << " " << "n_off_x : off_x" << n_offset[0] << " " << offset[0] << std::endl; + std::cout << rank << " " << "n_off_y : off_y" << n_offset[1] << " " << offset[1] << std::endl; + std::cout << rank << " " << "n_off_z : off_z" << n_offset[2] << " " << offset[2] << std::endl; + std::cout << rank << " " << "n_bx_x : bx_x" << n_box_x[0] << " " << box_x[0] << std::endl; + std::cout << rank << " " << "n_bx_y : bx_y" << n_box_x[1] << " " << box_x[1] << std::endl; + std::cout << rank << " " << "n_bx_z : bx_z" << n_box_x[2] << " " << box_x[2] << std::endl; + std::cout << rank << " " << "n_by_x : by_x" << n_box_y[0] << " " << box_y[0] << std::endl; + std::cout << rank << " " << "n_by_y : by_y" << n_box_y[1] << " " << box_y[1] << std::endl; + std::cout << rank << " " << "n_by_z : by_z" << n_box_y[2] << " " << box_y[2] << std::endl; + std::cout << rank << " " << "n_bz_x : bz_x" << n_box_z[0] << " " << box_z[0] << std::endl; + std::cout << rank << " " << "n_bz_y : bz_y" << n_box_z[1] << " " << box_z[1] << std::endl; + std::cout << rank << " " << "n_bz_z : bz_z" << n_box_z[2] << " " << box_z[2] << std::endl; + std::cout << rank << " " << "n_total : total" << n_total_particles << " " << total_particles << std::endl; + } +*/ + return changed; +} + + + +/* ---------------------------------------------------------------------- + check of ScaFaCoS result +------------------------------------------------------------------------- */ +bool FixScafacos::check_result(FCSResult result, int comm_rank) +{ + if (result) + { + std::cout << "ScaFaCoS ERROR: Caught error on task " << comm_rank << "!" << std::endl; + std::string err_msg; + std::stringstream ss; + + ss << fcs_result_get_function(result) << "\n" << fcs_result_get_message(result) << "\n"; + err_msg = ss.str(); + + error -> all(FLERR, err_msg.c_str()); + fcs_result_destroy(result); + } + return true; +} + diff --git a/src/SCAFACOS/fix_scafacos.h b/src/SCAFACOS/fix_scafacos.h new file mode 100644 index 0000000000..ffd4a94d32 --- /dev/null +++ b/src/SCAFACOS/fix_scafacos.h @@ -0,0 +1,164 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef FIX_CLASS + +FixStyle(scafacos,FixScafacos) + +#else + +#ifndef LMP_FIX_SCAFACOS_H +#define LMP_FIX_SCAFACOS_H + +#include "fix.h" +#include "fcs.h" +#include + +namespace LAMMPS_NS { + +class FixScafacos : public Fix { + public: + FixScafacos(class LAMMPS *, int, char **); + virtual ~FixScafacos(); + int setmask(); + void init(); + void init_list(int, NeighList*); + void setup(int); + void min_setup(int); + void setup_pre_reverse(int, int); + void initial_integrate(int); + void pre_reverse(int, int); + void post_force(int); + void min_post_force(int); + void final_integrate(); + void reset_dt(); + double compute_scalar(); + double memory_usage(); + + protected: + std::string method; + + // MPI rank + int rank; + + // source arrays for positions and charges + double *x, *q; + // result arrays for potentials and field + double *pot, *field; + + // box vectors for each dimension + fcs_float box_x[3], box_y[3], box_z[3]; + // offset of the box from the origin + fcs_float offset[3]; + + // periodicity of the system + fcs_int periodicity[3]; + + // ScaFaCoS handle + FCS fcs; + + // ScaFaCoS result variable + FCSResult result; + + // function to check results + bool check_result(FCSResult, int); + + // function to set up handle with common parameters + void setup_handle(); + + // function to check if the box parameters changed, so that a new tuning step is required + bool box_has_changed(); + + // store total number of particles (to check if tune needs to be called again) + fcs_int total_particles; + + // store number of local particles (to be able to readjust the size of result arrays, when needed) + int local_array_size; + + // should the near field calculations be computed by LAMMPS? + fcs_int near_field_flag; + + // type of accuracy chosen (if customized) + fcs_int tolerance_type; + + // value of tolerance + fcs_float tolerance_value; + + // is tolerance set? + bool tolerance_set; + + // check if fmm is chosen (ghost particles, since the implementation needs at least 1 particle on each process!) + bool fmm_chosen; + + // FMM: fmm particle array size + int fmm_array_size; +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Must use units metal with fix latte command + +UNDOCUMENTED + +E: Fix latte currently runs only in serial + +UNDOCUMENTED + +E: LAMMPS is linked against incompatible LATTE library + +UNDOCUMENTED + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: Fix latte does not yet support a LAMMPS calculation of a Coulomb potential + +UNDOCUMENTED + +E: Could not find fix latte compute ID + +UNDOCUMENTED + +E: Fix latte compute ID does not compute pe/atom + +UNDOCUMENTED + +E: Fix latte requires 3d problem + +UNDOCUMENTED + +E: Fix latte cannot compute Coulomb potential + +UNDOCUMENTED + +E: Fix latte requires 3d simulation + +UNDOCUMENTED + +W: Fix latte should come after all other integration fixes + +UNDOCUMENTED + +E: Internal LATTE problem + +UNDOCUMENTED + +*/ From 400ae7226765d17234fb2e2c57191e2fc5b21fb8 Mon Sep 17 00:00:00 2001 From: Rene Halver Date: Mon, 9 Jul 2018 13:18:28 -0600 Subject: [PATCH 036/302] added tolerance to the example --- examples/scafacos/in.scafacos | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/examples/scafacos/in.scafacos b/examples/scafacos/in.scafacos index a2849583f5..2a7e830110 100644 --- a/examples/scafacos/in.scafacos +++ b/examples/scafacos/in.scafacos @@ -5,8 +5,6 @@ atom_style full read_data data.NaCl -# need both mass settings due to hybrid atom style - velocity all set 0.0 0.0 0.0 mom no pair_style zero 1.0 @@ -15,7 +13,8 @@ pair_coeff * * neighbor 1.0 bin neigh_modify delay 0 -fix 1 all scafacos fmm +# using the fmm solver with a tolerance in energy of 10^-3 +fix 1 all scafacos fmm energy 0.001 timestep 0.005 From 4743bb3c30c207b1a9b51ed821e5b96ceb9c4080 Mon Sep 17 00:00:00 2001 From: Rene Halver Date: Mon, 9 Jul 2018 13:35:46 -0600 Subject: [PATCH 037/302] rename of the ScaFaCoS package --- cmake/CMakeLists.txt | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index a335a441da..de3f54b9e1 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -119,7 +119,7 @@ option(ENABLE_ALL "Build all default packages" OFF) set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GRANULAR KSPACE MANYBODY MC MEAM MISC MOLECULE PERI QEQ REAX REPLICA RIGID SHOCK SNAP SRD) -set(OTHER_PACKAGES KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE SCAFACOS +set(OTHER_PACKAGES KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE USER-SCAFACOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-MESO USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD USER-LB USER-MANIFOLD USER-MEAMC USER-MGPT USER-MISC @@ -150,11 +150,11 @@ pkg_depends(CORESHELL KSPACE) ###################################################### # packages with special compiler needs or external libs ###################################################### -if(PKG_REAX OR PKG_MEAM OR PKG_USER-QUIP OR PKG_USER-QMMM OR PKG_LATTE OR PKG_SCAFACOS) +if(PKG_REAX OR PKG_MEAM OR PKG_USER-QUIP OR PKG_USER-QMMM OR PKG_LATTE OR PKG_USER-SCAFACOS) enable_language(Fortran) endif() -if(PKG_MEAM OR PKG_USER-H5MD OR PKG_USER-QMMM OR PKG_SCAFACOS) +if(PKG_MEAM OR PKG_USER-H5MD OR PKG_USER-QMMM OR PKG_USER-SCAFACOS) enable_language(C) endif() From dbfea0e6170c4a894fa65a086503b33c9944cc4c Mon Sep 17 00:00:00 2001 From: Rene Halver Date: Mon, 9 Jul 2018 13:53:31 -0600 Subject: [PATCH 038/302] update folder structure to comply to LAMMPS contribution rules --- cmake/CMakeLists.txt | 2 +- src/{SCAFACOS => USER-SCAFACOS}/Install.sh | 0 src/{SCAFACOS => USER-SCAFACOS}/fix_scafacos.cpp | 0 src/{SCAFACOS => USER-SCAFACOS}/fix_scafacos.h | 0 4 files changed, 1 insertion(+), 1 deletion(-) rename src/{SCAFACOS => USER-SCAFACOS}/Install.sh (100%) rename src/{SCAFACOS => USER-SCAFACOS}/fix_scafacos.cpp (100%) rename src/{SCAFACOS => USER-SCAFACOS}/fix_scafacos.h (100%) diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index 05e4964e0b..afb93b9d1b 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -348,7 +348,7 @@ if(PKG_LATTE) list(APPEND LAMMPS_LINK_LIBS ${LATTE_LIBRARIES} ${LAPACK_LIBRARIES}) endif() -if(PKG_SCAFACOS) +if(PKG_USER-SCAFACOS) FIND_PACKAGE(PkgConfig) PKG_CHECK_MODULES(SCAFACOS scafacos) include_directories(${SCAFACOS_INCLUDE_DIRS}) diff --git a/src/SCAFACOS/Install.sh b/src/USER-SCAFACOS/Install.sh similarity index 100% rename from src/SCAFACOS/Install.sh rename to src/USER-SCAFACOS/Install.sh diff --git a/src/SCAFACOS/fix_scafacos.cpp b/src/USER-SCAFACOS/fix_scafacos.cpp similarity index 100% rename from src/SCAFACOS/fix_scafacos.cpp rename to src/USER-SCAFACOS/fix_scafacos.cpp diff --git a/src/SCAFACOS/fix_scafacos.h b/src/USER-SCAFACOS/fix_scafacos.h similarity index 100% rename from src/SCAFACOS/fix_scafacos.h rename to src/USER-SCAFACOS/fix_scafacos.h From 4c4d8372e45ca2ca16dab99b32a34fd8e8e94ecf Mon Sep 17 00:00:00 2001 From: Rene Halver Date: Mon, 9 Jul 2018 14:01:06 -0600 Subject: [PATCH 039/302] removed C++ std::cout I/O and replaced it with printf --- src/USER-SCAFACOS/fix_scafacos.cpp | 52 ++++++++++++++++-------------- 1 file changed, 27 insertions(+), 25 deletions(-) diff --git a/src/USER-SCAFACOS/fix_scafacos.cpp b/src/USER-SCAFACOS/fix_scafacos.cpp index f888747047..40d2556cdd 100644 --- a/src/USER-SCAFACOS/fix_scafacos.cpp +++ b/src/USER-SCAFACOS/fix_scafacos.cpp @@ -31,7 +31,6 @@ #include "error.h" // ScaFaCoS library -#include #include #include #include "fcs.h" @@ -67,28 +66,28 @@ FixScafacos::FixScafacos(LAMMPS *lmp, int narg, char **arg) : // check if tolerance option is set if (strcmp(arg[arg_index],"tolerance") == 0) { - tolerance_set = true; - ++arg_index; - if (strcmp(arg[arg_index],"energy") == 0) - tolerance_type = FCS_TOLERANCE_TYPE_ENERGY; - else if (strcmp(arg[arg_index],"energy_rel") == 0) - tolerance_type = FCS_TOLERANCE_TYPE_ENERGY_REL; - else if (strcmp(arg[arg_index],"field") == 0) - tolerance_type = FCS_TOLERANCE_TYPE_FIELD; - else if (strcmp(arg[arg_index],"field_rel") == 0) - tolerance_type = FCS_TOLERANCE_TYPE_FIELD_REL; - else if (strcmp(arg[arg_index],"potential") == 0) - tolerance_type = FCS_TOLERANCE_TYPE_POTENTIAL; - else if (strcmp(arg[arg_index],"potential_rel") == 0) - tolerance_type = FCS_TOLERANCE_TYPE_POTENTIAL_REL; - else - error->all(FLERR,"Illegal fix scafacos command"); - ++arg_index; - tolerance_value = atof(arg[arg_index]); - ++arg_index; + tolerance_set = true; + ++arg_index; + if (strcmp(arg[arg_index],"energy") == 0) + tolerance_type = FCS_TOLERANCE_TYPE_ENERGY; + else if (strcmp(arg[arg_index],"energy_rel") == 0) + tolerance_type = FCS_TOLERANCE_TYPE_ENERGY_REL; + else if (strcmp(arg[arg_index],"field") == 0) + tolerance_type = FCS_TOLERANCE_TYPE_FIELD; + else if (strcmp(arg[arg_index],"field_rel") == 0) + tolerance_type = FCS_TOLERANCE_TYPE_FIELD_REL; + else if (strcmp(arg[arg_index],"potential") == 0) + tolerance_type = FCS_TOLERANCE_TYPE_POTENTIAL; + else if (strcmp(arg[arg_index],"potential_rel") == 0) + tolerance_type = FCS_TOLERANCE_TYPE_POTENTIAL_REL; + else + error->all(FLERR,"Illegal fix scafacos command"); + ++arg_index; + tolerance_value = atof(arg[arg_index]); + ++arg_index; } else - error->all(FLERR,"Illegal fix scafacos command"); + error->all(FLERR,"Illegal fix scafacos command"); } } @@ -226,12 +225,14 @@ void FixScafacos::post_force(int vflag) if (box_has_changed()) { setup_handle(); - // print out parameters within handle + // print out parameters within handle TODO: should be done in C style + /* if (rank == 0) { - std::cout << " updated ScaFaCoS handle: " << std::endl; - fcs_print_parameters(fcs); + std::cout << " updated ScaFaCoS handle: " << std::endl; + fcs_print_parameters(fcs); } + */ // call the tuning routine (needs to be redone, if critical system parameters should change) result = fcs_tune(fcs,nlocal,x,q); if (!check_result(result, rank)) return; @@ -473,7 +474,8 @@ bool FixScafacos::check_result(FCSResult result, int comm_rank) { if (result) { - std::cout << "ScaFaCoS ERROR: Caught error on task " << comm_rank << "!" << std::endl; + printf("ScaFaCoS Error: Caught error on task %d.\n", comm_rank); + //std::cout << "ScaFaCoS ERROR: Caught error on task " << comm_rank << "!" << std::endl; std::string err_msg; std::stringstream ss; From dd38318f5f01e7efe1aeee229b89f0b113508f50 Mon Sep 17 00:00:00 2001 From: Rene Halver Date: Mon, 9 Jul 2018 14:12:06 -0600 Subject: [PATCH 040/302] adjustments to indention and line lengths (<=80 now) --- src/USER-SCAFACOS/fix_scafacos.cpp | 118 ++++++++++------------------- 1 file changed, 41 insertions(+), 77 deletions(-) diff --git a/src/USER-SCAFACOS/fix_scafacos.cpp b/src/USER-SCAFACOS/fix_scafacos.cpp index 40d2556cdd..6b89348a16 100644 --- a/src/USER-SCAFACOS/fix_scafacos.cpp +++ b/src/USER-SCAFACOS/fix_scafacos.cpp @@ -54,8 +54,6 @@ FixScafacos::FixScafacos(LAMMPS *lmp, int narg, char **arg) : // read method from fix input method = arg[3]; - // check if fmm method was chosen - fmm_chosen = !strcmp(method.c_str(),"fmm"); int arg_index = 4; @@ -149,23 +147,18 @@ void FixScafacos::init() // print out parameters within handle if (rank == 0) fcs_print_parameters(fcs); - // call the tuning routine (needs to be redone, if critical system parameters should change) + // call the tuning routine (needs to be redone, if critical system + // parameters should change) result = fcs_tune(fcs,nlocal,x,q); if (!check_result(result, rank)) return; - // allocate arrays larger in order to avoid fast reallocation due to fluctuations + // allocate arrays larger in order to avoid fast + // reallocation due to fluctuations local_array_size = (int)(1.25 * (double)nlocal); // allocate new result arrays memory->create(pot,local_array_size,"scafacos:potential"); memory->create(field,local_array_size*3,"scafacos:field"); - - // set result vectors to zero - for ( int i = 0; i < local_array_size; ++i) - { - pot[i] = 0.0; - field[3*i] = field[3*i+1] = field[3*i+2] = 0.0; - } } /* ---------------------------------------------------------------------- */ @@ -221,10 +214,12 @@ void FixScafacos::post_force(int vflag) x = &atom->x[0][0]; q = atom->q; - // check if box has changed since the last call of fcs_tune, if yes, call fcs_tune + // check if box has changed since the last call of fcs_tune, + // if it has, call fcs_tune if (box_has_changed()) { setup_handle(); + // print out parameters within handle TODO: should be done in C style /* if (rank == 0) @@ -233,23 +228,19 @@ void FixScafacos::post_force(int vflag) fcs_print_parameters(fcs); } */ - // call the tuning routine (needs to be redone, if critical system parameters should change) + + // call the tuning routine (needs to be redone, if critical + // system parameters should change) result = fcs_tune(fcs,nlocal,x,q); if (!check_result(result, rank)) return; } - /* - if (fmm_chosen && phantom_particle) - for (int i = 0; i < nlocal; ++i) - { - std::cout << rank << " " << i << " " << x[3*i] << " " << x[3*i+1] << " " << x[3*i+2] << " " << q[i] << std::endl; - } - */ - - // check if arrays for potentials and field are still large enough for the number of particles on process + // check if arrays for potentials and field are still large enough + // for the number of particles on process if (nlocal > local_array_size) { - // allocate arrays larger in order to avoid fast reallocation due to fluctuations + // allocate arrays larger in order to avoid fast + // reallocation due to fluctuations local_array_size = (int)(1.25 * (double)nlocal); // destroy old result arrays @@ -274,8 +265,6 @@ void FixScafacos::post_force(int vflag) if(!check_result(result,rank)) return; double E_coul_loc = 0.0; - // no reduction required (?) - //double E_coul = 0.0; for (int i = 0; i < atom->nlocal; ++i) { @@ -286,9 +275,6 @@ void FixScafacos::post_force(int vflag) E_coul_loc += 0.5 * q[i] * pot[i]; } - // not required (?) - // MPI_ALLREDUCE(&E_coul_loc, &E_coul, 1, MPI_DOUBLE, MPI_SUM, universe->uworld); - force->pair->eng_coul += E_coul_loc; } @@ -392,39 +378,39 @@ void FixScafacos::setup_handle() ------------------------------------------------------------------------- */ bool FixScafacos::box_has_changed() { - bool changed = false; + bool changed = false; - double n_periodicity[3]; - double n_offset[3]; - double n_box_x[3]; - double n_box_y[3]; - double n_box_z[3]; + double n_periodicity[3]; + double n_offset[3]; + double n_box_x[3]; + double n_box_y[3]; + double n_box_z[3]; - int n_total_particles; + int n_total_particles; - // store periodicity - n_periodicity[0] = domain->xperiodic; - n_periodicity[1] = domain->yperiodic; - n_periodicity[2] = domain->zperiodic; + // store periodicity + n_periodicity[0] = domain->xperiodic; + n_periodicity[1] = domain->yperiodic; + n_periodicity[2] = domain->zperiodic; - // store offset of the system - n_offset[0] = domain->boundary[0][0]; - n_offset[1] = domain->boundary[1][0]; - n_offset[2] = domain->boundary[2][0]; + // store offset of the system + n_offset[0] = domain->boundary[0][0]; + n_offset[1] = domain->boundary[1][0]; + n_offset[2] = domain->boundary[2][0]; - // calculate box vectors - n_box_x[0] = domain->prd[0]; - n_box_x[1] = n_box_x[2] = 0.0; + // calculate box vectors + n_box_x[0] = domain->prd[0]; + n_box_x[1] = n_box_x[2] = 0.0; - n_box_y[1] = domain->prd[1]; - n_box_y[0] = n_box_y[2] = 0.0; + n_box_y[1] = domain->prd[1]; + n_box_y[0] = n_box_y[2] = 0.0; - n_box_z[2] = domain->prd[2]; - n_box_z[1] = n_box_z[0] = 0.0; + n_box_z[2] = domain->prd[2]; + n_box_z[1] = n_box_z[0] = 0.0; - n_total_particles = atom->natoms; + n_total_particles = atom->natoms; - changed = changed || + changed = changed || ( n_periodicity[0] != periodicity[0] ) || ( n_periodicity[1] != periodicity[1] ) || ( n_periodicity[2] != periodicity[2] ) || @@ -441,28 +427,7 @@ bool FixScafacos::box_has_changed() ( n_box_z[1] != box_z[1] ) || ( n_box_z[2] != box_z[2] ) || ( n_total_particles != total_particles ); -/* - if (changed) - { - std::cout << rank << " " << "n_per_x : per_x" << n_periodicity[0] << " " << periodicity[0] << std::endl; - std::cout << rank << " " << "n_per_y : per_y" << n_periodicity[1] << " " << periodicity[1] << std::endl; - std::cout << rank << " " << "n_per_z : per_z" << n_periodicity[2] << " " << periodicity[2] << std::endl; - std::cout << rank << " " << "n_off_x : off_x" << n_offset[0] << " " << offset[0] << std::endl; - std::cout << rank << " " << "n_off_y : off_y" << n_offset[1] << " " << offset[1] << std::endl; - std::cout << rank << " " << "n_off_z : off_z" << n_offset[2] << " " << offset[2] << std::endl; - std::cout << rank << " " << "n_bx_x : bx_x" << n_box_x[0] << " " << box_x[0] << std::endl; - std::cout << rank << " " << "n_bx_y : bx_y" << n_box_x[1] << " " << box_x[1] << std::endl; - std::cout << rank << " " << "n_bx_z : bx_z" << n_box_x[2] << " " << box_x[2] << std::endl; - std::cout << rank << " " << "n_by_x : by_x" << n_box_y[0] << " " << box_y[0] << std::endl; - std::cout << rank << " " << "n_by_y : by_y" << n_box_y[1] << " " << box_y[1] << std::endl; - std::cout << rank << " " << "n_by_z : by_z" << n_box_y[2] << " " << box_y[2] << std::endl; - std::cout << rank << " " << "n_bz_x : bz_x" << n_box_z[0] << " " << box_z[0] << std::endl; - std::cout << rank << " " << "n_bz_y : bz_y" << n_box_z[1] << " " << box_z[1] << std::endl; - std::cout << rank << " " << "n_bz_z : bz_z" << n_box_z[2] << " " << box_z[2] << std::endl; - std::cout << rank << " " << "n_total : total" << n_total_particles << " " << total_particles << std::endl; - } -*/ - return changed; + return changed; } @@ -475,11 +440,11 @@ bool FixScafacos::check_result(FCSResult result, int comm_rank) if (result) { printf("ScaFaCoS Error: Caught error on task %d.\n", comm_rank); - //std::cout << "ScaFaCoS ERROR: Caught error on task " << comm_rank << "!" << std::endl; std::string err_msg; std::stringstream ss; - ss << fcs_result_get_function(result) << "\n" << fcs_result_get_message(result) << "\n"; + ss << fcs_result_get_function(result) << "\n" + << fcs_result_get_message(result) << "\n"; err_msg = ss.str(); error -> all(FLERR, err_msg.c_str()); @@ -487,4 +452,3 @@ bool FixScafacos::check_result(FCSResult result, int comm_rank) } return true; } - From ee98d026dcbf8b0884b012b06a744b4a807777e9 Mon Sep 17 00:00:00 2001 From: Rene Halver Date: Mon, 9 Jul 2018 14:28:25 -0600 Subject: [PATCH 041/302] preliminary documentation added (to be improved) --- doc/src/fix_scafacos.txt | 44 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 doc/src/fix_scafacos.txt diff --git a/doc/src/fix_scafacos.txt b/doc/src/fix_scafacos.txt new file mode 100644 index 0000000000..1a65ed0c5e --- /dev/null +++ b/doc/src/fix_scafacos.txt @@ -0,0 +1,44 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +fix scafacos command :h3 + +[Syntax:] + +fix ID group-ID scafacos solver tol_type tolerance :pre + +ID, group-ID are documented in "fix"_fix.html command +scafacos = style name of this fix command +solver = NULL or name of solver for electro-statics computation :ul +tol_type = NULL or one of (energy, energy_rel, field, field_rel, potential, potential_rel) +tolerance = only of tol_type is given, value of tolerance + +[Examples:] + +fix 1 all scafacos fmm +fix 1 all scafacos p3m field 0.001 + +[Description:] + +This fix style is a wrapper for the Coulomb solver library ScaFaCoS, +which provides a selection of different solvers for the compuation +of electro-static interaction. If you download and build ScaFaCoS, +it can be called as libray by LAMMPS via this fix, which allows the +selection of a solver as well as setting the tolerance of a chosen +parameter (if compatible with the chosen solver). + +ScaFaCoS was developed by a consortium of German research facilities +with a BMBF (German Ministry of Science and Education) funded project +in 2009-2012. Participants of the consortium were the Universities of +Bonn, Chemnitz, Stuttgart, and Wuppertal as well as the +Forschungszentrum Juelich. + +The library is available at "http://scafacos.de" or can be cloned +from the git-repository "git://github.com/scafacos/scafacos.git". + +:line From 55980294f1aaf712b841ad4016bb5eea993ea1f6 Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Mon, 9 Jul 2018 18:47:17 -0600 Subject: [PATCH 042/302] Fix issues in atom_vec_sphere_kokkos --- src/KOKKOS/atom_vec_sphere_kokkos.cpp | 30 +++++++++++++-------------- 1 file changed, 15 insertions(+), 15 deletions(-) diff --git a/src/KOKKOS/atom_vec_sphere_kokkos.cpp b/src/KOKKOS/atom_vec_sphere_kokkos.cpp index d34e2f9c61..3facc7b4ce 100644 --- a/src/KOKKOS/atom_vec_sphere_kokkos.cpp +++ b/src/KOKKOS/atom_vec_sphere_kokkos.cpp @@ -1005,9 +1005,9 @@ struct AtomVecSphereKokkos_PackBorder { _buf(i,1) = _x(j,1) + _dy; _buf(i,2) = _x(j,2) + _dz; } - _buf(i,3) = _tag(j); - _buf(i,4) = _type(j); - _buf(i,5) = _mask(j); + _buf(i,3) = d_ubuf(_tag(j)).d; + _buf(i,4) = d_ubuf(_type(j)).d; + _buf(i,5) = d_ubuf(_mask(j)).d; _buf(i,6) = _radius(j); _buf(i,7) = _rmass(j); } @@ -1066,7 +1066,7 @@ int AtomVecSphereKokkos::pack_border_kokkos(int n, DAT::tdual_int_2d k_sendlist, Kokkos::parallel_for(n,f); } } - return n*6; + return n*8; } /* ---------------------------------------------------------------------- */ @@ -1264,9 +1264,9 @@ struct AtomVecSphereKokkos_UnpackBorder { _x(i+_first,0) = _buf(i,0); _x(i+_first,1) = _buf(i,1); _x(i+_first,2) = _buf(i,2); - _tag(i+_first) = static_cast (_buf(i,3)); - _type(i+_first) = static_cast (_buf(i,4)); - _mask(i+_first) = static_cast (_buf(i,5)); + _tag(i+_first) = static_cast (d_ubuf(_buf(i,3)).i); + _type(i+_first) = static_cast (d_ubuf(_buf(i,4)).i); + _mask(i+_first) = static_cast (d_ubuf(_buf(i,5)).i); _radius(i+_first) = _buf(i,6); _rmass(i+_first) = _buf(i,7); } @@ -1440,10 +1440,10 @@ struct AtomVecSphereKokkos_PackExchangeFunctor { _buf(mysend,4) = _v(i,0); _buf(mysend,5) = _v(i,1); _buf(mysend,6) = _v(i,2); - _buf(mysend,7) = _tag[i]; - _buf(mysend,8) = _type[i]; - _buf(mysend,9) = _mask[i]; - _buf(mysend,10) = _image[i]; + _buf(mysend,7) = d_ubuf(_tag[i]).d; + _buf(mysend,8) = d_ubuf(_type[i]).d; + _buf(mysend,9) = d_ubuf(_mask[i]).d; + _buf(mysend,10) = d_ubuf(_image[i]).d; _buf(mysend,11) = _radius[i]; _buf(mysend,12) = _rmass[i]; _buf(mysend,13) = _omega(i,0); @@ -1584,10 +1584,10 @@ struct AtomVecSphereKokkos_UnpackExchangeFunctor { _v(i,0) = _buf(myrecv,4); _v(i,1) = _buf(myrecv,5); _v(i,2) = _buf(myrecv,6); - _tag[i] = _buf(myrecv,7); - _type[i] = _buf(myrecv,8); - _mask[i] = _buf(myrecv,9); - _image[i] = _buf(myrecv,10); + _tag[i] = (tagint) d_ubuf(_buf(myrecv,7)).i; + _type[i] = (int) d_ubuf(_buf(myrecv,8)).i; + _mask[i] = (int) d_ubuf(_buf(myrecv,9)).i; + _image[i] = (imageint) d_ubuf(_buf(myrecv,10)).i; _radius[i] = _buf(myrecv,11); _rmass[i] = _buf(myrecv,12); _omega(i,0) = _buf(myrecv,13); From ca8b109a1c447b2551723ad08af56086d2db7653 Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Tue, 10 Jul 2018 08:59:06 -0600 Subject: [PATCH 043/302] Fix issues with rmass in KOKKOS package --- src/KOKKOS/fix_langevin_kokkos.cpp | 34 +++++++++++------------ src/KOKKOS/fix_langevin_kokkos.h | 2 +- src/KOKKOS/fix_nh_kokkos.cpp | 4 +-- src/KOKKOS/fix_nh_kokkos.h | 4 +-- src/KOKKOS/fix_nve_kokkos.cpp | 8 +++--- src/KOKKOS/fix_nve_kokkos.h | 2 +- src/KOKKOS/pair_dpd_fdt_energy_kokkos.cpp | 4 +-- src/KOKKOS/pair_dpd_fdt_energy_kokkos.h | 2 +- 8 files changed, 30 insertions(+), 30 deletions(-) diff --git a/src/KOKKOS/fix_langevin_kokkos.cpp b/src/KOKKOS/fix_langevin_kokkos.cpp index 24d505e08d..8c403d3325 100644 --- a/src/KOKKOS/fix_langevin_kokkos.cpp +++ b/src/KOKKOS/fix_langevin_kokkos.cpp @@ -133,7 +133,7 @@ void FixLangevinKokkos::post_force(int vflag) { // sync the device views which might have been modified on host atomKK->sync(execution_space,datamask_read); - rmass = atomKK->rmass; + rmass = atomKK->k_rmass.view(); f = atomKK->k_f.template view(); v = atomKK->k_v.template view(); type = atomKK->k_type.template view(); @@ -191,7 +191,7 @@ void FixLangevinKokkos::post_force(int vflag) if (gjfflag) if (tallyflag) if (tbiasflag == BIAS) - if (rmass) + if (rmass.data()) if (zeroflag) { FixLangevinKokkosPostForceFunctor post_functor(this); Kokkos::parallel_reduce(nlocal,post_functor,s_fsum); @@ -210,7 +210,7 @@ void FixLangevinKokkos::post_force(int vflag) Kokkos::parallel_for(nlocal,post_functor); } else - if (rmass) + if (rmass.data()) if (zeroflag) { FixLangevinKokkosPostForceFunctor post_functor(this); Kokkos::parallel_reduce(nlocal,post_functor,s_fsum); @@ -230,7 +230,7 @@ void FixLangevinKokkos::post_force(int vflag) } else if (tbiasflag == BIAS) - if (rmass) + if (rmass.data()) if (zeroflag) { FixLangevinKokkosPostForceFunctor post_functor(this); Kokkos::parallel_reduce(nlocal,post_functor,s_fsum); @@ -249,7 +249,7 @@ void FixLangevinKokkos::post_force(int vflag) Kokkos::parallel_for(nlocal,post_functor); } else - if (rmass) + if (rmass.data()) if (zeroflag) { FixLangevinKokkosPostForceFunctor post_functor(this); Kokkos::parallel_reduce(nlocal,post_functor,s_fsum); @@ -270,7 +270,7 @@ void FixLangevinKokkos::post_force(int vflag) else if (tallyflag) if (tbiasflag == BIAS) - if (rmass) + if (rmass.data()) if (zeroflag) { FixLangevinKokkosPostForceFunctor post_functor(this); Kokkos::parallel_reduce(nlocal,post_functor,s_fsum); @@ -289,7 +289,7 @@ void FixLangevinKokkos::post_force(int vflag) Kokkos::parallel_for(nlocal,post_functor); } else - if (rmass) + if (rmass.data()) if (zeroflag) { FixLangevinKokkosPostForceFunctor post_functor(this); Kokkos::parallel_reduce(nlocal,post_functor,s_fsum); @@ -309,7 +309,7 @@ void FixLangevinKokkos::post_force(int vflag) } else if (tbiasflag == BIAS) - if (rmass) + if (rmass.data()) if (zeroflag) { FixLangevinKokkosPostForceFunctor post_functor(this); Kokkos::parallel_reduce(nlocal,post_functor,s_fsum); @@ -328,7 +328,7 @@ void FixLangevinKokkos::post_force(int vflag) Kokkos::parallel_for(nlocal,post_functor); } else - if (rmass) + if (rmass.data()) if (zeroflag) { FixLangevinKokkosPostForceFunctor post_functor(this); Kokkos::parallel_reduce(nlocal,post_functor,s_fsum); @@ -350,7 +350,7 @@ void FixLangevinKokkos::post_force(int vflag) if (gjfflag) if (tallyflag) if (tbiasflag == BIAS) - if (rmass) + if (rmass.data()) if (zeroflag) { FixLangevinKokkosPostForceFunctor post_functor(this); Kokkos::parallel_reduce(nlocal,post_functor,s_fsum); @@ -369,7 +369,7 @@ void FixLangevinKokkos::post_force(int vflag) Kokkos::parallel_for(nlocal,post_functor); } else - if (rmass) + if (rmass.data()) if (zeroflag) { FixLangevinKokkosPostForceFunctor post_functor(this); Kokkos::parallel_reduce(nlocal,post_functor,s_fsum); @@ -389,7 +389,7 @@ void FixLangevinKokkos::post_force(int vflag) } else if (tbiasflag == BIAS) - if (rmass) + if (rmass.data()) if (zeroflag) { FixLangevinKokkosPostForceFunctor post_functor(this); Kokkos::parallel_reduce(nlocal,post_functor,s_fsum); @@ -408,7 +408,7 @@ void FixLangevinKokkos::post_force(int vflag) Kokkos::parallel_for(nlocal,post_functor); } else - if (rmass) + if (rmass.data()) if (zeroflag) { FixLangevinKokkosPostForceFunctor post_functor(this); Kokkos::parallel_reduce(nlocal,post_functor,s_fsum); @@ -429,7 +429,7 @@ void FixLangevinKokkos::post_force(int vflag) else if (tallyflag) if (tbiasflag == BIAS) - if (rmass) + if (rmass.data()) if (zeroflag) { FixLangevinKokkosPostForceFunctor post_functor(this); Kokkos::parallel_reduce(nlocal,post_functor,s_fsum); @@ -448,7 +448,7 @@ void FixLangevinKokkos::post_force(int vflag) Kokkos::parallel_for(nlocal,post_functor); } else - if (rmass) + if (rmass.data()) if (zeroflag) { FixLangevinKokkosPostForceFunctor post_functor(this); Kokkos::parallel_reduce(nlocal,post_functor,s_fsum); @@ -468,7 +468,7 @@ void FixLangevinKokkos::post_force(int vflag) } else if (tbiasflag == BIAS) - if (rmass) + if (rmass.data()) if (zeroflag) { FixLangevinKokkosPostForceFunctor post_functor(this); Kokkos::parallel_reduce(nlocal,post_functor,s_fsum); @@ -487,7 +487,7 @@ void FixLangevinKokkos::post_force(int vflag) Kokkos::parallel_for(nlocal,post_functor); } else - if (rmass) + if (rmass.data()) if (zeroflag) { FixLangevinKokkosPostForceFunctor post_functor(this); Kokkos::parallel_reduce(nlocal,post_functor,s_fsum); diff --git a/src/KOKKOS/fix_langevin_kokkos.h b/src/KOKKOS/fix_langevin_kokkos.h index a9d015f6a1..140fea81d6 100644 --- a/src/KOKKOS/fix_langevin_kokkos.h +++ b/src/KOKKOS/fix_langevin_kokkos.h @@ -93,7 +93,7 @@ namespace LAMMPS_NS { private: class CommKokkos *commKK; - double *rmass; + typename ArrayTypes::t_float_1d rmass; typename ArrayTypes::tdual_double_2d k_franprev; typename ArrayTypes::t_double_2d d_franprev; HAT::t_double_2d h_franprev; diff --git a/src/KOKKOS/fix_nh_kokkos.cpp b/src/KOKKOS/fix_nh_kokkos.cpp index 679690ea82..43b1845f35 100644 --- a/src/KOKKOS/fix_nh_kokkos.cpp +++ b/src/KOKKOS/fix_nh_kokkos.cpp @@ -537,7 +537,7 @@ void FixNHKokkos::nve_v() v = atomKK->k_v.view(); f = atomKK->k_f.view(); - rmass = atomKK->rmass; + rmass = atomKK->k_rmass.view(); mass = atomKK->k_mass.view(); type = atomKK->k_type.view(); mask = atomKK->k_mask.view(); @@ -545,7 +545,7 @@ void FixNHKokkos::nve_v() if (igroup == atomKK->firstgroup) nlocal = atomKK->nfirst; copymode = 1; - if (rmass) + if (rmass.data()) Kokkos::parallel_for(Kokkos::RangePolicy >(0,nlocal),*this); else Kokkos::parallel_for(Kokkos::RangePolicy >(0,nlocal),*this); diff --git a/src/KOKKOS/fix_nh_kokkos.h b/src/KOKKOS/fix_nh_kokkos.h index a625cdbc20..ae18bd6dbd 100644 --- a/src/KOKKOS/fix_nh_kokkos.h +++ b/src/KOKKOS/fix_nh_kokkos.h @@ -71,8 +71,8 @@ class FixNHKokkos : public FixNH { typename ArrayTypes::t_x_array x; typename ArrayTypes::t_v_array v; typename ArrayTypes::t_f_array_const f; - double *rmass; - typename ArrayTypes::t_float_1d_randomread mass; + typename ArrayTypes::t_float_1d rmass; + typename ArrayTypes::t_float_1d mass; typename ArrayTypes::t_int_1d type; typename ArrayTypes::t_int_1d mask; }; diff --git a/src/KOKKOS/fix_nve_kokkos.cpp b/src/KOKKOS/fix_nve_kokkos.cpp index cb3eadcd90..621f16f420 100644 --- a/src/KOKKOS/fix_nve_kokkos.cpp +++ b/src/KOKKOS/fix_nve_kokkos.cpp @@ -62,14 +62,14 @@ void FixNVEKokkos::initial_integrate(int vflag) x = atomKK->k_x.view(); v = atomKK->k_v.view(); f = atomKK->k_f.view(); - rmass = atomKK->rmass; + rmass = atomKK->k_rmass.view(); mass = atomKK->k_mass.view(); type = atomKK->k_type.view(); mask = atomKK->k_mask.view(); int nlocal = atomKK->nlocal; if (igroup == atomKK->firstgroup) nlocal = atomKK->nfirst; - if (rmass) { + if (rmass.data()) { FixNVEKokkosInitialIntegrateFunctor functor(this); Kokkos::parallel_for(nlocal,functor); } else { @@ -118,14 +118,14 @@ void FixNVEKokkos::final_integrate() v = atomKK->k_v.view(); f = atomKK->k_f.view(); - rmass = atomKK->rmass; + rmass = atomKK->k_rmass.view(); mass = atomKK->k_mass.view(); type = atomKK->k_type.view(); mask = atomKK->k_mask.view(); int nlocal = atomKK->nlocal; if (igroup == atomKK->firstgroup) nlocal = atomKK->nfirst; - if (rmass) { + if (rmass.data()) { FixNVEKokkosFinalIntegrateFunctor functor(this); Kokkos::parallel_for(nlocal,functor); } else { diff --git a/src/KOKKOS/fix_nve_kokkos.h b/src/KOKKOS/fix_nve_kokkos.h index 578e0f46cc..3be4323f5b 100644 --- a/src/KOKKOS/fix_nve_kokkos.h +++ b/src/KOKKOS/fix_nve_kokkos.h @@ -60,7 +60,7 @@ class FixNVEKokkos : public FixNVE { typename ArrayTypes::t_x_array x; typename ArrayTypes::t_v_array v; typename ArrayTypes::t_f_array_const f; - double *rmass; + typename ArrayTypes::t_float_1d_randomread rmass; typename ArrayTypes::t_float_1d_randomread mass; typename ArrayTypes::t_int_1d type; typename ArrayTypes::t_int_1d mask; diff --git a/src/KOKKOS/pair_dpd_fdt_energy_kokkos.cpp b/src/KOKKOS/pair_dpd_fdt_energy_kokkos.cpp index 7ff536f8dd..63631119b0 100644 --- a/src/KOKKOS/pair_dpd_fdt_energy_kokkos.cpp +++ b/src/KOKKOS/pair_dpd_fdt_energy_kokkos.cpp @@ -186,7 +186,7 @@ void PairDPDfdtEnergyKokkos::compute(int eflag_in, int vflag_in) f = atomKK->k_f.view(); type = atomKK->k_type.view(); mass = atomKK->k_mass.view(); - rmass = atomKK->rmass; + rmass = atomKK->k_rmass.view(); dpdTheta = atomKK->k_dpdTheta.view(); k_cutsq.template sync(); @@ -564,7 +564,7 @@ void PairDPDfdtEnergyKokkos::operator()(TagPairDPDfdtEnergyComputeNo a_f(j,2) -= delz*fpair; } - if (rmass) { + if (rmass.data()) { mass_i = rmass[i]; mass_j = rmass[j]; } else { diff --git a/src/KOKKOS/pair_dpd_fdt_energy_kokkos.h b/src/KOKKOS/pair_dpd_fdt_energy_kokkos.h index 424779f839..c9f05e0400 100644 --- a/src/KOKKOS/pair_dpd_fdt_energy_kokkos.h +++ b/src/KOKKOS/pair_dpd_fdt_energy_kokkos.h @@ -132,7 +132,7 @@ class PairDPDfdtEnergyKokkos : public PairDPDfdtEnergy { typename ArrayTypes::t_f_array f; typename ArrayTypes::t_int_1d_randomread type; typename ArrayTypes::t_float_1d_randomread mass; - double *rmass; + typename ArrayTypes::t_float_1d_randomread rmass; typename AT::t_efloat_1d dpdTheta; typename AT::t_efloat_1d d_duCond,d_duMech; HAT::t_efloat_1d h_duCond,h_duMech; From 8c3cbad7aead2eaeb34ac1ca94e4a0b367f2325e Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Tue, 10 Jul 2018 09:15:24 -0600 Subject: [PATCH 044/302] Fix runtime error in fix_nve_kokkos --- src/KOKKOS/fix_nve_kokkos.h | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/KOKKOS/fix_nve_kokkos.h b/src/KOKKOS/fix_nve_kokkos.h index 3be4323f5b..e2230d86b6 100644 --- a/src/KOKKOS/fix_nve_kokkos.h +++ b/src/KOKKOS/fix_nve_kokkos.h @@ -60,8 +60,8 @@ class FixNVEKokkos : public FixNVE { typename ArrayTypes::t_x_array x; typename ArrayTypes::t_v_array v; typename ArrayTypes::t_f_array_const f; - typename ArrayTypes::t_float_1d_randomread rmass; - typename ArrayTypes::t_float_1d_randomread mass; + typename ArrayTypes::t_float_1d rmass; + typename ArrayTypes::t_float_1d mass; typename ArrayTypes::t_int_1d type; typename ArrayTypes::t_int_1d mask; }; From a49f946f2f3757bddc8dabbde1e20fd24dca94a5 Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Tue, 10 Jul 2018 10:04:13 -0600 Subject: [PATCH 045/302] Add missing modify in atom_vec_sphere_kokkos --- src/KOKKOS/atom_vec_sphere_kokkos.cpp | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/src/KOKKOS/atom_vec_sphere_kokkos.cpp b/src/KOKKOS/atom_vec_sphere_kokkos.cpp index 3facc7b4ce..05b84ce1fd 100644 --- a/src/KOKKOS/atom_vec_sphere_kokkos.cpp +++ b/src/KOKKOS/atom_vec_sphere_kokkos.cpp @@ -1839,6 +1839,8 @@ void AtomVecSphereKokkos::data_atom(double *coord, imageint imagetmp, char **val omega[nlocal][1] = 0.0; omega[nlocal][2] = 0.0; + atomKK->modified(Host,ALL_MASK); + atom->nlocal++; } @@ -1862,6 +1864,9 @@ int AtomVecSphereKokkos::data_atom_hybrid(int nlocal, char **values) rmass[nlocal] = 4.0*MY_PI/3.0 * radius[nlocal]*radius[nlocal]*radius[nlocal] * density; + + atomKK->modified(Host,RADIUS_MASK|RMASS_MASK); + return 2; } From af0eb52410742b6144cce68e4675575796c185b1 Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Tue, 10 Jul 2018 10:21:42 -0600 Subject: [PATCH 046/302] Error out if using fix pour with the KOKKOS package --- src/GRANULAR/fix_pour.cpp | 2 ++ src/GRANULAR/fix_pour.h | 4 ++++ 2 files changed, 6 insertions(+) diff --git a/src/GRANULAR/fix_pour.cpp b/src/GRANULAR/fix_pour.cpp index 95ed79ffc0..3ffca8db9d 100644 --- a/src/GRANULAR/fix_pour.cpp +++ b/src/GRANULAR/fix_pour.cpp @@ -53,6 +53,8 @@ FixPour::FixPour(LAMMPS *lmp, int narg, char **arg) : { if (narg < 6) error->all(FLERR,"Illegal fix pour command"); + if (lmp->kokkos) error->all(FLERR,"Cannot yet use fix pour with the KOKKOS package"); + time_depend = 1; if (!atom->radius_flag || !atom->rmass_flag) diff --git a/src/GRANULAR/fix_pour.h b/src/GRANULAR/fix_pour.h index c65fa6a18f..63d0d39152 100644 --- a/src/GRANULAR/fix_pour.h +++ b/src/GRANULAR/fix_pour.h @@ -89,6 +89,10 @@ Self-explanatory. Check the input script syntax and compare to the documentation for the command. You can use -echo screen as a command-line option when running LAMMPS to see the offending line. +E: Cannot yet use fix pour with the KOKKOS package + +This feature is not yet supported. + E: Fix pour requires atom attributes radius, rmass The atom style defined does not have these attributes. From 687a4427da0ab860e1a2427eb9ff212a520c8cdb Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Tue, 10 Jul 2018 12:15:08 -0600 Subject: [PATCH 047/302] Fix runtime error in pair_dpd_fdt_energy_kokkos due to rmass change --- src/KOKKOS/pair_dpd_fdt_energy_kokkos.h | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/KOKKOS/pair_dpd_fdt_energy_kokkos.h b/src/KOKKOS/pair_dpd_fdt_energy_kokkos.h index c9f05e0400..81aba715c5 100644 --- a/src/KOKKOS/pair_dpd_fdt_energy_kokkos.h +++ b/src/KOKKOS/pair_dpd_fdt_energy_kokkos.h @@ -132,7 +132,7 @@ class PairDPDfdtEnergyKokkos : public PairDPDfdtEnergy { typename ArrayTypes::t_f_array f; typename ArrayTypes::t_int_1d_randomread type; typename ArrayTypes::t_float_1d_randomread mass; - typename ArrayTypes::t_float_1d_randomread rmass; + typename ArrayTypes::t_float_1d rmass; typename AT::t_efloat_1d dpdTheta; typename AT::t_efloat_1d d_duCond,d_duMech; HAT::t_efloat_1d h_duCond,h_duMech; From c83b5ec2263ccbe8eb0c50c440660ef3183074e1 Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Tue, 10 Jul 2018 19:49:41 -0600 Subject: [PATCH 048/302] Prevent error when Kokkos debug mode turned on --- src/KOKKOS/verlet_kokkos.cpp | 3 +++ 1 file changed, 3 insertions(+) diff --git a/src/KOKKOS/verlet_kokkos.cpp b/src/KOKKOS/verlet_kokkos.cpp index 417de2d94a..f56e6015d0 100644 --- a/src/KOKKOS/verlet_kokkos.cpp +++ b/src/KOKKOS/verlet_kokkos.cpp @@ -585,6 +585,9 @@ void VerletKokkos::force_clear() { if (external_force_clear) return; + atomKK->k_f.modified_host() = 0; // ignore host forces/torques since device views + atomKK->k_torque.modified_host() = 0; // will be cleared below + // clear force on all particles // if either newton flag is set, also include ghosts // when using threads always clear all forces. From 0d1e55c99d10d2fdb3e1ba3ef1178e86df85da8f Mon Sep 17 00:00:00 2001 From: Denis Taniguchi Date: Wed, 11 Jul 2018 11:06:16 -0400 Subject: [PATCH 049/302] Removing unnecessary calls to sync/modified in AtomVecSphereKokkos. --- src/KOKKOS/atom_vec_sphere_kokkos.cpp | 15 +++++---------- 1 file changed, 5 insertions(+), 10 deletions(-) diff --git a/src/KOKKOS/atom_vec_sphere_kokkos.cpp b/src/KOKKOS/atom_vec_sphere_kokkos.cpp index 05b84ce1fd..8fa62bab39 100644 --- a/src/KOKKOS/atom_vec_sphere_kokkos.cpp +++ b/src/KOKKOS/atom_vec_sphere_kokkos.cpp @@ -549,7 +549,6 @@ void AtomVecSphereKokkos::unpack_comm_kokkos( return; } if(commKK->forward_comm_on_host) { - sync(Host,X_MASK|RADIUS_MASK|RMASS_MASK); modified(Host,X_MASK|RADIUS_MASK|RMASS_MASK); struct AtomVecSphereKokkos_UnpackComm f( atomKK->k_x, @@ -557,7 +556,6 @@ void AtomVecSphereKokkos::unpack_comm_kokkos( buf,first); Kokkos::parallel_for(n,f); } else { - sync(Device,X_MASK|RADIUS_MASK|RMASS_MASK); modified(Device,X_MASK|RADIUS_MASK|RMASS_MASK); struct AtomVecSphereKokkos_UnpackComm f( atomKK->k_x, @@ -926,7 +924,6 @@ int AtomVecSphereKokkos::pack_reverse_hybrid(int n, int first, double *buf) void AtomVecSphereKokkos::unpack_reverse(int n, int *list, double *buf) { if(n > 0) { - sync(Host,F_MASK|TORQUE_MASK); modified(Host,F_MASK|TORQUE_MASK); } @@ -947,7 +944,6 @@ void AtomVecSphereKokkos::unpack_reverse(int n, int *list, double *buf) int AtomVecSphereKokkos::unpack_reverse_hybrid(int n, int *list, double *buf) { if(n > 0) { - sync(Host,TORQUE_MASK); modified(Host,TORQUE_MASK); } @@ -1276,11 +1272,7 @@ struct AtomVecSphereKokkos_UnpackBorder { void AtomVecSphereKokkos::unpack_border_kokkos(const int &n, const int &first, const DAT::tdual_xfloat_2d &buf,ExecutionSpace space) { - modified(space,X_MASK|TAG_MASK|TYPE_MASK|MASK_MASK| - RADIUS_MASK|RMASS_MASK); while (first+n >= nmax) grow(0); - modified(space,X_MASK|TAG_MASK|TYPE_MASK|MASK_MASK| - RADIUS_MASK|RMASS_MASK); if(space==Host) { struct AtomVecSphereKokkos_UnpackBorder f(buf.view(), h_x,h_tag,h_type,h_mask, @@ -1294,6 +1286,9 @@ void AtomVecSphereKokkos::unpack_border_kokkos(const int &n, const int &first, first); Kokkos::parallel_for(n,f); } + + modified(space,X_MASK|TAG_MASK|TYPE_MASK|MASK_MASK| + RADIUS_MASK|RMASS_MASK); } /* ---------------------------------------------------------------------- */ @@ -1771,10 +1766,8 @@ void AtomVecSphereKokkos::create_atom(int itype, double *coord) { int nlocal = atom->nlocal; if (nlocal == nmax) { - atomKK->modified(Host,ALL_MASK); grow(0); } - atomKK->modified(Host,ALL_MASK); h_tag[nlocal] = 0; h_type[nlocal] = itype; @@ -1794,6 +1787,8 @@ void AtomVecSphereKokkos::create_atom(int itype, double *coord) h_omega(nlocal,1) = 0.0; h_omega(nlocal,2) = 0.0; + atomKK->modified(Host,ALL_MASK); + atom->nlocal++; } From b5816f2637e7636aa1c48ff4b534ea19bcc308d1 Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Wed, 11 Jul 2018 12:03:34 -0600 Subject: [PATCH 050/302] Update docs for Kokkos version of GRANULAR package --- doc/src/Section_commands.txt | 8 ++++---- doc/src/fix_freeze.txt | 14 ++++++++------ doc/src/fix_gravity.txt | 1 + doc/src/fix_nve_sphere.txt | 1 + doc/src/pair_gran.txt | 1 + 5 files changed, 15 insertions(+), 10 deletions(-) diff --git a/doc/src/Section_commands.txt b/doc/src/Section_commands.txt index e44595455f..3992c5bb54 100644 --- a/doc/src/Section_commands.txt +++ b/doc/src/Section_commands.txt @@ -585,10 +585,10 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT. "enforce2d"_fix_enforce2d.html, "evaporate"_fix_evaporate.html, "external"_fix_external.html, -"freeze"_fix_freeze.html, +"freeze (k)"_fix_freeze.html, "gcmc"_fix_gcmc.html, "gld"_fix_gld.html, -"gravity (o)"_fix_gravity.html, +"gravity (ko)"_fix_gravity.html, "halt"_fix_halt.html, "heat"_fix_heat.html, "indent"_fix_indent.html, @@ -617,7 +617,7 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT. "nve/limit"_fix_nve_limit.html, "nve/line"_fix_nve_line.html, "nve/noforce"_fix_nve_noforce.html, -"nve/sphere (o)"_fix_nve_sphere.html, +"nve/sphere (ko)"_fix_nve_sphere.html, "nve/spin"_fix_nve_spin.html, "nve/tri"_fix_nve_tri.html, "nvt (iko)"_fix_nh.html, @@ -971,7 +971,7 @@ KOKKOS, o = USER-OMP, t = OPT. "gayberne (gio)"_pair_gayberne.html, "gran/hertz/history (o)"_pair_gran.html, "gran/hooke (o)"_pair_gran.html, -"gran/hooke/history (o)"_pair_gran.html, +"gran/hooke/history (ko)"_pair_gran.html, "gw"_pair_gw.html, "gw/zbl"_pair_gw.html, "hbond/dreiding/lj (o)"_pair_hbond_dreiding.html, diff --git a/doc/src/fix_freeze.txt b/doc/src/fix_freeze.txt index a63ee4cb32..f57aa8b965 100644 --- a/doc/src/fix_freeze.txt +++ b/doc/src/fix_freeze.txt @@ -7,6 +7,7 @@ :line fix freeze command :h3 +fix freeze/kk command :h3 [Syntax:] @@ -31,12 +32,13 @@ using "fix setforce"_fix_setforce.html. :line -Styles with a suffix are functionally the same as the corresponding -style without the suffix. They have been optimized to run faster, -depending on your available hardware, as discussed in -"Section 5"_Section_accelerate.html of the manual. The -accelerated styles take the same arguments and should produce the same -results, except for round-off and precision issues. +Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed in "Section 5"_Section_accelerate.html +of the manual. The accelerated styles take the same arguments and +should produce the same results, except for round-off and precision +issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if diff --git a/doc/src/fix_gravity.txt b/doc/src/fix_gravity.txt index dae8ac5ed0..cbd257e44d 100644 --- a/doc/src/fix_gravity.txt +++ b/doc/src/fix_gravity.txt @@ -8,6 +8,7 @@ fix gravity command :h3 fix gravity/omp command :h3 +fix gravity/kk command :h3 [Syntax:] diff --git a/doc/src/fix_nve_sphere.txt b/doc/src/fix_nve_sphere.txt index 21dc6cba8a..f6e616785a 100644 --- a/doc/src/fix_nve_sphere.txt +++ b/doc/src/fix_nve_sphere.txt @@ -8,6 +8,7 @@ fix nve/sphere command :h3 fix nve/sphere/omp command :h3 +fix nve/sphere/kk command :h3 [Syntax:] diff --git a/doc/src/pair_gran.txt b/doc/src/pair_gran.txt index d7e87af013..541f13dc62 100644 --- a/doc/src/pair_gran.txt +++ b/doc/src/pair_gran.txt @@ -10,6 +10,7 @@ pair_style gran/hooke command :h3 pair_style gran/omp command :h3 pair_style gran/hooke/history command :h3 pair_style gran/hooke/history/omp command :h3 +pair_style gran/hooke/history/kk command :h3 pair_style gran/hertz/history command :h3 pair_style gran/hertz/history/omp command :h3 From 88d3233b66e68f54ac91cf4e3b3d4905d84d55e8 Mon Sep 17 00:00:00 2001 From: Rene Halver Date: Wed, 11 Jul 2018 14:02:30 -0600 Subject: [PATCH 051/302] replaced printf with fprintf as requested --- src/USER-SCAFACOS/fix_scafacos.cpp | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/USER-SCAFACOS/fix_scafacos.cpp b/src/USER-SCAFACOS/fix_scafacos.cpp index 6b89348a16..9446e3b60c 100644 --- a/src/USER-SCAFACOS/fix_scafacos.cpp +++ b/src/USER-SCAFACOS/fix_scafacos.cpp @@ -439,7 +439,7 @@ bool FixScafacos::check_result(FCSResult result, int comm_rank) { if (result) { - printf("ScaFaCoS Error: Caught error on task %d.\n", comm_rank); + fprintf(stdout,"ScaFaCoS Error: Caught error on task %d.\n", comm_rank); std::string err_msg; std::stringstream ss; @@ -447,7 +447,7 @@ bool FixScafacos::check_result(FCSResult result, int comm_rank) << fcs_result_get_message(result) << "\n"; err_msg = ss.str(); - error -> all(FLERR, err_msg.c_str()); + error -> one(FLERR, err_msg.c_str()); fcs_result_destroy(result); } return true; From 8cca44ae4541568df4a3dda4da902eabcb4a6138 Mon Sep 17 00:00:00 2001 From: Rene Halver Date: Wed, 11 Jul 2018 14:02:51 -0600 Subject: [PATCH 052/302] removed wrong error messages --- src/USER-SCAFACOS/fix_scafacos.h | 50 -------------------------------- 1 file changed, 50 deletions(-) diff --git a/src/USER-SCAFACOS/fix_scafacos.h b/src/USER-SCAFACOS/fix_scafacos.h index ffd4a94d32..c48f4d8388 100644 --- a/src/USER-SCAFACOS/fix_scafacos.h +++ b/src/USER-SCAFACOS/fix_scafacos.h @@ -111,54 +111,4 @@ class FixScafacos : public Fix { /* ERROR/WARNING messages: -E: Must use units metal with fix latte command - -UNDOCUMENTED - -E: Fix latte currently runs only in serial - -UNDOCUMENTED - -E: LAMMPS is linked against incompatible LATTE library - -UNDOCUMENTED - -E: Illegal ... command - -Self-explanatory. Check the input script syntax and compare to the -documentation for the command. You can use -echo screen as a -command-line option when running LAMMPS to see the offending line. - -E: Fix latte does not yet support a LAMMPS calculation of a Coulomb potential - -UNDOCUMENTED - -E: Could not find fix latte compute ID - -UNDOCUMENTED - -E: Fix latte compute ID does not compute pe/atom - -UNDOCUMENTED - -E: Fix latte requires 3d problem - -UNDOCUMENTED - -E: Fix latte cannot compute Coulomb potential - -UNDOCUMENTED - -E: Fix latte requires 3d simulation - -UNDOCUMENTED - -W: Fix latte should come after all other integration fixes - -UNDOCUMENTED - -E: Internal LATTE problem - -UNDOCUMENTED - */ From cdf091f228651c291aa02e9a585d708073c47756 Mon Sep 17 00:00:00 2001 From: Rene Halver Date: Fri, 13 Jul 2018 08:37:29 -0600 Subject: [PATCH 053/302] fixed an error in the scafacos example (added missing keyword tolerance) --- examples/scafacos/in.scafacos | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/examples/scafacos/in.scafacos b/examples/scafacos/in.scafacos index 2a7e830110..ae6b8e0193 100644 --- a/examples/scafacos/in.scafacos +++ b/examples/scafacos/in.scafacos @@ -14,7 +14,7 @@ neighbor 1.0 bin neigh_modify delay 0 # using the fmm solver with a tolerance in energy of 10^-3 -fix 1 all scafacos fmm energy 0.001 +fix 1 all scafacos fmm tolerance energy 0.001 timestep 0.005 From 6cfdcd1000360cbd1e53f319e9b51e2040505e4f Mon Sep 17 00:00:00 2001 From: Rene Halver Date: Fri, 13 Jul 2018 08:49:47 -0600 Subject: [PATCH 054/302] removed custom error message, information is added to error->one() call --- src/USER-SCAFACOS/fix_scafacos.cpp | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/src/USER-SCAFACOS/fix_scafacos.cpp b/src/USER-SCAFACOS/fix_scafacos.cpp index 9446e3b60c..f82b80dd5f 100644 --- a/src/USER-SCAFACOS/fix_scafacos.cpp +++ b/src/USER-SCAFACOS/fix_scafacos.cpp @@ -439,7 +439,6 @@ bool FixScafacos::check_result(FCSResult result, int comm_rank) { if (result) { - fprintf(stdout,"ScaFaCoS Error: Caught error on task %d.\n", comm_rank); std::string err_msg; std::stringstream ss; @@ -447,7 +446,7 @@ bool FixScafacos::check_result(FCSResult result, int comm_rank) << fcs_result_get_message(result) << "\n"; err_msg = ss.str(); - error -> one(FLERR, err_msg.c_str()); + error->one(FLERR, err_msg.c_str()); fcs_result_destroy(result); } return true; From e7f4e059cf1d552d9d809f48d26ff7ee4778f996 Mon Sep 17 00:00:00 2001 From: "Steven J. Plimpton" Date: Fri, 13 Jul 2018 16:46:06 -0600 Subject: [PATCH 055/302] convert to KSspace style rather than fix --- examples/scafacos/in.scafacos | 25 ++- lib/scafacos/Install.py | 168 ++++++++++++++++ src/Makefile | 4 +- src/USER-SCAFACOS/Install.sh | 21 +- src/USER-SCAFACOS/fix_scafacos.cpp | 7 +- src/USER-SCAFACOS/fix_scafacos.h | 50 +++++ src/USER-SCAFACOS/scafacos.cpp | 308 +++++++++++++++++++++++++++++ src/USER-SCAFACOS/scafacos.h | 69 +++++++ 8 files changed, 626 insertions(+), 26 deletions(-) create mode 100644 lib/scafacos/Install.py create mode 100644 src/USER-SCAFACOS/scafacos.cpp create mode 100644 src/USER-SCAFACOS/scafacos.h diff --git a/examples/scafacos/in.scafacos b/examples/scafacos/in.scafacos index ae6b8e0193..f9b6733eef 100644 --- a/examples/scafacos/in.scafacos +++ b/examples/scafacos/in.scafacos @@ -5,17 +5,32 @@ atom_style full read_data data.NaCl -velocity all set 0.0 0.0 0.0 mom no +replicate 8 8 8 -pair_style zero 1.0 -pair_coeff * * +velocity all create 1.5 49893 neighbor 1.0 bin neigh_modify delay 0 -# using the fmm solver with a tolerance in energy of 10^-3 -fix 1 all scafacos fmm tolerance energy 0.001 +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos p3m tolerance field 0.001 timestep 0.005 +thermo 10 run 100 diff --git a/lib/scafacos/Install.py b/lib/scafacos/Install.py new file mode 100644 index 0000000000..5d4ca7e96a --- /dev/null +++ b/lib/scafacos/Install.py @@ -0,0 +1,168 @@ +#!/usr/bin/env python + +# Install.py tool to download, unpack, build, and link to the Scafacos library +# used to automate the steps described in the README file in this dir + +from __future__ import print_function +import sys,os,re,subprocess + +# help message + +help = """ +Syntax from src dir: make lib-scafacos args="-b" + or: make lib-scafacos args="-p /usr/local/scafacos" +Syntax from lib dir: python Install.py -b + or: python Install.py -p /usr/local/scafacos + +specify zero or more options, order does not matter + + -b = download and build the Scafacos library + -p = specify folder of existing Scafacos installation + + always creates includelink, liblink to Scafacos dirs + +Example: + +make lib-scafacos args="-b" # download/build in lib/scafacos/scafacos +make lib-scafacos args="-p $HOME/scafacos" # use existing Scafacos installation in $HOME +""" + +# settings + +#version = "voro++-0.4.6" +#url = "http://math.lbl.gov/voro++/download/dir/%s.tar.gz" % version + +# print error message or help + +def error(str=None): + if not str: print(help) + else: print("ERROR",str) + sys.exit() + +# expand to full path name +# process leading '~' or relative path + +def fullpath(path): + return os.path.abspath(os.path.expanduser(path)) + +def which(program): + def is_exe(fpath): + return os.path.isfile(fpath) and os.access(fpath, os.X_OK) + + fpath, fname = os.path.split(program) + if fpath: + if is_exe(program): + return program + else: + for path in os.environ["PATH"].split(os.pathsep): + path = path.strip('"') + exe_file = os.path.join(path, program) + if is_exe(exe_file): + return exe_file + + return None + +def geturl(url,fname): + success = False + + if which('curl') != None: + cmd = 'curl -L -o "%s" %s' % (fname,url) + try: + subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) + success = True + except subprocess.CalledProcessError as e: + print("Calling curl failed with: %s" % e.output.decode('UTF-8')) + + if not success and which('wget') != None: + cmd = 'wget -O "%s" %s' % (fname,url) + try: + subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) + success = True + except subprocess.CalledProcessError as e: + print("Calling wget failed with: %s" % e.output.decode('UTF-8')) + + if not success: + error("Failed to download source code with 'curl' or 'wget'") + return + +# parse args + +args = sys.argv[1:] +nargs = len(args) +#if nargs == 0: error() + +homepath = "." + +buildflag = False +pathflag = False +linkflag = True + +iarg = 0 +while iarg < nargs: + if args[iarg] == "-v": + if iarg+2 > nargs: error() + version = args[iarg+1] + iarg += 2 + elif args[iarg] == "-p": + if iarg+2 > nargs: error() + scafacospath = fullpath(args[iarg+1]) + pathflag = True + iarg += 2 + elif args[iarg] == "-b": + buildflag = True + iarg += 1 + else: error() + +homepath = fullpath(homepath) +#homedir = "%s/%s" % (homepath,version) +homedir = homepath + +if (pathflag): + if not os.path.isdir(scafacospath): error("Scafacos path does not exist") + homedir =scafacospath + +if (buildflag and pathflag): + error("Cannot use -b and -p flag at the same time") + +#if (not buildflag and not pathflag): +# error("Have to use either -b or -p flag") + +# download and unpack Scafacos tarball + +if buildflag: + print("Downloading Scafacos ...") + geturl(url,"%s/%s.tar.gz" % (homepath,version)) + + print("Unpacking Voro++ tarball ...") + if os.path.exists("%s/%s" % (homepath,version)): + cmd = 'rm -rf "%s/%s"' % (homepath,version) + subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) + cmd = 'cd "%s"; tar -xzvf %s.tar.gz' % (homepath,version) + subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) + os.remove("%s/%s.tar.gz" % (homepath,version)) + if os.path.basename(homedir) != version: + if os.path.exists(homedir): + cmd = 'rm -rf "%s"' % homedir + subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) + os.rename("%s/%s" % (homepath,version),homedir) + +# build Scafacos + +if buildflag: + print("Building Scafacos ...") + cmd = 'cd "%s"; make CXX=g++ CFLAGS="-fPIC -O3"' % homedir + txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) + print(txt.decode('UTF-8')) + +# create 2 links in lib/scafacos to Scafacos include/lib dirs + +if linkflag: + print("Creating links to Scafacos include and lib files") + if os.path.isfile("includelink") or os.path.islink("includelink"): + os.remove("includelink") + if os.path.isfile("liblink") or os.path.islink("liblink"): + os.remove("liblink") + cmd = 'ln -s "scafacos/include" includelink' + subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) + cmd = 'ln -s "scafacos/lib" liblink' + subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) diff --git a/src/Makefile b/src/Makefile index 948d203cfe..5ca5e7ddc6 100644 --- a/src/Makefile +++ b/src/Makefile @@ -62,8 +62,8 @@ PACKUSER = user-atc user-awpmd user-bocs user-cgdna user-cgsdk user-colvars \ user-intel user-lb user-manifold user-meamc user-meso \ user-mgpt user-misc user-mofff user-molfile \ user-netcdf user-omp user-phonon user-qmmm user-qtb \ - user-quip user-reaxc user-smd user-smtbq user-sph user-tally \ - user-uef user-vtk + user-quip user-reaxc user-scafacos user-smd user-smtbq \ + user-sph user-tally user-uef user-vtk PACKLIB = compress gpu kim kokkos latte meam mpiio mscg poems \ python reax voronoi \ diff --git a/src/USER-SCAFACOS/Install.sh b/src/USER-SCAFACOS/Install.sh index ace610050b..964212fc51 100755 --- a/src/USER-SCAFACOS/Install.sh +++ b/src/USER-SCAFACOS/Install.sh @@ -37,31 +37,18 @@ done if (test $1 = 1) then if (test -e ../Makefile.package) then + sed -i -e 's/`.*scafacos.*` //' ../Makefile.package sed -i -e 's/[^ \t]*scafacos[^ \t]* //' ../Makefile.package sed -i -e 's|^PKG_INC =[ \t]*|&-I../../lib/scafacos/includelink |' ../Makefile.package sed -i -e 's|^PKG_PATH =[ \t]*|&-L../../lib/scafacos/liblink |' ../Makefile.package - #sed -i -e 's|^PKG_LIB =[ \t]*|&-lscafacos |' ../Makefile.package - sed -i -e 's|^PKG_SYSINC =[ \t]*|&$(scafacos_SYSINC) |' ../Makefile.package - sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(scafacos_SYSLIB) |' ../Makefile.package - sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(scafacos_SYSPATH) |' ../Makefile.package - fi - - if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*scafacos.*$/d' ../Makefile.package.settings - # multiline form needed for BSD sed on Macs - sed -i -e '4 i \ -include ..\/..\/lib\/scafacos\/Makefile.lammps -' ../Makefile.package.settings + sed -i -e 's%^PKG_LIB =[ \t]*%&`grep Libs: ../../lib/scafacos/liblink/pkgconfig/scafacos.pc | cut -d " " -f 2-` %' ../Makefile.package fi elif (test $1 = 0) then - if (test -e ../Makefile.package) then + if (test -e ../Makefile.package) then + sed -i -e 's/`.*scafacos.*` //' ../Makefile.package sed -i -e 's/[^ \t]*scafacos[^ \t]* //' ../Makefile.package fi - if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*scafacos.*$/d' ../Makefile.package.settings - fi - fi diff --git a/src/USER-SCAFACOS/fix_scafacos.cpp b/src/USER-SCAFACOS/fix_scafacos.cpp index f82b80dd5f..08aebb9f22 100644 --- a/src/USER-SCAFACOS/fix_scafacos.cpp +++ b/src/USER-SCAFACOS/fix_scafacos.cpp @@ -17,6 +17,7 @@ #include #include +#include #include "fix_scafacos.h" #include "atom.h" #include "comm.h" @@ -81,7 +82,7 @@ FixScafacos::FixScafacos(LAMMPS *lmp, int narg, char **arg) : else error->all(FLERR,"Illegal fix scafacos command"); ++arg_index; - tolerance_value = atof(arg[arg_index]); + tolerance_value = atof(arg[arg_index]); ++arg_index; } else @@ -439,6 +440,7 @@ bool FixScafacos::check_result(FCSResult result, int comm_rank) { if (result) { + printf("ScaFaCoS Error: Caught error on task %d.\n", comm_rank); std::string err_msg; std::stringstream ss; @@ -446,8 +448,9 @@ bool FixScafacos::check_result(FCSResult result, int comm_rank) << fcs_result_get_message(result) << "\n"; err_msg = ss.str(); - error->one(FLERR, err_msg.c_str()); + error -> all(FLERR, err_msg.c_str()); fcs_result_destroy(result); } return true; } + diff --git a/src/USER-SCAFACOS/fix_scafacos.h b/src/USER-SCAFACOS/fix_scafacos.h index c48f4d8388..ffd4a94d32 100644 --- a/src/USER-SCAFACOS/fix_scafacos.h +++ b/src/USER-SCAFACOS/fix_scafacos.h @@ -111,4 +111,54 @@ class FixScafacos : public Fix { /* ERROR/WARNING messages: +E: Must use units metal with fix latte command + +UNDOCUMENTED + +E: Fix latte currently runs only in serial + +UNDOCUMENTED + +E: LAMMPS is linked against incompatible LATTE library + +UNDOCUMENTED + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: Fix latte does not yet support a LAMMPS calculation of a Coulomb potential + +UNDOCUMENTED + +E: Could not find fix latte compute ID + +UNDOCUMENTED + +E: Fix latte compute ID does not compute pe/atom + +UNDOCUMENTED + +E: Fix latte requires 3d problem + +UNDOCUMENTED + +E: Fix latte cannot compute Coulomb potential + +UNDOCUMENTED + +E: Fix latte requires 3d simulation + +UNDOCUMENTED + +W: Fix latte should come after all other integration fixes + +UNDOCUMENTED + +E: Internal LATTE problem + +UNDOCUMENTED + */ diff --git a/src/USER-SCAFACOS/scafacos.cpp b/src/USER-SCAFACOS/scafacos.cpp new file mode 100644 index 0000000000..89c67b828b --- /dev/null +++ b/src/USER-SCAFACOS/scafacos.cpp @@ -0,0 +1,308 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Rene Halver (JSC) +------------------------------------------------------------------------- */ + +#include +#include +#include +#include "scafacos.h" +#include "atom.h" +#include "comm.h" +#include "domain.h" +#include "force.h" +#include "memory.h" +#include "error.h" + +// ScaFaCoS library + +#include +#include +#include "fcs.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +Scafacos::Scafacos(LAMMPS *lmp, int narg, char **arg) : KSpace(lmp, narg, arg) +{ + if (narg < 2) error->all(FLERR,"Illegal scafacos command"); + + int n = strlen(arg[0]) + 1; + method = new char[n]; + strcpy(method,arg[0]); + + // additional args + + int tflag = 0; + + int iarg = 1; + while (iarg < narg) { + if (strcmp(arg[iarg],"tolerance") == 0) { + if (iarg+3 > narg) error->all(FLERR,"Illegal scafacos command"); + tflag = 1; + if (strcmp(arg[iarg+1],"energy") == 0) + tolerance_type = FCS_TOLERANCE_TYPE_ENERGY; + else if (strcmp(arg[iarg+1],"energy_rel") == 0) + tolerance_type = FCS_TOLERANCE_TYPE_ENERGY_REL; + else if (strcmp(arg[iarg+1],"field") == 0) + tolerance_type = FCS_TOLERANCE_TYPE_FIELD; + else if (strcmp(arg[iarg+1],"field_rel") == 0) + tolerance_type = FCS_TOLERANCE_TYPE_FIELD_REL; + else if (strcmp(arg[iarg+1],"potential") == 0) + tolerance_type = FCS_TOLERANCE_TYPE_POTENTIAL; + else if (strcmp(arg[iarg+1],"potential_rel") == 0) + tolerance_type = FCS_TOLERANCE_TYPE_POTENTIAL_REL; + else error->all(FLERR,"Illegal scafacos command"); + tolerance = force->numeric(FLERR,arg[iarg+2]); + iarg += 3; + } else error->all(FLERR,"Illegal scafacos command"); + } + + if (!tflag) error->all(FLERR,"Must set tolerance in scafacos command"); + + // initializations + + me = comm->me; + initialized = 0; + + maxatom = 0; + epot = NULL; + efield = NULL; +} + +/* ---------------------------------------------------------------------- */ + +Scafacos::~Scafacos() +{ + delete [] method; + + memory->destroy(epot); + memory->destroy(efield); + + // NOTE: any clean-up call to ScaFaCoS needed? +} + +/* ---------------------------------------------------------------------- */ + +void Scafacos::init() +{ + // error checks + // NOTE: allow triclinic at some point + + if (domain->dimension == 2) + error->all(FLERR,"Cannot use ScaFaCoS with 2d simulation"); + + if (domain->triclinic) + error->all(FLERR,"Cannot use ScaFaCoS with triclinic domain yet"); + + // one-time initialization of ScaFaCoS + + if (!initialized) { + result = fcs_init(&fcs,method,world); + check_result(result); + + setup_handle(); + + result = fcs_set_tolerance(fcs,tolerance_type,tolerance); + check_result(result); + + if (me == 0) fcs_print_parameters(fcs); + + double **x = atom->x; + double *q = atom->q; + int nlocal = atom->nlocal; + + result = fcs_tune(fcs,nlocal,&x[0][0],q); + } + + initialized = 1; +} + +/* ---------------------------------------------------------------------- */ + +void Scafacos::setup() {} + +/* ---------------------------------------------------------------------- */ + +void Scafacos::compute(int eflag, int vflag) +{ + double **x = atom->x; + double *q = atom->q; + int nlocal = atom->nlocal; + + // if simluation box has changed, call fcs_tune() + + if (box_has_changed()) { + printf("AAA\n"); + setup_handle(); + result = fcs_tune(fcs,nlocal,&x[0][0],q); + check_result(result); + } + + // grow epot & efield if necessary + + if (nlocal > maxatom) { + memory->destroy(epot); + memory->destroy(efield); + maxatom = atom->nmax; + memory->create(epot,maxatom,"scafacos:epot"); + memory->create(efield,maxatom,3,"scafacos:efield"); + + } + + // initialize epot & efield + // NOTE: is this necessary? + + for (int i = 0; i < nlocal; i++) { + epot[i] = 0.0; + efield[i][0] = efield[i][1] = efield[i][2] = 0.0; + } + + // ScaFaCoS calculation of full Coulombics + + result = fcs_run(fcs,nlocal,&x[0][0],q,&efield[0][0],epot); + check_result(result); + + // apply Efield to each particle + // accumulate total energy + + double **f = atom->f; + + double qone; + double myeng = 0.0; + + for (int i = 0; i < nlocal; i++) { + qone = q[i]; + f[i][0] += qone * efield[i][0]; + f[i][1] += qone * efield[i][1]; + f[i][2] += qone * efield[i][2]; + myeng += 0.5 * qone * epot[i]; + } + + MPI_Allreduce(&myeng,&energy,1,MPI_DOUBLE,MPI_SUM,world); +} + +/* ---------------------------------------------------------------------- + memory usage of local arrays +------------------------------------------------------------------------- */ + +double Scafacos::memory_usage() +{ + double bytes = 0.0; + bytes += maxatom * sizeof(double); + bytes += 3*maxatom * sizeof(double); + return bytes; +} + +/* ---------------------------------------------------------------------- + setup of ScaFaCoS handle with common parameters +------------------------------------------------------------------------- */ + +void Scafacos::setup_handle() +{ + // store simulation box params + // NOTE: this assumes orthogonal box + // NOTE: total particles may not be a 4-byte int + // NOTE: what does SCFCS mean by offset? + // it's an integer flag in LAMMPS + + old_periodicity[0] = domain->xperiodic; + old_periodicity[1] = domain->yperiodic; + old_periodicity[2] = domain->zperiodic; + + old_offset[0] = domain->boundary[0][0]; + old_offset[1] = domain->boundary[1][0]; + old_offset[2] = domain->boundary[2][0]; + + old_box_x[0] = domain->prd[0]; + old_box_x[1] = old_box_x[2] = 0.0; + old_box_y[1] = domain->prd[1]; + old_box_y[0] = old_box_y[2] = 0.0; + old_box_z[2] = domain->prd[2]; + old_box_z[1] = old_box_z[0] = 0.0; + + old_natoms = atom->natoms; + + // set all required ScaFaCoS params + + result = fcs_set_box_a(fcs,old_box_x); + check_result(result); + + result = fcs_set_box_b(fcs,old_box_y); + check_result(result); + + result = fcs_set_box_c(fcs,old_box_z); + check_result(result); + + result = fcs_set_box_origin(fcs,old_offset); + check_result(result); + + result = fcs_set_periodicity(fcs,old_periodicity); + check_result(result); + + result = fcs_set_total_particles(fcs,old_natoms); + check_result(result); + + // NOTE: for now disable short-range calculations within LAMMPS + + int near_field_flag = 0; + result = fcs_set_near_field_flag(fcs,near_field_flag); + check_result(result); +} + +/* ---------------------------------------------------------------------- + check if box parameters changed, requiring a new call to fcs_tune +------------------------------------------------------------------------- */ + +bool Scafacos::box_has_changed() +{ + int *periodicity = domain->periodicity; + double *prd = domain->prd; + + bool changed = + (periodicity[0] != old_periodicity[0]) || + (periodicity[1] != old_periodicity[1]) || + (periodicity[2] != old_periodicity[2]) || + (domain->boundary[0][0] != old_offset[0]) || + (domain->boundary[1][0] != old_offset[1]) || + (domain->boundary[2][0] != old_offset[2]) || + (prd[0] != old_box_x[0]) || + (prd[1] != old_box_y[1]) || + (prd[2] != old_box_z[2]) || + (atom->natoms != old_natoms); + + return changed; +} + +/* ---------------------------------------------------------------------- + check ScaFaCoS result for error condition + NOTE: will all procs have same error? +------------------------------------------------------------------------- */ + +void Scafacos::check_result(FCSResult result) +{ + if (!result) return; + + std::stringstream ss; + ss << "ScaFaCoS: " << fcs_result_get_function(result) << "\n" + << fcs_result_get_message(result) << "\n"; + fcs_result_destroy(result); + std::string err_msg = ss.str(); + const char *str = err_msg.c_str(); + + error->one(FLERR,str); +} + diff --git a/src/USER-SCAFACOS/scafacos.h b/src/USER-SCAFACOS/scafacos.h new file mode 100644 index 0000000000..33911ee9fd --- /dev/null +++ b/src/USER-SCAFACOS/scafacos.h @@ -0,0 +1,69 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef KSPACE_CLASS + +KSpaceStyle(scafacos,Scafacos) + +#else + +#ifndef LMP_SCAFACOS_H +#define LMP_SCAFACOS_H + +#include "kspace.h" +#include "fcs.h" + +namespace LAMMPS_NS { + +class Scafacos : public KSpace { + public: + Scafacos(class LAMMPS *, int, char **); + ~Scafacos(); + void init(); + void setup(); + void compute(int, int); + double memory_usage(); + + private: + int me; + + char *method; + double tolerance; + double *epot,**efield; + int tolerance_type; + int initialized,maxatom; + + FCS fcs; // ScaFaCoS handle + FCSResult result; // result for each ScaFaCoS call + + // simulation state: box, natoms + // so ScaFaCoS can detect if changes, e.g. for NPT + + fcs_float old_box_x[3],old_box_y[3],old_box_z[3]; + fcs_float old_offset[3]; + fcs_int old_periodicity[3]; + fcs_int old_natoms; + + void check_result(FCSResult); + void setup_handle(); + bool box_has_changed(); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ From 406aaf011f185e30d2e58e5a31c41842fb9353a9 Mon Sep 17 00:00:00 2001 From: Denis Taniguchi Date: Mon, 16 Jul 2018 15:30:24 +0100 Subject: [PATCH 056/302] Improving global memory access pattern for firstflag and firstvalue in FixNeighHistoryKokkos. --- src/KOKKOS/fix_neigh_history_kokkos.cpp | 4 +- src/KOKKOS/fix_neigh_history_kokkos.h | 4 +- src/KOKKOS/pair_gran_hooke_history_kokkos.cpp | 38 +++++++++---------- src/KOKKOS/pair_gran_hooke_history_kokkos.h | 4 +- 4 files changed, 25 insertions(+), 25 deletions(-) diff --git a/src/KOKKOS/fix_neigh_history_kokkos.cpp b/src/KOKKOS/fix_neigh_history_kokkos.cpp index 8320d72545..d481c20818 100644 --- a/src/KOKKOS/fix_neigh_history_kokkos.cpp +++ b/src/KOKKOS/fix_neigh_history_kokkos.cpp @@ -174,8 +174,8 @@ void FixNeighHistoryKokkos::post_neighbor() if (maxatom < nlocal || k_list->maxneighs > d_firstflag.extent(1)) { maxatom = nall; - d_firstflag = typename ArrayTypes::t_int_2d("neighbor_history:firstflag",maxatom,k_list->maxneighs); - d_firstvalue = typename ArrayTypes::t_float_2d("neighbor_history:firstvalue",maxatom,k_list->maxneighs*dnum); + d_firstflag = Kokkos::View("neighbor_history:firstflag",maxatom,k_list->maxneighs); + d_firstvalue = Kokkos::View("neighbor_history:firstvalue",maxatom,k_list->maxneighs*dnum); } copymode = 1; diff --git a/src/KOKKOS/fix_neigh_history_kokkos.h b/src/KOKKOS/fix_neigh_history_kokkos.h index 4e2ca05e54..d5bb1c3971 100644 --- a/src/KOKKOS/fix_neigh_history_kokkos.h +++ b/src/KOKKOS/fix_neigh_history_kokkos.h @@ -49,8 +49,8 @@ class FixNeighHistoryKokkos : public FixNeighHistory { KOKKOS_INLINE_FUNCTION void post_neighbor_item(const int &ii) const; - typename ArrayTypes::t_int_2d d_firstflag; - typename ArrayTypes::t_float_2d d_firstvalue; + typename Kokkos::View d_firstflag; + typename Kokkos::View d_firstvalue; private: typename ArrayTypes::tdual_int_1d k_npartner; diff --git a/src/KOKKOS/pair_gran_hooke_history_kokkos.cpp b/src/KOKKOS/pair_gran_hooke_history_kokkos.cpp index b245896be5..e6c9756b94 100644 --- a/src/KOKKOS/pair_gran_hooke_history_kokkos.cpp +++ b/src/KOKKOS/pair_gran_hooke_history_kokkos.cpp @@ -278,14 +278,14 @@ void PairGranHookeHistoryKokkos::operator()(TagPairGranHookeHistoryC Kokkos::View::value> > a_f = f; Kokkos::View::value> > a_torque = torque; - int i = d_ilist[ii]; - X_FLOAT xtmp = x(i,0); - X_FLOAT ytmp = x(i,1); - X_FLOAT ztmp = x(i,2); - int itype = type[i]; - LMP_FLOAT imass = rmass[i]; - LMP_FLOAT irad = radius[i]; - int jnum = d_numneigh[i]; + const int i = d_ilist[ii]; + const X_FLOAT xtmp = x(i,0); + const X_FLOAT ytmp = x(i,1); + const X_FLOAT ztmp = x(i,2); + const int itype = type[i]; + const LMP_FLOAT imass = rmass[i]; + const LMP_FLOAT irad = radius[i]; + const int jnum = d_numneigh[i]; F_FLOAT fx_i = 0.0; F_FLOAT fy_i = 0.0; @@ -299,14 +299,14 @@ void PairGranHookeHistoryKokkos::operator()(TagPairGranHookeHistoryC int j = d_neighbors(i,jj); j &= NEIGHMASK; - X_FLOAT delx = xtmp - x(j,0); - X_FLOAT dely = ytmp - x(j,1); - X_FLOAT delz = ztmp - x(j,2); - X_FLOAT rsq = delx*delx + dely*dely + delz*delz; - int jtype = type[j]; - LMP_FLOAT jmass = rmass[j]; - LMP_FLOAT jrad = radius[j]; - LMP_FLOAT radsum = irad + jrad; + const X_FLOAT delx = xtmp - x(j,0); + const X_FLOAT dely = ytmp - x(j,1); + const X_FLOAT delz = ztmp - x(j,2); + const X_FLOAT rsq = delx*delx + dely*dely + delz*delz; + const int jtype = type[j]; + const LMP_FLOAT jmass = rmass[j]; + const LMP_FLOAT jrad = radius[j]; + const LMP_FLOAT radsum = irad + jrad; // check for touching neighbors @@ -316,9 +316,9 @@ void PairGranHookeHistoryKokkos::operator()(TagPairGranHookeHistoryC d_firstshear(i,3*jj+1) = 0; d_firstshear(i,3*jj+2) = 0; } else { - LMP_FLOAT r = sqrt(rsq); - LMP_FLOAT rinv = 1.0/r; - LMP_FLOAT rsqinv = 1/rsq; + const LMP_FLOAT r = sqrt(rsq); + const LMP_FLOAT rinv = 1.0/r; + const LMP_FLOAT rsqinv = 1/rsq; // relative translational velocity diff --git a/src/KOKKOS/pair_gran_hooke_history_kokkos.h b/src/KOKKOS/pair_gran_hooke_history_kokkos.h index dd5aac96d3..65a92f23cd 100644 --- a/src/KOKKOS/pair_gran_hooke_history_kokkos.h +++ b/src/KOKKOS/pair_gran_hooke_history_kokkos.h @@ -86,8 +86,8 @@ class PairGranHookeHistoryKokkos : public PairGranHookeHistory { typename AT::t_int_1d_randomread d_ilist; typename AT::t_int_1d_randomread d_numneigh; - typename AT::t_int_2d d_firsttouch; - typename AT::t_float_2d d_firstshear; + typename Kokkos::View d_firsttouch; + typename Kokkos::View d_firstshear; int newton_pair; double special_lj[4]; From eebd075a1523a6f5d49855d3f73f65651a69c558 Mon Sep 17 00:00:00 2001 From: Rene Halver Date: Wed, 18 Jul 2018 11:05:54 -0600 Subject: [PATCH 057/302] added scaling for different units (lj, metal, ...) and storage of atom-wise potentials (eatom / eatom_flag) --- src/USER-SCAFACOS/scafacos.cpp | 21 +++++++++++++++++++-- 1 file changed, 19 insertions(+), 2 deletions(-) diff --git a/src/USER-SCAFACOS/scafacos.cpp b/src/USER-SCAFACOS/scafacos.cpp index 89c67b828b..c5efd6a191 100644 --- a/src/USER-SCAFACOS/scafacos.cpp +++ b/src/USER-SCAFACOS/scafacos.cpp @@ -110,6 +110,10 @@ void Scafacos::init() // one-time initialization of ScaFaCoS + scale = 1.0; + qqrd2e = force->qqrd2e; + //qsum_qsq(); + if (!initialized) { result = fcs_init(&fcs,method,world); check_result(result); @@ -143,10 +147,15 @@ void Scafacos::compute(int eflag, int vflag) double *q = atom->q; int nlocal = atom->nlocal; + const double qscale = qqrd2e * scale; + // if simluation box has changed, call fcs_tune() + if (eflag || vflag) ev_setup(eflag,vflag); + else + eflag_atom = 0; + if (box_has_changed()) { - printf("AAA\n"); setup_handle(); result = fcs_tune(fcs,nlocal,&x[0][0],q); check_result(result); @@ -185,13 +194,21 @@ void Scafacos::compute(int eflag, int vflag) double myeng = 0.0; for (int i = 0; i < nlocal; i++) { - qone = q[i]; + qone = q[i] * qscale; f[i][0] += qone * efield[i][0]; f[i][1] += qone * efield[i][1]; f[i][2] += qone * efield[i][2]; myeng += 0.5 * qone * epot[i]; } + if (eflag_atom) + { + for (int i = 0; i < nlocal; i++) + { + eatom[i] = qscale * epot[i]; + } + } + MPI_Allreduce(&myeng,&energy,1,MPI_DOUBLE,MPI_SUM,world); } From 1a959a5683accbf9ad8c36198de73b9557d2c5f0 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 18 Jul 2018 13:26:45 -0400 Subject: [PATCH 058/302] must add USER-SCAFACOS to PACKLIB variable in Makefile We need "make no-lib" to be correct for automated testing to work, since only known packages with libraries can be successfully compiled through jenkins and other tools. Those scripts usually do "make yes-all no-lib" and then "make yes-XXX" for selected packages where it is known how to build the required libs. --- src/Makefile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/Makefile b/src/Makefile index 5ca5e7ddc6..4e19f43afb 100644 --- a/src/Makefile +++ b/src/Makefile @@ -68,7 +68,7 @@ PACKUSER = user-atc user-awpmd user-bocs user-cgdna user-cgsdk user-colvars \ PACKLIB = compress gpu kim kokkos latte meam mpiio mscg poems \ python reax voronoi \ user-atc user-awpmd user-colvars user-h5md user-lb user-molfile \ - user-netcdf user-qmmm user-quip user-smd user-vtk + user-netcdf user-qmmm user-quip user-scafacos user-smd user-vtk PACKSYS = compress mpiio python user-lb From b0c9fde1dd455194f4ef7767d5790ba022eaa7a9 Mon Sep 17 00:00:00 2001 From: "Steven J. Plimpton" Date: Wed, 18 Jul 2018 15:32:03 -0600 Subject: [PATCH 059/302] more changes from Steve --- doc/src/Section_packages.txt | 55 +++ doc/src/fix_scafacos.txt | 44 --- doc/src/kspace_modify.txt | 447 +++++++++++++--------- doc/src/kspace_style.txt | 91 ++++- examples/USER/scafacos/README | 10 + examples/{ => USER}/scafacos/data.NaCl | 0 examples/{ => USER}/scafacos/in.scafacos | 0 lib/scafacos/Install.py | 15 +- src/USER-SCAFACOS/README | 5 + src/USER-SCAFACOS/fix_scafacos.cpp | 456 ----------------------- src/USER-SCAFACOS/fix_scafacos.h | 164 -------- src/USER-SCAFACOS/scafacos.cpp | 103 ++--- src/USER-SCAFACOS/scafacos.h | 1 + src/kspace.cpp | 6 +- src/kspace.h | 2 + 15 files changed, 486 insertions(+), 913 deletions(-) delete mode 100644 doc/src/fix_scafacos.txt create mode 100644 examples/USER/scafacos/README rename examples/{ => USER}/scafacos/data.NaCl (100%) rename examples/{ => USER}/scafacos/in.scafacos (100%) create mode 100644 src/USER-SCAFACOS/README delete mode 100644 src/USER-SCAFACOS/fix_scafacos.cpp delete mode 100644 src/USER-SCAFACOS/fix_scafacos.h diff --git a/doc/src/Section_packages.txt b/doc/src/Section_packages.txt index 218866e271..ea03bdb74e 100644 --- a/doc/src/Section_packages.txt +++ b/doc/src/Section_packages.txt @@ -149,6 +149,7 @@ Package, Description, Doc page, Example, Library "USER-QTB"_#USER-QTB, quantum nuclear effects,"fix qtb"_fix_qtb.html "fix qbmsst"_fix_qbmsst.html, qtb, - "USER-QUIP"_#USER-QUIP, QUIP/libatoms interface,"pair_style quip"_pair_quip.html, USER/quip, ext "USER-REAXC"_#USER-REAXC, ReaxFF potential (C/C++) ,"pair_style reaxc"_pair_reaxc.html, reax, - +"USER-SCAFACOS"_#USER-SCAFACOS, ScaFaCoS long-range Coulombics,"kspace_style scafacos"_kspace_style.html, USER/scafacos, ext "USER-SMD"_#USER-SMD, smoothed Mach dynamics,"SMD User Guide"_PDF/SMD_LAMMPS_userguide.pdf, USER/smd, ext "USER-SMTBQ"_#USER-SMTBQ, second moment tight binding QEq potential,"pair_style smtbq"_pair_smtbq.html, USER/smtbq, - "USER-SPH"_#USER-SPH, smoothed particle hydrodynamics,"SPH User Guide"_PDF/SPH_LAMMPS_userguide.pdf, USER/sph, - @@ -2730,6 +2731,60 @@ examples/reax :ul :line +RENE: check this section + +USER-SCAFACOS package :link(USER-SCAFACOS),h4 + +[Contents:] + +A KSpace style which wraps the "ScaFaCoS Coulomb solver +library"_http://www.scafacos.de. + +To use this package you must have the ScaFaCoS library available on +your system. It is available for download at "http://scafacos.de" or +can be cloned from the git-repository +"git://github.com/scafacos/scafacos.git". + +[Author:] Rene Halver (JSC) wrote the scafacos LAMMPS command. + +ScaFaCoS was developed by a consortium of German research facilities +with a BMBF (German Ministry of Science and Education) funded project +in 2009-2012. Participants of the consortium were the Universities of +Bonn, Chemnitz, Stuttgart, and Wuppertal as well as the +Forschungszentrum Juelich. + +[Install or un-install:] + +Before building LAMMPS with this package, you must first download and +build the ScaFaCoS library. You can do this manually if you prefer; +follow the instructions in lib/scafacos/README. You can also do it in +one step from the lammps/src dir, using a command like these, which +simply invoke the lib/scafacos/Install.py script with the specified +args: + +make lib-scafacos # print help message +make lib-scafacos args="-b" # download and build in lib/scafacos/scafacos- +make lib-voronoi args="-p $HOME/scafacos # use existing ScaFaCoS installation in $HOME/scafacos + +You can then install/un-install the package and build LAMMPS in the +usual manner: + +make yes-user-scafacos +make machine :pre + +make no-user-scafacos +make machine :pre + +[Supporting info:] + +src/USER-SCAFACOS: filenames -> commands +src/USER-SCAFACOS/README +"kspace_style scafacos"_kspace_style.html +"kspace_modify"_kspace_modify.html +examples/USER/scafacos :ul + +:line + USER-SMD package :link(USER-SMD),h4 [Contents:] diff --git a/doc/src/fix_scafacos.txt b/doc/src/fix_scafacos.txt deleted file mode 100644 index 1a65ed0c5e..0000000000 --- a/doc/src/fix_scafacos.txt +++ /dev/null @@ -1,44 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Section_commands.html#comm) - -:line - -fix scafacos command :h3 - -[Syntax:] - -fix ID group-ID scafacos solver tol_type tolerance :pre - -ID, group-ID are documented in "fix"_fix.html command -scafacos = style name of this fix command -solver = NULL or name of solver for electro-statics computation :ul -tol_type = NULL or one of (energy, energy_rel, field, field_rel, potential, potential_rel) -tolerance = only of tol_type is given, value of tolerance - -[Examples:] - -fix 1 all scafacos fmm -fix 1 all scafacos p3m field 0.001 - -[Description:] - -This fix style is a wrapper for the Coulomb solver library ScaFaCoS, -which provides a selection of different solvers for the compuation -of electro-static interaction. If you download and build ScaFaCoS, -it can be called as libray by LAMMPS via this fix, which allows the -selection of a solver as well as setting the tolerance of a chosen -parameter (if compatible with the chosen solver). - -ScaFaCoS was developed by a consortium of German research facilities -with a BMBF (German Ministry of Science and Education) funded project -in 2009-2012. Participants of the consortium were the Universities of -Bonn, Chemnitz, Stuttgart, and Wuppertal as well as the -Forschungszentrum Juelich. - -The library is available at "http://scafacos.de" or can be cloned -from the git-repository "git://github.com/scafacos/scafacos.git". - -:line diff --git a/doc/src/kspace_modify.txt b/doc/src/kspace_modify.txt index 6d27bb7076..fbc569306c 100644 --- a/doc/src/kspace_modify.txt +++ b/doc/src/kspace_modify.txt @@ -13,47 +13,51 @@ kspace_modify command :h3 kspace_modify keyword value ... :pre one or more keyword/value pairs may be listed :ulb,l -keyword = {mesh} or {order} or {order/disp} or {mix/disp} or {overlap} or {minorder} or {force} or {gewald} or {gewald/disp} or {slab} or (nozforce} or {compute} or {cutoff/adjust} or {fftbench} or {collective} or {diff} or {kmax/ewald} or {force/disp/real} or {force/disp/kspace} or {splittol} or {disp/auto}:l - {mesh} value = x y z - x,y,z = grid size in each dimension for long-range Coulombics - {mesh/disp} value = x y z - x,y,z = grid size in each dimension for 1/r^6 dispersion - {order} value = N - N = extent of Gaussian for PPPM or MSM mapping of charge to grid - {order/disp} value = N - N = extent of Gaussian for PPPM mapping of dispersion term to grid - {mix/disp} value = {pair} or {geom} or {none} - {overlap} = {yes} or {no} = whether the grid stencil for PPPM is allowed to overlap into more than the nearest-neighbor processor - {minorder} value = M - M = min allowed extent of Gaussian when auto-adjusting to minimize grid communication +keyword = {collective} or {compute} or {cutoff/adjust} or {diff} or {disp/auto} or {fftbench} or {force/disp/kspace} or {force/disp/real} or {force} or {gewald/disp} or {gewald} or {kmax/ewald} or {mesh} or {minorder} or {mix/disp} or {order/disp} or {order} or {overlap} or {scafacos} or {slab} or {splittol} :l + {collective} value = {yes} or {no} + {compute} value = {yes} or {no} + {cutoff/adjust} value = {yes} or {no} + {diff} value = {ad} or {ik} = 2 or 4 FFTs for PPPM in smoothed or non-smoothed mode + {disp/auto} value = yes or no + {fftbench} value = {yes} or {no} + {force/disp/real} value = accuracy (force units) + {force/disp/kspace} value = accuracy (force units) {force} value = accuracy (force units) {gewald} value = rinv (1/distance units) rinv = G-ewald parameter for Coulombics {gewald/disp} value = rinv (1/distance units) rinv = G-ewald parameter for dispersion + {kmax/ewald} value = kx ky kz + kx,ky,kz = number of Ewald sum kspace vectors in each dimension + {mesh} value = x y z + x,y,z = grid size in each dimension for long-range Coulombics + {mesh/disp} value = x y z + x,y,z = grid size in each dimension for 1/r^6 dispersion + {minorder} value = M + M = min allowed extent of Gaussian when auto-adjusting to minimize grid communication + {mix/disp} value = {pair} or {geom} or {none} + {order} value = N + N = extent of Gaussian for PPPM or MSM mapping of charge to grid + {order/disp} value = N + N = extent of Gaussian for PPPM mapping of dispersion term to grid + {overlap} = {yes} or {no} = whether the grid stencil for PPPM is allowed to overlap into more than the nearest-neighbor processor + {pressure/scalar} value = {yes} or {no} + {scafacos} values = option value1 value2 ... + option = {tolerance} + value = {energy} or {energy_rel} or {field} or {field_rel} or {potential} or {potential_rel} {slab} value = volfactor or {nozforce} volfactor = ratio of the total extended volume used in the 2d approximation compared with the volume of the simulation domain {nozforce} turns off kspace forces in the z direction - {compute} value = {yes} or {no} - {cutoff/adjust} value = {yes} or {no} - {pressure/scalar} value = {yes} or {no} - {fftbench} value = {yes} or {no} - {collective} value = {yes} or {no} - {diff} value = {ad} or {ik} = 2 or 4 FFTs for PPPM in smoothed or non-smoothed mode - {kmax/ewald} value = kx ky kz - kx,ky,kz = number of Ewald sum kspace vectors in each dimension - {force/disp/real} value = accuracy (force units) - {force/disp/kspace} value = accuracy (force units) {splittol} value = tol - tol = relative size of two eigenvalues (see discussion below) - {disp/auto} value = yes or no :pre + tol = relative size of two eigenvalues (see discussion below) :pre :ule [Examples:] kspace_modify mesh 24 24 30 order 6 -kspace_modify slab 3.0 :pre +kspace_modify slab 3.0 +kspace_modify scafacos tolerance energy :pre [Description:] @@ -61,6 +65,132 @@ Set parameters used by the kspace solvers defined by the "kspace_style"_kspace_style.html command. Not all parameters are relevant to all kspace styles. +:line + +The {collective} keyword applies only to PPPM. It is set to {no} by +default, except on IBM BlueGene machines. If this option is set to +{yes}, LAMMPS will use MPI collective operations to remap data for +3d-FFT operations instead of the default point-to-point communication. +This is faster on IBM BlueGene machines, and may also be faster on +other machines if they have an efficient implementation of MPI +collective operations and adequate hardware. + +:line + +The {compute} keyword allows Kspace computations to be turned off, +even though a "kspace_style"_kspace_style.html is defined. This is +not useful for running a real simulation, but can be useful for +debugging purposes or for computing only partial forces that do not +include the Kspace contribution. You can also do this by simply not +defining a "kspace_style"_kspace_style.html, but a Kspace-compatible +"pair_style"_pair_style.html requires a kspace style to be defined. +This keyword gives you that option. + +:line + +The {cutoff/adjust} keyword applies only to MSM. If this option is +turned on, the Coulombic cutoff will be automatically adjusted at the +beginning of the run to give the desired estimated error. Other +cutoffs such as LJ will not be affected. If the grid is not set using +the {mesh} command, this command will also attempt to use the optimal +grid that minimizes cost using an estimate given by +"(Hardy)"_#Hardy1. Note that this cost estimate is not exact, somewhat +experimental, and still may not yield the optimal parameters. + +:line + +The {diff} keyword specifies the differentiation scheme used by the +PPPM method to compute forces on particles given electrostatic +potentials on the PPPM mesh. The {ik} approach is the default for +PPPM and is the original formulation used in "(Hockney)"_#Hockney1. It +performs differentiation in Kspace, and uses 3 FFTs to transfer each +component of the computed fields back to real space for total of 4 +FFTs per timestep. + +The analytic differentiation {ad} approach uses only 1 FFT to transfer +information back to real space for a total of 2 FFTs per timestep. It +then performs analytic differentiation on the single quantity to +generate the 3 components of the electric field at each grid point. +This is sometimes referred to as "smoothed" PPPM. This approach +requires a somewhat larger PPPM mesh to achieve the same accuracy as +the {ik} method. Currently, only the {ik} method (default) can be +used for a triclinic simulation cell with PPPM. The {ad} method is +always used for MSM. + +NOTE: Currently, not all PPPM styles support the {ad} option. Support +for those PPPM variants will be added later. + +:line + +The {disp/auto} option controls whether the pppm/disp is allowed to +generate PPPM parameters automatically. If set to {no}, parameters have +to be specified using the {gewald/disp}, {mesh/disp}, +{force/disp/real} or {force/disp/kspace} keywords, or +the code will stop with an error message. When this option is set to +{yes}, the error message will not appear and the simulation will start. +For a typical application, using the automatic parameter generation +will provide simulations that are either inaccurate or slow. Using this +option is thus not recommended. For guidelines on how to obtain good +parameters, see the "How-To"_Section_howto.html#howto_24 discussion. + +:line + +The {fftbench} keyword applies only to PPPM. It is off by default. If +this option is turned on, LAMMPS will perform a short FFT benchmark +computation and report its timings, and will thus finish a some seconds +later than it would if this option were off. + +:line + +The {force/disp/real} and {force/disp/kspace} keywords set the force +accuracy for the real and space computations for the dispersion part +of pppm/disp. As shown in "(Isele-Holder)"_#Isele-Holder1, optimal +performance and accuracy in the results is obtained when these values +are different. + +:line + +The {force} keyword overrides the relative accuracy parameter set by +the "kspace_style"_kspace_style.html command with an absolute +accuracy. The accuracy determines the RMS error in per-atom forces +calculated by the long-range solver and is thus specified in force +units. A negative value for the accuracy setting means to use the +relative accuracy parameter. The accuracy setting is used in +conjunction with the pairwise cutoff to determine the number of +K-space vectors for style {ewald}, the FFT grid size for style +{pppm}, or the real space grid size for style {msm}. + +:line + +The {gewald} keyword sets the value of the Ewald or PPPM G-ewald +parameter for charge as {rinv} in reciprocal distance units. Without +this setting, LAMMPS chooses the parameter automatically as a function +of cutoff, precision, grid spacing, etc. This means it can vary from +one simulation to the next which may not be desirable for matching a +KSpace solver to a pre-tabulated pairwise potential. This setting can +also be useful if Ewald or PPPM fails to choose a good grid spacing +and G-ewald parameter automatically. If the value is set to 0.0, +LAMMPS will choose the G-ewald parameter automatically. MSM does not +use the {gewald} parameter. + +:line + +The {gewald/disp} keyword sets the value of the Ewald or PPPM G-ewald +parameter for dispersion as {rinv} in reciprocal distance units. It +has the same meaning as the {gewald} setting for Coulombics. + +:line + +The {kmax/ewald} keyword sets the number of kspace vectors in each +dimension for kspace style {ewald}. The three values must be positive +integers, or else (0,0,0), which unsets the option. When this option +is not set, the Ewald sum scheme chooses its own kspace vectors, +consistent with the user-specified accuracy and pairwise cutoff. In +any case, if kspace style {ewald} is invoked, the values used are +printed to the screen and the log file at the start of the run. + +:line + The {mesh} keyword sets the grid size for kspace style {pppm} or {msm}. In the case of PPPM, this is the FFT mesh, and each dimension must be factorizable into powers of 2, 3, and 5. In the case of MSM, @@ -70,6 +200,8 @@ or MSM solver chooses its own grid size, consistent with the user-specified accuracy and pairwise cutoff. Values for x,y,z of 0,0,0 unset the option. +:line + The {mesh/disp} keyword sets the grid size for kspace style {pppm/disp}. This is the FFT mesh for long-range dispersion and ach dimension must be factorizable into powers of 2, 3, and 5. When this @@ -77,39 +209,7 @@ option is not set, the PPPM solver chooses its own grid size, consistent with the user-specified accuracy and pairwise cutoff. Values for x,y,z of 0,0,0 unset the option. -The {order} keyword determines how many grid spacings an atom's charge -extends when it is mapped to the grid in kspace style {pppm} or {msm}. -The default for this parameter is 5 for PPPM and 8 for MSM, which -means each charge spans 5 or 8 grid cells in each dimension, -respectively. For the LAMMPS implementation of MSM, the order can -range from 4 to 10 and must be even. For PPPM, the minimum allowed -setting is 2 and the maximum allowed setting is 7. The larger the -value of this parameter, the smaller that LAMMPS will set the grid -size, to achieve the requested accuracy. Conversely, the smaller the -order value, the larger the grid size will be. Note that there is an -inherent trade-off involved: a small grid will lower the cost of FFTs -or MSM direct sum, but a larger order parameter will increase the cost -of interpolating charge/fields to/from the grid. - -The {order/disp} keyword determines how many grid spacings an atom's -dispersion term extends when it is mapped to the grid in kspace style -{pppm/disp}. It has the same meaning as the {order} setting for -Coulombics. - -The {overlap} keyword can be used in conjunction with the {minorder} -keyword with the PPPM styles to adjust the amount of communication -that occurs when values on the FFT grid are exchanged between -processors. This communication is distinct from the communication -inherent in the parallel FFTs themselves, and is required because -processors interpolate charge and field values using grid point values -owned by neighboring processors (i.e. ghost point communication). If -the {overlap} keyword is set to {yes} then this communication is -allowed to extend beyond nearest-neighbor processors, e.g. when using -lots of processors on a small problem. If it is set to {no} then the -communication will be limited to nearest-neighbor processors and the -{order} setting will be reduced if necessary, as explained by the -{minorder} keyword discussion. The {overlap} keyword is always set to -{yes} in MSM. +:line The {minorder} keyword allows LAMMPS to reduce the {order} setting if necessary to keep the communication of ghost grid point limited to @@ -126,6 +226,42 @@ error if the grid communication is non-nearest-neighbor and {overlap} is set to {no}. The {minorder} keyword is not currently supported in MSM. +:line + +The {mix/disp} keyword selects the mixing rule for the dispersion +coefficients. With {pair}, the dispersion coefficients of unlike +types are computed as indicated with "pair_modify"_pair_modify.html. +With {geom}, geometric mixing is enforced on the dispersion +coefficients in the kspace coefficients. When using the arithmetic +mixing rule, this will speed-up the simulations but introduces some +error in the force computations, as shown in "(Wennberg)"_#Wennberg. +With {none}, it is assumed that no mixing rule is +applicable. Splitting of the dispersion coefficients will be performed +as described in "(Isele-Holder)"_#Isele-Holder1. + +This splitting can be influenced with the {splittol} keywords. Only +the eigenvalues that are larger than tol compared to the largest +eigenvalues are included. Using this keywords the original matrix of +dispersion coefficients is approximated. This leads to faster +computations, but the accuracy in the reciprocal space computations of +the dispersion part is decreased. + +:line + +The {order} keyword determines how many grid spacings an atom's charge +extends when it is mapped to the grid in kspace style {pppm} or {msm}. +The default for this parameter is 5 for PPPM and 8 for MSM, which +means each charge spans 5 or 8 grid cells in each dimension, +respectively. For the LAMMPS implementation of MSM, the order can +range from 4 to 10 and must be even. For PPPM, the minimum allowed +setting is 2 and the maximum allowed setting is 7. The larger the +value of this parameter, the smaller that LAMMPS will set the grid +size, to achieve the requested accuracy. Conversely, the smaller the +order value, the larger the grid size will be. Note that there is an +inherent trade-off involved: a small grid will lower the cost of FFTs +or MSM direct sum, but a larger order parameter will increase the cost +of interpolating charge/fields to/from the grid. + The PPPM order parameter may be reset by LAMMPS when it sets up the FFT grid if the implied grid stencil extends beyond the grid cells owned by neighboring processors. Typically this will only occur when @@ -134,30 +270,66 @@ be generated indicating the order parameter is being reduced to allow LAMMPS to run the problem. Automatic adjustment of the order parameter is not supported in MSM. -The {force} keyword overrides the relative accuracy parameter set by -the "kspace_style"_kspace_style.html command with an absolute -accuracy. The accuracy determines the RMS error in per-atom forces -calculated by the long-range solver and is thus specified in force -units. A negative value for the accuracy setting means to use the -relative accuracy parameter. The accuracy setting is used in -conjunction with the pairwise cutoff to determine the number of -K-space vectors for style {ewald}, the FFT grid size for style -{pppm}, or the real space grid size for style {msm}. +:line -The {gewald} keyword sets the value of the Ewald or PPPM G-ewald -parameter for charge as {rinv} in reciprocal distance units. Without -this setting, LAMMPS chooses the parameter automatically as a function -of cutoff, precision, grid spacing, etc. This means it can vary from -one simulation to the next which may not be desirable for matching a -KSpace solver to a pre-tabulated pairwise potential. This setting can -also be useful if Ewald or PPPM fails to choose a good grid spacing -and G-ewald parameter automatically. If the value is set to 0.0, -LAMMPS will choose the G-ewald parameter automatically. MSM does not -use the {gewald} parameter. +The {order/disp} keyword determines how many grid spacings an atom's +dispersion term extends when it is mapped to the grid in kspace style +{pppm/disp}. It has the same meaning as the {order} setting for +Coulombics. -The {gewald/disp} keyword sets the value of the Ewald or PPPM G-ewald -parameter for dispersion as {rinv} in reciprocal distance units. It -has the same meaning as the {gewald} setting for Coulombics. +:line + +The {overlap} keyword can be used in conjunction with the {minorder} +keyword with the PPPM styles to adjust the amount of communication +that occurs when values on the FFT grid are exchanged between +processors. This communication is distinct from the communication +inherent in the parallel FFTs themselves, and is required because +processors interpolate charge and field values using grid point values +owned by neighboring processors (i.e. ghost point communication). If +the {overlap} keyword is set to {yes} then this communication is +allowed to extend beyond nearest-neighbor processors, e.g. when using +lots of processors on a small problem. If it is set to {no} then the +communication will be limited to nearest-neighbor processors and the +{order} setting will be reduced if necessary, as explained by the +{minorder} keyword discussion. The {overlap} keyword is always set to +{yes} in MSM. + +:line + +The {pressure/scalar} keyword applies only to MSM. If this option is +turned on, only the scalar pressure (i.e. (Pxx + Pyy + Pzz)/3.0) will +be computed, which can be used, for example, to run an isotropic barostat. +Computing the full pressure tensor with MSM is expensive, and this option +provides a faster alternative. The scalar pressure is computed using a +relationship between the Coulombic energy and pressure "(Hummer)"_#Hummer +instead of using the virial equation. This option cannot be used to access +individual components of the pressure tensor, to compute per-atom virial, +or with suffix kspace/pair styles of MSM, like OMP or GPU. + +:line + +RENE: check this section + +The {scafacos} keyword is used for settings that are passed to the +ScaFaCoS library when using "kspace_style scafacos"_kspace_style.html. + +The {tolerance} option affects how the {accuracy} specified with +the "kspace_style"_kspace_style.html command is interpreted by ScaFaCoS. +The following values may be used: + +energy = absolute accuracy in total Coulomic energy +energy_rel = relative accuracy in total Coulomic energy +field = absolute accuracy in electric field +field_rel = relative accuracy in electric field +potential = absolute accuracy in total Coulomic potential +potential_rel = relative accuracy in total Coulomic potential + +RENE: which one is closest to what LAMMPS used (see kspace_style +command) - is it "field"? That's why I set it as the default. + +RENE: How is potential different than energy for this ?? + +:line The {slab} keyword allows an Ewald or PPPM solver to be used for a systems that are periodic in x,y but non-periodic in z - a @@ -191,109 +363,11 @@ the "fix efield"_fix_efield.html command, it will not give the correct dielectric constant due to the Yeh/Berkowitz "(Yeh)"_#Yeh correction not being compatible with how "fix efield"_fix_efield.html works. -The {compute} keyword allows Kspace computations to be turned off, -even though a "kspace_style"_kspace_style.html is defined. This is -not useful for running a real simulation, but can be useful for -debugging purposes or for computing only partial forces that do not -include the Kspace contribution. You can also do this by simply not -defining a "kspace_style"_kspace_style.html, but a Kspace-compatible -"pair_style"_pair_style.html requires a kspace style to be defined. -This keyword gives you that option. +:line -The {cutoff/adjust} keyword applies only to MSM. If this option is -turned on, the Coulombic cutoff will be automatically adjusted at the -beginning of the run to give the desired estimated error. Other -cutoffs such as LJ will not be affected. If the grid is not set using -the {mesh} command, this command will also attempt to use the optimal -grid that minimizes cost using an estimate given by -"(Hardy)"_#Hardy1. Note that this cost estimate is not exact, somewhat -experimental, and still may not yield the optimal parameters. +The {splittol} keyword is disussed above with the {mix/disp} keyword. -The {pressure/scalar} keyword applies only to MSM. If this option is -turned on, only the scalar pressure (i.e. (Pxx + Pyy + Pzz)/3.0) will -be computed, which can be used, for example, to run an isotropic barostat. -Computing the full pressure tensor with MSM is expensive, and this option -provides a faster alternative. The scalar pressure is computed using a -relationship between the Coulombic energy and pressure "(Hummer)"_#Hummer -instead of using the virial equation. This option cannot be used to access -individual components of the pressure tensor, to compute per-atom virial, -or with suffix kspace/pair styles of MSM, like OMP or GPU. - -The {fftbench} keyword applies only to PPPM. It is off by default. If -this option is turned on, LAMMPS will perform a short FFT benchmark -computation and report its timings, and will thus finish a some seconds -later than it would if this option were off. - -The {collective} keyword applies only to PPPM. It is set to {no} by -default, except on IBM BlueGene machines. If this option is set to -{yes}, LAMMPS will use MPI collective operations to remap data for -3d-FFT operations instead of the default point-to-point communication. -This is faster on IBM BlueGene machines, and may also be faster on -other machines if they have an efficient implementation of MPI -collective operations and adequate hardware. - -The {diff} keyword specifies the differentiation scheme used by the -PPPM method to compute forces on particles given electrostatic -potentials on the PPPM mesh. The {ik} approach is the default for -PPPM and is the original formulation used in "(Hockney)"_#Hockney1. It -performs differentiation in Kspace, and uses 3 FFTs to transfer each -component of the computed fields back to real space for total of 4 -FFTs per timestep. - -The analytic differentiation {ad} approach uses only 1 FFT to transfer -information back to real space for a total of 2 FFTs per timestep. It -then performs analytic differentiation on the single quantity to -generate the 3 components of the electric field at each grid point. -This is sometimes referred to as "smoothed" PPPM. This approach -requires a somewhat larger PPPM mesh to achieve the same accuracy as -the {ik} method. Currently, only the {ik} method (default) can be -used for a triclinic simulation cell with PPPM. The {ad} method is -always used for MSM. - -NOTE: Currently, not all PPPM styles support the {ad} option. Support -for those PPPM variants will be added later. - -The {kmax/ewald} keyword sets the number of kspace vectors in each -dimension for kspace style {ewald}. The three values must be positive -integers, or else (0,0,0), which unsets the option. When this option -is not set, the Ewald sum scheme chooses its own kspace vectors, -consistent with the user-specified accuracy and pairwise cutoff. In -any case, if kspace style {ewald} is invoked, the values used are -printed to the screen and the log file at the start of the run. - -With the {mix/disp} keyword one can select the mixing rule for the -dispersion coefficients. With {pair}, the dispersion coefficients of -unlike types are computed as indicated with -"pair_modify"_pair_modify.html. With {geom}, geometric mixing is -enforced on the dispersion coefficients in the kspace -coefficients. When using the arithmetic mixing rule, this will -speed-up the simulations but introduces some error in the force -computations, as shown in "(Wennberg)"_#Wennberg. With {none}, it is -assumed that no mixing rule is applicable. Splitting of the dispersion -coefficients will be performed as described in -"(Isele-Holder)"_#Isele-Holder1. This splitting can be influenced with -the {splittol} keywords. Only the eigenvalues that are larger than tol -compared to the largest eigenvalues are included. Using this keywords -the original matrix of dispersion coefficients is approximated. This -leads to faster computations, but the accuracy in the reciprocal space -computations of the dispersion part is decreased. - -The {force/disp/real} and {force/disp/kspace} keywords set the force -accuracy for the real and space computations for the dispersion part -of pppm/disp. As shown in "(Isele-Holder)"_#Isele-Holder1, optimal -performance and accuracy in the results is obtained when these values -are different. - -The {disp/auto} option controls whether the pppm/disp is allowed to -generate PPPM parameters automatically. If set to {no}, parameters have -to be specified using the {gewald/disp}, {mesh/disp}, -{force/disp/real} or {force/disp/kspace} keywords, or -the code will stop with an error message. When this option is set to -{yes}, the error message will not appear and the simulation will start. -For a typical application, using the automatic parameter generation -will provide simulations that are either inaccurate or slow. Using this -option is thus not recommended. For guidelines on how to obtain good -parameters, see the "How-To"_Section_howto.html#howto_24 discussion. +:line [Restrictions:] none @@ -306,10 +380,11 @@ parameters, see the "How-To"_Section_howto.html#howto_24 discussion. The option defaults are mesh = mesh/disp = 0 0 0, order = order/disp = 5 (PPPM), order = 10 (MSM), minorder = 2, overlap = yes, force = -1.0, gewald = gewald/disp = 0.0, slab = 1.0, compute = yes, cutoff/adjust = -yes (MSM), pressure/scalar = yes (MSM), fftbench = no (PPPM), diff = ik -(PPPM), mix/disp = pair, force/disp/real = -1.0, force/disp/kspace = -1.0, -split = 0, tol = 1.0e-6, and disp/auto = no. For pppm/intel, order = -order/disp = 7. +yes (MSM), pressure/scalar = yes (MSM), fftbench = no (PPPM), diff = +ik (PPPM), mix/disp = pair, force/disp/real = -1.0, force/disp/kspace += -1.0, split = 0, tol = 1.0e-6, and disp/auto = no. For pppm/intel, +order = order/disp = 7. For scafacos settings, scafacos tolerance +field. :line diff --git a/doc/src/kspace_style.txt b/doc/src/kspace_style.txt index 4f27c9aa78..e5333489cc 100644 --- a/doc/src/kspace_style.txt +++ b/doc/src/kspace_style.txt @@ -12,7 +12,7 @@ kspace_style command :h3 kspace_style style value :pre -style = {none} or {ewald} or {ewald/disp} or {ewald/omp} or {pppm} or {pppm/cg} or {pppm/disp} or {pppm/tip4p} or {pppm/stagger} or {pppm/disp/tip4p} or {pppm/gpu} or {pppm/kk} or {pppm/omp} or {pppm/cg/omp} or {pppm/tip4p/omp} or {msm} or {msm/cg} or {msm/omp} or {msm/cg/omp} :ulb,l +style = {none} or {ewald} or {ewald/disp} or {ewald/omp} or {pppm} or {pppm/cg} or {pppm/disp} or {pppm/tip4p} or {pppm/stagger} or {pppm/disp/tip4p} or {pppm/gpu} or {pppm/kk} or {pppm/omp} or {pppm/cg/omp} or {pppm/tip4p/omp} or {msm} or {msm/cg} or {msm/omp} or {msm/cg/omp} or {scafacos} :ulb,l {none} value = none {ewald} value = accuracy accuracy = desired relative error in forces @@ -22,7 +22,7 @@ style = {none} or {ewald} or {ewald/disp} or {ewald/omp} or {pppm} or {pppm/cg} accuracy = desired relative error in forces {pppm} value = accuracy accuracy = desired relative error in forces - {pppm/cg} value = accuracy (smallq) + {pppm/cg} values = accuracy (smallq) accuracy = desired relative error in forces smallq = cutoff for charges to be considered (optional) (charge units) {pppm/disp} value = accuracy @@ -56,7 +56,10 @@ style = {none} or {ewald} or {ewald/disp} or {ewald/omp} or {pppm} or {pppm/cg} accuracy = desired relative error in forces {msm/cg/omp} value = accuracy (smallq) accuracy = desired relative error in forces - smallq = cutoff for charges to be considered (optional) (charge units) :pre + smallq = cutoff for charges to be considered (optional) (charge units) + {scafacos} values = method accuracy + method = fmm or p3m or ... RENE + accuracy = desired relative error in forces :pre :ule [Examples:] @@ -64,6 +67,7 @@ style = {none} or {ewald} or {ewald/disp} or {ewald/omp} or {pppm} or {pppm/cg} kspace_style pppm 1.0e-4 kspace_style pppm/cg 1.0e-5 1.0e-6 kspace style msm 1.0e-4 +kspace style scafacos fmm 1.0e-4 kspace_style none :pre [Description:] @@ -210,6 +214,63 @@ pressure simulation with MSM will cause the code to run slower. :line +RENE: edit this section + +The {scafacos} style is a wrapper on the "ScaFaCoS Coulomb solver +library"_http://www.scafacos.de which provides a variety of solver +methods which can be used with LAMMPS. The paper by "(Who)"_#Who2012 +gives an overview of ScaFaCoS. + +ScaFaCoS was developed by a consortium of German research facilities +with a BMBF (German Ministry of Science and Education) funded project +in 2009-2012. Participants of the consortium were the Universities of +Bonn, Chemnitz, Stuttgart, and Wuppertal as well as the +Forschungszentrum Juelich. + +The library is available for download at "http://scafacos.de" or can +be cloned from the git-repository +"git://github.com/scafacos/scafacos.git". + +In order to use this KSpace style, you must download and build the +ScaFaCoS library, then build LAMMPS with the USER-SCAFACOS package +installed package which links LAMMPS to the ScaFaCoS library. +See details on "this page"_Section_packages.html#USER-SCAFACOS. + +NOTE: Unlike other KSpace solvers in LAMMPS, ScaFaCoS computes all +Coulombic interactions, both short- and long-range. Thus you should +NOT use a Coulmbic pair style when using kspace_style scafacos. Thus +the total Coulombic energy (short- and long-range) will be tallied for +"thermodynamic output"_thermo_style.html command as part of the +{elong} keyword; the {ecoul} keyword will be zero. + +NOTE: See the restriction below about use of ScaFaCoS in LAMMPS with +molecular charged systems or the TIP4P water model. + +Unlike other KSpace solvers in LAMMPS, ScaFaCoS computes all +Coulombic interactions, both short- and long-range. Thus you should +NOT use a Coulmbic pair style when using kspace_style scafacos. Thus +the total Coulombic energy (short- and long-range) will be tallied for +"thermodynamic output"_thermo_style.html command as part of the +{elong} keyword; the {ecoul} keyword will be zero. + +The specified {method} determines which ScaFaCoS algorithm is used. +The list of methods shown above are the ScaFaCoS methods currently +available from LAMMPS. + +RENE: explain this accuracy better compared to what +it means for other LAMMPS methods? + +The specified {accuracy} is similar to the accuracy setting for other +LAMMPS KSpace styles, but is passed to ScaFaCoS, which can interpret +it in different ways for different methods it supports. See the +"kspace_modify scafacos accuracy"_kspace_modify.html command for +details. + +The "kspace_modify scafacos"_kspace_modify.html command also explains +all the ScaFaCoS options currently exposed to LAMMPS. + +:line + The specified {accuracy} determines the relative RMS error in per-atom forces calculated by the long-range solver. It is set as a dimensionless number, relative to the force that two unit point @@ -321,12 +382,24 @@ dimensions. The only exception is if the slab option is set with "kspace_modify"_kspace_modify.html, in which case the xy dimensions must be periodic and the z dimension must be non-periodic. +The scafacos KSpace style will only be enabled if LAMMPS is built with +the USER-SCAFACOS package. See the "Making +LAMMPS"_Section_start.html#start_3 section for more info. + +The use of ScaFaCos in LAMMPS does not yet support molecular charged +systems where the short-range Coulombic interactions between atoms in +the same bond/angle/dihedral are weighted by the +"special_bonds"_special_bonds.html command. Likewise it does not +support the "TIP4P water style" where a fictitious charge site is +introduced in each water molecule. + [Related commands:] "kspace_modify"_kspace_modify.html, "pair_style lj/cut/coul/long"_pair_lj.html, "pair_style lj/charmm/coul/long"_pair_charmm.html, "pair_style -lj/long/coul/long"_pair_lj_long.html, "pair_style buck/coul/long"_pair_buck.html +lj/long/coul/long"_pair_lj_long.html, "pair_style +buck/coul/long"_pair_buck.html [Default:] @@ -384,5 +457,11 @@ Evaluation of Forces for the Simulation of Biomolecules, University of Illinois at Urbana-Champaign, (2006). :link(Hardy2009) -[(Hardy2)] Hardy, Stone, Schulten, Parallel Computing 35 (2009) -164-177. +[(Hardy2)] Hardy, Stone, Schulten, Parallel Computing, 35, 164-177 +(2009). + +RENE: + +:link(Who2012) +[(Who)] Who, Author2, Author3, J of Long Range Solvers, 35, 164-177 +(2012). diff --git a/examples/USER/scafacos/README b/examples/USER/scafacos/README new file mode 100644 index 0000000000..0ddd19d3ee --- /dev/null +++ b/examples/USER/scafacos/README @@ -0,0 +1,10 @@ +RENE: this dir needs a few short-running examples, +for both 1 and 4 procs, of using different Scafacos methods. +with sample log file outputs - so users can verify +they are running it correctly + +For each input script, there should be files like + +in.scafacos.fmm +log.20Jul18.scafacos.fmm.g++.1 +log.20Jul18.scafacos.fmm.g++.4 diff --git a/examples/scafacos/data.NaCl b/examples/USER/scafacos/data.NaCl similarity index 100% rename from examples/scafacos/data.NaCl rename to examples/USER/scafacos/data.NaCl diff --git a/examples/scafacos/in.scafacos b/examples/USER/scafacos/in.scafacos similarity index 100% rename from examples/scafacos/in.scafacos rename to examples/USER/scafacos/in.scafacos diff --git a/lib/scafacos/Install.py b/lib/scafacos/Install.py index 5d4ca7e96a..1b39335511 100644 --- a/lib/scafacos/Install.py +++ b/lib/scafacos/Install.py @@ -29,7 +29,7 @@ make lib-scafacos args="-p $HOME/scafacos" # use existing Scafacos installation # settings -#version = "voro++-0.4.6" +version = "scafacos-1.0" #url = "http://math.lbl.gov/voro++/download/dir/%s.tar.gz" % version # print error message or help @@ -89,7 +89,6 @@ def geturl(url,fname): args = sys.argv[1:] nargs = len(args) -#if nargs == 0: error() homepath = "." @@ -114,8 +113,7 @@ while iarg < nargs: else: error() homepath = fullpath(homepath) -#homedir = "%s/%s" % (homepath,version) -homedir = homepath +homedir = "%s/%s" % (homepath,version) if (pathflag): if not os.path.isdir(scafacospath): error("Scafacos path does not exist") @@ -124,16 +122,13 @@ if (pathflag): if (buildflag and pathflag): error("Cannot use -b and -p flag at the same time") -#if (not buildflag and not pathflag): -# error("Have to use either -b or -p flag") - # download and unpack Scafacos tarball if buildflag: print("Downloading Scafacos ...") geturl(url,"%s/%s.tar.gz" % (homepath,version)) - print("Unpacking Voro++ tarball ...") + print("Unpacking Scafacos tarball ...") if os.path.exists("%s/%s" % (homepath,version)): cmd = 'rm -rf "%s/%s"' % (homepath,version) subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) @@ -162,7 +157,7 @@ if linkflag: os.remove("includelink") if os.path.isfile("liblink") or os.path.islink("liblink"): os.remove("liblink") - cmd = 'ln -s "scafacos/include" includelink' + cmd = 'ln -s "%s/include" includelink' % homedir subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) - cmd = 'ln -s "scafacos/lib" liblink' + cmd = 'ln -s "%s/lib" liblink' % homedir subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) diff --git a/src/USER-SCAFACOS/README b/src/USER-SCAFACOS/README new file mode 100644 index 0000000000..30534499e4 --- /dev/null +++ b/src/USER-SCAFACOS/README @@ -0,0 +1,5 @@ +RENE: need a short README file - see other examples in the +USER package dirs within src + +give short background on ScaFaCos, authors, contact info +for LAMMPS users to have if needed, citation diff --git a/src/USER-SCAFACOS/fix_scafacos.cpp b/src/USER-SCAFACOS/fix_scafacos.cpp deleted file mode 100644 index 08aebb9f22..0000000000 --- a/src/USER-SCAFACOS/fix_scafacos.cpp +++ /dev/null @@ -1,456 +0,0 @@ -/* ---------------------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -/* ---------------------------------------------------------------------- - Contributing author: Rene Halver (JSC) -------------------------------------------------------------------------- */ - -#include -#include -#include -#include "fix_scafacos.h" -#include "atom.h" -#include "comm.h" -#include "update.h" -#include "neighbor.h" -#include "domain.h" -#include "force.h" -#include "pair.h" -#include "modify.h" -#include "compute.h" -#include "memory.h" -#include "error.h" - -// ScaFaCoS library -#include -#include -#include "fcs.h" -#include "universe.h" - -using namespace LAMMPS_NS; -using namespace FixConst; - -#define INVOKED_PERATOM 8 - -/* ---------------------------------------------------------------------- */ - -FixScafacos::FixScafacos(LAMMPS *lmp, int narg, char **arg) : - Fix(lmp, narg, arg) -{ - // form of fix string: - // fix <#> scafacos [ tolerance ] - - - if (narg < 4) error->all(FLERR,"Illegal fix scafacos command"); - - // read method from fix input - method = arg[3]; - - int arg_index = 4; - - tolerance_set = false; - - while(arg_index < narg) - { - // check if tolerance option is set - if (strcmp(arg[arg_index],"tolerance") == 0) - { - tolerance_set = true; - ++arg_index; - if (strcmp(arg[arg_index],"energy") == 0) - tolerance_type = FCS_TOLERANCE_TYPE_ENERGY; - else if (strcmp(arg[arg_index],"energy_rel") == 0) - tolerance_type = FCS_TOLERANCE_TYPE_ENERGY_REL; - else if (strcmp(arg[arg_index],"field") == 0) - tolerance_type = FCS_TOLERANCE_TYPE_FIELD; - else if (strcmp(arg[arg_index],"field_rel") == 0) - tolerance_type = FCS_TOLERANCE_TYPE_FIELD_REL; - else if (strcmp(arg[arg_index],"potential") == 0) - tolerance_type = FCS_TOLERANCE_TYPE_POTENTIAL; - else if (strcmp(arg[arg_index],"potential_rel") == 0) - tolerance_type = FCS_TOLERANCE_TYPE_POTENTIAL_REL; - else - error->all(FLERR,"Illegal fix scafacos command"); - ++arg_index; - tolerance_value = atof(arg[arg_index]); - ++arg_index; - } - else - error->all(FLERR,"Illegal fix scafacos command"); - } -} - -/* ---------------------------------------------------------------------- */ - -FixScafacos::~FixScafacos() -{ - memory->destroy(pot); - memory->destroy(field); -} - -/* ---------------------------------------------------------------------- */ - -int FixScafacos::setmask() -{ - int mask = 0; - //mask |= INITIAL_INTEGRATE; - //mask |= FINAL_INTEGRATE; - mask |= PRE_REVERSE; - mask |= POST_FORCE; - mask |= MIN_POST_FORCE; - mask |= THERMO_ENERGY; - return mask; -} - -/* ---------------------------------------------------------------------- */ - -void FixScafacos::init() -{ - // error checks - - if (domain->dimension == 2) - error->all(FLERR,"Fix scafacos requires 3d problem"); - - rank = comm->me; - - int nlocal = 0; - int proc_grid[3] = {comm->procgrid[0], comm->procgrid[1], comm->procgrid[2]}; - int myloc[3] = {comm->myloc[0], comm->myloc[1], comm->myloc[2]}; - - // call ScaFaCoS init - // TODO: check if universe->uworld is a good idea for computations - result = fcs_init(&fcs,method.c_str(),universe->uworld); - if (!check_result(result, rank)) return; - - setup_handle(); - - nlocal = atom -> nlocal; - // get particle data - x = &atom->x[0][0]; - q = atom->q; - - if (tolerance_set) - { - result = fcs_set_tolerance(fcs,tolerance_type,tolerance_value); - if (!check_result(result, rank)) return; - } - - // print out parameters within handle - if (rank == 0) fcs_print_parameters(fcs); - - // call the tuning routine (needs to be redone, if critical system - // parameters should change) - result = fcs_tune(fcs,nlocal,x,q); - if (!check_result(result, rank)) return; - - // allocate arrays larger in order to avoid fast - // reallocation due to fluctuations - local_array_size = (int)(1.25 * (double)nlocal); - - // allocate new result arrays - memory->create(pot,local_array_size,"scafacos:potential"); - memory->create(field,local_array_size*3,"scafacos:field"); -} - -/* ---------------------------------------------------------------------- */ - -void FixScafacos::init_list(int id, NeighList *ptr) -{ -} - -/* ---------------------------------------------------------------------- */ - -void FixScafacos::setup(int vflag) -{ - post_force(vflag); -} - -/* ---------------------------------------------------------------------- */ - -void FixScafacos::min_setup(int vflag) -{ - post_force(vflag); -} - -/* ---------------------------------------------------------------------- */ - -void FixScafacos::setup_pre_reverse(int eflag, int vflag) -{ - pre_reverse(eflag,vflag); -} - -/* ---------------------------------------------------------------------- - integrate electronic degrees of freedom -------------------------------------------------------------------------- */ - -void FixScafacos::initial_integrate(int vflag) {} - -/* ---------------------------------------------------------------------- - store eflag, so can use it in post_force to tally per-atom energies -------------------------------------------------------------------------- */ - -void FixScafacos::pre_reverse(int eflag, int vflag) -{ - int eflag_caller = eflag; -} - -/* ---------------------------------------------------------------------- */ - -void FixScafacos::post_force(int vflag) -{ - - int nlocal; - - nlocal = atom->nlocal; - x = &atom->x[0][0]; - q = atom->q; - - // check if box has changed since the last call of fcs_tune, - // if it has, call fcs_tune - if (box_has_changed()) - { - setup_handle(); - - // print out parameters within handle TODO: should be done in C style - /* - if (rank == 0) - { - std::cout << " updated ScaFaCoS handle: " << std::endl; - fcs_print_parameters(fcs); - } - */ - - // call the tuning routine (needs to be redone, if critical - // system parameters should change) - result = fcs_tune(fcs,nlocal,x,q); - if (!check_result(result, rank)) return; - } - - // check if arrays for potentials and field are still large enough - // for the number of particles on process - if (nlocal > local_array_size) - { - // allocate arrays larger in order to avoid fast - // reallocation due to fluctuations - local_array_size = (int)(1.25 * (double)nlocal); - - // destroy old result arrays - memory->destroy(pot); - memory->destroy(field); - - // allocate result arrays - memory->create(pot,local_array_size,"scafacos:potential"); - memory->create(field,3*local_array_size,"scafacos:field"); - - } - - // set result vectors to zero - for ( int i = 0; i < nlocal; ++i) - { - pot[i] = 0.0; - field[3*i] = field[3*i+1] = field[3*i+2] = 0.0; - } - - // compute Coulomb - fcs_run(fcs, nlocal, x, q, field, pot); - if(!check_result(result,rank)) return; - - double E_coul_loc = 0.0; - - for (int i = 0; i < atom->nlocal; ++i) - { - //std::cout << atom->f[i][0] << " " << field[3*i] << " " << q[i] << std::endl; - atom->f[i][0] += field[3*i] * q[i]; - atom->f[i][1] += field[3*i+1] * q[i]; - atom->f[i][2] += field[3*i+2] * q[i]; - E_coul_loc += 0.5 * q[i] * pot[i]; - } - - force->pair->eng_coul += E_coul_loc; - -} - -/* ---------------------------------------------------------------------- */ - -void FixScafacos::min_post_force(int vflag) -{ - post_force(vflag); -} - -/* ---------------------------------------------------------------------- - integrate electronic degrees of freedom -------------------------------------------------------------------------- */ - -void FixScafacos::final_integrate() {} - -/* ---------------------------------------------------------------------- */ - -void FixScafacos::reset_dt() -{ - //dtv = update->dt; - //dtf = 0.5 * update->dt * force->ftm2v; -} - -/* ---------------------------------------------------------------------- - DFTB energy from LATTE -------------------------------------------------------------------------- */ - -double FixScafacos::compute_scalar() -{ -} - -/* ---------------------------------------------------------------------- - memory usage of local arrays -------------------------------------------------------------------------- */ - -double FixScafacos::memory_usage() -{ - double bytes = 0.0; - bytes += local_array_size * sizeof(double); - bytes += local_array_size * 3 * sizeof(double); - return bytes; -} - -/* ---------------------------------------------------------------------- - setup of ScaFaCoS handle with common parameters -------------------------------------------------------------------------- */ -void FixScafacos::setup_handle() -{ - // store periodicity - periodicity[0] = domain->xperiodic; - periodicity[1] = domain->yperiodic; - periodicity[2] = domain->zperiodic; - - // store offset of the system - offset[0] = domain->boundary[0][0]; - offset[1] = domain->boundary[1][0]; - offset[2] = domain->boundary[2][0]; - - // calculate box vectors - box_x[0] = domain->prd[0]; - box_x[1] = box_x[2] = 0.0; - - box_y[1] = domain->prd[1]; - box_y[0] = box_y[2] = 0.0; - - box_z[2] = domain->prd[2]; - box_z[1] = box_z[0] = 0.0; - - total_particles = atom->natoms; - - // TODO: for now disable short-range calculations within LAMMPS - near_field_flag = 0; - - // enter all parameters required to ScaFaCoS handle - result = fcs_set_box_a(fcs, box_x); - if (!check_result(result, rank)) return; - - result = fcs_set_box_b(fcs, box_y); - if (!check_result(result, rank)) return; - - result = fcs_set_box_c(fcs, box_z); - if (!check_result(result, rank)) return; - - result = fcs_set_box_origin(fcs, offset); - if (!check_result(result, rank)) return; - - result = fcs_set_periodicity(fcs, periodicity); - if (!check_result(result, rank)) return; - - result = fcs_set_near_field_flag(fcs, near_field_flag); - if (!check_result(result, rank)) return; - - result = fcs_set_total_particles(fcs, atom->natoms); - if (!check_result(result, rank)) return; -} - -/* ---------------------------------------------------------------------- - check if box parameters changed, requiring a new call to fcs_tune -------------------------------------------------------------------------- */ -bool FixScafacos::box_has_changed() -{ - bool changed = false; - - double n_periodicity[3]; - double n_offset[3]; - double n_box_x[3]; - double n_box_y[3]; - double n_box_z[3]; - - int n_total_particles; - - // store periodicity - n_periodicity[0] = domain->xperiodic; - n_periodicity[1] = domain->yperiodic; - n_periodicity[2] = domain->zperiodic; - - // store offset of the system - n_offset[0] = domain->boundary[0][0]; - n_offset[1] = domain->boundary[1][0]; - n_offset[2] = domain->boundary[2][0]; - - // calculate box vectors - n_box_x[0] = domain->prd[0]; - n_box_x[1] = n_box_x[2] = 0.0; - - n_box_y[1] = domain->prd[1]; - n_box_y[0] = n_box_y[2] = 0.0; - - n_box_z[2] = domain->prd[2]; - n_box_z[1] = n_box_z[0] = 0.0; - - n_total_particles = atom->natoms; - - changed = changed || - ( n_periodicity[0] != periodicity[0] ) || - ( n_periodicity[1] != periodicity[1] ) || - ( n_periodicity[2] != periodicity[2] ) || - ( n_offset[0] != offset[0] ) || - ( n_offset[1] != offset[1] ) || - ( n_offset[2] != offset[2] ) || - ( n_box_x[0] != box_x[0] ) || - ( n_box_x[1] != box_x[1] ) || - ( n_box_x[2] != box_x[2] ) || - ( n_box_y[0] != box_y[0] ) || - ( n_box_y[1] != box_y[1] ) || - ( n_box_y[2] != box_y[2] ) || - ( n_box_z[0] != box_z[0] ) || - ( n_box_z[1] != box_z[1] ) || - ( n_box_z[2] != box_z[2] ) || - ( n_total_particles != total_particles ); - return changed; -} - - - -/* ---------------------------------------------------------------------- - check of ScaFaCoS result -------------------------------------------------------------------------- */ -bool FixScafacos::check_result(FCSResult result, int comm_rank) -{ - if (result) - { - printf("ScaFaCoS Error: Caught error on task %d.\n", comm_rank); - std::string err_msg; - std::stringstream ss; - - ss << fcs_result_get_function(result) << "\n" - << fcs_result_get_message(result) << "\n"; - err_msg = ss.str(); - - error -> all(FLERR, err_msg.c_str()); - fcs_result_destroy(result); - } - return true; -} - diff --git a/src/USER-SCAFACOS/fix_scafacos.h b/src/USER-SCAFACOS/fix_scafacos.h deleted file mode 100644 index ffd4a94d32..0000000000 --- a/src/USER-SCAFACOS/fix_scafacos.h +++ /dev/null @@ -1,164 +0,0 @@ -/* -*- c++ -*- ---------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -#ifdef FIX_CLASS - -FixStyle(scafacos,FixScafacos) - -#else - -#ifndef LMP_FIX_SCAFACOS_H -#define LMP_FIX_SCAFACOS_H - -#include "fix.h" -#include "fcs.h" -#include - -namespace LAMMPS_NS { - -class FixScafacos : public Fix { - public: - FixScafacos(class LAMMPS *, int, char **); - virtual ~FixScafacos(); - int setmask(); - void init(); - void init_list(int, NeighList*); - void setup(int); - void min_setup(int); - void setup_pre_reverse(int, int); - void initial_integrate(int); - void pre_reverse(int, int); - void post_force(int); - void min_post_force(int); - void final_integrate(); - void reset_dt(); - double compute_scalar(); - double memory_usage(); - - protected: - std::string method; - - // MPI rank - int rank; - - // source arrays for positions and charges - double *x, *q; - // result arrays for potentials and field - double *pot, *field; - - // box vectors for each dimension - fcs_float box_x[3], box_y[3], box_z[3]; - // offset of the box from the origin - fcs_float offset[3]; - - // periodicity of the system - fcs_int periodicity[3]; - - // ScaFaCoS handle - FCS fcs; - - // ScaFaCoS result variable - FCSResult result; - - // function to check results - bool check_result(FCSResult, int); - - // function to set up handle with common parameters - void setup_handle(); - - // function to check if the box parameters changed, so that a new tuning step is required - bool box_has_changed(); - - // store total number of particles (to check if tune needs to be called again) - fcs_int total_particles; - - // store number of local particles (to be able to readjust the size of result arrays, when needed) - int local_array_size; - - // should the near field calculations be computed by LAMMPS? - fcs_int near_field_flag; - - // type of accuracy chosen (if customized) - fcs_int tolerance_type; - - // value of tolerance - fcs_float tolerance_value; - - // is tolerance set? - bool tolerance_set; - - // check if fmm is chosen (ghost particles, since the implementation needs at least 1 particle on each process!) - bool fmm_chosen; - - // FMM: fmm particle array size - int fmm_array_size; -}; - -} - -#endif -#endif - -/* ERROR/WARNING messages: - -E: Must use units metal with fix latte command - -UNDOCUMENTED - -E: Fix latte currently runs only in serial - -UNDOCUMENTED - -E: LAMMPS is linked against incompatible LATTE library - -UNDOCUMENTED - -E: Illegal ... command - -Self-explanatory. Check the input script syntax and compare to the -documentation for the command. You can use -echo screen as a -command-line option when running LAMMPS to see the offending line. - -E: Fix latte does not yet support a LAMMPS calculation of a Coulomb potential - -UNDOCUMENTED - -E: Could not find fix latte compute ID - -UNDOCUMENTED - -E: Fix latte compute ID does not compute pe/atom - -UNDOCUMENTED - -E: Fix latte requires 3d problem - -UNDOCUMENTED - -E: Fix latte cannot compute Coulomb potential - -UNDOCUMENTED - -E: Fix latte requires 3d simulation - -UNDOCUMENTED - -W: Fix latte should come after all other integration fixes - -UNDOCUMENTED - -E: Internal LATTE problem - -UNDOCUMENTED - -*/ diff --git a/src/USER-SCAFACOS/scafacos.cpp b/src/USER-SCAFACOS/scafacos.cpp index c5efd6a191..10721b33c8 100644 --- a/src/USER-SCAFACOS/scafacos.cpp +++ b/src/USER-SCAFACOS/scafacos.cpp @@ -38,40 +38,16 @@ using namespace LAMMPS_NS; Scafacos::Scafacos(LAMMPS *lmp, int narg, char **arg) : KSpace(lmp, narg, arg) { - if (narg < 2) error->all(FLERR,"Illegal scafacos command"); + if (narg != 2) error->all(FLERR,"Illegal scafacos command"); int n = strlen(arg[0]) + 1; method = new char[n]; strcpy(method,arg[0]); + tolerance = force->numeric(FLERR,arg[1]); - // additional args + // optional ScaFaCoS library setting defaults - int tflag = 0; - - int iarg = 1; - while (iarg < narg) { - if (strcmp(arg[iarg],"tolerance") == 0) { - if (iarg+3 > narg) error->all(FLERR,"Illegal scafacos command"); - tflag = 1; - if (strcmp(arg[iarg+1],"energy") == 0) - tolerance_type = FCS_TOLERANCE_TYPE_ENERGY; - else if (strcmp(arg[iarg+1],"energy_rel") == 0) - tolerance_type = FCS_TOLERANCE_TYPE_ENERGY_REL; - else if (strcmp(arg[iarg+1],"field") == 0) - tolerance_type = FCS_TOLERANCE_TYPE_FIELD; - else if (strcmp(arg[iarg+1],"field_rel") == 0) - tolerance_type = FCS_TOLERANCE_TYPE_FIELD_REL; - else if (strcmp(arg[iarg+1],"potential") == 0) - tolerance_type = FCS_TOLERANCE_TYPE_POTENTIAL; - else if (strcmp(arg[iarg+1],"potential_rel") == 0) - tolerance_type = FCS_TOLERANCE_TYPE_POTENTIAL_REL; - else error->all(FLERR,"Illegal scafacos command"); - tolerance = force->numeric(FLERR,arg[iarg+2]); - iarg += 3; - } else error->all(FLERR,"Illegal scafacos command"); - } - - if (!tflag) error->all(FLERR,"Must set tolerance in scafacos command"); + tolerance_type = FCS_TOLERANCE_TYPE_FIELD; // initializations @@ -92,7 +68,7 @@ Scafacos::~Scafacos() memory->destroy(epot); memory->destroy(efield); - // NOTE: any clean-up call to ScaFaCoS needed? + // RENE: any clean-up/shut-down call to ScaFaCoS needed? } /* ---------------------------------------------------------------------- */ @@ -100,7 +76,6 @@ Scafacos::~Scafacos() void Scafacos::init() { // error checks - // NOTE: allow triclinic at some point if (domain->dimension == 2) error->all(FLERR,"Cannot use ScaFaCoS with 2d simulation"); @@ -108,11 +83,13 @@ void Scafacos::init() if (domain->triclinic) error->all(FLERR,"Cannot use ScaFaCoS with triclinic domain yet"); + if (atom->natoms > INT_MAX && sizeof(fcs_int) != 8) + error->all(FLERR,"Scafacos atom count exceeds 2B"); + // one-time initialization of ScaFaCoS scale = 1.0; qqrd2e = force->qqrd2e; - //qsum_qsq(); if (!initialized) { result = fcs_init(&fcs,method,world); @@ -147,13 +124,14 @@ void Scafacos::compute(int eflag, int vflag) double *q = atom->q; int nlocal = atom->nlocal; + // RENE: why is scale needed? + const double qscale = qqrd2e * scale; - // if simluation box has changed, call fcs_tune() - if (eflag || vflag) ev_setup(eflag,vflag); - else - eflag_atom = 0; + else eflag_atom = 0; + + // if simulation box has changed, call fcs_tune() if (box_has_changed()) { setup_handle(); @@ -173,7 +151,7 @@ void Scafacos::compute(int eflag, int vflag) } // initialize epot & efield - // NOTE: is this necessary? + // RENE: is this necessary? or does Scafacos just set them for (int i = 0; i < nlocal; i++) { epot[i] = 0.0; @@ -201,17 +179,47 @@ void Scafacos::compute(int eflag, int vflag) myeng += 0.5 * qone * epot[i]; } - if (eflag_atom) - { + if (eflag_atom) { for (int i = 0; i < nlocal; i++) - { eatom[i] = qscale * epot[i]; - } } MPI_Allreduce(&myeng,&energy,1,MPI_DOUBLE,MPI_SUM,world); } +/* ---------------------------------------------------------------------- */ + +int Scafacos::modify_param(int narg, char **arg) +{ + // RENE: add any Scafacos options here you want to expose to LAMMPS + // syntax: kspace_modify scafacos keyword value1 value2 ... + // keyword = tolerance + // value1 = energy, energy_rel, etc + // everyone of these should have a default, so user doesn't need to set + + if (strcmp(arg[0],"scafacos") != 0) return 0; + + if (strcmp(arg[1],"tolerance") == 0) { + if (narg < 2) error->all(FLERR,"Illegal kspace_modify command"); + if (strcmp(arg[2],"energy") == 0) + tolerance_type = FCS_TOLERANCE_TYPE_ENERGY; + else if (strcmp(arg[2],"energy_rel") == 0) + tolerance_type = FCS_TOLERANCE_TYPE_ENERGY_REL; + else if (strcmp(arg[2],"field") == 0) + tolerance_type = FCS_TOLERANCE_TYPE_FIELD; + else if (strcmp(arg[2],"field_rel") == 0) + tolerance_type = FCS_TOLERANCE_TYPE_FIELD_REL; + else if (strcmp(arg[2],"potential") == 0) + tolerance_type = FCS_TOLERANCE_TYPE_POTENTIAL; + else if (strcmp(arg[2],"potential_rel") == 0) + tolerance_type = FCS_TOLERANCE_TYPE_POTENTIAL_REL; + else error->all(FLERR,"Illegal kspace_modify command"); + return 3; + } + + return 0; +} + /* ---------------------------------------------------------------------- memory usage of local arrays ------------------------------------------------------------------------- */ @@ -231,15 +239,14 @@ double Scafacos::memory_usage() void Scafacos::setup_handle() { // store simulation box params - // NOTE: this assumes orthogonal box - // NOTE: total particles may not be a 4-byte int - // NOTE: what does SCFCS mean by offset? - // it's an integer flag in LAMMPS old_periodicity[0] = domain->xperiodic; old_periodicity[1] = domain->yperiodic; old_periodicity[2] = domain->zperiodic; + // RENE: what does SCFCS mean by offset? + // it's an integer flag in LAMMPS, but being stored in a float? + old_offset[0] = domain->boundary[0][0]; old_offset[1] = domain->boundary[1][0]; old_offset[2] = domain->boundary[2][0]; @@ -273,7 +280,9 @@ void Scafacos::setup_handle() result = fcs_set_total_particles(fcs,old_natoms); check_result(result); - // NOTE: for now disable short-range calculations within LAMMPS + // RENE: disable short-range calculations within LAMMPS + // not sure what this is doing + // is this the correct thing to do for now? int near_field_flag = 0; result = fcs_set_near_field_flag(fcs,near_field_flag); @@ -306,7 +315,6 @@ bool Scafacos::box_has_changed() /* ---------------------------------------------------------------------- check ScaFaCoS result for error condition - NOTE: will all procs have same error? ------------------------------------------------------------------------- */ void Scafacos::check_result(FCSResult result) @@ -320,6 +328,9 @@ void Scafacos::check_result(FCSResult result) std::string err_msg = ss.str(); const char *str = err_msg.c_str(); + // RENE: will all procs have same error? + // if so, then should call error->all(FLERR,str) + error->one(FLERR,str); } diff --git a/src/USER-SCAFACOS/scafacos.h b/src/USER-SCAFACOS/scafacos.h index 33911ee9fd..f3708129f1 100644 --- a/src/USER-SCAFACOS/scafacos.h +++ b/src/USER-SCAFACOS/scafacos.h @@ -32,6 +32,7 @@ class Scafacos : public KSpace { void init(); void setup(); void compute(int, int); + int modify_param(int, char **); double memory_usage(); private: diff --git a/src/kspace.cpp b/src/kspace.cpp index fc8b12288b..de96bee8b8 100644 --- a/src/kspace.cpp +++ b/src/kspace.cpp @@ -580,7 +580,11 @@ void KSpace::modify_params(int narg, char **arg) else if (strcmp(arg[iarg+1],"no") == 0) auto_disp_flag = 0; else error->all(FLERR,"Illegal kspace_modify command"); iarg += 2; - } else error->all(FLERR,"Illegal kspace_modify command"); + } else { + int n = modify_param(narg-iarg,&arg[iarg]); + if (n == 0) error->all(FLERR,"Illegal kspace_modify command"); + iarg += n; + } } } diff --git a/src/kspace.h b/src/kspace.h index 28c7bcef2a..c25dc93f45 100644 --- a/src/kspace.h +++ b/src/kspace.h @@ -126,6 +126,8 @@ class KSpace : protected Pointers { virtual int timing(int, double &, double &) {return 0;} virtual int timing_1d(int, double &) {return 0;} virtual int timing_3d(int, double &) {return 0;} + + virtual int modify_param(int, char **) {return 0;} virtual double memory_usage() {return 0.0;} /* ---------------------------------------------------------------------- From a62b65096bbdd10925feb9b08eea10d626b231fe Mon Sep 17 00:00:00 2001 From: "Steven J. Plimpton" Date: Wed, 18 Jul 2018 15:48:17 -0600 Subject: [PATCH 060/302] more error checks for Scafacos usage --- lib/scafacos/README | 7 +++++++ src/USER-SCAFACOS/scafacos.cpp | 5 +++++ 2 files changed, 12 insertions(+) create mode 100644 lib/scafacos/README diff --git a/lib/scafacos/README b/lib/scafacos/README new file mode 100644 index 0000000000..bdf167aef1 --- /dev/null +++ b/lib/scafacos/README @@ -0,0 +1,7 @@ +RENE - there needs to be a README like the one +for lib/voronoi/README, explaining how +to grab the correct version of Scafacos. + +And how to build, either via traditional make +and the Install.py script, or via CMake + diff --git a/src/USER-SCAFACOS/scafacos.cpp b/src/USER-SCAFACOS/scafacos.cpp index 10721b33c8..fef4b4948f 100644 --- a/src/USER-SCAFACOS/scafacos.cpp +++ b/src/USER-SCAFACOS/scafacos.cpp @@ -77,6 +77,8 @@ void Scafacos::init() { // error checks + if (!atom->q_flag) error->all(FLERR,"Kspace style requires atom attribute q"); + if (domain->dimension == 2) error->all(FLERR,"Cannot use ScaFaCoS with 2d simulation"); @@ -86,6 +88,9 @@ void Scafacos::init() if (atom->natoms > INT_MAX && sizeof(fcs_int) != 8) error->all(FLERR,"Scafacos atom count exceeds 2B"); + if (atom->molecular > 0) + error->all(FLERR,"Cannot use Scafacos with molecular charged systems yet"); + // one-time initialization of ScaFaCoS scale = 1.0; From 591e782415c7282095cacfd1c2279f18c8b9742c Mon Sep 17 00:00:00 2001 From: Denis Taniguchi Date: Thu, 19 Jul 2018 17:08:44 +0100 Subject: [PATCH 061/302] Optimizing PairGranHookeHistoryKokkos to be less divergent. --- src/KOKKOS/pair_gran_hooke_history_kokkos.cpp | 330 ++++++++++-------- src/KOKKOS/pair_gran_hooke_history_kokkos.h | 10 +- 2 files changed, 192 insertions(+), 148 deletions(-) diff --git a/src/KOKKOS/pair_gran_hooke_history_kokkos.cpp b/src/KOKKOS/pair_gran_hooke_history_kokkos.cpp index e6c9756b94..cd8beed583 100644 --- a/src/KOKKOS/pair_gran_hooke_history_kokkos.cpp +++ b/src/KOKKOS/pair_gran_hooke_history_kokkos.cpp @@ -159,9 +159,17 @@ void PairGranHookeHistoryKokkos::compute(int eflag_in, int vflag_in) d_neighbors = k_list->d_neighbors; d_ilist = k_list->d_ilist; + if (d_numneigh.extent(0) != d_numneigh_touch.extent(0)) + d_numneigh_touch = typename AT::t_int_1d("pair:numneigh_touch",d_numneigh.extent(0)); + if (d_neighbors.extent(0) != d_neighbors_touch.extent(0) || + d_neighbors.extent(1) != d_neighbors_touch.extent(1)) + d_neighbors_touch = typename AT::t_neighbors_2d("pair:neighbors_touch",d_neighbors.extent(0),d_neighbors.extent(1)); + d_firsttouch = fix_historyKK->d_firstflag; d_firstshear = fix_historyKK->d_firstvalue; - + + Kokkos::parallel_for(Kokkos::RangePolicy(0,inum),*this); + EV_FLOAT ev; if (lmp->kokkos->neighflag == HALF) { @@ -270,40 +278,24 @@ void PairGranHookeHistoryKokkos::compute(int eflag_in, int vflag_in) } template -template KOKKOS_INLINE_FUNCTION -void PairGranHookeHistoryKokkos::operator()(TagPairGranHookeHistoryCompute, const int ii, EV_FLOAT &ev) const { - - // The f and torque arrays are atomic for Half/Thread neighbor style - Kokkos::View::value> > a_f = f; - Kokkos::View::value> > a_torque = torque; - +void PairGranHookeHistoryKokkos::operator()(TagPairGranHookeHistoryReduce, const int ii) const { const int i = d_ilist[ii]; const X_FLOAT xtmp = x(i,0); const X_FLOAT ytmp = x(i,1); const X_FLOAT ztmp = x(i,2); - const int itype = type[i]; const LMP_FLOAT imass = rmass[i]; const LMP_FLOAT irad = radius[i]; const int jnum = d_numneigh[i]; - - F_FLOAT fx_i = 0.0; - F_FLOAT fy_i = 0.0; - F_FLOAT fz_i = 0.0; + int count = 0; - F_FLOAT torquex_i = 0.0; - F_FLOAT torquey_i = 0.0; - F_FLOAT torquez_i = 0.0; - for (int jj = 0; jj < jnum; jj++) { - int j = d_neighbors(i,jj); - j &= NEIGHMASK; + const int j = d_neighbors(i,jj) & NEIGHMASK; const X_FLOAT delx = xtmp - x(j,0); const X_FLOAT dely = ytmp - x(j,1); const X_FLOAT delz = ztmp - x(j,2); const X_FLOAT rsq = delx*delx + dely*dely + delz*delz; - const int jtype = type[j]; const LMP_FLOAT jmass = rmass[j]; const LMP_FLOAT jrad = radius[j]; const LMP_FLOAT radsum = irad + jrad; @@ -316,136 +308,180 @@ void PairGranHookeHistoryKokkos::operator()(TagPairGranHookeHistoryC d_firstshear(i,3*jj+1) = 0; d_firstshear(i,3*jj+2) = 0; } else { - const LMP_FLOAT r = sqrt(rsq); - const LMP_FLOAT rinv = 1.0/r; - const LMP_FLOAT rsqinv = 1/rsq; - - // relative translational velocity - - V_FLOAT vr1 = v(i,0) - v(j,0); - V_FLOAT vr2 = v(i,1) - v(j,1); - V_FLOAT vr3 = v(i,2) - v(j,2); - - // normal component - - V_FLOAT vnnr = vr1*delx + vr2*dely + vr3*delz; - V_FLOAT vn1 = delx*vnnr * rsqinv; - V_FLOAT vn2 = dely*vnnr * rsqinv; - V_FLOAT vn3 = delz*vnnr * rsqinv; - - // tangential component - - V_FLOAT vt1 = vr1 - vn1; - V_FLOAT vt2 = vr2 - vn2; - V_FLOAT vt3 = vr3 - vn3; - - // relative rotational velocity - - V_FLOAT wr1 = (irad*omega(i,0) + jrad*omega(j,0)) * rinv; - V_FLOAT wr2 = (irad*omega(i,1) + jrad*omega(j,1)) * rinv; - V_FLOAT wr3 = (irad*omega(i,2) + jrad*omega(j,2)) * rinv; - - LMP_FLOAT meff = imass*jmass / (imass+jmass); - if (mask[i] & freeze_group_bit) meff = jmass; - if (mask[j] & freeze_group_bit) meff = imass; - - F_FLOAT damp = meff*gamman*vnnr*rsqinv; - F_FLOAT ccel = kn*(radsum-r)*rinv - damp; - - // relative velocities - - V_FLOAT vtr1 = vt1 - (delz*wr2-dely*wr3); - V_FLOAT vtr2 = vt2 - (delx*wr3-delz*wr1); - V_FLOAT vtr3 = vt3 - (dely*wr1-delx*wr2); - V_FLOAT vrel = vtr1*vtr1 + vtr2*vtr2 + vtr3*vtr3; - vrel = sqrt(vrel); - - // shear history effects - d_firsttouch(i,jj) = 1; - X_FLOAT shear1 = d_firstshear(i,3*jj); - X_FLOAT shear2 = d_firstshear(i,3*jj+1); - X_FLOAT shear3 = d_firstshear(i,3*jj+2); - if (SHEARUPDATE) { - shear1 += vtr1*dt; - shear2 += vtr2*dt; - shear3 += vtr3*dt; - } - X_FLOAT shrmag = sqrt(shear1*shear1 + shear2*shear2 + - shear3*shear3); - - // rotate shear displacements - - X_FLOAT rsht = shear1*delx + shear2*dely + shear3*delz; - rsht *= rsqinv; - if (SHEARUPDATE) { - shear1 -= rsht*delx; - shear2 -= rsht*dely; - shear3 -= rsht*delz; - } - - // tangential forces = shear + tangential velocity damping - - F_FLOAT fs1 = - (kt*shear1 + meff*gammat*vtr1); - F_FLOAT fs2 = - (kt*shear2 + meff*gammat*vtr2); - F_FLOAT fs3 = - (kt*shear3 + meff*gammat*vtr3); - - // rescale frictional displacements and forces if needed - - F_FLOAT fs = sqrt(fs1*fs1 + fs2*fs2 + fs3*fs3); - F_FLOAT fn = xmu * fabs(ccel*r); - - if (fs > fn) { - if (shrmag != 0.0) { - shear1 = (fn/fs) * (shear1 + meff*gammat*vtr1/kt) - - meff*gammat*vtr1/kt; - shear2 = (fn/fs) * (shear2 + meff*gammat*vtr2/kt) - - meff*gammat*vtr2/kt; - shear3 = (fn/fs) * (shear3 + meff*gammat*vtr3/kt) - - meff*gammat*vtr3/kt; - fs1 *= fn/fs; - fs2 *= fn/fs; - fs3 *= fn/fs; - } else fs1 = fs2 = fs3 = 0.0; - } - - if (SHEARUPDATE) { - d_firstshear(i,3*jj) = shear1; - d_firstshear(i,3*jj+1) = shear2; - d_firstshear(i,3*jj+2) = shear3; - } - - // forces & torques - - F_FLOAT fx = delx*ccel + fs1; - F_FLOAT fy = dely*ccel + fs2; - F_FLOAT fz = delz*ccel + fs3; - fx_i += fx; - fy_i += fy; - fz_i += fz; - - F_FLOAT tor1 = rinv * (dely*fs3 - delz*fs2); - F_FLOAT tor2 = rinv * (delz*fs1 - delx*fs3); - F_FLOAT tor3 = rinv * (delx*fs2 - dely*fs1); - torquex_i -= irad*tor1; - torquey_i -= irad*tor2; - torquez_i -= irad*tor3; - - if (NEWTON_PAIR || j < nlocal) { - a_f(j,0) -= fx; - a_f(j,1) -= fy; - a_f(j,2) -= fz; - a_torque(j,0) -= jrad*tor1; - a_torque(j,1) -= jrad*tor2; - a_torque(j,2) -= jrad*tor3; - } - - if (EVFLAG == 2) - ev_tally_xyz_atom(ev, i, j, fx_i, fy_i, fz_i, delx, dely, delz); - if (EVFLAG == 1) - ev_tally_xyz(ev, i, j, fx_i, fy_i, fz_i, delx, dely, delz); + d_neighbors_touch(i,count++) = jj; } } + d_numneigh_touch[i] = count; +} + +template +template +KOKKOS_INLINE_FUNCTION +void PairGranHookeHistoryKokkos::operator()(TagPairGranHookeHistoryCompute, const int ii, EV_FLOAT &ev) const { + + // The f and torque arrays are atomic for Half/Thread neighbor style + Kokkos::View::value> > a_f = f; + Kokkos::View::value> > a_torque = torque; + + const int i = d_ilist[ii]; + const X_FLOAT xtmp = x(i,0); + const X_FLOAT ytmp = x(i,1); + const X_FLOAT ztmp = x(i,2); + const LMP_FLOAT imass = rmass[i]; + const LMP_FLOAT irad = radius[i]; + const int jnum = d_numneigh_touch[i]; + + F_FLOAT fx_i = 0.0; + F_FLOAT fy_i = 0.0; + F_FLOAT fz_i = 0.0; + + F_FLOAT torquex_i = 0.0; + F_FLOAT torquey_i = 0.0; + F_FLOAT torquez_i = 0.0; + + for (int jj = 0; jj < jnum; jj++) { + const int m = d_neighbors_touch(i, jj); + const int j = d_neighbors(i, m) & NEIGHMASK; + + const X_FLOAT delx = xtmp - x(j,0); + const X_FLOAT dely = ytmp - x(j,1); + const X_FLOAT delz = ztmp - x(j,2); + const X_FLOAT rsq = delx*delx + dely*dely + delz*delz; + const LMP_FLOAT jmass = rmass[j]; + const LMP_FLOAT jrad = radius[j]; + const LMP_FLOAT radsum = irad + jrad; + + // check for touching neighbors + + const LMP_FLOAT r = sqrt(rsq); + const LMP_FLOAT rinv = 1.0/r; + const LMP_FLOAT rsqinv = 1/rsq; + + // relative translational velocity + + V_FLOAT vr1 = v(i,0) - v(j,0); + V_FLOAT vr2 = v(i,1) - v(j,1); + V_FLOAT vr3 = v(i,2) - v(j,2); + + // normal component + + V_FLOAT vnnr = vr1*delx + vr2*dely + vr3*delz; + V_FLOAT vn1 = delx*vnnr * rsqinv; + V_FLOAT vn2 = dely*vnnr * rsqinv; + V_FLOAT vn3 = delz*vnnr * rsqinv; + + // tangential component + + V_FLOAT vt1 = vr1 - vn1; + V_FLOAT vt2 = vr2 - vn2; + V_FLOAT vt3 = vr3 - vn3; + + // relative rotational velocity + + V_FLOAT wr1 = (irad*omega(i,0) + jrad*omega(j,0)) * rinv; + V_FLOAT wr2 = (irad*omega(i,1) + jrad*omega(j,1)) * rinv; + V_FLOAT wr3 = (irad*omega(i,2) + jrad*omega(j,2)) * rinv; + + LMP_FLOAT meff = imass*jmass / (imass+jmass); + if (mask[i] & freeze_group_bit) meff = jmass; + if (mask[j] & freeze_group_bit) meff = imass; + + F_FLOAT damp = meff*gamman*vnnr*rsqinv; + F_FLOAT ccel = kn*(radsum-r)*rinv - damp; + + // relative velocities + + V_FLOAT vtr1 = vt1 - (delz*wr2-dely*wr3); + V_FLOAT vtr2 = vt2 - (delx*wr3-delz*wr1); + V_FLOAT vtr3 = vt3 - (dely*wr1-delx*wr2); + V_FLOAT vrel = vtr1*vtr1 + vtr2*vtr2 + vtr3*vtr3; + vrel = sqrt(vrel); + + // shear history effects + + X_FLOAT shear1 = d_firstshear(i,3*m); + X_FLOAT shear2 = d_firstshear(i,3*m+1); + X_FLOAT shear3 = d_firstshear(i,3*m+2); + if (SHEARUPDATE) { + shear1 += vtr1*dt; + shear2 += vtr2*dt; + shear3 += vtr3*dt; + } + X_FLOAT shrmag = sqrt(shear1*shear1 + shear2*shear2 + + shear3*shear3); + + // rotate shear displacements + + X_FLOAT rsht = shear1*delx + shear2*dely + shear3*delz; + rsht *= rsqinv; + if (SHEARUPDATE) { + shear1 -= rsht*delx; + shear2 -= rsht*dely; + shear3 -= rsht*delz; + } + + // tangential forces = shear + tangential velocity damping + + F_FLOAT fs1 = - (kt*shear1 + meff*gammat*vtr1); + F_FLOAT fs2 = - (kt*shear2 + meff*gammat*vtr2); + F_FLOAT fs3 = - (kt*shear3 + meff*gammat*vtr3); + + // rescale frictional displacements and forces if needed + + F_FLOAT fs = sqrt(fs1*fs1 + fs2*fs2 + fs3*fs3); + F_FLOAT fn = xmu * fabs(ccel*r); + + if (fs > fn) { + if (shrmag != 0.0) { + shear1 = (fn/fs) * (shear1 + meff*gammat*vtr1/kt) - + meff*gammat*vtr1/kt; + shear2 = (fn/fs) * (shear2 + meff*gammat*vtr2/kt) - + meff*gammat*vtr2/kt; + shear3 = (fn/fs) * (shear3 + meff*gammat*vtr3/kt) - + meff*gammat*vtr3/kt; + fs1 *= fn/fs; + fs2 *= fn/fs; + fs3 *= fn/fs; + } else fs1 = fs2 = fs3 = 0.0; + } + + if (SHEARUPDATE) { + d_firstshear(i,3*m) = shear1; + d_firstshear(i,3*m+1) = shear2; + d_firstshear(i,3*m+2) = shear3; + } + + // forces & torques + + F_FLOAT fx = delx*ccel + fs1; + F_FLOAT fy = dely*ccel + fs2; + F_FLOAT fz = delz*ccel + fs3; + fx_i += fx; + fy_i += fy; + fz_i += fz; + + F_FLOAT tor1 = rinv * (dely*fs3 - delz*fs2); + F_FLOAT tor2 = rinv * (delz*fs1 - delx*fs3); + F_FLOAT tor3 = rinv * (delx*fs2 - dely*fs1); + torquex_i -= irad*tor1; + torquey_i -= irad*tor2; + torquez_i -= irad*tor3; + + if (NEWTON_PAIR || j < nlocal) { + a_f(j,0) -= fx; + a_f(j,1) -= fy; + a_f(j,2) -= fz; + a_torque(j,0) -= jrad*tor1; + a_torque(j,1) -= jrad*tor2; + a_torque(j,2) -= jrad*tor3; + } + + if (EVFLAG == 2) + ev_tally_xyz_atom(ev, i, j, fx_i, fy_i, fz_i, delx, dely, delz); + if (EVFLAG == 1) + ev_tally_xyz(ev, i, j, fx_i, fy_i, fz_i, delx, dely, delz); + } a_f(i,0) += fx_i; a_f(i,1) += fy_i; diff --git a/src/KOKKOS/pair_gran_hooke_history_kokkos.h b/src/KOKKOS/pair_gran_hooke_history_kokkos.h index 65a92f23cd..822b9203a4 100644 --- a/src/KOKKOS/pair_gran_hooke_history_kokkos.h +++ b/src/KOKKOS/pair_gran_hooke_history_kokkos.h @@ -32,7 +32,9 @@ template class FixNeighHistoryKokkos; template -struct TagPairGranHookeHistoryCompute{}; +struct TagPairGranHookeHistoryCompute {}; + +struct TagPairGranHookeHistoryReduce {}; template class PairGranHookeHistoryKokkos : public PairGranHookeHistory { @@ -46,6 +48,9 @@ class PairGranHookeHistoryKokkos : public PairGranHookeHistory { virtual void compute(int, int); void init_style(); + KOKKOS_INLINE_FUNCTION + void operator()(TagPairGranHookeHistoryReduce, const int ii) const; + template KOKKOS_INLINE_FUNCTION void operator()(TagPairGranHookeHistoryCompute, const int, EV_FLOAT &ev) const; @@ -88,6 +93,9 @@ class PairGranHookeHistoryKokkos : public PairGranHookeHistory { typename Kokkos::View d_firsttouch; typename Kokkos::View d_firstshear; + + typename AT::t_neighbors_2d d_neighbors_touch; + typename AT::t_int_1d d_numneigh_touch; int newton_pair; double special_lj[4]; From fba165d6b28451d9eca389d77fa3aa0a4ef30dff Mon Sep 17 00:00:00 2001 From: Rene Halver Date: Thu, 19 Jul 2018 11:46:56 -0600 Subject: [PATCH 062/302] changed the files according to remarks by Steve (compare to previous commit) --- src/USER-SCAFACOS/scafacos.cpp | 74 ++++++++++++++++------------------ src/USER-SCAFACOS/scafacos.h | 2 +- 2 files changed, 35 insertions(+), 41 deletions(-) diff --git a/src/USER-SCAFACOS/scafacos.cpp b/src/USER-SCAFACOS/scafacos.cpp index fef4b4948f..8779796a54 100644 --- a/src/USER-SCAFACOS/scafacos.cpp +++ b/src/USER-SCAFACOS/scafacos.cpp @@ -38,16 +38,24 @@ using namespace LAMMPS_NS; Scafacos::Scafacos(LAMMPS *lmp, int narg, char **arg) : KSpace(lmp, narg, arg) { - if (narg != 2) error->all(FLERR,"Illegal scafacos command"); + if (narg > 2) error->all(FLERR,"Illegal scafacos command"); int n = strlen(arg[0]) + 1; method = new char[n]; strcpy(method,arg[0]); - tolerance = force->numeric(FLERR,arg[1]); + // to allow 'kspace scafacos ' with default values + if (narg == 2) + tolerance = force->numeric(FLERR,arg[1]); + else + tolerance = 0.001; // optional ScaFaCoS library setting defaults - - tolerance_type = FCS_TOLERANCE_TYPE_FIELD; + // choose the correct default tolerance type for chosen method + // TODO: needs to be expanded for all solvers, currently mainly used ones + if (strcmp(method,"fmm") == 0) + tolerance_type = FCS_TOLERANCE_TYPE_ENERGY; + else if (strcmp(method,"p3m") == 0 || strcmp(method,"p2nfft") == 0) + tolerance_type = FCS_TOLERANCE_TYPE_FIELD; // initializations @@ -68,7 +76,8 @@ Scafacos::~Scafacos() memory->destroy(epot); memory->destroy(efield); - // RENE: any clean-up/shut-down call to ScaFaCoS needed? + // clean up of the ScaFaCoS handle and internal arrays + fcs_destroy(fcs); } /* ---------------------------------------------------------------------- */ @@ -93,7 +102,6 @@ void Scafacos::init() // one-time initialization of ScaFaCoS - scale = 1.0; qqrd2e = force->qqrd2e; if (!initialized) { @@ -129,9 +137,7 @@ void Scafacos::compute(int eflag, int vflag) double *q = atom->q; int nlocal = atom->nlocal; - // RENE: why is scale needed? - - const double qscale = qqrd2e * scale; + const double qscale = qqrd2e; if (eflag || vflag) ev_setup(eflag,vflag); else eflag_atom = 0; @@ -155,16 +161,6 @@ void Scafacos::compute(int eflag, int vflag) } - // initialize epot & efield - // RENE: is this necessary? or does Scafacos just set them - - for (int i = 0; i < nlocal; i++) { - epot[i] = 0.0; - efield[i][0] = efield[i][1] = efield[i][2] = 0.0; - } - - // ScaFaCoS calculation of full Coulombics - result = fcs_run(fcs,nlocal,&x[0][0],q,&efield[0][0],epot); check_result(result); @@ -196,7 +192,7 @@ void Scafacos::compute(int eflag, int vflag) int Scafacos::modify_param(int narg, char **arg) { - // RENE: add any Scafacos options here you want to expose to LAMMPS + // add any Scafacos options here you want to expose to LAMMPS // syntax: kspace_modify scafacos keyword value1 value2 ... // keyword = tolerance // value1 = energy, energy_rel, etc @@ -245,17 +241,17 @@ void Scafacos::setup_handle() { // store simulation box params + // setup periodicity old_periodicity[0] = domain->xperiodic; old_periodicity[1] = domain->yperiodic; old_periodicity[2] = domain->zperiodic; - // RENE: what does SCFCS mean by offset? - // it's an integer flag in LAMMPS, but being stored in a float? - - old_offset[0] = domain->boundary[0][0]; - old_offset[1] = domain->boundary[1][0]; - old_offset[2] = domain->boundary[2][0]; + // setup box origin (lower left front corner of the system) + old_origin[0] = domain->boundary[0][0]; + old_origin[1] = domain->boundary[1][0]; + old_origin[2] = domain->boundary[2][0]; + // setup box vectors (base vectors of the system box) old_box_x[0] = domain->prd[0]; old_box_x[1] = old_box_x[2] = 0.0; old_box_y[1] = domain->prd[1]; @@ -263,10 +259,10 @@ void Scafacos::setup_handle() old_box_z[2] = domain->prd[2]; old_box_z[1] = old_box_z[0] = 0.0; + // setup number of atoms in the system old_natoms = atom->natoms; - // set all required ScaFaCoS params - + // store parameters to ScaFaCoS handle result = fcs_set_box_a(fcs,old_box_x); check_result(result); @@ -276,7 +272,7 @@ void Scafacos::setup_handle() result = fcs_set_box_c(fcs,old_box_z); check_result(result); - result = fcs_set_box_origin(fcs,old_offset); + result = fcs_set_box_origin(fcs,old_origin); check_result(result); result = fcs_set_periodicity(fcs,old_periodicity); @@ -285,11 +281,12 @@ void Scafacos::setup_handle() result = fcs_set_total_particles(fcs,old_natoms); check_result(result); - // RENE: disable short-range calculations within LAMMPS - // not sure what this is doing - // is this the correct thing to do for now? - - int near_field_flag = 0; + // allow ScaFaCoS to calculate the near field computations for now + // TODO: allow the delegation of the near field computations + // within LAMMPS + // (near_field_flag = 1 -> enables the internal near field calcs + // 0 -> disables the internal near field calcs + int near_field_flag = 1; result = fcs_set_near_field_flag(fcs,near_field_flag); check_result(result); } @@ -307,9 +304,9 @@ bool Scafacos::box_has_changed() (periodicity[0] != old_periodicity[0]) || (periodicity[1] != old_periodicity[1]) || (periodicity[2] != old_periodicity[2]) || - (domain->boundary[0][0] != old_offset[0]) || - (domain->boundary[1][0] != old_offset[1]) || - (domain->boundary[2][0] != old_offset[2]) || + (domain->boundary[0][0] != old_origin[0]) || + (domain->boundary[1][0] != old_origin[1]) || + (domain->boundary[2][0] != old_origin[2]) || (prd[0] != old_box_x[0]) || (prd[1] != old_box_y[1]) || (prd[2] != old_box_z[2]) || @@ -333,9 +330,6 @@ void Scafacos::check_result(FCSResult result) std::string err_msg = ss.str(); const char *str = err_msg.c_str(); - // RENE: will all procs have same error? - // if so, then should call error->all(FLERR,str) - error->one(FLERR,str); } diff --git a/src/USER-SCAFACOS/scafacos.h b/src/USER-SCAFACOS/scafacos.h index f3708129f1..3e549cf64e 100644 --- a/src/USER-SCAFACOS/scafacos.h +++ b/src/USER-SCAFACOS/scafacos.h @@ -51,7 +51,7 @@ class Scafacos : public KSpace { // so ScaFaCoS can detect if changes, e.g. for NPT fcs_float old_box_x[3],old_box_y[3],old_box_z[3]; - fcs_float old_offset[3]; + fcs_float old_origin[3]; fcs_int old_periodicity[3]; fcs_int old_natoms; From 407708dcd294e86cfa676489253691f496a650de Mon Sep 17 00:00:00 2001 From: Rene Halver Date: Fri, 20 Jul 2018 10:38:18 -0600 Subject: [PATCH 063/302] reverted change to kspace call and using domain->boxlo for origin for now --- src/USER-SCAFACOS/scafacos.cpp | 14 +++++--------- 1 file changed, 5 insertions(+), 9 deletions(-) diff --git a/src/USER-SCAFACOS/scafacos.cpp b/src/USER-SCAFACOS/scafacos.cpp index 8779796a54..b9390aea47 100644 --- a/src/USER-SCAFACOS/scafacos.cpp +++ b/src/USER-SCAFACOS/scafacos.cpp @@ -38,16 +38,12 @@ using namespace LAMMPS_NS; Scafacos::Scafacos(LAMMPS *lmp, int narg, char **arg) : KSpace(lmp, narg, arg) { - if (narg > 2) error->all(FLERR,"Illegal scafacos command"); + if (narg != 2) error->all(FLERR,"Illegal scafacos command"); int n = strlen(arg[0]) + 1; method = new char[n]; strcpy(method,arg[0]); - // to allow 'kspace scafacos ' with default values - if (narg == 2) - tolerance = force->numeric(FLERR,arg[1]); - else - tolerance = 0.001; + tolerance = force->numeric(FLERR,arg[1]); // optional ScaFaCoS library setting defaults // choose the correct default tolerance type for chosen method @@ -247,9 +243,9 @@ void Scafacos::setup_handle() old_periodicity[2] = domain->zperiodic; // setup box origin (lower left front corner of the system) - old_origin[0] = domain->boundary[0][0]; - old_origin[1] = domain->boundary[1][0]; - old_origin[2] = domain->boundary[2][0]; + old_origin[0] = domain->boxlo[0]; + old_origin[1] = domain->boxlo[1]; + old_origin[2] = domain->boxlo[2]; // setup box vectors (base vectors of the system box) old_box_x[0] = domain->prd[0]; From 5c934cdb6f111b6dc6b4a115776482e90cb341d1 Mon Sep 17 00:00:00 2001 From: Rene Halver Date: Fri, 20 Jul 2018 10:40:29 -0600 Subject: [PATCH 064/302] fixed examples to work with charged molecular restriction and new kspace call format --- examples/USER/scafacos/data.NaCl | 16 ++++++++-------- examples/USER/scafacos/in.scafacos | 3 ++- 2 files changed, 10 insertions(+), 9 deletions(-) diff --git a/examples/USER/scafacos/data.NaCl b/examples/USER/scafacos/data.NaCl index 1a599b957d..2d804dec95 100644 --- a/examples/USER/scafacos/data.NaCl +++ b/examples/USER/scafacos/data.NaCl @@ -15,11 +15,11 @@ Atoms - 1 1 1 1.0 0.0 0.0 0.0 - 2 1 2 -1.0 1.0 0.0 0.0 - 3 1 2 -1.0 0.0 1.0 0.0 - 4 1 1 1.0 1.0 1.0 0.0 - 5 1 2 -1.0 0.0 0.0 1.0 - 6 1 1 1.0 1.0 0.0 1.0 - 7 1 1 1.0 0.0 1.0 1.0 - 8 1 2 -1.0 1.0 1.0 1.0 + 1 1 1.0 0.0 0.0 0.0 + 2 2 -1.0 1.0 0.0 0.0 + 3 2 -1.0 0.0 1.0 0.0 + 4 1 1.0 1.0 1.0 0.0 + 5 2 -1.0 0.0 0.0 1.0 + 6 1 1.0 1.0 0.0 1.0 + 7 1 1.0 0.0 1.0 1.0 + 8 2 -1.0 1.0 1.0 1.0 diff --git a/examples/USER/scafacos/in.scafacos b/examples/USER/scafacos/in.scafacos index f9b6733eef..9a1f0f321e 100644 --- a/examples/USER/scafacos/in.scafacos +++ b/examples/USER/scafacos/in.scafacos @@ -28,7 +28,8 @@ pair_coeff * * #fix 2 all scafacos p3m tolerance field 0.001 -kspace_style scafacos p3m tolerance field 0.001 +kspace_style scafacos p3m 0.001 +kspace_style scafacos tolerance field timestep 0.005 thermo 10 From 0e0afdeb51b7eefaff3da277d7c4db437dc3e870 Mon Sep 17 00:00:00 2001 From: Rene Halver Date: Fri, 20 Jul 2018 10:41:19 -0600 Subject: [PATCH 065/302] fixed typo and removed comment --- doc/src/Section_packages.txt | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/doc/src/Section_packages.txt b/doc/src/Section_packages.txt index ea03bdb74e..18ae1a75e6 100644 --- a/doc/src/Section_packages.txt +++ b/doc/src/Section_packages.txt @@ -2731,8 +2731,6 @@ examples/reax :ul :line -RENE: check this section - USER-SCAFACOS package :link(USER-SCAFACOS),h4 [Contents:] @@ -2764,7 +2762,7 @@ args: make lib-scafacos # print help message make lib-scafacos args="-b" # download and build in lib/scafacos/scafacos- -make lib-voronoi args="-p $HOME/scafacos # use existing ScaFaCoS installation in $HOME/scafacos +make lib-scafacos args="-p $HOME/scafacos # use existing ScaFaCoS installation in $HOME/scafacos You can then install/un-install the package and build LAMMPS in the usual manner: From ef3fd1374a1ddc557c78abd8631415234d874db4 Mon Sep 17 00:00:00 2001 From: Rene Halver Date: Mon, 23 Jul 2018 16:11:18 -0600 Subject: [PATCH 066/302] added kspace_style for internal fmm tuning (for inhomogenous systems) and fixed the call to fcs_set_tolerance --- src/USER-SCAFACOS/scafacos.cpp | 45 ++++++++++++++++++++++++++++------ src/USER-SCAFACOS/scafacos.h | 2 ++ 2 files changed, 40 insertions(+), 7 deletions(-) diff --git a/src/USER-SCAFACOS/scafacos.cpp b/src/USER-SCAFACOS/scafacos.cpp index b9390aea47..352a298b86 100644 --- a/src/USER-SCAFACOS/scafacos.cpp +++ b/src/USER-SCAFACOS/scafacos.cpp @@ -49,7 +49,10 @@ Scafacos::Scafacos(LAMMPS *lmp, int narg, char **arg) : KSpace(lmp, narg, arg) // choose the correct default tolerance type for chosen method // TODO: needs to be expanded for all solvers, currently mainly used ones if (strcmp(method,"fmm") == 0) + { tolerance_type = FCS_TOLERANCE_TYPE_ENERGY; + fmm_tuning_flag = 0; + } else if (strcmp(method,"p3m") == 0 || strcmp(method,"p2nfft") == 0) tolerance_type = FCS_TOLERANCE_TYPE_FIELD; @@ -81,6 +84,8 @@ Scafacos::~Scafacos() void Scafacos::init() { // error checks + if (screen && me == 0) fprintf(screen,"Setting up ScaFaCoS with solver %s ...\n",method); + if (logfile && me == 0) fprintf(logfile,"Setting up ScaFaCoS with solver %s ...\n",method); if (!atom->q_flag) error->all(FLERR,"Kspace style requires atom attribute q"); @@ -106,18 +111,31 @@ void Scafacos::init() setup_handle(); - result = fcs_set_tolerance(fcs,tolerance_type,tolerance); - check_result(result); - + // using other methods lead to termination of the program, + // since they have no tolerance tuning methods + if ( strcmp(method,"fmm") == 0 || + strcmp(method,"p3m") == 0 || + strcmp(method,"p2nfft") == 0 || + strcmp(method,"ewald") == 0) + { + result = fcs_set_tolerance(fcs,tolerance_type,tolerance); + check_result(result); + } if (me == 0) fcs_print_parameters(fcs); double **x = atom->x; double *q = atom->q; int nlocal = atom->nlocal; - result = fcs_tune(fcs,nlocal,&x[0][0],q); - } + if (strcmp(method,"fmm") == 0) + { + if (fmm_tuning_flag == 1) + fcs_fmm_set_internal_tuning(fcs,fmm_tuning_flag); + } + result = fcs_tune(fcs,nlocal,&x[0][0],q); + check_result(result); + } initialized = 1; } @@ -197,7 +215,7 @@ int Scafacos::modify_param(int narg, char **arg) if (strcmp(arg[0],"scafacos") != 0) return 0; if (strcmp(arg[1],"tolerance") == 0) { - if (narg < 2) error->all(FLERR,"Illegal kspace_modify command"); + if (narg < 3) error->all(FLERR,"Illegal kspace_modify command (tolerance)"); if (strcmp(arg[2],"energy") == 0) tolerance_type = FCS_TOLERANCE_TYPE_ENERGY; else if (strcmp(arg[2],"energy_rel") == 0) @@ -210,7 +228,20 @@ int Scafacos::modify_param(int narg, char **arg) tolerance_type = FCS_TOLERANCE_TYPE_POTENTIAL; else if (strcmp(arg[2],"potential_rel") == 0) tolerance_type = FCS_TOLERANCE_TYPE_POTENTIAL_REL; - else error->all(FLERR,"Illegal kspace_modify command"); + else error->all(FLERR,"Illegal kspace_modify command (tolerance argument)"); + return 3; + } + + // keyword = fmm_inhomogen_tuning + // value1 = 0, 1 + // 0 -> homogenous system (default) + // 1 -> inhomogenous system (more internal tuning is provided (sequential!)) + if (strcmp(arg[1],"fmm_tuning") == 0) + { + if (screen && me == 0) fprintf(screen,"ScaFaCoS setting fmm inhomogen tuning ...%d\n", narg); + if (logfile && me == 0) fprintf(logfile,"ScaFaCoS setting fmm inhomogen tuning ...%d\n", narg); + if (narg < 3) error->all(FLERR,"Illegal kspace_modify command (fmm_tuning)"); + fmm_tuning_flag = atoi(arg[2]); return 3; } diff --git a/src/USER-SCAFACOS/scafacos.h b/src/USER-SCAFACOS/scafacos.h index 3e549cf64e..857036bb7a 100644 --- a/src/USER-SCAFACOS/scafacos.h +++ b/src/USER-SCAFACOS/scafacos.h @@ -44,6 +44,8 @@ class Scafacos : public KSpace { int tolerance_type; int initialized,maxatom; + int fmm_tuning_flag; + FCS fcs; // ScaFaCoS handle FCSResult result; // result for each ScaFaCoS call From a90e019ec7d9315fc359cb5eff01ac941e007921 Mon Sep 17 00:00:00 2001 From: Rene Halver Date: Mon, 23 Jul 2018 16:13:15 -0600 Subject: [PATCH 067/302] updated ScaFaCoS examples, added open-boundary Hammersley distributed sphere and charged cloud near a charged wall examples --- examples/USER/scafacos/data.NaCl | 50 +- examples/USER/scafacos/data.cloud_wall | 316 +++++ .../USER/scafacos/data.hammersley_shphere | 1016 +++++++++++++++++ examples/USER/scafacos/in.scafacos.cw.ewald | 31 + examples/USER/scafacos/in.scafacos.cw.fmm | 37 + examples/USER/scafacos/in.scafacos.cw.p2nfft | 31 + examples/USER/scafacos/in.scafacos.ewald | 37 + examples/USER/scafacos/in.scafacos.fmm | 37 + .../USER/scafacos/in.scafacos.hsph.direct | 34 + examples/USER/scafacos/in.scafacos.hsph.fmm | 37 + .../USER/scafacos/in.scafacos.hsph.p2nfft | 36 + examples/USER/scafacos/in.scafacos.p2nfft | 37 + .../log.23Jul18.scafacos.cw.g++.ewald.16 | 92 ++ .../log.23Jul18.scafacos.cw.g++.ewald.8 | 92 ++ .../log.23Jul18.scafacos.cw.g++.fmm.1 | 99 ++ .../log.23Jul18.scafacos.cw.g++.fmm.16 | 99 ++ .../log.23Jul18.scafacos.cw.g++.fmm.2 | 99 ++ .../log.23Jul18.scafacos.cw.g++.fmm.4 | 99 ++ .../log.23Jul18.scafacos.cw.g++.fmm.8 | 99 ++ .../log.23Jul18.scafacos.cw.g++.p2nfft.1 | 92 ++ .../log.23Jul18.scafacos.cw.g++.p2nfft.16 | 92 ++ .../log.23Jul18.scafacos.cw.g++.p2nfft.2 | 92 ++ .../log.23Jul18.scafacos.cw.g++.p2nfft.4 | 92 ++ .../log.23Jul18.scafacos.cw.g++.p2nfft.8 | 92 ++ .../log.23Jul18.scafacos.g++.ewald.16 | 102 ++ .../scafacos/log.23Jul18.scafacos.g++.ewald.8 | 102 ++ .../scafacos/log.23Jul18.scafacos.g++.fmm.1 | 102 ++ .../scafacos/log.23Jul18.scafacos.g++.fmm.16 | 102 ++ .../scafacos/log.23Jul18.scafacos.g++.fmm.2 | 102 ++ .../scafacos/log.23Jul18.scafacos.g++.fmm.4 | 102 ++ .../scafacos/log.23Jul18.scafacos.g++.fmm.8 | 102 ++ .../log.23Jul18.scafacos.g++.p2nfft.1 | 102 ++ .../log.23Jul18.scafacos.g++.p2nfft.16 | 102 ++ .../log.23Jul18.scafacos.g++.p2nfft.2 | 102 ++ .../log.23Jul18.scafacos.g++.p2nfft.4 | 102 ++ .../log.23Jul18.scafacos.g++.p2nfft.8 | 102 ++ .../log.23Jul18.scafacos.hsph.g++.direct.1 | 105 ++ .../log.23Jul18.scafacos.hsph.g++.direct.2 | 105 ++ .../log.23Jul18.scafacos.hsph.g++.direct.4 | 105 ++ .../log.23Jul18.scafacos.hsph.g++.direct.8 | 105 ++ .../log.23Jul18.scafacos.hsph.g++.fmm.1 | 109 ++ .../log.23Jul18.scafacos.hsph.g++.fmm.2 | 109 ++ .../log.23Jul18.scafacos.hsph.g++.fmm.4 | 109 ++ .../log.23Jul18.scafacos.hsph.g++.fmm.8 | 109 ++ .../log.23Jul18.scafacos.hsph.g++.p2nfft.1 | 107 ++ .../log.23Jul18.scafacos.hsph.g++.p2nfft.2 | 107 ++ .../log.23Jul18.scafacos.hsph.g++.p2nfft.4 | 107 ++ .../log.23Jul18.scafacos.hsph.g++.p2nfft.8 | 107 ++ 48 files changed, 5321 insertions(+), 25 deletions(-) create mode 100644 examples/USER/scafacos/data.cloud_wall create mode 100644 examples/USER/scafacos/data.hammersley_shphere create mode 100644 examples/USER/scafacos/in.scafacos.cw.ewald create mode 100644 examples/USER/scafacos/in.scafacos.cw.fmm create mode 100644 examples/USER/scafacos/in.scafacos.cw.p2nfft create mode 100644 examples/USER/scafacos/in.scafacos.ewald create mode 100644 examples/USER/scafacos/in.scafacos.fmm create mode 100644 examples/USER/scafacos/in.scafacos.hsph.direct create mode 100644 examples/USER/scafacos/in.scafacos.hsph.fmm create mode 100644 examples/USER/scafacos/in.scafacos.hsph.p2nfft create mode 100644 examples/USER/scafacos/in.scafacos.p2nfft create mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.ewald.16 create mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.ewald.8 create mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.1 create mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.16 create mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.2 create mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.4 create mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.8 create mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.p2nfft.1 create mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.p2nfft.16 create mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.p2nfft.2 create mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.p2nfft.4 create mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.p2nfft.8 create mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.g++.ewald.16 create mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.g++.ewald.8 create mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.g++.fmm.1 create mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.g++.fmm.16 create mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.g++.fmm.2 create mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.g++.fmm.4 create mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.g++.fmm.8 create mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.g++.p2nfft.1 create mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.g++.p2nfft.16 create mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.g++.p2nfft.2 create mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.g++.p2nfft.4 create mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.g++.p2nfft.8 create mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.direct.1 create mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.direct.2 create mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.direct.4 create mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.direct.8 create mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.fmm.1 create mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.fmm.2 create mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.fmm.4 create mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.fmm.8 create mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.p2nfft.1 create mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.p2nfft.2 create mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.p2nfft.4 create mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.p2nfft.8 diff --git a/examples/USER/scafacos/data.NaCl b/examples/USER/scafacos/data.NaCl index 2d804dec95..23807e23d5 100644 --- a/examples/USER/scafacos/data.NaCl +++ b/examples/USER/scafacos/data.NaCl @@ -1,25 +1,25 @@ - LAMMPS Description - - 8 atoms - - 2 atom types - - 0.0000000000000000 2.000000000000000 xlo xhi - 0.0000000000000000 2.000000000000000 ylo yhi - 0.0000000000000000 2.000000000000000 zlo zhi - - Masses - - 1 22.98976928 - 2 35.45 - - Atoms - - 1 1 1.0 0.0 0.0 0.0 - 2 2 -1.0 1.0 0.0 0.0 - 3 2 -1.0 0.0 1.0 0.0 - 4 1 1.0 1.0 1.0 0.0 - 5 2 -1.0 0.0 0.0 1.0 - 6 1 1.0 1.0 0.0 1.0 - 7 1 1.0 0.0 1.0 1.0 - 8 2 -1.0 1.0 1.0 1.0 +LAMMPS Description + +8 atoms + +2 atom types + +0 2 xlo xhi +0 2 ylo yhi +0 2 zlo zhi + +Masses + +1 22.98976928 +2 35.45 + +Atoms + +1 2 1 0 0 0 +2 1 -1 1 0 0 +3 1 -1 0 1 0 +4 2 1 1 1 0 +5 1 -1 0 0 1 +6 2 1 1 0 1 +7 2 1 0 1 1 +8 1 -1 1 1 1 diff --git a/examples/USER/scafacos/data.cloud_wall b/examples/USER/scafacos/data.cloud_wall new file mode 100644 index 0000000000..1592ec666a --- /dev/null +++ b/examples/USER/scafacos/data.cloud_wall @@ -0,0 +1,316 @@ +LAMMPS Description + +300 atoms + +1 atom types + +0 10 xlo xhi +0 10 ylo yhi +0 10 zlo zhi + +Masses + +1 1.0 + +Atoms + +1 1 1 0 0 4.5 +2 1 -1 0 0 5.5 +3 1 1 0 1 4.5 +4 1 -1 0 1 5.5 +5 1 1 0 2 4.5 +6 1 -1 0 2 5.5 +7 1 1 0 3 4.5 +8 1 -1 0 3 5.5 +9 1 1 0 4 4.5 +10 1 -1 0 4 5.5 +11 1 1 0 5 4.5 +12 1 -1 0 5 5.5 +13 1 1 0 6 4.5 +14 1 -1 0 6 5.5 +15 1 1 0 7 4.5 +16 1 -1 0 7 5.5 +17 1 1 0 8 4.5 +18 1 -1 0 8 5.5 +19 1 1 0 9 4.5 +20 1 -1 0 9 5.5 +21 1 1 1 0 4.5 +22 1 -1 1 0 5.5 +23 1 1 1 1 4.5 +24 1 -1 1 1 5.5 +25 1 1 1 2 4.5 +26 1 -1 1 2 5.5 +27 1 1 1 3 4.5 +28 1 -1 1 3 5.5 +29 1 1 1 4 4.5 +30 1 -1 1 4 5.5 +31 1 1 1 5 4.5 +32 1 -1 1 5 5.5 +33 1 1 1 6 4.5 +34 1 -1 1 6 5.5 +35 1 1 1 7 4.5 +36 1 -1 1 7 5.5 +37 1 1 1 8 4.5 +38 1 -1 1 8 5.5 +39 1 1 1 9 4.5 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8.91223 +298 1 1 3.91118 5.22253 6.29642 +299 1 -1 9.17618 3.98313 9.82158 +300 1 1 4.95424 5.93521 1.3652 diff --git a/examples/USER/scafacos/data.hammersley_shphere b/examples/USER/scafacos/data.hammersley_shphere new file mode 100644 index 0000000000..e0d067adfb --- /dev/null +++ b/examples/USER/scafacos/data.hammersley_shphere @@ -0,0 +1,1016 @@ +LAMMPS Description + +1000 atoms + +1 atom types + +-50.5 51.5 xlo xhi +-50.5 51.5 ylo yhi +-50.5 51.5 zlo zhi + +Masses + +1 1.0 + +Atoms + +1 1 1 0.5 0.5 0 +2 1 1 0.468393 0.5 0.001 +3 1 1 0.5 0.544677 0.002 +4 1 -1 0.5 0.44531 0.003 +5 1 -1 0.544632 0.544632 0.004 +6 1 1 0.450125 0.450125 0.005 +7 1 1 0.445392 0.554608 0.006 +8 1 -1 0.558953 0.441047 0.007 +9 1 -1 0.582303 0.534091 0.008 +10 1 -1 0.412748 0.463859 0.009 +11 1 -1 0.461923 0.591925 0.01 +12 1 -1 0.539915 0.403637 0.011 +13 1 -1 0.541669 0.600597 0.012 +14 1 -1 0.456652 0.395348 0.013 +15 1 -1 0.391453 0.544962 0.014 +16 1 1 0.6123 0.453484 0.015 +17 1 1 0.623064 0.524479 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-1 0.646729 0.543528 0.976 +978 1 -1 0.356287 0.457366 0.977 +979 1 -1 0.458282 0.640626 0.978 +980 1 1 0.54078 0.362537 0.979 +981 1 -1 0.566752 0.623062 0.98 +982 1 -1 0.434905 0.379993 0.981 +983 1 -1 0.383134 0.563391 0.982 +984 1 -1 0.613631 0.438364 0.983 +985 1 -1 0.59748 0.579004 0.984 +986 1 1 0.405567 0.423466 0.985 +987 1 -1 0.426024 0.591277 0.986 +988 1 -1 0.571322 0.411999 0.987 +989 1 1 0.511337 0.608293 0.988 +990 1 1 0.48914 0.396264 0.989 +991 1 -1 0.401042 0.51036 0.99 +992 1 1 0.593927 0.490167 0.991 +993 1 1 0.587477 0.516843 0.992 +994 1 1 0.418131 0.484237 0.993 +995 1 1 0.485399 0.575834 0.994 +996 1 -1 0.513336 0.430738 0.995 +997 1 -1 0.535388 0.552265 0.996 +998 1 -1 0.469337 0.454714 0.997 +999 1 1 0.463006 0.525048 0.998 +1000 1 -1 0.526172 0.482279 0.999 diff --git a/examples/USER/scafacos/in.scafacos.cw.ewald b/examples/USER/scafacos/in.scafacos.cw.ewald new file mode 100644 index 0000000000..f8444dd01f --- /dev/null +++ b/examples/USER/scafacos/in.scafacos.cw.ewald @@ -0,0 +1,31 @@ + +units lj +atom_style charge + +read_data data.cloud_wall + +velocity all set 0.0 0.0 0.0 mom no + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve +kspace_style scafacos ewald 0.001 +kspace_modify scafacos tolerance field + +timestep 0.005 + +thermo_style custom step atoms cpu temp pe ke etotal ecoul + +run_style verlet + +#dump simple all custom 1000 id x y z vx vy vz +#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass +#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass +#dump_modify dmpvtk pad 7 + +thermo 10 +run 100 diff --git a/examples/USER/scafacos/in.scafacos.cw.fmm b/examples/USER/scafacos/in.scafacos.cw.fmm new file mode 100644 index 0000000000..24a2739581 --- /dev/null +++ b/examples/USER/scafacos/in.scafacos.cw.fmm @@ -0,0 +1,37 @@ +units lj +atom_style charge + +read_data data.cloud_wall + +velocity all set 0.0 0.0 0.0 mom no + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +kspace_style scafacos fmm 1.0e-3 +kspace_modify scafacos tolerance energy_rel +kspace_modify scafacos fmm_tuning 1 + +timestep 0.005 + +thermo_style custom step atoms cpu temp pe ke etotal ecoul + +run_style verlet + +#dump simple all custom 1000 id x y z vx vy vz +#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass +#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass +#dump_modify dmpvtk pad 7 + +thermo 10 +run 100 diff --git a/examples/USER/scafacos/in.scafacos.cw.p2nfft b/examples/USER/scafacos/in.scafacos.cw.p2nfft new file mode 100644 index 0000000000..7a2391bc77 --- /dev/null +++ b/examples/USER/scafacos/in.scafacos.cw.p2nfft @@ -0,0 +1,31 @@ + +units lj +atom_style charge + +read_data data.cloud_wall + +velocity all set 0.0 0.0 0.0 mom no + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve +kspace_style scafacos p2nfft 0.001 +kspace_modify scafacos tolerance field + +timestep 0.005 + +thermo_style custom step atoms cpu temp pe ke etotal ecoul + +run_style verlet + +#dump simple all custom 1000 id x y z vx vy vz +#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass +#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass +#dump_modify dmpvtk pad 7 + +thermo 10 +run 100 diff --git a/examples/USER/scafacos/in.scafacos.ewald b/examples/USER/scafacos/in.scafacos.ewald new file mode 100644 index 0000000000..6c26c71884 --- /dev/null +++ b/examples/USER/scafacos/in.scafacos.ewald @@ -0,0 +1,37 @@ +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.NaCl + +replicate 8 8 8 + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos ewald 0.001 +kspace_modify scafacos tolerance field + +timestep 0.005 +thermo 10 + +run 100 diff --git a/examples/USER/scafacos/in.scafacos.fmm b/examples/USER/scafacos/in.scafacos.fmm new file mode 100644 index 0000000000..18d7464fb8 --- /dev/null +++ b/examples/USER/scafacos/in.scafacos.fmm @@ -0,0 +1,37 @@ +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.NaCl + +replicate 8 8 8 + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos fmm 0.001 +kspace_modify scafacos tolerance energy_rel + +timestep 0.005 +thermo 10 + +run 100 diff --git a/examples/USER/scafacos/in.scafacos.hsph.direct b/examples/USER/scafacos/in.scafacos.hsph.direct new file mode 100644 index 0000000000..60448880ec --- /dev/null +++ b/examples/USER/scafacos/in.scafacos.hsph.direct @@ -0,0 +1,34 @@ +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.hammersley_shphere +change_box all boundary f f f + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos direct 0.001 + +timestep 0.005 +thermo 1 +run 20 diff --git a/examples/USER/scafacos/in.scafacos.hsph.fmm b/examples/USER/scafacos/in.scafacos.hsph.fmm new file mode 100644 index 0000000000..515809dbde --- /dev/null +++ b/examples/USER/scafacos/in.scafacos.hsph.fmm @@ -0,0 +1,37 @@ +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.hammersley_shphere +change_box all boundary f f f + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos fmm 0.001 +kspace_modify scafacos tolerance energy_rel +kspace_modify scafacos fmm_tuning 1 + +timestep 0.005 +thermo 1 + +run 20 diff --git a/examples/USER/scafacos/in.scafacos.hsph.p2nfft b/examples/USER/scafacos/in.scafacos.hsph.p2nfft new file mode 100644 index 0000000000..d690a29e49 --- /dev/null +++ b/examples/USER/scafacos/in.scafacos.hsph.p2nfft @@ -0,0 +1,36 @@ +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.hammersley_shphere +change_box all boundary f f f + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos p2nfft 0.001 +kspace_modify scafacos tolerance potential + +timestep 0.005 +thermo 1 + +run 20 diff --git a/examples/USER/scafacos/in.scafacos.p2nfft b/examples/USER/scafacos/in.scafacos.p2nfft new file mode 100644 index 0000000000..7fa2ccdd9e --- /dev/null +++ b/examples/USER/scafacos/in.scafacos.p2nfft @@ -0,0 +1,37 @@ +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.NaCl + +replicate 8 8 8 + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos p2nfft 0.001 +kspace_modify scafacos tolerance field + +timestep 0.005 +thermo 10 + +run 100 diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.ewald.16 b/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.ewald.16 new file mode 100644 index 0000000000..ffdc7e3a3c --- /dev/null +++ b/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.ewald.16 @@ -0,0 +1,92 @@ +LAMMPS (29 Jun 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task + +units lj +atom_style charge + +read_data data.cloud_wall + orthogonal box = (0 0 0) to (10 10 10) + 2 by 2 by 4 MPI processor grid + reading atoms ... + 300 atoms + +velocity all set 0.0 0.0 0.0 mom no + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve +kspace_style scafacos ewald 0.001 +kspace_modify scafacos tolerance field + +timestep 0.005 + +thermo_style custom step atoms cpu temp pe ke etotal ecoul + +run_style verlet + +#dump simple all custom 1000 id x y z vx vy vz +#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass +#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass +#dump_modify dmpvtk pad 7 + +thermo 10 +run 100 +Setting up ScaFaCoS with solver ewald ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 10 10 10 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.313 | 3.501 | 3.689 Mbytes +Step Atoms CPU Temp PotEng KinEng TotEng E_coul + 0 300 0 0 0.49647271 0 0.49647271 0 + 10 300 0.061254978 0.014582562 0.44286522 0.02180093 0.46466616 0 + 20 300 0.12240911 0.058693359 0.37869251 0.087746571 0.46643909 0 + 30 300 0.18348265 0.13468789 0.26730177 0.2013584 0.46866017 0 + 40 300 0.24441123 0.50949535 0.083356437 0.76169555 0.84505198 0 + 50 300 0.30493236 1.1731116 -0.055261984 1.7538018 1.6985399 0 + 60 300 0.36615515 1.3589639 -0.33351524 2.031651 1.6981358 0 + 70 300 0.42717433 1.6482648 -0.76570045 2.4641559 1.6984554 0 + 80 300 0.48137259 2.8640899 -2.4038488 4.2818144 1.8779656 0 + 90 300 0.5323379 93.168442 -2.5911448 139.28682 136.69568 0 + 100 300 0.5756321 94.146897 -1.3480439 140.74961 139.40157 0 +Loop time of 0.575655 on 16 procs for 100 steps with 300 atoms + +Performance: 75045.007 tau/day, 173.715 timesteps/s +98.7% CPU use with 16 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.2159e-05 | 1.739e-05 | 2.3127e-05 | 0.0 | 0.00 +Kspace | 0.57008 | 0.57086 | 0.57137 | 0.1 | 99.17 +Neigh | 0.00025606 | 0.00061357 | 0.001369 | 0.0 | 0.11 +Comm | 0.0023558 | 0.0027267 | 0.003104 | 0.4 | 0.47 +Output | 0.00029898 | 0.00032344 | 0.00037599 | 0.0 | 0.06 +Modify | 8.2493e-05 | 0.00014143 | 0.00021815 | 0.0 | 0.02 +Other | | 0.0009701 | | | 0.17 + +Nlocal: 18.75 ave 39 max 6 min +Histogram: 6 1 1 0 1 2 2 1 1 1 +Nghost: 122.812 ave 195 max 63 min +Histogram: 8 0 0 0 0 0 0 1 3 4 +Neighs: 160.625 ave 598 max 13 min +Histogram: 8 2 1 1 1 0 0 2 0 1 + +Total # of neighbors = 2570 +Ave neighs/atom = 8.56667 +Neighbor list builds = 23 +Dangerous builds = 16 +Total wall time: 0:00:00 diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.ewald.8 b/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.ewald.8 new file mode 100644 index 0000000000..52d887f475 --- /dev/null +++ b/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.ewald.8 @@ -0,0 +1,92 @@ +LAMMPS (29 Jun 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task + +units lj +atom_style charge + +read_data data.cloud_wall + orthogonal box = (0 0 0) to (10 10 10) + 2 by 2 by 2 MPI processor grid + reading atoms ... + 300 atoms + +velocity all set 0.0 0.0 0.0 mom no + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve +kspace_style scafacos ewald 0.001 +kspace_modify scafacos tolerance field + +timestep 0.005 + +thermo_style custom step atoms cpu temp pe ke etotal ecoul + +run_style verlet + +#dump simple all custom 1000 id x y z vx vy vz +#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass +#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass +#dump_modify dmpvtk pad 7 + +thermo 10 +run 100 +Setting up ScaFaCoS with solver ewald ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 10 10 10 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.317 | 3.317 | 3.317 Mbytes +Step Atoms CPU Temp PotEng KinEng TotEng E_coul + 0 300 0 0 0.49647271 0 0.49647271 0 + 10 300 0.067519665 0.014718629 0.45088339 0.02200435 0.47288774 0 + 20 300 0.13502312 0.05922597 0.38470912 0.088542825 0.47325194 0 + 30 300 0.20248008 0.13587829 0.27058048 0.20313804 0.47371852 0 + 40 300 0.26985955 0.51353118 0.088432648 0.76772911 0.85616176 0 + 50 300 0.33801103 1.1760001 -0.058088247 1.7581201 1.7000319 0 + 60 300 0.40665984 1.3627885 -0.33736672 2.0373688 1.7000021 0 + 70 300 0.47533679 1.6529365 -0.77082139 2.4711401 1.7003187 0 + 80 300 0.54396391 2.9569837 -2.4624654 4.4206907 1.9582253 0 + 90 300 0.61429667 81.642726 -2.5370215 122.05588 119.51885 0 + 100 300 0.68513632 85.047974 -1.128107 127.14672 126.01861 0 +Loop time of 0.685155 on 8 procs for 100 steps with 300 atoms + +Performance: 63051.442 tau/day, 145.952 timesteps/s +99.7% CPU use with 8 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.0967e-05 | 1.4216e-05 | 1.8358e-05 | 0.0 | 0.00 +Kspace | 0.67942 | 0.67981 | 0.6803 | 0.0 | 99.22 +Neigh | 0.00073242 | 0.0010653 | 0.0015635 | 0.8 | 0.16 +Comm | 0.0029492 | 0.0031102 | 0.0033047 | 0.2 | 0.45 +Output | 0.00021768 | 0.00023454 | 0.00028443 | 0.0 | 0.03 +Modify | 0.00016046 | 0.00018132 | 0.00019431 | 0.0 | 0.03 +Other | | 0.0007433 | | | 0.11 + +Nlocal: 37.5 ave 46 max 31 min +Histogram: 2 0 0 2 1 0 2 0 0 1 +Nghost: 203.875 ave 212 max 192 min +Histogram: 1 0 1 0 0 2 1 0 0 3 +Neighs: 321.625 ave 599 max 112 min +Histogram: 1 2 0 1 1 0 1 1 0 1 + +Total # of neighbors = 2573 +Ave neighs/atom = 8.57667 +Neighbor list builds = 23 +Dangerous builds = 16 +Total wall time: 0:00:00 diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.1 b/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.1 new file mode 100644 index 0000000000..47e0be01ce --- /dev/null +++ b/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.1 @@ -0,0 +1,99 @@ +LAMMPS (29 Jun 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +units lj +atom_style charge + +read_data data.cloud_wall + orthogonal box = (0 0 0) to (10 10 10) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 300 atoms + +velocity all set 0.0 0.0 0.0 mom no + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +kspace_style scafacos fmm 1.0e-3 +kspace_modify scafacos tolerance energy_rel +kspace_modify scafacos fmm_tuning 1 +ScaFaCoS setting fmm inhomogen tuning ...3 + +timestep 0.005 + +thermo_style custom step atoms cpu temp pe ke etotal ecoul + +run_style verlet + +#dump simple all custom 1000 id x y z vx vy vz +#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass +#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass +#dump_modify dmpvtk pad 7 + +thermo 10 +run 100 +Setting up ScaFaCoS with solver fmm ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 10 10 10 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.34 | 3.34 | 3.34 Mbytes +Step Atoms CPU Temp PotEng KinEng TotEng E_coul + 0 300 0 0 0.49646402 0 0.49646402 0 + 10 300 0.036603451 0.015455559 0.47335833 0.02310606 0.49646439 0 + 20 300 0.073534727 0.06229069 0.40334177 0.093124582 0.49646635 0 + 30 300 0.10984373 0.14310163 0.28254277 0.21393694 0.49647971 0 + 40 300 0.14610171 0.52929788 0.089669015 0.79130033 0.88096934 0 + 50 300 0.18255496 1.1963022 -0.082792461 1.7884718 1.7056794 0 + 60 300 0.2194376 1.3928167 -0.37659239 2.082261 1.7056686 0 + 70 300 0.25588369 1.7069009 -0.84571914 2.5518169 1.7060978 0 + 80 300 0.29101205 15.358343 -3.368063 22.960722 19.592659 0 + 90 300 0.32697225 42.280432 -2.1623864 63.209247 61.04686 0 + 100 300 0.36395645 41.48079 -0.89904529 62.013782 61.114736 0 +Loop time of 0.363968 on 1 procs for 100 steps with 300 atoms + +Performance: 118691.709 tau/day, 274.749 timesteps/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.2875e-05 | 1.2875e-05 | 1.2875e-05 | 0.0 | 0.00 +Kspace | 0.35715 | 0.35715 | 0.35715 | 0.0 | 98.13 +Neigh | 0.0039768 | 0.0039768 | 0.0039768 | 0.0 | 1.09 +Comm | 0.0012023 | 0.0012023 | 0.0012023 | 0.0 | 0.33 +Output | 0.0001502 | 0.0001502 | 0.0001502 | 0.0 | 0.04 +Modify | 0.0009768 | 0.0009768 | 0.0009768 | 0.0 | 0.27 +Other | | 0.0005031 | | | 0.14 + +Nlocal: 300 ave 300 max 300 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 374 ave 374 max 374 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 2459 ave 2459 max 2459 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 2459 +Ave neighs/atom = 8.19667 +Neighbor list builds = 15 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.16 b/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.16 new file mode 100644 index 0000000000..f104355d87 --- /dev/null +++ b/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.16 @@ -0,0 +1,99 @@ +LAMMPS (29 Jun 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +units lj +atom_style charge + +read_data data.cloud_wall + orthogonal box = (0 0 0) to (10 10 10) + 2 by 2 by 4 MPI processor grid + reading atoms ... + 300 atoms + +velocity all set 0.0 0.0 0.0 mom no + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +kspace_style scafacos fmm 1.0e-3 +kspace_modify scafacos tolerance energy_rel +kspace_modify scafacos fmm_tuning 1 +ScaFaCoS setting fmm inhomogen tuning ...3 + +timestep 0.005 + +thermo_style custom step atoms cpu temp pe ke etotal ecoul + +run_style verlet + +#dump simple all custom 1000 id x y z vx vy vz +#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass +#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass +#dump_modify dmpvtk pad 7 + +thermo 10 +run 100 +Setting up ScaFaCoS with solver fmm ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 10 10 10 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.313 | 3.501 | 3.689 Mbytes +Step Atoms CPU Temp PotEng KinEng TotEng E_coul + 0 300 0 0 0.49646402 0 0.49646402 0 + 10 300 0.018873215 0.015455559 0.47335833 0.02310606 0.49646439 0 + 20 300 0.035197735 0.06229069 0.40334177 0.093124582 0.49646635 0 + 30 300 0.051513195 0.14310163 0.28254277 0.21393694 0.49647971 0 + 40 300 0.067400217 0.52929788 0.089669015 0.79130033 0.88096934 0 + 50 300 0.083569527 1.1963022 -0.082792461 1.7884718 1.7056794 0 + 60 300 0.099931955 1.3928167 -0.37659239 2.082261 1.7056686 0 + 70 300 0.11602688 1.7069009 -0.84571914 2.5518169 1.7060978 0 + 80 300 0.13271379 15.358343 -3.368063 22.960722 19.592659 0 + 90 300 0.15055513 42.280432 -2.1623864 63.209247 61.04686 0 + 100 300 0.16817498 41.48079 -0.89904529 62.013782 61.114736 0 +Loop time of 0.168194 on 16 procs for 100 steps with 300 atoms + +Performance: 256846.586 tau/day, 594.552 timesteps/s +97.7% CPU use with 16 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.4544e-05 | 2.0206e-05 | 2.6941e-05 | 0.0 | 0.01 +Kspace | 0.16313 | 0.16373 | 0.16423 | 0.1 | 97.34 +Neigh | 0.00016737 | 0.00039591 | 0.00084519 | 0.0 | 0.24 +Comm | 0.0021157 | 0.0026083 | 0.0032525 | 0.7 | 1.55 +Output | 0.00026298 | 0.00030228 | 0.00035977 | 0.0 | 0.18 +Modify | 0.00010705 | 0.00015062 | 0.00020647 | 0.0 | 0.09 +Other | | 0.0009913 | | | 0.59 + +Nlocal: 18.75 ave 36 max 6 min +Histogram: 4 3 1 0 0 1 2 1 2 2 +Nghost: 127 ave 196 max 71 min +Histogram: 8 0 0 0 0 0 0 1 6 1 +Neighs: 153.688 ave 491 max 10 min +Histogram: 8 1 1 1 1 1 0 0 0 3 + +Total # of neighbors = 2459 +Ave neighs/atom = 8.19667 +Neighbor list builds = 15 +Dangerous builds = 0 +Total wall time: 0:00:01 diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.2 b/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.2 new file mode 100644 index 0000000000..43ded2d4da --- /dev/null +++ b/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.2 @@ -0,0 +1,99 @@ +LAMMPS (29 Jun 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +units lj +atom_style charge + +read_data data.cloud_wall + orthogonal box = (0 0 0) to (10 10 10) + 1 by 1 by 2 MPI processor grid + reading atoms ... + 300 atoms + +velocity all set 0.0 0.0 0.0 mom no + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +kspace_style scafacos fmm 1.0e-3 +kspace_modify scafacos tolerance energy_rel +kspace_modify scafacos fmm_tuning 1 +ScaFaCoS setting fmm inhomogen tuning ...3 + +timestep 0.005 + +thermo_style custom step atoms cpu temp pe ke etotal ecoul + +run_style verlet + +#dump simple all custom 1000 id x y z vx vy vz +#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass +#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass +#dump_modify dmpvtk pad 7 + +thermo 10 +run 100 +Setting up ScaFaCoS with solver fmm ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 10 10 10 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.354 | 3.354 | 3.355 Mbytes +Step Atoms CPU Temp PotEng KinEng TotEng E_coul + 0 300 0 0 0.49646402 0 0.49646402 0 + 10 300 0.021326542 0.015455559 0.47335833 0.02310606 0.49646439 0 + 20 300 0.043129683 0.06229069 0.40334177 0.093124582 0.49646635 0 + 30 300 0.064425707 0.14310163 0.28254277 0.21393694 0.49647971 0 + 40 300 0.085822344 0.52929788 0.089669015 0.79130033 0.88096934 0 + 50 300 0.10737753 1.1963022 -0.082792461 1.7884718 1.7056794 0 + 60 300 0.12947297 1.3928167 -0.37659239 2.082261 1.7056686 0 + 70 300 0.15108895 1.7069009 -0.84571914 2.5518169 1.7060978 0 + 80 300 0.17378163 15.358343 -3.368063 22.960722 19.592659 0 + 90 300 0.19809985 42.280432 -2.1623864 63.209247 61.04686 0 + 100 300 0.22268319 41.48079 -0.89904529 62.013782 61.114736 0 +Loop time of 0.222696 on 2 procs for 100 steps with 300 atoms + +Performance: 193986.156 tau/day, 449.042 timesteps/s +98.4% CPU use with 2 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.1683e-05 | 1.5378e-05 | 1.9073e-05 | 0.0 | 0.01 +Kspace | 0.21627 | 0.2168 | 0.21734 | 0.1 | 97.35 +Neigh | 0.0016344 | 0.0021609 | 0.0026875 | 1.1 | 0.97 +Comm | 0.0022857 | 0.0023286 | 0.0023715 | 0.1 | 1.05 +Output | 0.00015521 | 0.00019228 | 0.00022936 | 0.0 | 0.09 +Modify | 0.00052834 | 0.00054049 | 0.00055265 | 0.0 | 0.24 +Other | | 0.0006541 | | | 0.29 + +Nlocal: 150 ave 159 max 141 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Nghost: 392 ave 395 max 389 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Neighs: 1229.5 ave 1773 max 686 min +Histogram: 1 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 2459 +Ave neighs/atom = 8.19667 +Neighbor list builds = 15 +Dangerous builds = 0 +Total wall time: 0:00:01 diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.4 b/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.4 new file mode 100644 index 0000000000..12c74993e9 --- /dev/null +++ b/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.4 @@ -0,0 +1,99 @@ +LAMMPS (29 Jun 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +units lj +atom_style charge + +read_data data.cloud_wall + orthogonal box = (0 0 0) to (10 10 10) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 300 atoms + +velocity all set 0.0 0.0 0.0 mom no + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +kspace_style scafacos fmm 1.0e-3 +kspace_modify scafacos tolerance energy_rel +kspace_modify scafacos fmm_tuning 1 +ScaFaCoS setting fmm inhomogen tuning ...3 + +timestep 0.005 + +thermo_style custom step atoms cpu temp pe ke etotal ecoul + +run_style verlet + +#dump simple all custom 1000 id x y z vx vy vz +#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass +#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass +#dump_modify dmpvtk pad 7 + +thermo 10 +run 100 +Setting up ScaFaCoS with solver fmm ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 10 10 10 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.333 | 3.333 | 3.333 Mbytes +Step Atoms CPU Temp PotEng KinEng TotEng E_coul + 0 300 0 0 0.49646402 0 0.49646402 0 + 10 300 0.017563343 0.015455559 0.47335833 0.02310606 0.49646439 0 + 20 300 0.034884214 0.06229069 0.40334177 0.093124582 0.49646635 0 + 30 300 0.052014828 0.14310163 0.28254277 0.21393694 0.49647971 0 + 40 300 0.069101095 0.52929788 0.089669015 0.79130033 0.88096934 0 + 50 300 0.085633039 1.1963022 -0.082792461 1.7884718 1.7056794 0 + 60 300 0.10165119 1.3928167 -0.37659239 2.082261 1.7056686 0 + 70 300 0.11729789 1.7069009 -0.84571914 2.5518169 1.7060978 0 + 80 300 0.1342802 15.358343 -3.368063 22.960722 19.592659 0 + 90 300 0.15266848 42.280432 -2.1623864 63.209247 61.04686 0 + 100 300 0.17004442 41.48079 -0.89904529 62.013782 61.114736 0 +Loop time of 0.170072 on 4 procs for 100 steps with 300 atoms + +Performance: 254010.216 tau/day, 587.987 timesteps/s +98.8% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.5497e-05 | 1.6868e-05 | 1.9789e-05 | 0.0 | 0.01 +Kspace | 0.16417 | 0.16472 | 0.16507 | 0.1 | 96.86 +Neigh | 0.00082564 | 0.0012031 | 0.0015855 | 0.9 | 0.71 +Comm | 0.0026572 | 0.0029335 | 0.003197 | 0.4 | 1.72 +Output | 0.00019169 | 0.00021791 | 0.00026536 | 0.0 | 0.13 +Modify | 0.00031304 | 0.00032955 | 0.00035334 | 0.0 | 0.19 +Other | | 0.0006474 | | | 0.38 + +Nlocal: 75 ave 81 max 70 min +Histogram: 2 0 0 0 0 0 0 1 0 1 +Nghost: 282.5 ave 290 max 274 min +Histogram: 1 0 0 1 0 0 0 0 1 1 +Neighs: 614.75 ave 981 max 285 min +Histogram: 1 1 0 0 0 0 0 1 0 1 + +Total # of neighbors = 2459 +Ave neighs/atom = 8.19667 +Neighbor list builds = 15 +Dangerous builds = 0 +Total wall time: 0:00:01 diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.8 b/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.8 new file mode 100644 index 0000000000..1fea13cd13 --- /dev/null +++ b/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.8 @@ -0,0 +1,99 @@ +LAMMPS (29 Jun 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +units lj +atom_style charge + +read_data data.cloud_wall + orthogonal box = (0 0 0) to (10 10 10) + 2 by 2 by 2 MPI processor grid + reading atoms ... + 300 atoms + +velocity all set 0.0 0.0 0.0 mom no + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +kspace_style scafacos fmm 1.0e-3 +kspace_modify scafacos tolerance energy_rel +kspace_modify scafacos fmm_tuning 1 +ScaFaCoS setting fmm inhomogen tuning ...3 + +timestep 0.005 + +thermo_style custom step atoms cpu temp pe ke etotal ecoul + +run_style verlet + +#dump simple all custom 1000 id x y z vx vy vz +#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass +#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass +#dump_modify dmpvtk pad 7 + +thermo 10 +run 100 +Setting up ScaFaCoS with solver fmm ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 10 10 10 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.317 | 3.317 | 3.317 Mbytes +Step Atoms CPU Temp PotEng KinEng TotEng E_coul + 0 300 0 0 0.49646402 0 0.49646402 0 + 10 300 0.016258478 0.015455559 0.47335833 0.02310606 0.49646439 0 + 20 300 0.031442165 0.06229069 0.40334177 0.093124582 0.49646635 0 + 30 300 0.046462774 0.14310163 0.28254277 0.21393694 0.49647971 0 + 40 300 0.061176538 0.52929788 0.089669015 0.79130033 0.88096934 0 + 50 300 0.076244354 1.1963022 -0.082792461 1.7884718 1.7056794 0 + 60 300 0.091396809 1.3928167 -0.37659239 2.082261 1.7056686 0 + 70 300 0.10625911 1.7069009 -0.84571914 2.5518169 1.7060978 0 + 80 300 0.1204896 15.358343 -3.368063 22.960722 19.592659 0 + 90 300 0.13657618 42.280432 -2.1623864 63.209247 61.04686 0 + 100 300 0.15163732 41.48079 -0.89904529 62.013782 61.114736 0 +Loop time of 0.151654 on 8 procs for 100 steps with 300 atoms + +Performance: 284858.554 tau/day, 659.395 timesteps/s +97.7% CPU use with 8 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.3828e-05 | 1.6987e-05 | 1.955e-05 | 0.0 | 0.01 +Kspace | 0.14633 | 0.14689 | 0.14725 | 0.1 | 96.86 +Neigh | 0.00047135 | 0.00067887 | 0.00094771 | 0.0 | 0.45 +Comm | 0.0027649 | 0.0029218 | 0.0032592 | 0.3 | 1.93 +Output | 0.00022578 | 0.00024724 | 0.00030136 | 0.0 | 0.16 +Modify | 0.00018954 | 0.00021681 | 0.0002358 | 0.0 | 0.14 +Other | | 0.0006794 | | | 0.45 + +Nlocal: 37.5 ave 45 max 31 min +Histogram: 1 1 1 1 1 0 1 0 1 1 +Nghost: 200 ave 209 max 189 min +Histogram: 1 0 0 0 1 4 0 0 0 2 +Neighs: 307.375 ave 514 max 115 min +Histogram: 2 1 0 1 1 0 0 0 1 2 + +Total # of neighbors = 2459 +Ave neighs/atom = 8.19667 +Neighbor list builds = 15 +Dangerous builds = 0 +Total wall time: 0:00:01 diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.p2nfft.1 b/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.p2nfft.1 new file mode 100644 index 0000000000..bd9325dc4b --- /dev/null +++ b/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.p2nfft.1 @@ -0,0 +1,92 @@ +LAMMPS (29 Jun 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task + +units lj +atom_style charge + +read_data data.cloud_wall + orthogonal box = (0 0 0) to (10 10 10) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 300 atoms + +velocity all set 0.0 0.0 0.0 mom no + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve +kspace_style scafacos p2nfft 0.001 +kspace_modify scafacos tolerance field + +timestep 0.005 + +thermo_style custom step atoms cpu temp pe ke etotal ecoul + +run_style verlet + +#dump simple all custom 1000 id x y z vx vy vz +#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass +#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass +#dump_modify dmpvtk pad 7 + +thermo 10 +run 100 +Setting up ScaFaCoS with solver p2nfft ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 10 10 10 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.34 | 3.34 | 3.34 Mbytes +Step Atoms CPU Temp PotEng KinEng TotEng E_coul + 0 300 0 0 0.49683273 0 0.49683273 0 + 10 300 0.082981586 0.015479312 0.47369009 0.023141571 0.49683166 0 + 20 300 0.16677213 0.062386358 0.40356181 0.093267605 0.49682941 0 + 30 300 0.2506392 0.14331637 0.2825636 0.21425798 0.49682157 0 + 40 300 0.33466673 0.53041843 0.089505208 0.79297556 0.88248077 0 + 50 300 0.41812825 1.1948397 -0.083317439 1.7862853 1.7029679 0 + 60 300 0.50167894 1.3915614 -0.37745551 2.0803842 1.7029287 0 + 70 300 0.58574796 1.7061978 -0.84746071 2.5507657 1.703305 0 + 80 300 0.6700325 20.692093 -3.32971 30.93468 27.60497 0 + 90 300 0.75608635 48.999403 -2.1632167 73.254107 71.090891 0 + 100 300 0.84190726 51.199785 -0.81127924 76.543678 75.732399 0 +Loop time of 0.841921 on 1 procs for 100 steps with 300 atoms + +Performance: 51311.251 tau/day, 118.776 timesteps/s +100.0% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.1206e-05 | 1.1206e-05 | 1.1206e-05 | 0.0 | 0.00 +Kspace | 0.835 | 0.835 | 0.835 | 0.0 | 99.18 +Neigh | 0.0040102 | 0.0040102 | 0.0040102 | 0.0 | 0.48 +Comm | 0.0012431 | 0.0012431 | 0.0012431 | 0.0 | 0.15 +Output | 0.0001545 | 0.0001545 | 0.0001545 | 0.0 | 0.02 +Modify | 0.0010202 | 0.0010202 | 0.0010202 | 0.0 | 0.12 +Other | | 0.000484 | | | 0.06 + +Nlocal: 300 ave 300 max 300 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 381 ave 381 max 381 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 2461 ave 2461 max 2461 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 2461 +Ave neighs/atom = 8.20333 +Neighbor list builds = 15 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.p2nfft.16 b/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.p2nfft.16 new file mode 100644 index 0000000000..1e385c5fda --- /dev/null +++ b/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.p2nfft.16 @@ -0,0 +1,92 @@ +LAMMPS (29 Jun 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task + +units lj +atom_style charge + +read_data data.cloud_wall + orthogonal box = (0 0 0) to (10 10 10) + 2 by 2 by 4 MPI processor grid + reading atoms ... + 300 atoms + +velocity all set 0.0 0.0 0.0 mom no + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve +kspace_style scafacos p2nfft 0.001 +kspace_modify scafacos tolerance field + +timestep 0.005 + +thermo_style custom step atoms cpu temp pe ke etotal ecoul + +run_style verlet + +#dump simple all custom 1000 id x y z vx vy vz +#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass +#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass +#dump_modify dmpvtk pad 7 + +thermo 10 +run 100 +Setting up ScaFaCoS with solver p2nfft ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 10 10 10 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.313 | 3.501 | 3.689 Mbytes +Step Atoms CPU Temp PotEng KinEng TotEng E_coul + 0 300 0 0 0.49683273 0 0.49683273 0 + 10 300 0.029647827 0.015479312 0.47369009 0.023141571 0.49683166 0 + 20 300 0.059298515 0.062386358 0.40356181 0.093267605 0.49682941 0 + 30 300 0.088926077 0.14331637 0.2825636 0.21425798 0.49682157 0 + 40 300 0.11850166 0.53041843 0.089505208 0.79297556 0.88248077 0 + 50 300 0.14820433 1.1948397 -0.083317439 1.7862853 1.7029679 0 + 60 300 0.17807317 1.3915614 -0.37745551 2.0803842 1.7029287 0 + 70 300 0.20803642 1.7061978 -0.84746071 2.5507657 1.703305 0 + 80 300 0.23797083 20.692093 -3.32971 30.93468 27.60497 0 + 90 300 0.26835561 48.999403 -2.1632167 73.254107 71.090891 0 + 100 300 0.29766583 51.199785 -0.81127924 76.543678 75.732399 0 +Loop time of 0.297693 on 16 procs for 100 steps with 300 atoms + +Performance: 145116.000 tau/day, 335.917 timesteps/s +98.8% CPU use with 16 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.1683e-05 | 1.6928e-05 | 2.4557e-05 | 0.0 | 0.01 +Kspace | 0.29245 | 0.29325 | 0.29366 | 0.1 | 98.51 +Neigh | 0.00017214 | 0.00042973 | 0.0010228 | 0.0 | 0.14 +Comm | 0.0021176 | 0.0024613 | 0.0028479 | 0.5 | 0.83 +Output | 0.00028467 | 0.00033538 | 0.00041103 | 0.0 | 0.11 +Modify | 8.893e-05 | 0.00015014 | 0.00027537 | 0.0 | 0.05 +Other | | 0.001048 | | | 0.35 + +Nlocal: 18.75 ave 33 max 6 min +Histogram: 2 6 0 0 0 0 2 1 2 3 +Nghost: 128.875 ave 198 max 71 min +Histogram: 7 1 0 0 0 0 0 1 5 2 +Neighs: 153.812 ave 490 max 14 min +Histogram: 8 0 3 0 1 1 0 0 1 2 + +Total # of neighbors = 2461 +Ave neighs/atom = 8.20333 +Neighbor list builds = 15 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.p2nfft.2 b/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.p2nfft.2 new file mode 100644 index 0000000000..3f54069ffd --- /dev/null +++ b/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.p2nfft.2 @@ -0,0 +1,92 @@ +LAMMPS (29 Jun 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task + +units lj +atom_style charge + +read_data data.cloud_wall + orthogonal box = (0 0 0) to (10 10 10) + 1 by 1 by 2 MPI processor grid + reading atoms ... + 300 atoms + +velocity all set 0.0 0.0 0.0 mom no + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve +kspace_style scafacos p2nfft 0.001 +kspace_modify scafacos tolerance field + +timestep 0.005 + +thermo_style custom step atoms cpu temp pe ke etotal ecoul + +run_style verlet + +#dump simple all custom 1000 id x y z vx vy vz +#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass +#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass +#dump_modify dmpvtk pad 7 + +thermo 10 +run 100 +Setting up ScaFaCoS with solver p2nfft ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 10 10 10 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.354 | 3.354 | 3.355 Mbytes +Step Atoms CPU Temp PotEng KinEng TotEng E_coul + 0 300 0 0 0.49683273 0 0.49683273 0 + 10 300 0.049199581 0.015479312 0.47369009 0.023141571 0.49683166 0 + 20 300 0.09860301 0.062386358 0.40356181 0.093267605 0.49682941 0 + 30 300 0.14826894 0.14331637 0.2825636 0.21425798 0.49682157 0 + 40 300 0.19769144 0.53041843 0.089505208 0.79297556 0.88248077 0 + 50 300 0.24735355 1.1948397 -0.083317439 1.7862853 1.7029679 0 + 60 300 0.29692888 1.3915614 -0.37745551 2.0803842 1.7029287 0 + 70 300 0.34639764 1.7061978 -0.84746071 2.5507657 1.703305 0 + 80 300 0.39633083 20.692093 -3.32971 30.93468 27.60497 0 + 90 300 0.44779778 48.999403 -2.1632167 73.254107 71.090891 0 + 100 300 0.49988627 51.199785 -0.81127924 76.543678 75.732399 0 +Loop time of 0.499909 on 2 procs for 100 steps with 300 atoms + +Performance: 86415.782 tau/day, 200.037 timesteps/s +99.5% CPU use with 2 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 9.0599e-06 | 1.3709e-05 | 1.8358e-05 | 0.0 | 0.00 +Kspace | 0.49314 | 0.49365 | 0.49416 | 0.1 | 98.75 +Neigh | 0.0016146 | 0.0021083 | 0.0026021 | 1.1 | 0.42 +Comm | 0.002754 | 0.0028276 | 0.0029013 | 0.1 | 0.57 +Output | 0.00015783 | 0.00019348 | 0.00022912 | 0.0 | 0.04 +Modify | 0.00049257 | 0.00049472 | 0.00049686 | 0.0 | 0.10 +Other | | 0.0006217 | | | 0.12 + +Nlocal: 150 ave 157 max 143 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Nghost: 399 ave 402 max 396 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Neighs: 1230.5 ave 1756 max 705 min +Histogram: 1 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 2461 +Ave neighs/atom = 8.20333 +Neighbor list builds = 15 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.p2nfft.4 b/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.p2nfft.4 new file mode 100644 index 0000000000..8b94402658 --- /dev/null +++ b/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.p2nfft.4 @@ -0,0 +1,92 @@ +LAMMPS (29 Jun 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task + +units lj +atom_style charge + +read_data data.cloud_wall + orthogonal box = (0 0 0) to (10 10 10) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 300 atoms + +velocity all set 0.0 0.0 0.0 mom no + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve +kspace_style scafacos p2nfft 0.001 +kspace_modify scafacos tolerance field + +timestep 0.005 + +thermo_style custom step atoms cpu temp pe ke etotal ecoul + +run_style verlet + +#dump simple all custom 1000 id x y z vx vy vz +#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass +#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass +#dump_modify dmpvtk pad 7 + +thermo 10 +run 100 +Setting up ScaFaCoS with solver p2nfft ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 10 10 10 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.333 | 3.333 | 3.333 Mbytes +Step Atoms CPU Temp PotEng KinEng TotEng E_coul + 0 300 0 0 0.49683273 0 0.49683273 0 + 10 300 0.031973124 0.015479312 0.47369009 0.023141571 0.49683166 0 + 20 300 0.064628601 0.062386358 0.40356181 0.093267605 0.49682941 0 + 30 300 0.096747875 0.14331637 0.2825636 0.21425798 0.49682157 0 + 40 300 0.12864041 0.53041843 0.089505208 0.79297556 0.88248077 0 + 50 300 0.161134 1.1948397 -0.083317439 1.7862853 1.7029679 0 + 60 300 0.19359422 1.3915614 -0.37745551 2.0803842 1.7029287 0 + 70 300 0.22573543 1.7061978 -0.84746071 2.5507657 1.703305 0 + 80 300 0.25922132 20.692093 -3.32971 30.93468 27.60497 0 + 90 300 0.29452014 48.999403 -2.1632167 73.254107 71.090891 0 + 100 300 0.33031607 51.199785 -0.81127924 76.543678 75.732399 0 +Loop time of 0.330333 on 4 procs for 100 steps with 300 atoms + +Performance: 130777.056 tau/day, 302.725 timesteps/s +99.7% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.0014e-05 | 1.3471e-05 | 1.5497e-05 | 0.0 | 0.00 +Kspace | 0.32504 | 0.3255 | 0.3258 | 0.1 | 98.54 +Neigh | 0.00083303 | 0.0011883 | 0.0015609 | 0.8 | 0.36 +Comm | 0.0024087 | 0.0025436 | 0.0026674 | 0.2 | 0.77 +Output | 0.00017405 | 0.00020278 | 0.00024986 | 0.0 | 0.06 +Modify | 0.00028658 | 0.00031012 | 0.00033331 | 0.0 | 0.09 +Other | | 0.0005748 | | | 0.17 + +Nlocal: 75 ave 81 max 69 min +Histogram: 1 0 0 0 1 1 0 0 0 1 +Nghost: 287 ave 296 max 278 min +Histogram: 1 0 1 0 0 0 0 1 0 1 +Neighs: 615.25 ave 964 max 286 min +Histogram: 1 1 0 0 0 0 0 1 0 1 + +Total # of neighbors = 2461 +Ave neighs/atom = 8.20333 +Neighbor list builds = 15 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.p2nfft.8 b/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.p2nfft.8 new file mode 100644 index 0000000000..3de3c25017 --- /dev/null +++ b/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.p2nfft.8 @@ -0,0 +1,92 @@ +LAMMPS (29 Jun 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task + +units lj +atom_style charge + +read_data data.cloud_wall + orthogonal box = (0 0 0) to (10 10 10) + 2 by 2 by 2 MPI processor grid + reading atoms ... + 300 atoms + +velocity all set 0.0 0.0 0.0 mom no + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve +kspace_style scafacos p2nfft 0.001 +kspace_modify scafacos tolerance field + +timestep 0.005 + +thermo_style custom step atoms cpu temp pe ke etotal ecoul + +run_style verlet + +#dump simple all custom 1000 id x y z vx vy vz +#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass +#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass +#dump_modify dmpvtk pad 7 + +thermo 10 +run 100 +Setting up ScaFaCoS with solver p2nfft ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 10 10 10 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.317 | 3.317 | 3.317 Mbytes +Step Atoms CPU Temp PotEng KinEng TotEng E_coul + 0 300 0 0 0.49683273 0 0.49683273 0 + 10 300 0.023941755 0.015479312 0.47369009 0.023141571 0.49683166 0 + 20 300 0.047938108 0.062386358 0.40356181 0.093267605 0.49682941 0 + 30 300 0.071953773 0.14331637 0.2825636 0.21425798 0.49682157 0 + 40 300 0.095941782 0.53041843 0.089505208 0.79297556 0.88248077 0 + 50 300 0.12011361 1.1948397 -0.083317439 1.7862853 1.7029679 0 + 60 300 0.14433384 1.3915614 -0.37745551 2.0803842 1.7029287 0 + 70 300 0.16875505 1.7061978 -0.84746071 2.5507657 1.703305 0 + 80 300 0.193331 20.692093 -3.32971 30.93468 27.60497 0 + 90 300 0.21844888 48.999403 -2.1632167 73.254107 71.090891 0 + 100 300 0.24417853 51.199785 -0.81127924 76.543678 75.732399 0 +Loop time of 0.244198 on 8 procs for 100 steps with 300 atoms + +Performance: 176905.349 tau/day, 409.503 timesteps/s +99.7% CPU use with 8 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 9.7752e-06 | 1.4246e-05 | 1.955e-05 | 0.0 | 0.01 +Kspace | 0.23946 | 0.23972 | 0.24009 | 0.0 | 98.17 +Neigh | 0.00049043 | 0.00071204 | 0.00095773 | 0.0 | 0.29 +Comm | 0.0025063 | 0.0026675 | 0.0027597 | 0.2 | 1.09 +Output | 0.00019646 | 0.00021604 | 0.00026321 | 0.0 | 0.09 +Modify | 0.00017905 | 0.0001913 | 0.00020766 | 0.0 | 0.08 +Other | | 0.0006773 | | | 0.28 + +Nlocal: 37.5 ave 42 max 33 min +Histogram: 2 1 0 1 0 0 1 0 1 2 +Nghost: 202.25 ave 212 max 194 min +Histogram: 1 0 2 1 0 2 0 1 0 1 +Neighs: 307.625 ave 505 max 129 min +Histogram: 3 0 0 1 1 0 0 0 1 2 + +Total # of neighbors = 2461 +Ave neighs/atom = 8.20333 +Neighbor list builds = 15 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.g++.ewald.16 b/examples/USER/scafacos/log.23Jul18.scafacos.g++.ewald.16 new file mode 100644 index 0000000000..f2223064e0 --- /dev/null +++ b/examples/USER/scafacos/log.23Jul18.scafacos.g++.ewald.16 @@ -0,0 +1,102 @@ +LAMMPS (29 Jun 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.NaCl + orthogonal box = (0 0 0) to (2 2 2) + 2 by 2 by 4 MPI processor grid + reading atoms ... + 8 atoms + +replicate 8 8 8 + orthogonal box = (0 0 0) to (16 16 16) + 2 by 2 by 4 MPI processor grid + 4096 atoms + Time spent = 0.000503302 secs + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos ewald 0.001 +kspace_modify scafacos tolerance field + +timestep 0.005 +thermo 10 + +run 100 +Setting up ScaFaCoS with solver ewald ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 16 16 16 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.401 | 3.401 | 3.401 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -0.87413076 0 1.3753199 1.4996338 + 10 1.5001167 -0.84976141 0 1.3998642 1.4997504 + 20 1.5002402 -0.84977464 0 1.4000363 1.499874 + 30 1.5003611 -0.84978325 0 1.4002089 1.4999948 + 40 1.5004736 -0.84977869 0 1.4003823 1.5001073 + 50 1.5005703 -0.8497468 0 1.4005591 1.5002039 + 60 1.5006418 -0.84967646 0 1.4007366 1.5002754 + 70 1.5006785 -0.84955497 0 1.4009132 1.5003121 + 80 1.5006711 -0.849369 0 1.4010881 1.5003047 + 90 1.500611 -0.84910811 0 1.4012589 1.5002446 + 100 1.5004911 -0.84870167 0 1.4014854 1.5001247 +Loop time of 46.4857 on 16 procs for 100 steps with 4096 atoms + +Performance: 929.317 tau/day, 2.151 timesteps/s +99.8% CPU use with 16 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.00023437 | 0.00024788 | 0.00026894 | 0.0 | 0.00 +Kspace | 46.476 | 46.476 | 46.476 | 0.0 | 99.98 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.0062859 | 0.0067717 | 0.0072649 | 0.3 | 0.01 +Output | 0.0004127 | 0.00044075 | 0.00050807 | 0.0 | 0.00 +Modify | 0.00099325 | 0.0010343 | 0.0010939 | 0.1 | 0.00 +Other | | 0.001459 | | | 0.00 + +Nlocal: 256 ave 256 max 256 min +Histogram: 16 0 0 0 0 0 0 0 0 0 +Nghost: 1265 ave 1265 max 1265 min +Histogram: 16 0 0 0 0 0 0 0 0 0 +Neighs: 4096 ave 4096 max 4096 min +Histogram: 16 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 65536 +Ave neighs/atom = 16 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:47 diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.g++.ewald.8 b/examples/USER/scafacos/log.23Jul18.scafacos.g++.ewald.8 new file mode 100644 index 0000000000..8d3702a8b3 --- /dev/null +++ b/examples/USER/scafacos/log.23Jul18.scafacos.g++.ewald.8 @@ -0,0 +1,102 @@ +LAMMPS (29 Jun 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.NaCl + orthogonal box = (0 0 0) to (2 2 2) + 2 by 2 by 2 MPI processor grid + reading atoms ... + 8 atoms + +replicate 8 8 8 + orthogonal box = (0 0 0) to (16 16 16) + 2 by 2 by 2 MPI processor grid + 4096 atoms + Time spent = 0.000281811 secs + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos ewald 0.001 +kspace_modify scafacos tolerance field + +timestep 0.005 +thermo 10 + +run 100 +Setting up ScaFaCoS with solver ewald ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 16 16 16 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.416 | 3.416 | 3.416 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -0.87413076 0 1.3753199 1.4996338 + 10 1.5001095 -0.85040058 0 1.3992143 1.4997433 + 20 1.5002258 -0.85039456 0 1.3993947 1.4998595 + 30 1.5003395 -0.85038368 0 1.3995761 1.4999732 + 40 1.5004452 -0.85035944 0 1.3997589 1.5000789 + 50 1.5005354 -0.85030783 0 1.3999457 1.500169 + 60 1.5006008 -0.85021779 0 1.4001339 1.5002344 + 70 1.500632 -0.8500769 0 1.4003215 1.5002656 + 80 1.5006197 -0.84987187 0 1.4005081 1.5002533 + 90 1.5005554 -0.84959251 0 1.400691 1.500189 + 100 1.500432 -0.84916846 0 1.4009301 1.5000657 +Loop time of 86.1477 on 8 procs for 100 steps with 4096 atoms + +Performance: 501.464 tau/day, 1.161 timesteps/s +99.9% CPU use with 8 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.000314 | 0.00033289 | 0.00035048 | 0.0 | 0.00 +Kspace | 86.136 | 86.136 | 86.136 | 0.0 | 99.99 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.0069821 | 0.0073864 | 0.0077834 | 0.3 | 0.01 +Output | 0.00038719 | 0.00041264 | 0.00047517 | 0.0 | 0.00 +Modify | 0.0018711 | 0.0019454 | 0.0020905 | 0.1 | 0.00 +Other | | 0.001762 | | | 0.00 + +Nlocal: 512 ave 512 max 512 min +Histogram: 8 0 0 0 0 0 0 0 0 0 +Nghost: 1685 ave 1685 max 1685 min +Histogram: 8 0 0 0 0 0 0 0 0 0 +Neighs: 8192 ave 8192 max 8192 min +Histogram: 8 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 65536 +Ave neighs/atom = 16 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:01:28 diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.g++.fmm.1 b/examples/USER/scafacos/log.23Jul18.scafacos.g++.fmm.1 new file mode 100644 index 0000000000..0749de3832 --- /dev/null +++ b/examples/USER/scafacos/log.23Jul18.scafacos.g++.fmm.1 @@ -0,0 +1,102 @@ +LAMMPS (29 Jun 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.NaCl + orthogonal box = (0 0 0) to (2 2 2) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 8 atoms + +replicate 8 8 8 + orthogonal box = (0 0 0) to (16 16 16) + 1 by 1 by 1 MPI processor grid + 4096 atoms + Time spent = 0.000584364 secs + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos fmm 0.001 +kspace_modify scafacos tolerance energy_rel + +timestep 0.005 +thermo 10 + +run 100 +Setting up ScaFaCoS with solver fmm ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 16 16 16 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.723 | 3.723 | 3.723 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -0.87378819 0 1.3756625 1.4996338 + 10 1.5000004 -0.87378882 0 1.3756625 1.4996342 + 20 1.4999998 -0.87378782 0 1.3756625 1.4996336 + 30 1.4999934 -0.87377823 0 1.3756625 1.4996272 + 40 1.4999745 -0.87374997 0 1.3756625 1.4996083 + 50 1.4999347 -0.87369019 0 1.3756625 1.4995685 + 60 1.4998637 -0.87358381 0 1.3756625 1.4994975 + 70 1.4997506 -0.87341428 0 1.3756624 1.4993845 + 80 1.4995842 -0.87316464 0 1.3756624 1.499218 + 90 1.4993536 -0.87281897 0 1.3756624 1.4989876 + 100 1.4990503 -0.87236411 0 1.3756624 1.4986843 +Loop time of 5.26537 on 1 procs for 100 steps with 4096 atoms + +Performance: 8204.550 tau/day, 18.992 timesteps/s +99.9% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0011349 | 0.0011349 | 0.0011349 | 0.0 | 0.02 +Kspace | 5.2375 | 5.2375 | 5.2375 | 0.0 | 99.47 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.0090225 | 0.0090225 | 0.0090225 | 0.0 | 0.17 +Output | 0.0004127 | 0.0004127 | 0.0004127 | 0.0 | 0.01 +Modify | 0.012851 | 0.012851 | 0.012851 | 0.0 | 0.24 +Other | | 0.004441 | | | 0.08 + +Nlocal: 4096 ave 4096 max 4096 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 5165 ave 5165 max 5165 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 65536 ave 65536 max 65536 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 65536 +Ave neighs/atom = 16 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:06 diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.g++.fmm.16 b/examples/USER/scafacos/log.23Jul18.scafacos.g++.fmm.16 new file mode 100644 index 0000000000..6af26f7b81 --- /dev/null +++ b/examples/USER/scafacos/log.23Jul18.scafacos.g++.fmm.16 @@ -0,0 +1,102 @@ +LAMMPS (29 Jun 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.NaCl + orthogonal box = (0 0 0) to (2 2 2) + 2 by 2 by 4 MPI processor grid + reading atoms ... + 8 atoms + +replicate 8 8 8 + orthogonal box = (0 0 0) to (16 16 16) + 2 by 2 by 4 MPI processor grid + 4096 atoms + Time spent = 0.000507593 secs + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos fmm 0.001 +kspace_modify scafacos tolerance energy_rel + +timestep 0.005 +thermo 10 + +run 100 +Setting up ScaFaCoS with solver fmm ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 16 16 16 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.401 | 3.401 | 3.401 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -0.87378819 0 1.3756625 1.4996338 + 10 1.5000004 -0.87378882 0 1.3756625 1.4996342 + 20 1.4999998 -0.87378782 0 1.3756625 1.4996336 + 30 1.4999934 -0.87377823 0 1.3756625 1.4996272 + 40 1.4999745 -0.87374997 0 1.3756625 1.4996083 + 50 1.4999347 -0.87369019 0 1.3756625 1.4995685 + 60 1.4998637 -0.87358381 0 1.3756625 1.4994975 + 70 1.4997506 -0.87341428 0 1.3756624 1.4993845 + 80 1.4995842 -0.87316464 0 1.3756624 1.499218 + 90 1.4993536 -0.87281897 0 1.3756624 1.4989876 + 100 1.4990503 -0.87236411 0 1.3756624 1.4986843 +Loop time of 0.570389 on 16 procs for 100 steps with 4096 atoms + +Performance: 75737.813 tau/day, 175.319 timesteps/s +99.3% CPU use with 16 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.00024104 | 0.00025283 | 0.00029206 | 0.0 | 0.04 +Kspace | 0.56153 | 0.56176 | 0.56189 | 0.0 | 98.49 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.0055203 | 0.0057825 | 0.0061858 | 0.2 | 1.01 +Output | 0.00038505 | 0.00040831 | 0.00048184 | 0.0 | 0.07 +Modify | 0.00096965 | 0.00099662 | 0.0010159 | 0.0 | 0.17 +Other | | 0.001192 | | | 0.21 + +Nlocal: 256 ave 256 max 256 min +Histogram: 16 0 0 0 0 0 0 0 0 0 +Nghost: 1265 ave 1265 max 1265 min +Histogram: 16 0 0 0 0 0 0 0 0 0 +Neighs: 4096 ave 4096 max 4096 min +Histogram: 16 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 65536 +Ave neighs/atom = 16 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:03 diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.g++.fmm.2 b/examples/USER/scafacos/log.23Jul18.scafacos.g++.fmm.2 new file mode 100644 index 0000000000..bcc61485ca --- /dev/null +++ b/examples/USER/scafacos/log.23Jul18.scafacos.g++.fmm.2 @@ -0,0 +1,102 @@ +LAMMPS (29 Jun 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.NaCl + orthogonal box = (0 0 0) to (2 2 2) + 1 by 1 by 2 MPI processor grid + reading atoms ... + 8 atoms + +replicate 8 8 8 + orthogonal box = (0 0 0) to (16 16 16) + 1 by 1 by 2 MPI processor grid + 4096 atoms + Time spent = 0.000455141 secs + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos fmm 0.001 +kspace_modify scafacos tolerance energy_rel + +timestep 0.005 +thermo 10 + +run 100 +Setting up ScaFaCoS with solver fmm ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 16 16 16 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.634 | 3.634 | 3.634 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -0.87378819 0 1.3756625 1.4996338 + 10 1.5000004 -0.87378882 0 1.3756625 1.4996342 + 20 1.4999998 -0.87378782 0 1.3756625 1.4996336 + 30 1.4999934 -0.87377823 0 1.3756625 1.4996272 + 40 1.4999745 -0.87374997 0 1.3756625 1.4996083 + 50 1.4999347 -0.87369019 0 1.3756625 1.4995685 + 60 1.4998637 -0.87358381 0 1.3756625 1.4994975 + 70 1.4997506 -0.87341428 0 1.3756624 1.4993845 + 80 1.4995842 -0.87316464 0 1.3756624 1.499218 + 90 1.4993536 -0.87281897 0 1.3756624 1.4989876 + 100 1.4990503 -0.87236411 0 1.3756624 1.4986843 +Loop time of 2.73149 on 2 procs for 100 steps with 4096 atoms + +Performance: 15815.560 tau/day, 36.610 timesteps/s +99.7% CPU use with 2 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.00070763 | 0.00071537 | 0.00072312 | 0.0 | 0.03 +Kspace | 2.7111 | 2.7112 | 2.7112 | 0.0 | 99.26 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.0096555 | 0.0097489 | 0.0098424 | 0.1 | 0.36 +Output | 0.00036025 | 0.0003823 | 0.00040436 | 0.0 | 0.01 +Modify | 0.0063472 | 0.0064594 | 0.0065715 | 0.1 | 0.24 +Other | | 0.00299 | | | 0.11 + +Nlocal: 2048 ave 2048 max 2048 min +Histogram: 2 0 0 0 0 0 0 0 0 0 +Nghost: 3685 ave 3685 max 3685 min +Histogram: 2 0 0 0 0 0 0 0 0 0 +Neighs: 32768 ave 32768 max 32768 min +Histogram: 2 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 65536 +Ave neighs/atom = 16 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:04 diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.g++.fmm.4 b/examples/USER/scafacos/log.23Jul18.scafacos.g++.fmm.4 new file mode 100644 index 0000000000..54e010c8fd --- /dev/null +++ b/examples/USER/scafacos/log.23Jul18.scafacos.g++.fmm.4 @@ -0,0 +1,102 @@ +LAMMPS (29 Jun 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.NaCl + orthogonal box = (0 0 0) to (2 2 2) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 8 atoms + +replicate 8 8 8 + orthogonal box = (0 0 0) to (16 16 16) + 1 by 2 by 2 MPI processor grid + 4096 atoms + Time spent = 0.000329494 secs + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos fmm 0.001 +kspace_modify scafacos tolerance energy_rel + +timestep 0.005 +thermo 10 + +run 100 +Setting up ScaFaCoS with solver fmm ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 16 16 16 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.497 | 3.497 | 3.497 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -0.87378819 0 1.3756625 1.4996338 + 10 1.5000004 -0.87378882 0 1.3756625 1.4996342 + 20 1.4999998 -0.87378782 0 1.3756625 1.4996336 + 30 1.4999934 -0.87377823 0 1.3756625 1.4996272 + 40 1.4999745 -0.87374997 0 1.3756625 1.4996083 + 50 1.4999347 -0.87369019 0 1.3756625 1.4995685 + 60 1.4998637 -0.87358381 0 1.3756625 1.4994975 + 70 1.4997506 -0.87341428 0 1.3756624 1.4993845 + 80 1.4995842 -0.87316464 0 1.3756624 1.499218 + 90 1.4993536 -0.87281897 0 1.3756624 1.4989876 + 100 1.4990503 -0.87236411 0 1.3756624 1.4986843 +Loop time of 1.53742 on 4 procs for 100 steps with 4096 atoms + +Performance: 28099.005 tau/day, 65.044 timesteps/s +99.7% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.00044894 | 0.00045562 | 0.0004611 | 0.0 | 0.03 +Kspace | 1.5223 | 1.5225 | 1.5225 | 0.0 | 99.03 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.0085156 | 0.0086777 | 0.0088782 | 0.1 | 0.56 +Output | 0.00034738 | 0.0003686 | 0.0004015 | 0.0 | 0.02 +Modify | 0.0032606 | 0.0033693 | 0.0034289 | 0.1 | 0.22 +Other | | 0.002084 | | | 0.14 + +Nlocal: 1024 ave 1024 max 1024 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2525 ave 2525 max 2525 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 16384 ave 16384 max 16384 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 65536 +Ave neighs/atom = 16 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:03 diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.g++.fmm.8 b/examples/USER/scafacos/log.23Jul18.scafacos.g++.fmm.8 new file mode 100644 index 0000000000..d5d38d6804 --- /dev/null +++ b/examples/USER/scafacos/log.23Jul18.scafacos.g++.fmm.8 @@ -0,0 +1,102 @@ +LAMMPS (29 Jun 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.NaCl + orthogonal box = (0 0 0) to (2 2 2) + 2 by 2 by 2 MPI processor grid + reading atoms ... + 8 atoms + +replicate 8 8 8 + orthogonal box = (0 0 0) to (16 16 16) + 2 by 2 by 2 MPI processor grid + 4096 atoms + Time spent = 0.000284672 secs + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos fmm 0.001 +kspace_modify scafacos tolerance energy_rel + +timestep 0.005 +thermo 10 + +run 100 +Setting up ScaFaCoS with solver fmm ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 16 16 16 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.416 | 3.416 | 3.416 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -0.87378819 0 1.3756625 1.4996338 + 10 1.5000004 -0.87378882 0 1.3756625 1.4996342 + 20 1.4999998 -0.87378782 0 1.3756625 1.4996336 + 30 1.4999934 -0.87377823 0 1.3756625 1.4996272 + 40 1.4999745 -0.87374997 0 1.3756625 1.4996083 + 50 1.4999347 -0.87369019 0 1.3756625 1.4995685 + 60 1.4998637 -0.87358381 0 1.3756625 1.4994975 + 70 1.4997506 -0.87341428 0 1.3756624 1.4993845 + 80 1.4995842 -0.87316464 0 1.3756624 1.499218 + 90 1.4993536 -0.87281897 0 1.3756624 1.4989876 + 100 1.4990503 -0.87236411 0 1.3756624 1.4986843 +Loop time of 0.902102 on 8 procs for 100 steps with 4096 atoms + +Performance: 47888.152 tau/day, 110.852 timesteps/s +99.7% CPU use with 8 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.00030732 | 0.00031349 | 0.00032663 | 0.0 | 0.03 +Kspace | 0.89112 | 0.89138 | 0.8916 | 0.0 | 98.81 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.0064399 | 0.0066807 | 0.0070164 | 0.2 | 0.74 +Output | 0.00034571 | 0.00036666 | 0.00041723 | 0.0 | 0.04 +Modify | 0.0018673 | 0.0019273 | 0.0020192 | 0.1 | 0.21 +Other | | 0.001431 | | | 0.16 + +Nlocal: 512 ave 512 max 512 min +Histogram: 8 0 0 0 0 0 0 0 0 0 +Nghost: 1685 ave 1685 max 1685 min +Histogram: 8 0 0 0 0 0 0 0 0 0 +Neighs: 8192 ave 8192 max 8192 min +Histogram: 8 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 65536 +Ave neighs/atom = 16 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:02 diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.g++.p2nfft.1 b/examples/USER/scafacos/log.23Jul18.scafacos.g++.p2nfft.1 new file mode 100644 index 0000000000..d8b782e41d --- /dev/null +++ b/examples/USER/scafacos/log.23Jul18.scafacos.g++.p2nfft.1 @@ -0,0 +1,102 @@ +LAMMPS (29 Jun 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.NaCl + orthogonal box = (0 0 0) to (2 2 2) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 8 atoms + +replicate 8 8 8 + orthogonal box = (0 0 0) to (16 16 16) + 1 by 1 by 1 MPI processor grid + 4096 atoms + Time spent = 0.000631332 secs + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos p2nfft 0.001 +kspace_modify scafacos tolerance field + +timestep 0.005 +thermo 10 + +run 100 +Setting up ScaFaCoS with solver p2nfft ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 16 16 16 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.723 | 3.723 | 3.723 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -0.87394226 0 1.3755084 1.4996338 + 10 1.5000144 -0.87365638 0 1.375816 1.4996482 + 20 1.5000284 -0.87366526 0 1.3758281 1.4996622 + 30 1.5000364 -0.87366516 0 1.3758401 1.4996702 + 40 1.5000313 -0.8736496 0 1.375848 1.4996651 + 50 1.5000039 -0.87360069 0 1.3758558 1.4996377 + 60 1.4999432 -0.87350118 0 1.3758644 1.499577 + 70 1.499838 -0.87333517 0 1.3758726 1.4994719 + 80 1.4996772 -0.87308644 0 1.3758801 1.4993111 + 90 1.4994505 -0.87274307 0 1.3758836 1.4990844 + 100 1.4991498 -0.8722911 0 1.3758846 1.4987838 +Loop time of 9.59682 on 1 procs for 100 steps with 4096 atoms + +Performance: 4501.489 tau/day, 10.420 timesteps/s +100.0% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0011375 | 0.0011375 | 0.0011375 | 0.0 | 0.01 +Kspace | 9.5688 | 9.5688 | 9.5688 | 0.0 | 99.71 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.009017 | 0.009017 | 0.009017 | 0.0 | 0.09 +Output | 0.0004344 | 0.0004344 | 0.0004344 | 0.0 | 0.00 +Modify | 0.012987 | 0.012987 | 0.012987 | 0.0 | 0.14 +Other | | 0.004481 | | | 0.05 + +Nlocal: 4096 ave 4096 max 4096 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 5165 ave 5165 max 5165 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 65536 ave 65536 max 65536 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 65536 +Ave neighs/atom = 16 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:10 diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.g++.p2nfft.16 b/examples/USER/scafacos/log.23Jul18.scafacos.g++.p2nfft.16 new file mode 100644 index 0000000000..43bcfb6770 --- /dev/null +++ b/examples/USER/scafacos/log.23Jul18.scafacos.g++.p2nfft.16 @@ -0,0 +1,102 @@ +LAMMPS (29 Jun 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.NaCl + orthogonal box = (0 0 0) to (2 2 2) + 2 by 2 by 4 MPI processor grid + reading atoms ... + 8 atoms + +replicate 8 8 8 + orthogonal box = (0 0 0) to (16 16 16) + 2 by 2 by 4 MPI processor grid + 4096 atoms + Time spent = 0.000500917 secs + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos p2nfft 0.001 +kspace_modify scafacos tolerance field + +timestep 0.005 +thermo 10 + +run 100 +Setting up ScaFaCoS with solver p2nfft ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 16 16 16 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.401 | 3.401 | 3.401 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -0.87394226 0 1.3755084 1.4996338 + 10 1.5000144 -0.87365638 0 1.375816 1.4996482 + 20 1.5000284 -0.87366526 0 1.3758281 1.4996622 + 30 1.5000364 -0.87366516 0 1.3758401 1.4996702 + 40 1.5000313 -0.8736496 0 1.375848 1.4996651 + 50 1.5000039 -0.87360069 0 1.3758558 1.4996377 + 60 1.4999432 -0.87350118 0 1.3758644 1.499577 + 70 1.499838 -0.87333517 0 1.3758726 1.4994719 + 80 1.4996772 -0.87308644 0 1.3758801 1.4993111 + 90 1.4994505 -0.87274307 0 1.3758836 1.4990844 + 100 1.4991498 -0.8722911 0 1.3758846 1.4987838 +Loop time of 1.20528 on 16 procs for 100 steps with 4096 atoms + +Performance: 35842.175 tau/day, 82.968 timesteps/s +99.3% CPU use with 16 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.00021839 | 0.00025332 | 0.00029278 | 0.0 | 0.02 +Kspace | 1.1945 | 1.1948 | 1.195 | 0.0 | 99.13 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.0066545 | 0.0069329 | 0.0072389 | 0.2 | 0.58 +Output | 0.0003922 | 0.00042732 | 0.00054955 | 0.0 | 0.04 +Modify | 0.0010166 | 0.0011965 | 0.0014412 | 0.3 | 0.10 +Other | | 0.001724 | | | 0.14 + +Nlocal: 256 ave 256 max 256 min +Histogram: 16 0 0 0 0 0 0 0 0 0 +Nghost: 1265 ave 1265 max 1265 min +Histogram: 16 0 0 0 0 0 0 0 0 0 +Neighs: 4096 ave 4096 max 4096 min +Histogram: 16 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 65536 +Ave neighs/atom = 16 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:01 diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.g++.p2nfft.2 b/examples/USER/scafacos/log.23Jul18.scafacos.g++.p2nfft.2 new file mode 100644 index 0000000000..9f4f44153b --- /dev/null +++ b/examples/USER/scafacos/log.23Jul18.scafacos.g++.p2nfft.2 @@ -0,0 +1,102 @@ +LAMMPS (29 Jun 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.NaCl + orthogonal box = (0 0 0) to (2 2 2) + 1 by 1 by 2 MPI processor grid + reading atoms ... + 8 atoms + +replicate 8 8 8 + orthogonal box = (0 0 0) to (16 16 16) + 1 by 1 by 2 MPI processor grid + 4096 atoms + Time spent = 0.00044775 secs + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos p2nfft 0.001 +kspace_modify scafacos tolerance field + +timestep 0.005 +thermo 10 + +run 100 +Setting up ScaFaCoS with solver p2nfft ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 16 16 16 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.634 | 3.634 | 3.634 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -0.87394226 0 1.3755084 1.4996338 + 10 1.5000144 -0.87365638 0 1.375816 1.4996482 + 20 1.5000284 -0.87366526 0 1.3758281 1.4996622 + 30 1.5000364 -0.87366516 0 1.3758401 1.4996702 + 40 1.5000313 -0.8736496 0 1.375848 1.4996651 + 50 1.5000039 -0.87360069 0 1.3758558 1.4996377 + 60 1.4999432 -0.87350118 0 1.3758644 1.499577 + 70 1.499838 -0.87333517 0 1.3758726 1.4994719 + 80 1.4996772 -0.87308644 0 1.3758801 1.4993111 + 90 1.4994505 -0.87274307 0 1.3758836 1.4990844 + 100 1.4991498 -0.8722911 0 1.3758846 1.4987838 +Loop time of 5.14681 on 2 procs for 100 steps with 4096 atoms + +Performance: 8393.542 tau/day, 19.429 timesteps/s +99.9% CPU use with 2 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.00070882 | 0.00072873 | 0.00074863 | 0.0 | 0.01 +Kspace | 5.1257 | 5.1258 | 5.1258 | 0.0 | 99.59 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.010188 | 0.010291 | 0.010394 | 0.1 | 0.20 +Output | 0.00042391 | 0.00044322 | 0.00046253 | 0.0 | 0.01 +Modify | 0.0063772 | 0.006551 | 0.0067248 | 0.2 | 0.13 +Other | | 0.003026 | | | 0.06 + +Nlocal: 2048 ave 2048 max 2048 min +Histogram: 2 0 0 0 0 0 0 0 0 0 +Nghost: 3685 ave 3685 max 3685 min +Histogram: 2 0 0 0 0 0 0 0 0 0 +Neighs: 32768 ave 32768 max 32768 min +Histogram: 2 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 65536 +Ave neighs/atom = 16 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:05 diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.g++.p2nfft.4 b/examples/USER/scafacos/log.23Jul18.scafacos.g++.p2nfft.4 new file mode 100644 index 0000000000..d6a78bb193 --- /dev/null +++ b/examples/USER/scafacos/log.23Jul18.scafacos.g++.p2nfft.4 @@ -0,0 +1,102 @@ +LAMMPS (29 Jun 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.NaCl + orthogonal box = (0 0 0) to (2 2 2) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 8 atoms + +replicate 8 8 8 + orthogonal box = (0 0 0) to (16 16 16) + 1 by 2 by 2 MPI processor grid + 4096 atoms + Time spent = 0.000317335 secs + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos p2nfft 0.001 +kspace_modify scafacos tolerance field + +timestep 0.005 +thermo 10 + +run 100 +Setting up ScaFaCoS with solver p2nfft ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 16 16 16 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.497 | 3.497 | 3.497 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -0.87394226 0 1.3755084 1.4996338 + 10 1.5000144 -0.87365638 0 1.375816 1.4996482 + 20 1.5000284 -0.87366526 0 1.3758281 1.4996622 + 30 1.5000364 -0.87366516 0 1.3758401 1.4996702 + 40 1.5000313 -0.8736496 0 1.375848 1.4996651 + 50 1.5000039 -0.87360069 0 1.3758558 1.4996377 + 60 1.4999432 -0.87350118 0 1.3758644 1.499577 + 70 1.499838 -0.87333517 0 1.3758726 1.4994719 + 80 1.4996772 -0.87308644 0 1.3758801 1.4993111 + 90 1.4994505 -0.87274307 0 1.3758836 1.4990844 + 100 1.4991498 -0.8722911 0 1.3758846 1.4987838 +Loop time of 2.94274 on 4 procs for 100 steps with 4096 atoms + +Performance: 14680.187 tau/day, 33.982 timesteps/s +99.7% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.00048852 | 0.00049287 | 0.00050163 | 0.0 | 0.02 +Kspace | 2.9277 | 2.9279 | 2.928 | 0.0 | 99.49 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.0081494 | 0.0083126 | 0.0084655 | 0.1 | 0.28 +Output | 0.00034475 | 0.00040233 | 0.00043464 | 0.0 | 0.01 +Modify | 0.0034239 | 0.0035145 | 0.0036252 | 0.1 | 0.12 +Other | | 0.00216 | | | 0.07 + +Nlocal: 1024 ave 1024 max 1024 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 2525 ave 2525 max 2525 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 16384 ave 16384 max 16384 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 65536 +Ave neighs/atom = 16 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:03 diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.g++.p2nfft.8 b/examples/USER/scafacos/log.23Jul18.scafacos.g++.p2nfft.8 new file mode 100644 index 0000000000..70716bbcbd --- /dev/null +++ b/examples/USER/scafacos/log.23Jul18.scafacos.g++.p2nfft.8 @@ -0,0 +1,102 @@ +LAMMPS (29 Jun 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.NaCl + orthogonal box = (0 0 0) to (2 2 2) + 2 by 2 by 2 MPI processor grid + reading atoms ... + 8 atoms + +replicate 8 8 8 + orthogonal box = (0 0 0) to (16 16 16) + 2 by 2 by 2 MPI processor grid + 4096 atoms + Time spent = 0.000422239 secs + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos p2nfft 0.001 +kspace_modify scafacos tolerance field + +timestep 0.005 +thermo 10 + +run 100 +Setting up ScaFaCoS with solver p2nfft ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 16 16 16 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.416 | 3.416 | 3.416 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -0.87394226 0 1.3755084 1.4996338 + 10 1.5000144 -0.87365638 0 1.375816 1.4996482 + 20 1.5000284 -0.87366526 0 1.3758281 1.4996622 + 30 1.5000364 -0.87366516 0 1.3758401 1.4996702 + 40 1.5000313 -0.8736496 0 1.375848 1.4996651 + 50 1.5000039 -0.87360069 0 1.3758558 1.4996377 + 60 1.4999432 -0.87350118 0 1.3758644 1.499577 + 70 1.499838 -0.87333517 0 1.3758726 1.4994719 + 80 1.4996772 -0.87308644 0 1.3758801 1.4993111 + 90 1.4994505 -0.87274307 0 1.3758836 1.4990844 + 100 1.4991498 -0.8722911 0 1.3758846 1.4987838 +Loop time of 1.75933 on 8 procs for 100 steps with 4096 atoms + +Performance: 24554.819 tau/day, 56.840 timesteps/s +99.4% CPU use with 8 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.00030684 | 0.00031838 | 0.00032926 | 0.0 | 0.02 +Kspace | 1.7474 | 1.7477 | 1.748 | 0.0 | 99.34 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.0068667 | 0.0072413 | 0.0075011 | 0.2 | 0.41 +Output | 0.00036955 | 0.00038695 | 0.00044942 | 0.0 | 0.02 +Modify | 0.0018206 | 0.0019438 | 0.0020213 | 0.1 | 0.11 +Other | | 0.001739 | | | 0.10 + +Nlocal: 512 ave 512 max 512 min +Histogram: 8 0 0 0 0 0 0 0 0 0 +Nghost: 1685 ave 1685 max 1685 min +Histogram: 8 0 0 0 0 0 0 0 0 0 +Neighs: 8192 ave 8192 max 8192 min +Histogram: 8 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 65536 +Ave neighs/atom = 16 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:02 diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.direct.1 b/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.direct.1 new file mode 100644 index 0000000000..37d12bb37d --- /dev/null +++ b/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.direct.1 @@ -0,0 +1,105 @@ +LAMMPS (29 Jun 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.hammersley_shphere + orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 1000 atoms +change_box all boundary f f f + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos direct 0.001 + +timestep 0.005 +thermo 1 +run 20 +Setting up ScaFaCoS with solver direct ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 102 102 102 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 10.3 | 10.3 | 10.3 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -0.62417787 0 1.6235721 0.00141207 + 1 18.780041 -10.770002 0 17.371889 0.017679155 + 2 65.289192 -11.084705 0 86.751149 0.06146194 + 3 121.92987 -7.0625759 0 175.64933 0.11478234 + 4 185.78164 -5.8777512 0 272.51604 0.17489112 + 5 286.36222 -4.382053 0 424.73173 0.26957567 + 6 481.42206 -4.3095567 0 717.1014 0.4532011 + 7 488.59167 -3.8685194 0 728.2861 0.45995044 + 8 497.85287 -3.0417966 0 742.99073 0.46866874 + 9 499.61615 -3.419003 0 745.2558 0.47032866 + 10 502.63684 -2.8360961 0 750.36521 0.47317227 + 11 504.4846 -2.7628105 0 753.20736 0.47491172 + 12 506.54485 -2.8460356 0 756.21142 0.47685119 + 13 508.27211 -2.730935 0 758.91482 0.4784772 + 14 510.57045 -2.6094877 0 762.48033 0.48064081 + 15 513.14798 -2.7150827 0 766.23717 0.48306726 + 16 515.78124 -2.3961811 0 770.50201 0.48554615 + 17 515.70265 -2.2982683 0 770.48215 0.48547216 + 18 515.7081 -2.1515983 0 770.63699 0.4854773 + 19 515.74906 -2.0581436 0 770.79182 0.48551586 + 20 515.70883 -1.8922577 0 770.89742 0.48547798 +Loop time of 0.52055 on 1 procs for 20 steps with 1000 atoms + +Performance: 16597.836 tau/day, 38.421 timesteps/s +99.7% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.00027752 | 0.00027752 | 0.00027752 | 0.0 | 0.05 +Kspace | 0.35879 | 0.35879 | 0.35879 | 0.0 | 68.93 +Neigh | 0.15946 | 0.15946 | 0.15946 | 0.0 | 30.63 +Comm | 0.00024056 | 0.00024056 | 0.00024056 | 0.0 | 0.05 +Output | 0.00034761 | 0.00034761 | 0.00034761 | 0.0 | 0.07 +Modify | 0.00071192 | 0.00071192 | 0.00071192 | 0.0 | 0.14 +Other | | 0.0007269 | | | 0.14 + +Nlocal: 1000 ave 1000 max 1000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 247817 ave 247817 max 247817 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 247817 +Ave neighs/atom = 247.817 +Neighbor list builds = 19 +Dangerous builds = 18 +Total wall time: 0:00:00 diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.direct.2 b/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.direct.2 new file mode 100644 index 0000000000..7a22e62bce --- /dev/null +++ b/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.direct.2 @@ -0,0 +1,105 @@ +LAMMPS (29 Jun 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.hammersley_shphere + orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5) + 1 by 1 by 2 MPI processor grid + reading atoms ... + 1000 atoms +change_box all boundary f f f + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos direct 0.001 + +timestep 0.005 +thermo 1 +run 20 +Setting up ScaFaCoS with solver direct ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 102 102 102 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 6.48 | 6.861 | 7.243 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -0.62417787 0 1.6235721 0.00141207 + 1 18.780041 -10.770002 0 17.371889 0.017679155 + 2 65.289192 -11.084705 0 86.751149 0.06146194 + 3 121.92987 -7.0625759 0 175.64933 0.11478234 + 4 185.78164 -5.8777512 0 272.51604 0.17489112 + 5 286.36222 -4.382053 0 424.73173 0.26957567 + 6 481.42206 -4.3095567 0 717.1014 0.4532011 + 7 488.59167 -3.8685194 0 728.2861 0.45995044 + 8 497.85287 -3.0417966 0 742.99073 0.46866874 + 9 499.61615 -3.419003 0 745.2558 0.47032866 + 10 502.63684 -2.8360961 0 750.36521 0.47317227 + 11 504.4846 -2.7628105 0 753.20736 0.47491172 + 12 506.54485 -2.8460356 0 756.21142 0.47685119 + 13 508.27211 -2.730935 0 758.91482 0.4784772 + 14 510.57045 -2.6094877 0 762.48033 0.48064081 + 15 513.14798 -2.7150827 0 766.23717 0.48306726 + 16 515.78124 -2.3961811 0 770.50201 0.48554615 + 17 515.70265 -2.2982683 0 770.48215 0.48547216 + 18 515.7081 -2.1515983 0 770.63699 0.4854773 + 19 515.74906 -2.0581436 0 770.79182 0.48551586 + 20 515.70883 -1.8922577 0 770.89742 0.48547798 +Loop time of 0.330519 on 2 procs for 20 steps with 1000 atoms + +Performance: 26140.700 tau/day, 60.511 timesteps/s +99.6% CPU use with 2 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0002749 | 0.00027692 | 0.00027895 | 0.0 | 0.08 +Kspace | 0.21565 | 0.24173 | 0.26782 | 5.3 | 73.14 +Neigh | 0.058644 | 0.084906 | 0.11117 | 9.0 | 25.69 +Comm | 0.002033 | 0.0022832 | 0.0025334 | 0.5 | 0.69 +Output | 0.00035667 | 0.0004549 | 0.00055313 | 0.0 | 0.14 +Modify | 0.0004704 | 0.00050521 | 0.00054002 | 0.0 | 0.15 +Other | | 0.0003613 | | | 0.11 + +Nlocal: 500 ave 516 max 484 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Nghost: 456.5 ave 475 max 438 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Neighs: 123908 ave 172139 max 75678 min +Histogram: 1 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 247817 +Ave neighs/atom = 247.817 +Neighbor list builds = 19 +Dangerous builds = 18 +Total wall time: 0:00:00 diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.direct.4 b/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.direct.4 new file mode 100644 index 0000000000..51d0f8c47e --- /dev/null +++ b/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.direct.4 @@ -0,0 +1,105 @@ +LAMMPS (29 Jun 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.hammersley_shphere + orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 1000 atoms +change_box all boundary f f f + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos direct 0.001 + +timestep 0.005 +thermo 1 +run 20 +Setting up ScaFaCoS with solver direct ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 102 102 102 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.837 | 5.123 | 5.6 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -0.62417787 0 1.6235721 0.00141207 + 1 18.780041 -10.770002 0 17.371889 0.017679155 + 2 65.289192 -11.084705 0 86.751149 0.06146194 + 3 121.92987 -7.0625759 0 175.64933 0.11478234 + 4 185.78164 -5.8777512 0 272.51604 0.17489112 + 5 286.36222 -4.382053 0 424.73173 0.26957567 + 6 481.42206 -4.3095567 0 717.1014 0.4532011 + 7 488.59167 -3.8685194 0 728.2861 0.45995044 + 8 497.85287 -3.0417966 0 742.99073 0.46866874 + 9 499.61615 -3.419003 0 745.2558 0.47032866 + 10 502.63684 -2.8360961 0 750.36521 0.47317227 + 11 504.4846 -2.7628105 0 753.20736 0.47491172 + 12 506.54485 -2.8460356 0 756.21142 0.47685119 + 13 508.27211 -2.730935 0 758.91482 0.4784772 + 14 510.57045 -2.6094877 0 762.48033 0.48064081 + 15 513.14798 -2.7150827 0 766.23717 0.48306726 + 16 515.78124 -2.3961811 0 770.50201 0.48554615 + 17 515.70265 -2.2982683 0 770.48215 0.48547216 + 18 515.7081 -2.1515983 0 770.63699 0.4854773 + 19 515.74906 -2.0581436 0 770.79182 0.48551586 + 20 515.70883 -1.8922577 0 770.89742 0.48547798 +Loop time of 0.197141 on 4 procs for 20 steps with 1000 atoms + +Performance: 43826.435 tau/day, 101.450 timesteps/s +99.6% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0002718 | 0.00027621 | 0.00028539 | 0.0 | 0.14 +Kspace | 0.12861 | 0.14654 | 0.16542 | 3.7 | 74.33 +Neigh | 0.027906 | 0.046895 | 0.064943 | 6.6 | 23.79 +Comm | 0.0022087 | 0.0024236 | 0.0026295 | 0.4 | 1.23 +Output | 0.0003252 | 0.00044608 | 0.0006001 | 0.0 | 0.23 +Modify | 0.00016618 | 0.0001756 | 0.00018811 | 0.0 | 0.09 +Other | | 0.0003839 | | | 0.19 + +Nlocal: 250 ave 259 max 238 min +Histogram: 1 0 0 1 0 0 0 0 0 2 +Nghost: 672.25 ave 683 max 663 min +Histogram: 2 0 0 0 0 0 0 0 1 1 +Neighs: 61954.2 ave 97157 max 25016 min +Histogram: 1 0 0 1 0 0 1 0 0 1 + +Total # of neighbors = 247817 +Ave neighs/atom = 247.817 +Neighbor list builds = 19 +Dangerous builds = 18 +Total wall time: 0:00:00 diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.direct.8 b/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.direct.8 new file mode 100644 index 0000000000..90119a101b --- /dev/null +++ b/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.direct.8 @@ -0,0 +1,105 @@ +LAMMPS (29 Jun 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.hammersley_shphere + orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5) + 2 by 2 by 2 MPI processor grid + reading atoms ... + 1000 atoms +change_box all boundary f f f + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos direct 0.001 + +timestep 0.005 +thermo 1 +run 20 +Setting up ScaFaCoS with solver direct ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 102 102 102 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.164 | 4.26 | 4.546 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -0.62417787 0 1.6235721 0.00141207 + 1 18.780041 -10.770002 0 17.371889 0.017679155 + 2 65.289192 -11.084705 0 86.751149 0.06146194 + 3 121.92987 -7.0625759 0 175.64933 0.11478234 + 4 185.78164 -5.8777512 0 272.51604 0.17489112 + 5 286.36222 -4.382053 0 424.73173 0.26957567 + 6 481.42206 -4.3095567 0 717.1014 0.4532011 + 7 488.59167 -3.8685194 0 728.2861 0.45995044 + 8 497.85287 -3.0417966 0 742.99073 0.46866874 + 9 499.61615 -3.419003 0 745.2558 0.47032866 + 10 502.63684 -2.8360961 0 750.36521 0.47317227 + 11 504.4846 -2.7628105 0 753.20736 0.47491172 + 12 506.54485 -2.8460356 0 756.21142 0.47685119 + 13 508.27211 -2.730935 0 758.91482 0.4784772 + 14 510.57045 -2.6094877 0 762.48033 0.48064081 + 15 513.14798 -2.7150827 0 766.23717 0.48306726 + 16 515.78124 -2.3961811 0 770.50201 0.48554615 + 17 515.70265 -2.2982683 0 770.48215 0.48547216 + 18 515.7081 -2.1515983 0 770.63699 0.4854773 + 19 515.74906 -2.0581436 0 770.79182 0.48551586 + 20 515.70883 -1.8922577 0 770.89742 0.48547798 +Loop time of 0.107014 on 8 procs for 20 steps with 1000 atoms + +Performance: 80736.875 tau/day, 186.891 timesteps/s +98.8% CPU use with 8 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.00027704 | 0.00029281 | 0.00035691 | 0.0 | 0.27 +Kspace | 0.069458 | 0.07877 | 0.089146 | 2.5 | 73.61 +Neigh | 0.013525 | 0.024156 | 0.033524 | 4.7 | 22.57 +Comm | 0.002552 | 0.0029828 | 0.0033691 | 0.5 | 2.79 +Output | 0.00037909 | 0.00051123 | 0.00070429 | 0.0 | 0.48 +Modify | 8.9645e-05 | 9.5487e-05 | 0.000103 | 0.0 | 0.09 +Other | | 0.0002059 | | | 0.19 + +Nlocal: 125 ave 133 max 113 min +Histogram: 2 0 0 0 0 1 1 0 2 2 +Nghost: 773.625 ave 788 max 764 min +Histogram: 1 1 2 1 1 0 0 0 1 1 +Neighs: 30977.1 ave 50690 max 10447 min +Histogram: 1 1 1 0 1 1 0 0 2 1 + +Total # of neighbors = 247817 +Ave neighs/atom = 247.817 +Neighbor list builds = 19 +Dangerous builds = 18 +Total wall time: 0:00:00 diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.fmm.1 b/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.fmm.1 new file mode 100644 index 0000000000..432ea72b67 --- /dev/null +++ b/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.fmm.1 @@ -0,0 +1,109 @@ +LAMMPS (29 Jun 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.hammersley_shphere + orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 1000 atoms +change_box all boundary f f f + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos fmm 0.001 +kspace_modify scafacos tolerance energy_rel +kspace_modify scafacos fmm_tuning 1 +ScaFaCoS setting fmm inhomogen tuning ...3 + +timestep 0.005 +thermo 1 + +run 20 +Setting up ScaFaCoS with solver fmm ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 102 102 102 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 10.3 | 10.3 | 10.3 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -0.62417141 0 1.6235786 0.00141207 + 1 18.780412 -10.770009 0 17.372438 0.017679504 + 2 65.294131 -11.084501 0 86.758754 0.06146659 + 3 121.92555 -7.0612033 0 175.64423 0.11477827 + 4 185.71165 -5.8781334 0 272.41077 0.17482523 + 5 286.28339 -4.3800108 0 424.61565 0.26950146 + 6 481.28097 -4.3052012 0 716.89433 0.45306828 + 7 487.26022 -3.8672741 0 726.29216 0.45869703 + 8 493.65478 -3.0242687 0 736.71742 0.46471675 + 9 495.66203 -3.4336343 0 739.31592 0.46660633 + 10 498.41831 -2.8837072 0 743.99613 0.46920104 + 11 499.20944 -2.7724783 0 745.29287 0.46994579 + 12 500.97345 -2.8281484 0 747.88057 0.4716064 + 13 507.46412 -2.7752775 0 757.65971 0.47771658 + 14 525.35729 -2.5749814 0 784.67292 0.49456085 + 15 563.9578 -2.9982381 0 842.09253 0.5308986 + 16 645.47602 -2.5519203 0 964.69389 0.60763822 + 17 647.09276 -2.2568468 0 967.41166 0.60916019 + 18 647.12596 -2.2791003 0 967.43915 0.60919144 + 19 647.24862 -2.2495226 0 967.65253 0.60930691 + 20 647.51175 -2.0239179 0 968.27244 0.60955462 +Loop time of 0.644143 on 1 procs for 20 steps with 1000 atoms + +Performance: 13413.173 tau/day, 31.049 timesteps/s +99.7% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.00027657 | 0.00027657 | 0.00027657 | 0.0 | 0.04 +Kspace | 0.4788 | 0.4788 | 0.4788 | 0.0 | 74.33 +Neigh | 0.16279 | 0.16279 | 0.16279 | 0.0 | 25.27 +Comm | 0.00021696 | 0.00021696 | 0.00021696 | 0.0 | 0.03 +Output | 0.00054836 | 0.00054836 | 0.00054836 | 0.0 | 0.09 +Modify | 0.00075102 | 0.00075102 | 0.00075102 | 0.0 | 0.12 +Other | | 0.000757 | | | 0.12 + +Nlocal: 1000 ave 1000 max 1000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 244342 ave 244342 max 244342 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 244342 +Ave neighs/atom = 244.342 +Neighbor list builds = 19 +Dangerous builds = 18 +Total wall time: 0:00:00 diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.fmm.2 b/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.fmm.2 new file mode 100644 index 0000000000..4d4b1100e3 --- /dev/null +++ b/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.fmm.2 @@ -0,0 +1,109 @@ +LAMMPS (29 Jun 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.hammersley_shphere + orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5) + 1 by 1 by 2 MPI processor grid + reading atoms ... + 1000 atoms +change_box all boundary f f f + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos fmm 0.001 +kspace_modify scafacos tolerance energy_rel +kspace_modify scafacos fmm_tuning 1 +ScaFaCoS setting fmm inhomogen tuning ...3 + +timestep 0.005 +thermo 1 + +run 20 +Setting up ScaFaCoS with solver fmm ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 102 102 102 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 6.48 | 6.861 | 7.243 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -0.62417141 0 1.6235786 0.00141207 + 1 18.780412 -10.770009 0 17.372438 0.017679504 + 2 65.294131 -11.084501 0 86.758754 0.06146659 + 3 121.92555 -7.0612033 0 175.64423 0.11477827 + 4 185.71165 -5.8781334 0 272.41077 0.17482523 + 5 286.28339 -4.3800108 0 424.61565 0.26950146 + 6 481.28097 -4.3052012 0 716.89433 0.45306828 + 7 487.26022 -3.8672741 0 726.29216 0.45869703 + 8 493.65478 -3.0242687 0 736.71742 0.46471675 + 9 495.66203 -3.4336343 0 739.31592 0.46660633 + 10 498.41831 -2.8837072 0 743.99613 0.46920104 + 11 499.20944 -2.7724783 0 745.29287 0.46994579 + 12 500.97345 -2.8281484 0 747.88057 0.4716064 + 13 507.46412 -2.7752775 0 757.65971 0.47771658 + 14 525.35729 -2.5749814 0 784.67292 0.49456085 + 15 563.9578 -2.9982381 0 842.09253 0.5308986 + 16 645.47602 -2.5519203 0 964.69389 0.60763822 + 17 647.09276 -2.2568468 0 967.41166 0.60916019 + 18 647.12596 -2.2791003 0 967.43915 0.60919144 + 19 647.24862 -2.2495226 0 967.65253 0.60930691 + 20 647.51175 -2.0239179 0 968.27244 0.60955462 +Loop time of 0.563049 on 2 procs for 20 steps with 1000 atoms + +Performance: 15345.024 tau/day, 35.521 timesteps/s +99.4% CPU use with 2 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.00024986 | 0.00026596 | 0.00028205 | 0.0 | 0.05 +Kspace | 0.45103 | 0.47692 | 0.50281 | 3.7 | 84.70 +Neigh | 0.055771 | 0.081813 | 0.10785 | 9.1 | 14.53 +Comm | 0.0022206 | 0.0024507 | 0.0026808 | 0.5 | 0.44 +Output | 0.00050044 | 0.00061882 | 0.00073719 | 0.0 | 0.11 +Modify | 0.00029945 | 0.00044227 | 0.00058508 | 0.0 | 0.08 +Other | | 0.0005381 | | | 0.10 + +Nlocal: 500 ave 509 max 491 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Nghost: 455.5 ave 467 max 444 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Neighs: 122171 ave 171834 max 72508 min +Histogram: 1 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 244342 +Ave neighs/atom = 244.342 +Neighbor list builds = 19 +Dangerous builds = 18 +Total wall time: 0:00:01 diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.fmm.4 b/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.fmm.4 new file mode 100644 index 0000000000..9634a0174b --- /dev/null +++ b/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.fmm.4 @@ -0,0 +1,109 @@ +LAMMPS (29 Jun 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.hammersley_shphere + orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 1000 atoms +change_box all boundary f f f + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos fmm 0.001 +kspace_modify scafacos tolerance energy_rel +kspace_modify scafacos fmm_tuning 1 +ScaFaCoS setting fmm inhomogen tuning ...3 + +timestep 0.005 +thermo 1 + +run 20 +Setting up ScaFaCoS with solver fmm ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 102 102 102 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.837 | 5.123 | 5.6 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -0.62417141 0 1.6235786 0.00141207 + 1 18.780412 -10.770009 0 17.372438 0.017679504 + 2 65.294131 -11.084501 0 86.758754 0.06146659 + 3 121.92555 -7.0612033 0 175.64423 0.11477827 + 4 185.71165 -5.8781334 0 272.41077 0.17482523 + 5 286.28339 -4.3800108 0 424.61565 0.26950146 + 6 481.28097 -4.3052012 0 716.89433 0.45306828 + 7 487.26022 -3.8672741 0 726.29216 0.45869703 + 8 493.65478 -3.0242687 0 736.71742 0.46471675 + 9 495.66203 -3.4336343 0 739.31592 0.46660633 + 10 498.41831 -2.8837072 0 743.99613 0.46920104 + 11 499.20944 -2.7724783 0 745.29287 0.46994579 + 12 500.97345 -2.8281484 0 747.88057 0.4716064 + 13 507.46412 -2.7752775 0 757.65971 0.47771658 + 14 525.35729 -2.5749814 0 784.67292 0.49456085 + 15 563.9578 -2.9982381 0 842.09253 0.5308986 + 16 645.47602 -2.5519203 0 964.69389 0.60763822 + 17 647.09276 -2.2568468 0 967.41166 0.60916019 + 18 647.12596 -2.2791003 0 967.43915 0.60919144 + 19 647.24862 -2.2495226 0 967.65253 0.60930691 + 20 647.51175 -2.0239179 0 968.27244 0.60955462 +Loop time of 0.508149 on 4 procs for 20 steps with 1000 atoms + +Performance: 17002.884 tau/day, 39.359 timesteps/s +99.4% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.00024509 | 0.00026453 | 0.00028753 | 0.0 | 0.05 +Kspace | 0.43933 | 0.45836 | 0.47734 | 2.2 | 90.20 +Neigh | 0.025956 | 0.045068 | 0.064242 | 7.2 | 8.87 +Comm | 0.002799 | 0.0030612 | 0.0033174 | 0.4 | 0.60 +Output | 0.00047231 | 0.00058293 | 0.00076509 | 0.0 | 0.11 +Modify | 0.00016856 | 0.0002442 | 0.00042009 | 0.0 | 0.05 +Other | | 0.0005655 | | | 0.11 + +Nlocal: 250 ave 259 max 240 min +Histogram: 1 0 0 0 0 2 0 0 0 1 +Nghost: 668.75 ave 679 max 657 min +Histogram: 1 0 0 0 0 1 1 0 0 1 +Neighs: 61085.5 ave 95363 max 24964 min +Histogram: 1 0 0 1 0 0 0 1 0 1 + +Total # of neighbors = 244342 +Ave neighs/atom = 244.342 +Neighbor list builds = 19 +Dangerous builds = 18 +Total wall time: 0:00:01 diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.fmm.8 b/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.fmm.8 new file mode 100644 index 0000000000..a6a020b031 --- /dev/null +++ b/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.fmm.8 @@ -0,0 +1,109 @@ +LAMMPS (29 Jun 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.hammersley_shphere + orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5) + 2 by 2 by 2 MPI processor grid + reading atoms ... + 1000 atoms +change_box all boundary f f f + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos fmm 0.001 +kspace_modify scafacos tolerance energy_rel +kspace_modify scafacos fmm_tuning 1 +ScaFaCoS setting fmm inhomogen tuning ...3 + +timestep 0.005 +thermo 1 + +run 20 +Setting up ScaFaCoS with solver fmm ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 102 102 102 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.164 | 4.26 | 4.546 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -0.62417141 0 1.6235786 0.00141207 + 1 18.780412 -10.770009 0 17.372438 0.017679504 + 2 65.294131 -11.084501 0 86.758754 0.06146659 + 3 121.92555 -7.0612033 0 175.64423 0.11477827 + 4 185.71165 -5.8781334 0 272.41077 0.17482523 + 5 286.28339 -4.3800108 0 424.61565 0.26950146 + 6 481.28097 -4.3052012 0 716.89433 0.45306828 + 7 487.26022 -3.8672741 0 726.29216 0.45869703 + 8 493.65478 -3.0242687 0 736.71742 0.46471675 + 9 495.66203 -3.4336343 0 739.31592 0.46660633 + 10 498.41831 -2.8837072 0 743.99613 0.46920104 + 11 499.20944 -2.7724783 0 745.29287 0.46994579 + 12 500.97345 -2.8281484 0 747.88057 0.4716064 + 13 507.46412 -2.7752775 0 757.65971 0.47771658 + 14 525.35729 -2.5749814 0 784.67292 0.49456085 + 15 563.9578 -2.9982381 0 842.09253 0.5308986 + 16 645.47602 -2.5519203 0 964.69389 0.60763822 + 17 647.09276 -2.2568468 0 967.41166 0.60916019 + 18 647.12596 -2.2791003 0 967.43915 0.60919144 + 19 647.24862 -2.2495226 0 967.65253 0.60930691 + 20 647.51175 -2.0239179 0 968.27244 0.60955462 +Loop time of 0.494261 on 8 procs for 20 steps with 1000 atoms + +Performance: 17480.630 tau/day, 40.464 timesteps/s +99.3% CPU use with 8 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.00027752 | 0.00030088 | 0.0003736 | 0.0 | 0.06 +Kspace | 0.45443 | 0.46295 | 0.47316 | 1.0 | 93.67 +Neigh | 0.014408 | 0.02515 | 0.034048 | 4.6 | 5.09 +Comm | 0.0036254 | 0.0041741 | 0.0048032 | 0.6 | 0.84 +Output | 0.00072742 | 0.0009357 | 0.0012984 | 0.0 | 0.19 +Modify | 0.00011778 | 0.00015756 | 0.00019836 | 0.0 | 0.03 +Other | | 0.000589 | | | 0.12 + +Nlocal: 125 ave 137 max 111 min +Histogram: 1 1 0 0 0 2 2 1 0 1 +Nghost: 768.875 ave 788 max 761 min +Histogram: 4 0 2 0 0 0 1 0 0 1 +Neighs: 30542.8 ave 48077 max 10011 min +Histogram: 1 1 1 0 1 1 0 0 0 3 + +Total # of neighbors = 244342 +Ave neighs/atom = 244.342 +Neighbor list builds = 19 +Dangerous builds = 18 +Total wall time: 0:00:01 diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.p2nfft.1 b/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.p2nfft.1 new file mode 100644 index 0000000000..f9192cdfaf --- /dev/null +++ b/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.p2nfft.1 @@ -0,0 +1,107 @@ +LAMMPS (29 Jun 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.hammersley_shphere + orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 1000 atoms +change_box all boundary f f f + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos p2nfft 0.001 +kspace_modify scafacos tolerance potential + +timestep 0.005 +thermo 1 + +run 20 +Setting up ScaFaCoS with solver p2nfft ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 102 102 102 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 10.3 | 10.3 | 10.3 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -0.62417787 0 1.6235721 0.00141207 + 1 18.780041 -10.770002 0 17.371889 0.017679155 + 2 65.289192 -11.084705 0 86.751149 0.06146194 + 3 121.92987 -7.0625759 0 175.64933 0.11478234 + 4 185.78164 -5.8777511 0 272.51603 0.17489112 + 5 286.36221 -4.3820531 0 424.73172 0.26957566 + 6 481.42203 -4.3095567 0 717.10136 0.45320108 + 7 488.59165 -3.8685193 0 728.28607 0.45995042 + 8 497.85288 -3.0417938 0 742.99075 0.46866875 + 9 499.61619 -3.4190063 0 745.25585 0.47032869 + 10 502.63691 -2.8360951 0 750.36531 0.47317234 + 11 504.4847 -2.7628089 0 753.20751 0.47491181 + 12 506.54494 -2.8460319 0 756.21157 0.47685128 + 13 508.2722 -2.7309328 0 758.91497 0.47847729 + 14 510.57053 -2.6094792 0 762.48045 0.48064089 + 15 513.14804 -2.7150819 0 766.23726 0.48306731 + 16 515.78127 -2.3961749 0 770.50206 0.48554618 + 17 515.70267 -2.2982581 0 770.48219 0.48547219 + 18 515.70813 -2.1516075 0 770.63702 0.48547732 + 19 515.74908 -2.0581483 0 770.79185 0.48551588 + 20 515.70881 -1.892235 0 770.89742 0.48547797 +Loop time of 1.34132 on 1 procs for 20 steps with 1000 atoms + +Performance: 6441.409 tau/day, 14.911 timesteps/s +100.0% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.00028849 | 0.00028849 | 0.00028849 | 0.0 | 0.02 +Kspace | 1.1744 | 1.1744 | 1.1744 | 0.0 | 87.56 +Neigh | 0.16435 | 0.16435 | 0.16435 | 0.0 | 12.25 +Comm | 0.00021219 | 0.00021219 | 0.00021219 | 0.0 | 0.02 +Output | 0.00051928 | 0.00051928 | 0.00051928 | 0.0 | 0.04 +Modify | 0.00079513 | 0.00079513 | 0.00079513 | 0.0 | 0.06 +Other | | 0.0007439 | | | 0.06 + +Nlocal: 1000 ave 1000 max 1000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 247817 ave 247817 max 247817 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 247817 +Ave neighs/atom = 247.817 +Neighbor list builds = 19 +Dangerous builds = 18 +Total wall time: 0:00:01 diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.p2nfft.2 b/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.p2nfft.2 new file mode 100644 index 0000000000..4db3e28dbf --- /dev/null +++ b/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.p2nfft.2 @@ -0,0 +1,107 @@ +LAMMPS (29 Jun 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.hammersley_shphere + orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5) + 1 by 1 by 2 MPI processor grid + reading atoms ... + 1000 atoms +change_box all boundary f f f + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos p2nfft 0.001 +kspace_modify scafacos tolerance potential + +timestep 0.005 +thermo 1 + +run 20 +Setting up ScaFaCoS with solver p2nfft ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 102 102 102 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 6.48 | 6.861 | 7.243 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -0.62417787 0 1.6235721 0.00141207 + 1 18.780041 -10.770002 0 17.371889 0.017679155 + 2 65.289192 -11.084705 0 86.751149 0.06146194 + 3 121.92987 -7.0625759 0 175.64933 0.11478234 + 4 185.78164 -5.8777511 0 272.51603 0.17489112 + 5 286.36221 -4.3820531 0 424.73172 0.26957566 + 6 481.42203 -4.3095567 0 717.10136 0.45320108 + 7 488.59165 -3.8685193 0 728.28607 0.45995042 + 8 497.85288 -3.0417938 0 742.99075 0.46866875 + 9 499.61619 -3.4190063 0 745.25585 0.47032869 + 10 502.63691 -2.8360951 0 750.36531 0.47317234 + 11 504.4847 -2.7628089 0 753.20751 0.47491181 + 12 506.54494 -2.8460319 0 756.21157 0.47685128 + 13 508.2722 -2.7309328 0 758.91497 0.47847729 + 14 510.57053 -2.6094792 0 762.48045 0.48064089 + 15 513.14804 -2.7150819 0 766.23726 0.48306731 + 16 515.78127 -2.3961749 0 770.50206 0.48554618 + 17 515.70267 -2.2982581 0 770.48219 0.48547219 + 18 515.70813 -2.1516075 0 770.63702 0.48547732 + 19 515.74908 -2.0581483 0 770.79185 0.48551588 + 20 515.70881 -1.892235 0 770.89742 0.48547797 +Loop time of 0.858675 on 2 procs for 20 steps with 1000 atoms + +Performance: 10062.016 tau/day, 23.292 timesteps/s +100.0% CPU use with 2 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.00026321 | 0.00026667 | 0.00027013 | 0.0 | 0.03 +Kspace | 0.74531 | 0.77182 | 0.79833 | 3.0 | 89.89 +Neigh | 0.055915 | 0.082578 | 0.10924 | 9.3 | 9.62 +Comm | 0.0021703 | 0.002401 | 0.0026317 | 0.5 | 0.28 +Output | 0.00048423 | 0.00061262 | 0.000741 | 0.0 | 0.07 +Modify | 0.00034285 | 0.0004636 | 0.00058436 | 0.0 | 0.05 +Other | | 0.0005329 | | | 0.06 + +Nlocal: 500 ave 516 max 484 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Nghost: 456.5 ave 475 max 438 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Neighs: 123908 ave 172139 max 75678 min +Histogram: 1 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 247817 +Ave neighs/atom = 247.817 +Neighbor list builds = 19 +Dangerous builds = 18 +Total wall time: 0:00:01 diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.p2nfft.4 b/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.p2nfft.4 new file mode 100644 index 0000000000..3a2d653106 --- /dev/null +++ b/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.p2nfft.4 @@ -0,0 +1,107 @@ +LAMMPS (29 Jun 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.hammersley_shphere + orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 1000 atoms +change_box all boundary f f f + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos p2nfft 0.001 +kspace_modify scafacos tolerance potential + +timestep 0.005 +thermo 1 + +run 20 +Setting up ScaFaCoS with solver p2nfft ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 102 102 102 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.837 | 5.123 | 5.6 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -0.62417787 0 1.6235721 0.00141207 + 1 18.780041 -10.770002 0 17.371889 0.017679155 + 2 65.289192 -11.084705 0 86.751149 0.06146194 + 3 121.92987 -7.0625759 0 175.64933 0.11478234 + 4 185.78164 -5.8777511 0 272.51603 0.17489112 + 5 286.36221 -4.3820531 0 424.73172 0.26957566 + 6 481.42203 -4.3095567 0 717.10136 0.45320108 + 7 488.59165 -3.8685193 0 728.28607 0.45995042 + 8 497.85288 -3.0417938 0 742.99075 0.46866875 + 9 499.61619 -3.4190063 0 745.25585 0.47032869 + 10 502.63691 -2.8360951 0 750.36531 0.47317234 + 11 504.4847 -2.7628089 0 753.20751 0.47491181 + 12 506.54494 -2.8460319 0 756.21157 0.47685128 + 13 508.2722 -2.7309328 0 758.91497 0.47847729 + 14 510.57053 -2.6094792 0 762.48045 0.48064089 + 15 513.14804 -2.7150819 0 766.23726 0.48306731 + 16 515.78127 -2.3961749 0 770.50206 0.48554618 + 17 515.70267 -2.2982581 0 770.48219 0.48547219 + 18 515.70813 -2.1516075 0 770.63702 0.48547732 + 19 515.74908 -2.0581483 0 770.79185 0.48551588 + 20 515.70881 -1.892235 0 770.89742 0.48547797 +Loop time of 0.540235 on 4 procs for 20 steps with 1000 atoms + +Performance: 15993.051 tau/day, 37.021 timesteps/s +99.3% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.00025725 | 0.00028253 | 0.00031233 | 0.0 | 0.05 +Kspace | 0.47152 | 0.48989 | 0.50709 | 1.9 | 90.68 +Neigh | 0.028196 | 0.045694 | 0.064338 | 6.3 | 8.46 +Comm | 0.0026579 | 0.003028 | 0.0033965 | 0.5 | 0.56 +Output | 0.00049663 | 0.00064254 | 0.00084853 | 0.0 | 0.12 +Modify | 0.00019264 | 0.0002293 | 0.00030923 | 0.0 | 0.04 +Other | | 0.0004709 | | | 0.09 + +Nlocal: 250 ave 259 max 238 min +Histogram: 1 0 0 1 0 0 0 0 0 2 +Nghost: 672.25 ave 683 max 663 min +Histogram: 2 0 0 0 0 0 0 0 1 1 +Neighs: 61954.2 ave 97157 max 25016 min +Histogram: 1 0 0 1 0 0 1 0 0 1 + +Total # of neighbors = 247817 +Ave neighs/atom = 247.817 +Neighbor list builds = 19 +Dangerous builds = 18 +Total wall time: 0:00:00 diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.p2nfft.8 b/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.p2nfft.8 new file mode 100644 index 0000000000..08e68531a9 --- /dev/null +++ b/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.p2nfft.8 @@ -0,0 +1,107 @@ +LAMMPS (29 Jun 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.hammersley_shphere + orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5) + 2 by 2 by 2 MPI processor grid + reading atoms ... + 1000 atoms +change_box all boundary f f f + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos p2nfft 0.001 +kspace_modify scafacos tolerance potential + +timestep 0.005 +thermo 1 + +run 20 +Setting up ScaFaCoS with solver p2nfft ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 102 102 102 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.164 | 4.26 | 4.546 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -0.62417787 0 1.6235721 0.00141207 + 1 18.780041 -10.770002 0 17.371889 0.017679155 + 2 65.289192 -11.084705 0 86.751149 0.06146194 + 3 121.92987 -7.0625759 0 175.64933 0.11478234 + 4 185.78164 -5.8777511 0 272.51603 0.17489112 + 5 286.36221 -4.3820531 0 424.73172 0.26957566 + 6 481.42203 -4.3095567 0 717.10136 0.45320108 + 7 488.59165 -3.8685193 0 728.28607 0.45995042 + 8 497.85288 -3.0417938 0 742.99075 0.46866875 + 9 499.61619 -3.4190063 0 745.25585 0.47032869 + 10 502.63691 -2.8360951 0 750.36531 0.47317234 + 11 504.4847 -2.7628089 0 753.20751 0.47491181 + 12 506.54494 -2.8460319 0 756.21157 0.47685128 + 13 508.2722 -2.7309328 0 758.91497 0.47847729 + 14 510.57053 -2.6094792 0 762.48045 0.48064089 + 15 513.14804 -2.7150819 0 766.23726 0.48306731 + 16 515.78127 -2.3961749 0 770.50206 0.48554618 + 17 515.70267 -2.2982581 0 770.48219 0.48547219 + 18 515.70813 -2.1516075 0 770.63702 0.48547732 + 19 515.74908 -2.0581483 0 770.79185 0.48551588 + 20 515.70881 -1.892235 0 770.89742 0.48547797 +Loop time of 0.317433 on 8 procs for 20 steps with 1000 atoms + +Performance: 27218.342 tau/day, 63.005 timesteps/s +99.6% CPU use with 8 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.00027013 | 0.00028479 | 0.00029206 | 0.0 | 0.09 +Kspace | 0.27742 | 0.28666 | 0.29702 | 1.4 | 90.31 +Neigh | 0.014795 | 0.025382 | 0.03481 | 4.8 | 8.00 +Comm | 0.0034907 | 0.0038758 | 0.0042439 | 0.5 | 1.22 +Output | 0.00055361 | 0.00073573 | 0.0010755 | 0.0 | 0.23 +Modify | 0.00012279 | 0.00014156 | 0.00016165 | 0.0 | 0.04 +Other | | 0.0003535 | | | 0.11 + +Nlocal: 125 ave 133 max 113 min +Histogram: 2 0 0 0 0 1 1 0 2 2 +Nghost: 773.625 ave 788 max 764 min +Histogram: 1 1 2 1 1 0 0 0 1 1 +Neighs: 30977.1 ave 50690 max 10447 min +Histogram: 1 1 1 0 1 1 0 0 2 1 + +Total # of neighbors = 247817 +Ave neighs/atom = 247.817 +Neighbor list builds = 19 +Dangerous builds = 18 +Total wall time: 0:00:00 From 1b7af5d93bd77d791a1ae6b3fef6cbb373ea2fcb Mon Sep 17 00:00:00 2001 From: Rene Halver Date: Mon, 23 Jul 2018 16:24:16 -0600 Subject: [PATCH 068/302] added the computation of the global virial by ScaFaCoS --- src/USER-SCAFACOS/scafacos.cpp | 16 +++++++++++++++- 1 file changed, 15 insertions(+), 1 deletion(-) diff --git a/src/USER-SCAFACOS/scafacos.cpp b/src/USER-SCAFACOS/scafacos.cpp index 352a298b86..e7dbcb4523 100644 --- a/src/USER-SCAFACOS/scafacos.cpp +++ b/src/USER-SCAFACOS/scafacos.cpp @@ -154,7 +154,11 @@ void Scafacos::compute(int eflag, int vflag) const double qscale = qqrd2e; if (eflag || vflag) ev_setup(eflag,vflag); - else eflag_atom = 0; + else + { + eflag_atom = 0; + vflag_global = 0; + } // if simulation box has changed, call fcs_tune() @@ -175,9 +179,19 @@ void Scafacos::compute(int eflag, int vflag) } + if (vflag_global) + { + fcs_set_compute_virial(fcs,1); + } + result = fcs_run(fcs,nlocal,&x[0][0],q,&efield[0][0],epot); check_result(result); + if (vflag_global) + { + fcs_get_virial(fcs,virial); + } + // apply Efield to each particle // accumulate total energy From ae2d43031bfd2c7b345478091fe3a2b8879b68f0 Mon Sep 17 00:00:00 2001 From: Rene Halver Date: Mon, 23 Jul 2018 16:25:02 -0600 Subject: [PATCH 069/302] added pressure output, to compare results with global virial (with internal PPPM) --- examples/USER/scafacos/in.scafacos.cw.ewald | 2 +- examples/USER/scafacos/in.scafacos.cw.fmm | 2 +- examples/USER/scafacos/in.scafacos.cw.p2nfft | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/examples/USER/scafacos/in.scafacos.cw.ewald b/examples/USER/scafacos/in.scafacos.cw.ewald index f8444dd01f..55ebd0e7b3 100644 --- a/examples/USER/scafacos/in.scafacos.cw.ewald +++ b/examples/USER/scafacos/in.scafacos.cw.ewald @@ -18,7 +18,7 @@ kspace_modify scafacos tolerance field timestep 0.005 -thermo_style custom step atoms cpu temp pe ke etotal ecoul +thermo_style custom step atoms cpu temp pe ke etotal ecoul press run_style verlet diff --git a/examples/USER/scafacos/in.scafacos.cw.fmm b/examples/USER/scafacos/in.scafacos.cw.fmm index 24a2739581..c63e241d63 100644 --- a/examples/USER/scafacos/in.scafacos.cw.fmm +++ b/examples/USER/scafacos/in.scafacos.cw.fmm @@ -24,7 +24,7 @@ kspace_modify scafacos fmm_tuning 1 timestep 0.005 -thermo_style custom step atoms cpu temp pe ke etotal ecoul +thermo_style custom step atoms cpu temp pe ke etotal ecoul press run_style verlet diff --git a/examples/USER/scafacos/in.scafacos.cw.p2nfft b/examples/USER/scafacos/in.scafacos.cw.p2nfft index 7a2391bc77..96be1b7d3c 100644 --- a/examples/USER/scafacos/in.scafacos.cw.p2nfft +++ b/examples/USER/scafacos/in.scafacos.cw.p2nfft @@ -18,7 +18,7 @@ kspace_modify scafacos tolerance field timestep 0.005 -thermo_style custom step atoms cpu temp pe ke etotal ecoul +thermo_style custom step atoms cpu temp pe ke etotal ecoul press run_style verlet From 81abd8bc0a3bc7eec25ce4a1a634e148ea69a05a Mon Sep 17 00:00:00 2001 From: Rene Halver Date: Tue, 24 Jul 2018 11:59:44 -0600 Subject: [PATCH 070/302] extended scafacos documentation --- doc/src/kspace_modify.txt | 32 +++++++++++++++++++++++++++----- doc/src/kspace_style.txt | 29 ++++++++++++++++++----------- 2 files changed, 45 insertions(+), 16 deletions(-) diff --git a/doc/src/kspace_modify.txt b/doc/src/kspace_modify.txt index fbc569306c..d21bb379e7 100644 --- a/doc/src/kspace_modify.txt +++ b/doc/src/kspace_modify.txt @@ -45,6 +45,8 @@ keyword = {collective} or {compute} or {cutoff/adjust} or {diff} or {disp/auto} {scafacos} values = option value1 value2 ... option = {tolerance} value = {energy} or {energy_rel} or {field} or {field_rel} or {potential} or {potential_rel} + option = {fmm_tuning} + value = {0} or {1} {slab} value = volfactor or {nozforce} volfactor = ratio of the total extended volume used in the 2d approximation compared with the volume of the simulation domain @@ -308,8 +310,6 @@ or with suffix kspace/pair styles of MSM, like OMP or GPU. :line -RENE: check this section - The {scafacos} keyword is used for settings that are passed to the ScaFaCoS library when using "kspace_style scafacos"_kspace_style.html. @@ -324,10 +324,32 @@ field_rel = relative accuracy in electric field potential = absolute accuracy in total Coulomic potential potential_rel = relative accuracy in total Coulomic potential -RENE: which one is closest to what LAMMPS used (see kspace_style -command) - is it "field"? That's why I set it as the default. +Potential and potential_rel impose a tolerance on a per-atom basis, +in comparison to the energy and energy_rel tolerance types, where +the tolerance is computed with regard to the total Coulomic energy +in the system. In comparison to that, the field and field_rel +tolerance types set a tolerance for the field values calculated +within ScaFaCoS. Since the forces are derived from the field +values, it indirectly sets a tolerance for the forces, comparable +to other LAMMPS KSpace styles, see "kspace_style"_kspace_modify.html. +The suffix '_rel' indicates that the tolerance is a relative tolerance, +whereas the other case imposes an absolute tolerance on the given +quantity. -RENE: How is potential different than energy for this ?? +What needs to be taken into account is that not all solvers within +the ScaFaCoS library support all kinds of tolerance types. + +fmm = energy and energy_rel +p2nfft = field (1d-,2d-,3d-periodic systems) or potential (0d-periodic) +ewald = field +direct = has no tolerance tuning + +The {fmm_tuning} option (de-)activates the internal tuning mechanism +for the fmm solver. Since the internal tuning mechanism is sequential, +it can be very time-consuming and usually it is not required for +systems with a homogenous charge distribution. The default of the +setting there for is {0}, disabling the internal tuning. {1} +activates the internal tuning. :line diff --git a/doc/src/kspace_style.txt b/doc/src/kspace_style.txt index e5333489cc..49fb13ac37 100644 --- a/doc/src/kspace_style.txt +++ b/doc/src/kspace_style.txt @@ -58,7 +58,7 @@ style = {none} or {ewald} or {ewald/disp} or {ewald/omp} or {pppm} or {pppm/cg} accuracy = desired relative error in forces smallq = cutoff for charges to be considered (optional) (charge units) {scafacos} values = method accuracy - method = fmm or p3m or ... RENE + method = fmm or p2nfft or ewald or direct accuracy = desired relative error in forces :pre :ule @@ -214,8 +214,6 @@ pressure simulation with MSM will cause the code to run slower. :line -RENE: edit this section - The {scafacos} style is a wrapper on the "ScaFaCoS Coulomb solver library"_http://www.scafacos.de which provides a variety of solver methods which can be used with LAMMPS. The paper by "(Who)"_#Who2012 @@ -255,16 +253,24 @@ the total Coulombic energy (short- and long-range) will be tallied for The specified {method} determines which ScaFaCoS algorithm is used. The list of methods shown above are the ScaFaCoS methods currently -available from LAMMPS. - -RENE: explain this accuracy better compared to what -it means for other LAMMPS methods? +available from LAMMPS. Currently the following solvers are +supported for use with LAMMPS: {fmm} (Fast Multi-Pole method), +{p2nfft} (FFT-based Coulomb solver), {ewald} (Ewald-Summation) +and {direct} (direct summation). The other ScaFaCoS solvers +will be supported later on, but for the time being are +experimental in connection with LAMMPS, e.g. {p3m} (PPPM-method). +Use unsupported methods at your own discretion. To get an overview +about the included solvers, refer to "(Sutmann)"_#Sutmann2013 The specified {accuracy} is similar to the accuracy setting for other LAMMPS KSpace styles, but is passed to ScaFaCoS, which can interpret -it in different ways for different methods it supports. See the -"kspace_modify scafacos accuracy"_kspace_modify.html command for -details. +it in different ways for different methods it supports. +Within the ScaFaCoS library the {accuracy} is treated as a tolerance +level (either absolute or relative) for the chosen quantity, where +the quantity can be either the Columic field values, the per-atom +Columic energy or the total Columic energy. Different solver support +different tolerance types, for more information on that, please +refer to "kspace_modify scafacos accuracy"_kspace_modify.html. The "kspace_modify scafacos"_kspace_modify.html command also explains all the ScaFaCoS options currently exposed to LAMMPS. @@ -460,7 +466,8 @@ Illinois at Urbana-Champaign, (2006). [(Hardy2)] Hardy, Stone, Schulten, Parallel Computing, 35, 164-177 (2009). -RENE: +:link(Sutmann2013) +[(Sutmann)] Sutmann, Arnold, Fahrenberger, et. al., Physical review / E 88(6), 063308 (2013) :link(Who2012) [(Who)] Who, Author2, Author3, J of Long Range Solvers, 35, 164-177 From 655bd10db6279c947fba9a32120ca32077eabef5 Mon Sep 17 00:00:00 2001 From: "Steven J. Plimpton" Date: Tue, 24 Jul 2018 15:20:37 -0600 Subject: [PATCH 071/302] doc changes to 2 files --- doc/src/kspace_modify.txt | 75 ++++++++++++++++++++++++++------------- doc/src/kspace_style.txt | 51 ++++++++++++-------------- 2 files changed, 72 insertions(+), 54 deletions(-) diff --git a/doc/src/kspace_modify.txt b/doc/src/kspace_modify.txt index d21bb379e7..c41e9a9336 100644 --- a/doc/src/kspace_modify.txt +++ b/doc/src/kspace_modify.txt @@ -313,43 +313,67 @@ or with suffix kspace/pair styles of MSM, like OMP or GPU. The {scafacos} keyword is used for settings that are passed to the ScaFaCoS library when using "kspace_style scafacos"_kspace_style.html. -The {tolerance} option affects how the {accuracy} specified with -the "kspace_style"_kspace_style.html command is interpreted by ScaFaCoS. +The {tolerance} option affects how the {accuracy} specified with the +"kspace_style"_kspace_style.html command is interpreted by ScaFaCoS. The following values may be used: energy = absolute accuracy in total Coulomic energy energy_rel = relative accuracy in total Coulomic energy -field = absolute accuracy in electric field -field_rel = relative accuracy in electric field potential = absolute accuracy in total Coulomic potential potential_rel = relative accuracy in total Coulomic potential +field = absolute accuracy in electric field +field_rel = relative accuracy in electric field :ul -Potential and potential_rel impose a tolerance on a per-atom basis, -in comparison to the energy and energy_rel tolerance types, where -the tolerance is computed with regard to the total Coulomic energy -in the system. In comparison to that, the field and field_rel -tolerance types set a tolerance for the field values calculated -within ScaFaCoS. Since the forces are derived from the field -values, it indirectly sets a tolerance for the forces, comparable -to other LAMMPS KSpace styles, see "kspace_style"_kspace_modify.html. -The suffix '_rel' indicates that the tolerance is a relative tolerance, -whereas the other case imposes an absolute tolerance on the given +The values with suffix "_rel" indicate the tolerance is a relative +tolerance; the other values impose an absolute tolerance on the given quantity. -What needs to be taken into account is that not all solvers within -the ScaFaCoS library support all kinds of tolerance types. +The energy and energy_rel values, set a tolerance based on the total +Coulomic energy of the system. The potential and potential_rel set a +tolerance based on the per-atom Coulomic energy. The field and +field_rel tolerance types set a tolerance based on the electric field +values computed by ScaFaCoS. Since per-atom forces are derived from +the per-atom electric field, this effectively sets a tolerance on the +forces, simimlar to other LAMMPS KSpace styles, as explained on the +"kspace_style"_kspace_style.html doc page. + +RENE: Can you add some explanation of the difference between relative +and absolute? Something like this (if it's correct). If the total +Coul energy is computed to be -1000.0, then an absolute tolerance of +1.0e-3 means the actual energy is between -999.999 and -1000.001. +Whereas a relative tolerance means it is between -999 and -1001. Thus +an absolute tolerance is generally much more stringent? + +RENE: Also, can you explain more what is the difference between energy +(total) and potential (per-atom)? Which one is more vs less accurate? +Does potential mean that the maximum of any atom's energy error is < +tolerance? I.e. it is a max across all per-atom values? Ditto for +field, since it is computed on a per-atom basis? + +Note that not all ScaFaCoS solvers support all tolerance types. +These are the allowed values for each method: fmm = energy and energy_rel p2nfft = field (1d-,2d-,3d-periodic systems) or potential (0d-periodic) ewald = field -direct = has no tolerance tuning +direct = has no tolerance tuning :ul -The {fmm_tuning} option (de-)activates the internal tuning mechanism -for the fmm solver. Since the internal tuning mechanism is sequential, -it can be very time-consuming and usually it is not required for -systems with a homogenous charge distribution. The default of the -setting there for is {0}, disabling the internal tuning. {1} -activates the internal tuning. +RENE: I think this means that the default tolerance setting +is differnet for different methods. If so, it should +be documented in the above list, i.e. by listing the default +value first. + +RENE: Does the code (LAMMPS or Scafacos) generate an error +if an unsupported tolerance is specified for a method? + +The {fmm_tuning} option is only relevant when using the FMM method. +It activates (value=1) or deactivates (value=0) an internal tuning +mechanism for the FMM solver. The tuning operation runs sequentially +and can be very time-consuming. Usually it is not needed for systems +with a homogenous charge distribution. The default for this option is +therefore {0}. + +RENE: is the tuning a one-time (start-up) operation if enabled? :line @@ -405,8 +429,9 @@ gewald = gewald/disp = 0.0, slab = 1.0, compute = yes, cutoff/adjust = yes (MSM), pressure/scalar = yes (MSM), fftbench = no (PPPM), diff = ik (PPPM), mix/disp = pair, force/disp/real = -1.0, force/disp/kspace = -1.0, split = 0, tol = 1.0e-6, and disp/auto = no. For pppm/intel, -order = order/disp = 7. For scafacos settings, scafacos tolerance -field. +order = order/disp = 7. For scafacos settings, the scafacos tolerance +option depends on the method chosen, as documented above. The +scafacos fmm_tuning default = 0. :line diff --git a/doc/src/kspace_style.txt b/doc/src/kspace_style.txt index 49fb13ac37..742d71ffb8 100644 --- a/doc/src/kspace_style.txt +++ b/doc/src/kspace_style.txt @@ -236,41 +236,34 @@ See details on "this page"_Section_packages.html#USER-SCAFACOS. NOTE: Unlike other KSpace solvers in LAMMPS, ScaFaCoS computes all Coulombic interactions, both short- and long-range. Thus you should -NOT use a Coulmbic pair style when using kspace_style scafacos. Thus -the total Coulombic energy (short- and long-range) will be tallied for -"thermodynamic output"_thermo_style.html command as part of the -{elong} keyword; the {ecoul} keyword will be zero. +NOT use a Coulmbic pair style when using kspace_style scafacos. This +also means the total Coulombic energy (short- and long-range) will be +tallied for "thermodynamic output"_thermo_style.html command as part +of the {elong} keyword; the {ecoul} keyword will be zero. -NOTE: See the restriction below about use of ScaFaCoS in LAMMPS with -molecular charged systems or the TIP4P water model. - -Unlike other KSpace solvers in LAMMPS, ScaFaCoS computes all -Coulombic interactions, both short- and long-range. Thus you should -NOT use a Coulmbic pair style when using kspace_style scafacos. Thus -the total Coulombic energy (short- and long-range) will be tallied for -"thermodynamic output"_thermo_style.html command as part of the -{elong} keyword; the {ecoul} keyword will be zero. +NOTE: See the current restriction below about use of ScaFaCoS in +LAMMPS with molecular charged systems or the TIP4P water model. The specified {method} determines which ScaFaCoS algorithm is used. -The list of methods shown above are the ScaFaCoS methods currently -available from LAMMPS. Currently the following solvers are -supported for use with LAMMPS: {fmm} (Fast Multi-Pole method), -{p2nfft} (FFT-based Coulomb solver), {ewald} (Ewald-Summation) -and {direct} (direct summation). The other ScaFaCoS solvers -will be supported later on, but for the time being are -experimental in connection with LAMMPS, e.g. {p3m} (PPPM-method). -Use unsupported methods at your own discretion. To get an overview -about the included solvers, refer to "(Sutmann)"_#Sutmann2013 +These are the ScaFaCoS methods currently available from LAMMPS: + +{fmm} = Fast Multi-Pole method +{p2nfft} = FFT-based Coulomb solver +{ewald} = Ewald summation +{direct} = direct O(N^2) summation + +We plan to support additional ScaFaCoS solvers from LAMMPS in the +future. For an overview of the included solvers, refer to +"(Sutmann)"_#Sutmann2013 The specified {accuracy} is similar to the accuracy setting for other LAMMPS KSpace styles, but is passed to ScaFaCoS, which can interpret -it in different ways for different methods it supports. -Within the ScaFaCoS library the {accuracy} is treated as a tolerance -level (either absolute or relative) for the chosen quantity, where -the quantity can be either the Columic field values, the per-atom -Columic energy or the total Columic energy. Different solver support -different tolerance types, for more information on that, please -refer to "kspace_modify scafacos accuracy"_kspace_modify.html. +it in different ways for different methods it supports. Within the +ScaFaCoS library the {accuracy} is treated as a tolerance level +(either absolute or relative) for the chosen quantity, where the +quantity can be either the Columic field values, the per-atom Columic +energy or the total Columic energy. To select from these options, see +the "kspace_modify scafacos accuracy"_kspace_modify.html doc page. The "kspace_modify scafacos"_kspace_modify.html command also explains all the ScaFaCoS options currently exposed to LAMMPS. From 8846f97868f24ef75cecf9dd4547640cf8cb06e7 Mon Sep 17 00:00:00 2001 From: Rene Halver Date: Tue, 24 Jul 2018 15:46:28 -0600 Subject: [PATCH 072/302] explained differences between absolute and relative tolerance more --- doc/src/kspace_modify.txt | 25 +++++++++++++------------ 1 file changed, 13 insertions(+), 12 deletions(-) diff --git a/doc/src/kspace_modify.txt b/doc/src/kspace_modify.txt index c41e9a9336..f552f9b9b6 100644 --- a/doc/src/kspace_modify.txt +++ b/doc/src/kspace_modify.txt @@ -326,7 +326,16 @@ field_rel = relative accuracy in electric field :ul The values with suffix "_rel" indicate the tolerance is a relative tolerance; the other values impose an absolute tolerance on the given -quantity. +quantity. Absoulte tolerance in this case means, that for a given +quantity q and a given absolute tolerance of t_a the result should +be between q-t_a and q+t_a. For a relative tolerance t_r the relative +error should not be greater than t_r, i.e. abs(1 - (result/q)) < t_r. +As a consequence of this, the tolerance type should be checked, when +performing computations with a high absolute field / energy. E.g. +if the total energy in the system is 1000000.0 an absolute tolerance +of 1e-3 would mean that the result has to be between 999999.999 and +1000000.001, which would be equivalent to a relative tolerance of +1e-9. The energy and energy_rel values, set a tolerance based on the total Coulomic energy of the system. The potential and potential_rel set a @@ -337,13 +346,6 @@ the per-atom electric field, this effectively sets a tolerance on the forces, simimlar to other LAMMPS KSpace styles, as explained on the "kspace_style"_kspace_style.html doc page. -RENE: Can you add some explanation of the difference between relative -and absolute? Something like this (if it's correct). If the total -Coul energy is computed to be -1000.0, then an absolute tolerance of -1.0e-3 means the actual energy is between -999.999 and -1000.001. -Whereas a relative tolerance means it is between -999 and -1001. Thus -an absolute tolerance is generally much more stringent? - RENE: Also, can you explain more what is the difference between energy (total) and potential (per-atom)? Which one is more vs less accurate? Does potential mean that the maximum of any atom's energy error is < @@ -358,10 +360,9 @@ p2nfft = field (1d-,2d-,3d-periodic systems) or potential (0d-periodic) ewald = field direct = has no tolerance tuning :ul -RENE: I think this means that the default tolerance setting -is differnet for different methods. If so, it should -be documented in the above list, i.e. by listing the default -value first. +If the tolerance type is not changed, the default values for the +tolerance type are the first values in the above list, e.g. energy +is the default tolerance type for the fmm solver. RENE: Does the code (LAMMPS or Scafacos) generate an error if an unsupported tolerance is specified for a method? From 37a0a7b49bb54cedeb475772c7f64b3e83b8153c Mon Sep 17 00:00:00 2001 From: Rene Halver Date: Tue, 24 Jul 2018 15:55:48 -0600 Subject: [PATCH 073/302] fixed compilation error --- doc/src/kspace_modify.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/src/kspace_modify.txt b/doc/src/kspace_modify.txt index f552f9b9b6..57cff18d7e 100644 --- a/doc/src/kspace_modify.txt +++ b/doc/src/kspace_modify.txt @@ -324,7 +324,7 @@ potential_rel = relative accuracy in total Coulomic potential field = absolute accuracy in electric field field_rel = relative accuracy in electric field :ul -The values with suffix "_rel" indicate the tolerance is a relative +The values with suffix _rel indicate the tolerance is a relative tolerance; the other values impose an absolute tolerance on the given quantity. Absoulte tolerance in this case means, that for a given quantity q and a given absolute tolerance of t_a the result should From ae04fd0beaba1c3561cd17354d2c1fa05bde79ae Mon Sep 17 00:00:00 2001 From: Rene Halver Date: Tue, 31 Jul 2018 09:48:59 -0600 Subject: [PATCH 074/302] fixed error: if no particles are on a process, the arrays for efield and epot were not allocated, leading to segfaults; shifted the parameter output to after the tuning step, so if the values are changed, the changed values are displayed --- src/USER-SCAFACOS/scafacos.cpp | 26 +++++++++++++++++++++----- 1 file changed, 21 insertions(+), 5 deletions(-) diff --git a/src/USER-SCAFACOS/scafacos.cpp b/src/USER-SCAFACOS/scafacos.cpp index e7dbcb4523..21e46f76ad 100644 --- a/src/USER-SCAFACOS/scafacos.cpp +++ b/src/USER-SCAFACOS/scafacos.cpp @@ -121,7 +121,6 @@ void Scafacos::init() result = fcs_set_tolerance(fcs,tolerance_type,tolerance); check_result(result); } - if (me == 0) fcs_print_parameters(fcs); double **x = atom->x; double *q = atom->q; @@ -130,11 +129,15 @@ void Scafacos::init() if (strcmp(method,"fmm") == 0) { if (fmm_tuning_flag == 1) - fcs_fmm_set_internal_tuning(fcs,fmm_tuning_flag); + fcs_fmm_set_internal_tuning(fcs,FCS_FMM_INHOMOGENOUS_SYSTEM); + else + fcs_fmm_set_internal_tuning(fcs,FCS_FMM_HOMOGENOUS_SYSTEM); } result = fcs_tune(fcs,nlocal,&x[0][0],q); check_result(result); + // more useful here, since the parameters should be tuned now + if (me == 0) fcs_print_parameters(fcs); } initialized = 1; } @@ -170,13 +173,20 @@ void Scafacos::compute(int eflag, int vflag) // grow epot & efield if necessary + if (nlocal == 0 && maxatom == 0) { + memory->destroy(epot); + memory->destroy(efield); + maxatom = 1; + memory->create(epot,maxatom,"scafacos:epot"); + memory->create(efield,maxatom,3,"scafacos:efield"); + } + if (nlocal > maxatom) { memory->destroy(epot); memory->destroy(efield); maxatom = atom->nmax; memory->create(epot,maxatom,"scafacos:epot"); memory->create(efield,maxatom,3,"scafacos:efield"); - } if (vflag_global) @@ -184,6 +194,12 @@ void Scafacos::compute(int eflag, int vflag) fcs_set_compute_virial(fcs,1); } + if (strcmp(method,"p3m")==0) + { + result = fcs_tune(fcs,nlocal,&x[0][0],q); + check_result(result); + } + result = fcs_run(fcs,nlocal,&x[0][0],q,&efield[0][0],epot); check_result(result); @@ -252,8 +268,8 @@ int Scafacos::modify_param(int narg, char **arg) // 1 -> inhomogenous system (more internal tuning is provided (sequential!)) if (strcmp(arg[1],"fmm_tuning") == 0) { - if (screen && me == 0) fprintf(screen,"ScaFaCoS setting fmm inhomogen tuning ...%d\n", narg); - if (logfile && me == 0) fprintf(logfile,"ScaFaCoS setting fmm inhomogen tuning ...%d\n", narg); + if (screen && me == 0) fprintf(screen,"ScaFaCoS setting fmm inhomogen tuning ...\n"); + if (logfile && me == 0) fprintf(logfile,"ScaFaCoS setting fmm inhomogen tuning ...\n"); if (narg < 3) error->all(FLERR,"Illegal kspace_modify command (fmm_tuning)"); fmm_tuning_flag = atoi(arg[2]); return 3; From ac0ab4ba346e951e17cb7ad85bd5cd8a5867e666 Mon Sep 17 00:00:00 2001 From: Rene Halver Date: Tue, 31 Jul 2018 13:31:50 -0600 Subject: [PATCH 075/302] changed CMake file to require pkg_config for ScaFaCoS and removed Fortran/C dependencies --- cmake/CMakeLists.txt | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index afb93b9d1b..bfaf9243b1 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -185,11 +185,11 @@ pkg_depends(CORESHELL KSPACE) ###################################################### # packages with special compiler needs or external libs ###################################################### -if(PKG_REAX OR PKG_MEAM OR PKG_USER-QUIP OR PKG_USER-QMMM OR PKG_LATTE OR PKG_USER-SCAFACOS) +if(PKG_REAX OR PKG_MEAM OR PKG_USER-QUIP OR PKG_USER-QMMM OR PKG_LATTE) enable_language(Fortran) endif() -if(PKG_MEAM OR PKG_USER-H5MD OR PKG_USER-QMMM OR PKG_USER-SCAFACOS) +if(PKG_MEAM OR PKG_USER-H5MD OR PKG_USER-QMMM) enable_language(C) endif() @@ -349,7 +349,7 @@ if(PKG_LATTE) endif() if(PKG_USER-SCAFACOS) - FIND_PACKAGE(PkgConfig) + FIND_PACKAGE(PkgConfig REQUIRED) PKG_CHECK_MODULES(SCAFACOS scafacos) include_directories(${SCAFACOS_INCLUDE_DIRS}) list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_LDFLAGS}) From a8f0200fe9636afeccf464f08b0bf242bf2992fe Mon Sep 17 00:00:00 2001 From: Rene Halver Date: Tue, 31 Jul 2018 13:33:10 -0600 Subject: [PATCH 076/302] Install.py works on dummy tar-ball --- lib/scafacos/Install.py | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/lib/scafacos/Install.py b/lib/scafacos/Install.py index 1b39335511..c478589144 100644 --- a/lib/scafacos/Install.py +++ b/lib/scafacos/Install.py @@ -29,8 +29,9 @@ make lib-scafacos args="-p $HOME/scafacos" # use existing Scafacos installation # settings -version = "scafacos-1.0" -#url = "http://math.lbl.gov/voro++/download/dir/%s.tar.gz" % version +version = "scafacos-0.9" +url = "https://gigamove.rz.rwth-aachen.de/d/id/fTmrTm4EUAUSAp/dd/100" +#url = "https://gigamove.rz.rwth-aachen.de/d/id/CTzyApN76MXMJ6/dd/100" % version # print error message or help @@ -75,6 +76,7 @@ def geturl(url,fname): if not success and which('wget') != None: cmd = 'wget -O "%s" %s' % (fname,url) + print("Wget command: %s" % cmd) try: subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) success = True @@ -92,7 +94,7 @@ nargs = len(args) homepath = "." -buildflag = False +buildflag = True pathflag = False linkflag = True @@ -145,7 +147,7 @@ if buildflag: if buildflag: print("Building Scafacos ...") - cmd = 'cd "%s"; make CXX=g++ CFLAGS="-fPIC -O3"' % homedir + cmd = 'cd "%s"; CC=mpicc FC=mpif90 CXX=mpicxx ./configure --prefix="`pwd`/build" --disable-doc --enable-fcs-solvers=fmm,p2nfft,direct,ewald > log.txt; make -j 4; make install' % homedir txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) print(txt.decode('UTF-8')) @@ -157,7 +159,7 @@ if linkflag: os.remove("includelink") if os.path.isfile("liblink") or os.path.islink("liblink"): os.remove("liblink") - cmd = 'ln -s "%s/include" includelink' % homedir + cmd = 'ln -s "%s/build/include" includelink' % homedir subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) - cmd = 'ln -s "%s/lib" liblink' % homedir + cmd = 'ln -s "%s/build/lib" liblink' % homedir subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) From efaebe0eb02d9970c6a03c0e20bca077885ae3d2 Mon Sep 17 00:00:00 2001 From: Rene Halver Date: Thu, 2 Aug 2018 13:44:12 -0600 Subject: [PATCH 077/302] READMEs for USER-SCAFACOS completed --- lib/scafacos/README | 79 +++++++++++++++++++++++++++++++++++++--- src/USER-SCAFACOS/README | 28 ++++++++++++-- 2 files changed, 98 insertions(+), 9 deletions(-) diff --git a/lib/scafacos/README b/lib/scafacos/README index bdf167aef1..e5f1ecd92c 100644 --- a/lib/scafacos/README +++ b/lib/scafacos/README @@ -1,7 +1,76 @@ -RENE - there needs to be a README like the one -for lib/voronoi/README, explaining how -to grab the correct version of Scafacos. +This directory contains links to the ScaFaCoS library which +is required to use the KSPACE scafacos and its kspace_style +scafacos command in a LAMMPS input script. -And how to build, either via traditional make -and the Install.py script, or via CMake +The ScaFaCoS library is available at http://scafacos.de or +on github at https://github.com/scafacos, the libary was +developed by a consortium of different universities in +Germany (Bonn, Chemnitz, Stuttgart, Wuppertal) and +the Research Centre Juelich (Juelich Supercomputing Centre). +----------------- + +Instructions: + +1.) Download ScaFaCoS at http://scafacos.de or directly from github + https://github.com/scafacos where you can either clone the + repository or download the latest stable release. + NOTE: For the P2NFFT solver, you require an installation of the + GNU Scientific Library (GSL). Also to ensure the correct + linker-flags are used, ScaFaCoS employs the pkg-config + tool, which is also required. + If you cloned the repository, please refer to 2.), else continue + with 3.) + +2.) If you cloned the git repository, you require autotools to setup + the library. For that the following packages are required: + m4 + autotools + automake + libtools + In the build_aux folder of the scafacos folder, you can find the + get_autotools.sh script, that downloads and installs the tools + to ${HOME}/local. To change the target folder, please change the + value of 'myprefix' in that script. + To start the auto-configuration process, please run the './bootstrap' + command in the scafacos base-folder. + +3.) If you downloaded the library as a tarball, please extract the file + to somewhere in your file system, or if you finished running + './bootstrap', please run './configure' in the base folder. + Important flags for './configure' are: + --prefix=: sets the directory the compiled files will + be installed to [default: /usr/local] + --fcs-enable-solvers=: sets the list of solvers that are going to + be built. By default all solvers will be + built. Currently supported by the kspace in LAMMPS + are: direct, ewald, fmm, p2nfft + The other solvers might work, but support + is purely experimental at the moment. To + give a list of solvers, use a comma seperated + list. + --fcs-disable-doc: disables the compilation of the documentation, + e.g. if no Latex is available on the system. + +4.) To build the library after configuration, run 'make' from the base folder. + +5.) To install the libray in the designated installation folder, run 'make install'. + Installation is required, as ScaFaCoS does not support an in-source build! + +6.) Create two soft links to this directory (lib/scafacos) to where the libary + is installed. E.g. if you built ScaFaCoS in the default install directory: + % ln -s /usr/local/include includelink + % ln -s /usr/local/lib liblink + for any custom directory : + % ln -s /include includelink + % ln -s /lib liblink + +7.) ScaFaCoS uses the pkg-config tool to supply the correct, so you need to setup your + PKG_CONFIG_PATH environment variable to include the lib/pkgconfig folder in the + installation directory. + Depending on the shell you use, this can be done either by: + % export PKG_CONFIG_PATH=/lib/pkgconfig:${PKG_CONFIG_PATH} + or + % setenv PKG_CONFIG_PATH=/lib/pkgconfig:${PKG_CONFIG_PATH} + +----------------- diff --git a/src/USER-SCAFACOS/README b/src/USER-SCAFACOS/README index 30534499e4..42d2e2c0f7 100644 --- a/src/USER-SCAFACOS/README +++ b/src/USER-SCAFACOS/README @@ -1,5 +1,25 @@ -RENE: need a short README file - see other examples in the -USER package dirs within src +This package provides a kspace style which is a wrapper for the +ScaFaCoS long-range Coulomb solver library. The library provides +a selection of different long-range Coulomb solvers, which can be +used to calculate the Coloumic forces between charged particles. +More information about the ScaFaCoS library can be found on this +web site: http://scafacos.de. ScaFaCoS was designed and implemented +by a consortium of German universities (Bonn, Chemnitz, Stuttgart, +Wuppertal and others) and the Juelich Supercomputing Centre +(Forschungszentrum Juelich). -give short background on ScaFaCos, authors, contact info -for LAMMPS users to have if needed, citation +The use of the scafacos kspace requires the download and installation +of the library on the system. This can be done in lib/scafacos or +elsewhere in your system. Details of the download and build process +for ScaFaCoS are given in the lib/scafacos/README file and it can also +be done via the make lib-user-scafacos command from the LAMMPS +source directory. + +Once you have successfully built LAMMPS with this package and the +ScaFaCoS library, you can test it using an input file from the +examples scafacos dir, e.g.: + +lmp_serial -in lammps/examples/USER/scafacos/in.scafacos.fmm + +For questions about ScaFaCoS, please contact: +r.halver@fz-juelich.de or g.sutmann@fz-juelich.de From e8774dce9792d3289bcb2fbd8f722796af3ec675 Mon Sep 17 00:00:00 2001 From: Rene Halver Date: Fri, 3 Aug 2018 11:31:11 -0600 Subject: [PATCH 078/302] removed thread restriction on make command, should make the building process faster --- lib/scafacos/Install.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/scafacos/Install.py b/lib/scafacos/Install.py index c478589144..df82780438 100644 --- a/lib/scafacos/Install.py +++ b/lib/scafacos/Install.py @@ -147,7 +147,7 @@ if buildflag: if buildflag: print("Building Scafacos ...") - cmd = 'cd "%s"; CC=mpicc FC=mpif90 CXX=mpicxx ./configure --prefix="`pwd`/build" --disable-doc --enable-fcs-solvers=fmm,p2nfft,direct,ewald > log.txt; make -j 4; make install' % homedir + cmd = 'cd "%s"; CC=mpicc FC=mpif90 CXX=mpicxx ./configure --prefix="`pwd`/build" --disable-doc --enable-fcs-solvers=fmm,p2nfft,direct,ewald > log.txt; make -j; make install' % homedir txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) print(txt.decode('UTF-8')) From 94bf221258af6fa48fe568a21171c492148ccf71 Mon Sep 17 00:00:00 2001 From: Rene Halver Date: Fri, 3 Aug 2018 11:31:50 -0600 Subject: [PATCH 079/302] implemented checks for unsupported solvers --- src/USER-SCAFACOS/scafacos.cpp | 18 ++++++++++++++++-- 1 file changed, 16 insertions(+), 2 deletions(-) diff --git a/src/USER-SCAFACOS/scafacos.cpp b/src/USER-SCAFACOS/scafacos.cpp index 21e46f76ad..d4b106b26c 100644 --- a/src/USER-SCAFACOS/scafacos.cpp +++ b/src/USER-SCAFACOS/scafacos.cpp @@ -47,14 +47,26 @@ Scafacos::Scafacos(LAMMPS *lmp, int narg, char **arg) : KSpace(lmp, narg, arg) // optional ScaFaCoS library setting defaults // choose the correct default tolerance type for chosen method - // TODO: needs to be expanded for all solvers, currently mainly used ones + // throw an error if a not yet supported solver is chosen if (strcmp(method,"fmm") == 0) { tolerance_type = FCS_TOLERANCE_TYPE_ENERGY; fmm_tuning_flag = 0; } - else if (strcmp(method,"p3m") == 0 || strcmp(method,"p2nfft") == 0) + else if (strcmp(method,"p3m") == 0 || + strcmp(method,"p2nfft") == 0 || + strcmp(method,"ewald") == 0) + { tolerance_type = FCS_TOLERANCE_TYPE_FIELD; + } + else if (strcmp(method,"direct") == 0) + { + // direct summation has no tolerance type + } + else + { + error->all(FLERR,"Unsupported ScaFaCoS method"); + } // initializations @@ -194,11 +206,13 @@ void Scafacos::compute(int eflag, int vflag) fcs_set_compute_virial(fcs,1); } + /* if (strcmp(method,"p3m")==0) { result = fcs_tune(fcs,nlocal,&x[0][0],q); check_result(result); } + */ result = fcs_run(fcs,nlocal,&x[0][0],q,&efield[0][0],epot); check_result(result); From 446a8da8e7a0129875840bde675bbe77b3a22a4b Mon Sep 17 00:00:00 2001 From: Stefan Paquay Date: Mon, 6 Aug 2018 10:25:12 -0400 Subject: [PATCH 080/302] Commit before merge. --- src/lammps.cpp | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/src/lammps.cpp b/src/lammps.cpp index 56af95767b..d25d5473e8 100644 --- a/src/lammps.cpp +++ b/src/lammps.cpp @@ -249,7 +249,11 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) helpflag = 1; citeflag = 0; iarg += 1; - } else error->universe_all(FLERR,"Invalid command-line argument"); + } else { + char msg[2048]; + sprintf( msg, "Invalid command-line argument \"%s\"\n", arg[iarg] ); + error->universe_all(FLERR,msg); + } } // if no partition command-line switch, universe is one world with all procs From b97195d48f69d984005b81d33da4fc161e3806f8 Mon Sep 17 00:00:00 2001 From: Rene Halver Date: Mon, 6 Aug 2018 15:58:53 -0600 Subject: [PATCH 081/302] CMake: download ScaFaCoS, compile and link it - required resorting, as Fortran MPI is required --- cmake/CMakeLists.txt | 103 +++++++++++++++++++++++++++++++------------ 1 file changed, 75 insertions(+), 28 deletions(-) diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index 401bdca99c..b2cc7e613d 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -115,6 +115,34 @@ set(LAMMPS_LINK_LIBS) set(LAMMPS_DEPS) set(LAMMPS_API_DEFINES) +set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE GRANULAR + KSPACE MANYBODY MC MEAM MISC MOLECULE PERI REAX REPLICA RIGID SHOCK SPIN SNAP + SRD KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE USER-ATC USER-AWPMD USER-BOCS + USER-CGDNA USER-MESO USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE + USER-EFF USER-FEP USER-H5MD USER-LB USER-MANIFOLD USER-MEAMC USER-MGPT USER-MISC + USER-MOFFF USER-MOLFILE USER-NETCDF USER-PHONON USER-QTB USER-REAXC USER-SCAFACOS + USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM) +set(ACCEL_PACKAGES USER-OMP KOKKOS OPT USER-INTEL GPU) +set(OTHER_PACKAGES CORESHELL QEQ) +foreach(PKG ${DEFAULT_PACKAGES}) + option(PKG_${PKG} "Build ${PKG} Package" OFF) +endforeach() +foreach(PKG ${ACCEL_PACKAGES} ${OTHER_PACKAGES}) + option(PKG_${PKG} "Build ${PKG} Package" OFF) +endforeach() + +###################################################### +# packages with special compiler needs or external libs +###################################################### +if(PKG_REAX OR PKG_MEAM OR PKG_USER-QUIP OR PKG_USER-QMMM OR PKG_LATTE OR PKG_USER-SCAFACOS) + enable_language(Fortran) +endif() + +if(PKG_MEAM OR PKG_USER-H5MD OR PKG_USER-QMMM OR PKG_USER-SCAFACOS) + enable_language(C) +endif() + +# do MPI detection after language activation, if MPI for these language is required find_package(MPI QUIET) option(BUILD_MPI "Build MPI version" ${MPI_FOUND}) if(BUILD_MPI) @@ -154,22 +182,6 @@ if(ENABLE_TESTING) enable_testing() endif(ENABLE_TESTING) -set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE GRANULAR - KSPACE MANYBODY MC MEAM MISC MOLECULE PERI REAX REPLICA RIGID SHOCK SPIN SNAP - SRD KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE USER-ATC USER-AWPMD USER-BOCS - USER-CGDNA USER-MESO USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE - USER-EFF USER-FEP USER-H5MD USER-LB USER-MANIFOLD USER-MEAMC USER-MGPT USER-MISC - USER-MOFFF USER-MOLFILE USER-NETCDF USER-PHONON USER-QTB USER-REAXC USER-SCAFACOS - USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM) -set(ACCEL_PACKAGES USER-OMP KOKKOS OPT USER-INTEL GPU) -set(OTHER_PACKAGES CORESHELL QEQ) -foreach(PKG ${DEFAULT_PACKAGES}) - option(PKG_${PKG} "Build ${PKG} Package" OFF) -endforeach() -foreach(PKG ${ACCEL_PACKAGES} ${OTHER_PACKAGES}) - option(PKG_${PKG} "Build ${PKG} Package" OFF) -endforeach() - macro(pkg_depends PKG1 PKG2) if(PKG_${PKG1} AND NOT (PKG_${PKG2} OR BUILD_${PKG2})) message(FATAL_ERROR "${PKG1} package needs LAMMPS to be build with ${PKG2}") @@ -182,17 +194,7 @@ pkg_depends(MPIIO MPI) pkg_depends(USER-ATC MANYBODY) pkg_depends(USER-LB MPI) pkg_depends(USER-PHONON KSPACE) - -###################################################### -# packages with special compiler needs or external libs -###################################################### -if(PKG_REAX OR PKG_MEAM OR PKG_USER-QUIP OR PKG_USER-QMMM OR PKG_LATTE) - enable_language(Fortran) -endif() - -if(PKG_MEAM OR PKG_USER-H5MD OR PKG_USER-QMMM) - enable_language(C) -endif() +pkg_depends(USER-SCAFACOS MPI) find_package(OpenMP QUIET) option(BUILD_OMP "Build with OpenMP support" ${OpenMP_FOUND}) @@ -350,10 +352,55 @@ if(PKG_LATTE) endif() if(PKG_USER-SCAFACOS) + find_package(GSL REQUIRED) + option(DOWNLOAD_SCAFACOS "Download ScaFaCoS (instead of using the system's one)" OFF) + if(DOWNLOAD_SCAFACOS) + include(ExternalProject) + ExternalProject_Add(scafacos_build + URL https://github.com/scafacos/scafacos/releases/download/v1.0.0/scafacos-1.0.0.tar.gz + URL_MD5 c75d75d8a4cb9757faddb8b205a2b20f + CONFIGURE_COMMAND /configure --prefix= + --disable-doc + --enable-fcs-solvers=fmm,p2nfft,direct,ewald + FC=${CMAKE_MPI_Fortran_COMPILER} + CXX=${CMAKE_MPI_CXX_COMPILER} + CC=${CMAKE_MPI_C_COMPILER} + F77= + ) + ExternalProject_get_property(scafacos_build INSTALL_DIR) + set(SCAFACOS_BUILD_DIR ${INSTALL_DIR}) + set(SCAFACOS_INCLUDE_DIRS ${SCAFACOS_BUILD_DIR}/include) + list(APPEND LAMMPS_DEPS scafacos_build) + # list and order from pkg_config file of ScaFaCoS build + list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs.a) + list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_direct.a) + list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_ewald.a) + list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_fmm.a) + list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_p2nfft.a) + list(APPEND LAMMPS_LINK_LIBS ${GSL_LIBRARIES}) + #list(APPEND LAMMPS_LINK_LIBS gsl) + #list(APPEND LAMMPS_LINK_LIBS gslcblas) + list(APPEND LAMMPS_LINK_LIBS m) + list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_near.a) + list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_gridsort.a) + list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_resort.a) + list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_common.a) + list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_pnfft.a) + list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_pfft.a) + list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_fftw3_mpi.a) + list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_fftw3.a) + list(APPEND LAMMPS_LINK_LIBS ${MPI_Fortran_LIBRARIES}) + list(APPEND LAMMPS_LINK_LIBS ${MPI_C_LIBRARIES}) +# -L${libdir} -lfcs4fortran -lfcs -lfcs_direct -lfcs_ewald -lfcs_fmm -lfcs_p2nfft -lgsl -lgslcblas -lm -lfcs_near -lfcs_gridsort -lfcs_resort -lfcs_common -lfcs_pnfft -lfcs_pfft -lfcs_fftw3_mpi -lfcs_fftw3 -L/projects/opt/centos7/mpich/3.2-gcc_6.2.0/lib -L/projects/opt/centos7/gcc/6.2.0/packages/gcc-6.2.0/bin/../lib/gcc/x86_64-pc-linux-gnu/6.2.0 -L/projects/opt/centos7/gcc/6.2.0/packages/gcc-6.2.0/bin/../lib/gcc -L/projects/opt/centos7/gcc/6.2.0/packages/gcc-6.2.0/bin/../lib/gcc/x86_64-pc-linux-gnu/6.2.0/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/projects/opt/centos7/gcc/6.2.0/packages/gcc-6.2.0/bin/../lib/gcc/x86_64-pc-linux-gnu/6.2.0/../../.. -lmpifort -lmpi -lgfortran -lm -lquadmath +#libfcs4fortran.a libfcs_common.a libfcs_direct.la libfcs_fftw3.a libfcs_fftw3_mpi.la libfcs_gridsort.a libfcs_near.a libfcs_p2nfft.la libfcs_pnfft.a libfcs_resort.la +#libfcs4fortran.la libfcs_common.la libfcs_ewald.a libfcs_fftw3.la libfcs_fmm.a libfcs_gridsort.la libfcs_near.la libfcs_pfft.a libfcs_pnfft.la pkgconfig +#libfcs.a libfcs_direct.a libfcs_ewald.la libfcs_fftw3_mpi.a libfcs_fmm.la libfcs.la libfcs_p2nfft.a libfcs_pfft.la libfcs_resort.a + else() FIND_PACKAGE(PkgConfig REQUIRED) PKG_CHECK_MODULES(SCAFACOS scafacos) - include_directories(${SCAFACOS_INCLUDE_DIRS}) list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_LDFLAGS}) + endif() + include_directories(${SCAFACOS_INCLUDE_DIRS}) endif() if(PKG_USER-MOLFILE) From 953b2837739501df789721655447c6c14a6236f7 Mon Sep 17 00:00:00 2001 From: Rene Halver Date: Mon, 6 Aug 2018 15:59:46 -0600 Subject: [PATCH 082/302] updated URL for tarball download --- lib/scafacos/Install.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/lib/scafacos/Install.py b/lib/scafacos/Install.py index df82780438..4e00e805d1 100644 --- a/lib/scafacos/Install.py +++ b/lib/scafacos/Install.py @@ -29,8 +29,8 @@ make lib-scafacos args="-p $HOME/scafacos" # use existing Scafacos installation # settings -version = "scafacos-0.9" -url = "https://gigamove.rz.rwth-aachen.de/d/id/fTmrTm4EUAUSAp/dd/100" +version = "scafacos-1.0.0" +url = "https://github.com/scafacos/scafacos/releases/download/v1.0.0/scafacos-1.0.0.tar.gz" #url = "https://gigamove.rz.rwth-aachen.de/d/id/CTzyApN76MXMJ6/dd/100" % version # print error message or help From 0a27b7065b0476e1fc3c9834bf783a7278b4053d Mon Sep 17 00:00:00 2001 From: Rene Halver Date: Mon, 6 Aug 2018 16:01:39 -0600 Subject: [PATCH 083/302] bug fixes: ScaFaCoS returns virial as 9-value array, requires copies to Lammps 6-value array; fixed error in compuation of per-atom energy calculation --- src/USER-SCAFACOS/scafacos.cpp | 22 ++++++++++++++++++++-- src/USER-SCAFACOS/scafacos.h | 2 ++ 2 files changed, 22 insertions(+), 2 deletions(-) diff --git a/src/USER-SCAFACOS/scafacos.cpp b/src/USER-SCAFACOS/scafacos.cpp index d4b106b26c..27828b1da1 100644 --- a/src/USER-SCAFACOS/scafacos.cpp +++ b/src/USER-SCAFACOS/scafacos.cpp @@ -219,7 +219,25 @@ void Scafacos::compute(int eflag, int vflag) if (vflag_global) { - fcs_get_virial(fcs,virial); + fcs_get_virial(fcs,virial_int); + /* + printf(" %lf %lf %lf \n %lf %lf %lf \n %lf %lf %lf \n ", + virial_int[0], + virial_int[1], + virial_int[2], + virial_int[3], + virial_int[4], + virial_int[5], + virial_int[6], + virial_int[7], + virial_int[8]); + */ + virial[0] = virial_int[0]; + virial[1] = virial_int[1]; + virial[2] = virial_int[2]; + virial[3] = virial_int[4]; + virial[4] = virial_int[5]; + virial[5] = virial_int[8]; } // apply Efield to each particle @@ -240,7 +258,7 @@ void Scafacos::compute(int eflag, int vflag) if (eflag_atom) { for (int i = 0; i < nlocal; i++) - eatom[i] = qscale * epot[i]; + eatom[i] = 0.5 * qscale * q[i] * epot[i]; } MPI_Allreduce(&myeng,&energy,1,MPI_DOUBLE,MPI_SUM,world); diff --git a/src/USER-SCAFACOS/scafacos.h b/src/USER-SCAFACOS/scafacos.h index 857036bb7a..8f7c46dc6b 100644 --- a/src/USER-SCAFACOS/scafacos.h +++ b/src/USER-SCAFACOS/scafacos.h @@ -57,6 +57,8 @@ class Scafacos : public KSpace { fcs_int old_periodicity[3]; fcs_int old_natoms; + fcs_float virial_int[9]; + void check_result(FCSResult); void setup_handle(); bool box_has_changed(); From ba693a74be0b785818ae592d82daf0282871ebb0 Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Tue, 7 Aug 2018 12:27:32 -0600 Subject: [PATCH 084/302] Add contribute method to pair_table_kokkos --- src/KOKKOS/pair_table_kokkos.cpp | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/src/KOKKOS/pair_table_kokkos.cpp b/src/KOKKOS/pair_table_kokkos.cpp index 7b06f814bb..b72df04c5f 100644 --- a/src/KOKKOS/pair_table_kokkos.cpp +++ b/src/KOKKOS/pair_table_kokkos.cpp @@ -128,21 +128,25 @@ void PairTableKokkos::compute_style(int eflag_in, int vflag_in) ff(this,(NeighListKokkos*) list); if (eflag || vflag) Kokkos::parallel_reduce(list->inum,ff,ev); else Kokkos::parallel_for(list->inum,ff); + ff.contribute(); } else if (neighflag == HALFTHREAD) { PairComputeFunctor,HALFTHREAD,false,S_TableCompute > ff(this,(NeighListKokkos*) list); if (eflag || vflag) Kokkos::parallel_reduce(list->inum,ff,ev); else Kokkos::parallel_for(list->inum,ff); + ff.contribute(); } else if (neighflag == HALF) { PairComputeFunctor,HALF,false,S_TableCompute > f(this,(NeighListKokkos*) list); if (eflag || vflag) Kokkos::parallel_reduce(list->inum,f,ev); else Kokkos::parallel_for(list->inum,f); + f.contribute(); } else if (neighflag == N2) { PairComputeFunctor,N2,false,S_TableCompute > f(this,(NeighListKokkos*) list); if (eflag || vflag) Kokkos::parallel_reduce(list->inum,f,ev); else Kokkos::parallel_for(list->inum,f); + f.contribute(); } } else { if (neighflag == FULL) { @@ -150,21 +154,25 @@ void PairTableKokkos::compute_style(int eflag_in, int vflag_in) f(this,(NeighListKokkos*) list); if (eflag || vflag) Kokkos::parallel_reduce(list->inum,f,ev); else Kokkos::parallel_for(list->inum,f); + f.contribute(); } else if (neighflag == HALFTHREAD) { PairComputeFunctor,HALFTHREAD,true,S_TableCompute > f(this,(NeighListKokkos*) list); if (eflag || vflag) Kokkos::parallel_reduce(list->inum,f,ev); else Kokkos::parallel_for(list->inum,f); + f.contribute(); } else if (neighflag == HALF) { PairComputeFunctor,HALF,true,S_TableCompute > f(this,(NeighListKokkos*) list); if (eflag || vflag) Kokkos::parallel_reduce(list->inum,f,ev); else Kokkos::parallel_for(list->inum,f); + f.contribute(); } else if (neighflag == N2) { PairComputeFunctor,N2,true,S_TableCompute > f(this,(NeighListKokkos*) list); if (eflag || vflag) Kokkos::parallel_reduce(list->inum,f,ev); else Kokkos::parallel_for(list->inum,f); + f.contribute(); } } From a944d1c913350cbe4378637a5f458b251bc5334e Mon Sep 17 00:00:00 2001 From: Rene Halver Date: Tue, 7 Aug 2018 14:26:53 -0600 Subject: [PATCH 085/302] fixed missing REQUIRED and introduced the compilation of internal sub-libraries (FFTW,PFFT,PNFFT) --- cmake/CMakeLists.txt | 14 ++++++-------- 1 file changed, 6 insertions(+), 8 deletions(-) diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index b2cc7e613d..0ec2d2086c 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -361,7 +361,10 @@ if(PKG_USER-SCAFACOS) URL_MD5 c75d75d8a4cb9757faddb8b205a2b20f CONFIGURE_COMMAND /configure --prefix= --disable-doc - --enable-fcs-solvers=fmm,p2nfft,direct,ewald + --enable-fcs-solvers=fmm,p2nfft,direct,ewald,p3m + --with-internal-fftw + --with-internal-pfft + --with-internal-pnfft FC=${CMAKE_MPI_Fortran_COMPILER} CXX=${CMAKE_MPI_CXX_COMPILER} CC=${CMAKE_MPI_C_COMPILER} @@ -377,9 +380,8 @@ if(PKG_USER-SCAFACOS) list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_ewald.a) list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_fmm.a) list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_p2nfft.a) + list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_p3m.a) list(APPEND LAMMPS_LINK_LIBS ${GSL_LIBRARIES}) - #list(APPEND LAMMPS_LINK_LIBS gsl) - #list(APPEND LAMMPS_LINK_LIBS gslcblas) list(APPEND LAMMPS_LINK_LIBS m) list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_near.a) list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_gridsort.a) @@ -391,13 +393,9 @@ if(PKG_USER-SCAFACOS) list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_fftw3.a) list(APPEND LAMMPS_LINK_LIBS ${MPI_Fortran_LIBRARIES}) list(APPEND LAMMPS_LINK_LIBS ${MPI_C_LIBRARIES}) -# -L${libdir} -lfcs4fortran -lfcs -lfcs_direct -lfcs_ewald -lfcs_fmm -lfcs_p2nfft -lgsl -lgslcblas -lm -lfcs_near -lfcs_gridsort -lfcs_resort -lfcs_common -lfcs_pnfft -lfcs_pfft -lfcs_fftw3_mpi -lfcs_fftw3 -L/projects/opt/centos7/mpich/3.2-gcc_6.2.0/lib -L/projects/opt/centos7/gcc/6.2.0/packages/gcc-6.2.0/bin/../lib/gcc/x86_64-pc-linux-gnu/6.2.0 -L/projects/opt/centos7/gcc/6.2.0/packages/gcc-6.2.0/bin/../lib/gcc -L/projects/opt/centos7/gcc/6.2.0/packages/gcc-6.2.0/bin/../lib/gcc/x86_64-pc-linux-gnu/6.2.0/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/projects/opt/centos7/gcc/6.2.0/packages/gcc-6.2.0/bin/../lib/gcc/x86_64-pc-linux-gnu/6.2.0/../../.. -lmpifort -lmpi -lgfortran -lm -lquadmath -#libfcs4fortran.a libfcs_common.a libfcs_direct.la libfcs_fftw3.a libfcs_fftw3_mpi.la libfcs_gridsort.a libfcs_near.a libfcs_p2nfft.la libfcs_pnfft.a libfcs_resort.la -#libfcs4fortran.la libfcs_common.la libfcs_ewald.a libfcs_fftw3.la libfcs_fmm.a libfcs_gridsort.la libfcs_near.la libfcs_pfft.a libfcs_pnfft.la pkgconfig -#libfcs.a libfcs_direct.a libfcs_ewald.la libfcs_fftw3_mpi.a libfcs_fmm.la libfcs.la libfcs_p2nfft.a libfcs_pfft.la libfcs_resort.a else() FIND_PACKAGE(PkgConfig REQUIRED) - PKG_CHECK_MODULES(SCAFACOS scafacos) + PKG_CHECK_MODULES(SCAFACOS scafacos REQUIRED) list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_LDFLAGS}) endif() include_directories(${SCAFACOS_INCLUDE_DIRS}) From cdde51d8af3d38679fbd311e942fd94359305560 Mon Sep 17 00:00:00 2001 From: Rene Halver Date: Tue, 7 Aug 2018 14:29:04 -0600 Subject: [PATCH 086/302] fixed example so that P3M also works, changed tolerance type in the FMM example --- examples/USER/scafacos/data.NaCl | 22 +++++++++++----------- examples/USER/scafacos/in.scafacos.fmm | 2 +- 2 files changed, 12 insertions(+), 12 deletions(-) diff --git a/examples/USER/scafacos/data.NaCl b/examples/USER/scafacos/data.NaCl index 23807e23d5..2fd6077983 100644 --- a/examples/USER/scafacos/data.NaCl +++ b/examples/USER/scafacos/data.NaCl @@ -4,9 +4,9 @@ LAMMPS Description 2 atom types -0 2 xlo xhi -0 2 ylo yhi -0 2 zlo zhi +0 1 xlo xhi +0 1 ylo yhi +0 1 zlo zhi Masses @@ -15,11 +15,11 @@ Masses Atoms -1 2 1 0 0 0 -2 1 -1 1 0 0 -3 1 -1 0 1 0 -4 2 1 1 1 0 -5 1 -1 0 0 1 -6 2 1 1 0 1 -7 2 1 0 1 1 -8 1 -1 1 1 1 +1 2 1 0.25 0.25 0.25 +2 1 -1 0.75 0.25 0.25 +3 1 -1 0.25 0.75 0.25 +4 2 1 0.75 0.75 0.25 +5 1 -1 0.25 0.25 0.75 +6 2 1 0.75 0.25 0.75 +7 2 1 0.25 0.75 0.75 +8 1 -1 0.75 0.75 0.75 diff --git a/examples/USER/scafacos/in.scafacos.fmm b/examples/USER/scafacos/in.scafacos.fmm index 18d7464fb8..054188ede2 100644 --- a/examples/USER/scafacos/in.scafacos.fmm +++ b/examples/USER/scafacos/in.scafacos.fmm @@ -29,7 +29,7 @@ pair_coeff * * #fix 2 all scafacos p3m tolerance field 0.001 kspace_style scafacos fmm 0.001 -kspace_modify scafacos tolerance energy_rel +kspace_modify scafacos tolerance energy timestep 0.005 thermo 10 From eb86ec3eea994ad1828f5db9b7e2db11ba5ff91b Mon Sep 17 00:00:00 2001 From: Rene Halver Date: Tue, 7 Aug 2018 15:03:48 -0600 Subject: [PATCH 087/302] added support for p3m, added check for compatible tolerance / method combinations (should they not be caught by ScaFaCoS itself) --- src/USER-SCAFACOS/scafacos.cpp | 80 ++++++++++++++++++++++------------ 1 file changed, 51 insertions(+), 29 deletions(-) diff --git a/src/USER-SCAFACOS/scafacos.cpp b/src/USER-SCAFACOS/scafacos.cpp index 27828b1da1..fdbd5e34e0 100644 --- a/src/USER-SCAFACOS/scafacos.cpp +++ b/src/USER-SCAFACOS/scafacos.cpp @@ -96,10 +96,13 @@ Scafacos::~Scafacos() void Scafacos::init() { // error checks - if (screen && me == 0) fprintf(screen,"Setting up ScaFaCoS with solver %s ...\n",method); - if (logfile && me == 0) fprintf(logfile,"Setting up ScaFaCoS with solver %s ...\n",method); + if (screen && me == 0) fprintf(screen, + "Setting up ScaFaCoS with solver %s ...\n",method); + if (logfile && me == 0) fprintf(logfile, + "Setting up ScaFaCoS with solver %s ...\n",method); - if (!atom->q_flag) error->all(FLERR,"Kspace style requires atom attribute q"); + if (!atom->q_flag) error->all(FLERR, + "Kspace style requires atom attribute q"); if (domain->dimension == 2) error->all(FLERR,"Cannot use ScaFaCoS with 2d simulation"); @@ -111,7 +114,8 @@ void Scafacos::init() error->all(FLERR,"Scafacos atom count exceeds 2B"); if (atom->molecular > 0) - error->all(FLERR,"Cannot use Scafacos with molecular charged systems yet"); + error->all(FLERR, + "Cannot use Scafacos with molecular charged systems yet"); // one-time initialization of ScaFaCoS @@ -204,34 +208,16 @@ void Scafacos::compute(int eflag, int vflag) if (vflag_global) { fcs_set_compute_virial(fcs,1); + if (strcmp(method,"p3m") == 0) + error->all(FLERR,"ScaFaCoS p3m does not support the computation of virial"); } - /* - if (strcmp(method,"p3m")==0) - { - result = fcs_tune(fcs,nlocal,&x[0][0],q); - check_result(result); - } - */ - result = fcs_run(fcs,nlocal,&x[0][0],q,&efield[0][0],epot); check_result(result); if (vflag_global) { fcs_get_virial(fcs,virial_int); - /* - printf(" %lf %lf %lf \n %lf %lf %lf \n %lf %lf %lf \n ", - virial_int[0], - virial_int[1], - virial_int[2], - virial_int[3], - virial_int[4], - virial_int[5], - virial_int[6], - virial_int[7], - virial_int[8]); - */ virial[0] = virial_int[0]; virial[1] = virial_int[1]; virial[2] = virial_int[2]; @@ -277,7 +263,8 @@ int Scafacos::modify_param(int narg, char **arg) if (strcmp(arg[0],"scafacos") != 0) return 0; if (strcmp(arg[1],"tolerance") == 0) { - if (narg < 3) error->all(FLERR,"Illegal kspace_modify command (tolerance)"); + if (narg < 3) error->all(FLERR, + "Illegal kspace_modify command (tolerance)"); if (strcmp(arg[2],"energy") == 0) tolerance_type = FCS_TOLERANCE_TYPE_ENERGY; else if (strcmp(arg[2],"energy_rel") == 0) @@ -290,7 +277,39 @@ int Scafacos::modify_param(int narg, char **arg) tolerance_type = FCS_TOLERANCE_TYPE_POTENTIAL; else if (strcmp(arg[2],"potential_rel") == 0) tolerance_type = FCS_TOLERANCE_TYPE_POTENTIAL_REL; - else error->all(FLERR,"Illegal kspace_modify command (tolerance argument)"); + else error->all(FLERR, + "Illegal kspace_modify command (tolerance argument)"); + // check if method is compatatible to chosen tolerance type + if( + ( + strcmp(method,"fmm") == 0 && + ( + tolerance_type != FCS_TOLERANCE_TYPE_ENERGY && + tolerance_type != FCS_TOLERANCE_TYPE_ENERGY_REL + ) + ) && + ( + strcmp(method,"p2nfft") == 0 && + ( + tolerance_type != FCS_TOLERANCE_TYPE_FIELD && + tolerance_type != FCS_TOLERANCE_TYPE_POTENTIAL + ) + ) && + ( + strcmp(method,"p3m") == 0 && + ( + tolerance_type != FCS_TOLERANCE_TYPE_FIELD + ) + ) && + ( + strcmp(method,"ewald") == 0 && + ( + tolerance_type != FCS_TOLERANCE_TYPE_FIELD + ) + ) + ) + error->all(FLERR,"Illegal kspace_modify command \ + (invalid tolerance / method combination)"); return 3; } @@ -300,9 +319,12 @@ int Scafacos::modify_param(int narg, char **arg) // 1 -> inhomogenous system (more internal tuning is provided (sequential!)) if (strcmp(arg[1],"fmm_tuning") == 0) { - if (screen && me == 0) fprintf(screen,"ScaFaCoS setting fmm inhomogen tuning ...\n"); - if (logfile && me == 0) fprintf(logfile,"ScaFaCoS setting fmm inhomogen tuning ...\n"); - if (narg < 3) error->all(FLERR,"Illegal kspace_modify command (fmm_tuning)"); + if (screen && me == 0) fprintf(screen, + "ScaFaCoS setting fmm inhomogen tuning ...\n"); + if (logfile && me == 0) fprintf(logfile, + "ScaFaCoS setting fmm inhomogen tuning ...\n"); + if (narg < 3) error->all(FLERR, + "Illegal kspace_modify command (fmm_tuning)"); fmm_tuning_flag = atoi(arg[2]); return 3; } From 48fd8b46ee49b8b56d0c9470a4114091b2d7a25b Mon Sep 17 00:00:00 2001 From: Rene Halver Date: Tue, 7 Aug 2018 15:04:37 -0600 Subject: [PATCH 088/302] cleaned documentation, added p3m entry for allowed tolerance type --- doc/src/kspace_modify.txt | 15 +++------------ doc/src/kspace_style.txt | 1 + 2 files changed, 4 insertions(+), 12 deletions(-) diff --git a/doc/src/kspace_modify.txt b/doc/src/kspace_modify.txt index 57cff18d7e..b05bd6dccb 100644 --- a/doc/src/kspace_modify.txt +++ b/doc/src/kspace_modify.txt @@ -346,17 +346,12 @@ the per-atom electric field, this effectively sets a tolerance on the forces, simimlar to other LAMMPS KSpace styles, as explained on the "kspace_style"_kspace_style.html doc page. -RENE: Also, can you explain more what is the difference between energy -(total) and potential (per-atom)? Which one is more vs less accurate? -Does potential mean that the maximum of any atom's energy error is < -tolerance? I.e. it is a max across all per-atom values? Ditto for -field, since it is computed on a per-atom basis? - Note that not all ScaFaCoS solvers support all tolerance types. These are the allowed values for each method: fmm = energy and energy_rel p2nfft = field (1d-,2d-,3d-periodic systems) or potential (0d-periodic) +p3m = field ewald = field direct = has no tolerance tuning :ul @@ -364,17 +359,13 @@ If the tolerance type is not changed, the default values for the tolerance type are the first values in the above list, e.g. energy is the default tolerance type for the fmm solver. -RENE: Does the code (LAMMPS or Scafacos) generate an error -if an unsupported tolerance is specified for a method? - The {fmm_tuning} option is only relevant when using the FMM method. It activates (value=1) or deactivates (value=0) an internal tuning mechanism for the FMM solver. The tuning operation runs sequentially and can be very time-consuming. Usually it is not needed for systems with a homogenous charge distribution. The default for this option is -therefore {0}. - -RENE: is the tuning a one-time (start-up) operation if enabled? +therefore {0}. The FMM internal tuning is performed once, when the +solver is set up. :line diff --git a/doc/src/kspace_style.txt b/doc/src/kspace_style.txt index cff196ed69..9e26f8e2e4 100644 --- a/doc/src/kspace_style.txt +++ b/doc/src/kspace_style.txt @@ -251,6 +251,7 @@ These are the ScaFaCoS methods currently available from LAMMPS: {p2nfft} = FFT-based Coulomb solver {ewald} = Ewald summation {direct} = direct O(N^2) summation +{p3m} = PPPM We plan to support additional ScaFaCoS solvers from LAMMPS in the future. For an overview of the included solvers, refer to From 7f5476b4081eccbf6f9ddf398ea3f46e92204535 Mon Sep 17 00:00:00 2001 From: Rene Halver Date: Wed, 8 Aug 2018 14:04:41 -0600 Subject: [PATCH 089/302] removed deprecated log files (will be replaced with more current ones) --- .../log.23Jul18.scafacos.cw.g++.ewald.16 | 92 --------------- .../log.23Jul18.scafacos.cw.g++.ewald.8 | 92 --------------- .../log.23Jul18.scafacos.cw.g++.fmm.1 | 99 ---------------- .../log.23Jul18.scafacos.cw.g++.fmm.16 | 99 ---------------- .../log.23Jul18.scafacos.cw.g++.fmm.2 | 99 ---------------- .../log.23Jul18.scafacos.cw.g++.fmm.4 | 99 ---------------- .../log.23Jul18.scafacos.cw.g++.fmm.8 | 99 ---------------- .../log.23Jul18.scafacos.cw.g++.p2nfft.1 | 92 --------------- .../log.23Jul18.scafacos.cw.g++.p2nfft.16 | 92 --------------- .../log.23Jul18.scafacos.cw.g++.p2nfft.2 | 92 --------------- .../log.23Jul18.scafacos.cw.g++.p2nfft.4 | 92 --------------- .../log.23Jul18.scafacos.cw.g++.p2nfft.8 | 92 --------------- .../log.23Jul18.scafacos.g++.ewald.16 | 102 ---------------- .../scafacos/log.23Jul18.scafacos.g++.ewald.8 | 102 ---------------- .../scafacos/log.23Jul18.scafacos.g++.fmm.1 | 102 ---------------- .../scafacos/log.23Jul18.scafacos.g++.fmm.16 | 102 ---------------- .../scafacos/log.23Jul18.scafacos.g++.fmm.2 | 102 ---------------- .../scafacos/log.23Jul18.scafacos.g++.fmm.4 | 102 ---------------- .../scafacos/log.23Jul18.scafacos.g++.fmm.8 | 102 ---------------- .../log.23Jul18.scafacos.g++.p2nfft.1 | 102 ---------------- .../log.23Jul18.scafacos.g++.p2nfft.16 | 102 ---------------- .../log.23Jul18.scafacos.g++.p2nfft.2 | 102 ---------------- .../log.23Jul18.scafacos.g++.p2nfft.4 | 102 ---------------- .../log.23Jul18.scafacos.g++.p2nfft.8 | 102 ---------------- .../log.23Jul18.scafacos.hsph.g++.direct.1 | 105 ----------------- .../log.23Jul18.scafacos.hsph.g++.direct.2 | 105 ----------------- .../log.23Jul18.scafacos.hsph.g++.direct.4 | 105 ----------------- .../log.23Jul18.scafacos.hsph.g++.direct.8 | 105 ----------------- .../log.23Jul18.scafacos.hsph.g++.fmm.1 | 109 ------------------ .../log.23Jul18.scafacos.hsph.g++.fmm.2 | 109 ------------------ .../log.23Jul18.scafacos.hsph.g++.fmm.4 | 109 ------------------ .../log.23Jul18.scafacos.hsph.g++.fmm.8 | 109 ------------------ .../log.23Jul18.scafacos.hsph.g++.p2nfft.1 | 107 ----------------- .../log.23Jul18.scafacos.hsph.g++.p2nfft.2 | 107 ----------------- .../log.23Jul18.scafacos.hsph.g++.p2nfft.4 | 107 ----------------- .../log.23Jul18.scafacos.hsph.g++.p2nfft.8 | 107 ----------------- 36 files changed, 3647 deletions(-) delete mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.ewald.16 delete mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.ewald.8 delete mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.1 delete mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.16 delete mode 100644 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100644 examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.fmm.4 delete mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.fmm.8 delete mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.p2nfft.1 delete mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.p2nfft.2 delete mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.p2nfft.4 delete mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.p2nfft.8 diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.ewald.16 b/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.ewald.16 deleted file mode 100644 index ffdc7e3a3c..0000000000 --- a/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.ewald.16 +++ /dev/null @@ -1,92 +0,0 @@ -LAMMPS (29 Jun 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) - using 1 OpenMP thread(s) per MPI task - -units lj -atom_style charge - -read_data data.cloud_wall - orthogonal box = (0 0 0) to (10 10 10) - 2 by 2 by 4 MPI processor grid - reading atoms ... - 300 atoms - -velocity all set 0.0 0.0 0.0 mom no - -pair_style zero 1.0 -pair_coeff * * - -neighbor 1.0 bin -neigh_modify delay 0 - -fix 1 all nve -kspace_style scafacos ewald 0.001 -kspace_modify scafacos tolerance field - -timestep 0.005 - -thermo_style custom step atoms cpu temp pe ke etotal ecoul - -run_style verlet - -#dump simple all custom 1000 id x y z vx vy vz -#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass -#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass -#dump_modify dmpvtk pad 7 - -thermo 10 -run 100 -Setting up ScaFaCoS with solver ewald ... -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2 - ghost atom cutoff = 2 - binsize = 1, bins = 10 10 10 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair zero, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.313 | 3.501 | 3.689 Mbytes -Step Atoms CPU Temp PotEng KinEng TotEng E_coul - 0 300 0 0 0.49647271 0 0.49647271 0 - 10 300 0.061254978 0.014582562 0.44286522 0.02180093 0.46466616 0 - 20 300 0.12240911 0.058693359 0.37869251 0.087746571 0.46643909 0 - 30 300 0.18348265 0.13468789 0.26730177 0.2013584 0.46866017 0 - 40 300 0.24441123 0.50949535 0.083356437 0.76169555 0.84505198 0 - 50 300 0.30493236 1.1731116 -0.055261984 1.7538018 1.6985399 0 - 60 300 0.36615515 1.3589639 -0.33351524 2.031651 1.6981358 0 - 70 300 0.42717433 1.6482648 -0.76570045 2.4641559 1.6984554 0 - 80 300 0.48137259 2.8640899 -2.4038488 4.2818144 1.8779656 0 - 90 300 0.5323379 93.168442 -2.5911448 139.28682 136.69568 0 - 100 300 0.5756321 94.146897 -1.3480439 140.74961 139.40157 0 -Loop time of 0.575655 on 16 procs for 100 steps with 300 atoms - -Performance: 75045.007 tau/day, 173.715 timesteps/s -98.7% CPU use with 16 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 1.2159e-05 | 1.739e-05 | 2.3127e-05 | 0.0 | 0.00 -Kspace | 0.57008 | 0.57086 | 0.57137 | 0.1 | 99.17 -Neigh | 0.00025606 | 0.00061357 | 0.001369 | 0.0 | 0.11 -Comm | 0.0023558 | 0.0027267 | 0.003104 | 0.4 | 0.47 -Output | 0.00029898 | 0.00032344 | 0.00037599 | 0.0 | 0.06 -Modify | 8.2493e-05 | 0.00014143 | 0.00021815 | 0.0 | 0.02 -Other | | 0.0009701 | | | 0.17 - -Nlocal: 18.75 ave 39 max 6 min -Histogram: 6 1 1 0 1 2 2 1 1 1 -Nghost: 122.812 ave 195 max 63 min -Histogram: 8 0 0 0 0 0 0 1 3 4 -Neighs: 160.625 ave 598 max 13 min -Histogram: 8 2 1 1 1 0 0 2 0 1 - -Total # of neighbors = 2570 -Ave neighs/atom = 8.56667 -Neighbor list builds = 23 -Dangerous builds = 16 -Total wall time: 0:00:00 diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.ewald.8 b/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.ewald.8 deleted file mode 100644 index 52d887f475..0000000000 --- a/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.ewald.8 +++ /dev/null @@ -1,92 +0,0 @@ -LAMMPS (29 Jun 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) - using 1 OpenMP thread(s) per MPI task - -units lj -atom_style charge - -read_data data.cloud_wall - orthogonal box = (0 0 0) to (10 10 10) - 2 by 2 by 2 MPI processor grid - reading atoms ... - 300 atoms - -velocity all set 0.0 0.0 0.0 mom no - -pair_style zero 1.0 -pair_coeff * * - -neighbor 1.0 bin -neigh_modify delay 0 - -fix 1 all nve -kspace_style scafacos ewald 0.001 -kspace_modify scafacos tolerance field - -timestep 0.005 - -thermo_style custom step atoms cpu temp pe ke etotal ecoul - -run_style verlet - -#dump simple all custom 1000 id x y z vx vy vz -#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass -#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass -#dump_modify dmpvtk pad 7 - -thermo 10 -run 100 -Setting up ScaFaCoS with solver ewald ... -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2 - ghost atom cutoff = 2 - binsize = 1, bins = 10 10 10 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair zero, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.317 | 3.317 | 3.317 Mbytes -Step Atoms CPU Temp PotEng KinEng TotEng E_coul - 0 300 0 0 0.49647271 0 0.49647271 0 - 10 300 0.067519665 0.014718629 0.45088339 0.02200435 0.47288774 0 - 20 300 0.13502312 0.05922597 0.38470912 0.088542825 0.47325194 0 - 30 300 0.20248008 0.13587829 0.27058048 0.20313804 0.47371852 0 - 40 300 0.26985955 0.51353118 0.088432648 0.76772911 0.85616176 0 - 50 300 0.33801103 1.1760001 -0.058088247 1.7581201 1.7000319 0 - 60 300 0.40665984 1.3627885 -0.33736672 2.0373688 1.7000021 0 - 70 300 0.47533679 1.6529365 -0.77082139 2.4711401 1.7003187 0 - 80 300 0.54396391 2.9569837 -2.4624654 4.4206907 1.9582253 0 - 90 300 0.61429667 81.642726 -2.5370215 122.05588 119.51885 0 - 100 300 0.68513632 85.047974 -1.128107 127.14672 126.01861 0 -Loop time of 0.685155 on 8 procs for 100 steps with 300 atoms - -Performance: 63051.442 tau/day, 145.952 timesteps/s -99.7% CPU use with 8 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 1.0967e-05 | 1.4216e-05 | 1.8358e-05 | 0.0 | 0.00 -Kspace | 0.67942 | 0.67981 | 0.6803 | 0.0 | 99.22 -Neigh | 0.00073242 | 0.0010653 | 0.0015635 | 0.8 | 0.16 -Comm | 0.0029492 | 0.0031102 | 0.0033047 | 0.2 | 0.45 -Output | 0.00021768 | 0.00023454 | 0.00028443 | 0.0 | 0.03 -Modify | 0.00016046 | 0.00018132 | 0.00019431 | 0.0 | 0.03 -Other | | 0.0007433 | | | 0.11 - -Nlocal: 37.5 ave 46 max 31 min -Histogram: 2 0 0 2 1 0 2 0 0 1 -Nghost: 203.875 ave 212 max 192 min -Histogram: 1 0 1 0 0 2 1 0 0 3 -Neighs: 321.625 ave 599 max 112 min -Histogram: 1 2 0 1 1 0 1 1 0 1 - -Total # of neighbors = 2573 -Ave neighs/atom = 8.57667 -Neighbor list builds = 23 -Dangerous builds = 16 -Total wall time: 0:00:00 diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.1 b/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.1 deleted file mode 100644 index 47e0be01ce..0000000000 --- a/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.1 +++ /dev/null @@ -1,99 +0,0 @@ -LAMMPS (29 Jun 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) - using 1 OpenMP thread(s) per MPI task -units lj -atom_style charge - -read_data data.cloud_wall - orthogonal box = (0 0 0) to (10 10 10) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 300 atoms - -velocity all set 0.0 0.0 0.0 mom no - -pair_style zero 1.0 -pair_coeff * * - -neighbor 1.0 bin -neigh_modify delay 0 - -fix 1 all nve - - -#pair_style coul/long 3.0 -#pair_coeff * * -#kspace_style pppm 1.0e-3 - -kspace_style scafacos fmm 1.0e-3 -kspace_modify scafacos tolerance energy_rel -kspace_modify scafacos fmm_tuning 1 -ScaFaCoS setting fmm inhomogen tuning ...3 - -timestep 0.005 - -thermo_style custom step atoms cpu temp pe ke etotal ecoul - -run_style verlet - -#dump simple all custom 1000 id x y z vx vy vz -#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass -#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass -#dump_modify dmpvtk pad 7 - -thermo 10 -run 100 -Setting up ScaFaCoS with solver fmm ... -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2 - ghost atom cutoff = 2 - binsize = 1, bins = 10 10 10 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair zero, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.34 | 3.34 | 3.34 Mbytes -Step Atoms CPU Temp PotEng KinEng TotEng E_coul - 0 300 0 0 0.49646402 0 0.49646402 0 - 10 300 0.036603451 0.015455559 0.47335833 0.02310606 0.49646439 0 - 20 300 0.073534727 0.06229069 0.40334177 0.093124582 0.49646635 0 - 30 300 0.10984373 0.14310163 0.28254277 0.21393694 0.49647971 0 - 40 300 0.14610171 0.52929788 0.089669015 0.79130033 0.88096934 0 - 50 300 0.18255496 1.1963022 -0.082792461 1.7884718 1.7056794 0 - 60 300 0.2194376 1.3928167 -0.37659239 2.082261 1.7056686 0 - 70 300 0.25588369 1.7069009 -0.84571914 2.5518169 1.7060978 0 - 80 300 0.29101205 15.358343 -3.368063 22.960722 19.592659 0 - 90 300 0.32697225 42.280432 -2.1623864 63.209247 61.04686 0 - 100 300 0.36395645 41.48079 -0.89904529 62.013782 61.114736 0 -Loop time of 0.363968 on 1 procs for 100 steps with 300 atoms - -Performance: 118691.709 tau/day, 274.749 timesteps/s -99.8% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 1.2875e-05 | 1.2875e-05 | 1.2875e-05 | 0.0 | 0.00 -Kspace | 0.35715 | 0.35715 | 0.35715 | 0.0 | 98.13 -Neigh | 0.0039768 | 0.0039768 | 0.0039768 | 0.0 | 1.09 -Comm | 0.0012023 | 0.0012023 | 0.0012023 | 0.0 | 0.33 -Output | 0.0001502 | 0.0001502 | 0.0001502 | 0.0 | 0.04 -Modify | 0.0009768 | 0.0009768 | 0.0009768 | 0.0 | 0.27 -Other | | 0.0005031 | | | 0.14 - -Nlocal: 300 ave 300 max 300 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 374 ave 374 max 374 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 2459 ave 2459 max 2459 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 2459 -Ave neighs/atom = 8.19667 -Neighbor list builds = 15 -Dangerous builds = 0 -Total wall time: 0:00:00 diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.16 b/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.16 deleted file mode 100644 index f104355d87..0000000000 --- a/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.16 +++ /dev/null @@ -1,99 +0,0 @@ -LAMMPS (29 Jun 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) - using 1 OpenMP thread(s) per MPI task -units lj -atom_style charge - -read_data data.cloud_wall - orthogonal box = (0 0 0) to (10 10 10) - 2 by 2 by 4 MPI processor grid - reading atoms ... - 300 atoms - -velocity all set 0.0 0.0 0.0 mom no - -pair_style zero 1.0 -pair_coeff * * - -neighbor 1.0 bin -neigh_modify delay 0 - -fix 1 all nve - - -#pair_style coul/long 3.0 -#pair_coeff * * -#kspace_style pppm 1.0e-3 - -kspace_style scafacos fmm 1.0e-3 -kspace_modify scafacos tolerance energy_rel -kspace_modify scafacos fmm_tuning 1 -ScaFaCoS setting fmm inhomogen tuning ...3 - -timestep 0.005 - -thermo_style custom step atoms cpu temp pe ke etotal ecoul - -run_style verlet - -#dump simple all custom 1000 id x y z vx vy vz -#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass -#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass -#dump_modify dmpvtk pad 7 - -thermo 10 -run 100 -Setting up ScaFaCoS with solver fmm ... -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2 - ghost atom cutoff = 2 - binsize = 1, bins = 10 10 10 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair zero, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.313 | 3.501 | 3.689 Mbytes -Step Atoms CPU Temp PotEng KinEng TotEng E_coul - 0 300 0 0 0.49646402 0 0.49646402 0 - 10 300 0.018873215 0.015455559 0.47335833 0.02310606 0.49646439 0 - 20 300 0.035197735 0.06229069 0.40334177 0.093124582 0.49646635 0 - 30 300 0.051513195 0.14310163 0.28254277 0.21393694 0.49647971 0 - 40 300 0.067400217 0.52929788 0.089669015 0.79130033 0.88096934 0 - 50 300 0.083569527 1.1963022 -0.082792461 1.7884718 1.7056794 0 - 60 300 0.099931955 1.3928167 -0.37659239 2.082261 1.7056686 0 - 70 300 0.11602688 1.7069009 -0.84571914 2.5518169 1.7060978 0 - 80 300 0.13271379 15.358343 -3.368063 22.960722 19.592659 0 - 90 300 0.15055513 42.280432 -2.1623864 63.209247 61.04686 0 - 100 300 0.16817498 41.48079 -0.89904529 62.013782 61.114736 0 -Loop time of 0.168194 on 16 procs for 100 steps with 300 atoms - -Performance: 256846.586 tau/day, 594.552 timesteps/s -97.7% CPU use with 16 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 1.4544e-05 | 2.0206e-05 | 2.6941e-05 | 0.0 | 0.01 -Kspace | 0.16313 | 0.16373 | 0.16423 | 0.1 | 97.34 -Neigh | 0.00016737 | 0.00039591 | 0.00084519 | 0.0 | 0.24 -Comm | 0.0021157 | 0.0026083 | 0.0032525 | 0.7 | 1.55 -Output | 0.00026298 | 0.00030228 | 0.00035977 | 0.0 | 0.18 -Modify | 0.00010705 | 0.00015062 | 0.00020647 | 0.0 | 0.09 -Other | | 0.0009913 | | | 0.59 - -Nlocal: 18.75 ave 36 max 6 min -Histogram: 4 3 1 0 0 1 2 1 2 2 -Nghost: 127 ave 196 max 71 min -Histogram: 8 0 0 0 0 0 0 1 6 1 -Neighs: 153.688 ave 491 max 10 min -Histogram: 8 1 1 1 1 1 0 0 0 3 - -Total # of neighbors = 2459 -Ave neighs/atom = 8.19667 -Neighbor list builds = 15 -Dangerous builds = 0 -Total wall time: 0:00:01 diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.2 b/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.2 deleted file mode 100644 index 43ded2d4da..0000000000 --- a/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.2 +++ /dev/null @@ -1,99 +0,0 @@ -LAMMPS (29 Jun 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) - using 1 OpenMP thread(s) per MPI task -units lj -atom_style charge - -read_data data.cloud_wall - orthogonal box = (0 0 0) to (10 10 10) - 1 by 1 by 2 MPI processor grid - reading atoms ... - 300 atoms - -velocity all set 0.0 0.0 0.0 mom no - -pair_style zero 1.0 -pair_coeff * * - -neighbor 1.0 bin -neigh_modify delay 0 - -fix 1 all nve - - -#pair_style coul/long 3.0 -#pair_coeff * * -#kspace_style pppm 1.0e-3 - -kspace_style scafacos fmm 1.0e-3 -kspace_modify scafacos tolerance energy_rel -kspace_modify scafacos fmm_tuning 1 -ScaFaCoS setting fmm inhomogen tuning ...3 - -timestep 0.005 - -thermo_style custom step atoms cpu temp pe ke etotal ecoul - -run_style verlet - -#dump simple all custom 1000 id x y z vx vy vz -#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass -#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass -#dump_modify dmpvtk pad 7 - -thermo 10 -run 100 -Setting up ScaFaCoS with solver fmm ... -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2 - ghost atom cutoff = 2 - binsize = 1, bins = 10 10 10 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair zero, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.354 | 3.354 | 3.355 Mbytes -Step Atoms CPU Temp PotEng KinEng TotEng E_coul - 0 300 0 0 0.49646402 0 0.49646402 0 - 10 300 0.021326542 0.015455559 0.47335833 0.02310606 0.49646439 0 - 20 300 0.043129683 0.06229069 0.40334177 0.093124582 0.49646635 0 - 30 300 0.064425707 0.14310163 0.28254277 0.21393694 0.49647971 0 - 40 300 0.085822344 0.52929788 0.089669015 0.79130033 0.88096934 0 - 50 300 0.10737753 1.1963022 -0.082792461 1.7884718 1.7056794 0 - 60 300 0.12947297 1.3928167 -0.37659239 2.082261 1.7056686 0 - 70 300 0.15108895 1.7069009 -0.84571914 2.5518169 1.7060978 0 - 80 300 0.17378163 15.358343 -3.368063 22.960722 19.592659 0 - 90 300 0.19809985 42.280432 -2.1623864 63.209247 61.04686 0 - 100 300 0.22268319 41.48079 -0.89904529 62.013782 61.114736 0 -Loop time of 0.222696 on 2 procs for 100 steps with 300 atoms - -Performance: 193986.156 tau/day, 449.042 timesteps/s -98.4% CPU use with 2 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 1.1683e-05 | 1.5378e-05 | 1.9073e-05 | 0.0 | 0.01 -Kspace | 0.21627 | 0.2168 | 0.21734 | 0.1 | 97.35 -Neigh | 0.0016344 | 0.0021609 | 0.0026875 | 1.1 | 0.97 -Comm | 0.0022857 | 0.0023286 | 0.0023715 | 0.1 | 1.05 -Output | 0.00015521 | 0.00019228 | 0.00022936 | 0.0 | 0.09 -Modify | 0.00052834 | 0.00054049 | 0.00055265 | 0.0 | 0.24 -Other | | 0.0006541 | | | 0.29 - -Nlocal: 150 ave 159 max 141 min -Histogram: 1 0 0 0 0 0 0 0 0 1 -Nghost: 392 ave 395 max 389 min -Histogram: 1 0 0 0 0 0 0 0 0 1 -Neighs: 1229.5 ave 1773 max 686 min -Histogram: 1 0 0 0 0 0 0 0 0 1 - -Total # of neighbors = 2459 -Ave neighs/atom = 8.19667 -Neighbor list builds = 15 -Dangerous builds = 0 -Total wall time: 0:00:01 diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.4 b/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.4 deleted file mode 100644 index 12c74993e9..0000000000 --- a/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.4 +++ /dev/null @@ -1,99 +0,0 @@ -LAMMPS (29 Jun 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) - using 1 OpenMP thread(s) per MPI task -units lj -atom_style charge - -read_data data.cloud_wall - orthogonal box = (0 0 0) to (10 10 10) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 300 atoms - -velocity all set 0.0 0.0 0.0 mom no - -pair_style zero 1.0 -pair_coeff * * - -neighbor 1.0 bin -neigh_modify delay 0 - -fix 1 all nve - - -#pair_style coul/long 3.0 -#pair_coeff * * -#kspace_style pppm 1.0e-3 - -kspace_style scafacos fmm 1.0e-3 -kspace_modify scafacos tolerance energy_rel -kspace_modify scafacos fmm_tuning 1 -ScaFaCoS setting fmm inhomogen tuning ...3 - -timestep 0.005 - -thermo_style custom step atoms cpu temp pe ke etotal ecoul - -run_style verlet - -#dump simple all custom 1000 id x y z vx vy vz -#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass -#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass -#dump_modify dmpvtk pad 7 - -thermo 10 -run 100 -Setting up ScaFaCoS with solver fmm ... -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2 - ghost atom cutoff = 2 - binsize = 1, bins = 10 10 10 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair zero, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.333 | 3.333 | 3.333 Mbytes -Step Atoms CPU Temp PotEng KinEng TotEng E_coul - 0 300 0 0 0.49646402 0 0.49646402 0 - 10 300 0.017563343 0.015455559 0.47335833 0.02310606 0.49646439 0 - 20 300 0.034884214 0.06229069 0.40334177 0.093124582 0.49646635 0 - 30 300 0.052014828 0.14310163 0.28254277 0.21393694 0.49647971 0 - 40 300 0.069101095 0.52929788 0.089669015 0.79130033 0.88096934 0 - 50 300 0.085633039 1.1963022 -0.082792461 1.7884718 1.7056794 0 - 60 300 0.10165119 1.3928167 -0.37659239 2.082261 1.7056686 0 - 70 300 0.11729789 1.7069009 -0.84571914 2.5518169 1.7060978 0 - 80 300 0.1342802 15.358343 -3.368063 22.960722 19.592659 0 - 90 300 0.15266848 42.280432 -2.1623864 63.209247 61.04686 0 - 100 300 0.17004442 41.48079 -0.89904529 62.013782 61.114736 0 -Loop time of 0.170072 on 4 procs for 100 steps with 300 atoms - -Performance: 254010.216 tau/day, 587.987 timesteps/s -98.8% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 1.5497e-05 | 1.6868e-05 | 1.9789e-05 | 0.0 | 0.01 -Kspace | 0.16417 | 0.16472 | 0.16507 | 0.1 | 96.86 -Neigh | 0.00082564 | 0.0012031 | 0.0015855 | 0.9 | 0.71 -Comm | 0.0026572 | 0.0029335 | 0.003197 | 0.4 | 1.72 -Output | 0.00019169 | 0.00021791 | 0.00026536 | 0.0 | 0.13 -Modify | 0.00031304 | 0.00032955 | 0.00035334 | 0.0 | 0.19 -Other | | 0.0006474 | | | 0.38 - -Nlocal: 75 ave 81 max 70 min -Histogram: 2 0 0 0 0 0 0 1 0 1 -Nghost: 282.5 ave 290 max 274 min -Histogram: 1 0 0 1 0 0 0 0 1 1 -Neighs: 614.75 ave 981 max 285 min -Histogram: 1 1 0 0 0 0 0 1 0 1 - -Total # of neighbors = 2459 -Ave neighs/atom = 8.19667 -Neighbor list builds = 15 -Dangerous builds = 0 -Total wall time: 0:00:01 diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.8 b/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.8 deleted file mode 100644 index 1fea13cd13..0000000000 --- a/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.8 +++ /dev/null @@ -1,99 +0,0 @@ -LAMMPS (29 Jun 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) - using 1 OpenMP thread(s) per MPI task -units lj -atom_style charge - -read_data data.cloud_wall - orthogonal box = (0 0 0) to (10 10 10) - 2 by 2 by 2 MPI processor grid - reading atoms ... - 300 atoms - -velocity all set 0.0 0.0 0.0 mom no - -pair_style zero 1.0 -pair_coeff * * - -neighbor 1.0 bin -neigh_modify delay 0 - -fix 1 all nve - - -#pair_style coul/long 3.0 -#pair_coeff * * -#kspace_style pppm 1.0e-3 - -kspace_style scafacos fmm 1.0e-3 -kspace_modify scafacos tolerance energy_rel -kspace_modify scafacos fmm_tuning 1 -ScaFaCoS setting fmm inhomogen tuning ...3 - -timestep 0.005 - -thermo_style custom step atoms cpu temp pe ke etotal ecoul - -run_style verlet - -#dump simple all custom 1000 id x y z vx vy vz -#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass -#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass -#dump_modify dmpvtk pad 7 - -thermo 10 -run 100 -Setting up ScaFaCoS with solver fmm ... -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2 - ghost atom cutoff = 2 - binsize = 1, bins = 10 10 10 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair zero, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.317 | 3.317 | 3.317 Mbytes -Step Atoms CPU Temp PotEng KinEng TotEng E_coul - 0 300 0 0 0.49646402 0 0.49646402 0 - 10 300 0.016258478 0.015455559 0.47335833 0.02310606 0.49646439 0 - 20 300 0.031442165 0.06229069 0.40334177 0.093124582 0.49646635 0 - 30 300 0.046462774 0.14310163 0.28254277 0.21393694 0.49647971 0 - 40 300 0.061176538 0.52929788 0.089669015 0.79130033 0.88096934 0 - 50 300 0.076244354 1.1963022 -0.082792461 1.7884718 1.7056794 0 - 60 300 0.091396809 1.3928167 -0.37659239 2.082261 1.7056686 0 - 70 300 0.10625911 1.7069009 -0.84571914 2.5518169 1.7060978 0 - 80 300 0.1204896 15.358343 -3.368063 22.960722 19.592659 0 - 90 300 0.13657618 42.280432 -2.1623864 63.209247 61.04686 0 - 100 300 0.15163732 41.48079 -0.89904529 62.013782 61.114736 0 -Loop time of 0.151654 on 8 procs for 100 steps with 300 atoms - -Performance: 284858.554 tau/day, 659.395 timesteps/s -97.7% CPU use with 8 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 1.3828e-05 | 1.6987e-05 | 1.955e-05 | 0.0 | 0.01 -Kspace | 0.14633 | 0.14689 | 0.14725 | 0.1 | 96.86 -Neigh | 0.00047135 | 0.00067887 | 0.00094771 | 0.0 | 0.45 -Comm | 0.0027649 | 0.0029218 | 0.0032592 | 0.3 | 1.93 -Output | 0.00022578 | 0.00024724 | 0.00030136 | 0.0 | 0.16 -Modify | 0.00018954 | 0.00021681 | 0.0002358 | 0.0 | 0.14 -Other | | 0.0006794 | | | 0.45 - -Nlocal: 37.5 ave 45 max 31 min -Histogram: 1 1 1 1 1 0 1 0 1 1 -Nghost: 200 ave 209 max 189 min -Histogram: 1 0 0 0 1 4 0 0 0 2 -Neighs: 307.375 ave 514 max 115 min -Histogram: 2 1 0 1 1 0 0 0 1 2 - -Total # of neighbors = 2459 -Ave neighs/atom = 8.19667 -Neighbor list builds = 15 -Dangerous builds = 0 -Total wall time: 0:00:01 diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.p2nfft.1 b/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.p2nfft.1 deleted file mode 100644 index bd9325dc4b..0000000000 --- a/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.p2nfft.1 +++ /dev/null @@ -1,92 +0,0 @@ -LAMMPS (29 Jun 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) - using 1 OpenMP thread(s) per MPI task - -units lj -atom_style charge - -read_data data.cloud_wall - orthogonal box = (0 0 0) to (10 10 10) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 300 atoms - -velocity all set 0.0 0.0 0.0 mom no - -pair_style zero 1.0 -pair_coeff * * - -neighbor 1.0 bin -neigh_modify delay 0 - -fix 1 all nve -kspace_style scafacos p2nfft 0.001 -kspace_modify scafacos tolerance field - -timestep 0.005 - -thermo_style custom step atoms cpu temp pe ke etotal ecoul - -run_style verlet - -#dump simple all custom 1000 id x y z vx vy vz -#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass -#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass -#dump_modify dmpvtk pad 7 - -thermo 10 -run 100 -Setting up ScaFaCoS with solver p2nfft ... -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2 - ghost atom cutoff = 2 - binsize = 1, bins = 10 10 10 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair zero, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.34 | 3.34 | 3.34 Mbytes -Step Atoms CPU Temp PotEng KinEng TotEng E_coul - 0 300 0 0 0.49683273 0 0.49683273 0 - 10 300 0.082981586 0.015479312 0.47369009 0.023141571 0.49683166 0 - 20 300 0.16677213 0.062386358 0.40356181 0.093267605 0.49682941 0 - 30 300 0.2506392 0.14331637 0.2825636 0.21425798 0.49682157 0 - 40 300 0.33466673 0.53041843 0.089505208 0.79297556 0.88248077 0 - 50 300 0.41812825 1.1948397 -0.083317439 1.7862853 1.7029679 0 - 60 300 0.50167894 1.3915614 -0.37745551 2.0803842 1.7029287 0 - 70 300 0.58574796 1.7061978 -0.84746071 2.5507657 1.703305 0 - 80 300 0.6700325 20.692093 -3.32971 30.93468 27.60497 0 - 90 300 0.75608635 48.999403 -2.1632167 73.254107 71.090891 0 - 100 300 0.84190726 51.199785 -0.81127924 76.543678 75.732399 0 -Loop time of 0.841921 on 1 procs for 100 steps with 300 atoms - -Performance: 51311.251 tau/day, 118.776 timesteps/s -100.0% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 1.1206e-05 | 1.1206e-05 | 1.1206e-05 | 0.0 | 0.00 -Kspace | 0.835 | 0.835 | 0.835 | 0.0 | 99.18 -Neigh | 0.0040102 | 0.0040102 | 0.0040102 | 0.0 | 0.48 -Comm | 0.0012431 | 0.0012431 | 0.0012431 | 0.0 | 0.15 -Output | 0.0001545 | 0.0001545 | 0.0001545 | 0.0 | 0.02 -Modify | 0.0010202 | 0.0010202 | 0.0010202 | 0.0 | 0.12 -Other | | 0.000484 | | | 0.06 - -Nlocal: 300 ave 300 max 300 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 381 ave 381 max 381 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 2461 ave 2461 max 2461 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 2461 -Ave neighs/atom = 8.20333 -Neighbor list builds = 15 -Dangerous builds = 0 -Total wall time: 0:00:00 diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.p2nfft.16 b/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.p2nfft.16 deleted file mode 100644 index 1e385c5fda..0000000000 --- a/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.p2nfft.16 +++ /dev/null @@ -1,92 +0,0 @@ -LAMMPS (29 Jun 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) - using 1 OpenMP thread(s) per MPI task - -units lj -atom_style charge - -read_data data.cloud_wall - orthogonal box = (0 0 0) to (10 10 10) - 2 by 2 by 4 MPI processor grid - reading atoms ... - 300 atoms - -velocity all set 0.0 0.0 0.0 mom no - -pair_style zero 1.0 -pair_coeff * * - -neighbor 1.0 bin -neigh_modify delay 0 - -fix 1 all nve -kspace_style scafacos p2nfft 0.001 -kspace_modify scafacos tolerance field - -timestep 0.005 - -thermo_style custom step atoms cpu temp pe ke etotal ecoul - -run_style verlet - -#dump simple all custom 1000 id x y z vx vy vz -#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass -#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass -#dump_modify dmpvtk pad 7 - -thermo 10 -run 100 -Setting up ScaFaCoS with solver p2nfft ... -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2 - ghost atom cutoff = 2 - binsize = 1, bins = 10 10 10 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair zero, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.313 | 3.501 | 3.689 Mbytes -Step Atoms CPU Temp PotEng KinEng TotEng E_coul - 0 300 0 0 0.49683273 0 0.49683273 0 - 10 300 0.029647827 0.015479312 0.47369009 0.023141571 0.49683166 0 - 20 300 0.059298515 0.062386358 0.40356181 0.093267605 0.49682941 0 - 30 300 0.088926077 0.14331637 0.2825636 0.21425798 0.49682157 0 - 40 300 0.11850166 0.53041843 0.089505208 0.79297556 0.88248077 0 - 50 300 0.14820433 1.1948397 -0.083317439 1.7862853 1.7029679 0 - 60 300 0.17807317 1.3915614 -0.37745551 2.0803842 1.7029287 0 - 70 300 0.20803642 1.7061978 -0.84746071 2.5507657 1.703305 0 - 80 300 0.23797083 20.692093 -3.32971 30.93468 27.60497 0 - 90 300 0.26835561 48.999403 -2.1632167 73.254107 71.090891 0 - 100 300 0.29766583 51.199785 -0.81127924 76.543678 75.732399 0 -Loop time of 0.297693 on 16 procs for 100 steps with 300 atoms - -Performance: 145116.000 tau/day, 335.917 timesteps/s -98.8% CPU use with 16 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 1.1683e-05 | 1.6928e-05 | 2.4557e-05 | 0.0 | 0.01 -Kspace | 0.29245 | 0.29325 | 0.29366 | 0.1 | 98.51 -Neigh | 0.00017214 | 0.00042973 | 0.0010228 | 0.0 | 0.14 -Comm | 0.0021176 | 0.0024613 | 0.0028479 | 0.5 | 0.83 -Output | 0.00028467 | 0.00033538 | 0.00041103 | 0.0 | 0.11 -Modify | 8.893e-05 | 0.00015014 | 0.00027537 | 0.0 | 0.05 -Other | | 0.001048 | | | 0.35 - -Nlocal: 18.75 ave 33 max 6 min -Histogram: 2 6 0 0 0 0 2 1 2 3 -Nghost: 128.875 ave 198 max 71 min -Histogram: 7 1 0 0 0 0 0 1 5 2 -Neighs: 153.812 ave 490 max 14 min -Histogram: 8 0 3 0 1 1 0 0 1 2 - -Total # of neighbors = 2461 -Ave neighs/atom = 8.20333 -Neighbor list builds = 15 -Dangerous builds = 0 -Total wall time: 0:00:00 diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.p2nfft.2 b/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.p2nfft.2 deleted file mode 100644 index 3f54069ffd..0000000000 --- a/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.p2nfft.2 +++ /dev/null @@ -1,92 +0,0 @@ -LAMMPS (29 Jun 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) - using 1 OpenMP thread(s) per MPI task - -units lj -atom_style charge - -read_data data.cloud_wall - orthogonal box = (0 0 0) to (10 10 10) - 1 by 1 by 2 MPI processor grid - reading atoms ... - 300 atoms - -velocity all set 0.0 0.0 0.0 mom no - -pair_style zero 1.0 -pair_coeff * * - -neighbor 1.0 bin -neigh_modify delay 0 - -fix 1 all nve -kspace_style scafacos p2nfft 0.001 -kspace_modify scafacos tolerance field - -timestep 0.005 - -thermo_style custom step atoms cpu temp pe ke etotal ecoul - -run_style verlet - -#dump simple all custom 1000 id x y z vx vy vz -#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass -#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass -#dump_modify dmpvtk pad 7 - -thermo 10 -run 100 -Setting up ScaFaCoS with solver p2nfft ... -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2 - ghost atom cutoff = 2 - binsize = 1, bins = 10 10 10 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair zero, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.354 | 3.354 | 3.355 Mbytes -Step Atoms CPU Temp PotEng KinEng TotEng E_coul - 0 300 0 0 0.49683273 0 0.49683273 0 - 10 300 0.049199581 0.015479312 0.47369009 0.023141571 0.49683166 0 - 20 300 0.09860301 0.062386358 0.40356181 0.093267605 0.49682941 0 - 30 300 0.14826894 0.14331637 0.2825636 0.21425798 0.49682157 0 - 40 300 0.19769144 0.53041843 0.089505208 0.79297556 0.88248077 0 - 50 300 0.24735355 1.1948397 -0.083317439 1.7862853 1.7029679 0 - 60 300 0.29692888 1.3915614 -0.37745551 2.0803842 1.7029287 0 - 70 300 0.34639764 1.7061978 -0.84746071 2.5507657 1.703305 0 - 80 300 0.39633083 20.692093 -3.32971 30.93468 27.60497 0 - 90 300 0.44779778 48.999403 -2.1632167 73.254107 71.090891 0 - 100 300 0.49988627 51.199785 -0.81127924 76.543678 75.732399 0 -Loop time of 0.499909 on 2 procs for 100 steps with 300 atoms - -Performance: 86415.782 tau/day, 200.037 timesteps/s -99.5% CPU use with 2 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 9.0599e-06 | 1.3709e-05 | 1.8358e-05 | 0.0 | 0.00 -Kspace | 0.49314 | 0.49365 | 0.49416 | 0.1 | 98.75 -Neigh | 0.0016146 | 0.0021083 | 0.0026021 | 1.1 | 0.42 -Comm | 0.002754 | 0.0028276 | 0.0029013 | 0.1 | 0.57 -Output | 0.00015783 | 0.00019348 | 0.00022912 | 0.0 | 0.04 -Modify | 0.00049257 | 0.00049472 | 0.00049686 | 0.0 | 0.10 -Other | | 0.0006217 | | | 0.12 - -Nlocal: 150 ave 157 max 143 min -Histogram: 1 0 0 0 0 0 0 0 0 1 -Nghost: 399 ave 402 max 396 min -Histogram: 1 0 0 0 0 0 0 0 0 1 -Neighs: 1230.5 ave 1756 max 705 min -Histogram: 1 0 0 0 0 0 0 0 0 1 - -Total # of neighbors = 2461 -Ave neighs/atom = 8.20333 -Neighbor list builds = 15 -Dangerous builds = 0 -Total wall time: 0:00:00 diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.p2nfft.4 b/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.p2nfft.4 deleted file mode 100644 index 8b94402658..0000000000 --- a/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.p2nfft.4 +++ /dev/null @@ -1,92 +0,0 @@ -LAMMPS (29 Jun 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) - using 1 OpenMP thread(s) per MPI task - -units lj -atom_style charge - -read_data data.cloud_wall - orthogonal box = (0 0 0) to (10 10 10) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 300 atoms - -velocity all set 0.0 0.0 0.0 mom no - -pair_style zero 1.0 -pair_coeff * * - -neighbor 1.0 bin -neigh_modify delay 0 - -fix 1 all nve -kspace_style scafacos p2nfft 0.001 -kspace_modify scafacos tolerance field - -timestep 0.005 - -thermo_style custom step atoms cpu temp pe ke etotal ecoul - -run_style verlet - -#dump simple all custom 1000 id x y z vx vy vz -#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass -#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass -#dump_modify dmpvtk pad 7 - -thermo 10 -run 100 -Setting up ScaFaCoS with solver p2nfft ... -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2 - ghost atom cutoff = 2 - binsize = 1, bins = 10 10 10 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair zero, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.333 | 3.333 | 3.333 Mbytes -Step Atoms CPU Temp PotEng KinEng TotEng E_coul - 0 300 0 0 0.49683273 0 0.49683273 0 - 10 300 0.031973124 0.015479312 0.47369009 0.023141571 0.49683166 0 - 20 300 0.064628601 0.062386358 0.40356181 0.093267605 0.49682941 0 - 30 300 0.096747875 0.14331637 0.2825636 0.21425798 0.49682157 0 - 40 300 0.12864041 0.53041843 0.089505208 0.79297556 0.88248077 0 - 50 300 0.161134 1.1948397 -0.083317439 1.7862853 1.7029679 0 - 60 300 0.19359422 1.3915614 -0.37745551 2.0803842 1.7029287 0 - 70 300 0.22573543 1.7061978 -0.84746071 2.5507657 1.703305 0 - 80 300 0.25922132 20.692093 -3.32971 30.93468 27.60497 0 - 90 300 0.29452014 48.999403 -2.1632167 73.254107 71.090891 0 - 100 300 0.33031607 51.199785 -0.81127924 76.543678 75.732399 0 -Loop time of 0.330333 on 4 procs for 100 steps with 300 atoms - -Performance: 130777.056 tau/day, 302.725 timesteps/s -99.7% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 1.0014e-05 | 1.3471e-05 | 1.5497e-05 | 0.0 | 0.00 -Kspace | 0.32504 | 0.3255 | 0.3258 | 0.1 | 98.54 -Neigh | 0.00083303 | 0.0011883 | 0.0015609 | 0.8 | 0.36 -Comm | 0.0024087 | 0.0025436 | 0.0026674 | 0.2 | 0.77 -Output | 0.00017405 | 0.00020278 | 0.00024986 | 0.0 | 0.06 -Modify | 0.00028658 | 0.00031012 | 0.00033331 | 0.0 | 0.09 -Other | | 0.0005748 | | | 0.17 - -Nlocal: 75 ave 81 max 69 min -Histogram: 1 0 0 0 1 1 0 0 0 1 -Nghost: 287 ave 296 max 278 min -Histogram: 1 0 1 0 0 0 0 1 0 1 -Neighs: 615.25 ave 964 max 286 min -Histogram: 1 1 0 0 0 0 0 1 0 1 - -Total # of neighbors = 2461 -Ave neighs/atom = 8.20333 -Neighbor list builds = 15 -Dangerous builds = 0 -Total wall time: 0:00:00 diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.p2nfft.8 b/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.p2nfft.8 deleted file mode 100644 index 3de3c25017..0000000000 --- a/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.p2nfft.8 +++ /dev/null @@ -1,92 +0,0 @@ -LAMMPS (29 Jun 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) - using 1 OpenMP thread(s) per MPI task - -units lj -atom_style charge - -read_data data.cloud_wall - orthogonal box = (0 0 0) to (10 10 10) - 2 by 2 by 2 MPI processor grid - reading atoms ... - 300 atoms - -velocity all set 0.0 0.0 0.0 mom no - -pair_style zero 1.0 -pair_coeff * * - -neighbor 1.0 bin -neigh_modify delay 0 - -fix 1 all nve -kspace_style scafacos p2nfft 0.001 -kspace_modify scafacos tolerance field - -timestep 0.005 - -thermo_style custom step atoms cpu temp pe ke etotal ecoul - -run_style verlet - -#dump simple all custom 1000 id x y z vx vy vz -#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass -#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass -#dump_modify dmpvtk pad 7 - -thermo 10 -run 100 -Setting up ScaFaCoS with solver p2nfft ... -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2 - ghost atom cutoff = 2 - binsize = 1, bins = 10 10 10 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair zero, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.317 | 3.317 | 3.317 Mbytes -Step Atoms CPU Temp PotEng KinEng TotEng E_coul - 0 300 0 0 0.49683273 0 0.49683273 0 - 10 300 0.023941755 0.015479312 0.47369009 0.023141571 0.49683166 0 - 20 300 0.047938108 0.062386358 0.40356181 0.093267605 0.49682941 0 - 30 300 0.071953773 0.14331637 0.2825636 0.21425798 0.49682157 0 - 40 300 0.095941782 0.53041843 0.089505208 0.79297556 0.88248077 0 - 50 300 0.12011361 1.1948397 -0.083317439 1.7862853 1.7029679 0 - 60 300 0.14433384 1.3915614 -0.37745551 2.0803842 1.7029287 0 - 70 300 0.16875505 1.7061978 -0.84746071 2.5507657 1.703305 0 - 80 300 0.193331 20.692093 -3.32971 30.93468 27.60497 0 - 90 300 0.21844888 48.999403 -2.1632167 73.254107 71.090891 0 - 100 300 0.24417853 51.199785 -0.81127924 76.543678 75.732399 0 -Loop time of 0.244198 on 8 procs for 100 steps with 300 atoms - -Performance: 176905.349 tau/day, 409.503 timesteps/s -99.7% CPU use with 8 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 9.7752e-06 | 1.4246e-05 | 1.955e-05 | 0.0 | 0.01 -Kspace | 0.23946 | 0.23972 | 0.24009 | 0.0 | 98.17 -Neigh | 0.00049043 | 0.00071204 | 0.00095773 | 0.0 | 0.29 -Comm | 0.0025063 | 0.0026675 | 0.0027597 | 0.2 | 1.09 -Output | 0.00019646 | 0.00021604 | 0.00026321 | 0.0 | 0.09 -Modify | 0.00017905 | 0.0001913 | 0.00020766 | 0.0 | 0.08 -Other | | 0.0006773 | | | 0.28 - -Nlocal: 37.5 ave 42 max 33 min -Histogram: 2 1 0 1 0 0 1 0 1 2 -Nghost: 202.25 ave 212 max 194 min -Histogram: 1 0 2 1 0 2 0 1 0 1 -Neighs: 307.625 ave 505 max 129 min -Histogram: 3 0 0 1 1 0 0 0 1 2 - -Total # of neighbors = 2461 -Ave neighs/atom = 8.20333 -Neighbor list builds = 15 -Dangerous builds = 0 -Total wall time: 0:00:00 diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.g++.ewald.16 b/examples/USER/scafacos/log.23Jul18.scafacos.g++.ewald.16 deleted file mode 100644 index f2223064e0..0000000000 --- a/examples/USER/scafacos/log.23Jul18.scafacos.g++.ewald.16 +++ /dev/null @@ -1,102 +0,0 @@ -LAMMPS (29 Jun 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) - using 1 OpenMP thread(s) per MPI task -# Point dipoles in a 2d box - -units lj -atom_style charge - -read_data data.NaCl - orthogonal box = (0 0 0) to (2 2 2) - 2 by 2 by 4 MPI processor grid - reading atoms ... - 8 atoms - -replicate 8 8 8 - orthogonal box = (0 0 0) to (16 16 16) - 2 by 2 by 4 MPI processor grid - 4096 atoms - Time spent = 0.000503302 secs - -velocity all create 1.5 49893 - -neighbor 1.0 bin -neigh_modify delay 0 - -fix 1 all nve - -# LAMMPS computes pairwise and long-range Coulombics - -#pair_style coul/long 3.0 -#pair_coeff * * -#kspace_style pppm 1.0e-3 - -# Scafacos computes entire long-range Coulombics -# use dummy pair style to perform atom sorting - -pair_style zero 1.0 -pair_coeff * * - -#fix 2 all scafacos p3m tolerance field 0.001 - -kspace_style scafacos ewald 0.001 -kspace_modify scafacos tolerance field - -timestep 0.005 -thermo 10 - -run 100 -Setting up ScaFaCoS with solver ewald ... -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2 - ghost atom cutoff = 2 - binsize = 1, bins = 16 16 16 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair zero, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.401 | 3.401 | 3.401 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1.5 -0.87413076 0 1.3753199 1.4996338 - 10 1.5001167 -0.84976141 0 1.3998642 1.4997504 - 20 1.5002402 -0.84977464 0 1.4000363 1.499874 - 30 1.5003611 -0.84978325 0 1.4002089 1.4999948 - 40 1.5004736 -0.84977869 0 1.4003823 1.5001073 - 50 1.5005703 -0.8497468 0 1.4005591 1.5002039 - 60 1.5006418 -0.84967646 0 1.4007366 1.5002754 - 70 1.5006785 -0.84955497 0 1.4009132 1.5003121 - 80 1.5006711 -0.849369 0 1.4010881 1.5003047 - 90 1.500611 -0.84910811 0 1.4012589 1.5002446 - 100 1.5004911 -0.84870167 0 1.4014854 1.5001247 -Loop time of 46.4857 on 16 procs for 100 steps with 4096 atoms - -Performance: 929.317 tau/day, 2.151 timesteps/s -99.8% CPU use with 16 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.00023437 | 0.00024788 | 0.00026894 | 0.0 | 0.00 -Kspace | 46.476 | 46.476 | 46.476 | 0.0 | 99.98 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.0062859 | 0.0067717 | 0.0072649 | 0.3 | 0.01 -Output | 0.0004127 | 0.00044075 | 0.00050807 | 0.0 | 0.00 -Modify | 0.00099325 | 0.0010343 | 0.0010939 | 0.1 | 0.00 -Other | | 0.001459 | | | 0.00 - -Nlocal: 256 ave 256 max 256 min -Histogram: 16 0 0 0 0 0 0 0 0 0 -Nghost: 1265 ave 1265 max 1265 min -Histogram: 16 0 0 0 0 0 0 0 0 0 -Neighs: 4096 ave 4096 max 4096 min -Histogram: 16 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 65536 -Ave neighs/atom = 16 -Neighbor list builds = 0 -Dangerous builds = 0 -Total wall time: 0:00:47 diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.g++.ewald.8 b/examples/USER/scafacos/log.23Jul18.scafacos.g++.ewald.8 deleted file mode 100644 index 8d3702a8b3..0000000000 --- a/examples/USER/scafacos/log.23Jul18.scafacos.g++.ewald.8 +++ /dev/null @@ -1,102 +0,0 @@ -LAMMPS (29 Jun 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) - using 1 OpenMP thread(s) per MPI task -# Point dipoles in a 2d box - -units lj -atom_style charge - -read_data data.NaCl - orthogonal box = (0 0 0) to (2 2 2) - 2 by 2 by 2 MPI processor grid - reading atoms ... - 8 atoms - -replicate 8 8 8 - orthogonal box = (0 0 0) to (16 16 16) - 2 by 2 by 2 MPI processor grid - 4096 atoms - Time spent = 0.000281811 secs - -velocity all create 1.5 49893 - -neighbor 1.0 bin -neigh_modify delay 0 - -fix 1 all nve - -# LAMMPS computes pairwise and long-range Coulombics - -#pair_style coul/long 3.0 -#pair_coeff * * -#kspace_style pppm 1.0e-3 - -# Scafacos computes entire long-range Coulombics -# use dummy pair style to perform atom sorting - -pair_style zero 1.0 -pair_coeff * * - -#fix 2 all scafacos p3m tolerance field 0.001 - -kspace_style scafacos ewald 0.001 -kspace_modify scafacos tolerance field - -timestep 0.005 -thermo 10 - -run 100 -Setting up ScaFaCoS with solver ewald ... -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2 - ghost atom cutoff = 2 - binsize = 1, bins = 16 16 16 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair zero, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.416 | 3.416 | 3.416 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1.5 -0.87413076 0 1.3753199 1.4996338 - 10 1.5001095 -0.85040058 0 1.3992143 1.4997433 - 20 1.5002258 -0.85039456 0 1.3993947 1.4998595 - 30 1.5003395 -0.85038368 0 1.3995761 1.4999732 - 40 1.5004452 -0.85035944 0 1.3997589 1.5000789 - 50 1.5005354 -0.85030783 0 1.3999457 1.500169 - 60 1.5006008 -0.85021779 0 1.4001339 1.5002344 - 70 1.500632 -0.8500769 0 1.4003215 1.5002656 - 80 1.5006197 -0.84987187 0 1.4005081 1.5002533 - 90 1.5005554 -0.84959251 0 1.400691 1.500189 - 100 1.500432 -0.84916846 0 1.4009301 1.5000657 -Loop time of 86.1477 on 8 procs for 100 steps with 4096 atoms - -Performance: 501.464 tau/day, 1.161 timesteps/s -99.9% CPU use with 8 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.000314 | 0.00033289 | 0.00035048 | 0.0 | 0.00 -Kspace | 86.136 | 86.136 | 86.136 | 0.0 | 99.99 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.0069821 | 0.0073864 | 0.0077834 | 0.3 | 0.01 -Output | 0.00038719 | 0.00041264 | 0.00047517 | 0.0 | 0.00 -Modify | 0.0018711 | 0.0019454 | 0.0020905 | 0.1 | 0.00 -Other | | 0.001762 | | | 0.00 - -Nlocal: 512 ave 512 max 512 min -Histogram: 8 0 0 0 0 0 0 0 0 0 -Nghost: 1685 ave 1685 max 1685 min -Histogram: 8 0 0 0 0 0 0 0 0 0 -Neighs: 8192 ave 8192 max 8192 min -Histogram: 8 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 65536 -Ave neighs/atom = 16 -Neighbor list builds = 0 -Dangerous builds = 0 -Total wall time: 0:01:28 diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.g++.fmm.1 b/examples/USER/scafacos/log.23Jul18.scafacos.g++.fmm.1 deleted file mode 100644 index 0749de3832..0000000000 --- a/examples/USER/scafacos/log.23Jul18.scafacos.g++.fmm.1 +++ /dev/null @@ -1,102 +0,0 @@ -LAMMPS (29 Jun 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) - using 1 OpenMP thread(s) per MPI task -# Point dipoles in a 2d box - -units lj -atom_style charge - -read_data data.NaCl - orthogonal box = (0 0 0) to (2 2 2) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 8 atoms - -replicate 8 8 8 - orthogonal box = (0 0 0) to (16 16 16) - 1 by 1 by 1 MPI processor grid - 4096 atoms - Time spent = 0.000584364 secs - -velocity all create 1.5 49893 - -neighbor 1.0 bin -neigh_modify delay 0 - -fix 1 all nve - -# LAMMPS computes pairwise and long-range Coulombics - -#pair_style coul/long 3.0 -#pair_coeff * * -#kspace_style pppm 1.0e-3 - -# Scafacos computes entire long-range Coulombics -# use dummy pair style to perform atom sorting - -pair_style zero 1.0 -pair_coeff * * - -#fix 2 all scafacos p3m tolerance field 0.001 - -kspace_style scafacos fmm 0.001 -kspace_modify scafacos tolerance energy_rel - -timestep 0.005 -thermo 10 - -run 100 -Setting up ScaFaCoS with solver fmm ... -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2 - ghost atom cutoff = 2 - binsize = 1, bins = 16 16 16 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair zero, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.723 | 3.723 | 3.723 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1.5 -0.87378819 0 1.3756625 1.4996338 - 10 1.5000004 -0.87378882 0 1.3756625 1.4996342 - 20 1.4999998 -0.87378782 0 1.3756625 1.4996336 - 30 1.4999934 -0.87377823 0 1.3756625 1.4996272 - 40 1.4999745 -0.87374997 0 1.3756625 1.4996083 - 50 1.4999347 -0.87369019 0 1.3756625 1.4995685 - 60 1.4998637 -0.87358381 0 1.3756625 1.4994975 - 70 1.4997506 -0.87341428 0 1.3756624 1.4993845 - 80 1.4995842 -0.87316464 0 1.3756624 1.499218 - 90 1.4993536 -0.87281897 0 1.3756624 1.4989876 - 100 1.4990503 -0.87236411 0 1.3756624 1.4986843 -Loop time of 5.26537 on 1 procs for 100 steps with 4096 atoms - -Performance: 8204.550 tau/day, 18.992 timesteps/s -99.9% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0011349 | 0.0011349 | 0.0011349 | 0.0 | 0.02 -Kspace | 5.2375 | 5.2375 | 5.2375 | 0.0 | 99.47 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.0090225 | 0.0090225 | 0.0090225 | 0.0 | 0.17 -Output | 0.0004127 | 0.0004127 | 0.0004127 | 0.0 | 0.01 -Modify | 0.012851 | 0.012851 | 0.012851 | 0.0 | 0.24 -Other | | 0.004441 | | | 0.08 - -Nlocal: 4096 ave 4096 max 4096 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 5165 ave 5165 max 5165 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 65536 ave 65536 max 65536 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 65536 -Ave neighs/atom = 16 -Neighbor list builds = 0 -Dangerous builds = 0 -Total wall time: 0:00:06 diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.g++.fmm.16 b/examples/USER/scafacos/log.23Jul18.scafacos.g++.fmm.16 deleted file mode 100644 index 6af26f7b81..0000000000 --- a/examples/USER/scafacos/log.23Jul18.scafacos.g++.fmm.16 +++ /dev/null @@ -1,102 +0,0 @@ -LAMMPS (29 Jun 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) - using 1 OpenMP thread(s) per MPI task -# Point dipoles in a 2d box - -units lj -atom_style charge - -read_data data.NaCl - orthogonal box = (0 0 0) to (2 2 2) - 2 by 2 by 4 MPI processor grid - reading atoms ... - 8 atoms - -replicate 8 8 8 - orthogonal box = (0 0 0) to (16 16 16) - 2 by 2 by 4 MPI processor grid - 4096 atoms - Time spent = 0.000507593 secs - -velocity all create 1.5 49893 - -neighbor 1.0 bin -neigh_modify delay 0 - -fix 1 all nve - -# LAMMPS computes pairwise and long-range Coulombics - -#pair_style coul/long 3.0 -#pair_coeff * * -#kspace_style pppm 1.0e-3 - -# Scafacos computes entire long-range Coulombics -# use dummy pair style to perform atom sorting - -pair_style zero 1.0 -pair_coeff * * - -#fix 2 all scafacos p3m tolerance field 0.001 - -kspace_style scafacos fmm 0.001 -kspace_modify scafacos tolerance energy_rel - -timestep 0.005 -thermo 10 - -run 100 -Setting up ScaFaCoS with solver fmm ... -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2 - ghost atom cutoff = 2 - binsize = 1, bins = 16 16 16 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair zero, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.401 | 3.401 | 3.401 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1.5 -0.87378819 0 1.3756625 1.4996338 - 10 1.5000004 -0.87378882 0 1.3756625 1.4996342 - 20 1.4999998 -0.87378782 0 1.3756625 1.4996336 - 30 1.4999934 -0.87377823 0 1.3756625 1.4996272 - 40 1.4999745 -0.87374997 0 1.3756625 1.4996083 - 50 1.4999347 -0.87369019 0 1.3756625 1.4995685 - 60 1.4998637 -0.87358381 0 1.3756625 1.4994975 - 70 1.4997506 -0.87341428 0 1.3756624 1.4993845 - 80 1.4995842 -0.87316464 0 1.3756624 1.499218 - 90 1.4993536 -0.87281897 0 1.3756624 1.4989876 - 100 1.4990503 -0.87236411 0 1.3756624 1.4986843 -Loop time of 0.570389 on 16 procs for 100 steps with 4096 atoms - -Performance: 75737.813 tau/day, 175.319 timesteps/s -99.3% CPU use with 16 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.00024104 | 0.00025283 | 0.00029206 | 0.0 | 0.04 -Kspace | 0.56153 | 0.56176 | 0.56189 | 0.0 | 98.49 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.0055203 | 0.0057825 | 0.0061858 | 0.2 | 1.01 -Output | 0.00038505 | 0.00040831 | 0.00048184 | 0.0 | 0.07 -Modify | 0.00096965 | 0.00099662 | 0.0010159 | 0.0 | 0.17 -Other | | 0.001192 | | | 0.21 - -Nlocal: 256 ave 256 max 256 min -Histogram: 16 0 0 0 0 0 0 0 0 0 -Nghost: 1265 ave 1265 max 1265 min -Histogram: 16 0 0 0 0 0 0 0 0 0 -Neighs: 4096 ave 4096 max 4096 min -Histogram: 16 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 65536 -Ave neighs/atom = 16 -Neighbor list builds = 0 -Dangerous builds = 0 -Total wall time: 0:00:03 diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.g++.fmm.2 b/examples/USER/scafacos/log.23Jul18.scafacos.g++.fmm.2 deleted file mode 100644 index bcc61485ca..0000000000 --- a/examples/USER/scafacos/log.23Jul18.scafacos.g++.fmm.2 +++ /dev/null @@ -1,102 +0,0 @@ -LAMMPS (29 Jun 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) - using 1 OpenMP thread(s) per MPI task -# Point dipoles in a 2d box - -units lj -atom_style charge - -read_data data.NaCl - orthogonal box = (0 0 0) to (2 2 2) - 1 by 1 by 2 MPI processor grid - reading atoms ... - 8 atoms - -replicate 8 8 8 - orthogonal box = (0 0 0) to (16 16 16) - 1 by 1 by 2 MPI processor grid - 4096 atoms - Time spent = 0.000455141 secs - -velocity all create 1.5 49893 - -neighbor 1.0 bin -neigh_modify delay 0 - -fix 1 all nve - -# LAMMPS computes pairwise and long-range Coulombics - -#pair_style coul/long 3.0 -#pair_coeff * * -#kspace_style pppm 1.0e-3 - -# Scafacos computes entire long-range Coulombics -# use dummy pair style to perform atom sorting - -pair_style zero 1.0 -pair_coeff * * - -#fix 2 all scafacos p3m tolerance field 0.001 - -kspace_style scafacos fmm 0.001 -kspace_modify scafacos tolerance energy_rel - -timestep 0.005 -thermo 10 - -run 100 -Setting up ScaFaCoS with solver fmm ... -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2 - ghost atom cutoff = 2 - binsize = 1, bins = 16 16 16 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair zero, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.634 | 3.634 | 3.634 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1.5 -0.87378819 0 1.3756625 1.4996338 - 10 1.5000004 -0.87378882 0 1.3756625 1.4996342 - 20 1.4999998 -0.87378782 0 1.3756625 1.4996336 - 30 1.4999934 -0.87377823 0 1.3756625 1.4996272 - 40 1.4999745 -0.87374997 0 1.3756625 1.4996083 - 50 1.4999347 -0.87369019 0 1.3756625 1.4995685 - 60 1.4998637 -0.87358381 0 1.3756625 1.4994975 - 70 1.4997506 -0.87341428 0 1.3756624 1.4993845 - 80 1.4995842 -0.87316464 0 1.3756624 1.499218 - 90 1.4993536 -0.87281897 0 1.3756624 1.4989876 - 100 1.4990503 -0.87236411 0 1.3756624 1.4986843 -Loop time of 2.73149 on 2 procs for 100 steps with 4096 atoms - -Performance: 15815.560 tau/day, 36.610 timesteps/s -99.7% CPU use with 2 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.00070763 | 0.00071537 | 0.00072312 | 0.0 | 0.03 -Kspace | 2.7111 | 2.7112 | 2.7112 | 0.0 | 99.26 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.0096555 | 0.0097489 | 0.0098424 | 0.1 | 0.36 -Output | 0.00036025 | 0.0003823 | 0.00040436 | 0.0 | 0.01 -Modify | 0.0063472 | 0.0064594 | 0.0065715 | 0.1 | 0.24 -Other | | 0.00299 | | | 0.11 - -Nlocal: 2048 ave 2048 max 2048 min -Histogram: 2 0 0 0 0 0 0 0 0 0 -Nghost: 3685 ave 3685 max 3685 min -Histogram: 2 0 0 0 0 0 0 0 0 0 -Neighs: 32768 ave 32768 max 32768 min -Histogram: 2 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 65536 -Ave neighs/atom = 16 -Neighbor list builds = 0 -Dangerous builds = 0 -Total wall time: 0:00:04 diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.g++.fmm.4 b/examples/USER/scafacos/log.23Jul18.scafacos.g++.fmm.4 deleted file mode 100644 index 54e010c8fd..0000000000 --- a/examples/USER/scafacos/log.23Jul18.scafacos.g++.fmm.4 +++ /dev/null @@ -1,102 +0,0 @@ -LAMMPS (29 Jun 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) - using 1 OpenMP thread(s) per MPI task -# Point dipoles in a 2d box - -units lj -atom_style charge - -read_data data.NaCl - orthogonal box = (0 0 0) to (2 2 2) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 8 atoms - -replicate 8 8 8 - orthogonal box = (0 0 0) to (16 16 16) - 1 by 2 by 2 MPI processor grid - 4096 atoms - Time spent = 0.000329494 secs - -velocity all create 1.5 49893 - -neighbor 1.0 bin -neigh_modify delay 0 - -fix 1 all nve - -# LAMMPS computes pairwise and long-range Coulombics - -#pair_style coul/long 3.0 -#pair_coeff * * -#kspace_style pppm 1.0e-3 - -# Scafacos computes entire long-range Coulombics -# use dummy pair style to perform atom sorting - -pair_style zero 1.0 -pair_coeff * * - -#fix 2 all scafacos p3m tolerance field 0.001 - -kspace_style scafacos fmm 0.001 -kspace_modify scafacos tolerance energy_rel - -timestep 0.005 -thermo 10 - -run 100 -Setting up ScaFaCoS with solver fmm ... -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2 - ghost atom cutoff = 2 - binsize = 1, bins = 16 16 16 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair zero, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.497 | 3.497 | 3.497 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1.5 -0.87378819 0 1.3756625 1.4996338 - 10 1.5000004 -0.87378882 0 1.3756625 1.4996342 - 20 1.4999998 -0.87378782 0 1.3756625 1.4996336 - 30 1.4999934 -0.87377823 0 1.3756625 1.4996272 - 40 1.4999745 -0.87374997 0 1.3756625 1.4996083 - 50 1.4999347 -0.87369019 0 1.3756625 1.4995685 - 60 1.4998637 -0.87358381 0 1.3756625 1.4994975 - 70 1.4997506 -0.87341428 0 1.3756624 1.4993845 - 80 1.4995842 -0.87316464 0 1.3756624 1.499218 - 90 1.4993536 -0.87281897 0 1.3756624 1.4989876 - 100 1.4990503 -0.87236411 0 1.3756624 1.4986843 -Loop time of 1.53742 on 4 procs for 100 steps with 4096 atoms - -Performance: 28099.005 tau/day, 65.044 timesteps/s -99.7% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.00044894 | 0.00045562 | 0.0004611 | 0.0 | 0.03 -Kspace | 1.5223 | 1.5225 | 1.5225 | 0.0 | 99.03 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.0085156 | 0.0086777 | 0.0088782 | 0.1 | 0.56 -Output | 0.00034738 | 0.0003686 | 0.0004015 | 0.0 | 0.02 -Modify | 0.0032606 | 0.0033693 | 0.0034289 | 0.1 | 0.22 -Other | | 0.002084 | | | 0.14 - -Nlocal: 1024 ave 1024 max 1024 min -Histogram: 4 0 0 0 0 0 0 0 0 0 -Nghost: 2525 ave 2525 max 2525 min -Histogram: 4 0 0 0 0 0 0 0 0 0 -Neighs: 16384 ave 16384 max 16384 min -Histogram: 4 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 65536 -Ave neighs/atom = 16 -Neighbor list builds = 0 -Dangerous builds = 0 -Total wall time: 0:00:03 diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.g++.fmm.8 b/examples/USER/scafacos/log.23Jul18.scafacos.g++.fmm.8 deleted file mode 100644 index d5d38d6804..0000000000 --- a/examples/USER/scafacos/log.23Jul18.scafacos.g++.fmm.8 +++ /dev/null @@ -1,102 +0,0 @@ -LAMMPS (29 Jun 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) - using 1 OpenMP thread(s) per MPI task -# Point dipoles in a 2d box - -units lj -atom_style charge - -read_data data.NaCl - orthogonal box = (0 0 0) to (2 2 2) - 2 by 2 by 2 MPI processor grid - reading atoms ... - 8 atoms - -replicate 8 8 8 - orthogonal box = (0 0 0) to (16 16 16) - 2 by 2 by 2 MPI processor grid - 4096 atoms - Time spent = 0.000284672 secs - -velocity all create 1.5 49893 - -neighbor 1.0 bin -neigh_modify delay 0 - -fix 1 all nve - -# LAMMPS computes pairwise and long-range Coulombics - -#pair_style coul/long 3.0 -#pair_coeff * * -#kspace_style pppm 1.0e-3 - -# Scafacos computes entire long-range Coulombics -# use dummy pair style to perform atom sorting - -pair_style zero 1.0 -pair_coeff * * - -#fix 2 all scafacos p3m tolerance field 0.001 - -kspace_style scafacos fmm 0.001 -kspace_modify scafacos tolerance energy_rel - -timestep 0.005 -thermo 10 - -run 100 -Setting up ScaFaCoS with solver fmm ... -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2 - ghost atom cutoff = 2 - binsize = 1, bins = 16 16 16 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair zero, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.416 | 3.416 | 3.416 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1.5 -0.87378819 0 1.3756625 1.4996338 - 10 1.5000004 -0.87378882 0 1.3756625 1.4996342 - 20 1.4999998 -0.87378782 0 1.3756625 1.4996336 - 30 1.4999934 -0.87377823 0 1.3756625 1.4996272 - 40 1.4999745 -0.87374997 0 1.3756625 1.4996083 - 50 1.4999347 -0.87369019 0 1.3756625 1.4995685 - 60 1.4998637 -0.87358381 0 1.3756625 1.4994975 - 70 1.4997506 -0.87341428 0 1.3756624 1.4993845 - 80 1.4995842 -0.87316464 0 1.3756624 1.499218 - 90 1.4993536 -0.87281897 0 1.3756624 1.4989876 - 100 1.4990503 -0.87236411 0 1.3756624 1.4986843 -Loop time of 0.902102 on 8 procs for 100 steps with 4096 atoms - -Performance: 47888.152 tau/day, 110.852 timesteps/s -99.7% CPU use with 8 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.00030732 | 0.00031349 | 0.00032663 | 0.0 | 0.03 -Kspace | 0.89112 | 0.89138 | 0.8916 | 0.0 | 98.81 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.0064399 | 0.0066807 | 0.0070164 | 0.2 | 0.74 -Output | 0.00034571 | 0.00036666 | 0.00041723 | 0.0 | 0.04 -Modify | 0.0018673 | 0.0019273 | 0.0020192 | 0.1 | 0.21 -Other | | 0.001431 | | | 0.16 - -Nlocal: 512 ave 512 max 512 min -Histogram: 8 0 0 0 0 0 0 0 0 0 -Nghost: 1685 ave 1685 max 1685 min -Histogram: 8 0 0 0 0 0 0 0 0 0 -Neighs: 8192 ave 8192 max 8192 min -Histogram: 8 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 65536 -Ave neighs/atom = 16 -Neighbor list builds = 0 -Dangerous builds = 0 -Total wall time: 0:00:02 diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.g++.p2nfft.1 b/examples/USER/scafacos/log.23Jul18.scafacos.g++.p2nfft.1 deleted file mode 100644 index d8b782e41d..0000000000 --- a/examples/USER/scafacos/log.23Jul18.scafacos.g++.p2nfft.1 +++ /dev/null @@ -1,102 +0,0 @@ -LAMMPS (29 Jun 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) - using 1 OpenMP thread(s) per MPI task -# Point dipoles in a 2d box - -units lj -atom_style charge - -read_data data.NaCl - orthogonal box = (0 0 0) to (2 2 2) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 8 atoms - -replicate 8 8 8 - orthogonal box = (0 0 0) to (16 16 16) - 1 by 1 by 1 MPI processor grid - 4096 atoms - Time spent = 0.000631332 secs - -velocity all create 1.5 49893 - -neighbor 1.0 bin -neigh_modify delay 0 - -fix 1 all nve - -# LAMMPS computes pairwise and long-range Coulombics - -#pair_style coul/long 3.0 -#pair_coeff * * -#kspace_style pppm 1.0e-3 - -# Scafacos computes entire long-range Coulombics -# use dummy pair style to perform atom sorting - -pair_style zero 1.0 -pair_coeff * * - -#fix 2 all scafacos p3m tolerance field 0.001 - -kspace_style scafacos p2nfft 0.001 -kspace_modify scafacos tolerance field - -timestep 0.005 -thermo 10 - -run 100 -Setting up ScaFaCoS with solver p2nfft ... -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2 - ghost atom cutoff = 2 - binsize = 1, bins = 16 16 16 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair zero, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.723 | 3.723 | 3.723 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1.5 -0.87394226 0 1.3755084 1.4996338 - 10 1.5000144 -0.87365638 0 1.375816 1.4996482 - 20 1.5000284 -0.87366526 0 1.3758281 1.4996622 - 30 1.5000364 -0.87366516 0 1.3758401 1.4996702 - 40 1.5000313 -0.8736496 0 1.375848 1.4996651 - 50 1.5000039 -0.87360069 0 1.3758558 1.4996377 - 60 1.4999432 -0.87350118 0 1.3758644 1.499577 - 70 1.499838 -0.87333517 0 1.3758726 1.4994719 - 80 1.4996772 -0.87308644 0 1.3758801 1.4993111 - 90 1.4994505 -0.87274307 0 1.3758836 1.4990844 - 100 1.4991498 -0.8722911 0 1.3758846 1.4987838 -Loop time of 9.59682 on 1 procs for 100 steps with 4096 atoms - -Performance: 4501.489 tau/day, 10.420 timesteps/s -100.0% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0011375 | 0.0011375 | 0.0011375 | 0.0 | 0.01 -Kspace | 9.5688 | 9.5688 | 9.5688 | 0.0 | 99.71 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.009017 | 0.009017 | 0.009017 | 0.0 | 0.09 -Output | 0.0004344 | 0.0004344 | 0.0004344 | 0.0 | 0.00 -Modify | 0.012987 | 0.012987 | 0.012987 | 0.0 | 0.14 -Other | | 0.004481 | | | 0.05 - -Nlocal: 4096 ave 4096 max 4096 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 5165 ave 5165 max 5165 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 65536 ave 65536 max 65536 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 65536 -Ave neighs/atom = 16 -Neighbor list builds = 0 -Dangerous builds = 0 -Total wall time: 0:00:10 diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.g++.p2nfft.16 b/examples/USER/scafacos/log.23Jul18.scafacos.g++.p2nfft.16 deleted file mode 100644 index 43bcfb6770..0000000000 --- a/examples/USER/scafacos/log.23Jul18.scafacos.g++.p2nfft.16 +++ /dev/null @@ -1,102 +0,0 @@ -LAMMPS (29 Jun 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) - using 1 OpenMP thread(s) per MPI task -# Point dipoles in a 2d box - -units lj -atom_style charge - -read_data data.NaCl - orthogonal box = (0 0 0) to (2 2 2) - 2 by 2 by 4 MPI processor grid - reading atoms ... - 8 atoms - -replicate 8 8 8 - orthogonal box = (0 0 0) to (16 16 16) - 2 by 2 by 4 MPI processor grid - 4096 atoms - Time spent = 0.000500917 secs - -velocity all create 1.5 49893 - -neighbor 1.0 bin -neigh_modify delay 0 - -fix 1 all nve - -# LAMMPS computes pairwise and long-range Coulombics - -#pair_style coul/long 3.0 -#pair_coeff * * -#kspace_style pppm 1.0e-3 - -# Scafacos computes entire long-range Coulombics -# use dummy pair style to perform atom sorting - -pair_style zero 1.0 -pair_coeff * * - -#fix 2 all scafacos p3m tolerance field 0.001 - -kspace_style scafacos p2nfft 0.001 -kspace_modify scafacos tolerance field - -timestep 0.005 -thermo 10 - -run 100 -Setting up ScaFaCoS with solver p2nfft ... -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2 - ghost atom cutoff = 2 - binsize = 1, bins = 16 16 16 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair zero, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.401 | 3.401 | 3.401 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1.5 -0.87394226 0 1.3755084 1.4996338 - 10 1.5000144 -0.87365638 0 1.375816 1.4996482 - 20 1.5000284 -0.87366526 0 1.3758281 1.4996622 - 30 1.5000364 -0.87366516 0 1.3758401 1.4996702 - 40 1.5000313 -0.8736496 0 1.375848 1.4996651 - 50 1.5000039 -0.87360069 0 1.3758558 1.4996377 - 60 1.4999432 -0.87350118 0 1.3758644 1.499577 - 70 1.499838 -0.87333517 0 1.3758726 1.4994719 - 80 1.4996772 -0.87308644 0 1.3758801 1.4993111 - 90 1.4994505 -0.87274307 0 1.3758836 1.4990844 - 100 1.4991498 -0.8722911 0 1.3758846 1.4987838 -Loop time of 1.20528 on 16 procs for 100 steps with 4096 atoms - -Performance: 35842.175 tau/day, 82.968 timesteps/s -99.3% CPU use with 16 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.00021839 | 0.00025332 | 0.00029278 | 0.0 | 0.02 -Kspace | 1.1945 | 1.1948 | 1.195 | 0.0 | 99.13 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.0066545 | 0.0069329 | 0.0072389 | 0.2 | 0.58 -Output | 0.0003922 | 0.00042732 | 0.00054955 | 0.0 | 0.04 -Modify | 0.0010166 | 0.0011965 | 0.0014412 | 0.3 | 0.10 -Other | | 0.001724 | | | 0.14 - -Nlocal: 256 ave 256 max 256 min -Histogram: 16 0 0 0 0 0 0 0 0 0 -Nghost: 1265 ave 1265 max 1265 min -Histogram: 16 0 0 0 0 0 0 0 0 0 -Neighs: 4096 ave 4096 max 4096 min -Histogram: 16 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 65536 -Ave neighs/atom = 16 -Neighbor list builds = 0 -Dangerous builds = 0 -Total wall time: 0:00:01 diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.g++.p2nfft.2 b/examples/USER/scafacos/log.23Jul18.scafacos.g++.p2nfft.2 deleted file mode 100644 index 9f4f44153b..0000000000 --- a/examples/USER/scafacos/log.23Jul18.scafacos.g++.p2nfft.2 +++ /dev/null @@ -1,102 +0,0 @@ -LAMMPS (29 Jun 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) - using 1 OpenMP thread(s) per MPI task -# Point dipoles in a 2d box - -units lj -atom_style charge - -read_data data.NaCl - orthogonal box = (0 0 0) to (2 2 2) - 1 by 1 by 2 MPI processor grid - reading atoms ... - 8 atoms - -replicate 8 8 8 - orthogonal box = (0 0 0) to (16 16 16) - 1 by 1 by 2 MPI processor grid - 4096 atoms - Time spent = 0.00044775 secs - -velocity all create 1.5 49893 - -neighbor 1.0 bin -neigh_modify delay 0 - -fix 1 all nve - -# LAMMPS computes pairwise and long-range Coulombics - -#pair_style coul/long 3.0 -#pair_coeff * * -#kspace_style pppm 1.0e-3 - -# Scafacos computes entire long-range Coulombics -# use dummy pair style to perform atom sorting - -pair_style zero 1.0 -pair_coeff * * - -#fix 2 all scafacos p3m tolerance field 0.001 - -kspace_style scafacos p2nfft 0.001 -kspace_modify scafacos tolerance field - -timestep 0.005 -thermo 10 - -run 100 -Setting up ScaFaCoS with solver p2nfft ... -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2 - ghost atom cutoff = 2 - binsize = 1, bins = 16 16 16 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair zero, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.634 | 3.634 | 3.634 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1.5 -0.87394226 0 1.3755084 1.4996338 - 10 1.5000144 -0.87365638 0 1.375816 1.4996482 - 20 1.5000284 -0.87366526 0 1.3758281 1.4996622 - 30 1.5000364 -0.87366516 0 1.3758401 1.4996702 - 40 1.5000313 -0.8736496 0 1.375848 1.4996651 - 50 1.5000039 -0.87360069 0 1.3758558 1.4996377 - 60 1.4999432 -0.87350118 0 1.3758644 1.499577 - 70 1.499838 -0.87333517 0 1.3758726 1.4994719 - 80 1.4996772 -0.87308644 0 1.3758801 1.4993111 - 90 1.4994505 -0.87274307 0 1.3758836 1.4990844 - 100 1.4991498 -0.8722911 0 1.3758846 1.4987838 -Loop time of 5.14681 on 2 procs for 100 steps with 4096 atoms - -Performance: 8393.542 tau/day, 19.429 timesteps/s -99.9% CPU use with 2 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.00070882 | 0.00072873 | 0.00074863 | 0.0 | 0.01 -Kspace | 5.1257 | 5.1258 | 5.1258 | 0.0 | 99.59 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.010188 | 0.010291 | 0.010394 | 0.1 | 0.20 -Output | 0.00042391 | 0.00044322 | 0.00046253 | 0.0 | 0.01 -Modify | 0.0063772 | 0.006551 | 0.0067248 | 0.2 | 0.13 -Other | | 0.003026 | | | 0.06 - -Nlocal: 2048 ave 2048 max 2048 min -Histogram: 2 0 0 0 0 0 0 0 0 0 -Nghost: 3685 ave 3685 max 3685 min -Histogram: 2 0 0 0 0 0 0 0 0 0 -Neighs: 32768 ave 32768 max 32768 min -Histogram: 2 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 65536 -Ave neighs/atom = 16 -Neighbor list builds = 0 -Dangerous builds = 0 -Total wall time: 0:00:05 diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.g++.p2nfft.4 b/examples/USER/scafacos/log.23Jul18.scafacos.g++.p2nfft.4 deleted file mode 100644 index d6a78bb193..0000000000 --- a/examples/USER/scafacos/log.23Jul18.scafacos.g++.p2nfft.4 +++ /dev/null @@ -1,102 +0,0 @@ -LAMMPS (29 Jun 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) - using 1 OpenMP thread(s) per MPI task -# Point dipoles in a 2d box - -units lj -atom_style charge - -read_data data.NaCl - orthogonal box = (0 0 0) to (2 2 2) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 8 atoms - -replicate 8 8 8 - orthogonal box = (0 0 0) to (16 16 16) - 1 by 2 by 2 MPI processor grid - 4096 atoms - Time spent = 0.000317335 secs - -velocity all create 1.5 49893 - -neighbor 1.0 bin -neigh_modify delay 0 - -fix 1 all nve - -# LAMMPS computes pairwise and long-range Coulombics - -#pair_style coul/long 3.0 -#pair_coeff * * -#kspace_style pppm 1.0e-3 - -# Scafacos computes entire long-range Coulombics -# use dummy pair style to perform atom sorting - -pair_style zero 1.0 -pair_coeff * * - -#fix 2 all scafacos p3m tolerance field 0.001 - -kspace_style scafacos p2nfft 0.001 -kspace_modify scafacos tolerance field - -timestep 0.005 -thermo 10 - -run 100 -Setting up ScaFaCoS with solver p2nfft ... -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2 - ghost atom cutoff = 2 - binsize = 1, bins = 16 16 16 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair zero, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.497 | 3.497 | 3.497 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1.5 -0.87394226 0 1.3755084 1.4996338 - 10 1.5000144 -0.87365638 0 1.375816 1.4996482 - 20 1.5000284 -0.87366526 0 1.3758281 1.4996622 - 30 1.5000364 -0.87366516 0 1.3758401 1.4996702 - 40 1.5000313 -0.8736496 0 1.375848 1.4996651 - 50 1.5000039 -0.87360069 0 1.3758558 1.4996377 - 60 1.4999432 -0.87350118 0 1.3758644 1.499577 - 70 1.499838 -0.87333517 0 1.3758726 1.4994719 - 80 1.4996772 -0.87308644 0 1.3758801 1.4993111 - 90 1.4994505 -0.87274307 0 1.3758836 1.4990844 - 100 1.4991498 -0.8722911 0 1.3758846 1.4987838 -Loop time of 2.94274 on 4 procs for 100 steps with 4096 atoms - -Performance: 14680.187 tau/day, 33.982 timesteps/s -99.7% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.00048852 | 0.00049287 | 0.00050163 | 0.0 | 0.02 -Kspace | 2.9277 | 2.9279 | 2.928 | 0.0 | 99.49 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.0081494 | 0.0083126 | 0.0084655 | 0.1 | 0.28 -Output | 0.00034475 | 0.00040233 | 0.00043464 | 0.0 | 0.01 -Modify | 0.0034239 | 0.0035145 | 0.0036252 | 0.1 | 0.12 -Other | | 0.00216 | | | 0.07 - -Nlocal: 1024 ave 1024 max 1024 min -Histogram: 4 0 0 0 0 0 0 0 0 0 -Nghost: 2525 ave 2525 max 2525 min -Histogram: 4 0 0 0 0 0 0 0 0 0 -Neighs: 16384 ave 16384 max 16384 min -Histogram: 4 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 65536 -Ave neighs/atom = 16 -Neighbor list builds = 0 -Dangerous builds = 0 -Total wall time: 0:00:03 diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.g++.p2nfft.8 b/examples/USER/scafacos/log.23Jul18.scafacos.g++.p2nfft.8 deleted file mode 100644 index 70716bbcbd..0000000000 --- a/examples/USER/scafacos/log.23Jul18.scafacos.g++.p2nfft.8 +++ /dev/null @@ -1,102 +0,0 @@ -LAMMPS (29 Jun 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) - using 1 OpenMP thread(s) per MPI task -# Point dipoles in a 2d box - -units lj -atom_style charge - -read_data data.NaCl - orthogonal box = (0 0 0) to (2 2 2) - 2 by 2 by 2 MPI processor grid - reading atoms ... - 8 atoms - -replicate 8 8 8 - orthogonal box = (0 0 0) to (16 16 16) - 2 by 2 by 2 MPI processor grid - 4096 atoms - Time spent = 0.000422239 secs - -velocity all create 1.5 49893 - -neighbor 1.0 bin -neigh_modify delay 0 - -fix 1 all nve - -# LAMMPS computes pairwise and long-range Coulombics - -#pair_style coul/long 3.0 -#pair_coeff * * -#kspace_style pppm 1.0e-3 - -# Scafacos computes entire long-range Coulombics -# use dummy pair style to perform atom sorting - -pair_style zero 1.0 -pair_coeff * * - -#fix 2 all scafacos p3m tolerance field 0.001 - -kspace_style scafacos p2nfft 0.001 -kspace_modify scafacos tolerance field - -timestep 0.005 -thermo 10 - -run 100 -Setting up ScaFaCoS with solver p2nfft ... -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2 - ghost atom cutoff = 2 - binsize = 1, bins = 16 16 16 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair zero, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.416 | 3.416 | 3.416 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1.5 -0.87394226 0 1.3755084 1.4996338 - 10 1.5000144 -0.87365638 0 1.375816 1.4996482 - 20 1.5000284 -0.87366526 0 1.3758281 1.4996622 - 30 1.5000364 -0.87366516 0 1.3758401 1.4996702 - 40 1.5000313 -0.8736496 0 1.375848 1.4996651 - 50 1.5000039 -0.87360069 0 1.3758558 1.4996377 - 60 1.4999432 -0.87350118 0 1.3758644 1.499577 - 70 1.499838 -0.87333517 0 1.3758726 1.4994719 - 80 1.4996772 -0.87308644 0 1.3758801 1.4993111 - 90 1.4994505 -0.87274307 0 1.3758836 1.4990844 - 100 1.4991498 -0.8722911 0 1.3758846 1.4987838 -Loop time of 1.75933 on 8 procs for 100 steps with 4096 atoms - -Performance: 24554.819 tau/day, 56.840 timesteps/s -99.4% CPU use with 8 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.00030684 | 0.00031838 | 0.00032926 | 0.0 | 0.02 -Kspace | 1.7474 | 1.7477 | 1.748 | 0.0 | 99.34 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.0068667 | 0.0072413 | 0.0075011 | 0.2 | 0.41 -Output | 0.00036955 | 0.00038695 | 0.00044942 | 0.0 | 0.02 -Modify | 0.0018206 | 0.0019438 | 0.0020213 | 0.1 | 0.11 -Other | | 0.001739 | | | 0.10 - -Nlocal: 512 ave 512 max 512 min -Histogram: 8 0 0 0 0 0 0 0 0 0 -Nghost: 1685 ave 1685 max 1685 min -Histogram: 8 0 0 0 0 0 0 0 0 0 -Neighs: 8192 ave 8192 max 8192 min -Histogram: 8 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 65536 -Ave neighs/atom = 16 -Neighbor list builds = 0 -Dangerous builds = 0 -Total wall time: 0:00:02 diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.direct.1 b/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.direct.1 deleted file mode 100644 index 37d12bb37d..0000000000 --- a/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.direct.1 +++ /dev/null @@ -1,105 +0,0 @@ -LAMMPS (29 Jun 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) - using 1 OpenMP thread(s) per MPI task -# Point dipoles in a 2d box - -units lj -atom_style charge - -read_data data.hammersley_shphere - orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 1000 atoms -change_box all boundary f f f - -velocity all create 1.5 49893 - -neighbor 1.0 bin -neigh_modify delay 0 - -fix 1 all nve - -# LAMMPS computes pairwise and long-range Coulombics - -#pair_style coul/long 3.0 -#pair_coeff * * -#kspace_style pppm 1.0e-3 - -# Scafacos computes entire long-range Coulombics -# use dummy pair style to perform atom sorting - -pair_style zero 1.0 -pair_coeff * * - -#fix 2 all scafacos p3m tolerance field 0.001 - -kspace_style scafacos direct 0.001 - -timestep 0.005 -thermo 1 -run 20 -Setting up ScaFaCoS with solver direct ... -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2 - ghost atom cutoff = 2 - binsize = 1, bins = 102 102 102 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair zero, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 10.3 | 10.3 | 10.3 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1.5 -0.62417787 0 1.6235721 0.00141207 - 1 18.780041 -10.770002 0 17.371889 0.017679155 - 2 65.289192 -11.084705 0 86.751149 0.06146194 - 3 121.92987 -7.0625759 0 175.64933 0.11478234 - 4 185.78164 -5.8777512 0 272.51604 0.17489112 - 5 286.36222 -4.382053 0 424.73173 0.26957567 - 6 481.42206 -4.3095567 0 717.1014 0.4532011 - 7 488.59167 -3.8685194 0 728.2861 0.45995044 - 8 497.85287 -3.0417966 0 742.99073 0.46866874 - 9 499.61615 -3.419003 0 745.2558 0.47032866 - 10 502.63684 -2.8360961 0 750.36521 0.47317227 - 11 504.4846 -2.7628105 0 753.20736 0.47491172 - 12 506.54485 -2.8460356 0 756.21142 0.47685119 - 13 508.27211 -2.730935 0 758.91482 0.4784772 - 14 510.57045 -2.6094877 0 762.48033 0.48064081 - 15 513.14798 -2.7150827 0 766.23717 0.48306726 - 16 515.78124 -2.3961811 0 770.50201 0.48554615 - 17 515.70265 -2.2982683 0 770.48215 0.48547216 - 18 515.7081 -2.1515983 0 770.63699 0.4854773 - 19 515.74906 -2.0581436 0 770.79182 0.48551586 - 20 515.70883 -1.8922577 0 770.89742 0.48547798 -Loop time of 0.52055 on 1 procs for 20 steps with 1000 atoms - -Performance: 16597.836 tau/day, 38.421 timesteps/s -99.7% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.00027752 | 0.00027752 | 0.00027752 | 0.0 | 0.05 -Kspace | 0.35879 | 0.35879 | 0.35879 | 0.0 | 68.93 -Neigh | 0.15946 | 0.15946 | 0.15946 | 0.0 | 30.63 -Comm | 0.00024056 | 0.00024056 | 0.00024056 | 0.0 | 0.05 -Output | 0.00034761 | 0.00034761 | 0.00034761 | 0.0 | 0.07 -Modify | 0.00071192 | 0.00071192 | 0.00071192 | 0.0 | 0.14 -Other | | 0.0007269 | | | 0.14 - -Nlocal: 1000 ave 1000 max 1000 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 247817 ave 247817 max 247817 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 247817 -Ave neighs/atom = 247.817 -Neighbor list builds = 19 -Dangerous builds = 18 -Total wall time: 0:00:00 diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.direct.2 b/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.direct.2 deleted file mode 100644 index 7a22e62bce..0000000000 --- a/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.direct.2 +++ /dev/null @@ -1,105 +0,0 @@ -LAMMPS (29 Jun 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) - using 1 OpenMP thread(s) per MPI task -# Point dipoles in a 2d box - -units lj -atom_style charge - -read_data data.hammersley_shphere - orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5) - 1 by 1 by 2 MPI processor grid - reading atoms ... - 1000 atoms -change_box all boundary f f f - -velocity all create 1.5 49893 - -neighbor 1.0 bin -neigh_modify delay 0 - -fix 1 all nve - -# LAMMPS computes pairwise and long-range Coulombics - -#pair_style coul/long 3.0 -#pair_coeff * * -#kspace_style pppm 1.0e-3 - -# Scafacos computes entire long-range Coulombics -# use dummy pair style to perform atom sorting - -pair_style zero 1.0 -pair_coeff * * - -#fix 2 all scafacos p3m tolerance field 0.001 - -kspace_style scafacos direct 0.001 - -timestep 0.005 -thermo 1 -run 20 -Setting up ScaFaCoS with solver direct ... -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2 - ghost atom cutoff = 2 - binsize = 1, bins = 102 102 102 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair zero, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 6.48 | 6.861 | 7.243 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1.5 -0.62417787 0 1.6235721 0.00141207 - 1 18.780041 -10.770002 0 17.371889 0.017679155 - 2 65.289192 -11.084705 0 86.751149 0.06146194 - 3 121.92987 -7.0625759 0 175.64933 0.11478234 - 4 185.78164 -5.8777512 0 272.51604 0.17489112 - 5 286.36222 -4.382053 0 424.73173 0.26957567 - 6 481.42206 -4.3095567 0 717.1014 0.4532011 - 7 488.59167 -3.8685194 0 728.2861 0.45995044 - 8 497.85287 -3.0417966 0 742.99073 0.46866874 - 9 499.61615 -3.419003 0 745.2558 0.47032866 - 10 502.63684 -2.8360961 0 750.36521 0.47317227 - 11 504.4846 -2.7628105 0 753.20736 0.47491172 - 12 506.54485 -2.8460356 0 756.21142 0.47685119 - 13 508.27211 -2.730935 0 758.91482 0.4784772 - 14 510.57045 -2.6094877 0 762.48033 0.48064081 - 15 513.14798 -2.7150827 0 766.23717 0.48306726 - 16 515.78124 -2.3961811 0 770.50201 0.48554615 - 17 515.70265 -2.2982683 0 770.48215 0.48547216 - 18 515.7081 -2.1515983 0 770.63699 0.4854773 - 19 515.74906 -2.0581436 0 770.79182 0.48551586 - 20 515.70883 -1.8922577 0 770.89742 0.48547798 -Loop time of 0.330519 on 2 procs for 20 steps with 1000 atoms - -Performance: 26140.700 tau/day, 60.511 timesteps/s -99.6% CPU use with 2 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0002749 | 0.00027692 | 0.00027895 | 0.0 | 0.08 -Kspace | 0.21565 | 0.24173 | 0.26782 | 5.3 | 73.14 -Neigh | 0.058644 | 0.084906 | 0.11117 | 9.0 | 25.69 -Comm | 0.002033 | 0.0022832 | 0.0025334 | 0.5 | 0.69 -Output | 0.00035667 | 0.0004549 | 0.00055313 | 0.0 | 0.14 -Modify | 0.0004704 | 0.00050521 | 0.00054002 | 0.0 | 0.15 -Other | | 0.0003613 | | | 0.11 - -Nlocal: 500 ave 516 max 484 min -Histogram: 1 0 0 0 0 0 0 0 0 1 -Nghost: 456.5 ave 475 max 438 min -Histogram: 1 0 0 0 0 0 0 0 0 1 -Neighs: 123908 ave 172139 max 75678 min -Histogram: 1 0 0 0 0 0 0 0 0 1 - -Total # of neighbors = 247817 -Ave neighs/atom = 247.817 -Neighbor list builds = 19 -Dangerous builds = 18 -Total wall time: 0:00:00 diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.direct.4 b/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.direct.4 deleted file mode 100644 index 51d0f8c47e..0000000000 --- a/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.direct.4 +++ /dev/null @@ -1,105 +0,0 @@ -LAMMPS (29 Jun 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) - using 1 OpenMP thread(s) per MPI task -# Point dipoles in a 2d box - -units lj -atom_style charge - -read_data data.hammersley_shphere - orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 1000 atoms -change_box all boundary f f f - -velocity all create 1.5 49893 - -neighbor 1.0 bin -neigh_modify delay 0 - -fix 1 all nve - -# LAMMPS computes pairwise and long-range Coulombics - -#pair_style coul/long 3.0 -#pair_coeff * * -#kspace_style pppm 1.0e-3 - -# Scafacos computes entire long-range Coulombics -# use dummy pair style to perform atom sorting - -pair_style zero 1.0 -pair_coeff * * - -#fix 2 all scafacos p3m tolerance field 0.001 - -kspace_style scafacos direct 0.001 - -timestep 0.005 -thermo 1 -run 20 -Setting up ScaFaCoS with solver direct ... -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2 - ghost atom cutoff = 2 - binsize = 1, bins = 102 102 102 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair zero, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 4.837 | 5.123 | 5.6 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1.5 -0.62417787 0 1.6235721 0.00141207 - 1 18.780041 -10.770002 0 17.371889 0.017679155 - 2 65.289192 -11.084705 0 86.751149 0.06146194 - 3 121.92987 -7.0625759 0 175.64933 0.11478234 - 4 185.78164 -5.8777512 0 272.51604 0.17489112 - 5 286.36222 -4.382053 0 424.73173 0.26957567 - 6 481.42206 -4.3095567 0 717.1014 0.4532011 - 7 488.59167 -3.8685194 0 728.2861 0.45995044 - 8 497.85287 -3.0417966 0 742.99073 0.46866874 - 9 499.61615 -3.419003 0 745.2558 0.47032866 - 10 502.63684 -2.8360961 0 750.36521 0.47317227 - 11 504.4846 -2.7628105 0 753.20736 0.47491172 - 12 506.54485 -2.8460356 0 756.21142 0.47685119 - 13 508.27211 -2.730935 0 758.91482 0.4784772 - 14 510.57045 -2.6094877 0 762.48033 0.48064081 - 15 513.14798 -2.7150827 0 766.23717 0.48306726 - 16 515.78124 -2.3961811 0 770.50201 0.48554615 - 17 515.70265 -2.2982683 0 770.48215 0.48547216 - 18 515.7081 -2.1515983 0 770.63699 0.4854773 - 19 515.74906 -2.0581436 0 770.79182 0.48551586 - 20 515.70883 -1.8922577 0 770.89742 0.48547798 -Loop time of 0.197141 on 4 procs for 20 steps with 1000 atoms - -Performance: 43826.435 tau/day, 101.450 timesteps/s -99.6% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0002718 | 0.00027621 | 0.00028539 | 0.0 | 0.14 -Kspace | 0.12861 | 0.14654 | 0.16542 | 3.7 | 74.33 -Neigh | 0.027906 | 0.046895 | 0.064943 | 6.6 | 23.79 -Comm | 0.0022087 | 0.0024236 | 0.0026295 | 0.4 | 1.23 -Output | 0.0003252 | 0.00044608 | 0.0006001 | 0.0 | 0.23 -Modify | 0.00016618 | 0.0001756 | 0.00018811 | 0.0 | 0.09 -Other | | 0.0003839 | | | 0.19 - -Nlocal: 250 ave 259 max 238 min -Histogram: 1 0 0 1 0 0 0 0 0 2 -Nghost: 672.25 ave 683 max 663 min -Histogram: 2 0 0 0 0 0 0 0 1 1 -Neighs: 61954.2 ave 97157 max 25016 min -Histogram: 1 0 0 1 0 0 1 0 0 1 - -Total # of neighbors = 247817 -Ave neighs/atom = 247.817 -Neighbor list builds = 19 -Dangerous builds = 18 -Total wall time: 0:00:00 diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.direct.8 b/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.direct.8 deleted file mode 100644 index 90119a101b..0000000000 --- a/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.direct.8 +++ /dev/null @@ -1,105 +0,0 @@ -LAMMPS (29 Jun 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) - using 1 OpenMP thread(s) per MPI task -# Point dipoles in a 2d box - -units lj -atom_style charge - -read_data data.hammersley_shphere - orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5) - 2 by 2 by 2 MPI processor grid - reading atoms ... - 1000 atoms -change_box all boundary f f f - -velocity all create 1.5 49893 - -neighbor 1.0 bin -neigh_modify delay 0 - -fix 1 all nve - -# LAMMPS computes pairwise and long-range Coulombics - -#pair_style coul/long 3.0 -#pair_coeff * * -#kspace_style pppm 1.0e-3 - -# Scafacos computes entire long-range Coulombics -# use dummy pair style to perform atom sorting - -pair_style zero 1.0 -pair_coeff * * - -#fix 2 all scafacos p3m tolerance field 0.001 - -kspace_style scafacos direct 0.001 - -timestep 0.005 -thermo 1 -run 20 -Setting up ScaFaCoS with solver direct ... -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2 - ghost atom cutoff = 2 - binsize = 1, bins = 102 102 102 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair zero, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 4.164 | 4.26 | 4.546 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1.5 -0.62417787 0 1.6235721 0.00141207 - 1 18.780041 -10.770002 0 17.371889 0.017679155 - 2 65.289192 -11.084705 0 86.751149 0.06146194 - 3 121.92987 -7.0625759 0 175.64933 0.11478234 - 4 185.78164 -5.8777512 0 272.51604 0.17489112 - 5 286.36222 -4.382053 0 424.73173 0.26957567 - 6 481.42206 -4.3095567 0 717.1014 0.4532011 - 7 488.59167 -3.8685194 0 728.2861 0.45995044 - 8 497.85287 -3.0417966 0 742.99073 0.46866874 - 9 499.61615 -3.419003 0 745.2558 0.47032866 - 10 502.63684 -2.8360961 0 750.36521 0.47317227 - 11 504.4846 -2.7628105 0 753.20736 0.47491172 - 12 506.54485 -2.8460356 0 756.21142 0.47685119 - 13 508.27211 -2.730935 0 758.91482 0.4784772 - 14 510.57045 -2.6094877 0 762.48033 0.48064081 - 15 513.14798 -2.7150827 0 766.23717 0.48306726 - 16 515.78124 -2.3961811 0 770.50201 0.48554615 - 17 515.70265 -2.2982683 0 770.48215 0.48547216 - 18 515.7081 -2.1515983 0 770.63699 0.4854773 - 19 515.74906 -2.0581436 0 770.79182 0.48551586 - 20 515.70883 -1.8922577 0 770.89742 0.48547798 -Loop time of 0.107014 on 8 procs for 20 steps with 1000 atoms - -Performance: 80736.875 tau/day, 186.891 timesteps/s -98.8% CPU use with 8 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.00027704 | 0.00029281 | 0.00035691 | 0.0 | 0.27 -Kspace | 0.069458 | 0.07877 | 0.089146 | 2.5 | 73.61 -Neigh | 0.013525 | 0.024156 | 0.033524 | 4.7 | 22.57 -Comm | 0.002552 | 0.0029828 | 0.0033691 | 0.5 | 2.79 -Output | 0.00037909 | 0.00051123 | 0.00070429 | 0.0 | 0.48 -Modify | 8.9645e-05 | 9.5487e-05 | 0.000103 | 0.0 | 0.09 -Other | | 0.0002059 | | | 0.19 - -Nlocal: 125 ave 133 max 113 min -Histogram: 2 0 0 0 0 1 1 0 2 2 -Nghost: 773.625 ave 788 max 764 min -Histogram: 1 1 2 1 1 0 0 0 1 1 -Neighs: 30977.1 ave 50690 max 10447 min -Histogram: 1 1 1 0 1 1 0 0 2 1 - -Total # of neighbors = 247817 -Ave neighs/atom = 247.817 -Neighbor list builds = 19 -Dangerous builds = 18 -Total wall time: 0:00:00 diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.fmm.1 b/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.fmm.1 deleted file mode 100644 index 432ea72b67..0000000000 --- a/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.fmm.1 +++ /dev/null @@ -1,109 +0,0 @@ -LAMMPS (29 Jun 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) - using 1 OpenMP thread(s) per MPI task -# Point dipoles in a 2d box - -units lj -atom_style charge - -read_data data.hammersley_shphere - orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 1000 atoms -change_box all boundary f f f - -velocity all create 1.5 49893 - -neighbor 1.0 bin -neigh_modify delay 0 - -fix 1 all nve - -# LAMMPS computes pairwise and long-range Coulombics - -#pair_style coul/long 3.0 -#pair_coeff * * -#kspace_style pppm 1.0e-3 - -# Scafacos computes entire long-range Coulombics -# use dummy pair style to perform atom sorting - -pair_style zero 1.0 -pair_coeff * * - -#fix 2 all scafacos p3m tolerance field 0.001 - -kspace_style scafacos fmm 0.001 -kspace_modify scafacos tolerance energy_rel -kspace_modify scafacos fmm_tuning 1 -ScaFaCoS setting fmm inhomogen tuning ...3 - -timestep 0.005 -thermo 1 - -run 20 -Setting up ScaFaCoS with solver fmm ... -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2 - ghost atom cutoff = 2 - binsize = 1, bins = 102 102 102 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair zero, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 10.3 | 10.3 | 10.3 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1.5 -0.62417141 0 1.6235786 0.00141207 - 1 18.780412 -10.770009 0 17.372438 0.017679504 - 2 65.294131 -11.084501 0 86.758754 0.06146659 - 3 121.92555 -7.0612033 0 175.64423 0.11477827 - 4 185.71165 -5.8781334 0 272.41077 0.17482523 - 5 286.28339 -4.3800108 0 424.61565 0.26950146 - 6 481.28097 -4.3052012 0 716.89433 0.45306828 - 7 487.26022 -3.8672741 0 726.29216 0.45869703 - 8 493.65478 -3.0242687 0 736.71742 0.46471675 - 9 495.66203 -3.4336343 0 739.31592 0.46660633 - 10 498.41831 -2.8837072 0 743.99613 0.46920104 - 11 499.20944 -2.7724783 0 745.29287 0.46994579 - 12 500.97345 -2.8281484 0 747.88057 0.4716064 - 13 507.46412 -2.7752775 0 757.65971 0.47771658 - 14 525.35729 -2.5749814 0 784.67292 0.49456085 - 15 563.9578 -2.9982381 0 842.09253 0.5308986 - 16 645.47602 -2.5519203 0 964.69389 0.60763822 - 17 647.09276 -2.2568468 0 967.41166 0.60916019 - 18 647.12596 -2.2791003 0 967.43915 0.60919144 - 19 647.24862 -2.2495226 0 967.65253 0.60930691 - 20 647.51175 -2.0239179 0 968.27244 0.60955462 -Loop time of 0.644143 on 1 procs for 20 steps with 1000 atoms - -Performance: 13413.173 tau/day, 31.049 timesteps/s -99.7% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.00027657 | 0.00027657 | 0.00027657 | 0.0 | 0.04 -Kspace | 0.4788 | 0.4788 | 0.4788 | 0.0 | 74.33 -Neigh | 0.16279 | 0.16279 | 0.16279 | 0.0 | 25.27 -Comm | 0.00021696 | 0.00021696 | 0.00021696 | 0.0 | 0.03 -Output | 0.00054836 | 0.00054836 | 0.00054836 | 0.0 | 0.09 -Modify | 0.00075102 | 0.00075102 | 0.00075102 | 0.0 | 0.12 -Other | | 0.000757 | | | 0.12 - -Nlocal: 1000 ave 1000 max 1000 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 244342 ave 244342 max 244342 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 244342 -Ave neighs/atom = 244.342 -Neighbor list builds = 19 -Dangerous builds = 18 -Total wall time: 0:00:00 diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.fmm.2 b/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.fmm.2 deleted file mode 100644 index 4d4b1100e3..0000000000 --- a/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.fmm.2 +++ /dev/null @@ -1,109 +0,0 @@ -LAMMPS (29 Jun 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) - using 1 OpenMP thread(s) per MPI task -# Point dipoles in a 2d box - -units lj -atom_style charge - -read_data data.hammersley_shphere - orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5) - 1 by 1 by 2 MPI processor grid - reading atoms ... - 1000 atoms -change_box all boundary f f f - -velocity all create 1.5 49893 - -neighbor 1.0 bin -neigh_modify delay 0 - -fix 1 all nve - -# LAMMPS computes pairwise and long-range Coulombics - -#pair_style coul/long 3.0 -#pair_coeff * * -#kspace_style pppm 1.0e-3 - -# Scafacos computes entire long-range Coulombics -# use dummy pair style to perform atom sorting - -pair_style zero 1.0 -pair_coeff * * - -#fix 2 all scafacos p3m tolerance field 0.001 - -kspace_style scafacos fmm 0.001 -kspace_modify scafacos tolerance energy_rel -kspace_modify scafacos fmm_tuning 1 -ScaFaCoS setting fmm inhomogen tuning ...3 - -timestep 0.005 -thermo 1 - -run 20 -Setting up ScaFaCoS with solver fmm ... -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2 - ghost atom cutoff = 2 - binsize = 1, bins = 102 102 102 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair zero, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 6.48 | 6.861 | 7.243 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1.5 -0.62417141 0 1.6235786 0.00141207 - 1 18.780412 -10.770009 0 17.372438 0.017679504 - 2 65.294131 -11.084501 0 86.758754 0.06146659 - 3 121.92555 -7.0612033 0 175.64423 0.11477827 - 4 185.71165 -5.8781334 0 272.41077 0.17482523 - 5 286.28339 -4.3800108 0 424.61565 0.26950146 - 6 481.28097 -4.3052012 0 716.89433 0.45306828 - 7 487.26022 -3.8672741 0 726.29216 0.45869703 - 8 493.65478 -3.0242687 0 736.71742 0.46471675 - 9 495.66203 -3.4336343 0 739.31592 0.46660633 - 10 498.41831 -2.8837072 0 743.99613 0.46920104 - 11 499.20944 -2.7724783 0 745.29287 0.46994579 - 12 500.97345 -2.8281484 0 747.88057 0.4716064 - 13 507.46412 -2.7752775 0 757.65971 0.47771658 - 14 525.35729 -2.5749814 0 784.67292 0.49456085 - 15 563.9578 -2.9982381 0 842.09253 0.5308986 - 16 645.47602 -2.5519203 0 964.69389 0.60763822 - 17 647.09276 -2.2568468 0 967.41166 0.60916019 - 18 647.12596 -2.2791003 0 967.43915 0.60919144 - 19 647.24862 -2.2495226 0 967.65253 0.60930691 - 20 647.51175 -2.0239179 0 968.27244 0.60955462 -Loop time of 0.563049 on 2 procs for 20 steps with 1000 atoms - -Performance: 15345.024 tau/day, 35.521 timesteps/s -99.4% CPU use with 2 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.00024986 | 0.00026596 | 0.00028205 | 0.0 | 0.05 -Kspace | 0.45103 | 0.47692 | 0.50281 | 3.7 | 84.70 -Neigh | 0.055771 | 0.081813 | 0.10785 | 9.1 | 14.53 -Comm | 0.0022206 | 0.0024507 | 0.0026808 | 0.5 | 0.44 -Output | 0.00050044 | 0.00061882 | 0.00073719 | 0.0 | 0.11 -Modify | 0.00029945 | 0.00044227 | 0.00058508 | 0.0 | 0.08 -Other | | 0.0005381 | | | 0.10 - -Nlocal: 500 ave 509 max 491 min -Histogram: 1 0 0 0 0 0 0 0 0 1 -Nghost: 455.5 ave 467 max 444 min -Histogram: 1 0 0 0 0 0 0 0 0 1 -Neighs: 122171 ave 171834 max 72508 min -Histogram: 1 0 0 0 0 0 0 0 0 1 - -Total # of neighbors = 244342 -Ave neighs/atom = 244.342 -Neighbor list builds = 19 -Dangerous builds = 18 -Total wall time: 0:00:01 diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.fmm.4 b/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.fmm.4 deleted file mode 100644 index 9634a0174b..0000000000 --- a/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.fmm.4 +++ /dev/null @@ -1,109 +0,0 @@ -LAMMPS (29 Jun 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) - using 1 OpenMP thread(s) per MPI task -# Point dipoles in a 2d box - -units lj -atom_style charge - -read_data data.hammersley_shphere - orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 1000 atoms -change_box all boundary f f f - -velocity all create 1.5 49893 - -neighbor 1.0 bin -neigh_modify delay 0 - -fix 1 all nve - -# LAMMPS computes pairwise and long-range Coulombics - -#pair_style coul/long 3.0 -#pair_coeff * * -#kspace_style pppm 1.0e-3 - -# Scafacos computes entire long-range Coulombics -# use dummy pair style to perform atom sorting - -pair_style zero 1.0 -pair_coeff * * - -#fix 2 all scafacos p3m tolerance field 0.001 - -kspace_style scafacos fmm 0.001 -kspace_modify scafacos tolerance energy_rel -kspace_modify scafacos fmm_tuning 1 -ScaFaCoS setting fmm inhomogen tuning ...3 - -timestep 0.005 -thermo 1 - -run 20 -Setting up ScaFaCoS with solver fmm ... -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2 - ghost atom cutoff = 2 - binsize = 1, bins = 102 102 102 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair zero, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 4.837 | 5.123 | 5.6 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1.5 -0.62417141 0 1.6235786 0.00141207 - 1 18.780412 -10.770009 0 17.372438 0.017679504 - 2 65.294131 -11.084501 0 86.758754 0.06146659 - 3 121.92555 -7.0612033 0 175.64423 0.11477827 - 4 185.71165 -5.8781334 0 272.41077 0.17482523 - 5 286.28339 -4.3800108 0 424.61565 0.26950146 - 6 481.28097 -4.3052012 0 716.89433 0.45306828 - 7 487.26022 -3.8672741 0 726.29216 0.45869703 - 8 493.65478 -3.0242687 0 736.71742 0.46471675 - 9 495.66203 -3.4336343 0 739.31592 0.46660633 - 10 498.41831 -2.8837072 0 743.99613 0.46920104 - 11 499.20944 -2.7724783 0 745.29287 0.46994579 - 12 500.97345 -2.8281484 0 747.88057 0.4716064 - 13 507.46412 -2.7752775 0 757.65971 0.47771658 - 14 525.35729 -2.5749814 0 784.67292 0.49456085 - 15 563.9578 -2.9982381 0 842.09253 0.5308986 - 16 645.47602 -2.5519203 0 964.69389 0.60763822 - 17 647.09276 -2.2568468 0 967.41166 0.60916019 - 18 647.12596 -2.2791003 0 967.43915 0.60919144 - 19 647.24862 -2.2495226 0 967.65253 0.60930691 - 20 647.51175 -2.0239179 0 968.27244 0.60955462 -Loop time of 0.508149 on 4 procs for 20 steps with 1000 atoms - -Performance: 17002.884 tau/day, 39.359 timesteps/s -99.4% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.00024509 | 0.00026453 | 0.00028753 | 0.0 | 0.05 -Kspace | 0.43933 | 0.45836 | 0.47734 | 2.2 | 90.20 -Neigh | 0.025956 | 0.045068 | 0.064242 | 7.2 | 8.87 -Comm | 0.002799 | 0.0030612 | 0.0033174 | 0.4 | 0.60 -Output | 0.00047231 | 0.00058293 | 0.00076509 | 0.0 | 0.11 -Modify | 0.00016856 | 0.0002442 | 0.00042009 | 0.0 | 0.05 -Other | | 0.0005655 | | | 0.11 - -Nlocal: 250 ave 259 max 240 min -Histogram: 1 0 0 0 0 2 0 0 0 1 -Nghost: 668.75 ave 679 max 657 min -Histogram: 1 0 0 0 0 1 1 0 0 1 -Neighs: 61085.5 ave 95363 max 24964 min -Histogram: 1 0 0 1 0 0 0 1 0 1 - -Total # of neighbors = 244342 -Ave neighs/atom = 244.342 -Neighbor list builds = 19 -Dangerous builds = 18 -Total wall time: 0:00:01 diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.fmm.8 b/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.fmm.8 deleted file mode 100644 index a6a020b031..0000000000 --- a/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.fmm.8 +++ /dev/null @@ -1,109 +0,0 @@ -LAMMPS (29 Jun 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) - using 1 OpenMP thread(s) per MPI task -# Point dipoles in a 2d box - -units lj -atom_style charge - -read_data data.hammersley_shphere - orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5) - 2 by 2 by 2 MPI processor grid - reading atoms ... - 1000 atoms -change_box all boundary f f f - -velocity all create 1.5 49893 - -neighbor 1.0 bin -neigh_modify delay 0 - -fix 1 all nve - -# LAMMPS computes pairwise and long-range Coulombics - -#pair_style coul/long 3.0 -#pair_coeff * * -#kspace_style pppm 1.0e-3 - -# Scafacos computes entire long-range Coulombics -# use dummy pair style to perform atom sorting - -pair_style zero 1.0 -pair_coeff * * - -#fix 2 all scafacos p3m tolerance field 0.001 - -kspace_style scafacos fmm 0.001 -kspace_modify scafacos tolerance energy_rel -kspace_modify scafacos fmm_tuning 1 -ScaFaCoS setting fmm inhomogen tuning ...3 - -timestep 0.005 -thermo 1 - -run 20 -Setting up ScaFaCoS with solver fmm ... -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2 - ghost atom cutoff = 2 - binsize = 1, bins = 102 102 102 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair zero, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 4.164 | 4.26 | 4.546 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1.5 -0.62417141 0 1.6235786 0.00141207 - 1 18.780412 -10.770009 0 17.372438 0.017679504 - 2 65.294131 -11.084501 0 86.758754 0.06146659 - 3 121.92555 -7.0612033 0 175.64423 0.11477827 - 4 185.71165 -5.8781334 0 272.41077 0.17482523 - 5 286.28339 -4.3800108 0 424.61565 0.26950146 - 6 481.28097 -4.3052012 0 716.89433 0.45306828 - 7 487.26022 -3.8672741 0 726.29216 0.45869703 - 8 493.65478 -3.0242687 0 736.71742 0.46471675 - 9 495.66203 -3.4336343 0 739.31592 0.46660633 - 10 498.41831 -2.8837072 0 743.99613 0.46920104 - 11 499.20944 -2.7724783 0 745.29287 0.46994579 - 12 500.97345 -2.8281484 0 747.88057 0.4716064 - 13 507.46412 -2.7752775 0 757.65971 0.47771658 - 14 525.35729 -2.5749814 0 784.67292 0.49456085 - 15 563.9578 -2.9982381 0 842.09253 0.5308986 - 16 645.47602 -2.5519203 0 964.69389 0.60763822 - 17 647.09276 -2.2568468 0 967.41166 0.60916019 - 18 647.12596 -2.2791003 0 967.43915 0.60919144 - 19 647.24862 -2.2495226 0 967.65253 0.60930691 - 20 647.51175 -2.0239179 0 968.27244 0.60955462 -Loop time of 0.494261 on 8 procs for 20 steps with 1000 atoms - -Performance: 17480.630 tau/day, 40.464 timesteps/s -99.3% CPU use with 8 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.00027752 | 0.00030088 | 0.0003736 | 0.0 | 0.06 -Kspace | 0.45443 | 0.46295 | 0.47316 | 1.0 | 93.67 -Neigh | 0.014408 | 0.02515 | 0.034048 | 4.6 | 5.09 -Comm | 0.0036254 | 0.0041741 | 0.0048032 | 0.6 | 0.84 -Output | 0.00072742 | 0.0009357 | 0.0012984 | 0.0 | 0.19 -Modify | 0.00011778 | 0.00015756 | 0.00019836 | 0.0 | 0.03 -Other | | 0.000589 | | | 0.12 - -Nlocal: 125 ave 137 max 111 min -Histogram: 1 1 0 0 0 2 2 1 0 1 -Nghost: 768.875 ave 788 max 761 min -Histogram: 4 0 2 0 0 0 1 0 0 1 -Neighs: 30542.8 ave 48077 max 10011 min -Histogram: 1 1 1 0 1 1 0 0 0 3 - -Total # of neighbors = 244342 -Ave neighs/atom = 244.342 -Neighbor list builds = 19 -Dangerous builds = 18 -Total wall time: 0:00:01 diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.p2nfft.1 b/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.p2nfft.1 deleted file mode 100644 index f9192cdfaf..0000000000 --- a/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.p2nfft.1 +++ /dev/null @@ -1,107 +0,0 @@ -LAMMPS (29 Jun 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) - using 1 OpenMP thread(s) per MPI task -# Point dipoles in a 2d box - -units lj -atom_style charge - -read_data data.hammersley_shphere - orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 1000 atoms -change_box all boundary f f f - -velocity all create 1.5 49893 - -neighbor 1.0 bin -neigh_modify delay 0 - -fix 1 all nve - -# LAMMPS computes pairwise and long-range Coulombics - -#pair_style coul/long 3.0 -#pair_coeff * * -#kspace_style pppm 1.0e-3 - -# Scafacos computes entire long-range Coulombics -# use dummy pair style to perform atom sorting - -pair_style zero 1.0 -pair_coeff * * - -#fix 2 all scafacos p3m tolerance field 0.001 - -kspace_style scafacos p2nfft 0.001 -kspace_modify scafacos tolerance potential - -timestep 0.005 -thermo 1 - -run 20 -Setting up ScaFaCoS with solver p2nfft ... -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2 - ghost atom cutoff = 2 - binsize = 1, bins = 102 102 102 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair zero, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 10.3 | 10.3 | 10.3 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1.5 -0.62417787 0 1.6235721 0.00141207 - 1 18.780041 -10.770002 0 17.371889 0.017679155 - 2 65.289192 -11.084705 0 86.751149 0.06146194 - 3 121.92987 -7.0625759 0 175.64933 0.11478234 - 4 185.78164 -5.8777511 0 272.51603 0.17489112 - 5 286.36221 -4.3820531 0 424.73172 0.26957566 - 6 481.42203 -4.3095567 0 717.10136 0.45320108 - 7 488.59165 -3.8685193 0 728.28607 0.45995042 - 8 497.85288 -3.0417938 0 742.99075 0.46866875 - 9 499.61619 -3.4190063 0 745.25585 0.47032869 - 10 502.63691 -2.8360951 0 750.36531 0.47317234 - 11 504.4847 -2.7628089 0 753.20751 0.47491181 - 12 506.54494 -2.8460319 0 756.21157 0.47685128 - 13 508.2722 -2.7309328 0 758.91497 0.47847729 - 14 510.57053 -2.6094792 0 762.48045 0.48064089 - 15 513.14804 -2.7150819 0 766.23726 0.48306731 - 16 515.78127 -2.3961749 0 770.50206 0.48554618 - 17 515.70267 -2.2982581 0 770.48219 0.48547219 - 18 515.70813 -2.1516075 0 770.63702 0.48547732 - 19 515.74908 -2.0581483 0 770.79185 0.48551588 - 20 515.70881 -1.892235 0 770.89742 0.48547797 -Loop time of 1.34132 on 1 procs for 20 steps with 1000 atoms - -Performance: 6441.409 tau/day, 14.911 timesteps/s -100.0% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.00028849 | 0.00028849 | 0.00028849 | 0.0 | 0.02 -Kspace | 1.1744 | 1.1744 | 1.1744 | 0.0 | 87.56 -Neigh | 0.16435 | 0.16435 | 0.16435 | 0.0 | 12.25 -Comm | 0.00021219 | 0.00021219 | 0.00021219 | 0.0 | 0.02 -Output | 0.00051928 | 0.00051928 | 0.00051928 | 0.0 | 0.04 -Modify | 0.00079513 | 0.00079513 | 0.00079513 | 0.0 | 0.06 -Other | | 0.0007439 | | | 0.06 - -Nlocal: 1000 ave 1000 max 1000 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 247817 ave 247817 max 247817 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 247817 -Ave neighs/atom = 247.817 -Neighbor list builds = 19 -Dangerous builds = 18 -Total wall time: 0:00:01 diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.p2nfft.2 b/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.p2nfft.2 deleted file mode 100644 index 4db3e28dbf..0000000000 --- a/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.p2nfft.2 +++ /dev/null @@ -1,107 +0,0 @@ -LAMMPS (29 Jun 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) - using 1 OpenMP thread(s) per MPI task -# Point dipoles in a 2d box - -units lj -atom_style charge - -read_data data.hammersley_shphere - orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5) - 1 by 1 by 2 MPI processor grid - reading atoms ... - 1000 atoms -change_box all boundary f f f - -velocity all create 1.5 49893 - -neighbor 1.0 bin -neigh_modify delay 0 - -fix 1 all nve - -# LAMMPS computes pairwise and long-range Coulombics - -#pair_style coul/long 3.0 -#pair_coeff * * -#kspace_style pppm 1.0e-3 - -# Scafacos computes entire long-range Coulombics -# use dummy pair style to perform atom sorting - -pair_style zero 1.0 -pair_coeff * * - -#fix 2 all scafacos p3m tolerance field 0.001 - -kspace_style scafacos p2nfft 0.001 -kspace_modify scafacos tolerance potential - -timestep 0.005 -thermo 1 - -run 20 -Setting up ScaFaCoS with solver p2nfft ... -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2 - ghost atom cutoff = 2 - binsize = 1, bins = 102 102 102 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair zero, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 6.48 | 6.861 | 7.243 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1.5 -0.62417787 0 1.6235721 0.00141207 - 1 18.780041 -10.770002 0 17.371889 0.017679155 - 2 65.289192 -11.084705 0 86.751149 0.06146194 - 3 121.92987 -7.0625759 0 175.64933 0.11478234 - 4 185.78164 -5.8777511 0 272.51603 0.17489112 - 5 286.36221 -4.3820531 0 424.73172 0.26957566 - 6 481.42203 -4.3095567 0 717.10136 0.45320108 - 7 488.59165 -3.8685193 0 728.28607 0.45995042 - 8 497.85288 -3.0417938 0 742.99075 0.46866875 - 9 499.61619 -3.4190063 0 745.25585 0.47032869 - 10 502.63691 -2.8360951 0 750.36531 0.47317234 - 11 504.4847 -2.7628089 0 753.20751 0.47491181 - 12 506.54494 -2.8460319 0 756.21157 0.47685128 - 13 508.2722 -2.7309328 0 758.91497 0.47847729 - 14 510.57053 -2.6094792 0 762.48045 0.48064089 - 15 513.14804 -2.7150819 0 766.23726 0.48306731 - 16 515.78127 -2.3961749 0 770.50206 0.48554618 - 17 515.70267 -2.2982581 0 770.48219 0.48547219 - 18 515.70813 -2.1516075 0 770.63702 0.48547732 - 19 515.74908 -2.0581483 0 770.79185 0.48551588 - 20 515.70881 -1.892235 0 770.89742 0.48547797 -Loop time of 0.858675 on 2 procs for 20 steps with 1000 atoms - -Performance: 10062.016 tau/day, 23.292 timesteps/s -100.0% CPU use with 2 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.00026321 | 0.00026667 | 0.00027013 | 0.0 | 0.03 -Kspace | 0.74531 | 0.77182 | 0.79833 | 3.0 | 89.89 -Neigh | 0.055915 | 0.082578 | 0.10924 | 9.3 | 9.62 -Comm | 0.0021703 | 0.002401 | 0.0026317 | 0.5 | 0.28 -Output | 0.00048423 | 0.00061262 | 0.000741 | 0.0 | 0.07 -Modify | 0.00034285 | 0.0004636 | 0.00058436 | 0.0 | 0.05 -Other | | 0.0005329 | | | 0.06 - -Nlocal: 500 ave 516 max 484 min -Histogram: 1 0 0 0 0 0 0 0 0 1 -Nghost: 456.5 ave 475 max 438 min -Histogram: 1 0 0 0 0 0 0 0 0 1 -Neighs: 123908 ave 172139 max 75678 min -Histogram: 1 0 0 0 0 0 0 0 0 1 - -Total # of neighbors = 247817 -Ave neighs/atom = 247.817 -Neighbor list builds = 19 -Dangerous builds = 18 -Total wall time: 0:00:01 diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.p2nfft.4 b/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.p2nfft.4 deleted file mode 100644 index 3a2d653106..0000000000 --- a/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.p2nfft.4 +++ /dev/null @@ -1,107 +0,0 @@ -LAMMPS (29 Jun 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) - using 1 OpenMP thread(s) per MPI task -# Point dipoles in a 2d box - -units lj -atom_style charge - -read_data data.hammersley_shphere - orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 1000 atoms -change_box all boundary f f f - -velocity all create 1.5 49893 - -neighbor 1.0 bin -neigh_modify delay 0 - -fix 1 all nve - -# LAMMPS computes pairwise and long-range Coulombics - -#pair_style coul/long 3.0 -#pair_coeff * * -#kspace_style pppm 1.0e-3 - -# Scafacos computes entire long-range Coulombics -# use dummy pair style to perform atom sorting - -pair_style zero 1.0 -pair_coeff * * - -#fix 2 all scafacos p3m tolerance field 0.001 - -kspace_style scafacos p2nfft 0.001 -kspace_modify scafacos tolerance potential - -timestep 0.005 -thermo 1 - -run 20 -Setting up ScaFaCoS with solver p2nfft ... -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2 - ghost atom cutoff = 2 - binsize = 1, bins = 102 102 102 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair zero, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 4.837 | 5.123 | 5.6 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1.5 -0.62417787 0 1.6235721 0.00141207 - 1 18.780041 -10.770002 0 17.371889 0.017679155 - 2 65.289192 -11.084705 0 86.751149 0.06146194 - 3 121.92987 -7.0625759 0 175.64933 0.11478234 - 4 185.78164 -5.8777511 0 272.51603 0.17489112 - 5 286.36221 -4.3820531 0 424.73172 0.26957566 - 6 481.42203 -4.3095567 0 717.10136 0.45320108 - 7 488.59165 -3.8685193 0 728.28607 0.45995042 - 8 497.85288 -3.0417938 0 742.99075 0.46866875 - 9 499.61619 -3.4190063 0 745.25585 0.47032869 - 10 502.63691 -2.8360951 0 750.36531 0.47317234 - 11 504.4847 -2.7628089 0 753.20751 0.47491181 - 12 506.54494 -2.8460319 0 756.21157 0.47685128 - 13 508.2722 -2.7309328 0 758.91497 0.47847729 - 14 510.57053 -2.6094792 0 762.48045 0.48064089 - 15 513.14804 -2.7150819 0 766.23726 0.48306731 - 16 515.78127 -2.3961749 0 770.50206 0.48554618 - 17 515.70267 -2.2982581 0 770.48219 0.48547219 - 18 515.70813 -2.1516075 0 770.63702 0.48547732 - 19 515.74908 -2.0581483 0 770.79185 0.48551588 - 20 515.70881 -1.892235 0 770.89742 0.48547797 -Loop time of 0.540235 on 4 procs for 20 steps with 1000 atoms - -Performance: 15993.051 tau/day, 37.021 timesteps/s -99.3% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.00025725 | 0.00028253 | 0.00031233 | 0.0 | 0.05 -Kspace | 0.47152 | 0.48989 | 0.50709 | 1.9 | 90.68 -Neigh | 0.028196 | 0.045694 | 0.064338 | 6.3 | 8.46 -Comm | 0.0026579 | 0.003028 | 0.0033965 | 0.5 | 0.56 -Output | 0.00049663 | 0.00064254 | 0.00084853 | 0.0 | 0.12 -Modify | 0.00019264 | 0.0002293 | 0.00030923 | 0.0 | 0.04 -Other | | 0.0004709 | | | 0.09 - -Nlocal: 250 ave 259 max 238 min -Histogram: 1 0 0 1 0 0 0 0 0 2 -Nghost: 672.25 ave 683 max 663 min -Histogram: 2 0 0 0 0 0 0 0 1 1 -Neighs: 61954.2 ave 97157 max 25016 min -Histogram: 1 0 0 1 0 0 1 0 0 1 - -Total # of neighbors = 247817 -Ave neighs/atom = 247.817 -Neighbor list builds = 19 -Dangerous builds = 18 -Total wall time: 0:00:00 diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.p2nfft.8 b/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.p2nfft.8 deleted file mode 100644 index 08e68531a9..0000000000 --- a/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.p2nfft.8 +++ /dev/null @@ -1,107 +0,0 @@ -LAMMPS (29 Jun 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) - using 1 OpenMP thread(s) per MPI task -# Point dipoles in a 2d box - -units lj -atom_style charge - -read_data data.hammersley_shphere - orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5) - 2 by 2 by 2 MPI processor grid - reading atoms ... - 1000 atoms -change_box all boundary f f f - -velocity all create 1.5 49893 - -neighbor 1.0 bin -neigh_modify delay 0 - -fix 1 all nve - -# LAMMPS computes pairwise and long-range Coulombics - -#pair_style coul/long 3.0 -#pair_coeff * * -#kspace_style pppm 1.0e-3 - -# Scafacos computes entire long-range Coulombics -# use dummy pair style to perform atom sorting - -pair_style zero 1.0 -pair_coeff * * - -#fix 2 all scafacos p3m tolerance field 0.001 - -kspace_style scafacos p2nfft 0.001 -kspace_modify scafacos tolerance potential - -timestep 0.005 -thermo 1 - -run 20 -Setting up ScaFaCoS with solver p2nfft ... -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2 - ghost atom cutoff = 2 - binsize = 1, bins = 102 102 102 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair zero, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 4.164 | 4.26 | 4.546 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1.5 -0.62417787 0 1.6235721 0.00141207 - 1 18.780041 -10.770002 0 17.371889 0.017679155 - 2 65.289192 -11.084705 0 86.751149 0.06146194 - 3 121.92987 -7.0625759 0 175.64933 0.11478234 - 4 185.78164 -5.8777511 0 272.51603 0.17489112 - 5 286.36221 -4.3820531 0 424.73172 0.26957566 - 6 481.42203 -4.3095567 0 717.10136 0.45320108 - 7 488.59165 -3.8685193 0 728.28607 0.45995042 - 8 497.85288 -3.0417938 0 742.99075 0.46866875 - 9 499.61619 -3.4190063 0 745.25585 0.47032869 - 10 502.63691 -2.8360951 0 750.36531 0.47317234 - 11 504.4847 -2.7628089 0 753.20751 0.47491181 - 12 506.54494 -2.8460319 0 756.21157 0.47685128 - 13 508.2722 -2.7309328 0 758.91497 0.47847729 - 14 510.57053 -2.6094792 0 762.48045 0.48064089 - 15 513.14804 -2.7150819 0 766.23726 0.48306731 - 16 515.78127 -2.3961749 0 770.50206 0.48554618 - 17 515.70267 -2.2982581 0 770.48219 0.48547219 - 18 515.70813 -2.1516075 0 770.63702 0.48547732 - 19 515.74908 -2.0581483 0 770.79185 0.48551588 - 20 515.70881 -1.892235 0 770.89742 0.48547797 -Loop time of 0.317433 on 8 procs for 20 steps with 1000 atoms - -Performance: 27218.342 tau/day, 63.005 timesteps/s -99.6% CPU use with 8 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.00027013 | 0.00028479 | 0.00029206 | 0.0 | 0.09 -Kspace | 0.27742 | 0.28666 | 0.29702 | 1.4 | 90.31 -Neigh | 0.014795 | 0.025382 | 0.03481 | 4.8 | 8.00 -Comm | 0.0034907 | 0.0038758 | 0.0042439 | 0.5 | 1.22 -Output | 0.00055361 | 0.00073573 | 0.0010755 | 0.0 | 0.23 -Modify | 0.00012279 | 0.00014156 | 0.00016165 | 0.0 | 0.04 -Other | | 0.0003535 | | | 0.11 - -Nlocal: 125 ave 133 max 113 min -Histogram: 2 0 0 0 0 1 1 0 2 2 -Nghost: 773.625 ave 788 max 764 min -Histogram: 1 1 2 1 1 0 0 0 1 1 -Neighs: 30977.1 ave 50690 max 10447 min -Histogram: 1 1 1 0 1 1 0 0 2 1 - -Total # of neighbors = 247817 -Ave neighs/atom = 247.817 -Neighbor list builds = 19 -Dangerous builds = 18 -Total wall time: 0:00:00 From fc93a79fdd04234f041aab2a9f7f07d5242585a0 Mon Sep 17 00:00:00 2001 From: Rene Halver Date: Wed, 8 Aug 2018 14:05:28 -0600 Subject: [PATCH 090/302] updated to support ScaFaCoS 1.0.1 --- cmake/CMakeLists.txt | 5 +++-- lib/scafacos/Install.py | 6 +++--- src/USER-SCAFACOS/scafacos.cpp | 22 ++++++++++++++++++++++ 3 files changed, 28 insertions(+), 5 deletions(-) diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index a03548c712..9f1f3a7526 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -360,8 +360,8 @@ if(PKG_USER-SCAFACOS) if(DOWNLOAD_SCAFACOS) include(ExternalProject) ExternalProject_Add(scafacos_build - URL https://github.com/scafacos/scafacos/releases/download/v1.0.0/scafacos-1.0.0.tar.gz - URL_MD5 c75d75d8a4cb9757faddb8b205a2b20f + URL https://github.com/scafacos/scafacos/releases/download/v1.0.1/scafacos-1.0.1.tar.gz + URL_MD5 bd46d74e3296bd8a444d731bb10c1738 CONFIGURE_COMMAND /configure --prefix= --disable-doc --enable-fcs-solvers=fmm,p2nfft,direct,ewald,p3m @@ -389,6 +389,7 @@ if(PKG_USER-SCAFACOS) list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_near.a) list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_gridsort.a) list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_resort.a) + list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_redist.a) list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_common.a) list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_pnfft.a) list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_pfft.a) diff --git a/lib/scafacos/Install.py b/lib/scafacos/Install.py index 4e00e805d1..d23e8a3686 100644 --- a/lib/scafacos/Install.py +++ b/lib/scafacos/Install.py @@ -29,8 +29,8 @@ make lib-scafacos args="-p $HOME/scafacos" # use existing Scafacos installation # settings -version = "scafacos-1.0.0" -url = "https://github.com/scafacos/scafacos/releases/download/v1.0.0/scafacos-1.0.0.tar.gz" +version = "scafacos-1.0.1" +url = "https://github.com/scafacos/scafacos/releases/download/v1.0.1/scafacos-1.0.1.tar.gz" #url = "https://gigamove.rz.rwth-aachen.de/d/id/CTzyApN76MXMJ6/dd/100" % version # print error message or help @@ -147,7 +147,7 @@ if buildflag: if buildflag: print("Building Scafacos ...") - cmd = 'cd "%s"; CC=mpicc FC=mpif90 CXX=mpicxx ./configure --prefix="`pwd`/build" --disable-doc --enable-fcs-solvers=fmm,p2nfft,direct,ewald > log.txt; make -j; make install' % homedir + cmd = 'cd "%s"; ./configure --prefix="`pwd`/build" --disable-doc --enable-fcs-solvers=fmm,p2nfft,direct,ewald,p3m --with-internal-fftw --with-internal-pfft --with-internal-pnfft CC=mpicc FC=mpif90 CXX=mpicxx F77= > log.txt; make -j; make install' % homedir txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) print(txt.decode('UTF-8')) diff --git a/src/USER-SCAFACOS/scafacos.cpp b/src/USER-SCAFACOS/scafacos.cpp index fdbd5e34e0..5832f5b052 100644 --- a/src/USER-SCAFACOS/scafacos.cpp +++ b/src/USER-SCAFACOS/scafacos.cpp @@ -150,6 +150,17 @@ void Scafacos::init() fcs_fmm_set_internal_tuning(fcs,FCS_FMM_HOMOGENOUS_SYSTEM); } + // for the FMM at least one particle is required per process + if (strcmp(method,"fmm") == 0) + { + int empty = (nlocal==0)?1:0; + MPI_Allreduce(MPI_IN_PLACE,&empty,1,MPI_INT,MPI_SUM,world); + if (empty > 0) + fcs_set_redistribute(fcs,1); + else + fcs_set_redistribute(fcs,0); + } + result = fcs_tune(fcs,nlocal,&x[0][0],q); check_result(result); // more useful here, since the parameters should be tuned now @@ -172,6 +183,17 @@ void Scafacos::compute(int eflag, int vflag) const double qscale = qqrd2e; + // for the FMM at least one particle is required per process + if (strcmp(method,"fmm")) + { + int empty = (nlocal==0)?1:0; + MPI_Allreduce(MPI_IN_PLACE,&empty,1,MPI_INT,MPI_SUM,world); + if (empty > 0) + fcs_set_redistribute(fcs,1); + else + fcs_set_redistribute(fcs,0); + } + if (eflag || vflag) ev_setup(eflag,vflag); else { From 2a5e550bdacb74abba6136db9a8c4b80e147774f Mon Sep 17 00:00:00 2001 From: Rene Halver Date: Wed, 8 Aug 2018 15:02:19 -0600 Subject: [PATCH 091/302] updated log files --- .../log.08Aug18.scafacos.cw.g++.ewald.16 | 92 +++++++++++++++ .../log.08Aug18.scafacos.cw.g++.ewald.8 | 92 +++++++++++++++ .../log.08Aug18.scafacos.cw.g++.fmm.1 | 99 ++++++++++++++++ .../log.08Aug18.scafacos.cw.g++.fmm.16 | 99 ++++++++++++++++ .../log.08Aug18.scafacos.cw.g++.fmm.2 | 99 ++++++++++++++++ .../log.08Aug18.scafacos.cw.g++.fmm.4 | 99 ++++++++++++++++ .../log.08Aug18.scafacos.cw.g++.fmm.8 | 99 ++++++++++++++++ .../log.08Aug18.scafacos.cw.g++.p2nfft.1 | 92 +++++++++++++++ .../log.08Aug18.scafacos.cw.g++.p2nfft.16 | 92 +++++++++++++++ .../log.08Aug18.scafacos.cw.g++.p2nfft.2 | 92 +++++++++++++++ .../log.08Aug18.scafacos.cw.g++.p2nfft.4 | 92 +++++++++++++++ .../log.08Aug18.scafacos.cw.g++.p2nfft.8 | 92 +++++++++++++++ .../scafacos/log.08Aug18.scafacos.g++.ewald.1 | 102 ++++++++++++++++ .../log.08Aug18.scafacos.g++.ewald.16 | 102 ++++++++++++++++ .../scafacos/log.08Aug18.scafacos.g++.ewald.2 | 102 ++++++++++++++++ .../scafacos/log.08Aug18.scafacos.g++.ewald.4 | 102 ++++++++++++++++ .../scafacos/log.08Aug18.scafacos.g++.ewald.8 | 102 ++++++++++++++++ .../scafacos/log.08Aug18.scafacos.g++.fmm.1 | 102 ++++++++++++++++ .../scafacos/log.08Aug18.scafacos.g++.fmm.16 | 102 ++++++++++++++++ .../scafacos/log.08Aug18.scafacos.g++.fmm.2 | 102 ++++++++++++++++ .../scafacos/log.08Aug18.scafacos.g++.fmm.4 | 102 ++++++++++++++++ .../scafacos/log.08Aug18.scafacos.g++.fmm.8 | 102 ++++++++++++++++ .../log.08Aug18.scafacos.g++.p2nfft.1 | 102 ++++++++++++++++ .../log.08Aug18.scafacos.g++.p2nfft.16 | 102 ++++++++++++++++ .../log.08Aug18.scafacos.g++.p2nfft.2 | 102 ++++++++++++++++ .../log.08Aug18.scafacos.g++.p2nfft.4 | 102 ++++++++++++++++ .../log.08Aug18.scafacos.g++.p2nfft.8 | 102 ++++++++++++++++ .../scafacos/log.08Aug18.scafacos.g++.p3m.2 | 0 .../log.08Aug18.scafacos.hsph.g++.direct.1 | 105 +++++++++++++++++ .../log.08Aug18.scafacos.hsph.g++.direct.2 | 105 +++++++++++++++++ .../log.08Aug18.scafacos.hsph.g++.direct.4 | 105 +++++++++++++++++ .../log.08Aug18.scafacos.hsph.g++.direct.8 | 105 +++++++++++++++++ .../log.08Aug18.scafacos.hsph.g++.fmm.1 | 109 ++++++++++++++++++ .../log.08Aug18.scafacos.hsph.g++.fmm.2 | 109 ++++++++++++++++++ .../log.08Aug18.scafacos.hsph.g++.fmm.4 | 109 ++++++++++++++++++ .../log.08Aug18.scafacos.hsph.g++.fmm.8 | 109 ++++++++++++++++++ .../log.08Aug18.scafacos.hsph.g++.p2nfft.1 | 107 +++++++++++++++++ .../log.08Aug18.scafacos.hsph.g++.p2nfft.2 | 107 +++++++++++++++++ .../log.08Aug18.scafacos.hsph.g++.p2nfft.4 | 107 +++++++++++++++++ .../log.08Aug18.scafacos.hsph.g++.p2nfft.8 | 107 +++++++++++++++++ 40 files changed, 3953 insertions(+) create mode 100644 examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.ewald.16 create mode 100644 examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.ewald.8 create mode 100644 examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.fmm.1 create mode 100644 examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.fmm.16 create mode 100644 examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.fmm.2 create mode 100644 examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.fmm.4 create mode 100644 examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.fmm.8 create mode 100644 examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.p2nfft.1 create mode 100644 examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.p2nfft.16 create mode 100644 examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.p2nfft.2 create mode 100644 examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.p2nfft.4 create mode 100644 examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.p2nfft.8 create mode 100644 examples/USER/scafacos/log.08Aug18.scafacos.g++.ewald.1 create mode 100644 examples/USER/scafacos/log.08Aug18.scafacos.g++.ewald.16 create mode 100644 examples/USER/scafacos/log.08Aug18.scafacos.g++.ewald.2 create mode 100644 examples/USER/scafacos/log.08Aug18.scafacos.g++.ewald.4 create mode 100644 examples/USER/scafacos/log.08Aug18.scafacos.g++.ewald.8 create mode 100644 examples/USER/scafacos/log.08Aug18.scafacos.g++.fmm.1 create mode 100644 examples/USER/scafacos/log.08Aug18.scafacos.g++.fmm.16 create mode 100644 examples/USER/scafacos/log.08Aug18.scafacos.g++.fmm.2 create mode 100644 examples/USER/scafacos/log.08Aug18.scafacos.g++.fmm.4 create mode 100644 examples/USER/scafacos/log.08Aug18.scafacos.g++.fmm.8 create mode 100644 examples/USER/scafacos/log.08Aug18.scafacos.g++.p2nfft.1 create mode 100644 examples/USER/scafacos/log.08Aug18.scafacos.g++.p2nfft.16 create mode 100644 examples/USER/scafacos/log.08Aug18.scafacos.g++.p2nfft.2 create mode 100644 examples/USER/scafacos/log.08Aug18.scafacos.g++.p2nfft.4 create mode 100644 examples/USER/scafacos/log.08Aug18.scafacos.g++.p2nfft.8 create mode 100644 examples/USER/scafacos/log.08Aug18.scafacos.g++.p3m.2 create mode 100644 examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.direct.1 create mode 100644 examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.direct.2 create mode 100644 examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.direct.4 create mode 100644 examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.direct.8 create mode 100644 examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.fmm.1 create mode 100644 examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.fmm.2 create mode 100644 examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.fmm.4 create mode 100644 examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.fmm.8 create mode 100644 examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.p2nfft.1 create mode 100644 examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.p2nfft.2 create mode 100644 examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.p2nfft.4 create mode 100644 examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.p2nfft.8 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.ewald.16 b/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.ewald.16 new file mode 100644 index 0000000000..20d3faaf7f --- /dev/null +++ b/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.ewald.16 @@ -0,0 +1,92 @@ +LAMMPS (2 Aug 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task + +units lj +atom_style charge + +read_data data.cloud_wall + orthogonal box = (0 0 0) to (10 10 10) + 2 by 2 by 4 MPI processor grid + reading atoms ... + 300 atoms + +velocity all set 0.0 0.0 0.0 mom no + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve +kspace_style scafacos ewald 0.001 +kspace_modify scafacos tolerance field + +timestep 0.005 + +thermo_style custom step atoms cpu temp pe ke etotal ecoul press + +run_style verlet + +#dump simple all custom 1000 id x y z vx vy vz +#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass +#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass +#dump_modify dmpvtk pad 7 + +thermo 10 +run 100 +Setting up ScaFaCoS with solver ewald ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 10 10 10 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.313 | 3.501 | 3.689 Mbytes +Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press + 0 300 0 0 0.49647271 0 0.49647271 0 0 + 10 300 0.051135063 0.014582562 0.44286522 0.02180093 0.46466616 0 0.0043601861 + 20 300 0.10210872 0.058693359 0.37869251 0.087746571 0.46643909 0 0.017549314 + 30 300 0.15278506 0.13468789 0.26730177 0.2013584 0.46866017 0 0.040271679 + 40 300 0.19430375 0.50949535 0.083356437 0.76169555 0.84505198 0 0.15233911 + 50 300 0.23220921 1.1731116 -0.055261984 1.7538018 1.6985399 0 0.35076037 + 60 300 0.27002859 1.3589639 -0.33351524 2.031651 1.6981358 0 0.4063302 + 70 300 0.30781388 1.6482648 -0.76570045 2.4641559 1.6984554 0 0.49283118 + 80 300 0.34566283 2.8640899 -2.4038488 4.2818144 1.8779656 0 0.85636288 + 90 300 0.38424087 93.168442 -2.5911448 139.28682 136.69568 0 27.857364 + 100 300 0.42331123 94.146897 -1.3480439 140.74961 139.40157 0 28.149922 +Loop time of 0.423331 on 16 procs for 100 steps with 300 atoms + +Performance: 102047.913 tau/day, 236.222 timesteps/s +99.2% CPU use with 16 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.5988e-05 | 3.6508e-05 | 5.5075e-05 | 0.0 | 0.01 +Kspace | 0.41852 | 0.41925 | 0.41976 | 0.1 | 99.04 +Neigh | 0.00023413 | 0.00056887 | 0.0012875 | 0.0 | 0.13 +Comm | 0.0019519 | 0.0022772 | 0.0027158 | 0.5 | 0.54 +Output | 0.00028276 | 0.00030752 | 0.0003624 | 0.0 | 0.07 +Modify | 8.3685e-05 | 0.0001286 | 0.00018764 | 0.0 | 0.03 +Other | | 0.000758 | | | 0.18 + +Nlocal: 18.75 ave 39 max 6 min +Histogram: 6 1 1 0 1 2 2 1 1 1 +Nghost: 122.812 ave 195 max 63 min +Histogram: 8 0 0 0 0 0 0 1 3 4 +Neighs: 160.625 ave 598 max 13 min +Histogram: 8 2 1 1 1 0 0 2 0 1 + +Total # of neighbors = 2570 +Ave neighs/atom = 8.56667 +Neighbor list builds = 23 +Dangerous builds = 16 +Total wall time: 0:00:00 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.ewald.8 b/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.ewald.8 new file mode 100644 index 0000000000..d26138522a --- /dev/null +++ b/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.ewald.8 @@ -0,0 +1,92 @@ +LAMMPS (2 Aug 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task + +units lj +atom_style charge + +read_data data.cloud_wall + orthogonal box = (0 0 0) to (10 10 10) + 2 by 2 by 2 MPI processor grid + reading atoms ... + 300 atoms + +velocity all set 0.0 0.0 0.0 mom no + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve +kspace_style scafacos ewald 0.001 +kspace_modify scafacos tolerance field + +timestep 0.005 + +thermo_style custom step atoms cpu temp pe ke etotal ecoul press + +run_style verlet + +#dump simple all custom 1000 id x y z vx vy vz +#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass +#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass +#dump_modify dmpvtk pad 7 + +thermo 10 +run 100 +Setting up ScaFaCoS with solver ewald ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 10 10 10 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.317 | 3.317 | 3.317 Mbytes +Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press + 0 300 0 0 0.49647271 0 0.49647271 0 0 + 10 300 0.057411432 0.014718629 0.45088339 0.02200435 0.47288774 0 0.00440087 + 20 300 0.11482716 0.05922597 0.38470912 0.088542825 0.47325194 0 0.017708565 + 30 300 0.17278481 0.13587829 0.27058048 0.20313804 0.47371852 0 0.040627608 + 40 300 0.23021507 0.51353118 0.088432648 0.76772911 0.85616176 0 0.15354582 + 50 300 0.28812647 1.1760001 -0.058088247 1.7581201 1.7000319 0 0.35162403 + 60 300 0.34651113 1.3627885 -0.33736672 2.0373688 1.7000021 0 0.40747376 + 70 300 0.40509939 1.6529365 -0.77082139 2.4711401 1.7003187 0 0.49422802 + 80 300 0.46342874 2.9569837 -2.4624654 4.4206907 1.9582253 0 0.88413814 + 90 300 0.52329254 81.642726 -2.5370215 122.05588 119.51885 0 24.411175 + 100 300 0.58335209 85.047974 -1.128107 127.14672 126.01861 0 25.429344 +Loop time of 0.583369 on 8 procs for 100 steps with 300 atoms + +Performance: 74052.598 tau/day, 171.418 timesteps/s +99.7% CPU use with 8 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 4.0531e-05 | 4.6492e-05 | 4.8876e-05 | 0.0 | 0.01 +Kspace | 0.57805 | 0.5785 | 0.57893 | 0.0 | 99.17 +Neigh | 0.00062275 | 0.00091892 | 0.0013313 | 0.0 | 0.16 +Comm | 0.002604 | 0.0028289 | 0.0031538 | 0.3 | 0.48 +Output | 0.0002265 | 0.0002434 | 0.00029039 | 0.0 | 0.04 +Modify | 0.00016117 | 0.00017747 | 0.00019884 | 0.0 | 0.03 +Other | | 0.00065 | | | 0.11 + +Nlocal: 37.5 ave 46 max 31 min +Histogram: 2 0 0 2 1 0 2 0 0 1 +Nghost: 203.875 ave 212 max 192 min +Histogram: 1 0 1 0 0 2 1 0 0 3 +Neighs: 321.625 ave 599 max 112 min +Histogram: 1 2 0 1 1 0 1 1 0 1 + +Total # of neighbors = 2573 +Ave neighs/atom = 8.57667 +Neighbor list builds = 23 +Dangerous builds = 16 +Total wall time: 0:00:00 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.fmm.1 b/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.fmm.1 new file mode 100644 index 0000000000..714ce85a5f --- /dev/null +++ b/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.fmm.1 @@ -0,0 +1,99 @@ +LAMMPS (2 Aug 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +units lj +atom_style charge + +read_data data.cloud_wall + orthogonal box = (0 0 0) to (10 10 10) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 300 atoms + +velocity all set 0.0 0.0 0.0 mom no + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +kspace_style scafacos fmm 1.0e-3 +kspace_modify scafacos tolerance energy_rel +kspace_modify scafacos fmm_tuning 1 +ScaFaCoS setting fmm inhomogen tuning ... + +timestep 0.005 + +thermo_style custom step atoms cpu temp pe ke etotal ecoul press + +run_style verlet + +#dump simple all custom 1000 id x y z vx vy vz +#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass +#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass +#dump_modify dmpvtk pad 7 + +thermo 10 +run 100 +Setting up ScaFaCoS with solver fmm ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 10 10 10 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.34 | 3.34 | 3.34 Mbytes +Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press + 0 300 0 0 0.49646402 0 0.49646402 0 0.016548801 + 10 300 0.063865185 0.015455559 0.47335833 0.02310606 0.49646439 0 0.020399823 + 20 300 0.12760854 0.06229069 0.40334177 0.093124582 0.49646635 0 0.032069642 + 30 300 0.19143319 0.14310163 0.28254277 0.21393694 0.49647971 0 0.05220548 + 40 300 0.25553131 0.52929788 0.089669015 0.79130033 0.88096934 0 0.16124903 + 50 300 0.31961966 1.1963022 -0.082792461 1.7884718 1.7056794 0 0.35493462 + 60 300 0.38388991 1.3928167 -0.37659239 2.082261 1.7056686 0 0.40389911 + 70 300 0.44797421 1.7069009 -0.84571914 2.5518169 1.7060978 0 0.48217274 + 80 300 0.50961447 15.358343 -3.368063 22.960722 19.592659 0 4.4798757 + 90 300 0.57181501 42.280432 -2.1623864 63.209247 61.04686 0 12.56977 + 100 300 0.63501096 41.48079 -0.89904529 62.013782 61.114736 0 12.372788 +Loop time of 0.635022 on 1 procs for 100 steps with 300 atoms + +Performance: 68029.122 tau/day, 157.475 timesteps/s +99.7% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 9.0837e-05 | 9.0837e-05 | 9.0837e-05 | 0.0 | 0.01 +Kspace | 0.62877 | 0.62877 | 0.62877 | 0.0 | 99.01 +Neigh | 0.0035319 | 0.0035319 | 0.0035319 | 0.0 | 0.56 +Comm | 0.0010211 | 0.0010211 | 0.0010211 | 0.0 | 0.16 +Output | 0.00014758 | 0.00014758 | 0.00014758 | 0.0 | 0.02 +Modify | 0.0010428 | 0.0010428 | 0.0010428 | 0.0 | 0.16 +Other | | 0.0004218 | | | 0.07 + +Nlocal: 300 ave 300 max 300 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 374 ave 374 max 374 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 2459 ave 2459 max 2459 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 2459 +Ave neighs/atom = 8.19667 +Neighbor list builds = 15 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.fmm.16 b/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.fmm.16 new file mode 100644 index 0000000000..c9c1e0d155 --- /dev/null +++ b/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.fmm.16 @@ -0,0 +1,99 @@ +LAMMPS (2 Aug 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +units lj +atom_style charge + +read_data data.cloud_wall + orthogonal box = (0 0 0) to (10 10 10) + 2 by 2 by 4 MPI processor grid + reading atoms ... + 300 atoms + +velocity all set 0.0 0.0 0.0 mom no + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +kspace_style scafacos fmm 1.0e-3 +kspace_modify scafacos tolerance energy_rel +kspace_modify scafacos fmm_tuning 1 +ScaFaCoS setting fmm inhomogen tuning ... + +timestep 0.005 + +thermo_style custom step atoms cpu temp pe ke etotal ecoul press + +run_style verlet + +#dump simple all custom 1000 id x y z vx vy vz +#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass +#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass +#dump_modify dmpvtk pad 7 + +thermo 10 +run 100 +Setting up ScaFaCoS with solver fmm ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 10 10 10 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.313 | 3.501 | 3.689 Mbytes +Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press + 0 300 0 0 0.49646402 0 0.49646402 0 0.016548801 + 10 300 0.023007393 0.015455559 0.47335833 0.02310606 0.49646439 0 0.020399823 + 20 300 0.045746088 0.06229069 0.40334177 0.093124582 0.49646635 0 0.032069642 + 30 300 0.068123341 0.14310163 0.28254277 0.21393694 0.49647971 0 0.05220548 + 40 300 0.090359211 0.52929788 0.089669015 0.79130033 0.88096934 0 0.16124903 + 50 300 0.11304998 1.1963022 -0.082792461 1.7884718 1.7056794 0 0.35493462 + 60 300 0.13585806 1.3928167 -0.37659239 2.082261 1.7056686 0 0.40389911 + 70 300 0.15867376 1.7069009 -0.84571914 2.5518169 1.7060978 0 0.48217274 + 80 300 0.18324137 15.358343 -3.368063 22.960722 19.592659 0 4.4798757 + 90 300 0.20960689 42.280432 -2.1623864 63.209247 61.04686 0 12.56977 + 100 300 0.23539281 41.48079 -0.89904529 62.013782 61.114736 0 12.372788 +Loop time of 0.235411 on 16 procs for 100 steps with 300 atoms + +Performance: 183509.107 tau/day, 424.790 timesteps/s +97.9% CPU use with 16 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 3.2425e-05 | 4.4718e-05 | 6.1274e-05 | 0.0 | 0.02 +Kspace | 0.23097 | 0.23143 | 0.2318 | 0.1 | 98.31 +Neigh | 0.00015116 | 0.00035347 | 0.00075746 | 0.0 | 0.15 +Comm | 0.0020316 | 0.002282 | 0.0025339 | 0.3 | 0.97 +Output | 0.00034404 | 0.00037053 | 0.00042701 | 0.0 | 0.16 +Modify | 9.3937e-05 | 0.00014532 | 0.00018811 | 0.0 | 0.06 +Other | | 0.0007878 | | | 0.33 + +Nlocal: 18.75 ave 36 max 6 min +Histogram: 4 3 1 0 0 1 2 1 2 2 +Nghost: 127 ave 196 max 71 min +Histogram: 8 0 0 0 0 0 0 1 6 1 +Neighs: 153.688 ave 491 max 10 min +Histogram: 8 1 1 1 1 1 0 0 0 3 + +Total # of neighbors = 2459 +Ave neighs/atom = 8.19667 +Neighbor list builds = 15 +Dangerous builds = 0 +Total wall time: 0:00:01 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.fmm.2 b/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.fmm.2 new file mode 100644 index 0000000000..1a9bc77146 --- /dev/null +++ b/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.fmm.2 @@ -0,0 +1,99 @@ +LAMMPS (2 Aug 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +units lj +atom_style charge + +read_data data.cloud_wall + orthogonal box = (0 0 0) to (10 10 10) + 1 by 1 by 2 MPI processor grid + reading atoms ... + 300 atoms + +velocity all set 0.0 0.0 0.0 mom no + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +kspace_style scafacos fmm 1.0e-3 +kspace_modify scafacos tolerance energy_rel +kspace_modify scafacos fmm_tuning 1 +ScaFaCoS setting fmm inhomogen tuning ... + +timestep 0.005 + +thermo_style custom step atoms cpu temp pe ke etotal ecoul press + +run_style verlet + +#dump simple all custom 1000 id x y z vx vy vz +#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass +#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass +#dump_modify dmpvtk pad 7 + +thermo 10 +run 100 +Setting up ScaFaCoS with solver fmm ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 10 10 10 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.354 | 3.354 | 3.355 Mbytes +Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press + 0 300 0 0 0.49646402 0 0.49646402 0 0.016548801 + 10 300 0.038181543 0.015455559 0.47335833 0.02310606 0.49646439 0 0.020399823 + 20 300 0.076276302 0.06229069 0.40334177 0.093124582 0.49646635 0 0.032069642 + 30 300 0.11437607 0.14310163 0.28254277 0.21393694 0.49647971 0 0.05220548 + 40 300 0.15244293 0.52929788 0.089669015 0.79130033 0.88096934 0 0.16124903 + 50 300 0.19081283 1.1963022 -0.082792461 1.7884718 1.7056794 0 0.35493462 + 60 300 0.22923493 1.3928167 -0.37659239 2.082261 1.7056686 0 0.40389911 + 70 300 0.26754427 1.7069009 -0.84571914 2.5518169 1.7060978 0 0.48217274 + 80 300 0.30721259 15.358343 -3.368063 22.960722 19.592659 0 4.4798757 + 90 300 0.34865618 42.280432 -2.1623864 63.209247 61.04686 0 12.56977 + 100 300 0.39100981 41.48079 -0.89904529 62.013782 61.114736 0 12.372788 +Loop time of 0.391022 on 2 procs for 100 steps with 300 atoms + +Performance: 110479.760 tau/day, 255.740 timesteps/s +99.6% CPU use with 2 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 8.0109e-05 | 8.1539e-05 | 8.297e-05 | 0.0 | 0.02 +Kspace | 0.38534 | 0.38582 | 0.3863 | 0.1 | 98.67 +Neigh | 0.0014851 | 0.0019699 | 0.0024548 | 1.1 | 0.50 +Comm | 0.0019314 | 0.0020101 | 0.0020888 | 0.2 | 0.51 +Output | 0.00014496 | 0.00017297 | 0.00020099 | 0.0 | 0.04 +Modify | 0.0005033 | 0.00052273 | 0.00054216 | 0.0 | 0.13 +Other | | 0.0004461 | | | 0.11 + +Nlocal: 150 ave 159 max 141 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Nghost: 392 ave 395 max 389 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Neighs: 1229.5 ave 1773 max 686 min +Histogram: 1 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 2459 +Ave neighs/atom = 8.19667 +Neighbor list builds = 15 +Dangerous builds = 0 +Total wall time: 0:00:01 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.fmm.4 b/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.fmm.4 new file mode 100644 index 0000000000..eae3f2b840 --- /dev/null +++ b/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.fmm.4 @@ -0,0 +1,99 @@ +LAMMPS (2 Aug 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +units lj +atom_style charge + +read_data data.cloud_wall + orthogonal box = (0 0 0) to (10 10 10) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 300 atoms + +velocity all set 0.0 0.0 0.0 mom no + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +kspace_style scafacos fmm 1.0e-3 +kspace_modify scafacos tolerance energy_rel +kspace_modify scafacos fmm_tuning 1 +ScaFaCoS setting fmm inhomogen tuning ... + +timestep 0.005 + +thermo_style custom step atoms cpu temp pe ke etotal ecoul press + +run_style verlet + +#dump simple all custom 1000 id x y z vx vy vz +#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass +#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass +#dump_modify dmpvtk pad 7 + +thermo 10 +run 100 +Setting up ScaFaCoS with solver fmm ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 10 10 10 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.333 | 3.333 | 3.333 Mbytes +Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press + 0 300 0 0 0.49646402 0 0.49646402 0 0.016548801 + 10 300 0.029414415 0.015455559 0.47335833 0.02310606 0.49646439 0 0.020399823 + 20 300 0.058616877 0.06229069 0.40334177 0.093124582 0.49646635 0 0.032069642 + 30 300 0.087769508 0.14310163 0.28254277 0.21393694 0.49647971 0 0.05220548 + 40 300 0.1168611 0.52929788 0.089669015 0.79130033 0.88096934 0 0.16124903 + 50 300 0.14482284 1.1963022 -0.082792461 1.7884718 1.7056794 0 0.35493462 + 60 300 0.17198443 1.3928167 -0.37659239 2.082261 1.7056686 0 0.40389911 + 70 300 0.19868851 1.7069009 -0.84571914 2.5518169 1.7060978 0 0.48217274 + 80 300 0.22835517 15.358343 -3.368063 22.960722 19.592659 0 4.4798757 + 90 300 0.26023602 42.280432 -2.1623864 63.209247 61.04686 0 12.56977 + 100 300 0.29043221 41.48079 -0.89904529 62.013782 61.114736 0 12.372788 +Loop time of 0.290448 on 4 procs for 100 steps with 300 atoms + +Performance: 148735.741 tau/day, 344.296 timesteps/s +99.0% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 5.9605e-05 | 6.187e-05 | 6.4135e-05 | 0.0 | 0.02 +Kspace | 0.28551 | 0.28584 | 0.28604 | 0.0 | 98.41 +Neigh | 0.00077796 | 0.0010615 | 0.0013225 | 0.7 | 0.37 +Comm | 0.002372 | 0.0024325 | 0.002497 | 0.1 | 0.84 +Output | 0.00025368 | 0.0002659 | 0.00029516 | 0.0 | 0.09 +Modify | 0.00030279 | 0.00031865 | 0.00033021 | 0.0 | 0.11 +Other | | 0.0004706 | | | 0.16 + +Nlocal: 75 ave 81 max 70 min +Histogram: 2 0 0 0 0 0 0 1 0 1 +Nghost: 282.5 ave 290 max 274 min +Histogram: 1 0 0 1 0 0 0 0 1 1 +Neighs: 614.75 ave 981 max 285 min +Histogram: 1 1 0 0 0 0 0 1 0 1 + +Total # of neighbors = 2459 +Ave neighs/atom = 8.19667 +Neighbor list builds = 15 +Dangerous builds = 0 +Total wall time: 0:00:01 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.fmm.8 b/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.fmm.8 new file mode 100644 index 0000000000..feb7e2a5a6 --- /dev/null +++ b/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.fmm.8 @@ -0,0 +1,99 @@ +LAMMPS (2 Aug 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +units lj +atom_style charge + +read_data data.cloud_wall + orthogonal box = (0 0 0) to (10 10 10) + 2 by 2 by 2 MPI processor grid + reading atoms ... + 300 atoms + +velocity all set 0.0 0.0 0.0 mom no + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +kspace_style scafacos fmm 1.0e-3 +kspace_modify scafacos tolerance energy_rel +kspace_modify scafacos fmm_tuning 1 +ScaFaCoS setting fmm inhomogen tuning ... + +timestep 0.005 + +thermo_style custom step atoms cpu temp pe ke etotal ecoul press + +run_style verlet + +#dump simple all custom 1000 id x y z vx vy vz +#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass +#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass +#dump_modify dmpvtk pad 7 + +thermo 10 +run 100 +Setting up ScaFaCoS with solver fmm ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 10 10 10 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.317 | 3.317 | 3.317 Mbytes +Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press + 0 300 0 0 0.49646402 0 0.49646402 0 0.016548801 + 10 300 0.026465416 0.015455559 0.47335833 0.02310606 0.49646439 0 0.020399823 + 20 300 0.057377338 0.06229069 0.40334177 0.093124582 0.49646635 0 0.032069642 + 30 300 0.088356495 0.14310163 0.28254277 0.21393694 0.49647971 0 0.05220548 + 40 300 0.11900806 0.52929788 0.089669015 0.79130033 0.88096934 0 0.16124903 + 50 300 0.15157914 1.1963022 -0.082792461 1.7884718 1.7056794 0 0.35493462 + 60 300 0.18608141 1.3928167 -0.37659239 2.082261 1.7056686 0 0.40389911 + 70 300 0.21956491 1.7069009 -0.84571914 2.5518169 1.7060978 0 0.48217274 + 80 300 0.24269128 15.358343 -3.368063 22.960722 19.592659 0 4.4798757 + 90 300 0.26847005 42.280432 -2.1623864 63.209247 61.04686 0 12.56977 + 100 300 0.29283834 41.48079 -0.89904529 62.013782 61.114736 0 12.372788 +Loop time of 0.292855 on 8 procs for 100 steps with 300 atoms + +Performance: 147513.337 tau/day, 341.466 timesteps/s +98.4% CPU use with 8 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 4.7207e-05 | 5.5045e-05 | 6.9618e-05 | 0.0 | 0.02 +Kspace | 0.28739 | 0.28773 | 0.2881 | 0.0 | 98.25 +Neigh | 0.00040698 | 0.00060901 | 0.00082922 | 0.0 | 0.21 +Comm | 0.0029533 | 0.0031788 | 0.0034056 | 0.3 | 1.09 +Output | 0.00029063 | 0.00030866 | 0.00035119 | 0.0 | 0.11 +Modify | 0.00018978 | 0.00022188 | 0.00026703 | 0.0 | 0.08 +Other | | 0.0007486 | | | 0.26 + +Nlocal: 37.5 ave 45 max 31 min +Histogram: 1 1 1 1 1 0 1 0 1 1 +Nghost: 200 ave 209 max 189 min +Histogram: 1 0 0 0 1 4 0 0 0 2 +Neighs: 307.375 ave 514 max 115 min +Histogram: 2 1 0 1 1 0 0 0 1 2 + +Total # of neighbors = 2459 +Ave neighs/atom = 8.19667 +Neighbor list builds = 15 +Dangerous builds = 0 +Total wall time: 0:00:01 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.p2nfft.1 b/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.p2nfft.1 new file mode 100644 index 0000000000..f47f24edee --- /dev/null +++ b/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.p2nfft.1 @@ -0,0 +1,92 @@ +LAMMPS (2 Aug 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task + +units lj +atom_style charge + +read_data data.cloud_wall + orthogonal box = (0 0 0) to (10 10 10) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 300 atoms + +velocity all set 0.0 0.0 0.0 mom no + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve +kspace_style scafacos p2nfft 0.001 +kspace_modify scafacos tolerance field + +timestep 0.005 + +thermo_style custom step atoms cpu temp pe ke etotal ecoul press + +run_style verlet + +#dump simple all custom 1000 id x y z vx vy vz +#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass +#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass +#dump_modify dmpvtk pad 7 + +thermo 10 +run 100 +Setting up ScaFaCoS with solver p2nfft ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 10 10 10 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.34 | 3.34 | 3.34 Mbytes +Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press + 0 300 0 0 0.49683273 0 0.49683273 0 0.016561091 + 10 300 0.071435928 0.015479312 0.47369009 0.023141571 0.49683166 0 0.020417984 + 20 300 0.14302707 0.062386358 0.40356181 0.093267605 0.49682941 0 0.032105581 + 30 300 0.21480989 0.14331637 0.2825636 0.21425798 0.49682157 0 0.052270382 + 40 300 0.28638172 0.53041843 0.089505208 0.79297556 0.88248077 0 0.16157862 + 50 300 0.35810781 1.1948397 -0.083317439 1.7862853 1.7029679 0 0.35447982 + 60 300 0.42993116 1.3915614 -0.37745551 2.0803842 1.7029287 0 0.40349499 + 70 300 0.50181961 1.7061978 -0.84746071 2.5507657 1.703305 0 0.48190445 + 80 300 0.57404566 20.692093 -3.32971 30.93468 27.60497 0 6.0759456 + 90 300 0.64724708 48.999403 -2.1632167 73.254107 71.090891 0 14.578714 + 100 300 0.72128963 51.199785 -0.81127924 76.543678 75.732399 0 15.281693 +Loop time of 0.721302 on 1 procs for 100 steps with 300 atoms + +Performance: 59891.733 tau/day, 138.638 timesteps/s +100.0% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 8.893e-05 | 8.893e-05 | 8.893e-05 | 0.0 | 0.01 +Kspace | 0.71502 | 0.71502 | 0.71502 | 0.0 | 99.13 +Neigh | 0.0035415 | 0.0035415 | 0.0035415 | 0.0 | 0.49 +Comm | 0.001024 | 0.001024 | 0.001024 | 0.0 | 0.14 +Output | 0.00015044 | 0.00015044 | 0.00015044 | 0.0 | 0.02 +Modify | 0.0010409 | 0.0010409 | 0.0010409 | 0.0 | 0.14 +Other | | 0.0004385 | | | 0.06 + +Nlocal: 300 ave 300 max 300 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 381 ave 381 max 381 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 2461 ave 2461 max 2461 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 2461 +Ave neighs/atom = 8.20333 +Neighbor list builds = 15 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.p2nfft.16 b/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.p2nfft.16 new file mode 100644 index 0000000000..d6e7cbea37 --- /dev/null +++ b/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.p2nfft.16 @@ -0,0 +1,92 @@ +LAMMPS (2 Aug 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task + +units lj +atom_style charge + +read_data data.cloud_wall + orthogonal box = (0 0 0) to (10 10 10) + 2 by 2 by 4 MPI processor grid + reading atoms ... + 300 atoms + +velocity all set 0.0 0.0 0.0 mom no + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve +kspace_style scafacos p2nfft 0.001 +kspace_modify scafacos tolerance field + +timestep 0.005 + +thermo_style custom step atoms cpu temp pe ke etotal ecoul press + +run_style verlet + +#dump simple all custom 1000 id x y z vx vy vz +#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass +#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass +#dump_modify dmpvtk pad 7 + +thermo 10 +run 100 +Setting up ScaFaCoS with solver p2nfft ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 10 10 10 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.313 | 3.501 | 3.689 Mbytes +Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press + 0 300 0 0 0.49683273 0 0.49683273 0 0.016561091 + 10 300 0.015678644 0.015479312 0.47369009 0.023141571 0.49683166 0 0.020417984 + 20 300 0.031283855 0.062386358 0.40356181 0.093267605 0.49682941 0 0.032105581 + 30 300 0.046878099 0.14331637 0.2825636 0.21425798 0.49682157 0 0.052270382 + 40 300 0.062416077 0.53041843 0.089505208 0.79297556 0.88248077 0 0.16157862 + 50 300 0.078029871 1.1948397 -0.083317439 1.7862853 1.7029679 0 0.35447982 + 60 300 0.093806505 1.3915614 -0.37745551 2.0803842 1.7029287 0 0.40349499 + 70 300 0.1096344 1.7061978 -0.84746071 2.5507657 1.703305 0 0.48190445 + 80 300 0.12532592 20.692093 -3.32971 30.93468 27.60497 0 6.0759456 + 90 300 0.14175463 48.999403 -2.1632167 73.254107 71.090891 0 14.578714 + 100 300 0.15838337 51.199785 -0.81127924 76.543678 75.732399 0 15.281693 +Loop time of 0.158406 on 16 procs for 100 steps with 300 atoms + +Performance: 272716.448 tau/day, 631.288 timesteps/s +99.4% CPU use with 16 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.718e-05 | 3.7491e-05 | 5.6744e-05 | 0.0 | 0.02 +Kspace | 0.15435 | 0.15482 | 0.15516 | 0.1 | 97.74 +Neigh | 0.00014806 | 0.0003508 | 0.00074744 | 0.0 | 0.22 +Comm | 0.0016866 | 0.0019967 | 0.0023787 | 0.5 | 1.26 +Output | 0.00027871 | 0.00033027 | 0.00038028 | 0.0 | 0.21 +Modify | 8.0347e-05 | 0.00011933 | 0.00016522 | 0.0 | 0.08 +Other | | 0.0007506 | | | 0.47 + +Nlocal: 18.75 ave 33 max 6 min +Histogram: 2 6 0 0 0 0 2 1 2 3 +Nghost: 128.875 ave 198 max 71 min +Histogram: 7 1 0 0 0 0 0 1 5 2 +Neighs: 153.812 ave 490 max 14 min +Histogram: 8 0 3 0 1 1 0 0 1 2 + +Total # of neighbors = 2461 +Ave neighs/atom = 8.20333 +Neighbor list builds = 15 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.p2nfft.2 b/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.p2nfft.2 new file mode 100644 index 0000000000..fb863797f3 --- /dev/null +++ b/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.p2nfft.2 @@ -0,0 +1,92 @@ +LAMMPS (2 Aug 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task + +units lj +atom_style charge + +read_data data.cloud_wall + orthogonal box = (0 0 0) to (10 10 10) + 1 by 1 by 2 MPI processor grid + reading atoms ... + 300 atoms + +velocity all set 0.0 0.0 0.0 mom no + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve +kspace_style scafacos p2nfft 0.001 +kspace_modify scafacos tolerance field + +timestep 0.005 + +thermo_style custom step atoms cpu temp pe ke etotal ecoul press + +run_style verlet + +#dump simple all custom 1000 id x y z vx vy vz +#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass +#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass +#dump_modify dmpvtk pad 7 + +thermo 10 +run 100 +Setting up ScaFaCoS with solver p2nfft ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 10 10 10 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.354 | 3.354 | 3.355 Mbytes +Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press + 0 300 0 0 0.49683273 0 0.49683273 0 0.016561091 + 10 300 0.044083834 0.015479312 0.47369009 0.023141571 0.49683166 0 0.020417984 + 20 300 0.088379145 0.062386358 0.40356181 0.093267605 0.49682941 0 0.032105581 + 30 300 0.13264704 0.14331637 0.2825636 0.21425798 0.49682157 0 0.052270382 + 40 300 0.17687225 0.53041843 0.089505208 0.79297556 0.88248077 0 0.16157862 + 50 300 0.22116137 1.1948397 -0.083317439 1.7862853 1.7029679 0 0.35447982 + 60 300 0.26515126 1.3915614 -0.37745551 2.0803842 1.7029287 0 0.40349499 + 70 300 0.30891085 1.7061978 -0.84746071 2.5507657 1.703305 0 0.48190445 + 80 300 0.35292292 20.692093 -3.32971 30.93468 27.60497 0 6.0759456 + 90 300 0.39845228 48.999403 -2.1632167 73.254107 71.090891 0 14.578714 + 100 300 0.44492316 51.199785 -0.81127924 76.543678 75.732399 0 15.281693 +Loop time of 0.444937 on 2 procs for 100 steps with 300 atoms + +Performance: 97092.373 tau/day, 224.751 timesteps/s +100.0% CPU use with 2 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 7.7248e-05 | 7.844e-05 | 7.9632e-05 | 0.0 | 0.02 +Kspace | 0.43932 | 0.43979 | 0.44026 | 0.1 | 98.84 +Neigh | 0.0014915 | 0.0019662 | 0.0024409 | 1.1 | 0.44 +Comm | 0.0019331 | 0.0019941 | 0.0020552 | 0.1 | 0.45 +Output | 0.00013781 | 0.00016308 | 0.00018835 | 0.0 | 0.04 +Modify | 0.00050378 | 0.00050449 | 0.00050521 | 0.0 | 0.11 +Other | | 0.0004425 | | | 0.10 + +Nlocal: 150 ave 157 max 143 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Nghost: 399 ave 402 max 396 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Neighs: 1230.5 ave 1756 max 705 min +Histogram: 1 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 2461 +Ave neighs/atom = 8.20333 +Neighbor list builds = 15 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.p2nfft.4 b/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.p2nfft.4 new file mode 100644 index 0000000000..d5a07e0324 --- /dev/null +++ b/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.p2nfft.4 @@ -0,0 +1,92 @@ +LAMMPS (2 Aug 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task + +units lj +atom_style charge + +read_data data.cloud_wall + orthogonal box = (0 0 0) to (10 10 10) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 300 atoms + +velocity all set 0.0 0.0 0.0 mom no + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve +kspace_style scafacos p2nfft 0.001 +kspace_modify scafacos tolerance field + +timestep 0.005 + +thermo_style custom step atoms cpu temp pe ke etotal ecoul press + +run_style verlet + +#dump simple all custom 1000 id x y z vx vy vz +#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass +#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass +#dump_modify dmpvtk pad 7 + +thermo 10 +run 100 +Setting up ScaFaCoS with solver p2nfft ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 10 10 10 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.333 | 3.333 | 3.333 Mbytes +Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press + 0 300 0 0 0.49683273 0 0.49683273 0 0.016561091 + 10 300 0.02743125 0.015479312 0.47369009 0.023141571 0.49683166 0 0.020417984 + 20 300 0.05494833 0.062386358 0.40356181 0.093267605 0.49682941 0 0.032105581 + 30 300 0.082517862 0.14331637 0.2825636 0.21425798 0.49682157 0 0.052270382 + 40 300 0.11015558 0.53041843 0.089505208 0.79297556 0.88248077 0 0.16157862 + 50 300 0.13790298 1.1948397 -0.083317439 1.7862853 1.7029679 0 0.35447982 + 60 300 0.1660006 1.3915614 -0.37745551 2.0803842 1.7029287 0 0.40349499 + 70 300 0.1937964 1.7061978 -0.84746071 2.5507657 1.703305 0 0.48190445 + 80 300 0.22181106 20.692093 -3.32971 30.93468 27.60497 0 6.0759456 + 90 300 0.25105524 48.999403 -2.1632167 73.254107 71.090891 0 14.578714 + 100 300 0.28086019 51.199785 -0.81127924 76.543678 75.732399 0 15.281693 +Loop time of 0.280875 on 4 procs for 100 steps with 300 atoms + +Performance: 153805.254 tau/day, 356.031 timesteps/s +99.7% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 5.6744e-05 | 6.0022e-05 | 6.4135e-05 | 0.0 | 0.02 +Kspace | 0.27651 | 0.27682 | 0.27714 | 0.0 | 98.56 +Neigh | 0.00079465 | 0.001082 | 0.0014107 | 0.8 | 0.39 +Comm | 0.0019372 | 0.002014 | 0.0020835 | 0.1 | 0.72 +Output | 0.00018406 | 0.00019914 | 0.00023413 | 0.0 | 0.07 +Modify | 0.0002749 | 0.00028563 | 0.00029325 | 0.0 | 0.10 +Other | | 0.0004173 | | | 0.15 + +Nlocal: 75 ave 81 max 69 min +Histogram: 1 0 0 0 1 1 0 0 0 1 +Nghost: 287 ave 296 max 278 min +Histogram: 1 0 1 0 0 0 0 1 0 1 +Neighs: 615.25 ave 964 max 286 min +Histogram: 1 1 0 0 0 0 0 1 0 1 + +Total # of neighbors = 2461 +Ave neighs/atom = 8.20333 +Neighbor list builds = 15 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.p2nfft.8 b/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.p2nfft.8 new file mode 100644 index 0000000000..a6f9228673 --- /dev/null +++ b/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.p2nfft.8 @@ -0,0 +1,92 @@ +LAMMPS (2 Aug 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task + +units lj +atom_style charge + +read_data data.cloud_wall + orthogonal box = (0 0 0) to (10 10 10) + 2 by 2 by 2 MPI processor grid + reading atoms ... + 300 atoms + +velocity all set 0.0 0.0 0.0 mom no + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve +kspace_style scafacos p2nfft 0.001 +kspace_modify scafacos tolerance field + +timestep 0.005 + +thermo_style custom step atoms cpu temp pe ke etotal ecoul press + +run_style verlet + +#dump simple all custom 1000 id x y z vx vy vz +#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass +#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass +#dump_modify dmpvtk pad 7 + +thermo 10 +run 100 +Setting up ScaFaCoS with solver p2nfft ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 10 10 10 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.317 | 3.317 | 3.317 Mbytes +Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press + 0 300 0 0 0.49683273 0 0.49683273 0 0.016561091 + 10 300 0.01961565 0.015479312 0.47369009 0.023141571 0.49683166 0 0.020417984 + 20 300 0.039346695 0.062386358 0.40356181 0.093267605 0.49682941 0 0.032105581 + 30 300 0.059037447 0.14331637 0.2825636 0.21425798 0.49682157 0 0.052270382 + 40 300 0.078732729 0.53041843 0.089505208 0.79297556 0.88248077 0 0.16157862 + 50 300 0.098586798 1.1948397 -0.083317439 1.7862853 1.7029679 0 0.35447982 + 60 300 0.11857247 1.3915614 -0.37745551 2.0803842 1.7029287 0 0.40349499 + 70 300 0.1385541 1.7061978 -0.84746071 2.5507657 1.703305 0 0.48190445 + 80 300 0.15850091 20.692093 -3.32971 30.93468 27.60497 0 6.0759456 + 90 300 0.17892075 48.999403 -2.1632167 73.254107 71.090891 0 14.578714 + 100 300 0.19964767 51.199785 -0.81127924 76.543678 75.732399 0 15.281693 +Loop time of 0.199664 on 8 procs for 100 steps with 300 atoms + +Performance: 216363.074 tau/day, 500.840 timesteps/s +99.4% CPU use with 8 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 4.5061e-05 | 4.7535e-05 | 5.3167e-05 | 0.0 | 0.02 +Kspace | 0.19551 | 0.19584 | 0.19611 | 0.0 | 98.08 +Neigh | 0.00041366 | 0.00060952 | 0.00082064 | 0.0 | 0.31 +Comm | 0.0021496 | 0.0022282 | 0.0024025 | 0.2 | 1.12 +Output | 0.0002346 | 0.00024167 | 0.00027847 | 0.0 | 0.12 +Modify | 0.00016665 | 0.00017652 | 0.0001924 | 0.0 | 0.09 +Other | | 0.0005245 | | | 0.26 + +Nlocal: 37.5 ave 42 max 33 min +Histogram: 2 1 0 1 0 0 1 0 1 2 +Nghost: 202.25 ave 212 max 194 min +Histogram: 1 0 2 1 0 2 0 1 0 1 +Neighs: 307.625 ave 505 max 129 min +Histogram: 3 0 0 1 1 0 0 0 1 2 + +Total # of neighbors = 2461 +Ave neighs/atom = 8.20333 +Neighbor list builds = 15 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.g++.ewald.1 b/examples/USER/scafacos/log.08Aug18.scafacos.g++.ewald.1 new file mode 100644 index 0000000000..13212ede0c --- /dev/null +++ b/examples/USER/scafacos/log.08Aug18.scafacos.g++.ewald.1 @@ -0,0 +1,102 @@ +LAMMPS (2 Aug 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.NaCl + orthogonal box = (0 0 0) to (1 1 1) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 8 atoms + +replicate 8 8 8 + orthogonal box = (0 0 0) to (8 8 8) + 1 by 1 by 1 MPI processor grid + 4096 atoms + Time spent = 0.000498772 secs + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos ewald 0.001 +kspace_modify scafacos tolerance field + +timestep 0.005 +thermo 10 + +run 100 +Setting up ScaFaCoS with solver ewald ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 8 8 8 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.813 | 5.813 | 5.813 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -1.7475938 0 0.50185691 11.99707 + 10 1.500011 -1.747529 0 0.50193816 11.997158 + 20 1.5000023 -1.7475152 0 0.50193898 11.997089 + 30 1.4999308 -1.747404 0 0.50194285 11.996517 + 40 1.4997722 -1.7471622 0 0.50194686 11.995248 + 50 1.4995835 -1.746878 0 0.50194808 11.993739 + 60 1.4996054 -1.7469114 0 0.50194749 11.993914 + 70 1.5004341 -1.7481558 0 0.50194592 12.000543 + 80 1.5033218 -1.7524875 0 0.50194458 12.023638 + 90 1.5108306 -1.7637462 0 0.50194636 12.083694 + 100 1.5292479 -1.7913449 0 0.50196695 12.230996 +Loop time of 1121.22 on 1 procs for 100 steps with 4096 atoms + +Performance: 38.530 tau/day, 0.089 timesteps/s +100.0% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0015197 | 0.0015197 | 0.0015197 | 0.0 | 0.00 +Kspace | 1121.2 | 1121.2 | 1121.2 | 0.0 |100.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.013699 | 0.013699 | 0.013699 | 0.0 | 0.00 +Output | 0.00038314 | 0.00038314 | 0.00038314 | 0.0 | 0.00 +Modify | 0.011126 | 0.011126 | 0.011126 | 0.0 | 0.00 +Other | | 0.00418 | | | 0.00 + +Nlocal: 4096 ave 4096 max 4096 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 9728 ave 9728 max 9728 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 524288 ave 524288 max 524288 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 524288 +Ave neighs/atom = 128 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:18:57 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.g++.ewald.16 b/examples/USER/scafacos/log.08Aug18.scafacos.g++.ewald.16 new file mode 100644 index 0000000000..2fc46da3cd --- /dev/null +++ b/examples/USER/scafacos/log.08Aug18.scafacos.g++.ewald.16 @@ -0,0 +1,102 @@ +LAMMPS (2 Aug 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.NaCl + orthogonal box = (0 0 0) to (1 1 1) + 2 by 2 by 4 MPI processor grid + reading atoms ... + 8 atoms + +replicate 8 8 8 + orthogonal box = (0 0 0) to (8 8 8) + 2 by 2 by 4 MPI processor grid + 4096 atoms + Time spent = 0.000462294 secs + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos ewald 0.001 +kspace_modify scafacos tolerance field + +timestep 0.005 +thermo 10 + +run 100 +Setting up ScaFaCoS with solver ewald ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 8 8 8 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.501 | 3.501 | 3.501 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -1.7475938 0 0.50185691 -nan + 10 1.500011 -1.747529 0 0.50193816 -nan + 20 1.5000023 -1.7475152 0 0.50193898 -nan + 30 1.4999308 -1.747404 0 0.50194285 -nan + 40 1.4997722 -1.7471622 0 0.50194686 -nan + 50 1.4995835 -1.746878 0 0.50194808 -nan + 60 1.4996054 -1.7469114 0 0.50194749 -nan + 70 1.5004341 -1.7481558 0 0.50194592 -nan + 80 1.5033218 -1.7524875 0 0.50194458 -nan + 90 1.5108306 -1.7637462 0 0.50194636 -nan + 100 1.5292479 -1.7913449 0 0.50196695 -nan +Loop time of 80.2777 on 16 procs for 100 steps with 4096 atoms + +Performance: 538.132 tau/day, 1.246 timesteps/s +99.8% CPU use with 16 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0003705 | 0.00039807 | 0.00048542 | 0.0 | 0.00 +Kspace | 80.262 | 80.263 | 80.264 | 0.0 | 99.98 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.010191 | 0.011419 | 0.012416 | 0.6 | 0.01 +Output | 0.00028253 | 0.00033158 | 0.0004065 | 0.0 | 0.00 +Modify | 0.00082541 | 0.0008464 | 0.00087833 | 0.0 | 0.00 +Other | | 0.001511 | | | 0.00 + +Nlocal: 256 ave 256 max 256 min +Histogram: 16 0 0 0 0 0 0 0 0 0 +Nghost: 2816 ave 2816 max 2816 min +Histogram: 16 0 0 0 0 0 0 0 0 0 +Neighs: 32768 ave 32768 max 32768 min +Histogram: 16 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 524288 +Ave neighs/atom = 128 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:01:22 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.g++.ewald.2 b/examples/USER/scafacos/log.08Aug18.scafacos.g++.ewald.2 new file mode 100644 index 0000000000..b6bf41de24 --- /dev/null +++ b/examples/USER/scafacos/log.08Aug18.scafacos.g++.ewald.2 @@ -0,0 +1,102 @@ +LAMMPS (2 Aug 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.NaCl + orthogonal box = (0 0 0) to (1 1 1) + 1 by 1 by 2 MPI processor grid + reading atoms ... + 8 atoms + +replicate 8 8 8 + orthogonal box = (0 0 0) to (8 8 8) + 1 by 1 by 2 MPI processor grid + 4096 atoms + Time spent = 0.000344753 secs + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos ewald 0.001 +kspace_modify scafacos tolerance field + +timestep 0.005 +thermo 10 + +run 100 +Setting up ScaFaCoS with solver ewald ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 8 8 8 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.574 | 4.574 | 4.574 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -1.7475938 0 0.50185691 11.99707 + 10 1.500011 -1.747529 0 0.50193816 11.997158 + 20 1.5000023 -1.7475152 0 0.50193898 11.997089 + 30 1.4999308 -1.747404 0 0.50194285 11.996517 + 40 1.4997722 -1.7471622 0 0.50194686 11.995248 + 50 1.4995835 -1.746878 0 0.50194808 11.993739 + 60 1.4996054 -1.7469114 0 0.50194749 11.993914 + 70 1.5004341 -1.7481558 0 0.50194592 12.000543 + 80 1.5033218 -1.7524875 0 0.50194458 12.023638 + 90 1.5108306 -1.7637462 0 0.50194636 12.083694 + 100 1.5292479 -1.7913449 0 0.50196695 12.230996 +Loop time of 566.796 on 2 procs for 100 steps with 4096 atoms + +Performance: 76.218 tau/day, 0.176 timesteps/s +100.0% CPU use with 2 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0010231 | 0.0010413 | 0.0010595 | 0.1 | 0.00 +Kspace | 566.77 | 566.77 | 566.77 | 0.0 | 99.99 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.019707 | 0.01982 | 0.019932 | 0.1 | 0.00 +Output | 0.0002656 | 0.00029266 | 0.00031972 | 0.0 | 0.00 +Modify | 0.0055575 | 0.0055707 | 0.0055838 | 0.0 | 0.00 +Other | | 0.002497 | | | 0.00 + +Nlocal: 2048 ave 2048 max 2048 min +Histogram: 2 0 0 0 0 0 0 0 0 0 +Nghost: 7168 ave 7168 max 7168 min +Histogram: 2 0 0 0 0 0 0 0 0 0 +Neighs: 262144 ave 262144 max 262144 min +Histogram: 2 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 524288 +Ave neighs/atom = 128 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:09:38 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.g++.ewald.4 b/examples/USER/scafacos/log.08Aug18.scafacos.g++.ewald.4 new file mode 100644 index 0000000000..26c1953afa --- /dev/null +++ b/examples/USER/scafacos/log.08Aug18.scafacos.g++.ewald.4 @@ -0,0 +1,102 @@ +LAMMPS (2 Aug 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.NaCl + orthogonal box = (0 0 0) to (1 1 1) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 8 atoms + +replicate 8 8 8 + orthogonal box = (0 0 0) to (8 8 8) + 1 by 2 by 2 MPI processor grid + 4096 atoms + Time spent = 0.000261068 secs + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos ewald 0.001 +kspace_modify scafacos tolerance field + +timestep 0.005 +thermo 10 + +run 100 +Setting up ScaFaCoS with solver ewald ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 8 8 8 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.008 | 4.008 | 4.008 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -1.7475938 0 0.50185691 -nan + 10 1.500011 -1.747529 0 0.50193816 -nan + 20 1.5000023 -1.7475152 0 0.50193898 -nan + 30 1.4999308 -1.747404 0 0.50194285 -nan + 40 1.4997722 -1.7471622 0 0.50194686 -nan + 50 1.4995835 -1.746878 0 0.50194808 -nan + 60 1.4996054 -1.7469114 0 0.50194749 -nan + 70 1.5004341 -1.7481558 0 0.50194592 -nan + 80 1.5033218 -1.7524875 0 0.50194458 -nan + 90 1.5108306 -1.7637462 0 0.50194636 -nan + 100 1.5292479 -1.7913449 0 0.50196695 -nan +Loop time of 295.996 on 4 procs for 100 steps with 4096 atoms + +Performance: 145.948 tau/day, 0.338 timesteps/s +99.9% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.00071096 | 0.00071985 | 0.00072813 | 0.0 | 0.00 +Kspace | 295.98 | 295.98 | 295.98 | 0.0 | 99.99 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.013666 | 0.013736 | 0.013795 | 0.0 | 0.00 +Output | 0.00023484 | 0.00025135 | 0.00029254 | 0.0 | 0.00 +Modify | 0.0029099 | 0.002973 | 0.0030224 | 0.1 | 0.00 +Other | | 0.001821 | | | 0.00 + +Nlocal: 1024 ave 1024 max 1024 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 5120 ave 5120 max 5120 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 131072 ave 131072 max 131072 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 524288 +Ave neighs/atom = 128 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:05:02 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.g++.ewald.8 b/examples/USER/scafacos/log.08Aug18.scafacos.g++.ewald.8 new file mode 100644 index 0000000000..4a1a5b91ed --- /dev/null +++ b/examples/USER/scafacos/log.08Aug18.scafacos.g++.ewald.8 @@ -0,0 +1,102 @@ +LAMMPS (2 Aug 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.NaCl + orthogonal box = (0 0 0) to (1 1 1) + 2 by 2 by 2 MPI processor grid + reading atoms ... + 8 atoms + +replicate 8 8 8 + orthogonal box = (0 0 0) to (8 8 8) + 2 by 2 by 2 MPI processor grid + 4096 atoms + Time spent = 0.000232935 secs + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos ewald 0.001 +kspace_modify scafacos tolerance field + +timestep 0.005 +thermo 10 + +run 100 +Setting up ScaFaCoS with solver ewald ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 8 8 8 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.508 | 3.508 | 3.508 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -1.7475938 0 0.50185691 -nan + 10 1.500011 -1.747529 0 0.50193816 -nan + 20 1.5000023 -1.7475152 0 0.50193898 -nan + 30 1.4999308 -1.747404 0 0.50194285 -nan + 40 1.4997722 -1.7471622 0 0.50194686 -nan + 50 1.4995835 -1.746878 0 0.50194808 -nan + 60 1.4996054 -1.7469114 0 0.50194749 -nan + 70 1.5004341 -1.7481558 0 0.50194592 -nan + 80 1.5033218 -1.7524875 0 0.50194458 -nan + 90 1.5108306 -1.7637462 0 0.50194636 -nan + 100 1.5292479 -1.7913449 0 0.50196695 -nan +Loop time of 154.44 on 8 procs for 100 steps with 4096 atoms + +Performance: 279.720 tau/day, 0.647 timesteps/s +99.9% CPU use with 8 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.00049257 | 0.00051311 | 0.00059295 | 0.0 | 0.00 +Kspace | 154.42 | 154.42 | 154.42 | 0.0 | 99.99 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.012076 | 0.013177 | 0.014308 | 0.8 | 0.01 +Output | 0.00025177 | 0.00028065 | 0.00030136 | 0.0 | 0.00 +Modify | 0.0015776 | 0.0017182 | 0.0018268 | 0.2 | 0.00 +Other | | 0.001309 | | | 0.00 + +Nlocal: 512 ave 512 max 512 min +Histogram: 8 0 0 0 0 0 0 0 0 0 +Nghost: 3584 ave 3584 max 3584 min +Histogram: 8 0 0 0 0 0 0 0 0 0 +Neighs: 65536 ave 65536 max 65536 min +Histogram: 8 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 524288 +Ave neighs/atom = 128 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:02:38 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.g++.fmm.1 b/examples/USER/scafacos/log.08Aug18.scafacos.g++.fmm.1 new file mode 100644 index 0000000000..598585ae95 --- /dev/null +++ b/examples/USER/scafacos/log.08Aug18.scafacos.g++.fmm.1 @@ -0,0 +1,102 @@ +LAMMPS (2 Aug 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.NaCl + orthogonal box = (0 0 0) to (1 1 1) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 8 atoms + +replicate 8 8 8 + orthogonal box = (0 0 0) to (8 8 8) + 1 by 1 by 1 MPI processor grid + 4096 atoms + Time spent = 0.000518799 secs + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos fmm 0.001 +kspace_modify scafacos tolerance energy + +timestep 0.005 +thermo 10 + +run 100 +Setting up ScaFaCoS with solver fmm ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 8 8 8 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.813 | 5.813 | 5.813 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -1.7475646 0 0.50188608 10.44368 + 10 1.5000016 -1.7475671 0 0.50188602 10.44369 + 20 1.4999827 -1.7475388 0 0.50188592 10.443564 + 30 1.4999016 -1.7474173 0 0.5018858 10.443023 + 40 1.4997356 -1.7471685 0 0.50188572 10.441917 + 50 1.4995414 -1.7468771 0 0.5018858 10.440623 + 60 1.4995587 -1.7469027 0 0.50188622 10.440739 + 70 1.5003837 -1.7481389 0 0.50188727 10.446238 + 80 1.5032684 -1.7524625 0 0.50188958 10.465466 + 90 1.5107749 -1.763714 0 0.50189507 10.515502 + 100 1.52919 -1.791306 0 0.50191895 10.638261 +Loop time of 34.7058 on 1 procs for 100 steps with 4096 atoms + +Performance: 1244.749 tau/day, 2.881 timesteps/s +100.0% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0015228 | 0.0015228 | 0.0015228 | 0.0 | 0.00 +Kspace | 34.675 | 34.675 | 34.675 | 0.0 | 99.91 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.013741 | 0.013741 | 0.013741 | 0.0 | 0.04 +Output | 0.00041246 | 0.00041246 | 0.00041246 | 0.0 | 0.00 +Modify | 0.01107 | 0.01107 | 0.01107 | 0.0 | 0.03 +Other | | 0.004232 | | | 0.01 + +Nlocal: 4096 ave 4096 max 4096 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 9728 ave 9728 max 9728 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 524288 ave 524288 max 524288 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 524288 +Ave neighs/atom = 128 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:35 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.g++.fmm.16 b/examples/USER/scafacos/log.08Aug18.scafacos.g++.fmm.16 new file mode 100644 index 0000000000..4bd0c3d4f3 --- /dev/null +++ b/examples/USER/scafacos/log.08Aug18.scafacos.g++.fmm.16 @@ -0,0 +1,102 @@ +LAMMPS (2 Aug 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.NaCl + orthogonal box = (0 0 0) to (1 1 1) + 2 by 2 by 4 MPI processor grid + reading atoms ... + 8 atoms + +replicate 8 8 8 + orthogonal box = (0 0 0) to (8 8 8) + 2 by 2 by 4 MPI processor grid + 4096 atoms + Time spent = 0.000400543 secs + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos fmm 0.001 +kspace_modify scafacos tolerance energy + +timestep 0.005 +thermo 10 + +run 100 +Setting up ScaFaCoS with solver fmm ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 8 8 8 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.501 | 3.501 | 3.501 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -1.7475646 0 0.50188608 10.44368 + 10 1.5000016 -1.7475671 0 0.50188602 10.44369 + 20 1.4999827 -1.7475388 0 0.50188592 10.443564 + 30 1.4999016 -1.7474173 0 0.5018858 10.443023 + 40 1.4997356 -1.7471685 0 0.50188572 10.441917 + 50 1.4995414 -1.7468771 0 0.5018858 10.440623 + 60 1.4995587 -1.7469027 0 0.50188622 10.440739 + 70 1.5003837 -1.7481389 0 0.50188727 10.446238 + 80 1.5032684 -1.7524625 0 0.50188958 10.465466 + 90 1.5107749 -1.763714 0 0.50189507 10.515502 + 100 1.52919 -1.791306 0 0.50191895 10.638261 +Loop time of 4.23774 on 16 procs for 100 steps with 4096 atoms + +Performance: 10194.102 tau/day, 23.597 timesteps/s +99.6% CPU use with 16 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.00038028 | 0.00040729 | 0.00046206 | 0.0 | 0.01 +Kspace | 4.2206 | 4.2211 | 4.2216 | 0.0 | 99.61 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.011439 | 0.012491 | 0.013172 | 0.4 | 0.29 +Output | 0.00042915 | 0.000489 | 0.00061274 | 0.0 | 0.01 +Modify | 0.00093102 | 0.00099151 | 0.0010982 | 0.0 | 0.02 +Other | | 0.002255 | | | 0.05 + +Nlocal: 256 ave 256 max 256 min +Histogram: 16 0 0 0 0 0 0 0 0 0 +Nghost: 2816 ave 2816 max 2816 min +Histogram: 16 0 0 0 0 0 0 0 0 0 +Neighs: 32768 ave 32768 max 32768 min +Histogram: 16 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 524288 +Ave neighs/atom = 128 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:06 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.g++.fmm.2 b/examples/USER/scafacos/log.08Aug18.scafacos.g++.fmm.2 new file mode 100644 index 0000000000..50dcc99393 --- /dev/null +++ b/examples/USER/scafacos/log.08Aug18.scafacos.g++.fmm.2 @@ -0,0 +1,102 @@ +LAMMPS (2 Aug 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.NaCl + orthogonal box = (0 0 0) to (1 1 1) + 1 by 1 by 2 MPI processor grid + reading atoms ... + 8 atoms + +replicate 8 8 8 + orthogonal box = (0 0 0) to (8 8 8) + 1 by 1 by 2 MPI processor grid + 4096 atoms + Time spent = 0.0003407 secs + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos fmm 0.001 +kspace_modify scafacos tolerance energy + +timestep 0.005 +thermo 10 + +run 100 +Setting up ScaFaCoS with solver fmm ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 8 8 8 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.574 | 4.574 | 4.574 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -1.7475646 0 0.50188608 10.44368 + 10 1.5000016 -1.7475671 0 0.50188602 10.44369 + 20 1.4999827 -1.7475388 0 0.50188592 10.443564 + 30 1.4999016 -1.7474173 0 0.5018858 10.443023 + 40 1.4997356 -1.7471685 0 0.50188572 10.441917 + 50 1.4995414 -1.7468771 0 0.5018858 10.440623 + 60 1.4995587 -1.7469027 0 0.50188622 10.440739 + 70 1.5003837 -1.7481389 0 0.50188727 10.446238 + 80 1.5032684 -1.7524625 0 0.50188958 10.465466 + 90 1.5107749 -1.763714 0 0.50189507 10.515502 + 100 1.52919 -1.791306 0 0.50191895 10.638261 +Loop time of 17.9401 on 2 procs for 100 steps with 4096 atoms + +Performance: 2408.014 tau/day, 5.574 timesteps/s +99.9% CPU use with 2 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0010042 | 0.0010235 | 0.0010428 | 0.1 | 0.01 +Kspace | 17.912 | 17.912 | 17.912 | 0.0 | 99.84 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.018252 | 0.018528 | 0.018804 | 0.2 | 0.10 +Output | 0.00034094 | 0.00035989 | 0.00037885 | 0.0 | 0.00 +Modify | 0.0055602 | 0.0056567 | 0.0057533 | 0.1 | 0.03 +Other | | 0.002716 | | | 0.02 + +Nlocal: 2048 ave 2048 max 2048 min +Histogram: 2 0 0 0 0 0 0 0 0 0 +Nghost: 7168 ave 7168 max 7168 min +Histogram: 2 0 0 0 0 0 0 0 0 0 +Neighs: 262144 ave 262144 max 262144 min +Histogram: 2 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 524288 +Ave neighs/atom = 128 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:19 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.g++.fmm.4 b/examples/USER/scafacos/log.08Aug18.scafacos.g++.fmm.4 new file mode 100644 index 0000000000..27fdfcedcb --- /dev/null +++ b/examples/USER/scafacos/log.08Aug18.scafacos.g++.fmm.4 @@ -0,0 +1,102 @@ +LAMMPS (2 Aug 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.NaCl + orthogonal box = (0 0 0) to (1 1 1) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 8 atoms + +replicate 8 8 8 + orthogonal box = (0 0 0) to (8 8 8) + 1 by 2 by 2 MPI processor grid + 4096 atoms + Time spent = 0.000270367 secs + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos fmm 0.001 +kspace_modify scafacos tolerance energy + +timestep 0.005 +thermo 10 + +run 100 +Setting up ScaFaCoS with solver fmm ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 8 8 8 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.008 | 4.008 | 4.008 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -1.7475646 0 0.50188608 10.44368 + 10 1.5000016 -1.7475671 0 0.50188602 10.44369 + 20 1.4999827 -1.7475388 0 0.50188592 10.443564 + 30 1.4999016 -1.7474173 0 0.5018858 10.443023 + 40 1.4997356 -1.7471685 0 0.50188572 10.441917 + 50 1.4995414 -1.7468771 0 0.5018858 10.440623 + 60 1.4995587 -1.7469027 0 0.50188622 10.440739 + 70 1.5003837 -1.7481389 0 0.50188727 10.446238 + 80 1.5032684 -1.7524625 0 0.50188958 10.465466 + 90 1.5107749 -1.763714 0 0.50189507 10.515502 + 100 1.52919 -1.791306 0 0.50191895 10.638261 +Loop time of 10.0781 on 4 procs for 100 steps with 4096 atoms + +Performance: 4286.533 tau/day, 9.923 timesteps/s +99.9% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.00071096 | 0.00073177 | 0.00075269 | 0.0 | 0.01 +Kspace | 10.056 | 10.057 | 10.057 | 0.0 | 99.79 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.01492 | 0.015036 | 0.015207 | 0.1 | 0.15 +Output | 0.00036311 | 0.00039428 | 0.00046515 | 0.0 | 0.00 +Modify | 0.002944 | 0.0030704 | 0.0033708 | 0.3 | 0.03 +Other | | 0.002214 | | | 0.02 + +Nlocal: 1024 ave 1024 max 1024 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 5120 ave 5120 max 5120 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 131072 ave 131072 max 131072 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 524288 +Ave neighs/atom = 128 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:11 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.g++.fmm.8 b/examples/USER/scafacos/log.08Aug18.scafacos.g++.fmm.8 new file mode 100644 index 0000000000..02a5528c59 --- /dev/null +++ b/examples/USER/scafacos/log.08Aug18.scafacos.g++.fmm.8 @@ -0,0 +1,102 @@ +LAMMPS (2 Aug 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.NaCl + orthogonal box = (0 0 0) to (1 1 1) + 2 by 2 by 2 MPI processor grid + reading atoms ... + 8 atoms + +replicate 8 8 8 + orthogonal box = (0 0 0) to (8 8 8) + 2 by 2 by 2 MPI processor grid + 4096 atoms + Time spent = 0.000236988 secs + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos fmm 0.001 +kspace_modify scafacos tolerance energy + +timestep 0.005 +thermo 10 + +run 100 +Setting up ScaFaCoS with solver fmm ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 8 8 8 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.508 | 3.508 | 3.508 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -1.7475646 0 0.50188608 10.44368 + 10 1.5000016 -1.7475671 0 0.50188602 10.44369 + 20 1.4999827 -1.7475388 0 0.50188592 10.443564 + 30 1.4999016 -1.7474173 0 0.5018858 10.443023 + 40 1.4997356 -1.7471685 0 0.50188572 10.441917 + 50 1.4995414 -1.7468771 0 0.5018858 10.440623 + 60 1.4995587 -1.7469027 0 0.50188622 10.440739 + 70 1.5003837 -1.7481389 0 0.50188727 10.446238 + 80 1.5032684 -1.7524625 0 0.50188958 10.465466 + 90 1.5107749 -1.763714 0 0.50189507 10.515502 + 100 1.52919 -1.791306 0 0.50191895 10.638261 +Loop time of 5.96037 on 8 procs for 100 steps with 4096 atoms + +Performance: 7247.876 tau/day, 16.777 timesteps/s +99.8% CPU use with 8 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.00049591 | 0.0005368 | 0.00056005 | 0.0 | 0.01 +Kspace | 5.94 | 5.941 | 5.9419 | 0.0 | 99.68 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.013702 | 0.014631 | 0.015768 | 0.6 | 0.25 +Output | 0.00044751 | 0.00048846 | 0.00058961 | 0.0 | 0.01 +Modify | 0.0016675 | 0.0017205 | 0.0017893 | 0.1 | 0.03 +Other | | 0.001971 | | | 0.03 + +Nlocal: 512 ave 512 max 512 min +Histogram: 8 0 0 0 0 0 0 0 0 0 +Nghost: 3584 ave 3584 max 3584 min +Histogram: 8 0 0 0 0 0 0 0 0 0 +Neighs: 65536 ave 65536 max 65536 min +Histogram: 8 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 524288 +Ave neighs/atom = 128 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:07 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.g++.p2nfft.1 b/examples/USER/scafacos/log.08Aug18.scafacos.g++.p2nfft.1 new file mode 100644 index 0000000000..1876a0e52b --- /dev/null +++ b/examples/USER/scafacos/log.08Aug18.scafacos.g++.p2nfft.1 @@ -0,0 +1,102 @@ +LAMMPS (2 Aug 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.NaCl + orthogonal box = (0 0 0) to (1 1 1) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 8 atoms + +replicate 8 8 8 + orthogonal box = (0 0 0) to (8 8 8) + 1 by 1 by 1 MPI processor grid + 4096 atoms + Time spent = 0.00049448 secs + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos p2nfft 0.001 +kspace_modify scafacos tolerance field + +timestep 0.005 +thermo 10 + +run 100 +Setting up ScaFaCoS with solver p2nfft ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 8 8 8 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.813 | 5.813 | 5.813 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -1.7477245 0 0.50172614 10.443537 + 10 1.5000176 -1.7475898 0 0.50188725 10.443798 + 20 1.5000161 -1.7475262 0 0.50194874 10.443843 + 30 1.4999486 -1.7474019 0 0.50197176 10.443413 + 40 1.4997889 -1.7471525 0 0.50198161 10.442357 + 50 1.4995945 -1.7468614 0 0.50198122 10.441061 + 60 1.499609 -1.7468813 0 0.50198309 10.44116 + 70 1.5004314 -1.7481179 0 0.50197962 10.446638 + 80 1.5033149 -1.7524495 0 0.50197233 10.46585 + 90 1.5108219 -1.7637095 0 0.50197005 10.515883 + 100 1.529239 -1.7913105 0 0.501988 10.638649 +Loop time of 18.1113 on 1 procs for 100 steps with 4096 atoms + +Performance: 2385.257 tau/day, 5.521 timesteps/s +100.0% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0014985 | 0.0014985 | 0.0014985 | 0.0 | 0.01 +Kspace | 18.079 | 18.079 | 18.079 | 0.0 | 99.82 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.014229 | 0.014229 | 0.014229 | 0.0 | 0.08 +Output | 0.0004642 | 0.0004642 | 0.0004642 | 0.0 | 0.00 +Modify | 0.011227 | 0.011227 | 0.011227 | 0.0 | 0.06 +Other | | 0.004455 | | | 0.02 + +Nlocal: 4096 ave 4096 max 4096 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 9728 ave 9728 max 9728 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 524288 ave 524288 max 524288 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 524288 +Ave neighs/atom = 128 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:21 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.g++.p2nfft.16 b/examples/USER/scafacos/log.08Aug18.scafacos.g++.p2nfft.16 new file mode 100644 index 0000000000..6e6e8f6e94 --- /dev/null +++ b/examples/USER/scafacos/log.08Aug18.scafacos.g++.p2nfft.16 @@ -0,0 +1,102 @@ +LAMMPS (2 Aug 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.NaCl + orthogonal box = (0 0 0) to (1 1 1) + 2 by 2 by 4 MPI processor grid + reading atoms ... + 8 atoms + +replicate 8 8 8 + orthogonal box = (0 0 0) to (8 8 8) + 2 by 2 by 4 MPI processor grid + 4096 atoms + Time spent = 0.000361443 secs + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos p2nfft 0.001 +kspace_modify scafacos tolerance field + +timestep 0.005 +thermo 10 + +run 100 +Setting up ScaFaCoS with solver p2nfft ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 8 8 8 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.501 | 3.501 | 3.501 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -1.7477245 0 0.50172614 10.443537 + 10 1.5000176 -1.7475898 0 0.50188725 10.443798 + 20 1.5000161 -1.7475262 0 0.50194874 10.443843 + 30 1.4999486 -1.7474019 0 0.50197176 10.443413 + 40 1.4997889 -1.7471525 0 0.50198161 10.442357 + 50 1.4995945 -1.7468614 0 0.50198122 10.441061 + 60 1.499609 -1.7468813 0 0.50198309 10.44116 + 70 1.5004314 -1.7481179 0 0.50197962 10.446638 + 80 1.5033149 -1.7524495 0 0.50197233 10.46585 + 90 1.5108219 -1.7637095 0 0.50197005 10.515883 + 100 1.529239 -1.7913105 0 0.501988 10.638649 +Loop time of 1.56685 on 16 procs for 100 steps with 4096 atoms + +Performance: 27571.239 tau/day, 63.822 timesteps/s +99.8% CPU use with 16 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.00036407 | 0.00040755 | 0.00047517 | 0.0 | 0.03 +Kspace | 1.5521 | 1.553 | 1.5536 | 0.0 | 99.12 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.009537 | 0.010175 | 0.011894 | 0.6 | 0.65 +Output | 0.000319 | 0.00039139 | 0.00052881 | 0.0 | 0.02 +Modify | 0.00086999 | 0.00097834 | 0.0010362 | 0.0 | 0.06 +Other | | 0.001859 | | | 0.12 + +Nlocal: 256 ave 256 max 256 min +Histogram: 16 0 0 0 0 0 0 0 0 0 +Nghost: 2816 ave 2816 max 2816 min +Histogram: 16 0 0 0 0 0 0 0 0 0 +Neighs: 32768 ave 32768 max 32768 min +Histogram: 16 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 524288 +Ave neighs/atom = 128 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:01 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.g++.p2nfft.2 b/examples/USER/scafacos/log.08Aug18.scafacos.g++.p2nfft.2 new file mode 100644 index 0000000000..72a53c48ff --- /dev/null +++ b/examples/USER/scafacos/log.08Aug18.scafacos.g++.p2nfft.2 @@ -0,0 +1,102 @@ +LAMMPS (2 Aug 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.NaCl + orthogonal box = (0 0 0) to (1 1 1) + 1 by 1 by 2 MPI processor grid + reading atoms ... + 8 atoms + +replicate 8 8 8 + orthogonal box = (0 0 0) to (8 8 8) + 1 by 1 by 2 MPI processor grid + 4096 atoms + Time spent = 0.0003438 secs + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos p2nfft 0.001 +kspace_modify scafacos tolerance field + +timestep 0.005 +thermo 10 + +run 100 +Setting up ScaFaCoS with solver p2nfft ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 8 8 8 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.574 | 4.574 | 4.574 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -1.7477245 0 0.50172614 10.443537 + 10 1.5000176 -1.7475898 0 0.50188725 10.443798 + 20 1.5000161 -1.7475262 0 0.50194874 10.443843 + 30 1.4999486 -1.7474019 0 0.50197176 10.443413 + 40 1.4997889 -1.7471525 0 0.50198161 10.442357 + 50 1.4995945 -1.7468614 0 0.50198122 10.441061 + 60 1.499609 -1.7468813 0 0.50198309 10.44116 + 70 1.5004314 -1.7481179 0 0.50197962 10.446638 + 80 1.5033149 -1.7524495 0 0.50197233 10.46585 + 90 1.5108219 -1.7637095 0 0.50197005 10.515883 + 100 1.529239 -1.7913105 0 0.501988 10.638649 +Loop time of 9.38943 on 2 procs for 100 steps with 4096 atoms + +Performance: 4600.920 tau/day, 10.650 timesteps/s +99.9% CPU use with 2 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0010064 | 0.0010065 | 0.0010066 | 0.0 | 0.01 +Kspace | 9.3602 | 9.3603 | 9.3604 | 0.0 | 99.69 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.019444 | 0.01968 | 0.019916 | 0.2 | 0.21 +Output | 0.00033355 | 0.00035357 | 0.0003736 | 0.0 | 0.00 +Modify | 0.0055819 | 0.0056176 | 0.0056534 | 0.0 | 0.06 +Other | | 0.002495 | | | 0.03 + +Nlocal: 2048 ave 2048 max 2048 min +Histogram: 2 0 0 0 0 0 0 0 0 0 +Nghost: 7168 ave 7168 max 7168 min +Histogram: 2 0 0 0 0 0 0 0 0 0 +Neighs: 262144 ave 262144 max 262144 min +Histogram: 2 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 524288 +Ave neighs/atom = 128 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:11 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.g++.p2nfft.4 b/examples/USER/scafacos/log.08Aug18.scafacos.g++.p2nfft.4 new file mode 100644 index 0000000000..bf4494df8b --- /dev/null +++ b/examples/USER/scafacos/log.08Aug18.scafacos.g++.p2nfft.4 @@ -0,0 +1,102 @@ +LAMMPS (2 Aug 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.NaCl + orthogonal box = (0 0 0) to (1 1 1) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 8 atoms + +replicate 8 8 8 + orthogonal box = (0 0 0) to (8 8 8) + 1 by 2 by 2 MPI processor grid + 4096 atoms + Time spent = 0.000260592 secs + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos p2nfft 0.001 +kspace_modify scafacos tolerance field + +timestep 0.005 +thermo 10 + +run 100 +Setting up ScaFaCoS with solver p2nfft ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 8 8 8 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.008 | 4.008 | 4.008 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -1.7477245 0 0.50172614 10.443537 + 10 1.5000176 -1.7475898 0 0.50188725 10.443798 + 20 1.5000161 -1.7475262 0 0.50194874 10.443843 + 30 1.4999486 -1.7474019 0 0.50197176 10.443413 + 40 1.4997889 -1.7471525 0 0.50198161 10.442357 + 50 1.4995945 -1.7468614 0 0.50198122 10.441061 + 60 1.499609 -1.7468813 0 0.50198309 10.44116 + 70 1.5004314 -1.7481179 0 0.50197962 10.446638 + 80 1.5033149 -1.7524495 0 0.50197233 10.46585 + 90 1.5108219 -1.7637095 0 0.50197005 10.515883 + 100 1.529239 -1.7913105 0 0.501988 10.638649 +Loop time of 5.09997 on 4 procs for 100 steps with 4096 atoms + +Performance: 8470.643 tau/day, 19.608 timesteps/s +99.8% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.00069928 | 0.00071001 | 0.00073647 | 0.0 | 0.01 +Kspace | 5.0795 | 5.0796 | 5.0797 | 0.0 | 99.60 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.014101 | 0.014216 | 0.014331 | 0.1 | 0.28 +Output | 0.00030541 | 0.00033581 | 0.00039625 | 0.0 | 0.01 +Modify | 0.0030217 | 0.0030621 | 0.0030868 | 0.0 | 0.06 +Other | | 0.002036 | | | 0.04 + +Nlocal: 1024 ave 1024 max 1024 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 5120 ave 5120 max 5120 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 131072 ave 131072 max 131072 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 524288 +Ave neighs/atom = 128 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:05 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.g++.p2nfft.8 b/examples/USER/scafacos/log.08Aug18.scafacos.g++.p2nfft.8 new file mode 100644 index 0000000000..b5e889dfc1 --- /dev/null +++ b/examples/USER/scafacos/log.08Aug18.scafacos.g++.p2nfft.8 @@ -0,0 +1,102 @@ +LAMMPS (2 Aug 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.NaCl + orthogonal box = (0 0 0) to (1 1 1) + 2 by 2 by 2 MPI processor grid + reading atoms ... + 8 atoms + +replicate 8 8 8 + orthogonal box = (0 0 0) to (8 8 8) + 2 by 2 by 2 MPI processor grid + 4096 atoms + Time spent = 0.000324488 secs + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos p2nfft 0.001 +kspace_modify scafacos tolerance field + +timestep 0.005 +thermo 10 + +run 100 +Setting up ScaFaCoS with solver p2nfft ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 8 8 8 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.508 | 3.508 | 3.508 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -1.7477245 0 0.50172614 10.443537 + 10 1.5000176 -1.7475898 0 0.50188725 10.443798 + 20 1.5000161 -1.7475262 0 0.50194874 10.443843 + 30 1.4999486 -1.7474019 0 0.50197176 10.443413 + 40 1.4997889 -1.7471525 0 0.50198161 10.442357 + 50 1.4995945 -1.7468614 0 0.50198122 10.441061 + 60 1.499609 -1.7468813 0 0.50198309 10.44116 + 70 1.5004314 -1.7481179 0 0.50197962 10.446638 + 80 1.5033149 -1.7524495 0 0.50197233 10.46585 + 90 1.5108219 -1.7637095 0 0.50197005 10.515883 + 100 1.529239 -1.7913105 0 0.501988 10.638649 +Loop time of 2.88506 on 8 procs for 100 steps with 4096 atoms + +Performance: 14973.700 tau/day, 34.661 timesteps/s +99.6% CPU use with 8 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.000489 | 0.00051507 | 0.00052857 | 0.0 | 0.02 +Kspace | 2.8657 | 2.866 | 2.8664 | 0.0 | 99.34 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.014354 | 0.014851 | 0.015097 | 0.2 | 0.51 +Output | 0.00037169 | 0.00042769 | 0.00054169 | 0.0 | 0.01 +Modify | 0.0015774 | 0.0016578 | 0.0018044 | 0.2 | 0.06 +Other | | 0.001645 | | | 0.06 + +Nlocal: 512 ave 512 max 512 min +Histogram: 8 0 0 0 0 0 0 0 0 0 +Nghost: 3584 ave 3584 max 3584 min +Histogram: 8 0 0 0 0 0 0 0 0 0 +Neighs: 65536 ave 65536 max 65536 min +Histogram: 8 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 524288 +Ave neighs/atom = 128 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:03 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.g++.p3m.2 b/examples/USER/scafacos/log.08Aug18.scafacos.g++.p3m.2 new file mode 100644 index 0000000000..e69de29bb2 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.direct.1 b/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.direct.1 new file mode 100644 index 0000000000..b0a47e4f98 --- /dev/null +++ b/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.direct.1 @@ -0,0 +1,105 @@ +LAMMPS (2 Aug 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.hammersley_shphere + orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 1000 atoms +change_box all boundary f f f + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos direct 0.001 + +timestep 0.005 +thermo 1 +run 20 +Setting up ScaFaCoS with solver direct ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 102 102 102 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 10.3 | 10.3 | 10.3 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -0.62417787 0 1.6235721 0.0015678854 + 1 18.780041 -10.770002 0 17.371889 0.016718957 + 2 65.289192 -11.084705 0 86.751149 0.060353634 + 3 121.92987 -7.0625759 0 175.64933 0.11404974 + 4 185.78164 -5.8777512 0 272.51604 0.17462195 + 5 286.36222 -4.382053 0 424.73173 0.26918926 + 6 481.42206 -4.3095567 0 717.1014 0.45274088 + 7 488.59167 -3.8685194 0 728.2861 0.45956866 + 8 497.85287 -3.0417966 0 742.99073 0.46838116 + 9 499.61615 -3.419003 0 745.2558 0.46983345 + 10 502.63684 -2.8360961 0 750.36521 0.47280809 + 11 504.4846 -2.7628105 0 753.20736 0.47462793 + 12 506.54485 -2.8460356 0 756.21142 0.47651441 + 13 508.27211 -2.730935 0 758.91482 0.47813752 + 14 510.57045 -2.6094877 0 762.48033 0.48031431 + 15 513.14798 -2.7150827 0 766.23717 0.48275229 + 16 515.78124 -2.3961811 0 770.50201 0.48526333 + 17 515.70265 -2.2982683 0 770.48215 0.48526617 + 18 515.7081 -2.1515983 0 770.63699 0.48530393 + 19 515.74906 -2.0581436 0 770.79182 0.48530977 + 20 515.70883 -1.8922577 0 770.89742 0.48527105 +Loop time of 0.465839 on 1 procs for 20 steps with 1000 atoms + +Performance: 18547.165 tau/day, 42.933 timesteps/s +99.9% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.00021982 | 0.00021982 | 0.00021982 | 0.0 | 0.05 +Kspace | 0.3218 | 0.3218 | 0.3218 | 0.0 | 69.08 +Neigh | 0.14249 | 0.14249 | 0.14249 | 0.0 | 30.59 +Comm | 0.00014853 | 0.00014853 | 0.00014853 | 0.0 | 0.03 +Output | 0.00026131 | 0.00026131 | 0.00026131 | 0.0 | 0.06 +Modify | 0.00055146 | 0.00055146 | 0.00055146 | 0.0 | 0.12 +Other | | 0.0003715 | | | 0.08 + +Nlocal: 1000 ave 1000 max 1000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 247817 ave 247817 max 247817 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 247817 +Ave neighs/atom = 247.817 +Neighbor list builds = 19 +Dangerous builds = 18 +Total wall time: 0:00:00 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.direct.2 b/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.direct.2 new file mode 100644 index 0000000000..1ffab0ca6a --- /dev/null +++ b/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.direct.2 @@ -0,0 +1,105 @@ +LAMMPS (2 Aug 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.hammersley_shphere + orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5) + 1 by 1 by 2 MPI processor grid + reading atoms ... + 1000 atoms +change_box all boundary f f f + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos direct 0.001 + +timestep 0.005 +thermo 1 +run 20 +Setting up ScaFaCoS with solver direct ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 102 102 102 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 6.48 | 6.861 | 7.243 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -0.62417787 0 1.6235721 0.0015678854 + 1 18.780041 -10.770002 0 17.371889 0.016718957 + 2 65.289192 -11.084705 0 86.751149 0.060353634 + 3 121.92987 -7.0625759 0 175.64933 0.11404974 + 4 185.78164 -5.8777512 0 272.51604 0.17462195 + 5 286.36222 -4.382053 0 424.73173 0.26918926 + 6 481.42206 -4.3095567 0 717.1014 0.45274088 + 7 488.59167 -3.8685194 0 728.2861 0.45956866 + 8 497.85287 -3.0417966 0 742.99073 0.46838116 + 9 499.61615 -3.419003 0 745.2558 0.46983345 + 10 502.63684 -2.8360961 0 750.36521 0.47280809 + 11 504.4846 -2.7628105 0 753.20736 0.47462793 + 12 506.54485 -2.8460356 0 756.21142 0.47651441 + 13 508.27211 -2.730935 0 758.91482 0.47813752 + 14 510.57045 -2.6094877 0 762.48033 0.48031431 + 15 513.14798 -2.7150827 0 766.23717 0.48275229 + 16 515.78124 -2.3961811 0 770.50201 0.48526333 + 17 515.70265 -2.2982683 0 770.48215 0.48526617 + 18 515.7081 -2.1515983 0 770.63699 0.48530393 + 19 515.74906 -2.0581436 0 770.79182 0.48530977 + 20 515.70883 -1.8922577 0 770.89742 0.48527105 +Loop time of 0.284007 on 2 procs for 20 steps with 1000 atoms + +Performance: 30421.778 tau/day, 70.421 timesteps/s +99.1% CPU use with 2 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.00022578 | 0.00022626 | 0.00022674 | 0.0 | 0.08 +Kspace | 0.18253 | 0.20503 | 0.22752 | 5.0 | 72.19 +Neigh | 0.05363 | 0.076239 | 0.098848 | 8.2 | 26.84 +Comm | 0.0014737 | 0.0016443 | 0.0018148 | 0.4 | 0.58 +Output | 0.000247 | 0.00032353 | 0.00040007 | 0.0 | 0.11 +Modify | 0.00029159 | 0.00029731 | 0.00030303 | 0.0 | 0.10 +Other | | 0.0002506 | | | 0.09 + +Nlocal: 500 ave 516 max 484 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Nghost: 456.5 ave 475 max 438 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Neighs: 123908 ave 172139 max 75678 min +Histogram: 1 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 247817 +Ave neighs/atom = 247.817 +Neighbor list builds = 19 +Dangerous builds = 18 +Total wall time: 0:00:00 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.direct.4 b/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.direct.4 new file mode 100644 index 0000000000..1235c0a3cd --- /dev/null +++ b/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.direct.4 @@ -0,0 +1,105 @@ +LAMMPS (2 Aug 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.hammersley_shphere + orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 1000 atoms +change_box all boundary f f f + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos direct 0.001 + +timestep 0.005 +thermo 1 +run 20 +Setting up ScaFaCoS with solver direct ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 102 102 102 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.837 | 5.123 | 5.6 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -0.62417787 0 1.6235721 0.0015678854 + 1 18.780041 -10.770002 0 17.371889 0.016718957 + 2 65.289192 -11.084705 0 86.751149 0.060353634 + 3 121.92987 -7.0625759 0 175.64933 0.11404974 + 4 185.78164 -5.8777512 0 272.51604 0.17462195 + 5 286.36222 -4.382053 0 424.73173 0.26918926 + 6 481.42206 -4.3095567 0 717.1014 0.45274088 + 7 488.59167 -3.8685194 0 728.2861 0.45956866 + 8 497.85287 -3.0417966 0 742.99073 0.46838116 + 9 499.61615 -3.419003 0 745.2558 0.46983345 + 10 502.63684 -2.8360961 0 750.36521 0.47280809 + 11 504.4846 -2.7628105 0 753.20736 0.47462793 + 12 506.54485 -2.8460356 0 756.21142 0.47651441 + 13 508.27211 -2.730935 0 758.91482 0.47813752 + 14 510.57045 -2.6094877 0 762.48033 0.48031431 + 15 513.14798 -2.7150827 0 766.23717 0.48275229 + 16 515.78124 -2.3961811 0 770.50201 0.48526333 + 17 515.70265 -2.2982683 0 770.48215 0.48526617 + 18 515.7081 -2.1515983 0 770.63699 0.48530393 + 19 515.74906 -2.0581436 0 770.79182 0.48530977 + 20 515.70883 -1.8922577 0 770.89742 0.48527105 +Loop time of 0.161335 on 4 procs for 20 steps with 1000 atoms + +Performance: 53553.228 tau/day, 123.966 timesteps/s +99.5% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.00022721 | 0.00023353 | 0.000247 | 0.0 | 0.14 +Kspace | 0.10295 | 0.11808 | 0.13377 | 3.5 | 73.19 +Neigh | 0.023849 | 0.039717 | 0.055031 | 6.1 | 24.62 +Comm | 0.0023148 | 0.0025774 | 0.0028391 | 0.4 | 1.60 +Output | 0.00029063 | 0.00038403 | 0.00050664 | 0.0 | 0.24 +Modify | 0.00015664 | 0.00015944 | 0.00016165 | 0.0 | 0.10 +Other | | 0.0001805 | | | 0.11 + +Nlocal: 250 ave 259 max 238 min +Histogram: 1 0 0 1 0 0 0 0 0 2 +Nghost: 672.25 ave 683 max 663 min +Histogram: 2 0 0 0 0 0 0 0 1 1 +Neighs: 61954.2 ave 97157 max 25016 min +Histogram: 1 0 0 1 0 0 1 0 0 1 + +Total # of neighbors = 247817 +Ave neighs/atom = 247.817 +Neighbor list builds = 19 +Dangerous builds = 18 +Total wall time: 0:00:00 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.direct.8 b/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.direct.8 new file mode 100644 index 0000000000..e72ade73b5 --- /dev/null +++ b/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.direct.8 @@ -0,0 +1,105 @@ +LAMMPS (2 Aug 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.hammersley_shphere + orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5) + 2 by 2 by 2 MPI processor grid + reading atoms ... + 1000 atoms +change_box all boundary f f f + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos direct 0.001 + +timestep 0.005 +thermo 1 +run 20 +Setting up ScaFaCoS with solver direct ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 102 102 102 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.164 | 4.26 | 4.546 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -0.62417787 0 1.6235721 0.0015678854 + 1 18.780041 -10.770002 0 17.371889 0.016718957 + 2 65.289192 -11.084705 0 86.751149 0.060353634 + 3 121.92987 -7.0625759 0 175.64933 0.11404974 + 4 185.78164 -5.8777512 0 272.51604 0.17462195 + 5 286.36222 -4.382053 0 424.73173 0.26918926 + 6 481.42206 -4.3095567 0 717.1014 0.45274088 + 7 488.59167 -3.8685194 0 728.2861 0.45956866 + 8 497.85287 -3.0417966 0 742.99073 0.46838116 + 9 499.61615 -3.419003 0 745.2558 0.46983345 + 10 502.63684 -2.8360961 0 750.36521 0.47280809 + 11 504.4846 -2.7628105 0 753.20736 0.47462793 + 12 506.54485 -2.8460356 0 756.21142 0.47651441 + 13 508.27211 -2.730935 0 758.91482 0.47813752 + 14 510.57045 -2.6094877 0 762.48033 0.48031431 + 15 513.14798 -2.7150827 0 766.23717 0.48275229 + 16 515.78124 -2.3961811 0 770.50201 0.48526333 + 17 515.70265 -2.2982683 0 770.48215 0.48526617 + 18 515.7081 -2.1515983 0 770.63699 0.48530393 + 19 515.74906 -2.0581436 0 770.79182 0.48530977 + 20 515.70883 -1.8922577 0 770.89742 0.48527105 +Loop time of 0.0883947 on 8 procs for 20 steps with 1000 atoms + +Performance: 97743.448 tau/day, 226.258 timesteps/s +99.2% CPU use with 8 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0002284 | 0.00024167 | 0.00029922 | 0.0 | 0.27 +Kspace | 0.055725 | 0.063153 | 0.071883 | 2.4 | 71.44 +Neigh | 0.012251 | 0.021348 | 0.029026 | 4.3 | 24.15 +Comm | 0.0025573 | 0.0029825 | 0.0034359 | 0.5 | 3.37 +Output | 0.00034451 | 0.00044149 | 0.00057721 | 0.0 | 0.50 +Modify | 7.8917e-05 | 8.437e-05 | 8.9407e-05 | 0.0 | 0.10 +Other | | 0.0001439 | | | 0.16 + +Nlocal: 125 ave 133 max 113 min +Histogram: 2 0 0 0 0 1 1 0 2 2 +Nghost: 773.625 ave 788 max 764 min +Histogram: 1 1 2 1 1 0 0 0 1 1 +Neighs: 30977.1 ave 50690 max 10447 min +Histogram: 1 1 1 0 1 1 0 0 2 1 + +Total # of neighbors = 247817 +Ave neighs/atom = 247.817 +Neighbor list builds = 19 +Dangerous builds = 18 +Total wall time: 0:00:00 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.fmm.1 b/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.fmm.1 new file mode 100644 index 0000000000..4bef247e26 --- /dev/null +++ b/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.fmm.1 @@ -0,0 +1,109 @@ +LAMMPS (2 Aug 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.hammersley_shphere + orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 1000 atoms +change_box all boundary f f f + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos fmm 0.001 +kspace_modify scafacos tolerance energy_rel +kspace_modify scafacos fmm_tuning 1 +ScaFaCoS setting fmm inhomogen tuning ... + +timestep 0.005 +thermo 1 + +run 20 +Setting up ScaFaCoS with solver fmm ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 102 102 102 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 10.3 | 10.3 | 10.3 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -0.62417141 0 1.6235786 0.0015676581 + 1 18.780412 -10.770009 0 17.372438 0.016719188 + 2 65.294131 -11.084501 0 86.758754 0.06035827 + 3 121.92555 -7.0612033 0 175.64423 0.1140457 + 4 185.71165 -5.8781334 0 272.41077 0.17455524 + 5 286.28339 -4.3800108 0 424.61565 0.26911306 + 6 481.28097 -4.3052012 0 716.89433 0.45262045 + 7 487.26022 -3.8672741 0 726.29216 0.45830216 + 8 493.65478 -3.0242687 0 736.71742 0.46443761 + 9 495.66203 -3.4336343 0 739.31592 0.46613014 + 10 498.41831 -2.8837072 0 743.99613 0.46887706 + 11 499.20944 -2.7724783 0 745.29287 0.46966875 + 12 500.97345 -2.8281484 0 747.88057 0.47126462 + 13 507.46412 -2.7752775 0 757.65971 0.47728761 + 14 525.35729 -2.5749814 0 784.67292 0.49422171 + 15 563.9578 -2.9982381 0 842.09253 0.53043696 + 16 645.47602 -2.5519203 0 964.69389 0.60730795 + 17 647.09276 -2.2568468 0 967.41166 0.60891914 + 18 647.12596 -2.2791003 0 967.43915 0.60900309 + 19 647.24862 -2.2495226 0 967.65253 0.60908339 + 20 647.51175 -2.0239179 0 968.27244 0.60932598 +Loop time of 0.797289 on 1 procs for 20 steps with 1000 atoms + +Performance: 10836.721 tau/day, 25.085 timesteps/s +100.0% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.00022364 | 0.00022364 | 0.00022364 | 0.0 | 0.03 +Kspace | 0.6524 | 0.6524 | 0.6524 | 0.0 | 81.83 +Neigh | 0.14312 | 0.14312 | 0.14312 | 0.0 | 17.95 +Comm | 0.00020337 | 0.00020337 | 0.00020337 | 0.0 | 0.03 +Output | 0.00036621 | 0.00036621 | 0.00036621 | 0.0 | 0.05 +Modify | 0.00058126 | 0.00058126 | 0.00058126 | 0.0 | 0.07 +Other | | 0.0003934 | | | 0.05 + +Nlocal: 1000 ave 1000 max 1000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 244342 ave 244342 max 244342 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 244342 +Ave neighs/atom = 244.342 +Neighbor list builds = 19 +Dangerous builds = 18 +Total wall time: 0:00:01 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.fmm.2 b/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.fmm.2 new file mode 100644 index 0000000000..e8e614004d --- /dev/null +++ b/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.fmm.2 @@ -0,0 +1,109 @@ +LAMMPS (2 Aug 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.hammersley_shphere + orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5) + 1 by 1 by 2 MPI processor grid + reading atoms ... + 1000 atoms +change_box all boundary f f f + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos fmm 0.001 +kspace_modify scafacos tolerance energy_rel +kspace_modify scafacos fmm_tuning 1 +ScaFaCoS setting fmm inhomogen tuning ... + +timestep 0.005 +thermo 1 + +run 20 +Setting up ScaFaCoS with solver fmm ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 102 102 102 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 6.48 | 6.861 | 7.243 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -0.62417141 0 1.6235786 0.0015676581 + 1 18.780412 -10.770009 0 17.372438 0.016719188 + 2 65.294131 -11.084501 0 86.758754 0.06035827 + 3 121.92555 -7.0612033 0 175.64423 0.1140457 + 4 185.71165 -5.8781334 0 272.41077 0.17455524 + 5 286.28339 -4.3800108 0 424.61565 0.26911306 + 6 481.28097 -4.3052012 0 716.89433 0.45262045 + 7 487.26022 -3.8672741 0 726.29216 0.45830216 + 8 493.65478 -3.0242687 0 736.71742 0.46443761 + 9 495.66203 -3.4336343 0 739.31592 0.46613014 + 10 498.41831 -2.8837072 0 743.99613 0.46887706 + 11 499.20944 -2.7724783 0 745.29287 0.46966875 + 12 500.97345 -2.8281484 0 747.88057 0.47126462 + 13 507.46412 -2.7752775 0 757.65971 0.47728761 + 14 525.35729 -2.5749814 0 784.67292 0.49422171 + 15 563.9578 -2.9982381 0 842.09253 0.53043696 + 16 645.47602 -2.5519203 0 964.69389 0.60730795 + 17 647.09276 -2.2568468 0 967.41166 0.60891914 + 18 647.12596 -2.2791003 0 967.43915 0.60900309 + 19 647.24862 -2.2495226 0 967.65253 0.60908339 + 20 647.51175 -2.0239179 0 968.27244 0.60932598 +Loop time of 0.701186 on 2 procs for 20 steps with 1000 atoms + +Performance: 12321.981 tau/day, 28.523 timesteps/s +99.7% CPU use with 2 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.00022388 | 0.00022912 | 0.00023437 | 0.0 | 0.03 +Kspace | 0.60189 | 0.62405 | 0.64621 | 2.8 | 89.00 +Neigh | 0.051681 | 0.073973 | 0.096265 | 8.2 | 10.55 +Comm | 0.0016983 | 0.0018919 | 0.0020854 | 0.4 | 0.27 +Output | 0.00034356 | 0.00044572 | 0.00054789 | 0.0 | 0.06 +Modify | 0.00031281 | 0.0003171 | 0.00032139 | 0.0 | 0.05 +Other | | 0.0002786 | | | 0.04 + +Nlocal: 500 ave 509 max 491 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Nghost: 455.5 ave 467 max 444 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Neighs: 122171 ave 171834 max 72508 min +Histogram: 1 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 244342 +Ave neighs/atom = 244.342 +Neighbor list builds = 19 +Dangerous builds = 18 +Total wall time: 0:00:01 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.fmm.4 b/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.fmm.4 new file mode 100644 index 0000000000..e3f5bf44c9 --- /dev/null +++ b/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.fmm.4 @@ -0,0 +1,109 @@ +LAMMPS (2 Aug 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.hammersley_shphere + orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 1000 atoms +change_box all boundary f f f + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos fmm 0.001 +kspace_modify scafacos tolerance energy_rel +kspace_modify scafacos fmm_tuning 1 +ScaFaCoS setting fmm inhomogen tuning ... + +timestep 0.005 +thermo 1 + +run 20 +Setting up ScaFaCoS with solver fmm ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 102 102 102 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.837 | 5.123 | 5.6 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -0.62417141 0 1.6235786 0.0015676581 + 1 18.780412 -10.770009 0 17.372438 0.016719188 + 2 65.294131 -11.084501 0 86.758754 0.06035827 + 3 121.92555 -7.0612033 0 175.64423 0.1140457 + 4 185.71165 -5.8781334 0 272.41077 0.17455524 + 5 286.28339 -4.3800108 0 424.61565 0.26911306 + 6 481.28097 -4.3052012 0 716.89433 0.45262045 + 7 487.26022 -3.8672741 0 726.29216 0.45830216 + 8 493.65478 -3.0242687 0 736.71742 0.46443761 + 9 495.66203 -3.4336343 0 739.31592 0.46613014 + 10 498.41831 -2.8837072 0 743.99613 0.46887706 + 11 499.20944 -2.7724783 0 745.29287 0.46966875 + 12 500.97345 -2.8281484 0 747.88057 0.47126462 + 13 507.46412 -2.7752775 0 757.65971 0.47728761 + 14 525.35729 -2.5749814 0 784.67292 0.49422171 + 15 563.9578 -2.9982381 0 842.09253 0.53043696 + 16 645.47602 -2.5519203 0 964.69389 0.60730795 + 17 647.09276 -2.2568468 0 967.41166 0.60891914 + 18 647.12596 -2.2791003 0 967.43915 0.60900309 + 19 647.24862 -2.2495226 0 967.65253 0.60908339 + 20 647.51175 -2.0239179 0 968.27244 0.60932598 +Loop time of 0.666895 on 4 procs for 20 steps with 1000 atoms + +Performance: 12955.555 tau/day, 29.990 timesteps/s +99.5% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0002284 | 0.00024879 | 0.00025725 | 0.0 | 0.04 +Kspace | 0.6085 | 0.62278 | 0.6386 | 1.6 | 93.38 +Neigh | 0.023998 | 0.040044 | 0.054552 | 6.2 | 6.00 +Comm | 0.0025489 | 0.0028656 | 0.0031898 | 0.4 | 0.43 +Output | 0.0004077 | 0.00053912 | 0.00071406 | 0.0 | 0.08 +Modify | 0.00017953 | 0.00018525 | 0.00020218 | 0.0 | 0.03 +Other | | 0.0002366 | | | 0.04 + +Nlocal: 250 ave 259 max 240 min +Histogram: 1 0 0 0 0 2 0 0 0 1 +Nghost: 668.75 ave 679 max 657 min +Histogram: 1 0 0 0 0 1 1 0 0 1 +Neighs: 61085.5 ave 95363 max 24964 min +Histogram: 1 0 0 1 0 0 0 1 0 1 + +Total # of neighbors = 244342 +Ave neighs/atom = 244.342 +Neighbor list builds = 19 +Dangerous builds = 18 +Total wall time: 0:00:01 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.fmm.8 b/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.fmm.8 new file mode 100644 index 0000000000..22d1140813 --- /dev/null +++ b/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.fmm.8 @@ -0,0 +1,109 @@ +LAMMPS (2 Aug 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.hammersley_shphere + orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5) + 2 by 2 by 2 MPI processor grid + reading atoms ... + 1000 atoms +change_box all boundary f f f + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos fmm 0.001 +kspace_modify scafacos tolerance energy_rel +kspace_modify scafacos fmm_tuning 1 +ScaFaCoS setting fmm inhomogen tuning ... + +timestep 0.005 +thermo 1 + +run 20 +Setting up ScaFaCoS with solver fmm ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 102 102 102 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.164 | 4.26 | 4.546 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -0.62417141 0 1.6235786 0.0015676581 + 1 18.780412 -10.770009 0 17.372438 0.016719188 + 2 65.294131 -11.084501 0 86.758754 0.06035827 + 3 121.92555 -7.0612033 0 175.64423 0.1140457 + 4 185.71165 -5.8781334 0 272.41077 0.17455524 + 5 286.28339 -4.3800108 0 424.61565 0.26911306 + 6 481.28097 -4.3052012 0 716.89433 0.45262045 + 7 487.26022 -3.8672741 0 726.29216 0.45830216 + 8 493.65478 -3.0242687 0 736.71742 0.46443761 + 9 495.66203 -3.4336343 0 739.31592 0.46613014 + 10 498.41831 -2.8837072 0 743.99613 0.46887706 + 11 499.20944 -2.7724783 0 745.29287 0.46966875 + 12 500.97345 -2.8281484 0 747.88057 0.47126462 + 13 507.46412 -2.7752775 0 757.65971 0.47728761 + 14 525.35729 -2.5749814 0 784.67292 0.49422171 + 15 563.9578 -2.9982381 0 842.09253 0.53043696 + 16 645.47602 -2.5519203 0 964.69389 0.60730795 + 17 647.09276 -2.2568468 0 967.41166 0.60891914 + 18 647.12596 -2.2791003 0 967.43915 0.60900309 + 19 647.24862 -2.2495226 0 967.65253 0.60908339 + 20 647.51175 -2.0239179 0 968.27244 0.60932598 +Loop time of 0.569395 on 8 procs for 20 steps with 1000 atoms + +Performance: 15174.000 tau/day, 35.125 timesteps/s +99.3% CPU use with 8 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.00021982 | 0.00023353 | 0.0002408 | 0.0 | 0.04 +Kspace | 0.53679 | 0.54466 | 0.55292 | 0.8 | 95.66 +Neigh | 0.011844 | 0.02033 | 0.028357 | 4.2 | 3.57 +Comm | 0.0028894 | 0.0031579 | 0.0034704 | 0.4 | 0.55 +Output | 0.0005579 | 0.00067073 | 0.0008719 | 0.0 | 0.12 +Modify | 0.0001018 | 0.00011405 | 0.00012612 | 0.0 | 0.02 +Other | | 0.0002268 | | | 0.04 + +Nlocal: 125 ave 137 max 111 min +Histogram: 1 1 0 0 0 2 2 1 0 1 +Nghost: 768.875 ave 788 max 761 min +Histogram: 4 0 2 0 0 0 1 0 0 1 +Neighs: 30542.8 ave 48077 max 10011 min +Histogram: 1 1 1 0 1 1 0 0 0 3 + +Total # of neighbors = 244342 +Ave neighs/atom = 244.342 +Neighbor list builds = 19 +Dangerous builds = 18 +Total wall time: 0:00:01 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.p2nfft.1 b/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.p2nfft.1 new file mode 100644 index 0000000000..f8a85c6c6b --- /dev/null +++ b/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.p2nfft.1 @@ -0,0 +1,107 @@ +LAMMPS (2 Aug 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.hammersley_shphere + orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 1000 atoms +change_box all boundary f f f + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos p2nfft 0.001 +kspace_modify scafacos tolerance potential + +timestep 0.005 +thermo 1 + +run 20 +Setting up ScaFaCoS with solver p2nfft ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 102 102 102 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 10.3 | 10.3 | 10.3 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -0.62417787 0 1.6235721 0.0015678854 + 1 18.780041 -10.770002 0 17.371889 0.016718957 + 2 65.289192 -11.084705 0 86.751149 0.060353634 + 3 121.92987 -7.0625759 0 175.64933 0.11404974 + 4 185.78164 -5.8777511 0 272.51603 0.17462194 + 5 286.36221 -4.3820531 0 424.73172 0.26918925 + 6 481.42203 -4.3095567 0 717.10136 0.45274086 + 7 488.59165 -3.8685193 0 728.28607 0.45956865 + 8 497.85288 -3.0417938 0 742.99075 0.46838117 + 9 499.61619 -3.4190063 0 745.25585 0.46983349 + 10 502.63691 -2.8360951 0 750.36531 0.47280815 + 11 504.4847 -2.7628089 0 753.20751 0.47462802 + 12 506.54494 -2.8460319 0 756.21157 0.4765145 + 13 508.2722 -2.7309328 0 758.91497 0.47813761 + 14 510.57053 -2.6094792 0 762.48045 0.48031438 + 15 513.14804 -2.7150819 0 766.23726 0.48275234 + 16 515.78127 -2.3961749 0 770.50206 0.48526336 + 17 515.70267 -2.2982581 0 770.48219 0.48526619 + 18 515.70813 -2.1516075 0 770.63702 0.48530395 + 19 515.74908 -2.0581483 0 770.79185 0.48530979 + 20 515.70881 -1.892235 0 770.89742 0.48527104 +Loop time of 1.06008 on 1 procs for 20 steps with 1000 atoms + +Performance: 8150.306 tau/day, 18.866 timesteps/s +100.0% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.00022078 | 0.00022078 | 0.00022078 | 0.0 | 0.02 +Kspace | 0.91611 | 0.91611 | 0.91611 | 0.0 | 86.42 +Neigh | 0.14232 | 0.14232 | 0.14232 | 0.0 | 13.43 +Comm | 0.00015092 | 0.00015092 | 0.00015092 | 0.0 | 0.01 +Output | 0.00033736 | 0.00033736 | 0.00033736 | 0.0 | 0.03 +Modify | 0.00056243 | 0.00056243 | 0.00056243 | 0.0 | 0.05 +Other | | 0.0003803 | | | 0.04 + +Nlocal: 1000 ave 1000 max 1000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 247817 ave 247817 max 247817 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 247817 +Ave neighs/atom = 247.817 +Neighbor list builds = 19 +Dangerous builds = 18 +Total wall time: 0:00:01 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.p2nfft.2 b/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.p2nfft.2 new file mode 100644 index 0000000000..bd7e7fee1f --- /dev/null +++ b/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.p2nfft.2 @@ -0,0 +1,107 @@ +LAMMPS (2 Aug 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.hammersley_shphere + orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5) + 1 by 1 by 2 MPI processor grid + reading atoms ... + 1000 atoms +change_box all boundary f f f + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos p2nfft 0.001 +kspace_modify scafacos tolerance potential + +timestep 0.005 +thermo 1 + +run 20 +Setting up ScaFaCoS with solver p2nfft ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 102 102 102 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 6.48 | 6.861 | 7.243 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -0.62417787 0 1.6235721 0.0015678854 + 1 18.780041 -10.770002 0 17.371889 0.016718957 + 2 65.289192 -11.084705 0 86.751149 0.060353634 + 3 121.92987 -7.0625759 0 175.64933 0.11404974 + 4 185.78164 -5.8777511 0 272.51603 0.17462194 + 5 286.36221 -4.3820531 0 424.73172 0.26918925 + 6 481.42203 -4.3095567 0 717.10136 0.45274086 + 7 488.59165 -3.8685193 0 728.28607 0.45956865 + 8 497.85288 -3.0417938 0 742.99075 0.46838117 + 9 499.61619 -3.4190063 0 745.25585 0.46983349 + 10 502.63691 -2.8360951 0 750.36531 0.47280815 + 11 504.4847 -2.7628089 0 753.20751 0.47462802 + 12 506.54494 -2.8460319 0 756.21157 0.4765145 + 13 508.2722 -2.7309328 0 758.91497 0.47813761 + 14 510.57053 -2.6094792 0 762.48045 0.48031438 + 15 513.14804 -2.7150819 0 766.23726 0.48275234 + 16 515.78127 -2.3961749 0 770.50206 0.48526336 + 17 515.70267 -2.2982581 0 770.48219 0.48526619 + 18 515.70813 -2.1516075 0 770.63702 0.48530395 + 19 515.74908 -2.0581483 0 770.79185 0.48530979 + 20 515.70881 -1.892235 0 770.89742 0.48527104 +Loop time of 0.701267 on 2 procs for 20 steps with 1000 atoms + +Performance: 12320.557 tau/day, 28.520 timesteps/s +99.6% CPU use with 2 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0002265 | 0.00022769 | 0.00022888 | 0.0 | 0.03 +Kspace | 0.60195 | 0.62374 | 0.64554 | 2.8 | 88.95 +Neigh | 0.05268 | 0.074592 | 0.096504 | 8.0 | 10.64 +Comm | 0.0015199 | 0.0016934 | 0.0018668 | 0.4 | 0.24 +Output | 0.00031519 | 0.00041544 | 0.0005157 | 0.0 | 0.06 +Modify | 0.00029492 | 0.00030565 | 0.00031638 | 0.0 | 0.04 +Other | | 0.000288 | | | 0.04 + +Nlocal: 500 ave 516 max 484 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Nghost: 456.5 ave 475 max 438 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Neighs: 123908 ave 172139 max 75678 min +Histogram: 1 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 247817 +Ave neighs/atom = 247.817 +Neighbor list builds = 19 +Dangerous builds = 18 +Total wall time: 0:00:00 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.p2nfft.4 b/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.p2nfft.4 new file mode 100644 index 0000000000..8a7e591f9a --- /dev/null +++ b/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.p2nfft.4 @@ -0,0 +1,107 @@ +LAMMPS (2 Aug 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.hammersley_shphere + orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 1000 atoms +change_box all boundary f f f + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos p2nfft 0.001 +kspace_modify scafacos tolerance potential + +timestep 0.005 +thermo 1 + +run 20 +Setting up ScaFaCoS with solver p2nfft ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 102 102 102 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.837 | 5.123 | 5.6 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -0.62417787 0 1.6235721 0.0015678854 + 1 18.780041 -10.770002 0 17.371889 0.016718957 + 2 65.289192 -11.084705 0 86.751149 0.060353634 + 3 121.92987 -7.0625759 0 175.64933 0.11404974 + 4 185.78164 -5.8777511 0 272.51603 0.17462194 + 5 286.36221 -4.3820531 0 424.73172 0.26918925 + 6 481.42203 -4.3095567 0 717.10136 0.45274086 + 7 488.59165 -3.8685193 0 728.28607 0.45956865 + 8 497.85288 -3.0417938 0 742.99075 0.46838117 + 9 499.61619 -3.4190063 0 745.25585 0.46983349 + 10 502.63691 -2.8360951 0 750.36531 0.47280815 + 11 504.4847 -2.7628089 0 753.20751 0.47462802 + 12 506.54494 -2.8460319 0 756.21157 0.4765145 + 13 508.2722 -2.7309328 0 758.91497 0.47813761 + 14 510.57053 -2.6094792 0 762.48045 0.48031438 + 15 513.14804 -2.7150819 0 766.23726 0.48275234 + 16 515.78127 -2.3961749 0 770.50206 0.48526336 + 17 515.70267 -2.2982581 0 770.48219 0.48526619 + 18 515.70813 -2.1516075 0 770.63702 0.48530395 + 19 515.74908 -2.0581483 0 770.79185 0.48530979 + 20 515.70881 -1.892235 0 770.89742 0.48527104 +Loop time of 0.427495 on 4 procs for 20 steps with 1000 atoms + +Performance: 20210.785 tau/day, 46.784 timesteps/s +99.7% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0002327 | 0.00023341 | 0.00023437 | 0.0 | 0.05 +Kspace | 0.36897 | 0.38411 | 0.39988 | 1.9 | 89.85 +Neigh | 0.023831 | 0.039796 | 0.055124 | 6.1 | 9.31 +Comm | 0.0022776 | 0.0025444 | 0.0028152 | 0.4 | 0.60 +Output | 0.00033784 | 0.0004344 | 0.00057077 | 0.0 | 0.10 +Modify | 0.00016117 | 0.00016713 | 0.00017095 | 0.0 | 0.04 +Other | | 0.0002093 | | | 0.05 + +Nlocal: 250 ave 259 max 238 min +Histogram: 1 0 0 1 0 0 0 0 0 2 +Nghost: 672.25 ave 683 max 663 min +Histogram: 2 0 0 0 0 0 0 0 1 1 +Neighs: 61954.2 ave 97157 max 25016 min +Histogram: 1 0 0 1 0 0 1 0 0 1 + +Total # of neighbors = 247817 +Ave neighs/atom = 247.817 +Neighbor list builds = 19 +Dangerous builds = 18 +Total wall time: 0:00:00 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.p2nfft.8 b/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.p2nfft.8 new file mode 100644 index 0000000000..13922c09ac --- /dev/null +++ b/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.p2nfft.8 @@ -0,0 +1,107 @@ +LAMMPS (2 Aug 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.hammersley_shphere + orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5) + 2 by 2 by 2 MPI processor grid + reading atoms ... + 1000 atoms +change_box all boundary f f f + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos p2nfft 0.001 +kspace_modify scafacos tolerance potential + +timestep 0.005 +thermo 1 + +run 20 +Setting up ScaFaCoS with solver p2nfft ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 102 102 102 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.164 | 4.26 | 4.546 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -0.62417787 0 1.6235721 0.0015678854 + 1 18.780041 -10.770002 0 17.371889 0.016718957 + 2 65.289192 -11.084705 0 86.751149 0.060353634 + 3 121.92987 -7.0625759 0 175.64933 0.11404974 + 4 185.78164 -5.8777511 0 272.51603 0.17462194 + 5 286.36221 -4.3820531 0 424.73172 0.26918925 + 6 481.42203 -4.3095567 0 717.10136 0.45274086 + 7 488.59165 -3.8685193 0 728.28607 0.45956865 + 8 497.85288 -3.0417938 0 742.99075 0.46838117 + 9 499.61619 -3.4190063 0 745.25585 0.46983349 + 10 502.63691 -2.8360951 0 750.36531 0.47280815 + 11 504.4847 -2.7628089 0 753.20751 0.47462802 + 12 506.54494 -2.8460319 0 756.21157 0.4765145 + 13 508.2722 -2.7309328 0 758.91497 0.47813761 + 14 510.57053 -2.6094792 0 762.48045 0.48031438 + 15 513.14804 -2.7150819 0 766.23726 0.48275234 + 16 515.78127 -2.3961749 0 770.50206 0.48526336 + 17 515.70267 -2.2982581 0 770.48219 0.48526619 + 18 515.70813 -2.1516075 0 770.63702 0.48530395 + 19 515.74908 -2.0581483 0 770.79185 0.48530979 + 20 515.70881 -1.892235 0 770.89742 0.48527104 +Loop time of 0.242145 on 8 procs for 20 steps with 1000 atoms + +Performance: 35681.038 tau/day, 82.595 timesteps/s +99.2% CPU use with 8 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0002315 | 0.00023672 | 0.00024652 | 0.0 | 0.10 +Kspace | 0.20915 | 0.21666 | 0.22564 | 1.3 | 89.48 +Neigh | 0.012218 | 0.021341 | 0.029026 | 4.3 | 8.81 +Comm | 0.0028954 | 0.0031248 | 0.0033553 | 0.3 | 1.29 +Output | 0.00039291 | 0.00049406 | 0.00066066 | 0.0 | 0.20 +Modify | 8.7976e-05 | 9.2953e-05 | 9.7752e-05 | 0.0 | 0.04 +Other | | 0.0001938 | | | 0.08 + +Nlocal: 125 ave 133 max 113 min +Histogram: 2 0 0 0 0 1 1 0 2 2 +Nghost: 773.625 ave 788 max 764 min +Histogram: 1 1 2 1 1 0 0 0 1 1 +Neighs: 30977.1 ave 50690 max 10447 min +Histogram: 1 1 1 0 1 1 0 0 2 1 + +Total # of neighbors = 247817 +Ave neighs/atom = 247.817 +Neighbor list builds = 19 +Dangerous builds = 18 +Total wall time: 0:00:00 From e08aaa7e397987c370a836723126aca66db05932 Mon Sep 17 00:00:00 2001 From: Rene Halver Date: Wed, 8 Aug 2018 15:03:47 -0600 Subject: [PATCH 092/302] added examples for P3M with ScaFaCoS --- examples/USER/scafacos/in.scafacos.cw.p3m | 31 +++++++++++++++++++ examples/USER/scafacos/in.scafacos.p3m | 37 +++++++++++++++++++++++ 2 files changed, 68 insertions(+) create mode 100644 examples/USER/scafacos/in.scafacos.cw.p3m create mode 100644 examples/USER/scafacos/in.scafacos.p3m diff --git a/examples/USER/scafacos/in.scafacos.cw.p3m b/examples/USER/scafacos/in.scafacos.cw.p3m new file mode 100644 index 0000000000..50ff1a64a8 --- /dev/null +++ b/examples/USER/scafacos/in.scafacos.cw.p3m @@ -0,0 +1,31 @@ + +units lj +atom_style charge + +read_data data.cloud_wall + +velocity all set 0.0 0.0 0.0 mom no + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve +kspace_style scafacos p3m 0.001 +kspace_modify scafacos tolerance field + +timestep 0.005 + +thermo_style custom step atoms cpu temp pe ke etotal ecoul press + +run_style verlet + +#dump simple all custom 1000 id x y z vx vy vz +#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass +#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass +#dump_modify dmpvtk pad 7 + +thermo 10 +run 100 diff --git a/examples/USER/scafacos/in.scafacos.p3m b/examples/USER/scafacos/in.scafacos.p3m new file mode 100644 index 0000000000..874b1d151a --- /dev/null +++ b/examples/USER/scafacos/in.scafacos.p3m @@ -0,0 +1,37 @@ +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.NaCl + +replicate 8 8 8 + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos p3m 0.001 +kspace_modify scafacos tolerance field + +timestep 0.005 +thermo 10 + +run 100 From 120fdbb9fc94dc049d94488a771b3c19e1f56208 Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Fri, 10 Aug 2018 10:53:22 -0600 Subject: [PATCH 093/302] Add data duplication to pair_eam_kokkos --- src/KOKKOS/pair_eam_kokkos.cpp | 87 ++++++++++++++++++++++------------ src/KOKKOS/pair_eam_kokkos.h | 10 ++++ 2 files changed, 66 insertions(+), 31 deletions(-) diff --git a/src/KOKKOS/pair_eam_kokkos.cpp b/src/KOKKOS/pair_eam_kokkos.cpp index 1bfb8255dc..256cb8d55b 100644 --- a/src/KOKKOS/pair_eam_kokkos.cpp +++ b/src/KOKKOS/pair_eam_kokkos.cpp @@ -117,6 +117,19 @@ void PairEAMKokkos::compute(int eflag_in, int vflag_in) d_ilist = k_list->d_ilist; int inum = list->inum; + need_dup = lmp->kokkos->need_dup(); + if (need_dup) { + dup_rho = Kokkos::Experimental::create_scatter_view(d_rho); + dup_f = Kokkos::Experimental::create_scatter_view(f); + dup_eatom = Kokkos::Experimental::create_scatter_view(d_eatom); + dup_vatom = Kokkos::Experimental::create_scatter_view(d_vatom); + } else { + ndup_rho = Kokkos::Experimental::create_scatter_view(d_rho); + ndup_f = Kokkos::Experimental::create_scatter_view(f); + ndup_eatom = Kokkos::Experimental::create_scatter_view(d_eatom); + ndup_vatom = Kokkos::Experimental::create_scatter_view(d_vatom); + } + copymode = 1; // zero out density @@ -228,6 +241,9 @@ void PairEAMKokkos::compute(int eflag_in, int vflag_in) } } + if (need_dup) + Kokkos::Experimental::contribute(f, dup_f); + if (eflag_global) eng_vdwl += ev.evdwl; if (vflag_global) { virial[0] += ev.v[0]; @@ -241,11 +257,15 @@ void PairEAMKokkos::compute(int eflag_in, int vflag_in) if (vflag_fdotr) pair_virial_fdotr_compute(this); if (eflag_atom) { + if (need_dup) + Kokkos::Experimental::contribute(d_eatom, dup_eatom); k_eatom.template modify(); k_eatom.template sync(); } if (vflag_atom) { + if (need_dup) + Kokkos::Experimental::contribute(d_vatom, dup_vatom); k_vatom.template modify(); k_vatom.template sync(); } @@ -503,8 +523,9 @@ void PairEAMKokkos::operator()(TagPairEAMKernelA::value> > rho = v_rho; + // The rho array is duplicated for OpenMP, atomic for CUDA, and neither for Serial + auto v_rho = ScatterViewHelper::value,decltype(dup_rho),decltype(ndup_rho)>::get(dup_rho,ndup_rho); + auto a_rho = v_rho.template access::value>(); const int i = d_ilist[ii]; const X_FLOAT xtmp = x(i,0); @@ -538,13 +559,13 @@ void PairEAMKokkos::operator()(TagPairEAMKernelA KOKKOS_INLINE_FUNCTION void PairEAMKokkos::operator()(TagPairEAMKernelC, const int &ii, EV_FLOAT& ev) const { - // The f array is atomic for Half/Thread neighbor style - Kokkos::View::value> > a_f = f; + // The f array is duplicated for OpenMP, atomic for CUDA, and neither for Serial + auto v_f = ScatterViewHelper::value,decltype(dup_f),decltype(ndup_f)>::get(dup_f,ndup_f); + auto a_f = v_f.template access::value>(); const int i = d_ilist[ii]; const X_FLOAT xtmp = x(i,0); @@ -778,18 +800,21 @@ void PairEAMKokkos::ev_tally(EV_FLOAT &ev, const int &i, const int & const int EFLAG = eflag; const int VFLAG = vflag_either; - // The eatom and vatom arrays are atomic for Half/Thread neighbor style - Kokkos::View::value> > v_eatom = k_eatom.view(); - Kokkos::View::value> > v_vatom = k_vatom.view(); + // The eatom and vatom arrays are duplicated for OpenMP, atomic for CUDA, and neither for Serial + auto v_eatom = ScatterViewHelper::value,decltype(dup_eatom),decltype(ndup_eatom)>::get(dup_eatom,ndup_eatom); + auto a_eatom = v_eatom.template access::value>(); + + auto v_vatom = ScatterViewHelper::value,decltype(dup_vatom),decltype(ndup_vatom)>::get(dup_vatom,ndup_vatom); + auto a_vatom = v_vatom.template access::value>(); if (EFLAG) { if (eflag_atom) { const E_FLOAT epairhalf = 0.5 * epair; if (NEIGHFLAG!=FULL) { - if (NEWTON_PAIR || i < nlocal) v_eatom[i] += epairhalf; - if (NEWTON_PAIR || j < nlocal) v_eatom[j] += epairhalf; + if (NEWTON_PAIR || i < nlocal) a_eatom[i] += epairhalf; + if (NEWTON_PAIR || j < nlocal) a_eatom[j] += epairhalf; } else { - v_eatom[i] += epairhalf; + a_eatom[i] += epairhalf; } } } @@ -833,28 +858,28 @@ void PairEAMKokkos::ev_tally(EV_FLOAT &ev, const int &i, const int & if (vflag_atom) { if (NEIGHFLAG!=FULL) { if (NEWTON_PAIR || i < nlocal) { - v_vatom(i,0) += 0.5*v0; - v_vatom(i,1) += 0.5*v1; - v_vatom(i,2) += 0.5*v2; - v_vatom(i,3) += 0.5*v3; - v_vatom(i,4) += 0.5*v4; - v_vatom(i,5) += 0.5*v5; + a_vatom(i,0) += 0.5*v0; + a_vatom(i,1) += 0.5*v1; + a_vatom(i,2) += 0.5*v2; + a_vatom(i,3) += 0.5*v3; + a_vatom(i,4) += 0.5*v4; + a_vatom(i,5) += 0.5*v5; } if (NEWTON_PAIR || j < nlocal) { - v_vatom(j,0) += 0.5*v0; - v_vatom(j,1) += 0.5*v1; - v_vatom(j,2) += 0.5*v2; - v_vatom(j,3) += 0.5*v3; - v_vatom(j,4) += 0.5*v4; - v_vatom(j,5) += 0.5*v5; + a_vatom(j,0) += 0.5*v0; + a_vatom(j,1) += 0.5*v1; + a_vatom(j,2) += 0.5*v2; + a_vatom(j,3) += 0.5*v3; + a_vatom(j,4) += 0.5*v4; + a_vatom(j,5) += 0.5*v5; } } else { - v_vatom(i,0) += 0.5*v0; - v_vatom(i,1) += 0.5*v1; - v_vatom(i,2) += 0.5*v2; - v_vatom(i,3) += 0.5*v3; - v_vatom(i,4) += 0.5*v4; - v_vatom(i,5) += 0.5*v5; + a_vatom(i,0) += 0.5*v0; + a_vatom(i,1) += 0.5*v1; + a_vatom(i,2) += 0.5*v2; + a_vatom(i,3) += 0.5*v3; + a_vatom(i,4) += 0.5*v4; + a_vatom(i,5) += 0.5*v5; } } } diff --git a/src/KOKKOS/pair_eam_kokkos.h b/src/KOKKOS/pair_eam_kokkos.h index c821750da5..6523e3fe72 100644 --- a/src/KOKKOS/pair_eam_kokkos.h +++ b/src/KOKKOS/pair_eam_kokkos.h @@ -126,6 +126,16 @@ class PairEAMKokkos : public PairEAM, public KokkosBase { typename ArrayTypes::t_efloat_1d d_eatom; typename ArrayTypes::t_virial_array d_vatom; + int need_dup; + Kokkos::Experimental::ScatterView dup_rho; + Kokkos::Experimental::ScatterView dup_f; + Kokkos::Experimental::ScatterView dup_eatom; + Kokkos::Experimental::ScatterView dup_vatom; + Kokkos::Experimental::ScatterView ndup_rho; + Kokkos::Experimental::ScatterView ndup_f; + Kokkos::Experimental::ScatterView ndup_eatom; + Kokkos::Experimental::ScatterView ndup_vatom; + DAT::tdual_ffloat_1d k_rho; DAT::tdual_ffloat_1d k_fp; typename AT::t_ffloat_1d d_rho; From d9fb37e25ea1586f3e069c712ec77db45d83fb1a Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Fri, 10 Aug 2018 12:30:03 -0600 Subject: [PATCH 094/302] Add data duplication to pair_tersoff_kokkos and variants --- src/KOKKOS/pair_tersoff_kokkos.cpp | 79 +++++++++++++++++--------- src/KOKKOS/pair_tersoff_kokkos.h | 8 +++ src/KOKKOS/pair_tersoff_mod_kokkos.cpp | 79 +++++++++++++++++--------- src/KOKKOS/pair_tersoff_mod_kokkos.h | 8 +++ src/KOKKOS/pair_tersoff_zbl_kokkos.cpp | 79 +++++++++++++++++--------- src/KOKKOS/pair_tersoff_zbl_kokkos.h | 8 +++ 6 files changed, 180 insertions(+), 81 deletions(-) diff --git a/src/KOKKOS/pair_tersoff_kokkos.cpp b/src/KOKKOS/pair_tersoff_kokkos.cpp index cb4def2d37..7b21bf5793 100644 --- a/src/KOKKOS/pair_tersoff_kokkos.cpp +++ b/src/KOKKOS/pair_tersoff_kokkos.cpp @@ -200,6 +200,17 @@ void PairTersoffKokkos::compute(int eflag_in, int vflag_in) d_neighbors = k_list->d_neighbors; d_ilist = k_list->d_ilist; + need_dup = lmp->kokkos->need_dup(); + if (need_dup) { + dup_f = Kokkos::Experimental::create_scatter_view(f); + dup_eatom = Kokkos::Experimental::create_scatter_view(d_eatom); + dup_vatom = Kokkos::Experimental::create_scatter_view(d_vatom); + } else { + ndup_f = Kokkos::Experimental::create_scatter_view(f); + ndup_eatom = Kokkos::Experimental::create_scatter_view(d_eatom); + ndup_vatom = Kokkos::Experimental::create_scatter_view(d_vatom); + } + copymode = 1; EV_FLOAT ev; @@ -243,6 +254,9 @@ void PairTersoffKokkos::compute(int eflag_in, int vflag_in) ev_all += ev; } + if (need_dup) + Kokkos::Experimental::contribute(f, dup_f); + if (eflag_global) eng_vdwl += ev_all.evdwl; if (vflag_global) { virial[0] += ev_all.v[0]; @@ -254,11 +268,15 @@ void PairTersoffKokkos::compute(int eflag_in, int vflag_in) } if (eflag_atom) { + if (need_dup) + Kokkos::Experimental::contribute(d_eatom, dup_eatom); k_eatom.template modify(); k_eatom.template sync(); } if (vflag_atom) { + if (need_dup) + Kokkos::Experimental::contribute(d_vatom, dup_vatom); k_vatom.template modify(); k_vatom.template sync(); } @@ -304,8 +322,10 @@ template KOKKOS_INLINE_FUNCTION void PairTersoffKokkos::operator()(TagPairTersoffComputeHalf, const int &ii, EV_FLOAT& ev) const { - // The f array is atomic for Half/Thread neighbor style - Kokkos::View::value> > a_f = f; + // The f array is duplicated for OpenMP, atomic for CUDA, and neither for Serial + + auto v_f = ScatterViewHelper::value,decltype(dup_f),decltype(ndup_f)>::get(dup_f,ndup_f); + auto a_f = v_f.template access::value>(); const int i = d_ilist[ii]; if (i >= nlocal) return; @@ -1117,14 +1137,18 @@ void PairTersoffKokkos::ev_tally(EV_FLOAT &ev, const int &i, const i { const int VFLAG = vflag_either; - // The eatom and vatom arrays are atomic for Half/Thread neighbor style - Kokkos::View::value> > v_eatom = k_eatom.view(); - Kokkos::View::value> > v_vatom = k_vatom.view(); + // The eatom and vatom arrays are duplicated for OpenMP, atomic for CUDA, and neither for Serial + + auto v_eatom = ScatterViewHelper::value,decltype(dup_eatom),decltype(ndup_eatom)>::get(dup_eatom,ndup_eatom); + auto a_eatom = v_eatom.template access::value>(); + + auto v_vatom = ScatterViewHelper::value,decltype(dup_vatom),decltype(ndup_vatom)>::get(dup_vatom,ndup_vatom); + auto a_vatom = v_vatom.template access::value>(); if (eflag_atom) { const E_FLOAT epairhalf = 0.5 * epair; - v_eatom[i] += epairhalf; - if (NEIGHFLAG != FULL) v_eatom[j] += epairhalf; + a_eatom[i] += epairhalf; + if (NEIGHFLAG != FULL) a_eatom[j] += epairhalf; } if (VFLAG) { @@ -1154,20 +1178,20 @@ void PairTersoffKokkos::ev_tally(EV_FLOAT &ev, const int &i, const i } if (vflag_atom) { - v_vatom(i,0) += 0.5*v0; - v_vatom(i,1) += 0.5*v1; - v_vatom(i,2) += 0.5*v2; - v_vatom(i,3) += 0.5*v3; - v_vatom(i,4) += 0.5*v4; - v_vatom(i,5) += 0.5*v5; + a_vatom(i,0) += 0.5*v0; + a_vatom(i,1) += 0.5*v1; + a_vatom(i,2) += 0.5*v2; + a_vatom(i,3) += 0.5*v3; + a_vatom(i,4) += 0.5*v4; + a_vatom(i,5) += 0.5*v5; if (NEIGHFLAG != FULL) { - v_vatom(j,0) += 0.5*v0; - v_vatom(j,1) += 0.5*v1; - v_vatom(j,2) += 0.5*v2; - v_vatom(j,3) += 0.5*v3; - v_vatom(j,4) += 0.5*v4; - v_vatom(j,5) += 0.5*v5; + a_vatom(j,0) += 0.5*v0; + a_vatom(j,1) += 0.5*v1; + a_vatom(j,2) += 0.5*v2; + a_vatom(j,3) += 0.5*v3; + a_vatom(j,4) += 0.5*v4; + a_vatom(j,5) += 0.5*v5; } } } @@ -1181,9 +1205,10 @@ KOKKOS_INLINE_FUNCTION void PairTersoffKokkos::v_tally3(EV_FLOAT &ev, const int &i, const int &j, const int &k, F_FLOAT *fj, F_FLOAT *fk, F_FLOAT *drij, F_FLOAT *drik) const { + // The vatom array is duplicated for OpenMP, atomic for CUDA, and neither for Serial - // The eatom and vatom arrays are atomic for Half/Thread neighbor style - Kokkos::View::value> > v_vatom = k_vatom.view(); + auto v_vatom = ScatterViewHelper::value,decltype(dup_vatom),decltype(ndup_vatom)>::get(dup_vatom,ndup_vatom); + auto a_vatom = v_vatom.template access::value>(); F_FLOAT v[6]; @@ -1204,13 +1229,13 @@ void PairTersoffKokkos::v_tally3(EV_FLOAT &ev, const int &i, const i } if (vflag_atom) { - v_vatom(i,0) += v[0]; v_vatom(i,1) += v[1]; v_vatom(i,2) += v[2]; - v_vatom(i,3) += v[3]; v_vatom(i,4) += v[4]; v_vatom(i,5) += v[5]; + a_vatom(i,0) += v[0]; a_vatom(i,1) += v[1]; a_vatom(i,2) += v[2]; + a_vatom(i,3) += v[3]; a_vatom(i,4) += v[4]; a_vatom(i,5) += v[5]; if (NEIGHFLAG != FULL) { - v_vatom(j,0) += v[0]; v_vatom(j,1) += v[1]; v_vatom(j,2) += v[2]; - v_vatom(j,3) += v[3]; v_vatom(j,4) += v[4]; v_vatom(j,5) += v[5]; - v_vatom(k,0) += v[0]; v_vatom(k,1) += v[1]; v_vatom(k,2) += v[2]; - v_vatom(k,3) += v[3]; v_vatom(k,4) += v[4]; v_vatom(k,5) += v[5]; + a_vatom(j,0) += v[0]; a_vatom(j,1) += v[1]; a_vatom(j,2) += v[2]; + a_vatom(j,3) += v[3]; a_vatom(j,4) += v[4]; a_vatom(j,5) += v[5]; + a_vatom(k,0) += v[0]; a_vatom(k,1) += v[1]; a_vatom(k,2) += v[2]; + a_vatom(k,3) += v[3]; a_vatom(k,4) += v[4]; a_vatom(k,5) += v[5]; } } diff --git a/src/KOKKOS/pair_tersoff_kokkos.h b/src/KOKKOS/pair_tersoff_kokkos.h index 2dac2c5991..f73d4fe2d8 100644 --- a/src/KOKKOS/pair_tersoff_kokkos.h +++ b/src/KOKKOS/pair_tersoff_kokkos.h @@ -202,6 +202,14 @@ class PairTersoffKokkos : public PairTersoff { typename ArrayTypes::t_efloat_1d d_eatom; typename ArrayTypes::t_virial_array d_vatom; + int need_dup; + Kokkos::Experimental::ScatterView dup_f; + Kokkos::Experimental::ScatterView dup_eatom; + Kokkos::Experimental::ScatterView dup_vatom; + Kokkos::Experimental::ScatterView ndup_f; + Kokkos::Experimental::ScatterView ndup_eatom; + Kokkos::Experimental::ScatterView ndup_vatom; + typedef Kokkos::DualView tdual_ffloat_2d_n7; typedef typename tdual_ffloat_2d_n7::t_dev_const_randomread t_ffloat_2d_n7_randomread; typedef typename tdual_ffloat_2d_n7::t_host t_host_ffloat_2d_n7; diff --git a/src/KOKKOS/pair_tersoff_mod_kokkos.cpp b/src/KOKKOS/pair_tersoff_mod_kokkos.cpp index 0d150f83e4..2fe4361503 100644 --- a/src/KOKKOS/pair_tersoff_mod_kokkos.cpp +++ b/src/KOKKOS/pair_tersoff_mod_kokkos.cpp @@ -200,6 +200,17 @@ void PairTersoffMODKokkos::compute(int eflag_in, int vflag_in) d_neighbors = k_list->d_neighbors; d_ilist = k_list->d_ilist; + need_dup = lmp->kokkos->need_dup(); + if (need_dup) { + dup_f = Kokkos::Experimental::create_scatter_view(f); + dup_eatom = Kokkos::Experimental::create_scatter_view(d_eatom); + dup_vatom = Kokkos::Experimental::create_scatter_view(d_vatom); + } else { + ndup_f = Kokkos::Experimental::create_scatter_view(f); + ndup_eatom = Kokkos::Experimental::create_scatter_view(d_eatom); + ndup_vatom = Kokkos::Experimental::create_scatter_view(d_vatom); + } + copymode = 1; EV_FLOAT ev; @@ -243,6 +254,9 @@ void PairTersoffMODKokkos::compute(int eflag_in, int vflag_in) ev_all += ev; } + if (need_dup) + Kokkos::Experimental::contribute(f, dup_f); + if (eflag_global) eng_vdwl += ev_all.evdwl; if (vflag_global) { virial[0] += ev_all.v[0]; @@ -254,11 +268,15 @@ void PairTersoffMODKokkos::compute(int eflag_in, int vflag_in) } if (eflag_atom) { + if (need_dup) + Kokkos::Experimental::contribute(d_eatom, dup_eatom); k_eatom.template modify(); k_eatom.template sync(); } if (vflag_atom) { + if (need_dup) + Kokkos::Experimental::contribute(d_vatom, dup_vatom); k_vatom.template modify(); k_vatom.template sync(); } @@ -304,8 +322,10 @@ template KOKKOS_INLINE_FUNCTION void PairTersoffMODKokkos::operator()(TagPairTersoffMODComputeHalf, const int &ii, EV_FLOAT& ev) const { - // The f array is atomic for Half/Thread neighbor style - Kokkos::View::value> > a_f = f; + // The f array is duplicated for OpenMP, atomic for CUDA, and neither for Serial + + auto v_f = ScatterViewHelper::value,decltype(dup_f),decltype(ndup_f)>::get(dup_f,ndup_f); + auto a_f = v_f.template access::value>(); const int i = d_ilist[ii]; if (i >= nlocal) return; @@ -1120,14 +1140,18 @@ void PairTersoffMODKokkos::ev_tally(EV_FLOAT &ev, const int &i, cons { const int VFLAG = vflag_either; - // The eatom and vatom arrays are atomic for Half/Thread neighbor style - Kokkos::View::value> > v_eatom = k_eatom.view(); - Kokkos::View::value> > v_vatom = k_vatom.view(); + // The eatom and vatom arrays are duplicated for OpenMP, atomic for CUDA, and neither for Serial + + auto v_eatom = ScatterViewHelper::value,decltype(dup_eatom),decltype(ndup_eatom)>::get(dup_eatom,ndup_eatom); + auto a_eatom = v_eatom.template access::value>(); + + auto v_vatom = ScatterViewHelper::value,decltype(dup_vatom),decltype(ndup_vatom)>::get(dup_vatom,ndup_vatom); + auto a_vatom = v_vatom.template access::value>(); if (eflag_atom) { const E_FLOAT epairhalf = 0.5 * epair; - v_eatom[i] += epairhalf; - if (NEIGHFLAG != FULL) v_eatom[j] += epairhalf; + a_eatom[i] += epairhalf; + if (NEIGHFLAG != FULL) a_eatom[j] += epairhalf; } if (VFLAG) { @@ -1157,20 +1181,20 @@ void PairTersoffMODKokkos::ev_tally(EV_FLOAT &ev, const int &i, cons } if (vflag_atom) { - v_vatom(i,0) += 0.5*v0; - v_vatom(i,1) += 0.5*v1; - v_vatom(i,2) += 0.5*v2; - v_vatom(i,3) += 0.5*v3; - v_vatom(i,4) += 0.5*v4; - v_vatom(i,5) += 0.5*v5; + a_vatom(i,0) += 0.5*v0; + a_vatom(i,1) += 0.5*v1; + a_vatom(i,2) += 0.5*v2; + a_vatom(i,3) += 0.5*v3; + a_vatom(i,4) += 0.5*v4; + a_vatom(i,5) += 0.5*v5; if (NEIGHFLAG != FULL) { - v_vatom(j,0) += 0.5*v0; - v_vatom(j,1) += 0.5*v1; - v_vatom(j,2) += 0.5*v2; - v_vatom(j,3) += 0.5*v3; - v_vatom(j,4) += 0.5*v4; - v_vatom(j,5) += 0.5*v5; + a_vatom(j,0) += 0.5*v0; + a_vatom(j,1) += 0.5*v1; + a_vatom(j,2) += 0.5*v2; + a_vatom(j,3) += 0.5*v3; + a_vatom(j,4) += 0.5*v4; + a_vatom(j,5) += 0.5*v5; } } } @@ -1184,9 +1208,10 @@ KOKKOS_INLINE_FUNCTION void PairTersoffMODKokkos::v_tally3(EV_FLOAT &ev, const int &i, const int &j, const int &k, F_FLOAT *fj, F_FLOAT *fk, F_FLOAT *drij, F_FLOAT *drik) const { + // The vatom array is duplicated for OpenMP, atomic for CUDA, and neither for Serial - // The eatom and vatom arrays are atomic for Half/Thread neighbor style - Kokkos::View::value> > v_vatom = k_vatom.view(); + auto v_vatom = ScatterViewHelper::value,decltype(dup_vatom),decltype(ndup_vatom)>::get(dup_vatom,ndup_vatom); + auto a_vatom = v_vatom.template access::value>(); F_FLOAT v[6]; @@ -1207,13 +1232,13 @@ void PairTersoffMODKokkos::v_tally3(EV_FLOAT &ev, const int &i, cons } if (vflag_atom) { - v_vatom(i,0) += v[0]; v_vatom(i,1) += v[1]; v_vatom(i,2) += v[2]; - v_vatom(i,3) += v[3]; v_vatom(i,4) += v[4]; v_vatom(i,5) += v[5]; + a_vatom(i,0) += v[0]; a_vatom(i,1) += v[1]; a_vatom(i,2) += v[2]; + a_vatom(i,3) += v[3]; a_vatom(i,4) += v[4]; a_vatom(i,5) += v[5]; if (NEIGHFLAG != FULL) { - v_vatom(j,0) += v[0]; v_vatom(j,1) += v[1]; v_vatom(j,2) += v[2]; - v_vatom(j,3) += v[3]; v_vatom(j,4) += v[4]; v_vatom(j,5) += v[5]; - v_vatom(k,0) += v[0]; v_vatom(k,1) += v[1]; v_vatom(k,2) += v[2]; - v_vatom(k,3) += v[3]; v_vatom(k,4) += v[4]; v_vatom(k,5) += v[5]; + a_vatom(j,0) += v[0]; a_vatom(j,1) += v[1]; a_vatom(j,2) += v[2]; + a_vatom(j,3) += v[3]; a_vatom(j,4) += v[4]; a_vatom(j,5) += v[5]; + a_vatom(k,0) += v[0]; a_vatom(k,1) += v[1]; a_vatom(k,2) += v[2]; + a_vatom(k,3) += v[3]; a_vatom(k,4) += v[4]; a_vatom(k,5) += v[5]; } } diff --git a/src/KOKKOS/pair_tersoff_mod_kokkos.h b/src/KOKKOS/pair_tersoff_mod_kokkos.h index dd5efb50f1..d7c94ffc93 100644 --- a/src/KOKKOS/pair_tersoff_mod_kokkos.h +++ b/src/KOKKOS/pair_tersoff_mod_kokkos.h @@ -202,6 +202,14 @@ class PairTersoffMODKokkos : public PairTersoffMOD { typename ArrayTypes::t_efloat_1d d_eatom; typename ArrayTypes::t_virial_array d_vatom; + int need_dup; + Kokkos::Experimental::ScatterView dup_f; + Kokkos::Experimental::ScatterView dup_eatom; + Kokkos::Experimental::ScatterView dup_vatom; + Kokkos::Experimental::ScatterView ndup_f; + Kokkos::Experimental::ScatterView ndup_eatom; + Kokkos::Experimental::ScatterView ndup_vatom; + typedef Kokkos::DualView tdual_ffloat_2d_n7; typedef typename tdual_ffloat_2d_n7::t_dev_const_randomread t_ffloat_2d_n7_randomread; typedef typename tdual_ffloat_2d_n7::t_host t_host_ffloat_2d_n7; diff --git a/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp b/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp index 2fb9675db6..2892947f66 100644 --- a/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp +++ b/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp @@ -214,6 +214,17 @@ void PairTersoffZBLKokkos::compute(int eflag_in, int vflag_in) d_neighbors = k_list->d_neighbors; d_ilist = k_list->d_ilist; + need_dup = lmp->kokkos->need_dup(); + if (need_dup) { + dup_f = Kokkos::Experimental::create_scatter_view(f); + dup_eatom = Kokkos::Experimental::create_scatter_view(d_eatom); + dup_vatom = Kokkos::Experimental::create_scatter_view(d_vatom); + } else { + ndup_f = Kokkos::Experimental::create_scatter_view(f); + ndup_eatom = Kokkos::Experimental::create_scatter_view(d_eatom); + ndup_vatom = Kokkos::Experimental::create_scatter_view(d_vatom); + } + copymode = 1; EV_FLOAT ev; @@ -257,6 +268,9 @@ void PairTersoffZBLKokkos::compute(int eflag_in, int vflag_in) ev_all += ev; } + if (need_dup) + Kokkos::Experimental::contribute(f, dup_f); + if (eflag_global) eng_vdwl += ev_all.evdwl; if (vflag_global) { virial[0] += ev_all.v[0]; @@ -268,11 +282,15 @@ void PairTersoffZBLKokkos::compute(int eflag_in, int vflag_in) } if (eflag_atom) { + if (need_dup) + Kokkos::Experimental::contribute(d_eatom, dup_eatom); k_eatom.template modify(); k_eatom.template sync(); } if (vflag_atom) { + if (need_dup) + Kokkos::Experimental::contribute(d_vatom, dup_vatom); k_vatom.template modify(); k_vatom.template sync(); } @@ -318,8 +336,10 @@ template KOKKOS_INLINE_FUNCTION void PairTersoffZBLKokkos::operator()(TagPairTersoffZBLComputeHalf, const int &ii, EV_FLOAT& ev) const { - // The f array is atomic for Half/Thread neighbor style - Kokkos::View::value> > a_f = f; + // The f array is duplicated for OpenMP, atomic for CUDA, and neither for Serial + + auto v_f = ScatterViewHelper::value,decltype(dup_f),decltype(ndup_f)>::get(dup_f,ndup_f); + auto a_f = v_f.template access::value>(); const int i = d_ilist[ii]; if (i >= nlocal) return; @@ -1214,14 +1234,18 @@ void PairTersoffZBLKokkos::ev_tally(EV_FLOAT &ev, const int &i, cons { const int VFLAG = vflag_either; - // The eatom and vatom arrays are atomic for Half/Thread neighbor style - Kokkos::View::value> > v_eatom = k_eatom.view(); - Kokkos::View::value> > v_vatom = k_vatom.view(); + // The eatom and vatom arrays are duplicated for OpenMP, atomic for CUDA, and neither for Serial + + auto v_eatom = ScatterViewHelper::value,decltype(dup_eatom),decltype(ndup_eatom)>::get(dup_eatom,ndup_eatom); + auto a_eatom = v_eatom.template access::value>(); + + auto v_vatom = ScatterViewHelper::value,decltype(dup_vatom),decltype(ndup_vatom)>::get(dup_vatom,ndup_vatom); + auto a_vatom = v_vatom.template access::value>(); if (eflag_atom) { const E_FLOAT epairhalf = 0.5 * epair; - v_eatom[i] += epairhalf; - if (NEIGHFLAG != FULL) v_eatom[j] += epairhalf; + a_eatom[i] += epairhalf; + if (NEIGHFLAG != FULL) a_eatom[j] += epairhalf; } if (VFLAG) { @@ -1251,20 +1275,20 @@ void PairTersoffZBLKokkos::ev_tally(EV_FLOAT &ev, const int &i, cons } if (vflag_atom) { - v_vatom(i,0) += 0.5*v0; - v_vatom(i,1) += 0.5*v1; - v_vatom(i,2) += 0.5*v2; - v_vatom(i,3) += 0.5*v3; - v_vatom(i,4) += 0.5*v4; - v_vatom(i,5) += 0.5*v5; + a_vatom(i,0) += 0.5*v0; + a_vatom(i,1) += 0.5*v1; + a_vatom(i,2) += 0.5*v2; + a_vatom(i,3) += 0.5*v3; + a_vatom(i,4) += 0.5*v4; + a_vatom(i,5) += 0.5*v5; if (NEIGHFLAG != FULL) { - v_vatom(j,0) += 0.5*v0; - v_vatom(j,1) += 0.5*v1; - v_vatom(j,2) += 0.5*v2; - v_vatom(j,3) += 0.5*v3; - v_vatom(j,4) += 0.5*v4; - v_vatom(j,5) += 0.5*v5; + a_vatom(j,0) += 0.5*v0; + a_vatom(j,1) += 0.5*v1; + a_vatom(j,2) += 0.5*v2; + a_vatom(j,3) += 0.5*v3; + a_vatom(j,4) += 0.5*v4; + a_vatom(j,5) += 0.5*v5; } } } @@ -1278,9 +1302,10 @@ KOKKOS_INLINE_FUNCTION void PairTersoffZBLKokkos::v_tally3(EV_FLOAT &ev, const int &i, const int &j, const int &k, F_FLOAT *fj, F_FLOAT *fk, F_FLOAT *drij, F_FLOAT *drik) const { + // The vatom array is duplicated for OpenMP, atomic for CUDA, and neither for Serial - // The eatom and vatom arrays are atomic for Half/Thread neighbor style - Kokkos::View::value> > v_vatom = k_vatom.view(); + auto v_vatom = ScatterViewHelper::value,decltype(dup_vatom),decltype(ndup_vatom)>::get(dup_vatom,ndup_vatom); + auto a_vatom = v_vatom.template access::value>(); F_FLOAT v[6]; @@ -1301,13 +1326,13 @@ void PairTersoffZBLKokkos::v_tally3(EV_FLOAT &ev, const int &i, cons } if (vflag_atom) { - v_vatom(i,0) += v[0]; v_vatom(i,1) += v[1]; v_vatom(i,2) += v[2]; - v_vatom(i,3) += v[3]; v_vatom(i,4) += v[4]; v_vatom(i,5) += v[5]; + a_vatom(i,0) += v[0]; a_vatom(i,1) += v[1]; a_vatom(i,2) += v[2]; + a_vatom(i,3) += v[3]; a_vatom(i,4) += v[4]; a_vatom(i,5) += v[5]; if (NEIGHFLAG != FULL) { - v_vatom(j,0) += v[0]; v_vatom(j,1) += v[1]; v_vatom(j,2) += v[2]; - v_vatom(j,3) += v[3]; v_vatom(j,4) += v[4]; v_vatom(j,5) += v[5]; - v_vatom(k,0) += v[0]; v_vatom(k,1) += v[1]; v_vatom(k,2) += v[2]; - v_vatom(k,3) += v[3]; v_vatom(k,4) += v[4]; v_vatom(k,5) += v[5]; + a_vatom(j,0) += v[0]; a_vatom(j,1) += v[1]; a_vatom(j,2) += v[2]; + a_vatom(j,3) += v[3]; a_vatom(j,4) += v[4]; a_vatom(j,5) += v[5]; + a_vatom(k,0) += v[0]; a_vatom(k,1) += v[1]; a_vatom(k,2) += v[2]; + a_vatom(k,3) += v[3]; a_vatom(k,4) += v[4]; a_vatom(k,5) += v[5]; } } diff --git a/src/KOKKOS/pair_tersoff_zbl_kokkos.h b/src/KOKKOS/pair_tersoff_zbl_kokkos.h index 45982bd420..3af4e0d8eb 100644 --- a/src/KOKKOS/pair_tersoff_zbl_kokkos.h +++ b/src/KOKKOS/pair_tersoff_zbl_kokkos.h @@ -207,6 +207,14 @@ class PairTersoffZBLKokkos : public PairTersoffZBL { typename ArrayTypes::t_efloat_1d d_eatom; typename ArrayTypes::t_virial_array d_vatom; + int need_dup; + Kokkos::Experimental::ScatterView dup_f; + Kokkos::Experimental::ScatterView dup_eatom; + Kokkos::Experimental::ScatterView dup_vatom; + Kokkos::Experimental::ScatterView ndup_f; + Kokkos::Experimental::ScatterView ndup_eatom; + Kokkos::Experimental::ScatterView ndup_vatom; + typedef Kokkos::DualView tdual_ffloat_2d_n7; typedef typename tdual_ffloat_2d_n7::t_dev_const_randomread t_ffloat_2d_n7_randomread; typedef typename tdual_ffloat_2d_n7::t_host t_host_ffloat_2d_n7; From faa21a059196067e0b9adc3486a14ac4e2295dbc Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Fri, 10 Aug 2018 12:30:17 -0600 Subject: [PATCH 095/302] Add data duplication to pair_sw_kokkos --- src/KOKKOS/pair_sw_kokkos.cpp | 92 ++++++++++++++++++++++------------- src/KOKKOS/pair_sw_kokkos.h | 8 +++ 2 files changed, 66 insertions(+), 34 deletions(-) diff --git a/src/KOKKOS/pair_sw_kokkos.cpp b/src/KOKKOS/pair_sw_kokkos.cpp index 8f4903c767..22da4f7858 100644 --- a/src/KOKKOS/pair_sw_kokkos.cpp +++ b/src/KOKKOS/pair_sw_kokkos.cpp @@ -115,6 +115,17 @@ void PairSWKokkos::compute(int eflag_in, int vflag_in) d_numneigh = k_list->d_numneigh; d_neighbors = k_list->d_neighbors; + need_dup = lmp->kokkos->need_dup(); + if (need_dup) { + dup_f = Kokkos::Experimental::create_scatter_view(f); + dup_eatom = Kokkos::Experimental::create_scatter_view(d_eatom); + dup_vatom = Kokkos::Experimental::create_scatter_view(d_vatom); + } else { + ndup_f = Kokkos::Experimental::create_scatter_view(f); + ndup_eatom = Kokkos::Experimental::create_scatter_view(d_eatom); + ndup_vatom = Kokkos::Experimental::create_scatter_view(d_vatom); + } + copymode = 1; EV_FLOAT ev; @@ -160,6 +171,9 @@ void PairSWKokkos::compute(int eflag_in, int vflag_in) ev_all += ev; } + if (need_dup) + Kokkos::Experimental::contribute(f, dup_f); + if (eflag_global) eng_vdwl += ev_all.evdwl; if (vflag_global) { virial[0] += ev_all.v[0]; @@ -171,11 +185,15 @@ void PairSWKokkos::compute(int eflag_in, int vflag_in) } if (eflag_atom) { + if (need_dup) + Kokkos::Experimental::contribute(d_eatom, dup_eatom); k_eatom.template modify(); k_eatom.template sync(); } if (vflag_atom) { + if (need_dup) + Kokkos::Experimental::contribute(d_vatom, dup_vatom); k_vatom.template modify(); k_vatom.template sync(); } @@ -222,9 +240,10 @@ template KOKKOS_INLINE_FUNCTION void PairSWKokkos::operator()(TagPairSWComputeHalf, const int &ii, EV_FLOAT& ev) const { - // The f array is atomic + // The f array is duplicated for OpenMP, atomic for CUDA, and neither for Serial - Kokkos::View::value> > a_f = f; + auto v_f = ScatterViewHelper::value,decltype(dup_f),decltype(ndup_f)>::get(dup_f,ndup_f); + auto a_f = v_f.template access::value>(); F_FLOAT delr1[3],delr2[3],fj[3],fk[3]; F_FLOAT evdwl = 0.0; @@ -777,17 +796,19 @@ void PairSWKokkos::ev_tally(EV_FLOAT &ev, const int &i, const int &j { const int VFLAG = vflag_either; - // The eatom and vatom arrays are atomic for half/thread neighbor list + // The eatom and vatom arrays are duplicated for OpenMP, atomic for CUDA, and neither for Serial - Kokkos::View::value> > v_eatom = k_eatom.view(); - Kokkos::View::value> > v_vatom = k_vatom.view(); + auto v_eatom = ScatterViewHelper::value,decltype(dup_eatom),decltype(ndup_eatom)>::get(dup_eatom,ndup_eatom); + auto a_eatom = v_eatom.template access::value>(); + auto v_vatom = ScatterViewHelper::value,decltype(dup_vatom),decltype(ndup_vatom)>::get(dup_vatom,ndup_vatom); + auto a_vatom = v_vatom.template access::value>(); if (eflag_atom) { const E_FLOAT epairhalf = 0.5 * epair; - v_eatom[i] += epairhalf; + a_eatom[i] += epairhalf; if (NEIGHFLAG != FULL) - v_eatom[j] += epairhalf; + a_eatom[j] += epairhalf; } if (VFLAG) { @@ -817,20 +838,20 @@ void PairSWKokkos::ev_tally(EV_FLOAT &ev, const int &i, const int &j } if (vflag_atom) { - v_vatom(i,0) += 0.5*v0; - v_vatom(i,1) += 0.5*v1; - v_vatom(i,2) += 0.5*v2; - v_vatom(i,3) += 0.5*v3; - v_vatom(i,4) += 0.5*v4; - v_vatom(i,5) += 0.5*v5; + a_vatom(i,0) += 0.5*v0; + a_vatom(i,1) += 0.5*v1; + a_vatom(i,2) += 0.5*v2; + a_vatom(i,3) += 0.5*v3; + a_vatom(i,4) += 0.5*v4; + a_vatom(i,5) += 0.5*v5; if (NEIGHFLAG != FULL) { - v_vatom(j,0) += 0.5*v0; - v_vatom(j,1) += 0.5*v1; - v_vatom(j,2) += 0.5*v2; - v_vatom(j,3) += 0.5*v3; - v_vatom(j,4) += 0.5*v4; - v_vatom(j,5) += 0.5*v5; + a_vatom(j,0) += 0.5*v0; + a_vatom(j,1) += 0.5*v1; + a_vatom(j,2) += 0.5*v2; + a_vatom(j,3) += 0.5*v3; + a_vatom(j,4) += 0.5*v4; + a_vatom(j,5) += 0.5*v5; } } } @@ -853,17 +874,20 @@ void PairSWKokkos::ev_tally3(EV_FLOAT &ev, const int &i, const int & const int VFLAG = vflag_either; -// The eatom and vatom arrays are atomic for half/thread neighbor list + // The eatom and vatom arrays are duplicated for OpenMP, atomic for CUDA, and neither for Serial - Kokkos::View::value> > v_eatom = k_eatom.view(); - Kokkos::View::value> > v_vatom = k_vatom.view(); + auto v_eatom = ScatterViewHelper::value,decltype(dup_eatom),decltype(ndup_eatom)>::get(dup_eatom,ndup_eatom); + auto a_eatom = v_eatom.template access::value>(); + + auto v_vatom = ScatterViewHelper::value,decltype(dup_vatom),decltype(ndup_vatom)>::get(dup_vatom,ndup_vatom); + auto a_vatom = v_vatom.template access::value>(); if (eflag_atom) { epairthird = THIRD * (evdwl + ecoul); - v_eatom[i] += epairthird; + a_eatom[i] += epairthird; if (NEIGHFLAG != FULL) { - v_eatom[j] += epairthird; - v_eatom[k] += epairthird; + a_eatom[j] += epairthird; + a_eatom[k] += epairthird; } } @@ -885,18 +909,18 @@ void PairSWKokkos::ev_tally3(EV_FLOAT &ev, const int &i, const int & } if (vflag_atom) { - v_vatom(i,0) += THIRD*v[0]; v_vatom(i,1) += THIRD*v[1]; - v_vatom(i,2) += THIRD*v[2]; v_vatom(i,3) += THIRD*v[3]; - v_vatom(i,4) += THIRD*v[4]; v_vatom(i,5) += THIRD*v[5]; + a_vatom(i,0) += THIRD*v[0]; a_vatom(i,1) += THIRD*v[1]; + a_vatom(i,2) += THIRD*v[2]; a_vatom(i,3) += THIRD*v[3]; + a_vatom(i,4) += THIRD*v[4]; a_vatom(i,5) += THIRD*v[5]; if (NEIGHFLAG != FULL) { - v_vatom(j,0) += THIRD*v[0]; v_vatom(j,1) += THIRD*v[1]; - v_vatom(j,2) += THIRD*v[2]; v_vatom(j,3) += THIRD*v[3]; - v_vatom(j,4) += THIRD*v[4]; v_vatom(j,5) += THIRD*v[5]; + a_vatom(j,0) += THIRD*v[0]; a_vatom(j,1) += THIRD*v[1]; + a_vatom(j,2) += THIRD*v[2]; a_vatom(j,3) += THIRD*v[3]; + a_vatom(j,4) += THIRD*v[4]; a_vatom(j,5) += THIRD*v[5]; - v_vatom(k,0) += THIRD*v[0]; v_vatom(k,1) += THIRD*v[1]; - v_vatom(k,2) += THIRD*v[2]; v_vatom(k,3) += THIRD*v[3]; - v_vatom(k,4) += THIRD*v[4]; v_vatom(k,5) += THIRD*v[5]; + a_vatom(k,0) += THIRD*v[0]; a_vatom(k,1) += THIRD*v[1]; + a_vatom(k,2) += THIRD*v[2]; a_vatom(k,3) += THIRD*v[3]; + a_vatom(k,4) += THIRD*v[4]; a_vatom(k,5) += THIRD*v[5]; } } } diff --git a/src/KOKKOS/pair_sw_kokkos.h b/src/KOKKOS/pair_sw_kokkos.h index eb59d5bc3c..1a3f0b862f 100644 --- a/src/KOKKOS/pair_sw_kokkos.h +++ b/src/KOKKOS/pair_sw_kokkos.h @@ -134,6 +134,14 @@ class PairSWKokkos : public PairSW { typename AT::t_efloat_1d d_eatom; typename AT::t_virial_array d_vatom; + int need_dup; + Kokkos::Experimental::ScatterView dup_f; + Kokkos::Experimental::ScatterView dup_eatom; + Kokkos::Experimental::ScatterView dup_vatom; + Kokkos::Experimental::ScatterView ndup_f; + Kokkos::Experimental::ScatterView ndup_eatom; + Kokkos::Experimental::ScatterView ndup_vatom; + typename AT::t_int_1d_randomread d_type2frho; typename AT::t_int_2d_randomread d_type2rhor; typename AT::t_int_2d_randomread d_type2z2r; From ebc0abbb8d877c1c5fe370e721a132597b8aad21 Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Fri, 10 Aug 2018 12:30:37 -0600 Subject: [PATCH 096/302] Add data duplication to pair_eam_kokkos variants --- src/KOKKOS/pair_eam_alloy_kokkos.cpp | 86 ++++++++++++++++++---------- src/KOKKOS/pair_eam_alloy_kokkos.h | 10 ++++ src/KOKKOS/pair_eam_fs_kokkos.cpp | 85 +++++++++++++++++---------- src/KOKKOS/pair_eam_fs_kokkos.h | 10 ++++ src/KOKKOS/pair_eam_kokkos.cpp | 5 +- 5 files changed, 137 insertions(+), 59 deletions(-) diff --git a/src/KOKKOS/pair_eam_alloy_kokkos.cpp b/src/KOKKOS/pair_eam_alloy_kokkos.cpp index f21ea2335d..7c6510f311 100644 --- a/src/KOKKOS/pair_eam_alloy_kokkos.cpp +++ b/src/KOKKOS/pair_eam_alloy_kokkos.cpp @@ -38,6 +38,7 @@ using namespace LAMMPS_NS; // Cannot use virtual inheritance on the GPU, so must duplicate code + /* ---------------------------------------------------------------------- */ template @@ -122,6 +123,19 @@ void PairEAMAlloyKokkos::compute(int eflag_in, int vflag_in) d_ilist = k_list->d_ilist; int inum = list->inum; + need_dup = lmp->kokkos->need_dup(); + if (need_dup) { + dup_rho = Kokkos::Experimental::create_scatter_view(d_rho); + dup_f = Kokkos::Experimental::create_scatter_view(f); + dup_eatom = Kokkos::Experimental::create_scatter_view(d_eatom); + dup_vatom = Kokkos::Experimental::create_scatter_view(d_vatom); + } else { + ndup_rho = Kokkos::Experimental::create_scatter_view(d_rho); + ndup_f = Kokkos::Experimental::create_scatter_view(f); + ndup_eatom = Kokkos::Experimental::create_scatter_view(d_eatom); + ndup_vatom = Kokkos::Experimental::create_scatter_view(d_vatom); + } + copymode = 1; // zero out density @@ -233,6 +247,9 @@ void PairEAMAlloyKokkos::compute(int eflag_in, int vflag_in) } } + if (need_dup) + Kokkos::Experimental::contribute(f, dup_f); + if (eflag_global) eng_vdwl += ev.evdwl; if (vflag_global) { virial[0] += ev.v[0]; @@ -244,11 +261,15 @@ void PairEAMAlloyKokkos::compute(int eflag_in, int vflag_in) } if (eflag_atom) { + if (need_dup) + Kokkos::Experimental::contribute(d_eatom, dup_eatom); k_eatom.template modify(); k_eatom.template sync(); } if (vflag_atom) { + if (need_dup) + Kokkos::Experimental::contribute(d_vatom, dup_vatom); k_vatom.template modify(); k_vatom.template sync(); } @@ -503,8 +524,10 @@ void PairEAMAlloyKokkos::operator()(TagPairEAMAlloyKernelA::value> > rho = v_rho; + // The rho array is duplicated for OpenMP, atomic for CUDA, and neither for Serial + + auto v_rho = ScatterViewHelper::value,decltype(dup_rho),decltype(ndup_rho)>::get(dup_rho,ndup_rho); + auto a_rho = v_rho.template access::value>(); const int i = d_ilist[ii]; const X_FLOAT xtmp = x(i,0); @@ -672,8 +695,10 @@ template KOKKOS_INLINE_FUNCTION void PairEAMAlloyKokkos::operator()(TagPairEAMAlloyKernelC, const int &ii, EV_FLOAT& ev) const { - // The f array is atomic for Half/Thread neighbor style - Kokkos::View::value> > a_f = f; + // The f array is duplicated for OpenMP, atomic for CUDA, and neither for Serial + + auto v_f = ScatterViewHelper::value,decltype(dup_f),decltype(ndup_f)>::get(dup_f,ndup_f); + auto a_f = v_f.template access::value>(); const int i = d_ilist[ii]; const X_FLOAT xtmp = x(i,0); @@ -780,18 +805,22 @@ void PairEAMAlloyKokkos::ev_tally(EV_FLOAT &ev, const int &i, const const int EFLAG = eflag; const int VFLAG = vflag_either; - // The eatom and vatom arrays are atomic for Half/Thread neighbor style - Kokkos::View::value> > v_eatom = k_eatom.view(); - Kokkos::View::value> > v_vatom = k_vatom.view(); + // The eatom and vatom arrays are duplicated for OpenMP, atomic for CUDA, and neither for Serial + + auto v_eatom = ScatterViewHelper::value,decltype(dup_eatom),decltype(ndup_eatom)>::get(dup_eatom,ndup_eatom); + auto a_eatom = v_eatom.template access::value>(); + + auto v_vatom = ScatterViewHelper::value,decltype(dup_vatom),decltype(ndup_vatom)>::get(dup_vatom,ndup_vatom); + auto a_vatom = v_vatom.template access::value>(); if (EFLAG) { if (eflag_atom) { const E_FLOAT epairhalf = 0.5 * epair; if (NEIGHFLAG!=FULL) { - if (NEWTON_PAIR || i < nlocal) v_eatom[i] += epairhalf; - if (NEWTON_PAIR || j < nlocal) v_eatom[j] += epairhalf; + if (NEWTON_PAIR || i < nlocal) a_eatom[i] += epairhalf; + if (NEWTON_PAIR || j < nlocal) a_eatom[j] += epairhalf; } else { - v_eatom[i] += epairhalf; + a_eatom[i] += epairhalf; } } } @@ -835,28 +864,28 @@ void PairEAMAlloyKokkos::ev_tally(EV_FLOAT &ev, const int &i, const if (vflag_atom) { if (NEIGHFLAG!=FULL) { if (NEWTON_PAIR || i < nlocal) { - v_vatom(i,0) += 0.5*v0; - v_vatom(i,1) += 0.5*v1; - v_vatom(i,2) += 0.5*v2; - v_vatom(i,3) += 0.5*v3; - v_vatom(i,4) += 0.5*v4; - v_vatom(i,5) += 0.5*v5; + a_vatom(i,0) += 0.5*v0; + a_vatom(i,1) += 0.5*v1; + a_vatom(i,2) += 0.5*v2; + a_vatom(i,3) += 0.5*v3; + a_vatom(i,4) += 0.5*v4; + a_vatom(i,5) += 0.5*v5; } if (NEWTON_PAIR || j < nlocal) { - v_vatom(j,0) += 0.5*v0; - v_vatom(j,1) += 0.5*v1; - v_vatom(j,2) += 0.5*v2; - v_vatom(j,3) += 0.5*v3; - v_vatom(j,4) += 0.5*v4; - v_vatom(j,5) += 0.5*v5; + a_vatom(j,0) += 0.5*v0; + a_vatom(j,1) += 0.5*v1; + a_vatom(j,2) += 0.5*v2; + a_vatom(j,3) += 0.5*v3; + a_vatom(j,4) += 0.5*v4; + a_vatom(j,5) += 0.5*v5; } } else { - v_vatom(i,0) += 0.5*v0; - v_vatom(i,1) += 0.5*v1; - v_vatom(i,2) += 0.5*v2; - v_vatom(i,3) += 0.5*v3; - v_vatom(i,4) += 0.5*v4; - v_vatom(i,5) += 0.5*v5; + a_vatom(i,0) += 0.5*v0; + a_vatom(i,1) += 0.5*v1; + a_vatom(i,2) += 0.5*v2; + a_vatom(i,3) += 0.5*v3; + a_vatom(i,4) += 0.5*v4; + a_vatom(i,5) += 0.5*v5; } } } @@ -1165,4 +1194,3 @@ template class PairEAMAlloyKokkos; template class PairEAMAlloyKokkos; #endif } - diff --git a/src/KOKKOS/pair_eam_alloy_kokkos.h b/src/KOKKOS/pair_eam_alloy_kokkos.h index 5848399672..9c6b1342ea 100644 --- a/src/KOKKOS/pair_eam_alloy_kokkos.h +++ b/src/KOKKOS/pair_eam_alloy_kokkos.h @@ -129,6 +129,16 @@ class PairEAMAlloyKokkos : public PairEAM, public KokkosBase { typename ArrayTypes::t_efloat_1d d_eatom; typename ArrayTypes::t_virial_array d_vatom; + int need_dup; + Kokkos::Experimental::ScatterView dup_rho; + Kokkos::Experimental::ScatterView dup_f; + Kokkos::Experimental::ScatterView dup_eatom; + Kokkos::Experimental::ScatterView dup_vatom; + Kokkos::Experimental::ScatterView ndup_rho; + Kokkos::Experimental::ScatterView ndup_f; + Kokkos::Experimental::ScatterView ndup_eatom; + Kokkos::Experimental::ScatterView ndup_vatom; + DAT::tdual_ffloat_1d k_rho; DAT::tdual_ffloat_1d k_fp; typename AT::t_ffloat_1d d_rho; diff --git a/src/KOKKOS/pair_eam_fs_kokkos.cpp b/src/KOKKOS/pair_eam_fs_kokkos.cpp index 627b56b84a..e0e87ecfc5 100644 --- a/src/KOKKOS/pair_eam_fs_kokkos.cpp +++ b/src/KOKKOS/pair_eam_fs_kokkos.cpp @@ -122,6 +122,19 @@ void PairEAMFSKokkos::compute(int eflag_in, int vflag_in) d_ilist = k_list->d_ilist; int inum = list->inum; + need_dup = lmp->kokkos->need_dup(); + if (need_dup) { + dup_rho = Kokkos::Experimental::create_scatter_view(d_rho); + dup_f = Kokkos::Experimental::create_scatter_view(f); + dup_eatom = Kokkos::Experimental::create_scatter_view(d_eatom); + dup_vatom = Kokkos::Experimental::create_scatter_view(d_vatom); + } else { + ndup_rho = Kokkos::Experimental::create_scatter_view(d_rho); + ndup_f = Kokkos::Experimental::create_scatter_view(f); + ndup_eatom = Kokkos::Experimental::create_scatter_view(d_eatom); + ndup_vatom = Kokkos::Experimental::create_scatter_view(d_vatom); + } + copymode = 1; // zero out density @@ -233,6 +246,9 @@ void PairEAMFSKokkos::compute(int eflag_in, int vflag_in) } } + if (need_dup) + Kokkos::Experimental::contribute(f, dup_f); + if (eflag_global) eng_vdwl += ev.evdwl; if (vflag_global) { virial[0] += ev.v[0]; @@ -246,11 +262,15 @@ void PairEAMFSKokkos::compute(int eflag_in, int vflag_in) if (vflag_fdotr) pair_virial_fdotr_compute(this); if (eflag_atom) { + if (need_dup) + Kokkos::Experimental::contribute(d_eatom, dup_eatom); k_eatom.template modify(); k_eatom.template sync(); } if (vflag_atom) { + if (need_dup) + Kokkos::Experimental::contribute(d_vatom, dup_vatom); k_vatom.template modify(); k_vatom.template sync(); } @@ -503,8 +523,10 @@ void PairEAMFSKokkos::operator()(TagPairEAMFSKernelA::value> > rho = v_rho; + // The rho array is duplicated for OpenMP, atomic for CUDA, and neither for Serial + + auto v_rho = ScatterViewHelper::value,decltype(dup_rho),decltype(ndup_rho)>::get(dup_rho,ndup_rho); + auto a_rho = v_rho.template access::value>(); const int i = d_ilist[ii]; const X_FLOAT xtmp = x(i,0); @@ -672,8 +694,10 @@ template KOKKOS_INLINE_FUNCTION void PairEAMFSKokkos::operator()(TagPairEAMFSKernelC, const int &ii, EV_FLOAT& ev) const { - // The f array is atomic for Half/Thread neighbor style - Kokkos::View::value> > a_f = f; + // The f array is duplicated for OpenMP, atomic for CUDA, and neither for Serial + + auto v_f = ScatterViewHelper::value,decltype(dup_f),decltype(ndup_f)>::get(dup_f,ndup_f); + auto a_f = v_f.template access::value>(); const int i = d_ilist[ii]; const X_FLOAT xtmp = x(i,0); @@ -780,18 +804,22 @@ void PairEAMFSKokkos::ev_tally(EV_FLOAT &ev, const int &i, const int const int EFLAG = eflag; const int VFLAG = vflag_either; - // The eatom and vatom arrays are atomic for Half/Thread neighbor style - Kokkos::View::value> > v_eatom = k_eatom.view(); - Kokkos::View::value> > v_vatom = k_vatom.view(); + // The eatom and vatom arrays are duplicated for OpenMP, atomic for CUDA, and neither for Serial + + auto v_eatom = ScatterViewHelper::value,decltype(dup_eatom),decltype(ndup_eatom)>::get(dup_eatom,ndup_eatom); + auto a_eatom = v_eatom.template access::value>(); + + auto v_vatom = ScatterViewHelper::value,decltype(dup_vatom),decltype(ndup_vatom)>::get(dup_vatom,ndup_vatom); + auto a_vatom = v_vatom.template access::value>(); if (EFLAG) { if (eflag_atom) { const E_FLOAT epairhalf = 0.5 * epair; if (NEIGHFLAG!=FULL) { - if (NEWTON_PAIR || i < nlocal) v_eatom[i] += epairhalf; - if (NEWTON_PAIR || j < nlocal) v_eatom[j] += epairhalf; + if (NEWTON_PAIR || i < nlocal) a_eatom[i] += epairhalf; + if (NEWTON_PAIR || j < nlocal) a_eatom[j] += epairhalf; } else { - v_eatom[i] += epairhalf; + a_eatom[i] += epairhalf; } } } @@ -835,28 +863,28 @@ void PairEAMFSKokkos::ev_tally(EV_FLOAT &ev, const int &i, const int if (vflag_atom) { if (NEIGHFLAG!=FULL) { if (NEWTON_PAIR || i < nlocal) { - v_vatom(i,0) += 0.5*v0; - v_vatom(i,1) += 0.5*v1; - v_vatom(i,2) += 0.5*v2; - v_vatom(i,3) += 0.5*v3; - v_vatom(i,4) += 0.5*v4; - v_vatom(i,5) += 0.5*v5; + a_vatom(i,0) += 0.5*v0; + a_vatom(i,1) += 0.5*v1; + a_vatom(i,2) += 0.5*v2; + a_vatom(i,3) += 0.5*v3; + a_vatom(i,4) += 0.5*v4; + a_vatom(i,5) += 0.5*v5; } if (NEWTON_PAIR || j < nlocal) { - v_vatom(j,0) += 0.5*v0; - v_vatom(j,1) += 0.5*v1; - v_vatom(j,2) += 0.5*v2; - v_vatom(j,3) += 0.5*v3; - v_vatom(j,4) += 0.5*v4; - v_vatom(j,5) += 0.5*v5; + a_vatom(j,0) += 0.5*v0; + a_vatom(j,1) += 0.5*v1; + a_vatom(j,2) += 0.5*v2; + a_vatom(j,3) += 0.5*v3; + a_vatom(j,4) += 0.5*v4; + a_vatom(j,5) += 0.5*v5; } } else { - v_vatom(i,0) += 0.5*v0; - v_vatom(i,1) += 0.5*v1; - v_vatom(i,2) += 0.5*v2; - v_vatom(i,3) += 0.5*v3; - v_vatom(i,4) += 0.5*v4; - v_vatom(i,5) += 0.5*v5; + a_vatom(i,0) += 0.5*v0; + a_vatom(i,1) += 0.5*v1; + a_vatom(i,2) += 0.5*v2; + a_vatom(i,3) += 0.5*v3; + a_vatom(i,4) += 0.5*v4; + a_vatom(i,5) += 0.5*v5; } } } @@ -1174,4 +1202,3 @@ template class PairEAMFSKokkos; template class PairEAMFSKokkos; #endif } - diff --git a/src/KOKKOS/pair_eam_fs_kokkos.h b/src/KOKKOS/pair_eam_fs_kokkos.h index ce0b572ea2..432a486276 100644 --- a/src/KOKKOS/pair_eam_fs_kokkos.h +++ b/src/KOKKOS/pair_eam_fs_kokkos.h @@ -129,6 +129,16 @@ class PairEAMFSKokkos : public PairEAM, public KokkosBase { typename ArrayTypes::t_efloat_1d d_eatom; typename ArrayTypes::t_virial_array d_vatom; + int need_dup; + Kokkos::Experimental::ScatterView dup_rho; + Kokkos::Experimental::ScatterView dup_f; + Kokkos::Experimental::ScatterView dup_eatom; + Kokkos::Experimental::ScatterView dup_vatom; + Kokkos::Experimental::ScatterView ndup_rho; + Kokkos::Experimental::ScatterView ndup_f; + Kokkos::Experimental::ScatterView ndup_eatom; + Kokkos::Experimental::ScatterView ndup_vatom; + DAT::tdual_ffloat_1d k_rho; DAT::tdual_ffloat_1d k_fp; typename AT::t_ffloat_1d d_rho; diff --git a/src/KOKKOS/pair_eam_kokkos.cpp b/src/KOKKOS/pair_eam_kokkos.cpp index 256cb8d55b..f6271a5a04 100644 --- a/src/KOKKOS/pair_eam_kokkos.cpp +++ b/src/KOKKOS/pair_eam_kokkos.cpp @@ -1,3 +1,4 @@ +/* ---------------------------------------------------------------------- /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator http://lammps.sandia.gov, Sandia National Laboratories @@ -34,7 +35,6 @@ using namespace LAMMPS_NS; - /* ---------------------------------------------------------------------- */ template @@ -524,6 +524,7 @@ void PairEAMKokkos::operator()(TagPairEAMKernelA::value,decltype(dup_rho),decltype(ndup_rho)>::get(dup_rho,ndup_rho); auto a_rho = v_rho.template access::value>(); @@ -692,6 +693,7 @@ KOKKOS_INLINE_FUNCTION void PairEAMKokkos::operator()(TagPairEAMKernelC, const int &ii, EV_FLOAT& ev) const { // The f array is duplicated for OpenMP, atomic for CUDA, and neither for Serial + auto v_f = ScatterViewHelper::value,decltype(dup_f),decltype(ndup_f)>::get(dup_f,ndup_f); auto a_f = v_f.template access::value>(); @@ -801,6 +803,7 @@ void PairEAMKokkos::ev_tally(EV_FLOAT &ev, const int &i, const int & const int VFLAG = vflag_either; // The eatom and vatom arrays are duplicated for OpenMP, atomic for CUDA, and neither for Serial + auto v_eatom = ScatterViewHelper::value,decltype(dup_eatom),decltype(ndup_eatom)>::get(dup_eatom,ndup_eatom); auto a_eatom = v_eatom.template access::value>(); From 12ecc45b6a9d315f7e9bd0a9d4e4f3b42d07c812 Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Fri, 10 Aug 2018 12:30:58 -0600 Subject: [PATCH 097/302] Add data duplication to pair_snap_kokkos --- src/KOKKOS/pair_snap_kokkos.h | 6 ++++ src/KOKKOS/pair_snap_kokkos_impl.h | 52 +++++++++++++++++++++--------- 2 files changed, 42 insertions(+), 16 deletions(-) diff --git a/src/KOKKOS/pair_snap_kokkos.h b/src/KOKKOS/pair_snap_kokkos.h index 5c68284219..b2019879ed 100644 --- a/src/KOKKOS/pair_snap_kokkos.h +++ b/src/KOKKOS/pair_snap_kokkos.h @@ -129,6 +129,12 @@ inline double dist2(double* x,double* y); typename AT::t_f_array f; typename AT::t_int_1d_randomread type; + int need_dup; + Kokkos::Experimental::ScatterView dup_f; + Kokkos::Experimental::ScatterView dup_vatom; + Kokkos::Experimental::ScatterView ndup_f; + Kokkos::Experimental::ScatterView ndup_vatom; + friend void pair_virial_fdotr_compute(PairSNAPKokkos*); }; diff --git a/src/KOKKOS/pair_snap_kokkos_impl.h b/src/KOKKOS/pair_snap_kokkos_impl.h index a024e5cbd1..013a8f1ba9 100644 --- a/src/KOKKOS/pair_snap_kokkos_impl.h +++ b/src/KOKKOS/pair_snap_kokkos_impl.h @@ -170,6 +170,15 @@ void PairSNAPKokkos::compute(int eflag_in, int vflag_in) d_ilist = k_list->d_ilist; int inum = list->inum; + need_dup = lmp->kokkos->need_dup(); + if (need_dup) { + dup_f = Kokkos::Experimental::create_scatter_view(f); + dup_vatom = Kokkos::Experimental::create_scatter_view(d_vatom); + } else { + ndup_f = Kokkos::Experimental::create_scatter_view(f); + ndup_vatom = Kokkos::Experimental::create_scatter_view(d_vatom); + } + /* for (int i = 0; i < nlocal; i++) { typename t_neigh_list::t_neighs neighs_i = neigh_list.get_neighs(i); @@ -232,6 +241,9 @@ void PairSNAPKokkos::compute(int eflag_in, int vflag_in) //if (step%10==0) // printf(" %e %e %e %e %e (%e %e): %e\n",t1,t2,t3,t4,t5,t6,t7,t1+t2+t3+t4+t5); + if (need_dup) + Kokkos::Experimental::contribute(f, dup_f); + if (eflag_global) eng_vdwl += ev.evdwl; if (vflag_global) { virial[0] += ev.v[0]; @@ -244,12 +256,15 @@ void PairSNAPKokkos::compute(int eflag_in, int vflag_in) if (vflag_fdotr) pair_virial_fdotr_compute(this); + if (eflag_atom) { k_eatom.template modify(); k_eatom.template sync(); } if (vflag_atom) { + if (need_dup) + Kokkos::Experimental::contribute(d_vatom, dup_vatom); k_vatom.template modify(); k_vatom.template sync(); } @@ -349,8 +364,11 @@ template template KOKKOS_INLINE_FUNCTION void PairSNAPKokkos::operator() (TagPairSNAP,const typename Kokkos::TeamPolicy >::member_type& team, EV_FLOAT& ev) const { - // The f array is atomic for Half/Thread neighbor style - Kokkos::View::value> > a_f = f; + + // The f array is duplicated for OpenMP, atomic for CUDA, and neither for Serial + + auto v_f = ScatterViewHelper::value,decltype(dup_f),decltype(ndup_f)>::get(dup_f,ndup_f); + auto a_f = v_f.template access::value>(); const int ii = team.league_rank(); const int i = d_ilist[ii]; @@ -591,8 +609,10 @@ void PairSNAPKokkos::v_tally_xyz(EV_FLOAT &ev, const int &i, const i const F_FLOAT &fx, const F_FLOAT &fy, const F_FLOAT &fz, const F_FLOAT &delx, const F_FLOAT &dely, const F_FLOAT &delz) const { - // The vatom array is atomic for Half/Thread neighbor style - Kokkos::View::value> > v_vatom = k_vatom.view(); + // The vatom array is duplicated for OpenMP, atomic for CUDA, and neither for Serial + + auto v_vatom = ScatterViewHelper::value,decltype(dup_vatom),decltype(ndup_vatom)>::get(dup_vatom,ndup_vatom); + auto a_vatom = v_vatom.template access::value>(); const E_FLOAT v0 = delx*fx; const E_FLOAT v1 = dely*fy; @@ -611,18 +631,18 @@ void PairSNAPKokkos::v_tally_xyz(EV_FLOAT &ev, const int &i, const i } if (vflag_atom) { - v_vatom(i,0) += 0.5*v0; - v_vatom(i,1) += 0.5*v1; - v_vatom(i,2) += 0.5*v2; - v_vatom(i,3) += 0.5*v3; - v_vatom(i,4) += 0.5*v4; - v_vatom(i,5) += 0.5*v5; - v_vatom(j,0) += 0.5*v0; - v_vatom(j,1) += 0.5*v1; - v_vatom(j,2) += 0.5*v2; - v_vatom(j,3) += 0.5*v3; - v_vatom(j,4) += 0.5*v4; - v_vatom(j,5) += 0.5*v5; + a_vatom(i,0) += 0.5*v0; + a_vatom(i,1) += 0.5*v1; + a_vatom(i,2) += 0.5*v2; + a_vatom(i,3) += 0.5*v3; + a_vatom(i,4) += 0.5*v4; + a_vatom(i,5) += 0.5*v5; + a_vatom(j,0) += 0.5*v0; + a_vatom(j,1) += 0.5*v1; + a_vatom(j,2) += 0.5*v2; + a_vatom(j,3) += 0.5*v3; + a_vatom(j,4) += 0.5*v4; + a_vatom(j,5) += 0.5*v5; } } From 9f058f19bc5664f53fd9e0547d3699590dac7d17 Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Fri, 10 Aug 2018 12:49:02 -0600 Subject: [PATCH 098/302] Deallocate duplicated memory --- src/KOKKOS/fix_qeq_reax_kokkos.cpp | 7 ++++--- src/KOKKOS/pair_eam_alloy_kokkos.cpp | 8 ++++++++ src/KOKKOS/pair_eam_fs_kokkos.cpp | 8 ++++++++ src/KOKKOS/pair_eam_kokkos.cpp | 8 ++++++++ src/KOKKOS/pair_reaxc_kokkos.cpp | 4 ++-- src/KOKKOS/pair_snap_kokkos_impl.h | 7 +++++++ src/KOKKOS/pair_sw_kokkos.cpp | 7 +++++++ src/KOKKOS/pair_tersoff_kokkos.cpp | 7 +++++++ src/KOKKOS/pair_tersoff_mod_kokkos.cpp | 7 +++++++ src/KOKKOS/pair_tersoff_zbl_kokkos.cpp | 7 +++++++ 10 files changed, 65 insertions(+), 5 deletions(-) diff --git a/src/KOKKOS/fix_qeq_reax_kokkos.cpp b/src/KOKKOS/fix_qeq_reax_kokkos.cpp index bc9c935576..c2ad719a47 100644 --- a/src/KOKKOS/fix_qeq_reax_kokkos.cpp +++ b/src/KOKKOS/fix_qeq_reax_kokkos.cpp @@ -260,9 +260,6 @@ void FixQEqReaxKokkos::pre_force(int vflag) // 2nd cg solve over b_t, t cg_solve2(); - if (need_dup) - dup_o = decltype(dup_o)(); // free duplicated memory - // calculate_Q(); calculate_q(); k_s_hist.template modify(); @@ -272,6 +269,10 @@ void FixQEqReaxKokkos::pre_force(int vflag) if (!allocated_flag) allocated_flag = 1; + + // free duplicated memory + if (need_dup) + dup_o = decltype(dup_o)(); } /* ---------------------------------------------------------------------- */ diff --git a/src/KOKKOS/pair_eam_alloy_kokkos.cpp b/src/KOKKOS/pair_eam_alloy_kokkos.cpp index 7c6510f311..2684ede376 100644 --- a/src/KOKKOS/pair_eam_alloy_kokkos.cpp +++ b/src/KOKKOS/pair_eam_alloy_kokkos.cpp @@ -277,6 +277,14 @@ void PairEAMAlloyKokkos::compute(int eflag_in, int vflag_in) if (vflag_fdotr) pair_virial_fdotr_compute(this); copymode = 0; + + // free duplicated memory + if (need_dup) { + dup_rho = decltype(dup_rho)(); + dup_f = decltype(dup_f)(); + dup_eatom = decltype(dup_eatom)(); + dup_vatom = decltype(dup_vatom)(); + } } /* ---------------------------------------------------------------------- diff --git a/src/KOKKOS/pair_eam_fs_kokkos.cpp b/src/KOKKOS/pair_eam_fs_kokkos.cpp index e0e87ecfc5..d46b81b9ae 100644 --- a/src/KOKKOS/pair_eam_fs_kokkos.cpp +++ b/src/KOKKOS/pair_eam_fs_kokkos.cpp @@ -276,6 +276,14 @@ void PairEAMFSKokkos::compute(int eflag_in, int vflag_in) } copymode = 0; + + // free duplicated memory + if (need_dup) { + dup_rho = decltype(dup_rho)(); + dup_f = decltype(dup_f)(); + dup_eatom = decltype(dup_eatom)(); + dup_vatom = decltype(dup_vatom)(); + } } /* ---------------------------------------------------------------------- diff --git a/src/KOKKOS/pair_eam_kokkos.cpp b/src/KOKKOS/pair_eam_kokkos.cpp index f6271a5a04..5e3c06294b 100644 --- a/src/KOKKOS/pair_eam_kokkos.cpp +++ b/src/KOKKOS/pair_eam_kokkos.cpp @@ -271,6 +271,14 @@ void PairEAMKokkos::compute(int eflag_in, int vflag_in) } copymode = 0; + + // free duplicated memory + if (need_dup) { + dup_rho = decltype(dup_rho)(); + dup_f = decltype(dup_f)(); + dup_eatom = decltype(dup_eatom)(); + dup_vatom = decltype(dup_vatom)(); + } } /* ---------------------------------------------------------------------- diff --git a/src/KOKKOS/pair_reaxc_kokkos.cpp b/src/KOKKOS/pair_reaxc_kokkos.cpp index 4db6235ca6..6cf9b3979a 100644 --- a/src/KOKKOS/pair_reaxc_kokkos.cpp +++ b/src/KOKKOS/pair_reaxc_kokkos.cpp @@ -1063,6 +1063,8 @@ void PairReaxCKokkos::compute(int eflag_in, int vflag_in) if (fixspecies_flag) FindBondSpecies(); + copymode = 0; + // free duplicated memory if (need_dup) { dup_f = decltype(dup_f)(); @@ -1075,8 +1077,6 @@ void PairReaxCKokkos::compute(int eflag_in, int vflag_in) dup_eatom = decltype(dup_eatom)(); dup_vatom = decltype(dup_vatom)(); } - - copymode = 0; } /* ---------------------------------------------------------------------- */ diff --git a/src/KOKKOS/pair_snap_kokkos_impl.h b/src/KOKKOS/pair_snap_kokkos_impl.h index 013a8f1ba9..c452042cfe 100644 --- a/src/KOKKOS/pair_snap_kokkos_impl.h +++ b/src/KOKKOS/pair_snap_kokkos_impl.h @@ -270,7 +270,14 @@ void PairSNAPKokkos::compute(int eflag_in, int vflag_in) } atomKK->modified(execution_space,F_MASK); + copymode = 0; + + // free duplicated memory + if (need_dup) { + dup_f = decltype(dup_f)(); + dup_vatom = decltype(dup_vatom)(); + } } /* ---------------------------------------------------------------------- diff --git a/src/KOKKOS/pair_sw_kokkos.cpp b/src/KOKKOS/pair_sw_kokkos.cpp index 22da4f7858..5452d2293f 100644 --- a/src/KOKKOS/pair_sw_kokkos.cpp +++ b/src/KOKKOS/pair_sw_kokkos.cpp @@ -201,6 +201,13 @@ void PairSWKokkos::compute(int eflag_in, int vflag_in) if (vflag_fdotr) pair_virial_fdotr_compute(this); copymode = 0; + + // free duplicated memory + if (need_dup) { + dup_f = decltype(dup_f)(); + dup_eatom = decltype(dup_eatom)(); + dup_vatom = decltype(dup_vatom)(); + } } diff --git a/src/KOKKOS/pair_tersoff_kokkos.cpp b/src/KOKKOS/pair_tersoff_kokkos.cpp index 7b21bf5793..c3e1494d0b 100644 --- a/src/KOKKOS/pair_tersoff_kokkos.cpp +++ b/src/KOKKOS/pair_tersoff_kokkos.cpp @@ -284,6 +284,13 @@ void PairTersoffKokkos::compute(int eflag_in, int vflag_in) if (vflag_fdotr) pair_virial_fdotr_compute(this); copymode = 0; + + // free duplicated memory + if (need_dup) { + dup_f = decltype(dup_f)(); + dup_eatom = decltype(dup_eatom)(); + dup_vatom = decltype(dup_vatom)(); + } } /* ---------------------------------------------------------------------- */ diff --git a/src/KOKKOS/pair_tersoff_mod_kokkos.cpp b/src/KOKKOS/pair_tersoff_mod_kokkos.cpp index 2fe4361503..61493794ba 100644 --- a/src/KOKKOS/pair_tersoff_mod_kokkos.cpp +++ b/src/KOKKOS/pair_tersoff_mod_kokkos.cpp @@ -284,6 +284,13 @@ void PairTersoffMODKokkos::compute(int eflag_in, int vflag_in) if (vflag_fdotr) pair_virial_fdotr_compute(this); copymode = 0; + + // free duplicated memory + if (need_dup) { + dup_f = decltype(dup_f)(); + dup_eatom = decltype(dup_eatom)(); + dup_vatom = decltype(dup_vatom)(); + } } /* ---------------------------------------------------------------------- */ diff --git a/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp b/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp index 2892947f66..f51da2afde 100644 --- a/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp +++ b/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp @@ -298,6 +298,13 @@ void PairTersoffZBLKokkos::compute(int eflag_in, int vflag_in) if (vflag_fdotr) pair_virial_fdotr_compute(this); copymode = 0; + + // free duplicated memory + if (need_dup) { + dup_f = decltype(dup_f)(); + dup_eatom = decltype(dup_eatom)(); + dup_vatom = decltype(dup_vatom)(); + } } /* ---------------------------------------------------------------------- */ From eb4d5864937a6b0eb6634b04996f8fed1940d556 Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Fri, 10 Aug 2018 12:53:27 -0600 Subject: [PATCH 099/302] Remove duplicate if test in fix_qeq_reax_kokkos --- src/KOKKOS/fix_qeq_reax_kokkos.cpp | 12 ++++-------- 1 file changed, 4 insertions(+), 8 deletions(-) diff --git a/src/KOKKOS/fix_qeq_reax_kokkos.cpp b/src/KOKKOS/fix_qeq_reax_kokkos.cpp index c2ad719a47..578afd2077 100644 --- a/src/KOKKOS/fix_qeq_reax_kokkos.cpp +++ b/src/KOKKOS/fix_qeq_reax_kokkos.cpp @@ -496,8 +496,7 @@ void FixQEqReaxKokkos::cg_solve1() Kokkos::parallel_for(inum,sparse13_functor); } if (need_dup) - if (need_dup) - Kokkos::Experimental::contribute(d_o, dup_o); + Kokkos::Experimental::contribute(d_o, dup_o); } else { Kokkos::parallel_for(Kokkos::TeamPolicy (inum, teamsize), *this); } @@ -555,8 +554,7 @@ void FixQEqReaxKokkos::cg_solve1() Kokkos::parallel_for(inum,sparse23_functor); } if (need_dup) - if (need_dup) - Kokkos::Experimental::contribute(d_o, dup_o); + Kokkos::Experimental::contribute(d_o, dup_o); } else { Kokkos::parallel_for(Kokkos::TeamPolicy (inum, teamsize), *this); } @@ -635,8 +633,7 @@ void FixQEqReaxKokkos::cg_solve2() Kokkos::parallel_for(inum,sparse33_functor); } if (need_dup) - if (need_dup) - Kokkos::Experimental::contribute(d_o, dup_o); + Kokkos::Experimental::contribute(d_o, dup_o); } else { Kokkos::parallel_for(Kokkos::TeamPolicy (inum, teamsize), *this); } @@ -694,8 +691,7 @@ void FixQEqReaxKokkos::cg_solve2() Kokkos::parallel_for(inum,sparse23_functor); } if (need_dup) - if (need_dup) - Kokkos::Experimental::contribute(d_o, dup_o); + Kokkos::Experimental::contribute(d_o, dup_o); } else { Kokkos::parallel_for(Kokkos::TeamPolicy (inum, teamsize), *this); } From 6f1986a8f149dc4873d1c86fa1f031995983fc77 Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Fri, 10 Aug 2018 13:10:02 -0600 Subject: [PATCH 100/302] Small tweaks to Kokkos EAM --- src/KOKKOS/pair_eam_alloy_kokkos.cpp | 1 - src/KOKKOS/pair_eam_alloy_kokkos.h | 5 ++--- src/KOKKOS/pair_eam_fs_kokkos.cpp | 1 - src/KOKKOS/pair_eam_fs_kokkos.h | 5 ++--- src/KOKKOS/pair_eam_kokkos.cpp | 1 - src/KOKKOS/pair_eam_kokkos.h | 5 ++--- 6 files changed, 6 insertions(+), 12 deletions(-) diff --git a/src/KOKKOS/pair_eam_alloy_kokkos.cpp b/src/KOKKOS/pair_eam_alloy_kokkos.cpp index 2684ede376..d20e71fe4c 100644 --- a/src/KOKKOS/pair_eam_alloy_kokkos.cpp +++ b/src/KOKKOS/pair_eam_alloy_kokkos.cpp @@ -110,7 +110,6 @@ void PairEAMAlloyKokkos::compute(int eflag_in, int vflag_in) x = atomKK->k_x.view(); f = atomKK->k_f.view(); - v_rho = k_rho.view(); type = atomKK->k_type.view(); tag = atomKK->k_tag.view(); nlocal = atom->nlocal; diff --git a/src/KOKKOS/pair_eam_alloy_kokkos.h b/src/KOKKOS/pair_eam_alloy_kokkos.h index 9c6b1342ea..6593ccae73 100644 --- a/src/KOKKOS/pair_eam_alloy_kokkos.h +++ b/src/KOKKOS/pair_eam_alloy_kokkos.h @@ -130,11 +130,11 @@ class PairEAMAlloyKokkos : public PairEAM, public KokkosBase { typename ArrayTypes::t_virial_array d_vatom; int need_dup; - Kokkos::Experimental::ScatterView dup_rho; + Kokkos::Experimental::ScatterView dup_rho; Kokkos::Experimental::ScatterView dup_f; Kokkos::Experimental::ScatterView dup_eatom; Kokkos::Experimental::ScatterView dup_vatom; - Kokkos::Experimental::ScatterView ndup_rho; + Kokkos::Experimental::ScatterView ndup_rho; Kokkos::Experimental::ScatterView ndup_f; Kokkos::Experimental::ScatterView ndup_eatom; Kokkos::Experimental::ScatterView ndup_vatom; @@ -142,7 +142,6 @@ class PairEAMAlloyKokkos : public PairEAM, public KokkosBase { DAT::tdual_ffloat_1d k_rho; DAT::tdual_ffloat_1d k_fp; typename AT::t_ffloat_1d d_rho; - typename AT::t_ffloat_1d v_rho; typename AT::t_ffloat_1d d_fp; HAT::t_ffloat_1d h_rho; HAT::t_ffloat_1d h_fp; diff --git a/src/KOKKOS/pair_eam_fs_kokkos.cpp b/src/KOKKOS/pair_eam_fs_kokkos.cpp index d46b81b9ae..8f5571bf29 100644 --- a/src/KOKKOS/pair_eam_fs_kokkos.cpp +++ b/src/KOKKOS/pair_eam_fs_kokkos.cpp @@ -109,7 +109,6 @@ void PairEAMFSKokkos::compute(int eflag_in, int vflag_in) x = atomKK->k_x.view(); f = atomKK->k_f.view(); - v_rho = k_rho.view(); type = atomKK->k_type.view(); tag = atomKK->k_tag.view(); nlocal = atom->nlocal; diff --git a/src/KOKKOS/pair_eam_fs_kokkos.h b/src/KOKKOS/pair_eam_fs_kokkos.h index 432a486276..f75605ff6d 100644 --- a/src/KOKKOS/pair_eam_fs_kokkos.h +++ b/src/KOKKOS/pair_eam_fs_kokkos.h @@ -130,11 +130,11 @@ class PairEAMFSKokkos : public PairEAM, public KokkosBase { typename ArrayTypes::t_virial_array d_vatom; int need_dup; - Kokkos::Experimental::ScatterView dup_rho; + Kokkos::Experimental::ScatterView dup_rho; Kokkos::Experimental::ScatterView dup_f; Kokkos::Experimental::ScatterView dup_eatom; Kokkos::Experimental::ScatterView dup_vatom; - Kokkos::Experimental::ScatterView ndup_rho; + Kokkos::Experimental::ScatterView ndup_rho; Kokkos::Experimental::ScatterView ndup_f; Kokkos::Experimental::ScatterView ndup_eatom; Kokkos::Experimental::ScatterView ndup_vatom; @@ -142,7 +142,6 @@ class PairEAMFSKokkos : public PairEAM, public KokkosBase { DAT::tdual_ffloat_1d k_rho; DAT::tdual_ffloat_1d k_fp; typename AT::t_ffloat_1d d_rho; - typename AT::t_ffloat_1d v_rho; typename AT::t_ffloat_1d d_fp; HAT::t_ffloat_1d h_rho; HAT::t_ffloat_1d h_fp; diff --git a/src/KOKKOS/pair_eam_kokkos.cpp b/src/KOKKOS/pair_eam_kokkos.cpp index 5e3c06294b..1a49e1357c 100644 --- a/src/KOKKOS/pair_eam_kokkos.cpp +++ b/src/KOKKOS/pair_eam_kokkos.cpp @@ -104,7 +104,6 @@ void PairEAMKokkos::compute(int eflag_in, int vflag_in) x = atomKK->k_x.view(); f = atomKK->k_f.view(); - v_rho = k_rho.view(); type = atomKK->k_type.view(); tag = atomKK->k_tag.view(); nlocal = atom->nlocal; diff --git a/src/KOKKOS/pair_eam_kokkos.h b/src/KOKKOS/pair_eam_kokkos.h index 6523e3fe72..4040eba858 100644 --- a/src/KOKKOS/pair_eam_kokkos.h +++ b/src/KOKKOS/pair_eam_kokkos.h @@ -127,11 +127,11 @@ class PairEAMKokkos : public PairEAM, public KokkosBase { typename ArrayTypes::t_virial_array d_vatom; int need_dup; - Kokkos::Experimental::ScatterView dup_rho; + Kokkos::Experimental::ScatterView dup_rho; Kokkos::Experimental::ScatterView dup_f; Kokkos::Experimental::ScatterView dup_eatom; Kokkos::Experimental::ScatterView dup_vatom; - Kokkos::Experimental::ScatterView ndup_rho; + Kokkos::Experimental::ScatterView ndup_rho; Kokkos::Experimental::ScatterView ndup_f; Kokkos::Experimental::ScatterView ndup_eatom; Kokkos::Experimental::ScatterView ndup_vatom; @@ -139,7 +139,6 @@ class PairEAMKokkos : public PairEAM, public KokkosBase { DAT::tdual_ffloat_1d k_rho; DAT::tdual_ffloat_1d k_fp; typename AT::t_ffloat_1d d_rho; - typename AT::t_ffloat_1d v_rho; typename AT::t_ffloat_1d d_fp; HAT::t_ffloat_1d h_rho; HAT::t_ffloat_1d h_fp; From 8f665a5a0f35a3022655a530161f95ed285b8e50 Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Fri, 10 Aug 2018 13:46:03 -0600 Subject: [PATCH 101/302] Update Kokkos docs for data duplication --- doc/src/Speed_kokkos.txt | 21 +++++++++++++++++++++ src/KOKKOS/kokkos.cpp | 4 +++- 2 files changed, 24 insertions(+), 1 deletion(-) diff --git a/doc/src/Speed_kokkos.txt b/doc/src/Speed_kokkos.txt index 597ed73e53..5846781e66 100644 --- a/doc/src/Speed_kokkos.txt +++ b/doc/src/Speed_kokkos.txt @@ -178,6 +178,11 @@ this manner no modification to the input script is needed. Alternatively, one can run with the KOKKOS package by editing the input script as described below. +NOTE: When using a single OpenMP thread, the Kokkos Serial backend (i.e. +Makefile.kokkos_mpi_only) will give better performance than the OpenMP +backend (i.e. Makefile.kokkos_omp) because some of the overhead to make +the code thread-safe is removed. + NOTE: The default for the "package kokkos"_package.html command is to use "full" neighbor lists and set the Newton flag to "off" for both pairwise and bonded interactions. However, when running on CPUs, it @@ -194,6 +199,22 @@ mpirun -np 16 lmp_kokkos_mpi_only -k on -sf kk -pk kokkos newton on neigh half c If the "newton"_newton.html command is used in the input script, it can also override the Newton flag defaults. +For half neighbor lists and OpenMP, the KOKKOS package uses data +duplication (i.e. thread-private arrays) by default to avoid +thread-level write conflicts in the force arrays (and other data +structures as necessary). Data duplication is typically fastest for +small numbers of threads (i.e. 8 or less) but does increase memory +footprint and is not scalable to large numbers of threads. An +alternative to data duplication is to use thread-level atomics, which +don't require duplication. The use of atomics can be forced by compiling +with the "-DLMP_KOKKOS_USE_ATOMICS" compile switch. Most but not all +Kokkos-enabled pair_styles support data duplication. Alternatively, full +neighbor lists avoid the need for duplication or atomics but require +more compute operations per atom. When using the Kokkos Serial backend +or the OpenMP backend with a single thread, no duplication or atomics is +used. For CUDA and half neighbor lists, the KOKKOS package always uses +atomics. + [Core and Thread Affinity:] When using multi-threading, it is important for performance to bind diff --git a/src/KOKKOS/kokkos.cpp b/src/KOKKOS/kokkos.cpp index e8bc610de6..9973b5a688 100644 --- a/src/KOKKOS/kokkos.cpp +++ b/src/KOKKOS/kokkos.cpp @@ -168,7 +168,9 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) #ifndef KOKKOS_HAVE_SERIAL if (num_threads == 1) - error->warning(FLERR,"Using Kokkos Serial backend (i.e. Makefile.kokkos_mpi_only) performs better with 1 thread"); + error->warning(FLERR,"When using a single thread, the Kokkos Serial backend " + "(i.e. Makefile.kokkos_mpi_only) gives better performance " + "than the OpenMP backend"); #endif Kokkos::InitArguments args; From 165fa01a97816c7430f2f2f1283036d92408e926 Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Fri, 10 Aug 2018 14:23:51 -0600 Subject: [PATCH 102/302] Cleanup --- doc/src/Speed_kokkos.txt | 2 +- src/KOKKOS/pair_eam_alloy_kokkos.cpp | 1 - src/KOKKOS/pair_eam_kokkos.cpp | 1 - src/KOKKOS/pair_reaxc_kokkos.cpp | 79 ++++++++++------------------ 4 files changed, 29 insertions(+), 54 deletions(-) diff --git a/doc/src/Speed_kokkos.txt b/doc/src/Speed_kokkos.txt index 5846781e66..dc5dbd6049 100644 --- a/doc/src/Speed_kokkos.txt +++ b/doc/src/Speed_kokkos.txt @@ -211,7 +211,7 @@ with the "-DLMP_KOKKOS_USE_ATOMICS" compile switch. Most but not all Kokkos-enabled pair_styles support data duplication. Alternatively, full neighbor lists avoid the need for duplication or atomics but require more compute operations per atom. When using the Kokkos Serial backend -or the OpenMP backend with a single thread, no duplication or atomics is +or the OpenMP backend with a single thread, no duplication or atomics are used. For CUDA and half neighbor lists, the KOKKOS package always uses atomics. diff --git a/src/KOKKOS/pair_eam_alloy_kokkos.cpp b/src/KOKKOS/pair_eam_alloy_kokkos.cpp index d20e71fe4c..fc19da1c8a 100644 --- a/src/KOKKOS/pair_eam_alloy_kokkos.cpp +++ b/src/KOKKOS/pair_eam_alloy_kokkos.cpp @@ -38,7 +38,6 @@ using namespace LAMMPS_NS; // Cannot use virtual inheritance on the GPU, so must duplicate code - /* ---------------------------------------------------------------------- */ template diff --git a/src/KOKKOS/pair_eam_kokkos.cpp b/src/KOKKOS/pair_eam_kokkos.cpp index 1a49e1357c..a1431334b4 100644 --- a/src/KOKKOS/pair_eam_kokkos.cpp +++ b/src/KOKKOS/pair_eam_kokkos.cpp @@ -1,4 +1,3 @@ -/* ---------------------------------------------------------------------- /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator http://lammps.sandia.gov, Sandia National Laboratories diff --git a/src/KOKKOS/pair_reaxc_kokkos.cpp b/src/KOKKOS/pair_reaxc_kokkos.cpp index 6cf9b3979a..46ecddfd83 100644 --- a/src/KOKKOS/pair_reaxc_kokkos.cpp +++ b/src/KOKKOS/pair_reaxc_kokkos.cpp @@ -73,14 +73,6 @@ PairReaxCKokkos::PairReaxCKokkos(LAMMPS *lmp) : PairReaxC(lmp) k_error_flag = DAT::tdual_int_scalar("pair:error_flag"); k_nbuf_local = DAT::tdual_int_scalar("pair:nbuf_local"); - - static double t1 = 0.0; - static double t2 = 0.0; - static double t3 = 0.0; - static double t4 = 0.0; - static double t5 = 0.0; - static double t6 = 0.0; - static double t7 = 0.0; } /* ---------------------------------------------------------------------- */ @@ -678,8 +670,6 @@ void PairReaxCKokkos::LR_vdW_Coulomb( int i, int j, double r_ij, LR_ template void PairReaxCKokkos::compute(int eflag_in, int vflag_in) { - Kokkos::Timer timer; - copymode = 1; bocnt = hbcnt = 0; @@ -828,7 +818,6 @@ void PairReaxCKokkos::compute(int eflag_in, int vflag_in) // zero Kokkos::parallel_for(Kokkos::RangePolicy(0,nmax),*this); - if (neighflag == HALF) Kokkos::parallel_for(Kokkos::RangePolicy >(0,ignum),*this); else if (neighflag == HALFTHREAD) @@ -1115,8 +1104,8 @@ template KOKKOS_INLINE_FUNCTION void PairReaxCKokkos::operator()(PairReaxComputeLJCoulomb, const int &ii, EV_FLOAT_REAX& ev) const { - // The f array is atomic for Half/Thread neighbor style - //Kokkos::View::value> > a_f = f; + // The f array is duplicated for OpenMP, atomic for CUDA, and neither for Serial + auto v_f = ScatterViewHelper::value,decltype(dup_f),decltype(ndup_f)>::get(dup_f,ndup_f); auto a_f = v_f.template access::value>(); @@ -1276,8 +1265,8 @@ template KOKKOS_INLINE_FUNCTION void PairReaxCKokkos::operator()(PairReaxComputeTabulatedLJCoulomb, const int &ii, EV_FLOAT_REAX& ev) const { - // The f array is atomic for Half/Thread neighbor style - //Kokkos::View::value> > a_f = f; + // The f array is duplicated for OpenMP, atomic for CUDA, and neither for Serial + auto v_f = ScatterViewHelper::value,decltype(dup_f),decltype(ndup_f)>::get(dup_f,ndup_f); auto a_f = v_f.template access::value>(); @@ -1660,10 +1649,9 @@ void PairReaxCKokkos::operator()(PairReaxBuildListsHalf, if (d_resize_bo() || d_resize_hb()) return; - //Kokkos::View::value> > a_dDeltap_self = d_dDeltap_self; auto v_dDeltap_self = ScatterViewHelper::value,decltype(dup_dDeltap_self),decltype(ndup_dDeltap_self)>::get(dup_dDeltap_self,ndup_dDeltap_self); auto a_dDeltap_self = v_dDeltap_self.template access::value>(); - //Kokkos::View::value> > a_total_bo = d_total_bo; + auto v_total_bo = ScatterViewHelper::value,decltype(dup_total_bo),decltype(ndup_total_bo)>::get(dup_total_bo,ndup_total_bo); auto a_total_bo = v_total_bo.template access::value>(); @@ -2356,7 +2344,6 @@ template KOKKOS_INLINE_FUNCTION void PairReaxCKokkos::operator()(PairReaxComputeMulti2, const int &ii, EV_FLOAT_REAX& ev) const { - //Kokkos::View::value> > a_CdDelta = d_CdDelta; auto v_CdDelta = ScatterViewHelper::value,decltype(dup_CdDelta),decltype(ndup_CdDelta)>::get(dup_CdDelta,ndup_CdDelta); auto a_CdDelta = v_CdDelta.template access::value>(); @@ -2509,12 +2496,10 @@ template KOKKOS_INLINE_FUNCTION void PairReaxCKokkos::operator()(PairReaxComputeAngular, const int &ii, EV_FLOAT_REAX& ev) const { - //Kokkos::View::value> > a_f = f; auto v_f = ScatterViewHelper::value,decltype(dup_f),decltype(ndup_f)>::get(dup_f,ndup_f); auto a_f = v_f.template access::value>(); Kokkos::View::value> > a_Cdbo = d_Cdbo; - //auto a_Cdbo = dup_Cdbo.template access::value>(); - //Kokkos::View::value> > a_CdDelta = d_CdDelta; + auto v_CdDelta = ScatterViewHelper::value,decltype(dup_CdDelta),decltype(ndup_CdDelta)>::get(dup_CdDelta,ndup_CdDelta); auto a_CdDelta = v_CdDelta.template access::value>(); @@ -2758,10 +2743,10 @@ void PairReaxCKokkos::operator()(PairReaxComputeAngular::operator()(PairReaxComputeAngular KOKKOS_INLINE_FUNCTION void PairReaxCKokkos::operator()(PairReaxComputeTorsion, const int &ii, EV_FLOAT_REAX& ev) const { - //Kokkos::View::value> > a_f = f; auto v_f = ScatterViewHelper::value,decltype(dup_f),decltype(ndup_f)>::get(dup_f,ndup_f); auto a_f = v_f.template access::value>(); - //Kokkos::View::value> > a_CdDelta = d_CdDelta; + auto v_CdDelta = ScatterViewHelper::value,decltype(dup_CdDelta),decltype(ndup_CdDelta)>::get(dup_CdDelta,ndup_CdDelta); auto a_CdDelta = v_CdDelta.template access::value>(); Kokkos::View::value> > a_Cdbo = d_Cdbo; @@ -3131,9 +3115,9 @@ void PairReaxCKokkos::operator()(PairReaxComputeTorsion KOKKOS_INLINE_FUNCTION void PairReaxCKokkos::operator()(PairReaxComputeHydrogen, const int &ii, EV_FLOAT_REAX& ev) const { - //Kokkos::View::value> > a_f = f; auto v_f = ScatterViewHelper::value,decltype(dup_f),decltype(ndup_f)>::get(dup_f,ndup_f); auto a_f = v_f.template access::value>(); @@ -3387,9 +3370,9 @@ void PairReaxCKokkos::operator()(PairReaxUpdateBond, cons } if (flag) { - d_Cdbo(j,k_index) += Cdbo_i; - d_Cdbopi(j,k_index) += Cdbopi_i; - d_Cdbopi2(j,k_index) += Cdbopi2_i; + a_Cdbo(j,k_index) += Cdbo_i; + a_Cdbopi(j,k_index) += Cdbopi_i; + a_Cdbopi2(j,k_index) += Cdbopi2_i; } } } @@ -3401,14 +3384,12 @@ template KOKKOS_INLINE_FUNCTION void PairReaxCKokkos::operator()(PairReaxComputeBond1, const int &ii, EV_FLOAT_REAX& ev) const { - //Kokkos::View::value> > a_f = f; auto v_f = ScatterViewHelper::value,decltype(dup_f),decltype(ndup_f)>::get(dup_f,ndup_f); auto a_f = v_f.template access::value>(); - //Kokkos::View::value> > a_CdDelta = d_CdDelta; + auto v_CdDelta = ScatterViewHelper::value,decltype(dup_CdDelta),decltype(ndup_CdDelta)>::get(dup_CdDelta,ndup_CdDelta); auto a_CdDelta = v_CdDelta.template access::value>(); - F_FLOAT delij[3]; F_FLOAT p_be1, p_be2, De_s, De_p, De_pp, pow_BOs_be2, exp_be12, CEbo, ebond; @@ -3544,7 +3525,6 @@ template KOKKOS_INLINE_FUNCTION void PairReaxCKokkos::operator()(PairReaxComputeBond2, const int &ii, EV_FLOAT_REAX& ev) const { - //Kokkos::View::value> > a_f = f; auto v_f = ScatterViewHelper::value,decltype(dup_f),decltype(ndup_f)>::get(dup_f,ndup_f); auto a_f = v_f.template access::value>(); @@ -3758,11 +3738,11 @@ void PairReaxCKokkos::ev_tally(EV_FLOAT_REAX &ev, const int &i, cons { const int VFLAG = vflag_either; - // The eatom and vatom arrays are atomic for Half/Thread neighbor style - //Kokkos::View::value> > a_eatom = d_eatom; + // The eatom and vatom arrays are duplicated for OpenMP, atomic for CUDA, and neither for Serial + auto v_eatom = ScatterViewHelper::value,decltype(dup_eatom),decltype(ndup_eatom)>::get(dup_eatom,ndup_eatom); auto a_eatom = v_eatom.template access::value>(); - //Kokkos::View::value> > a_vatom = d_vatom; + auto v_vatom = ScatterViewHelper::value,decltype(dup_vatom),decltype(ndup_vatom)>::get(dup_vatom,ndup_vatom); auto a_vatom = v_vatom.template access::value>(); @@ -3827,10 +3807,10 @@ void PairReaxCKokkos::e_tally(EV_FLOAT_REAX &ev, const int &i, const const F_FLOAT &epair) const { - // The eatom array is atomic for Half/Thread neighbor style + // The eatom array is duplicated for OpenMP, atomic for CUDA, and neither for Serial + if (eflag_atom) { - //Kokkos::View::value> > a_eatom = d_eatom; auto v_eatom = ScatterViewHelper::value,decltype(dup_eatom),decltype(ndup_eatom)>::get(dup_eatom,ndup_eatom); auto a_eatom = v_eatom.template access::value>(); @@ -3848,8 +3828,7 @@ KOKKOS_INLINE_FUNCTION void PairReaxCKokkos::e_tally_single(EV_FLOAT_REAX &ev, const int &i, const F_FLOAT &epair) const { - // The eatom array is atomic for Half/Thread neighbor style - //Kokkos::View::value> > a_eatom = d_eatom; + // The eatom array is duplicated for OpenMP, atomic for CUDA, and neither for Serial auto v_eatom = ScatterViewHelper::value,decltype(dup_eatom),decltype(ndup_eatom)>::get(dup_eatom,ndup_eatom); auto a_eatom = v_eatom.template access::value>(); @@ -3884,7 +3863,6 @@ void PairReaxCKokkos::v_tally(EV_FLOAT_REAX &ev, const int &i, } if (vflag_atom) { - //Kokkos::View::value> > a_vatom = d_vatom; auto v_vatom = ScatterViewHelper::value,decltype(dup_vatom),decltype(ndup_vatom)>::get(dup_vatom,ndup_vatom); auto a_vatom = v_vatom.template access::value>(); @@ -3902,8 +3880,7 @@ void PairReaxCKokkos::v_tally3(EV_FLOAT_REAX &ev, const int &i, cons F_FLOAT *fj, F_FLOAT *fk, F_FLOAT *drij, F_FLOAT *drik) const { - // The eatom and vatom arrays are atomic for Half/Thread neighbor style - //Kokkos::View::value> > a_vatom = d_vatom; + // The eatom and vatom arrays are duplicated for OpenMP, atomic for CUDA, and neither for Serial auto v_vatom = ScatterViewHelper::value,decltype(dup_vatom),decltype(ndup_vatom)>::get(dup_vatom,ndup_vatom); auto a_vatom = v_vatom.template access::value>(); @@ -3945,7 +3922,8 @@ void PairReaxCKokkos::v_tally4(EV_FLOAT_REAX &ev, const int &i, cons const int &l, F_FLOAT *fi, F_FLOAT *fj, F_FLOAT *fk, F_FLOAT *dril, F_FLOAT *drjl, F_FLOAT *drkl) const { - // The vatom array is atomic for Half/Thread neighbor style + // The vatom array is duplicated for OpenMP, atomic for CUDA, and neither for Serial + F_FLOAT v[6]; v[0] = dril[0]*fi[0] + drjl[0]*fj[0] + drkl[0]*fk[0]; @@ -3965,7 +3943,6 @@ void PairReaxCKokkos::v_tally4(EV_FLOAT_REAX &ev, const int &i, cons } if (vflag_atom) { - //Kokkos::View::value> > a_vatom = d_vatom; auto v_vatom = ScatterViewHelper::value,decltype(dup_vatom),decltype(ndup_vatom)>::get(dup_vatom,ndup_vatom); auto a_vatom = v_vatom.template access::value>(); From 9765a9a4300dab5a12ca36a1edeebd54210be927 Mon Sep 17 00:00:00 2001 From: Denis Taniguchi Date: Mon, 13 Aug 2018 16:03:23 +0100 Subject: [PATCH 103/302] Implementing forward/border comm in Kokkos. --- src/KOKKOS/atom_vec_kokkos.h | 19 + src/KOKKOS/atom_vec_sphere_kokkos.cpp | 663 ++++++++++++++++++++++++-- src/KOKKOS/atom_vec_sphere_kokkos.h | 12 + src/KOKKOS/comm_kokkos.cpp | 93 ++-- 4 files changed, 711 insertions(+), 76 deletions(-) diff --git a/src/KOKKOS/atom_vec_kokkos.h b/src/KOKKOS/atom_vec_kokkos.h index b68fdc9b20..38ffed9d37 100644 --- a/src/KOKKOS/atom_vec_kokkos.h +++ b/src/KOKKOS/atom_vec_kokkos.h @@ -60,6 +60,15 @@ class AtomVecKokkos : public AtomVec { unpack_comm_kokkos(const int &n, const int &nfirst, const DAT::tdual_xfloat_2d &buf); + virtual int + pack_comm_vel_kokkos(const int &n, const DAT::tdual_int_2d &list, + const int & iswap, const DAT::tdual_xfloat_2d &buf, + const int &pbc_flag, const int pbc[]) { return 0; } + + virtual void + unpack_comm_vel_kokkos(const int &n, const int &nfirst, + const DAT::tdual_xfloat_2d &buf) {} + virtual int unpack_reverse_self(const int &n, const DAT::tdual_int_2d &list, const int & iswap, const int nfirst); @@ -82,6 +91,16 @@ class AtomVecKokkos : public AtomVec { const DAT::tdual_xfloat_2d &buf, ExecutionSpace space) = 0; + virtual int + pack_border_vel_kokkos(int n, DAT::tdual_int_2d k_sendlist, + DAT::tdual_xfloat_2d buf,int iswap, + int pbc_flag, int *pbc, ExecutionSpace space) { return 0; } + + virtual void + unpack_border_vel_kokkos(const int &n, const int &nfirst, + const DAT::tdual_xfloat_2d &buf, + ExecutionSpace space) {} + virtual int pack_exchange_kokkos(const int &nsend, DAT::tdual_xfloat_2d &buf, DAT::tdual_int_1d k_sendlist, diff --git a/src/KOKKOS/atom_vec_sphere_kokkos.cpp b/src/KOKKOS/atom_vec_sphere_kokkos.cpp index 8fa62bab39..76582086df 100644 --- a/src/KOKKOS/atom_vec_sphere_kokkos.cpp +++ b/src/KOKKOS/atom_vec_sphere_kokkos.cpp @@ -229,9 +229,9 @@ struct AtomVecSphereKokkos_PackComm { _list(list.view()),_iswap(iswap), _xprd(xprd),_yprd(yprd),_zprd(zprd), _xy(xy),_xz(xz),_yz(yz) { - const size_t maxsend = (buf.view().extent(0)*buf.view().extent(1))/3; const size_t elements = 5; - buffer_view(_buf,buf,maxsend,elements); + const size_t maxsend = (buf.view().extent(0)*buf.view().extent(1))/elements; + _buf = typename ArrayTypes::t_xfloat_2d_um(buf.view().data(),maxsend,elements); _pbc[0] = pbc[0]; _pbc[1] = pbc[1]; _pbc[2] = pbc[2]; _pbc[3] = pbc[3]; _pbc[4] = pbc[4]; _pbc[5] = pbc[5]; } @@ -358,6 +358,243 @@ int AtomVecSphereKokkos::pack_comm_kokkos( /* ---------------------------------------------------------------------- */ +template +struct AtomVecSphereKokkos_PackCommVel { + typedef DeviceType device_type; + + typename ArrayTypes::t_x_array_randomread _x; + typename ArrayTypes::t_int_1d _mask; + typename ArrayTypes::t_float_1d _radius,_rmass; + typename ArrayTypes::t_v_array _v, _omega; + typename ArrayTypes::t_xfloat_2d_um _buf; + typename ArrayTypes::t_int_2d_const _list; + const int _iswap; + X_FLOAT _xprd,_yprd,_zprd,_xy,_xz,_yz; + X_FLOAT _pbc[6]; + X_FLOAT _h_rate[6]; + const int _deform_vremap; + + AtomVecSphereKokkos_PackCommVel( + const typename DAT::tdual_x_array &x, + const typename DAT::tdual_int_1d &mask, + const typename DAT::tdual_float_1d &radius, + const typename DAT::tdual_float_1d &rmass, + const typename DAT::tdual_v_array &v, + const typename DAT::tdual_v_array &omega, + const typename DAT::tdual_xfloat_2d &buf, + const typename DAT::tdual_int_2d &list, + const int &iswap, + const X_FLOAT &xprd, const X_FLOAT &yprd, const X_FLOAT &zprd, + const X_FLOAT &xy, const X_FLOAT &xz, const X_FLOAT &yz, const int* const pbc, + const double * const h_rate, + const int &deform_vremap): + _x(x.view()), + _mask(mask.view()), + _radius(radius.view()), + _rmass(rmass.view()), + _v(v.view()), + _omega(omega.view()), + _list(list.view()),_iswap(iswap), + _xprd(xprd),_yprd(yprd),_zprd(zprd), + _xy(xy),_xz(xz),_yz(yz), + _deform_vremap(deform_vremap) + { + const size_t elements = 11; + const int maxsend = (buf.template view().extent(0)*buf.template view().extent(1))/elements; + _buf = typename ArrayTypes::t_xfloat_2d_um(buf.view().data(),maxsend,elements); + _pbc[0] = pbc[0]; _pbc[1] = pbc[1]; _pbc[2] = pbc[2]; + _pbc[3] = pbc[3]; _pbc[4] = pbc[4]; _pbc[5] = pbc[5]; + _h_rate[0] = h_rate[0]; _h_rate[1] = h_rate[1]; _h_rate[2] = h_rate[2]; + _h_rate[3] = h_rate[3]; _h_rate[4] = h_rate[4]; _h_rate[5] = h_rate[5]; + } + + KOKKOS_INLINE_FUNCTION + void operator() (const int& i) const { + const int j = _list(_iswap,i); + if (PBC_FLAG == 0) { + _buf(i,0) = _x(j,0); + _buf(i,1) = _x(j,1); + _buf(i,2) = _x(j,2); + } else { + if (TRICLINIC == 0) { + _buf(i,0) = _x(j,0) + _pbc[0]*_xprd; + _buf(i,1) = _x(j,1) + _pbc[1]*_yprd; + _buf(i,2) = _x(j,2) + _pbc[2]*_zprd; + } else { + _buf(i,0) = _x(j,0) + _pbc[0]*_xprd + _pbc[5]*_xy + _pbc[4]*_xz; + _buf(i,1) = _x(j,1) + _pbc[1]*_yprd + _pbc[3]*_yz; + _buf(i,2) = _x(j,2) + _pbc[2]*_zprd; + } + } + _buf(i,3) = _radius(j); + _buf(i,4) = _rmass(j); + if (DEFORM_VREMAP == 0) { + _buf(i,5) = _v(j,0); + _buf(i,6) = _v(j,1); + _buf(i,7) = _v(j,2); + } else { + if (_mask(i) & _deform_vremap) { + _buf(i,5) = _v(j,0) + _pbc[0]*_h_rate[0] + _pbc[5]*_h_rate[5] + _pbc[4]*_h_rate[4]; + _buf(i,6) = _v(j,1) + _pbc[1]*_h_rate[1] + _pbc[3]*_h_rate[3]; + _buf(i,7) = _v(j,2) + _pbc[2]*_h_rate[2]; + } else { + _buf(i,5) = _v(j,0); + _buf(i,6) = _v(j,1); + _buf(i,7) = _v(j,2); + } + } + _buf(i,8) = _omega(j,0); + _buf(i,9) = _omega(j,1); + _buf(i,10) = _omega(j,2); + } +}; + +/* ---------------------------------------------------------------------- */ + +int AtomVecSphereKokkos::pack_comm_vel_kokkos( + const int &n, + const DAT::tdual_int_2d &list, + const int & iswap, + const DAT::tdual_xfloat_2d &buf, + const int &pbc_flag, + const int* const pbc) +{ + if(commKK->forward_comm_on_host) { + sync(Host,X_MASK|RADIUS_MASK|RMASS_MASK|V_MASK|OMEGA_MASK); + if(pbc_flag) { + if(deform_vremap) { + if(domain->triclinic) { + struct AtomVecSphereKokkos_PackCommVel f( + atomKK->k_x,atomKK->k_mask, + atomKK->k_radius,atomKK->k_rmass, + atomKK->k_v,atomKK->k_omega, + buf,list,iswap, + domain->xprd,domain->yprd,domain->zprd, + domain->xy,domain->xz,domain->yz,pbc,h_rate,deform_vremap); + Kokkos::parallel_for(n,f); + } else { + struct AtomVecSphereKokkos_PackCommVel f( + atomKK->k_x,atomKK->k_mask, + atomKK->k_radius,atomKK->k_rmass, + atomKK->k_v,atomKK->k_omega, + buf,list,iswap, + domain->xprd,domain->yprd,domain->zprd, + domain->xy,domain->xz,domain->yz,pbc,h_rate,deform_vremap); + Kokkos::parallel_for(n,f); + } + } else { + if(domain->triclinic) { + struct AtomVecSphereKokkos_PackCommVel f( + atomKK->k_x,atomKK->k_mask, + atomKK->k_radius,atomKK->k_rmass, + atomKK->k_v,atomKK->k_omega, + buf,list,iswap, + domain->xprd,domain->yprd,domain->zprd, + domain->xy,domain->xz,domain->yz,pbc,h_rate,deform_vremap); + Kokkos::parallel_for(n,f); + } else { + struct AtomVecSphereKokkos_PackCommVel f( + atomKK->k_x,atomKK->k_mask, + atomKK->k_radius,atomKK->k_rmass, + atomKK->k_v,atomKK->k_omega, + buf,list,iswap, + domain->xprd,domain->yprd,domain->zprd, + domain->xy,domain->xz,domain->yz,pbc,h_rate,deform_vremap); + Kokkos::parallel_for(n,f); + } + } + } else { + if(domain->triclinic) { + struct AtomVecSphereKokkos_PackCommVel f( + atomKK->k_x,atomKK->k_mask, + atomKK->k_radius,atomKK->k_rmass, + atomKK->k_v,atomKK->k_omega, + buf,list,iswap, + domain->xprd,domain->yprd,domain->zprd, + domain->xy,domain->xz,domain->yz,pbc,h_rate,deform_vremap); + Kokkos::parallel_for(n,f); + } else { + struct AtomVecSphereKokkos_PackCommVel f( + atomKK->k_x,atomKK->k_mask, + atomKK->k_radius,atomKK->k_rmass, + atomKK->k_v,atomKK->k_omega, + buf,list,iswap, + domain->xprd,domain->yprd,domain->zprd, + domain->xy,domain->xz,domain->yz,pbc,h_rate,deform_vremap); + Kokkos::parallel_for(n,f); + } + } + } else { + sync(Device,X_MASK|RADIUS_MASK|RMASS_MASK|V_MASK|OMEGA_MASK); + if(pbc_flag) { + if(deform_vremap) { + if(domain->triclinic) { + struct AtomVecSphereKokkos_PackCommVel f( + atomKK->k_x,atomKK->k_mask, + atomKK->k_radius,atomKK->k_rmass, + atomKK->k_v,atomKK->k_omega, + buf,list,iswap, + domain->xprd,domain->yprd,domain->zprd, + domain->xy,domain->xz,domain->yz,pbc,h_rate,deform_vremap); + Kokkos::parallel_for(n,f); + } else { + struct AtomVecSphereKokkos_PackCommVel f( + atomKK->k_x,atomKK->k_mask, + atomKK->k_radius,atomKK->k_rmass, + atomKK->k_v,atomKK->k_omega, + buf,list,iswap, + domain->xprd,domain->yprd,domain->zprd, + domain->xy,domain->xz,domain->yz,pbc,h_rate,deform_vremap); + Kokkos::parallel_for(n,f); + } + } else { + if(domain->triclinic) { + struct AtomVecSphereKokkos_PackCommVel f( + atomKK->k_x,atomKK->k_mask, + atomKK->k_radius,atomKK->k_rmass, + atomKK->k_v,atomKK->k_omega, + buf,list,iswap, + domain->xprd,domain->yprd,domain->zprd, + domain->xy,domain->xz,domain->yz,pbc,h_rate,deform_vremap); + Kokkos::parallel_for(n,f); + } else { + struct AtomVecSphereKokkos_PackCommVel f( + atomKK->k_x,atomKK->k_mask, + atomKK->k_radius,atomKK->k_rmass, + atomKK->k_v,atomKK->k_omega, + buf,list,iswap, + domain->xprd,domain->yprd,domain->zprd, + domain->xy,domain->xz,domain->yz,pbc,h_rate,deform_vremap); + Kokkos::parallel_for(n,f); + } + } + } else { + if(domain->triclinic) { + struct AtomVecSphereKokkos_PackCommVel f( + atomKK->k_x,atomKK->k_mask, + atomKK->k_radius,atomKK->k_rmass, + atomKK->k_v,atomKK->k_omega, + buf,list,iswap, + domain->xprd,domain->yprd,domain->zprd, + domain->xy,domain->xz,domain->yz,pbc,h_rate,deform_vremap); + Kokkos::parallel_for(n,f); + } else { + struct AtomVecSphereKokkos_PackCommVel f( + atomKK->k_x,atomKK->k_mask, + atomKK->k_radius,atomKK->k_rmass, + atomKK->k_v,atomKK->k_omega, + buf,list,iswap, + domain->xprd,domain->yprd,domain->zprd, + domain->xy,domain->xz,domain->yz,pbc,h_rate,deform_vremap); + Kokkos::parallel_for(n,f); + } + } + } + return n*11; +} + +/* ---------------------------------------------------------------------- */ + template struct AtomVecSphereKokkos_PackCommSelf { typedef DeviceType device_type; @@ -416,7 +653,7 @@ struct AtomVecSphereKokkos_PackCommSelf { /* ---------------------------------------------------------------------- */ int AtomVecSphereKokkos::pack_comm_self( - const int &n, const DAT::tdual_int_2d &list, const int & iswap, + const int &n, const DAT::tdual_int_2d &list, const int &iswap, const int nfirst, const int &pbc_flag, const int* const pbc) { // Fallback to AtomVecKokkos if radvary == 0 if (radvary == 0) @@ -513,7 +750,7 @@ struct AtomVecSphereKokkos_UnpackComm { typename ArrayTypes::t_x_array _x; typename ArrayTypes::t_float_1d _radius,_rmass; - typename ArrayTypes::t_xfloat_2d_const _buf; + typename ArrayTypes::t_xfloat_2d_const_um _buf; int _first; AtomVecSphereKokkos_UnpackComm( @@ -525,8 +762,12 @@ struct AtomVecSphereKokkos_UnpackComm { _x(x.view()), _radius(radius.view()), _rmass(rmass.view()), - _buf(buf.view()), - _first(first) {}; + _first(first) + { + const size_t elements = 5; + const size_t maxsend = (buf.view().extent(0)*buf.view().extent(1))/elements; + _buf = typename ArrayTypes::t_xfloat_2d_const_um(buf.view().data(),maxsend,elements); + }; KOKKOS_INLINE_FUNCTION void operator() (const int& i) const { @@ -567,6 +808,78 @@ void AtomVecSphereKokkos::unpack_comm_kokkos( /* ---------------------------------------------------------------------- */ +template +struct AtomVecSphereKokkos_UnpackCommVel { + typedef DeviceType device_type; + + typename ArrayTypes::t_x_array _x; + typename ArrayTypes::t_float_1d _radius,_rmass; + typename ArrayTypes::t_v_array _v, _omega; + typename ArrayTypes::t_xfloat_2d_const _buf; + int _first; + + AtomVecSphereKokkos_UnpackCommVel( + const typename DAT::tdual_x_array &x, + const typename DAT::tdual_float_1d &radius, + const typename DAT::tdual_float_1d &rmass, + const typename DAT::tdual_v_array &v, + const typename DAT::tdual_v_array &omega, + const typename DAT::tdual_xfloat_2d &buf, + const int& first): + _x(x.view()), + _radius(radius.view()), + _rmass(rmass.view()), + _v(v.view()), + _omega(omega.view()), + _first(first) + { + const size_t elements = 11; + const int maxsend = (buf.template view().extent(0)*buf.template view().extent(1))/elements; + buffer_view(_buf,buf,maxsend,elements); + }; + + KOKKOS_INLINE_FUNCTION + void operator() (const int& i) const { + _x(i+_first,0) = _buf(i,0); + _x(i+_first,1) = _buf(i,1); + _x(i+_first,2) = _buf(i,2); + _radius(i+_first) = _buf(i,3); + _rmass(i+_first) = _buf(i,4); + _v(i+_first,0) = _buf(i,5); + _v(i+_first,1) = _buf(i,6); + _v(i+_first,2) = _buf(i,7); + _omega(i+_first,0) = _buf(i,8); + _omega(i+_first,1) = _buf(i,9); + _omega(i+_first,2) = _buf(i,10); + } +}; + +/* ---------------------------------------------------------------------- */ + +void AtomVecSphereKokkos::unpack_comm_vel_kokkos( + const int &n, const int &first, + const DAT::tdual_xfloat_2d &buf ) { + if(commKK->forward_comm_on_host) { + modified(Host,X_MASK|RADIUS_MASK|RMASS_MASK|V_MASK|OMEGA_MASK); + struct AtomVecSphereKokkos_UnpackCommVel f( + atomKK->k_x, + atomKK->k_radius,atomKK->k_rmass, + atomKK->k_v,atomKK->k_omega, + buf,first); + Kokkos::parallel_for(n,f); + } else { + modified(Device,X_MASK|RADIUS_MASK|RMASS_MASK|V_MASK|OMEGA_MASK); + struct AtomVecSphereKokkos_UnpackCommVel f( + atomKK->k_x, + atomKK->k_radius,atomKK->k_rmass, + atomKK->k_v,atomKK->k_omega, + buf,first); + Kokkos::parallel_for(n,f); + } +} + +/* ---------------------------------------------------------------------- */ + int AtomVecSphereKokkos::pack_comm(int n, int *list, double *buf, int pbc_flag, int *pbc) { @@ -708,7 +1021,6 @@ int AtomVecSphereKokkos::pack_comm_vel(int n, int *list, double *buf, } } } - } else { sync(Host,X_MASK|RADIUS_MASK|RMASS_MASK|V_MASK|OMEGA_MASK); m = 0; @@ -963,7 +1275,7 @@ template struct AtomVecSphereKokkos_PackBorder { typedef DeviceType device_type; - typename ArrayTypes::t_xfloat_2d _buf; + typename ArrayTypes::t_xfloat_2d_um _buf; const typename ArrayTypes::t_int_2d_const _list; const int _iswap; const typename ArrayTypes::t_x_array_randomread _x; @@ -973,21 +1285,27 @@ struct AtomVecSphereKokkos_PackBorder { typename ArrayTypes::t_float_1d _radius,_rmass; X_FLOAT _dx,_dy,_dz; - AtomVecSphereKokkos_PackBorder(const typename ArrayTypes::t_xfloat_2d &buf, - const typename ArrayTypes::t_int_2d_const &list, - const int & iswap, - const typename ArrayTypes::t_x_array &x, - const typename ArrayTypes::t_tagint_1d &tag, - const typename ArrayTypes::t_int_1d &type, - const typename ArrayTypes::t_int_1d &mask, - const typename ArrayTypes::t_float_1d &radius, - const typename ArrayTypes::t_float_1d &rmass, - const X_FLOAT &dx, const X_FLOAT &dy, const X_FLOAT &dz): - _buf(buf),_list(list),_iswap(iswap), + AtomVecSphereKokkos_PackBorder( + const typename ArrayTypes::t_xfloat_2d &buf, + const typename ArrayTypes::t_int_2d_const &list, + const int &iswap, + const typename ArrayTypes::t_x_array &x, + const typename ArrayTypes::t_tagint_1d &tag, + const typename ArrayTypes::t_int_1d &type, + const typename ArrayTypes::t_int_1d &mask, + const typename ArrayTypes::t_float_1d &radius, + const typename ArrayTypes::t_float_1d &rmass, + const X_FLOAT &dx, const X_FLOAT &dy, const X_FLOAT &dz): + _list(list),_iswap(iswap), _x(x),_tag(tag),_type(type),_mask(mask), _radius(radius), _rmass(rmass), - _dx(dx),_dy(dy),_dz(dz) {} + _dx(dx),_dy(dy),_dz(dz) + { + const size_t elements = 8; + const int maxsend = (buf.extent(0)*buf.extent(1))/elements; + _buf = typename ArrayTypes::t_xfloat_2d_um(buf.data(),maxsend,elements); + } KOKKOS_INLINE_FUNCTION void operator() (const int& i) const { @@ -1011,8 +1329,9 @@ struct AtomVecSphereKokkos_PackBorder { /* ---------------------------------------------------------------------- */ -int AtomVecSphereKokkos::pack_border_kokkos(int n, DAT::tdual_int_2d k_sendlist, DAT::tdual_xfloat_2d buf,int iswap, - int pbc_flag, int *pbc, ExecutionSpace space) +int AtomVecSphereKokkos::pack_border_kokkos( + int n, DAT::tdual_int_2d k_sendlist, DAT::tdual_xfloat_2d buf,int iswap, + int pbc_flag, int *pbc, ExecutionSpace space) { X_FLOAT dx,dy,dz; @@ -1067,8 +1386,9 @@ int AtomVecSphereKokkos::pack_border_kokkos(int n, DAT::tdual_int_2d k_sendlist, /* ---------------------------------------------------------------------- */ -int AtomVecSphereKokkos::pack_border(int n, int *list, double *buf, - int pbc_flag, int *pbc) +int AtomVecSphereKokkos::pack_border( + int n, int *list, double *buf, + int pbc_flag, int *pbc) { int i,j,m; double dx,dy,dz; @@ -1120,8 +1440,182 @@ int AtomVecSphereKokkos::pack_border(int n, int *list, double *buf, /* ---------------------------------------------------------------------- */ +template +struct AtomVecSphereKokkos_PackBorderVel { + typedef DeviceType device_type; + + typename ArrayTypes::t_xfloat_2d_um _buf; + const typename ArrayTypes::t_int_2d_const _list; + const int _iswap; + const typename ArrayTypes::t_x_array_randomread _x; + const typename ArrayTypes::t_tagint_1d _tag; + const typename ArrayTypes::t_int_1d _type; + const typename ArrayTypes::t_int_1d _mask; + typename ArrayTypes::t_float_1d _radius,_rmass; + typename ArrayTypes::t_v_array _v, _omega; + X_FLOAT _dx,_dy,_dz, _dvx, _dvy, _dvz; + const int _deform_groupbit; + + AtomVecSphereKokkos_PackBorderVel( + const typename ArrayTypes::t_xfloat_2d &buf, + const typename ArrayTypes::t_int_2d_const &list, + const int &iswap, + const typename ArrayTypes::t_x_array &x, + const typename ArrayTypes::t_tagint_1d &tag, + const typename ArrayTypes::t_int_1d &type, + const typename ArrayTypes::t_int_1d &mask, + const typename ArrayTypes::t_float_1d &radius, + const typename ArrayTypes::t_float_1d &rmass, + const typename ArrayTypes::t_v_array &v, + const typename ArrayTypes::t_v_array &omega, + const X_FLOAT &dx, const X_FLOAT &dy, const X_FLOAT &dz, + const X_FLOAT &dvx, const X_FLOAT &dvy, const X_FLOAT &dvz, + const int &deform_groupbit): + _buf(buf),_list(list),_iswap(iswap), + _x(x),_tag(tag),_type(type),_mask(mask), + _radius(radius), + _rmass(rmass), + _v(v), _omega(omega), + _dx(dx),_dy(dy),_dz(dz), + _dvx(dvx),_dvy(dvy),_dvz(dvz), + _deform_groupbit(deform_groupbit) + { + const size_t elements = 14; + const int maxsend = (buf.extent(0)*buf.extent(1))/elements; + _buf = typename ArrayTypes::t_xfloat_2d_um(buf.data(),maxsend,elements); + } + + KOKKOS_INLINE_FUNCTION + void operator() (const int& i) const { + const int j = _list(_iswap,i); + if (PBC_FLAG == 0) { + _buf(i,0) = _x(j,0); + _buf(i,1) = _x(j,1); + _buf(i,2) = _x(j,2); + } else { + _buf(i,0) = _x(j,0) + _dx; + _buf(i,1) = _x(j,1) + _dy; + _buf(i,2) = _x(j,2) + _dz; + } + _buf(i,3) = d_ubuf(_tag(j)).d; + _buf(i,4) = d_ubuf(_type(j)).d; + _buf(i,5) = d_ubuf(_mask(j)).d; + _buf(i,6) = _radius(j); + _buf(i,7) = _rmass(j); + if (DEFORM_VREMAP) { + if (_mask(i) & _deform_groupbit) { + _buf(i,8) = _v(j,0) + _dvx; + _buf(i,9) = _v(j,1) + _dvy; + _buf(i,10) = _v(j,2) + _dvz; + } + } + else { + _buf(i,8) = _v(j,0); + _buf(i,9) = _v(j,1); + _buf(i,10) = _v(j,2); + } + _buf(i,11) = _omega(j,0); + _buf(i,12) = _omega(j,1); + _buf(i,13) = _omega(j,2); + } +}; + +/* ---------------------------------------------------------------------- */ + +int AtomVecSphereKokkos::pack_border_vel_kokkos( + int n, DAT::tdual_int_2d k_sendlist, DAT::tdual_xfloat_2d buf,int iswap, + int pbc_flag, int *pbc, ExecutionSpace space) +{ + X_FLOAT dx=0,dy=0,dz=0; + X_FLOAT dvx=0,dvy=0,dvz=0; + + // This was in atom_vec_dpd_kokkos but doesn't appear in any other atom_vec + sync(space,ALL_MASK); + + if (pbc_flag != 0) { + if (domain->triclinic == 0) { + dx = pbc[0]*domain->xprd; + dy = pbc[1]*domain->yprd; + dz = pbc[2]*domain->zprd; + } else { + dx = pbc[0]; + dy = pbc[1]; + dz = pbc[2]; + } + if (!deform_vremap) { + if(space==Host) { + AtomVecSphereKokkos_PackBorderVel f( + buf.view(), k_sendlist.view(), + iswap,h_x,h_tag,h_type,h_mask, + h_radius,h_rmass, + h_v, h_omega, + dx,dy,dz,dvx,dvy,dvz, + deform_groupbit); + Kokkos::parallel_for(n,f); + } else { + AtomVecSphereKokkos_PackBorderVel f( + buf.view(), k_sendlist.view(), + iswap,d_x,d_tag,d_type,d_mask, + d_radius,d_rmass, + d_v, d_omega, + dx,dy,dz,dvx,dvy,dvz, + deform_groupbit); + Kokkos::parallel_for(n,f); + } + } + else { + dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4]; + dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3]; + dvz = pbc[2]*h_rate[2]; + if(space==Host) { + AtomVecSphereKokkos_PackBorderVel f( + buf.view(), k_sendlist.view(), + iswap,h_x,h_tag,h_type,h_mask, + h_radius,h_rmass, + h_v, h_omega, + dx,dy,dz,dvx,dvy,dvz, + deform_groupbit); + Kokkos::parallel_for(n,f); + } else { + AtomVecSphereKokkos_PackBorderVel f( + buf.view(), k_sendlist.view(), + iswap,d_x,d_tag,d_type,d_mask, + d_radius,d_rmass, + d_v, d_omega, + dx,dy,dz,dvx,dvy,dvz, + deform_groupbit); + Kokkos::parallel_for(n,f); + } + } + } else { + if(space==Host) { + AtomVecSphereKokkos_PackBorderVel f( + buf.view(), k_sendlist.view(), + iswap,h_x,h_tag,h_type,h_mask, + h_radius,h_rmass, + h_v, h_omega, + dx,dy,dz,dvx,dvy,dvz, + deform_groupbit); + Kokkos::parallel_for(n,f); + } else { + AtomVecSphereKokkos_PackBorderVel f( + buf.view(), k_sendlist.view(), + iswap,d_x,d_tag,d_type,d_mask, + d_radius,d_rmass, + d_v, d_omega, + dx,dy,dz,dvx,dvy,dvz, + deform_groupbit); + Kokkos::parallel_for(n,f); + } + } + + return n*14; +} + +/* ---------------------------------------------------------------------- */ + int AtomVecSphereKokkos::pack_border_vel(int n, int *list, double *buf, - int pbc_flag, int *pbc) + int pbc_flag, int *pbc) { int i,j,m; double dx,dy,dz,dvx,dvy,dvz; @@ -1233,7 +1727,7 @@ template struct AtomVecSphereKokkos_UnpackBorder { typedef DeviceType device_type; - const typename ArrayTypes::t_xfloat_2d_const _buf; + typename ArrayTypes::t_xfloat_2d_const_um _buf; typename ArrayTypes::t_x_array _x; typename ArrayTypes::t_tagint_1d _tag; typename ArrayTypes::t_int_1d _type; @@ -1242,18 +1736,23 @@ struct AtomVecSphereKokkos_UnpackBorder { int _first; AtomVecSphereKokkos_UnpackBorder( - const typename ArrayTypes::t_xfloat_2d_const &buf, - typename ArrayTypes::t_x_array &x, - typename ArrayTypes::t_tagint_1d &tag, - typename ArrayTypes::t_int_1d &type, - typename ArrayTypes::t_int_1d &mask, + const typename ArrayTypes::t_xfloat_2d &buf, + const typename ArrayTypes::t_x_array &x, + const typename ArrayTypes::t_tagint_1d &tag, + const typename ArrayTypes::t_int_1d &type, + const typename ArrayTypes::t_int_1d &mask, const typename ArrayTypes::t_float_1d &radius, const typename ArrayTypes::t_float_1d &rmass, const int& first): _buf(buf),_x(x),_tag(tag),_type(type),_mask(mask), _radius(radius), _rmass(rmass), - _first(first) {}; + _first(first) + { + const size_t elements = 8; + const int maxsend = (buf.extent(0)*buf.extent(1))/elements; + _buf = typename ArrayTypes::t_xfloat_2d_const_um(buf.data(),maxsend,elements); + }; KOKKOS_INLINE_FUNCTION void operator() (const int& i) const { @@ -1318,6 +1817,89 @@ void AtomVecSphereKokkos::unpack_border(int n, int first, double *buf) } +/* ---------------------------------------------------------------------- */ + +template +struct AtomVecSphereKokkos_UnpackBorderVel { + typedef DeviceType device_type; + + typename ArrayTypes::t_xfloat_2d_const_um _buf; + typename ArrayTypes::t_x_array _x; + typename ArrayTypes::t_tagint_1d _tag; + typename ArrayTypes::t_int_1d _type; + typename ArrayTypes::t_int_1d _mask; + typename ArrayTypes::t_float_1d _radius,_rmass; + typename ArrayTypes::t_v_array _v; + typename ArrayTypes::t_v_array _omega; + int _first; + + AtomVecSphereKokkos_UnpackBorderVel( + const typename ArrayTypes::t_xfloat_2d_const &buf, + const typename ArrayTypes::t_x_array &x, + const typename ArrayTypes::t_tagint_1d &tag, + const typename ArrayTypes::t_int_1d &type, + const typename ArrayTypes::t_int_1d &mask, + const typename ArrayTypes::t_float_1d &radius, + const typename ArrayTypes::t_float_1d &rmass, + const typename ArrayTypes::t_v_array &v, + const typename ArrayTypes::t_v_array &omega, + const int& first): + _buf(buf),_x(x),_tag(tag),_type(type),_mask(mask), + _radius(radius), + _rmass(rmass), + _v(v), _omega(omega), + _first(first) + { + const size_t elements = 14; + const int maxsend = (buf.extent(0)*buf.extent(1))/elements; + _buf = typename ArrayTypes::t_xfloat_2d_const_um(buf.data(),maxsend,elements); + }; + + KOKKOS_INLINE_FUNCTION + void operator() (const int& i) const { + _x(i+_first,0) = _buf(i,0); + _x(i+_first,1) = _buf(i,1); + _x(i+_first,2) = _buf(i,2); + _tag(i+_first) = static_cast (d_ubuf(_buf(i,3)).i); + _type(i+_first) = static_cast (d_ubuf(_buf(i,4)).i); + _mask(i+_first) = static_cast (d_ubuf(_buf(i,5)).i); + _radius(i+_first) = _buf(i,6); + _rmass(i+_first) = _buf(i,7); + _v(i+_first,0) = _buf(i,8); + _v(i+_first,1) = _buf(i,9); + _v(i+_first,2) = _buf(i,10); + _omega(i+_first,0) = _buf(i,11); + _omega(i+_first,1) = _buf(i,12); + _omega(i+_first,2) = _buf(i,13); + } +}; + +/* ---------------------------------------------------------------------- */ + +void AtomVecSphereKokkos::unpack_border_vel_kokkos( + const int &n, const int &first, + const DAT::tdual_xfloat_2d &buf,ExecutionSpace space) { + while (first+n >= nmax) grow(0); + if(space==Host) { + struct AtomVecSphereKokkos_UnpackBorderVel f(buf.view(), + h_x,h_tag,h_type,h_mask, + h_radius,h_rmass, + h_v, h_omega, + first); + Kokkos::parallel_for(n,f); + } else { + struct AtomVecSphereKokkos_UnpackBorderVel f(buf.view(), + d_x,d_tag,d_type,d_mask, + d_radius,d_rmass, + d_v, d_omega, + first); + Kokkos::parallel_for(n,f); + } + + modified(space,X_MASK|TAG_MASK|TYPE_MASK|MASK_MASK| + RADIUS_MASK|RMASS_MASK|V_MASK|OMEGA_MASK); +} + /* ---------------------------------------------------------------------- */ void AtomVecSphereKokkos::unpack_border_vel(int n, int first, double *buf) @@ -1418,11 +2000,12 @@ struct AtomVecSphereKokkos_PackExchangeFunctor { _sendlist(sendlist.template view()), _copylist(copylist.template view()), _nlocal(nlocal),_dim(dim), - _lo(lo),_hi(hi){ + _lo(lo),_hi(hi) + { const size_t elements = 16; - const int maxsendlist = (buf.template view().extent(0)*buf.template view().extent(1))/elements; + const int maxsend = (buf.template view().extent(0)*buf.template view().extent(1))/elements; - buffer_view(_buf,buf,maxsendlist,elements); + _buf = typename AT::t_xfloat_2d_um(buf.template view().data(),maxsend,elements); } KOKKOS_INLINE_FUNCTION @@ -1468,7 +2051,12 @@ struct AtomVecSphereKokkos_PackExchangeFunctor { /* ---------------------------------------------------------------------- */ -int AtomVecSphereKokkos::pack_exchange_kokkos(const int &nsend,DAT::tdual_xfloat_2d &k_buf, DAT::tdual_int_1d k_sendlist,DAT::tdual_int_1d k_copylist,ExecutionSpace space,int dim,X_FLOAT lo,X_FLOAT hi ) +int AtomVecSphereKokkos::pack_exchange_kokkos( + const int &nsend, + DAT::tdual_xfloat_2d &k_buf, + DAT::tdual_int_1d k_sendlist, + DAT::tdual_int_1d k_copylist, + ExecutionSpace space,int dim,X_FLOAT lo,X_FLOAT hi) { if(nsend > (int) (k_buf.view().extent(0)*k_buf.view().extent(1))/16) { int newsize = nsend*17/k_buf.view().extent(1)+1; @@ -1561,7 +2149,8 @@ struct AtomVecSphereKokkos_UnpackExchangeFunctor { _rmass(atom->k_rmass.view()), _omega(atom->k_omega.view()), _nlocal(nlocal.template view()),_dim(dim), - _lo(lo),_hi(hi){ + _lo(lo),_hi(hi) + { const size_t elements = 16; const int maxsendlist = (buf.template view().extent(0)*buf.template view().extent(1))/elements; diff --git a/src/KOKKOS/atom_vec_sphere_kokkos.h b/src/KOKKOS/atom_vec_sphere_kokkos.h index d6739cb714..d9fc061ada 100644 --- a/src/KOKKOS/atom_vec_sphere_kokkos.h +++ b/src/KOKKOS/atom_vec_sphere_kokkos.h @@ -75,6 +75,12 @@ class AtomVecSphereKokkos : public AtomVecKokkos { const int &pbc_flag, const int pbc[]); void unpack_comm_kokkos(const int &n, const int &nfirst, const DAT::tdual_xfloat_2d &buf); + int pack_comm_vel_kokkos(const int &n, const DAT::tdual_int_2d &k_sendlist, + const int & iswap, + const DAT::tdual_xfloat_2d &buf, + const int &pbc_flag, const int pbc[]); + void unpack_comm_vel_kokkos(const int &n, const int &nfirst, + const DAT::tdual_xfloat_2d &buf); int pack_comm_self(const int &n, const DAT::tdual_int_2d &list, const int & iswap, const int nfirst, const int &pbc_flag, const int pbc[]); @@ -84,6 +90,12 @@ class AtomVecSphereKokkos : public AtomVecKokkos { void unpack_border_kokkos(const int &n, const int &nfirst, const DAT::tdual_xfloat_2d &buf, ExecutionSpace space); + int pack_border_vel_kokkos(int n, DAT::tdual_int_2d k_sendlist, + DAT::tdual_xfloat_2d buf,int iswap, + int pbc_flag, int *pbc, ExecutionSpace space); + void unpack_border_vel_kokkos(const int &n, const int &nfirst, + const DAT::tdual_xfloat_2d &buf, + ExecutionSpace space); int pack_exchange_kokkos(const int &nsend,DAT::tdual_xfloat_2d &buf, DAT::tdual_int_1d k_sendlist, DAT::tdual_int_1d k_copylist, diff --git a/src/KOKKOS/comm_kokkos.cpp b/src/KOKKOS/comm_kokkos.cpp index d00d766318..f6256275fb 100644 --- a/src/KOKKOS/comm_kokkos.cpp +++ b/src/KOKKOS/comm_kokkos.cpp @@ -134,9 +134,6 @@ void CommKokkos::init() if (force->newton == 0) check_reverse = 0; if (force->pair) check_reverse += force->pair->comm_reverse_off; - if (ghost_velocity) - forward_comm_classic = true; - if (!comm_f_only) // not all Kokkos atom_vec styles have reverse pack/unpack routines yet reverse_comm_classic = true; } @@ -191,10 +188,10 @@ void CommKokkos::forward_comm_device(int dummy) if (sendproc[iswap] != me) { if (comm_x_only) { if (size_forward_recv[iswap]) { - buf = atomKK->k_x.view().data() + - firstrecv[iswap]*atomKK->k_x.view().extent(1); - MPI_Irecv(buf,size_forward_recv[iswap],MPI_DOUBLE, - recvproc[iswap],0,world,&request); + buf = atomKK->k_x.view().data() + + firstrecv[iswap]*atomKK->k_x.view().extent(1); + MPI_Irecv(buf,size_forward_recv[iswap],MPI_DOUBLE, + recvproc[iswap],0,world,&request); } n = avec->pack_comm_kokkos(sendnum[iswap],k_sendlist, iswap,k_buf_send,pbc_flag[iswap],pbc[iswap]); @@ -210,17 +207,21 @@ void CommKokkos::forward_comm_device(int dummy) space,X_MASK); } } else if (ghost_velocity) { - error->all(FLERR,"Ghost velocity forward comm not yet " - "implemented with Kokkos"); - if (size_forward_recv[iswap]) - MPI_Irecv(k_buf_recv.view().data(), + if (size_forward_recv[iswap]) { + MPI_Irecv(k_buf_recv.view().data(), size_forward_recv[iswap],MPI_DOUBLE, recvproc[iswap],0,world,&request); - n = avec->pack_comm_vel(sendnum[iswap],sendlist[iswap], - buf_send,pbc_flag[iswap],pbc[iswap]); - if (n) MPI_Send(buf_send,n,MPI_DOUBLE,sendproc[iswap],0,world); + } + n = avec->pack_comm_vel_kokkos(sendnum[iswap],k_sendlist,iswap, + k_buf_send,pbc_flag[iswap],pbc[iswap]); + DeviceType::fence(); + if (n) { + MPI_Send(k_buf_send.view().data(),n, + MPI_DOUBLE,sendproc[iswap],0,world); + } if (size_forward_recv[iswap]) MPI_Wait(&request,MPI_STATUS_IGNORE); - avec->unpack_comm_vel(recvnum[iswap],firstrecv[iswap],buf_recv); + avec->unpack_comm_vel_kokkos(recvnum[iswap],firstrecv[iswap],k_buf_recv); + DeviceType::fence(); } else { if (size_forward_recv[iswap]) MPI_Irecv(k_buf_recv.view().data(), @@ -236,18 +237,18 @@ void CommKokkos::forward_comm_device(int dummy) avec->unpack_comm_kokkos(recvnum[iswap],firstrecv[iswap],k_buf_recv); DeviceType::fence(); } - } else { if (!ghost_velocity) { if (sendnum[iswap]) n = avec->pack_comm_self(sendnum[iswap],k_sendlist,iswap, firstrecv[iswap],pbc_flag[iswap],pbc[iswap]); - } else if (ghost_velocity) { - error->all(FLERR,"Ghost velocity forward comm not yet " - "implemented with Kokkos"); - n = avec->pack_comm_vel(sendnum[iswap],sendlist[iswap], - buf_send,pbc_flag[iswap],pbc[iswap]); - avec->unpack_comm_vel(recvnum[iswap],firstrecv[iswap],buf_send); + DeviceType::fence(); + } else { + n = avec->pack_comm_vel_kokkos(sendnum[iswap],k_sendlist,iswap, + k_buf_send,pbc_flag[iswap],pbc[iswap]); + DeviceType::fence(); + avec->unpack_comm_vel_kokkos(recvnum[iswap],firstrecv[iswap],k_buf_send); + DeviceType::fence(); } } } @@ -613,10 +614,9 @@ void CommKokkos::exchange_device() nsend = avec->pack_exchange_kokkos(k_count.h_view(),k_buf_send, k_exchange_sendlist,k_exchange_copylist, - ExecutionSpaceFromDevice:: - space,dim,lo,hi); + ExecutionSpaceFromDevice::space, + dim,lo,hi); DeviceType::fence(); - } else { while (i < nlocal) { if (x[i][dim] < lo || x[i][dim] >= hi) { @@ -707,7 +707,7 @@ void CommKokkos::borders() if (!exchange_comm_classic) { static int print = 1; - if (mode != Comm::SINGLE || bordergroup || ghost_velocity) { + if (mode != Comm::SINGLE || bordergroup) { if (print && comm->me==0) { error->warning(FLERR,"Required border comm not yet implemented in Kokkos communication, " "switching to classic communication"); @@ -929,10 +929,10 @@ void CommKokkos::borders_device() { if (nsend*size_border > maxsend) grow_send_kokkos(nsend*size_border,0); if (ghost_velocity) { - error->all(FLERR,"Required border comm not yet " - "implemented with Kokkos"); - n = avec->pack_border_vel(nsend,sendlist[iswap],buf_send, - pbc_flag[iswap],pbc[iswap]); + n = avec-> + pack_border_vel_kokkos(nsend,k_sendlist,k_buf_send,iswap, + pbc_flag[iswap],pbc[iswap],exec_space); + DeviceType::fence(); } else { n = avec-> @@ -965,11 +965,16 @@ void CommKokkos::borders_device() { // unpack buffer if (ghost_velocity) { - error->all(FLERR,"Required border comm not yet " - "implemented with Kokkos"); - avec->unpack_border_vel(nrecv,atom->nlocal+atom->nghost,buf); - } - else + if (sendproc[iswap] != me) { + avec->unpack_border_vel_kokkos(nrecv,atom->nlocal+atom->nghost, + k_buf_recv,exec_space); + DeviceType::fence(); + } else { + avec->unpack_border_vel_kokkos(nrecv,atom->nlocal+atom->nghost, + k_buf_send,exec_space); + DeviceType::fence(); + } + } else { if (sendproc[iswap] != me) { avec->unpack_border_kokkos(nrecv,atom->nlocal+atom->nghost, k_buf_recv,exec_space); @@ -979,7 +984,7 @@ void CommKokkos::borders_device() { k_buf_send,exec_space); DeviceType::fence(); } - + } // set all pointers & counters smax = MAX(smax,nsend); @@ -1046,12 +1051,22 @@ void CommKokkos::grow_send_kokkos(int n, int flag, ExecutionSpace space) else k_buf_send.modify(); - k_buf_send.resize(maxsend_border,atom->avec->size_border); + if (ghost_velocity) + k_buf_send.resize(maxsend_border, + atom->avec->size_border + atom->avec->size_velocity); + else + k_buf_send.resize(maxsend_border,atom->avec->size_border); buf_send = k_buf_send.view().data(); } else { - k_buf_send = DAT:: - tdual_xfloat_2d("comm:k_buf_send",maxsend_border,atom->avec->size_border); + if (ghost_velocity) + k_buf_send = DAT:: + tdual_xfloat_2d("comm:k_buf_send", + maxsend_border, + atom->avec->size_border + atom->avec->size_velocity); + else + k_buf_send = DAT:: + tdual_xfloat_2d("comm:k_buf_send",maxsend_border,atom->avec->size_border); buf_send = k_buf_send.view().data(); } } From e0fc050bf40563d69c1b1fa71e9c204ed02c618b Mon Sep 17 00:00:00 2001 From: Stefan Paquay Date: Mon, 20 Aug 2018 15:12:05 -0400 Subject: [PATCH 104/302] Changes to linux makefile. --- lib/gpu/Makefile.linux | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/lib/gpu/Makefile.linux b/lib/gpu/Makefile.linux index ed5b6092d3..be103d7f89 100644 --- a/lib/gpu/Makefile.linux +++ b/lib/gpu/Makefile.linux @@ -8,7 +8,7 @@ EXTRAMAKE = Makefile.lammps.standard ifeq ($(CUDA_HOME),) -CUDA_HOME = /usr/local/cuda +CUDA_HOME = /opt/cuda endif NVCC = nvcc @@ -19,7 +19,7 @@ CUDA_ARCH = -arch=sm_21 #CUDA_ARCH = -arch=sm_13 # older CUDA #CUDA_ARCH = -arch=sm_10 -DCUDA_PRE_THREE -CUDA_ARCH = -arch=sm_35 +CUDA_ARCH = -arch=sm_61 # this setting should match LAMMPS Makefile # one of LAMMPS_SMALLBIG (default), LAMMPS_BIGBIG and LAMMPS_SMALLSMALL From fc7d9ff558482730137755ce86cfd26af1b37f77 Mon Sep 17 00:00:00 2001 From: "Steven J. Plimpton" Date: Tue, 21 Aug 2018 11:12:21 -0600 Subject: [PATCH 105/302] apply PBC to coords passed to scafacos --- src/USER-SCAFACOS/scafacos.cpp | 50 ++++++++++++++++++++++------------ src/USER-SCAFACOS/scafacos.h | 4 +-- 2 files changed, 34 insertions(+), 20 deletions(-) diff --git a/src/USER-SCAFACOS/scafacos.cpp b/src/USER-SCAFACOS/scafacos.cpp index 5832f5b052..23d51b07b8 100644 --- a/src/USER-SCAFACOS/scafacos.cpp +++ b/src/USER-SCAFACOS/scafacos.cpp @@ -101,8 +101,8 @@ void Scafacos::init() if (logfile && me == 0) fprintf(logfile, "Setting up ScaFaCoS with solver %s ...\n",method); - if (!atom->q_flag) error->all(FLERR, - "Kspace style requires atom attribute q"); + if (!atom->q_flag) + error->all(FLERR,"Kspace style requires atom attribute q"); if (domain->dimension == 2) error->all(FLERR,"Cannot use ScaFaCoS with 2d simulation"); @@ -166,15 +166,12 @@ void Scafacos::init() // more useful here, since the parameters should be tuned now if (me == 0) fcs_print_parameters(fcs); } + initialized = 1; } /* ---------------------------------------------------------------------- */ -void Scafacos::setup() {} - -/* ---------------------------------------------------------------------- */ - void Scafacos::compute(int eflag, int vflag) { double **x = atom->x; @@ -209,20 +206,14 @@ void Scafacos::compute(int eflag, int vflag) check_result(result); } - // grow epot & efield if necessary + // grow xpbc, epot, efield if necessary - if (nlocal == 0 && maxatom == 0) { - memory->destroy(epot); - memory->destroy(efield); - maxatom = 1; - memory->create(epot,maxatom,"scafacos:epot"); - memory->create(efield,maxatom,3,"scafacos:efield"); - } - - if (nlocal > maxatom) { + if (nlocal > maxatom || maxatom == 0) { + memory->destroy(xpbc); memory->destroy(epot); memory->destroy(efield); maxatom = atom->nmax; + memory->create(xpbc,3*maxatom,"scafacos:xpbc"); memory->create(epot,maxatom,"scafacos:epot"); memory->create(efield,maxatom,3,"scafacos:efield"); } @@ -231,12 +222,27 @@ void Scafacos::compute(int eflag, int vflag) { fcs_set_compute_virial(fcs,1); if (strcmp(method,"p3m") == 0) - error->all(FLERR,"ScaFaCoS p3m does not support the computation of virial"); + error->all(FLERR,"ScaFaCoS p3m does not support computation of virial"); } - result = fcs_run(fcs,nlocal,&x[0][0],q,&efield[0][0],epot); + // pack coords into xpbc and apply PBC + + double **x = atom->x; + memcpy(xpbc,&x[0][0],3*nlocal*sizeof(double)); + + int j = 0; + for (int i = 0; i < nlocal; i++) { + domain->remap(&xpbc[j]); + j += 3; + } + + // invoke ScaFaCoS solver + + result = fcs_run(fcs,nlocal,xpbc,q,&efield[0][0],epot); check_result(result); + // extract virial + if (vflag_global) { fcs_get_virial(fcs,virial_int); @@ -272,6 +278,14 @@ void Scafacos::compute(int eflag, int vflag) MPI_Allreduce(&myeng,&energy,1,MPI_DOUBLE,MPI_SUM,world); } +/* ---------------------------------------------------------------------- + pack local coords into xpbc, enforcing PBC +------------------------------------------------------------------------- */ + +void Scafacos::pack_coords() +{ +} + /* ---------------------------------------------------------------------- */ int Scafacos::modify_param(int narg, char **arg) diff --git a/src/USER-SCAFACOS/scafacos.h b/src/USER-SCAFACOS/scafacos.h index 8f7c46dc6b..bf07b3b45a 100644 --- a/src/USER-SCAFACOS/scafacos.h +++ b/src/USER-SCAFACOS/scafacos.h @@ -30,7 +30,7 @@ class Scafacos : public KSpace { Scafacos(class LAMMPS *, int, char **); ~Scafacos(); void init(); - void setup(); + void setup() {} void compute(int, int); int modify_param(int, char **); double memory_usage(); @@ -40,7 +40,7 @@ class Scafacos : public KSpace { char *method; double tolerance; - double *epot,**efield; + double *xpbc,*epot,**efield; int tolerance_type; int initialized,maxatom; From 3573970e4a168c409d3cef2a6c6c3008504c6043 Mon Sep 17 00:00:00 2001 From: Rene Halver Date: Tue, 21 Aug 2018 17:04:52 -0600 Subject: [PATCH 106/302] fixed double definition, removed virial check for p3m and removed unused function definition Scafacos::pack... --- src/USER-SCAFACOS/scafacos.cpp | 29 ++++++++++------------------- 1 file changed, 10 insertions(+), 19 deletions(-) diff --git a/src/USER-SCAFACOS/scafacos.cpp b/src/USER-SCAFACOS/scafacos.cpp index 23d51b07b8..d68d3db323 100644 --- a/src/USER-SCAFACOS/scafacos.cpp +++ b/src/USER-SCAFACOS/scafacos.cpp @@ -198,13 +198,6 @@ void Scafacos::compute(int eflag, int vflag) vflag_global = 0; } - // if simulation box has changed, call fcs_tune() - - if (box_has_changed()) { - setup_handle(); - result = fcs_tune(fcs,nlocal,&x[0][0],q); - check_result(result); - } // grow xpbc, epot, efield if necessary @@ -221,13 +214,11 @@ void Scafacos::compute(int eflag, int vflag) if (vflag_global) { fcs_set_compute_virial(fcs,1); - if (strcmp(method,"p3m") == 0) - error->all(FLERR,"ScaFaCoS p3m does not support computation of virial"); + //if (strcmp(method,"p3m") == 0) + // error->all(FLERR,"ScaFaCoS p3m does not support computation of virial"); } // pack coords into xpbc and apply PBC - - double **x = atom->x; memcpy(xpbc,&x[0][0],3*nlocal*sizeof(double)); int j = 0; @@ -236,6 +227,14 @@ void Scafacos::compute(int eflag, int vflag) j += 3; } + // if simulation box has changed, call fcs_tune() + + if (box_has_changed()) { + setup_handle(); + result = fcs_tune(fcs,nlocal,xpbc,q); + check_result(result); + } + // invoke ScaFaCoS solver result = fcs_run(fcs,nlocal,xpbc,q,&efield[0][0],epot); @@ -278,14 +277,6 @@ void Scafacos::compute(int eflag, int vflag) MPI_Allreduce(&myeng,&energy,1,MPI_DOUBLE,MPI_SUM,world); } -/* ---------------------------------------------------------------------- - pack local coords into xpbc, enforcing PBC -------------------------------------------------------------------------- */ - -void Scafacos::pack_coords() -{ -} - /* ---------------------------------------------------------------------- */ int Scafacos::modify_param(int narg, char **arg) From c23534019c5077ef208c3a36b439095e5376f5c6 Mon Sep 17 00:00:00 2001 From: Rene Halver Date: Tue, 21 Aug 2018 17:28:42 -0600 Subject: [PATCH 107/302] fixed typo in example file name --- .../{data.hammersley_shphere => data.hammersley_sphere} | 6 +++--- examples/USER/scafacos/in.scafacos.hsph.direct | 2 +- examples/USER/scafacos/in.scafacos.hsph.fmm | 2 +- examples/USER/scafacos/in.scafacos.hsph.p2nfft | 2 +- 4 files changed, 6 insertions(+), 6 deletions(-) rename examples/USER/scafacos/{data.hammersley_shphere => data.hammersley_sphere} (99%) diff --git a/examples/USER/scafacos/data.hammersley_shphere b/examples/USER/scafacos/data.hammersley_sphere similarity index 99% rename from examples/USER/scafacos/data.hammersley_shphere rename to examples/USER/scafacos/data.hammersley_sphere index e0d067adfb..0d238ebf8f 100644 --- a/examples/USER/scafacos/data.hammersley_shphere +++ b/examples/USER/scafacos/data.hammersley_sphere @@ -4,9 +4,9 @@ LAMMPS Description 1 atom types --50.5 51.5 xlo xhi --50.5 51.5 ylo yhi --50.5 51.5 zlo zhi +-51.5 51.5 xlo xhi +-51.5 51.5 ylo yhi +-51.5 51.5 zlo zhi Masses diff --git a/examples/USER/scafacos/in.scafacos.hsph.direct b/examples/USER/scafacos/in.scafacos.hsph.direct index 60448880ec..3688b5157c 100644 --- a/examples/USER/scafacos/in.scafacos.hsph.direct +++ b/examples/USER/scafacos/in.scafacos.hsph.direct @@ -3,7 +3,7 @@ units lj atom_style charge -read_data data.hammersley_shphere +read_data data.hammersley_sphere change_box all boundary f f f velocity all create 1.5 49893 diff --git a/examples/USER/scafacos/in.scafacos.hsph.fmm b/examples/USER/scafacos/in.scafacos.hsph.fmm index 515809dbde..48a60a4b8b 100644 --- a/examples/USER/scafacos/in.scafacos.hsph.fmm +++ b/examples/USER/scafacos/in.scafacos.hsph.fmm @@ -3,7 +3,7 @@ units lj atom_style charge -read_data data.hammersley_shphere +read_data data.hammersley_sphere change_box all boundary f f f velocity all create 1.5 49893 diff --git a/examples/USER/scafacos/in.scafacos.hsph.p2nfft b/examples/USER/scafacos/in.scafacos.hsph.p2nfft index d690a29e49..a91f8f91c7 100644 --- a/examples/USER/scafacos/in.scafacos.hsph.p2nfft +++ b/examples/USER/scafacos/in.scafacos.hsph.p2nfft @@ -3,7 +3,7 @@ units lj atom_style charge -read_data data.hammersley_shphere +read_data data.hammersley_sphere change_box all boundary f f f velocity all create 1.5 49893 From bfd711ad12e2a6fd56aba5ff69de7efc8d025fcc Mon Sep 17 00:00:00 2001 From: Rene Halver Date: Tue, 21 Aug 2018 17:29:38 -0600 Subject: [PATCH 108/302] fixed missing initialization of xpbc as well as deallocation in constructor --- src/USER-SCAFACOS/scafacos.cpp | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/src/USER-SCAFACOS/scafacos.cpp b/src/USER-SCAFACOS/scafacos.cpp index d68d3db323..f3e8ce64f7 100644 --- a/src/USER-SCAFACOS/scafacos.cpp +++ b/src/USER-SCAFACOS/scafacos.cpp @@ -74,6 +74,7 @@ Scafacos::Scafacos(LAMMPS *lmp, int narg, char **arg) : KSpace(lmp, narg, arg) initialized = 0; maxatom = 0; + xpbc = NULL; epot = NULL; efield = NULL; } @@ -84,6 +85,7 @@ Scafacos::~Scafacos() { delete [] method; + memory->destroy(xpbc); memory->destroy(epot); memory->destroy(efield); @@ -221,10 +223,12 @@ void Scafacos::compute(int eflag, int vflag) // pack coords into xpbc and apply PBC memcpy(xpbc,&x[0][0],3*nlocal*sizeof(double)); - int j = 0; + //int j = 0; for (int i = 0; i < nlocal; i++) { - domain->remap(&xpbc[j]); - j += 3; + if (domain->xperiodic) domain->remap(&xpbc[3*i]); + if (domain->yperiodic) domain->remap(&xpbc[3*i+1]); + if (domain->zperiodic) domain->remap(&xpbc[3*i+2]); + //j += 3; } // if simulation box has changed, call fcs_tune() From f466c6407129641e9e9c29ab57f99f826a68cb53 Mon Sep 17 00:00:00 2001 From: "Steven J. Plimpton" Date: Wed, 22 Aug 2018 09:21:54 -0600 Subject: [PATCH 109/302] enable merge to current GH master --- doc/src/Packages_details.txt | 1544 +++++++--------------------------- 1 file changed, 299 insertions(+), 1245 deletions(-) diff --git a/doc/src/Packages_details.txt b/doc/src/Packages_details.txt index 4bbb235245..892774be38 100644 --- a/doc/src/Packages_details.txt +++ b/doc/src/Packages_details.txt @@ -17,100 +17,97 @@ library it requires. It also gives links to documentation, example scripts, and pictures/movies (if available) that illustrate use of the package. +The majority of packages can be included in a LAMMPS build with a +single setting (-D PGK_NAME for CMake) or command ("make yes-name" for +make). See the "Build package"_Build_package.html doc page for more +info. A few packages may require additional steps; this is indicated +in the descriptions below. The "Build extras"_Build_extras.html doc +page gives those details. + NOTE: To see the complete list of commands a package adds to LAMMPS, you can examine the files in its src directory, e.g. "ls src/GRANULAR". Files with names that start with fix, compute, atom, pair, bond, angle, etc correspond to commands with the same style name as contained in the file name. -"ASPHERE"_#ASPHERE, -"BODY"_#BODY, -"CLASS2"_#CLASS2, -"COLLOID"_#COLLOID, -"COMPRESS"_#COMPRESS, -"CORESHELL"_#CORESHELL, -"DIPOLE"_#DIPOLE, -"GPU"_#GPU, -"GRANULAR"_#GRANULAR, -"KIM"_#KIM, -"KOKKOS"_#KOKKOS, -"KSPACE"_#KSPACE, -"LATTE"_#LATTE, -"MANYBODY"_#MANYBODY, -"MC"_#MC, -"MEAM"_#MEAM, -"MISC"_#MISC, -"MOLECULE"_#MOLECULE, -"MPIIO"_#MPIIO, -"MSCG"_#MSCG, -"OPT"_#OPT, -"PERI"_#PERI, -"POEMS"_#POEMS, -"PYTHON"_#PYTHON, -"QEQ"_#QEQ, -"REAX"_#REAX, -"REPLICA"_#REPLICA, -"RIGID"_#RIGID, -"SHOCK"_#SHOCK, -"SNAP"_#SNAP, -"SPIN"_#SPIN, -"SRD"_#SRD, -"VORONOI"_#VORONOI :tb(c=6,ea=c) +"ASPHERE"_#PKG-ASPHERE, +"BODY"_#PKG-BODY, +"CLASS2"_#PKG-CLASS2, +"COLLOID"_#PKG-COLLOID, +"COMPRESS"_#PKG-COMPRESS, +"CORESHELL"_#PKG-CORESHELL, +"DIPOLE"_#PKG-DIPOLE, +"GPU"_#PKG-GPU, +"GRANULAR"_#PKG-GRANULAR, +"KIM"_#PKG-KIM, +"KOKKOS"_#PKG-KOKKOS, +"KSPACE"_#PKG-KSPACE, +"LATTE"_#PKG-LATTE, +"MANYBODY"_#PKG-MANYBODY, +"MC"_#PKG-MC, +"MEAM"_#PKG-MEAM, +"MISC"_#PKG-MISC, +"MOLECULE"_#PKG-MOLECULE, +"MPIIO"_#PKG-MPIIO, +"MSCG"_#PKG-MSCG, +"OPT"_#PKG-OPT, +"PERI"_#PKG-PERI, +"POEMS"_#PKG-POEMS, +"PYTHON"_#PKG-PYTHON, +"QEQ"_#PKG-QEQ, +"REAX"_#PKG-REAX, +"REPLICA"_#PKG-REPLICA2, +"RIGID"_#PKG-RIGID, +"SHOCK"_#PKG-SHOCK, +"SNAP"_#PKG-SNAP, +"SPIN"_#PKG-SPIN, +"SRD"_#PKG-SRD, +"VORONOI"_#PKG-VORONOI :tb(c=6,ea=c) -"USER-ATC"_#USER-ATC, -"USER-AWPMD"_#USER-AWPMD, -"USER-BOCS"_#USER-BOCS, -"USER-CGDNA"_#USER-CGDNA, -"USER-CGSDK"_#USER-CGSDK, -"USER-COLVARS"_#USER-COLVARS, -"USER-DIFFRACTION"_#USER-DIFFRACTION, -"USER-DPD"_#USER-DPD, -"USER-DRUDE"_#USER-DRUDE, -"USER-EFF"_#USER-EFF, -"USER-FEP"_#USER-FEP, -"USER-H5MD"_#USER-H5MD, -"USER-INTEL"_#USER-INTEL, -"USER-LB"_#USER-LB, -"USER-MANIFOLD"_#USER-MANIFOLD, -"USER-MEAMC"_#USER-MEAMC, -"USER-MESO"_#USER-MESO, -"USER-MGPT"_#USER-MGPT, -"USER-MISC"_#USER-MISC, -"USER-MOFFF"_#USER-MOFFF, -"USER-MOLFILE"_#USER-MOLFILE, -"USER-NETCDF"_#USER-NETCDF, -"USER-OMP"_#USER-OMP, -"USER-PHONON"_#USER-PHONON, -"USER-QMMM"_#USER-QMMM, -"USER-QTB"_#USER-QTB, -"USER-QUIP"_#USER-QUIP, -"USER-REAXC"_#USER-REAXC, -"USER-SCAFACOS"_#USER-SCAFACOS, -"USER-SMD"_#USER-SMD, -"USER-SMTBQ"_#USER-SMTBQ, -"USER-SPH"_#USER-SPH, -"USER-TALLY"_#USER-TALLY, -"USER-UEF"_#USER-UEF, -"USER-VTK"_#USER-VTK :tb(c=6,ea=c) +"USER-ATC"_#PKG-USER-ATC, +"USER-AWPMD"_#PKG-USER-AWPMD, +"USER-BOCS"_#PKG-USER-BOCS, +"USER-CGDNA"_#PKG-USER-CGDNA, +"USER-CGSDK"_#PKG-USER-CGSDK, +"USER-COLVARS"_#PKG-USER-COLVARS, +"USER-DIFFRACTION"_#PKG-USER-DIFFRACTION, +"USER-DPD"_#PKG-USER-DPD, +"USER-DRUDE"_#PKG-USER-DRUDE, +"USER-EFF"_#PKG-USER-EFF, +"USER-FEP"_#PKG-USER-FEP, +"USER-H5MD"_#PKG-USER-H5MD, +"USER-INTEL"_#PKG-USER-INTEL, +"USER-LB"_#PKG-USER-LB, +"USER-MANIFOLD"_#PKG-USER-MANIFOLD, +"USER-MEAMC"_#PKG-USER-MEAMC, +"USER-MESO"_#PKG-USER-MESO, +"USER-MGPT"_#PKG-USER-MGPT, +"USER-MISC"_#PKG-USER-MISC, +"USER-MOFFF"_#PKG-USER-MOFFF, +"USER-MOLFILE"_#PKG-USER-MOLFILE, +"USER-NETCDF"_#PKG-USER-NETCDF, +"USER-OMP"_#PKG-USER-OMP, +"USER-PHONON"_#PKG-USER-PHONON, +"USER-QMMM"_#PKG-USER-QMMM, +"USER-QTB"_#PKG-USER-QTB, +"USER-QUIP"_#PKG-USER-QUIP, +"USER-REAXC"_#PKG-USER-REAXC, +"USER-SMD"_#PKG-USER-SMD, +"USER-SMTBQ"_#PKG-USER-SMTBQ, +"USER-SPH"_#PKG-USER-SPH, +"USER-TALLY"_#PKG-USER-TALLY, +"USER-UEF"_#PKG-USER-UEF, +"USER-VTK"_#PKG-USER-VTK :tb(c=6,ea=c) -:line :line -ASPHERE package :link(ASPHERE),h4 +ASPHERE package :link(PKG-ASPHERE),h4 [Contents:] Computes, time-integration fixes, and pair styles for aspherical particle models including ellipsoids, 2d lines, and 3d triangles. -[Install or un-install:] - -make yes-asphere -make machine :pre - -make no-asphere -make machine :pre - [Supporting info:] src/ASPHERE: filenames -> commands @@ -126,7 +123,7 @@ http://lammps.sandia.gov/movies.html#tri :ul :line -BODY package :link(BODY),h4 +BODY package :link(PKG-BODY),h4 [Contents:] @@ -135,14 +132,6 @@ time-integration fixes, pair styles, as well as the body styles themselves. See the "Howto body"_Howto_body.html doc page for an overview. -[Install or un-install:] - -make yes-body -make machine :pre - -make no-body -make machine :pre - [Supporting info:] src/BODY filenames -> commands @@ -154,21 +143,13 @@ examples/body :ul :line -CLASS2 package :link(CLASS2),h4 +CLASS2 package :link(PKG-CLASS2),h4 [Contents:] Bond, angle, dihedral, improper, and pair styles for the COMPASS CLASS2 molecular force field. -[Install or un-install:] - -make yes-class2 -make machine :pre - -make no-class2 -make machine :pre - [Supporting info:] src/CLASS2: filenames -> commands @@ -180,7 +161,7 @@ src/CLASS2: filenames -> commands :line -COLLOID package :link(COLLOID),h4 +COLLOID package :link(PKG-COLLOID),h4 [Contents:] @@ -193,14 +174,6 @@ simplified approximation to Stokesian dynamics. which were created by Amit Kumar and Michael Bybee from Jonathan Higdon's group at UIUC. -[Install or un-install:] - -make yes-colloid -make machine :pre - -make no-colloid -make machine :pre - [Supporting info:] src/COLLOID: filenames -> commands @@ -215,7 +188,7 @@ examples/srd :ul :line -COMPRESS package :link(COMPRESS),h4 +COMPRESS package :link(PKG-COMPRESS),h4 [Contents:] @@ -227,19 +200,11 @@ available on your system. [Author:] Axel Kohlmeyer (Temple U). -[Install or un-install:] +[Install:] -Note that building with this package assumes you have the zlib -compression library available on your system. The LAMMPS build uses -the settings in the lib/compress/Makefile.lammps file in the -compile/link process. You should only need to edit this file if the -LAMMPS build fails on your system. - -make yes-compress -make machine :pre - -make no-compress -make machine :pre +This package has "specific installation +instructions"_Build_extras.html#gpu on the "Build +extras"_Build_extras.html doc page. [Supporting info:] @@ -253,7 +218,7 @@ lib/compress/README :line -CORESHELL package :link(CORESHELL),h4 +CORESHELL package :link(PKG-CORESHELL),h4 [Contents:] @@ -267,14 +232,6 @@ this package. [Author:] Hendrik Heenen (Technical U of Munich). -[Install or un-install:] - -make yes-coreshell -make machine :pre - -make no-coreshell -make machine :pre - [Supporting info:] src/CORESHELL: filenames -> commands @@ -288,21 +245,13 @@ examples/coreshell :ul :line -DIPOLE package :link(DIPOLE),h4 +DIPOLE package :link(PKG-DIPOLE),h4 [Contents:] An atom style and several pair styles for point dipole models with short-range or long-range interactions. -[Install or un-install:] - -make yes-dipole -make machine :pre - -make no-dipole -make machine :pre - [Supporting info:] src/DIPOLE: filenames -> commands @@ -314,7 +263,7 @@ examples/dipole :ul :line -GPU package :link(GPU),h4 +GPU package :link(PKG-GPU),h4 [Contents:] @@ -326,66 +275,17 @@ and only the CUDA versions are regularly tested. The "Speed gpu"_Speed_gpu.html doc page gives details of what hardware and GPU software is required on your system, and details on how to build and use this package. Its styles can be invoked at run time via the "-sf -gpu" or "-suffix gpu" "command-line -switches"_Section_start.html#start_6. See also the "KOKKOS"_#KOKKOS -package, which has GPU-enabled styles. +gpu" or "-suffix gpu" "command-line switches"_Run_options.html. See +also the "KOKKOS"_#PKG-KOKKOS package, which has GPU-enabled styles. [Authors:] Mike Brown (Intel) while at Sandia and ORNL and Trung Nguyen (Northwestern U) while at ORNL. -[Install or un-install:] +[Install:] -Before building LAMMPS with this package, you must first build the GPU -library in lib/gpu from a set of provided C and CUDA files. You can -do this manually if you prefer; follow the instructions in -lib/gpu/README. Please note, that the GPU library uses MPI calls, so -you have to make certain to use the same MPI library (or the STUBS -library) settings as the main LAMMPS code. That same applies to the --DLAMMPS_BIGBIG, -DLAMMPS_SMALLBIG, or -DLAMMPS_SMALLSMALL define. - -You can also do it in one step from the lammps/src -dir, using a command like these, which simply invoke the -lib/gpu/Install.py script with the specified args: - -make lib-gpu # print help message -make lib-gpu args="-b" # build GPU library with default Makefile.linux -make lib-gpu args="-m xk7 -p single -o xk7.single" # create new Makefile.xk7.single, altered for single-precision -make lib-gpu args="-m mpi -p mixed -b" # build GPU library with mixed precision using settings in Makefile.mpi :pre - -Note that this procedure through the '-m machine' flag starts with one of -the existing Makefile.machine files in lib/gpu. For your convenience, -machine makefiles for "mpi" and "serial" are provided, which have the -same settings as the corresponding machine makefiles in the main LAMMPS -source folder. In addition you can alter 4 important settings in that -Makefile, via the -h, -a, -p, -e switches, and also save a copy of the -new Makefile, if desired: - -CUDA_HOME = where NVIDIA CUDA software is installed on your system -CUDA_ARCH = what GPU hardware you have (see help message for details) -CUDA_PRECISION = precision (double, mixed, single) -EXTRAMAKE = which Makefile.lammps.* file to copy to Makefile.lammps :ul - -If the library build is successful, at least 3 files should be created: -lib/gpu/libgpu.a, lib/gpu/nvc_get_devices, and lib/gpu/Makefile.lammps. -The latter has settings that enable LAMMPS to link with CUDA libraries. -If the settings in Makefile.lammps for your machine are not correct, -the LAMMPS build will fail, and lib/gpu/Makefile.lammps may need to -be edited. - -You can then install/un-install the package and build LAMMPS in the -usual manner: - -make yes-gpu -make machine :pre - -make no-gpu -make machine :pre - -NOTE: If you re-build the GPU library in lib/gpu, you should always -un-install the GPU package, then re-install it and re-build LAMMPS. -This is because the compilation of files in the GPU package use the -library settings from the lib/gpu/Makefile.machine used to build the -GPU library. +This package has "specific installation +instructions"_Build_extras.html#gpu on the "Build +extras"_Build_extras.html doc page. [Supporting info:] @@ -393,16 +293,16 @@ src/GPU: filenames -> commands src/GPU/README lib/gpu/README "Speed packages"_Speed_packages.html -"Speed gpu"_Speed_gpu.html.html -"Section 2.6 -sf gpu"_Section_start.html#start_6 -"Section 2.6 -pk gpu"_Section_start.html#start_6 +"Speed gpu"_Speed_gpu.html +"Section 2.6 -sf gpu"_Run_options.html +"Section 2.6 -pk gpu"_Run_options.html "package gpu"_package.html "Commands all"_Commands_all.html pages (pair,kspace) for styles followed by (g) "Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul :line -GRANULAR package :link(GRANULAR),h4 +GRANULAR package :link(PKG-GRANULAR),h4 [Contents:] @@ -410,14 +310,6 @@ Pair styles and fixes for finite-size granular particles, which interact with each other and boundaries via frictional and dissipative potentials. -[Install or un-install:] - -make yes-granular -make machine :pre - -make no-granular -make machine :pre - [Supporting info:] src/GRANULAR: filenames -> commands @@ -437,7 +329,7 @@ http://lammps.sandia.gov/movies.html#granregion :ul :line -KIM package :link(KIM),h4 +KIM package :link(PKG-KIM),h4 [Contents:] @@ -457,48 +349,11 @@ API which the "pair_style kim"_pair_kim.html command uses. He developed the pair style in collaboration with Valeriu Smirichinski (U Minnesota). -[Install or un-install:] +[Install:] -Before building LAMMPS with this package, you must first download and -build the KIM library and include the KIM models that you want to -use. You can do this manually if you prefer; follow the instructions -in lib/kim/README. You can also do it in one step from the lammps/src -dir, using a command like these, which simply invoke the -lib/kim/Install.py script with the specified args. - -make lib-kim # print help message -make lib-kim args="-b " # (re-)install KIM API lib with only example models -make lib-kim args="-b -a Glue_Ercolessi_Adams_Al__MO_324507536345_001" # ditto plus one model -make lib-kim args="-b -a everything" # install KIM API lib with all models -make lib-kim args="-n -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # add one model or model driver -make lib-kim args="-p /usr/local/kim-api" # use an existing KIM API installation at the provided location -make lib-kim args="-p /usr/local/kim-api -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # ditto but add one model or driver :pre - -Note that in LAMMPS lingo, a KIM model driver is a pair style -(e.g. EAM or Tersoff). A KIM model is a pair style for a particular -element or alloy and set of parameters, e.g. EAM for Cu with a -specific EAM potential file. Also note that installing the KIM API -library with all its models, may take around 30 min to build. Of -course you only need to do that once. - -See the list of KIM model drivers here: -https://openkim.org/kim-items/model-drivers/alphabetical - -See the list of all KIM models here: -https://openkim.org/kim-items/models/by-model-drivers - -See the list of example KIM models included by default here: -https://openkim.org/kim-api on the "What is in the KIM API source -package?" page. - -You can then install/un-install the package and build LAMMPS in the -usual manner: - -make yes-kim -make machine :pre - -make no-kim -make machine :pre +This package has "specific installation +instructions"_Build_extras.html#gpu on the "Build +extras"_Build_extras.html doc page. [Supporting info:] @@ -510,7 +365,7 @@ examples/kim :ul :line -KOKKOS package :link(KOKKOS),h4 +KOKKOS package :link(PKG-KOKKOS),h4 [Contents:] @@ -522,11 +377,16 @@ style name. The "Speed kokkos"_Speed_kokkos.html doc page gives details of what hardware and software is required on your system, and how to build and use this package. Its styles can be invoked at run time via the "-sf kk" or "-suffix kk" "command-line -switches"_Section_start.html#start_6. Also see the "GPU"_#GPU, -"OPT"_#OPT, "USER-INTEL"_#USER-INTEL, and "USER-OMP"_#USER-OMP -packages, which have styles optimized for CPUs, KNLs, and GPUs. +switches"_Run_options.html. Also see the "GPU"_#PKG-GPU, "OPT"_#PKG-OPT, +"USER-INTEL"_#PKG-USER-INTEL, and "USER-OMP"_#PKG-USER-OMP packages, which +have styles optimized for CPUs, KNLs, and GPUs. You must have a C++11 compatible compiler to use this package. +KOKKOS makes extensive use of advanced C++ features, which can +expose compiler bugs, especially when compiling for maximum +performance at high optimization levels. Please see the file +lib/kokkos/README for a list of compilers and their respective +platforms, that are known to work. [Authors:] The KOKKOS package was created primarily by Christian Trott and Stan Moore (Sandia), with contributions from other folks as well. @@ -535,53 +395,11 @@ which was developed by Carter Edwards, Christian Trott, and others at Sandia, and which is included in the LAMMPS distribution in lib/kokkos. -[Install or un-install:] +[Install:] -For the KOKKOS package, you have 3 choices when building. You can -build with either CPU or KNL or GPU support. Each choice requires -additional settings in your Makefile.machine for the KOKKOS_DEVICES -and KOKKOS_ARCH settings. See the src/MAKE/OPTIONS/Makefile.kokkos* -files for examples. - -For multicore CPUs using OpenMP: - -KOKKOS_DEVICES = OpenMP -KOKKOS_ARCH = HSW # HSW = Haswell, SNB = SandyBridge, BDW = Broadwell, etc :pre - -For Intel KNLs using OpenMP: - -KOKKOS_DEVICES = OpenMP -KOKKOS_ARCH = KNL :pre - -For NVIDIA GPUs using CUDA: - -KOKKOS_DEVICES = Cuda -KOKKOS_ARCH = Pascal60,Power8 # P100 hosted by an IBM Power8, etc -KOKKOS_ARCH = Kepler37,Power8 # K80 hosted by an IBM Power8, etc :pre - -For GPUs, you also need these 2 lines in your Makefile.machine before -the CC line is defined, in this case for use with OpenMPI mpicxx. The -2 lines define a nvcc wrapper compiler, which will use nvcc for -compiling CUDA files or use a C++ compiler for non-Kokkos, non-CUDA -files. - -KOKKOS_ABSOLUTE_PATH = $(shell cd $(KOKKOS_PATH); pwd) -export OMPI_CXX = $(KOKKOS_ABSOLUTE_PATH)/config/nvcc_wrapper -CC = mpicxx :pre - -Once you have an appropriate Makefile.machine, you can -install/un-install the package and build LAMMPS in the usual manner. -Note that you cannot build one executable to run on multiple hardware -targets (CPU or KNL or GPU). You need to build LAMMPS once for each -hardware target, to produce a separate executable. Also note that we -do not recommend building with other acceleration packages installed -(GPU, OPT, USER-INTEL, USER-OMP) when also building with KOKKOS. - -make yes-kokkos -make machine :pre - -make no-kokkos -make machine :pre +This package has "specific installation +instructions"_Build_extras.html#gpu on the "Build +extras"_Build_extras.html doc page. [Supporting info:] @@ -590,16 +408,16 @@ src/KOKKOS/README lib/kokkos/README "Speed packages"_Speed_packages.html "Speed kokkos"_Speed_kokkos.html -"Section 2.6 -k on ..."_Section_start.html#start_6 -"Section 2.6 -sf kk"_Section_start.html#start_6 -"Section 2.6 -pk kokkos"_Section_start.html#start_6 +"Section 2.6 -k on ..."_Run_options.html +"Section 2.6 -sf kk"_Run_options.html +"Section 2.6 -pk kokkos"_Run_options.html "package kokkos"_package.html "Commands all"_Commands_all.html pages (fix,compute,pair,etc) for styles followed by (k) "Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul :line -KSPACE package :link(KSPACE),h4 +KSPACE package :link(PKG-KSPACE),h4 [Contents:] @@ -608,20 +426,14 @@ which compute the corresponding short-range pairwise Coulombic interactions. These include Ewald, particle-particle particle-mesh (PPPM), and multilevel summation method (MSM) solvers. -[Install or un-install:] +[Install:] Building with this package requires a 1d FFT library be present on your system for use by the PPPM solvers. This can be the KISS FFT library provided with LAMMPS, 3rd party libraries like FFTW, or a -vendor-supplied FFT library. See step 6 of "Section -2.2.2"_Section_start.html#start_2_2 of the manual for details on how -to select different FFT options in your machine Makefile. - -make yes-kspace -make machine :pre - -make no-kspace -make machine :pre +vendor-supplied FFT library. See the "Build +settings"_Build_settings.html doc page for details on how to select +different FFT options for your LAMPMS build. [Supporting info:] @@ -638,7 +450,7 @@ bench/in.rhodo :ul :line -LATTE package :link(LATTE),h4 +LATTE package :link(PKG-LATTE),h4 [Contents:] @@ -656,36 +468,11 @@ description is given with the "fix latte"_fix_latte.html command. itself is developed at Los Alamos National Laboratory by Marc Cawkwell, Anders Niklasson, and Christian Negre. -[Install or un-install:] +[Install:] -Before building LAMMPS with this package, you must first download and -build the LATTE library. You can do this manually if you prefer; -follow the instructions in lib/latte/README. You can also do it in -one step from the lammps/src dir, using a command like these, which -simply invokes the lib/latte/Install.py script with the specified -args: - -make lib-latte # print help message -make lib-latte args="-b" # download and build in lib/latte/LATTE-master -make lib-latte args="-p $HOME/latte" # use existing LATTE installation in $HOME/latte -make lib-latte args="-b -m gfortran" # download and build in lib/latte and - # copy Makefile.lammps.gfortran to Makefile.lammps -:pre - -Note that 3 symbolic (soft) links, "includelink" and "liblink" and -"filelink.o", are created in lib/latte to point into the LATTE home dir. -When LAMMPS builds in src it will use these links. You should -also check that the Makefile.lammps file you create is appropriate -for the compiler you use on your system to build LATTE. - -You can then install/un-install the package and build LAMMPS in the -usual manner: - -make yes-latte -make machine :pre - -make no-latte -make machine :pre +This package has "specific installation +instructions"_Build_extras.html#gpu on the "Build +extras"_Build_extras.html doc page. [Supporting info:] @@ -698,21 +485,13 @@ examples/latte :line -MANYBODY package :link(MANYBODY),h4 +MANYBODY package :link(PKG-MANYBODY),h4 [Contents:] A variety of manybody and bond-order potentials. These include (AI)REBO, BOP, EAM, EIM, Stillinger-Weber, and Tersoff potentials. -[Install or un-install:] - -make yes-manybody -make machine :pre - -make no-manybody -make machine :pre - [Supporting info:] src/MANYBODY: filenames -> commands @@ -727,7 +506,7 @@ bench/in.eam :ul :line -MC package :link(MC),h4 +MC package :link(PKG-MC),h4 [Contents:] @@ -736,14 +515,6 @@ attributes. These include fixes for creating, breaking, and swapping bonds, for performing atomic swaps, and performing grand-canonical MC (GCMC) in conjuction with dynamics. -[Install or un-install:] - -make yes-mc -make machine :pre - -make no-mc -make machine :pre - [Supporting info:] src/MC: filenames -> commands @@ -757,51 +528,26 @@ http://lammps.sandia.gov/movies.html#gcmc :ul :line -MEAM package :link(MEAM),h4 +MEAM package :link(PKG-MEAM),h4 [Contents:] A pair style for the modified embedded atom (MEAM) potential. -Please note that the MEAM package has been superseded by the -"USER-MEAMC"_#USER-MEAMC package, which is a direct translation -of the MEAM package to C++. USER-MEAMC contains additional -optimizations making it run faster than MEAM on most machines, -while providing the identical features and USER interface. +Please note that the use of the MEAM package is discouraged as +it has been superseded by the "USER-MEAMC"_#PKG-USER-MEAMC package, +which is a direct translation of the MEAM package to C++. +USER-MEAMC contains additional optimizations making it run faster +than MEAM on most machines, while providing the identical features +and user interface. [Author:] Greg Wagner (Northwestern U) while at Sandia. -[Install or un-install:] +[Install:] -Before building LAMMPS with this package, you must first build the -MEAM library in lib/meam. You can do this manually if you prefer; -follow the instructions in lib/meam/README. You can also do it in one -step from the lammps/src dir, using a command like these, which simply -invoke the lib/meam/Install.py script with the specified args: - -make lib-meam # print help message -make lib-meam args="-m mpi" # build with default Fortran compiler compatible with your MPI library -make lib-meam args="-m serial" # build with compiler compatible with "make serial" (GNU Fortran) -make lib-meam args="-m ifort" # build with Intel Fortran compiler using Makefile.ifort :pre - -The build should produce two files: lib/meam/libmeam.a and -lib/meam/Makefile.lammps. The latter is copied from an existing -Makefile.lammps.* and has settings needed to link C++ (LAMMPS) with -Fortran (MEAM library). Typically the two compilers used for LAMMPS -and the MEAM library need to be consistent (e.g. both Intel or both -GNU compilers). If necessary, you can edit/create a new -lib/meam/Makefile.machine file for your system, which should define an -EXTRAMAKE variable to specify a corresponding Makefile.lammps.machine -file. - -You can then install/un-install the package and build LAMMPS in the -usual manner: - -make yes-meam -make machine :pre - -make no-meam -make machine :pre +This package has "specific installation +instructions"_Build_extras.html#gpu on the "Build +extras"_Build_extras.html doc page. NOTE: You should test building the MEAM library with both the Intel and GNU compilers to see if a simulation runs faster with one versus @@ -817,7 +563,7 @@ examples/meam :ul :line -MISC package :link(MISC),h4 +MISC package :link(PKG-MISC),h4 [Contents:] @@ -828,14 +574,6 @@ listing, "ls src/MISC", to see the list of commands. NOTE: the MISC package contains styles that require using the -restrict flag, when compiling with Intel compilers. -[Install or un-install:] - -make yes-misc -make machine :pre - -make no-misc -make machine :pre - [Supporting info:] src/MISC: filenames -> commands @@ -852,7 +590,7 @@ http://lammps.sandia.gov/movies.html#evaporation :ul :line -MOLECULE package :link(MOLECULE),h4 +MOLECULE package :link(PKG-MOLECULE),h4 [Contents:] @@ -861,14 +599,6 @@ that are used to model molecular systems with fixed covalent bonds. The pair styles include the Dreiding (hydrogen-bonding) and CHARMM force fields, and a TIP4P water model. -[Install or un-install:] - -make yes-molecule -make machine :pre - -make no-molecule -make machine :pre - [Supporting info:] src/MOLECULE: filenames -> commands @@ -889,7 +619,7 @@ bench/in.rhodo :ul :line -MPIIO package :link(MPIIO),h4 +MPIIO package :link(PKG-MPIIO),h4 [Contents:] @@ -898,18 +628,6 @@ MPIIO library. It adds "dump styles"_dump.html with a "mpiio" in their style name. Restart files with an ".mpiio" suffix are also written and read in parallel. -[Install or un-install:] - -Note that MPIIO is part of the standard message-passing interface -(MPI) library, so you should not need any additional compiler or link -settings, beyond what LAMMPS normally uses for MPI on your system. - -make yes-mpiio -make machine :pre - -make no-mpiio -make machine :pre - [Supporting info:] src/MPIIO: filenames -> commands @@ -920,7 +638,7 @@ src/MPIIO: filenames -> commands :line -MSCG package :link(mscg),h4 +MSCG package :link(PKG-mscg),h4 [Contents:] @@ -937,39 +655,11 @@ system. library was developed by Jacob Wagner in Greg Voth's group at the University of Chicago. -[Install or un-install:] +[Install:] -Before building LAMMPS with this package, you must first download and -build the MS-CG library. Building the MS-CG library and using it from -LAMMPS requires a C++11 compatible compiler and that the GSL -(GNU Scientific Library) headers and libraries are installed on your -machine. See the lib/mscg/README and MSCG/Install files for more details. - -Assuming these libraries are in place, you can do the download and -build of MS-CG manually if you prefer; follow the instructions in -lib/mscg/README. You can also do it in one step from the lammps/src -dir, using a command like these, which simply invoke the -lib/mscg/Install.py script with the specified args: - -make lib-mscg # print help message -make lib-mscg args="-b -m serial" # download and build in lib/mscg/MSCG-release-master - # with the settings compatible with "make serial" -make lib-mscg args="-b -m mpi" # download and build in lib/mscg/MSCG-release-master - # with the settings compatible with "make mpi" -make lib-mscg args="-p /usr/local/mscg-release" # use the existing MS-CG installation in /usr/local/mscg-release :pre - -Note that 2 symbolic (soft) links, "includelink" and "liblink", will be created in lib/mscg -to point to the MS-CG src/installation dir. When LAMMPS is built in src it will use these links. -You should not need to edit the lib/mscg/Makefile.lammps file. - -You can then install/un-install the package and build LAMMPS in the -usual manner: - -make yes-mscg -make machine :pre - -make no-mscg -make machine :pre +This package has "specific installation +instructions"_Build_extras.html#gpu on the "Build +extras"_Build_extras.html doc page. [Supporting info:] @@ -980,7 +670,7 @@ examples/mscg :ul :line -OPT package :link(OPT),h4 +OPT package :link(PKG-OPT),h4 [Contents:] @@ -990,40 +680,31 @@ CHARMM, and Morse potentials. The styles have an "opt" suffix in their style name. The "Speed opt"_Speed_opt.html doc page gives details of how to build and use this package. Its styles can be invoked at run time via the "-sf opt" or "-suffix opt" "command-line -switches"_Section_start.html#start_6. See also the "KOKKOS"_#KOKKOS, -"USER-INTEL"_#USER-INTEL, and "USER-OMP"_#USER-OMP packages, which +switches"_Run_options.html. See also the "KOKKOS"_#PKG-KOKKOS, +"USER-INTEL"_#PKG-USER-INTEL, and "USER-OMP"_#PKG-USER-OMP packages, which have styles optimized for CPU performance. [Authors:] James Fischer (High Performance Technologies), David Richie, and Vincent Natoli (Stone Ridge Technolgy). -[Install or un-install:] +[Install:] -make yes-opt -make machine :pre - -make no-opt -make machine :pre - -NOTE: The compile flag "-restrict" must be used to build LAMMPS with -the OPT package when using Intel compilers. It should be added to -the CCFLAGS line of your Makefile.machine. See Makefile.opt in -src/MAKE/OPTIONS for an example. - -CCFLAGS: add -restrict for Intel compilers :ul +This package has "specific installation +instructions"_Build_extras.html#gpu on the "Build +extras"_Build_extras.html doc page. [Supporting info:] src/OPT: filenames -> commands "Speed packages"_Speed_packages.html "Speed opt"_Speed_opt.html -"Section 2.6 -sf opt"_Section_start.html#start_6 +"Section 2.6 -sf opt"_Run_options.html "Commands pair"_Commands_pair.html for styles followed by (t) "Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul :line -PERI package :link(PERI),h4 +PERI package :link(PKG-PERI),h4 [Contents:] @@ -1036,14 +717,6 @@ model. Additional Peridynamics models were added by Rezwanur Rahman and John Foster (UTSA). -[Install or un-install:] - -make yes-peri -make machine :pre - -make no-peri -make machine :pre - [Supporting info:] src/PERI: filenames -> commands @@ -1059,7 +732,7 @@ http://lammps.sandia.gov/movies.html#peri :ul :line -POEMS package :link(POEMS),h4 +POEMS package :link(PKG-POEMS),h4 [Contents:] @@ -1071,35 +744,11 @@ connections at hinge points. [Author:] Rudra Mukherjee (JPL) while at RPI. -[Install or un-install:] +[Install:] -Before building LAMMPS with this package, you must first build the -POEMS library in lib/poems. You can do this manually if you prefer; -follow the instructions in lib/poems/README. You can also do it in -one step from the lammps/src dir, using a command like these, which -simply invoke the lib/poems/Install.py script with the specified args: - -make lib-poems # print help message -make lib-poems args="-m serial" # build with GNU g++ compiler (settings as with "make serial") -make lib-poems args="-m mpi" # build with default MPI C++ compiler (settings as with "make mpi") -make lib-poems args="-m icc" # build with Intel icc compiler :pre - -The build should produce two files: lib/poems/libpoems.a and -lib/poems/Makefile.lammps. The latter is copied from an existing -Makefile.lammps.* and has settings needed to build LAMMPS with the -POEMS library (though typically the settings are just blank). If -necessary, you can edit/create a new lib/poems/Makefile.machine file -for your system, which should define an EXTRAMAKE variable to specify -a corresponding Makefile.lammps.machine file. - -You can then install/un-install the package and build LAMMPS in the -usual manner: - -make yes-poems -make machine :pre - -make no-meam -make machine :pre +This package has "specific installation +instructions"_Build_extras.html#gpu on the "Build +extras"_Build_extras.html doc page. [Supporting info:] @@ -1111,7 +760,7 @@ examples/rigid :ul :line -PYTHON package :link(PYTHON),h4 +PYTHON package :link(PKG-PYTHON),h4 [Contents:] @@ -1119,35 +768,30 @@ A "python"_python.html command which allow you to execute Python code from a LAMMPS input script. The code can be in a separate file or embedded in the input script itself. See the "Python call"_Python_call.html doc page for an overview of using Python from -LAMMPS in this manner and all the "Python"_Python.html doc pages for -other ways to use LAMMPS and Python together. - -[Install or un-install:] - -make yes-python -make machine :pre - -make no-python -make machine :pre +LAMMPS in this manner and all the "Python"_Python_head.html doc pages +for other ways to use LAMMPS and Python together. NOTE: Building with the PYTHON package assumes you have a Python shared library available on your system, which needs to be a Python 2 version, 2.6 or later. Python 3 is not yet supported. See the -lib/python/README for more details. Note that the build uses the -lib/python/Makefile.lammps file in the compile/link process. You -should only need to create a new Makefile.lammps.* file (and copy it -to Makefile.lammps) if the LAMMPS build fails. +lib/python/README for more details. + +[Install:] + +This package has "specific installation +instructions"_Build_extras.html#gpu on the "Build +extras"_Build_extras.html doc page. [Supporting info:] src/PYTHON: filenames -> commands -"Python call"_Python.html +"Python call"_Python_head.html lib/python/README examples/python :ul :line -QEQ package :link(QEQ),h4 +QEQ package :link(PKG-QEQ),h4 [Contents:] @@ -1155,14 +799,6 @@ Several fixes for performing charge equilibration (QEq) via different algorithms. These can be used with pair styles that perform QEq as part of their formulation. -[Install or un-install:] - -make yes-qeq -make machine :pre - -make no-qeq -make machine :pre - [Supporting info:] src/QEQ: filenames -> commands @@ -1172,49 +808,27 @@ examples/streitz :ul :line -REAX package :link(REAX),h4 +REAX package :link(PKG-REAX),h4 [Contents:] +NOTE: the use of the REAX package is discouraged, as it is no longer +maintained. Please use the "USER-REAXC"_#PKG-USER-REAXC package instead, +and possibly the KOKKOS enabled variant of that, which has a more robust +memory management. + A pair style which wraps a Fortran library which implements the ReaxFF -potential, which is a universal reactive force field. See the -"USER-REAXC package"_#USER-REAXC for an alternate implementation in -C/C++. Also a "fix reax/bonds"_fix_reax_bonds.html command for -monitoring molecules as bonds are created and destroyed. +potential, which is a universal reactive force field. Also included is +a "fix reax/bonds"_fix_reax_bonds.html command for monitoring molecules +as bonds are created and destroyed. [Author:] Aidan Thompson (Sandia). -[Install or un-install:] +[Install:] -Before building LAMMPS with this package, you must first build the -REAX library in lib/reax. You can do this manually if you prefer; -follow the instructions in lib/reax/README. You can also do it in one -step from the lammps/src dir, using a command like these, which simply -invoke the lib/reax/Install.py script with the specified args: - -make lib-reax # print help message -make lib-reax args="-m serial" # build with GNU Fortran compiler (settings as with "make serial") -make lib-reax args="-m mpi" # build with default MPI Fortran compiler (settings as with "make mpi") -make lib-reax args="-m ifort" # build with Intel ifort compiler :pre - -The build should produce two files: lib/reax/libreax.a and -lib/reax/Makefile.lammps. The latter is copied from an existing -Makefile.lammps.* and has settings needed to link C++ (LAMMPS) with -Fortran (REAX library). Typically the two compilers used for LAMMPS -and the REAX library need to be consistent (e.g. both Intel or both -GNU compilers). If necessary, you can edit/create a new -lib/reax/Makefile.machine file for your system, which should define an -EXTRAMAKE variable to specify a corresponding Makefile.lammps.machine -file. - -You can then install/un-install the package and build LAMMPS in the -usual manner: - -make yes-reax -make machine :pre - -make no-reax -make machine :pre +This package has "specific installation +instructions"_Build_extras.html#gpu on the "Build +extras"_Build_extras.html doc page. [Supporting info:] @@ -1226,7 +840,7 @@ examples/reax :ul :line -REPLICA package :link(REPLICA),h4 +REPLICA package :link(PKG-REPLICA2),h4 [Contents:] @@ -1240,14 +854,6 @@ verlet/split algorithm for performing long-range Coulombics on one set of processors, and the remainder of the force field calcalation on another set. -[Install or un-install:] - -make yes-replica -make machine :pre - -make no-replica -make machine :pre - [Supporting info:] src/REPLICA: filenames -> commands @@ -1263,7 +869,7 @@ examples/tad :ul :line -RIGID package :link(RIGID),h4 +RIGID package :link(PKG-RIGID),h4 [Contents:] @@ -1272,16 +878,6 @@ particles. This includes SHAKE and RATTLE, as well as varous rigid-body integrators for a few large bodies or many small bodies. Also several computes which calculate properties of rigid bodies. -To install/build: - -make yes-rigid -make machine :pre - -To un-install/re-build: - -make no-rigid -make machine :pre - [Supporting info:] src/RIGID: filenames -> commands @@ -1297,21 +893,13 @@ http://lammps.sandia.gov/movies.html#star :ul :line -SHOCK package :link(SHOCK),h4 +SHOCK package :link(PKG-SHOCK),h4 [Contents:] Fixes for running impact simulations where a shock-wave passes through a material. -[Install or un-install:] - -make yes-shock -make machine :pre - -make no-shock -make machine :pre - [Supporting info:] src/SHOCK: filenames -> commands @@ -1324,7 +912,7 @@ examples/msst :ul :line -SNAP package :link(SNAP),h4 +SNAP package :link(PKG-SNAP),h4 [Contents:] @@ -1335,14 +923,6 @@ computes which analyze attributes of the potential. [Author:] Aidan Thompson (Sandia). -[Install or un-install:] - -make yes-snap -make machine :pre - -make no-snap -make machine :pre - [Supporting info:] src/SNAP: filenames -> commands @@ -1354,7 +934,7 @@ examples/snap :ul :line -SPIN package :link(SPIN),h4 +SPIN package :link(PKG-SPIN),h4 [Contents:] @@ -1363,18 +943,10 @@ the usual manner via MD. Various pair, fix, and compute styles. [Author:] Julian Tranchida (Sandia). -[Install or un-install:] - -make yes-spin -make machine :pre - -make no-spin -make machine :pre - [Supporting info:] src/SPIN: filenames -> commands -"Howto spin"_Howto_spin.html +"Howto spins"_Howto_spins.html "pair_style spin/dmi"_pair_spin_dmi.html "pair_style spin/exchange"_pair_spin_exchange.html "pair_style spin/magelec"_pair_spin_magelec.html @@ -1386,7 +958,7 @@ examples/SPIN :ul :line -SRD package :link(SRD),h4 +SRD package :link(PKG-SRD),h4 [Contents:] @@ -1394,16 +966,6 @@ A pair of fixes which implement the Stochastic Rotation Dynamics (SRD) method for coarse-graining of a solvent, typically around large colloidal particles. -To install/build: - -make yes-srd -make machine :pre - -To un-install/re-build: - -make no-srd -make machine :pre - [Supporting info:] src/SRD: filenames -> commands @@ -1417,7 +979,7 @@ http://lammps.sandia.gov/movies.html#poly :ul :line -VORONOI package :link(VORONOI),h4 +VORONOI package :link(PKG-VORONOI),h4 [Contents:] @@ -1435,33 +997,11 @@ system. library was written by Chris Rycroft (Harvard U) while at UC Berkeley and LBNL. -[Install or un-install:] +[Install:] -Before building LAMMPS with this package, you must first download and -build the Voro++ library. You can do this manually if you prefer; -follow the instructions in lib/voronoi/README. You can also do it in -one step from the lammps/src dir, using a command like these, which -simply invoke the lib/voronoi/Install.py script with the specified -args: - -make lib-voronoi # print help message -make lib-voronoi args="-b" # download and build the default version in lib/voronoi/voro++- -make lib-voronoi args="-p $HOME/voro++" # use existing Voro++ installation in $HOME/voro++ -make lib-voronoi args="-b -v voro++0.4.6" # download and build the 0.4.6 version in lib/voronoi/voro++-0.4.6 :pre - -Note that 2 symbolic (soft) links, "includelink" and "liblink", are -created in lib/voronoi to point to the Voro++ src dir. When LAMMPS -builds in src it will use these links. You should not need to edit -the lib/voronoi/Makefile.lammps file. - -You can then install/un-install the package and build LAMMPS in the -usual manner: - -make yes-voronoi -make machine :pre - -make no-voronoi -make machine :pre +This package has "specific installation +instructions"_Build_extras.html#gpu on the "Build +extras"_Build_extras.html doc page. [Supporting info:] @@ -1471,10 +1011,9 @@ lib/voronoi/README "compute voronoi/atom"_compute_voronoi_atom.html examples/voronoi :ul -:line :line -USER-ATC package :link(USER-ATC),h4 +USER-ATC package :link(PKG-USER-ATC),h4 [Contents:] @@ -1485,46 +1024,11 @@ atomic information to continuum fields. [Authors:] Reese Jones, Jeremy Templeton, Jon Zimmerman (Sandia). -[Install or un-install:] +[Install:] -Before building LAMMPS with this package, you must first build the ATC -library in lib/atc. You can do this manually if you prefer; follow -the instructions in lib/atc/README. You can also do it in one step -from the lammps/src dir, using a command like these, which simply -invoke the lib/atc/Install.py script with the specified args: - -make lib-atc # print help message -make lib-atc args="-m serial" # build with GNU g++ compiler and MPI STUBS (settings as with "make serial") -make lib-atc args="-m mpi" # build with default MPI compiler (settings as with "make mpi") -make lib-atc args="-m icc" # build with Intel icc compiler :pre - -The build should produce two files: lib/atc/libatc.a and -lib/atc/Makefile.lammps. The latter is copied from an existing -Makefile.lammps.* and has settings needed to build LAMMPS with the ATC -library. If necessary, you can edit/create a new -lib/atc/Makefile.machine file for your system, which should define an -EXTRAMAKE variable to specify a corresponding Makefile.lammps.machine -file. - -Note that the Makefile.lammps file has settings for the BLAS and -LAPACK linear algebra libraries. As explained in lib/atc/README these -can either exist on your system, or you can use the files provided in -lib/linalg. In the latter case you also need to build the library -in lib/linalg with a command like these: - -make lib-linalg # print help message -make lib-linalg args="-m serial" # build with GNU Fortran compiler (settings as with "make serial") -make lib-linalg args="-m mpi" # build with default MPI Fortran compiler (settings as with "make mpi") -make lib-linalg args="-m gfortran" # build with GNU Fortran compiler :pre - -You can then install/un-install the package and build LAMMPS in the -usual manner: - -make yes-user-atc -make machine :pre - -make no-user-atc -make machine :pre +This package has "specific installation +instructions"_Build_extras.html#gpu on the "Build +extras"_Build_extras.html doc page. [Supporting info:] @@ -1536,7 +1040,7 @@ http://lammps.sandia.gov/pictures.html#atc :ul :line -USER-AWPMD package :link(USER-AWPMD),h4 +USER-AWPMD package :link(PKG-USER-AWPMD),h4 [Contents:] @@ -1547,46 +1051,11 @@ model. [Author:] Ilya Valuev (JIHT, Russia). -[Install or un-install:] +[Install:] -Before building LAMMPS with this package, you must first build the -AWPMD library in lib/awpmd. You can do this manually if you prefer; -follow the instructions in lib/awpmd/README. You can also do it in -one step from the lammps/src dir, using a command like these, which -simply invoke the lib/awpmd/Install.py script with the specified args: - -make lib-awpmd # print help message -make lib-awpmd args="-m serial" # build with GNU g++ compiler and MPI STUBS (settings as with "make serial") -make lib-awpmd args="-m mpi" # build with default MPI compiler (settings as with "make mpi") -make lib-awpmd args="-m icc" # build with Intel icc compiler :pre - -The build should produce two files: lib/awpmd/libawpmd.a and -lib/awpmd/Makefile.lammps. The latter is copied from an existing -Makefile.lammps.* and has settings needed to build LAMMPS with the -AWPMD library. If necessary, you can edit/create a new -lib/awpmd/Makefile.machine file for your system, which should define -an EXTRAMAKE variable to specify a corresponding -Makefile.lammps.machine file. - -Note that the Makefile.lammps file has settings for the BLAS and -LAPACK linear algebra libraries. As explained in lib/awpmd/README -these can either exist on your system, or you can use the files -provided in lib/linalg. In the latter case you also need to build the -library in lib/linalg with a command like these: - -make lib-linalg # print help message -make lib-linalg args="-m serial" # build with GNU Fortran compiler (settings as with "make serial") -make lib-linalg args="-m mpi" # build with default MPI Fortran compiler (settings as with "make mpi") -make lib-linalg args="-m gfortran" # build with GNU Fortran compiler :pre - -You can then install/un-install the package and build LAMMPS in the -usual manner: - -make yes-user-awpmd -make machine :pre - -make no-user-awpmd -make machine :pre +This package has "specific installation +instructions"_Build_extras.html#gpu on the "Build +extras"_Build_extras.html doc page. [Supporting info:] @@ -1597,7 +1066,7 @@ examples/USER/awpmd :ul :line -USER-BOCS package :link(USER-BOCS),h4 +USER-BOCS package :link(PKG-USER-BOCS),h4 [Contents:] @@ -1609,15 +1078,8 @@ N. J. H. Dunn and W. G. Noid, "Bottom-up coarse-grained models that accurately describe the structure, pressure, and compressibility of molecular liquids," J. Chem. Phys. 143, 243148 (2015). -[Authors:] Nicholas J. H. Dunn and Michael R. DeLyser (The Pennsylvania State University) - -[Install or un-install:] - -make yes-user-bocs -make machine :pre - -make no-user-bocs -make machine :pre +[Authors:] Nicholas J. H. Dunn and Michael R. DeLyser (The +Pennsylvania State University) [Supporting info:] @@ -1634,7 +1096,7 @@ Example inputs are in the examples/USER/bocs folder. :line -USER-CGDNA package :link(USER-CGDNA),h4 +USER-CGDNA package :link(PKG-USER-CGDNA),h4 [Contents:] @@ -1646,14 +1108,6 @@ stability. [Author:] Oliver Henrich (University of Strathclyde, Glasgow). -[Install or un-install:] - -make yes-user-cgdna -make machine :pre - -make no-user-cgdna -make machine :pre - [Supporting info:] src/USER-CGDNA: filenames -> commands @@ -1666,7 +1120,7 @@ src/USER-CGDNA: filenames -> commands :line -USER-CGSDK package :link(USER-CGSDK),h4 +USER-CGSDK package :link(PKG-USER-CGSDK),h4 [Contents:] @@ -1677,14 +1131,6 @@ acids. [Author:] Axel Kohlmeyer (Temple U). -[Install or un-install:] - -make yes-user-cgsdk -make machine :pre - -make no-user-cgsdk -make machine :pre - [Supporting info:] src/USER-CGSDK: filenames -> commands @@ -1696,7 +1142,7 @@ http://lammps.sandia.gov/pictures.html#cg :ul :line -USER-COLVARS package :link(USER-COLVARS),h4 +USER-COLVARS package :link(PKG-USER-COLVARS),h4 [Contents:] @@ -1713,36 +1159,11 @@ and Jerome Henin (LISM, CNRS, Marseille, France), originally for the NAMD MD code, but with portability in mind. Axel Kohlmeyer (Temple U) provided the interface to LAMMPS. -[Install or un-install:] +[Install:] -Before building LAMMPS with this package, you must first build the -COLVARS library in lib/colvars. You can do this manually if you -prefer; follow the instructions in lib/colvars/README. You can also -do it in one step from the lammps/src dir, using a command like these, -which simply invoke the lib/colvars/Install.py script with the -specified args: - -make lib-colvars # print help message -make lib-colvars args="-m serial" # build with GNU g++ compiler (settings as with "make serial") -make lib-colvars args="-m mpi" # build with default MPI compiler (settings as with "make mpi") -make lib-colvars args="-m g++-debug" # build with GNU g++ compiler and colvars debugging enabled :pre - -The build should produce two files: lib/colvars/libcolvars.a and -lib/colvars/Makefile.lammps. The latter is copied from an existing -Makefile.lammps.* and has settings needed to build LAMMPS with the -COLVARS library (though typically the settings are just blank). If -necessary, you can edit/create a new lib/colvars/Makefile.machine file -for your system, which should define an EXTRAMAKE variable to specify -a corresponding Makefile.lammps.machine file. - -You can then install/un-install the package and build LAMMPS in the -usual manner: - -make yes-user-colvars -make machine :pre - -make no-user-colvars -make machine :pre +This package has "specific installation +instructions"_Build_extras.html#gpu on the "Build +extras"_Build_extras.html doc page. [Supporting info:] @@ -1755,7 +1176,7 @@ examples/USER/colvars :ul :line -USER-DIFFRACTION package :link(USER-DIFFRACTION),h4 +USER-DIFFRACTION package :link(PKG-USER-DIFFRACTION),h4 [Contents:] @@ -1764,14 +1185,6 @@ intensities based on kinematic diffraction theory. [Author:] Shawn Coleman while at the U Arkansas. -[Install or un-install:] - -make yes-user-diffraction -make machine :pre - -make no-user-diffraction -make machine :pre - [Supporting info:] src/USER-DIFFRACTION: filenames -> commands @@ -1782,7 +1195,7 @@ examples/USER/diffraction :ul :line -USER-DPD package :link(USER-DPD),h4 +USER-DPD package :link(PKG-USER-DPD),h4 [Contents:] @@ -1799,14 +1212,6 @@ algorithm. [Authors:] Jim Larentzos (ARL), Tim Mattox (Engility Corp), and and John Brennan (ARL). -[Install or un-install:] - -make yes-user-dpd -make machine :pre - -make no-user-dpd -make machine :pre - [Supporting info:] src/USER-DPD: filenames -> commands @@ -1828,7 +1233,7 @@ examples/USER/dpd :ul :line -USER-DRUDE package :link(USER-DRUDE),h4 +USER-DRUDE package :link(PKG-USER-DRUDE),h4 [Contents:] @@ -1841,14 +1246,6 @@ for using this package in tools/drude. [Authors:] Alain Dequidt (U Blaise Pascal Clermont-Ferrand), Julien Devemy (CNRS), and Agilio Padua (U Blaise Pascal). -[Install or un-install:] - -make yes-user-drude -make machine :pre - -make no-user-drude -make machine :pre - [Supporting info:] src/USER-DRUDE: filenames -> commands @@ -1866,7 +1263,7 @@ tools/drude :ul :line -USER-EFF package :link(USER-EFF),h4 +USER-EFF package :link(PKG-USER-EFF),h4 [Contents:] @@ -1880,14 +1277,6 @@ tools/eff; see its README file. [Author:] Andres Jaramillo-Botero (CalTech). -[Install or un-install:] - -make yes-user-eff -make machine :pre - -make no-user-eff -make machine :pre - [Supporting info:] src/USER-EFF: filenames -> commands @@ -1907,7 +1296,7 @@ http://lammps.sandia.gov/movies.html#eff :ul :line -USER-FEP package :link(USER-FEP),h4 +USER-FEP package :link(PKG-USER-FEP),h4 [Contents:] @@ -1919,14 +1308,6 @@ for using this package in tools/fep; see its README file. [Author:] Agilio Padua (Universite Blaise Pascal Clermont-Ferrand) -[Install or un-install:] - -make yes-user-fep -make machine :pre - -make no-user-fep -make machine :pre - [Supporting info:] src/USER-FEP: filenames -> commands @@ -1940,7 +1321,7 @@ tools/fep :ul :line -USER-H5MD package :link(USER-H5MD),h4 +USER-H5MD package :link(PKG-USER-H5MD),h4 [Contents:] @@ -1958,37 +1339,11 @@ system. [Author:] Pierre de Buyl (KU Leuven) created both the package and the H5MD format. -[Install or un-install:] +[Install:] -Note that to follow these steps to compile and link to the CH5MD -library, you need the standard HDF5 software package installed on your -system, which should include the h5cc compiler and the HDF5 library. - -Before building LAMMPS with this package, you must first build the -CH5MD library in lib/h5md. You can do this manually if you prefer; -follow the instructions in lib/h5md/README. You can also do it in one -step from the lammps/src dir, using a command like these, which simply -invoke the lib/h5md/Install.py script with the specified args: - -make lib-h5md # print help message -make lib-hm5d args="-m h5cc" # build with h5cc compiler :pre - -The build should produce two files: lib/h5md/libch5md.a and -lib/h5md/Makefile.lammps. The latter is copied from an existing -Makefile.lammps.* and has settings needed to build LAMMPS with the -system HDF5 library. If necessary, you can edit/create a new -lib/h5md/Makefile.machine file for your system, which should define an -EXTRAMAKE variable to specify a corresponding Makefile.lammps.machine -file. - -You can then install/un-install the package and build LAMMPS in the -usual manner: - -make yes-user-h5md -make machine :pre - -make no-user-h5md -make machine :pre +This package has "specific installation +instructions"_Build_extras.html#gpu on the "Build +extras"_Build_extras.html doc page. [Supporting info:] @@ -1999,7 +1354,7 @@ lib/h5md/README :line -USER-INTEL package :link(USER-INTEL),h4 +USER-INTEL package :link(PKG-USER-INTEL),h4 [Contents:] @@ -2009,9 +1364,9 @@ All of them have an "intel" in their style name. The "Speed intel"_Speed_intel.html doc page gives details of what hardware and compilers are required on your system, and how to build and use this package. Its styles can be invoked at run time via the "-sf intel" or -"-suffix intel" "command-line switches"_Section_start.html#start_6. -Also see the "KOKKOS"_#KOKKOS, "OPT"_#OPT, and "USER-OMP"_#USER-OMP -packages, which have styles optimized for CPUs and KNLs. +"-suffix intel" "command-line switches"_Run_options.html. Also see +the "KOKKOS"_#PKG-KOKKOS, "OPT"_#PKG-OPT, and "USER-OMP"_#PKG-USER-OMP packages, +which have styles optimized for CPUs and KNLs. You need to have an Intel compiler, version 14 or higher to take full advantage of this package. While compilation with GNU compilers is @@ -2020,49 +1375,13 @@ supported, performance will be suboptimal. NOTE: the USER-INTEL package contains styles that require using the -restrict flag, when compiling with Intel compilers. - [Author:] Mike Brown (Intel). -[Install or un-install:] +[Install:] -For the USER-INTEL package, you have 2 choices when building. You can -build with either CPU or KNL support. Each choice requires additional -settings in your Makefile.machine for CCFLAGS and LINKFLAGS and -optimized malloc libraries. See the -src/MAKE/OPTIONS/Makefile.intel_cpu and src/MAKE/OPTIONS/Makefile.knl -files for examples. - -For CPUs: - -OPTFLAGS = -xHost -O2 -fp-model fast=2 -no-prec-div -qoverride-limits -CCFLAGS = -g -qopenmp -DLAMMPS_MEMALIGN=64 -no-offload \ --fno-alias -ansi-alias -restrict $(OPTFLAGS) -LINKFLAGS = -g -qopenmp $(OPTFLAGS) -LIB = -ltbbmalloc -ltbbmalloc_proxy :pre - -For KNLs: - -OPTFLAGS = -xMIC-AVX512 -O2 -fp-model fast=2 -no-prec-div -qoverride-limits -CCFLAGS = -g -qopenmp -DLAMMPS_MEMALIGN=64 -no-offload \ --fno-alias -ansi-alias -restrict $(OPTFLAGS) -LINKFLAGS = -g -qopenmp $(OPTFLAGS) -LIB = -ltbbmalloc :pre - -Once you have an appropriate Makefile.machine, you can -install/un-install the package and build LAMMPS in the usual manner. -Note that you cannot build one executable to run on multiple hardware -targets (Intel CPUs or KNL). You need to build LAMMPS once for each -hardware target, to produce a separate executable. - -You should also typically install the USER-OMP package, as it can be -used in tandem with the USER-INTEL package to good effect, as -explained on the "Speed intel"_Speed_intel.html doc page. - -make yes-user-intel yes-user-omp -make machine :pre - -make no-user-intel no-user-omp -make machine :pre +This package has "specific installation +instructions"_Build_extras.html#gpu on the "Build +extras"_Build_extras.html doc page. [Supporting info:] @@ -2070,8 +1389,8 @@ src/USER-INTEL: filenames -> commands src/USER-INTEL/README "Speed packages"_Speed_packages.html "Speed intel"_Speed_intel.html -"Section 2.6 -sf intel"_Section_start.html#start_6 -"Section 2.6 -pk intel"_Section_start.html#start_6 +"Section 2.6 -sf intel"_Run_options.html +"Section 2.6 -pk intel"_Run_options.html "package intel"_package.html "Commands all"_Commands_all.html pages (fix,compute,pair,etc) for styles followed by (i) src/USER-INTEL/TEST @@ -2079,7 +1398,7 @@ src/USER-INTEL/TEST :line -USER-LB package :link(USER-LB),h4 +USER-LB package :link(PKG-USER-LB),h4 [Contents:] @@ -2089,14 +1408,6 @@ can be used to model MD particles influenced by hydrodynamic forces. [Authors:] Frances Mackay and Colin Denniston (University of Western Ontario). -[Install or un-install:] - -make yes-user-lb -make machine :pre - -make no-user-lb -make machine :pre - [Supporting info:] src/USER-LB: filenames -> commands @@ -2108,7 +1419,7 @@ examples/USER/lb :ul :line -USER-MGPT package :link(USER-MGPT),h4 +USER-MGPT package :link(PKG-USER-MGPT),h4 [Contents:] @@ -2123,14 +1434,6 @@ matrix-MGPT algorithm due to Tomas Oppelstrup at LLNL. [Authors:] Tomas Oppelstrup and John Moriarty (LLNL). -[Install or un-install:] - -make yes-user-mgpt -make machine :pre - -make no-user-mgpt -make machine :pre - [Supporting info:] src/USER-MGPT: filenames -> commands @@ -2140,7 +1443,7 @@ examples/USER/mgpt :ul :line -USER-MISC package :link(USER-MISC),h4 +USER-MISC package :link(PKG-USER-MISC),h4 [Contents:] @@ -2151,14 +1454,6 @@ dihedral, improper, or command style. [Authors:] The author for each style in the package is listed in the src/USER-MISC/README file. -[Install or un-install:] - -make yes-user-misc -make machine :pre - -make no-user-misc -make machine :pre - [Supporting info:] src/USER-MISC: filenames -> commands @@ -2168,7 +1463,7 @@ examples/USER/misc :ul :line -USER-MANIFOLD package :link(USER-MANIFOLD),h4 +USER-MANIFOLD package :link(PKG-USER-MANIFOLD),h4 [Contents:] @@ -2179,16 +1474,9 @@ algorithm to formulate single-particle constraint functions g(xi,yi,zi) = 0 and their derivative (i.e. the normal of the manifold) n = grad(g). -[Author:] Stefan Paquay (until 2017: Eindhoven University of Technology (TU/e), The -Netherlands; since 2017: Brandeis University, Waltham, MA, USA) - -[Install or un-install:] - -make yes-user-manifold -make machine :pre - -make no-user-manifold -make machine :pre +[Author:] Stefan Paquay (until 2017: Eindhoven University of +Technology (TU/e), The Netherlands; since 2017: Brandeis University, +Waltham, MA, USA) [Supporting info:] @@ -2203,7 +1491,7 @@ http://lammps.sandia.gov/movies.html#manifold :ul :line -USER-MEAMC package :link(USER-MEAMC),h4 +USER-MEAMC package :link(PKG-USER-MEAMC),h4 [Contents:] @@ -2217,14 +1505,6 @@ multiple times. based on the Fortran version of Greg Wagner (Northwestern U) while at Sandia. -[Install or un-install:] - -make yes-user-meamc -make machine :pre - -make no-user-meamc -make machine :pre - [Supporting info:] src/USER-MEAMC: filenames -> commands @@ -2234,7 +1514,7 @@ examples/meam :ul :line -USER-MESO package :link(USER-MESO),h4 +USER-MESO package :link(PKG-USER-MESO),h4 [Contents:] @@ -2248,14 +1528,6 @@ algorithm. [Author:] Zhen Li (Division of Applied Mathematics, Brown University) -[Install or un-install:] - -make yes-user-meso -make machine :pre - -make no-user-meso -make machine :pre - [Supporting info:] src/USER-MESO: filenames -> commands @@ -2270,7 +1542,7 @@ http://lammps.sandia.gov/movies.html#mesodpd :ul :line -USER-MOFFF package :link(USER-MOFFF),h4 +USER-MOFFF package :link(PKG-USER-MOFFF),h4 [Contents:] @@ -2288,14 +1560,6 @@ well as the "MOF+"_MOFplus website. [Author:] Hendrik Heenen (Technical U of Munich), Rochus Schmid (Ruhr-University Bochum). -[Install or un-install:] - -make yes-user-mofff -make machine :pre - -make no-user-mofff -make machine :pre - [Supporting info:] src/USER-MOFFF: filenames -> commands @@ -2308,7 +1572,7 @@ examples/USER/mofff :ul :line -USER-MOLFILE package :link(USER-MOLFILE),h4 +USER-MOLFILE package :link(PKG-USER-MOLFILE),h4 [Contents:] @@ -2336,20 +1600,11 @@ at [Author:] Axel Kohlmeyer (Temple U). -[Install or un-install:] +[Install:] -Note that the lib/molfile/Makefile.lammps file has a setting for a -dynamic loading library libdl.a that should is typically present on -all systems, which is required for LAMMPS to link with this package. -If the setting is not valid for your system, you will need to edit the -Makefile.lammps file. See lib/molfile/README and -lib/molfile/Makefile.lammps for details. - -make yes-user-molfile -make machine :pre - -make no-user-molfile -make machine :pre +This package has "specific installation +instructions"_Build_extras.html#gpu on the "Build +extras"_Build_extras.html doc page. [Supporting info:] @@ -2360,7 +1615,7 @@ lib/molfile/README :line -USER-NETCDF package :link(USER-NETCDF),h4 +USER-NETCDF package :link(PKG-USER-NETCDF),h4 [Contents:] @@ -2384,20 +1639,11 @@ tools: [Author:] Lars Pastewka (Karlsruhe Institute of Technology). -[Install or un-install:] +[Install:] -Note that to follow these steps, you need the standard NetCDF software -package installed on your system. The lib/netcdf/Makefile.lammps file -has settings for NetCDF include and library files that LAMMPS needs to -compile and linkk with this package. If the settings are not valid -for your system, you will need to edit the Makefile.lammps file. See -lib/netcdf/README for details. - -make yes-user-netcdf -make machine :pre - -make no-user-netcdf -make machine :pre +This package has "specific installation +instructions"_Build_extras.html#gpu on the "Build +extras"_Build_extras.html doc page. [Supporting info:] @@ -2408,7 +1654,7 @@ lib/netcdf/README :line -USER-OMP package :link(USER-OMP),h4 +USER-OMP package :link(PKG-USER-OMP),h4 [Contents:] @@ -2418,10 +1664,9 @@ via OpenMP directives. All of them have an "omp" in their style name. The "Speed omp"_Speed_omp.html doc page gives details of what hardware and compilers are required on your system, and how to build and use this package. Its styles can be invoked at run time via the "-sf omp" -or "-suffix omp" "command-line switches"_Section_start.html#start_6. -Also see the "KOKKOS"_#KOKKOS, "OPT"_#OPT, and -"USER-INTEL"_#USER-INTEL packages, which have styles optimized for -CPUs. +or "-suffix omp" "command-line switches"_Run_options.html. Also see +the "KOKKOS"_#PKG-KOKKOS, "OPT"_#PKG-OPT, and "USER-INTEL"_#PKG-USER-INTEL +packages, which have styles optimized for CPUs. [Author:] Axel Kohlmeyer (Temple U). @@ -2438,16 +1683,11 @@ See src/MAKE/OPTIONS/Makefile.omp for an example. Once you have an appropriate Makefile.machine, you can install/un-install the package and build LAMMPS in the usual manner: -[Install or un-install:] +[Install:] -make yes-user-omp -make machine :pre - -make no-user-omp -make machine :pre - -CCFLAGS: add -fopenmp (and -restrict when using Intel compilers) -LINKFLAGS: add -fopenmp :ul +This package has "specific installation +instructions"_Build_extras.html#gpu on the "Build +extras"_Build_extras.html doc page. [Supporting info:] @@ -2455,15 +1695,15 @@ src/USER-OMP: filenames -> commands src/USER-OMP/README "Speed packages"_Speed_packages.html "Speed omp"_Speed_omp.html -"Section 2.6 -sf omp"_Section_start.html#start_6 -"Section 2.6 -pk omp"_Section_start.html#start_6 +"Section 2.6 -sf omp"_Run_options.html +"Section 2.6 -pk omp"_Run_options.html "package omp"_package.html "Commands all"_Commands_all.html pages (fix,compute,pair,etc) for styles followed by (o) "Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul :line -USER-PHONON package :link(USER-PHONON),h4 +USER-PHONON package :link(PKG-USER-PHONON),h4 [Contents:] @@ -2473,14 +1713,6 @@ relations, directly from molecular dynamics simulations. [Author:] Ling-Ti Kong (Shanghai Jiao Tong University). -[Install or un-install:] - -make yes-user-phonon -make machine :pre - -make no-user-phonon -make machine :pre - [Supporting info:] src/USER-PHONON: filenames -> commands @@ -2490,7 +1722,7 @@ examples/USER/phonon :ul :line -USER-QMMM package :link(USER-QMMM),h4 +USER-QMMM package :link(PKG-USER-QMMM),h4 [Contents:] @@ -2511,42 +1743,11 @@ without changes to LAMMPS itself. [Author:] Axel Kohlmeyer (Temple U). -[Install or un-install:] +[Install:] -Before building LAMMPS with this package, you must first build the -QMMM library in lib/qmmm. You can do this manually if you prefer; -follow the first two steps explained in lib/qmmm/README. You can -also do it in one step from the lammps/src dir, using a command like -these, which simply invoke the lib/qmmm/Install.py script with the -specified args: - -make lib-qmmm # print help message -make lib-qmmm args="-m serial" # build with GNU Fortran compiler (settings as in "make serial") -make lib-qmmm args="-m mpi" # build with default MPI compiler (settings as in "make mpi") -make lib-qmmm args="-m gfortran" # build with GNU Fortran compiler :pre - -The build should produce two files: lib/qmmm/libqmmm.a and -lib/qmmm/Makefile.lammps. The latter is copied from an existing -Makefile.lammps.* and has settings needed to build LAMMPS with the -QMMM library (though typically the settings are just blank). If -necessary, you can edit/create a new lib/qmmm/Makefile.machine file -for your system, which should define an EXTRAMAKE variable to specify -a corresponding Makefile.lammps.machine file. - -You can then install/un-install the package and build LAMMPS in the -usual manner: - -make yes-user-qmmm -make machine :pre - -make no-user-qmmm -make machine :pre - -NOTE: The LAMMPS executable these steps produce is not yet functional -for a QM/MM simulation. You must also build Quantum ESPRESSO and -create a new executable which links LAMMPS and Quantum ESPRESSO -together. These are steps 3 and 4 described in the lib/qmmm/README -file. +This package has "specific installation +instructions"_Build_extras.html#gpu on the "Build +extras"_Build_extras.html doc page. [Supporting info:] @@ -2559,7 +1760,7 @@ lib/qmmm/example-mc/README :ul :line -USER-QTB package :link(USER-QTB),h4 +USER-QTB package :link(PKG-USER-QTB),h4 [Contents:] @@ -2574,14 +1775,6 @@ simulation. [Author:] Yuan Shen (Stanford U). -[Install or un-install:] - -make yes-user-qtb -make machine :pre - -make no-user-qtb -make machine :pre - [Supporting info:] src/USER-QTB: filenames -> commands @@ -2592,7 +1785,7 @@ examples/USER/qtb :ul :line -USER-QUIP package :link(USER-QUIP),h4 +USER-QUIP package :link(PKG-USER-QUIP),h4 [Contents:] @@ -2608,26 +1801,11 @@ on your system. [Author:] Albert Bartok (Cambridge University) -[Install or un-install:] +[Install:] -Note that to follow these steps to compile and link to the QUIP -library, you must first download and build QUIP on your systems. It -can be obtained from GitHub. See step 1 and step 1.1 in the -lib/quip/README file for details on how to do this. Note that it -requires setting two environment variables, QUIP_ROOT and QUIP_ARCH, -which will be accessed by the lib/quip/Makefile.lammps file which is -used when you compile and link LAMMPS with this package. You should -only need to edit this file if the LAMMPS build can not use its -settings to successfully build on your system. - -You can then install/un-install the package and build LAMMPS in the -usual manner: - -make yes-user-quip -make machine :pre - -make no-user-quip -make machine :pre +This package has "specific installation +instructions"_Build_extras.html#gpu on the "Build +extras"_Build_extras.html doc page. [Supporting info:] @@ -2638,26 +1816,18 @@ examples/USER/quip :ul :line -USER-REAXC package :link(USER-REAXC),h4 +USER-REAXC package :link(PKG-USER-REAXC),h4 [Contents:] A pair style which implements the ReaxFF potential in C/C++ (in -contrast to the "REAX package"_#REAX and its Fortran library). ReaxFF +contrast to the "REAX package"_#PKG-REAX and its Fortran library). ReaxFF is universal reactive force field. See the src/USER-REAXC/README file for more info on differences between the two packages. Also two fixes for monitoring molecules as bonds are created and destroyed. [Author:] Hasan Metin Aktulga (MSU) while at Purdue University. -[Install or un-install:] - -make yes-user-reaxc -make machine :pre - -make no-user-reaxc -make machine :pre - [Supporting info:] src/USER-REAXC: filenames -> commands @@ -2669,66 +1839,14 @@ examples/reax :ul :line -USER-SCAFACOS package :link(USER-SCAFACOS),h4 - -[Contents:] - -A KSpace style which wraps the "ScaFaCoS Coulomb solver -library"_http://www.scafacos.de. - -To use this package you must have the ScaFaCoS library available on -your system. It is available for download at "http://scafacos.de" or -can be cloned from the git-repository -"git://github.com/scafacos/scafacos.git". - -[Author:] Rene Halver (JSC) wrote the scafacos LAMMPS command. - -ScaFaCoS was developed by a consortium of German research facilities -with a BMBF (German Ministry of Science and Education) funded project -in 2009-2012. Participants of the consortium were the Universities of -Bonn, Chemnitz, Stuttgart, and Wuppertal as well as the -Forschungszentrum Juelich. - -[Install or un-install:] - -Before building LAMMPS with this package, you must first download and -build the ScaFaCoS library. You can do this manually if you prefer; -follow the instructions in lib/scafacos/README. You can also do it in -one step from the lammps/src dir, using a command like these, which -simply invoke the lib/scafacos/Install.py script with the specified -args: - -make lib-scafacos # print help message -make lib-scafacos args="-b" # download and build in lib/scafacos/scafacos- -make lib-scafacos args="-p $HOME/scafacos # use existing ScaFaCoS installation in $HOME/scafacos - -You can then install/un-install the package and build LAMMPS in the -usual manner: - -make yes-user-scafacos -make machine :pre - -make no-user-scafacos -make machine :pre - -[Supporting info:] - -src/USER-SCAFACOS: filenames -> commands -src/USER-SCAFACOS/README -"kspace_style scafacos"_kspace_style.html -"kspace_modify"_kspace_modify.html -examples/USER/scafacos :ul - -:line - -USER-SMD package :link(USER-SMD),h4 +USER-SMD package :link(PKG-USER-SMD),h4 [Contents:] An atom style, fixes, computes, and several pair styles which implements smoothed Mach dynamics (SMD) for solids, which is a model related to smoothed particle hydrodynamics (SPH) for liquids (see the -"USER-SPH package"_#USER-SPH). +"USER-SPH package"_#PKG-USER-SPH). This package solves solids mechanics problems via a state of the art stabilized meshless method with hourglass control. It can specify @@ -2742,31 +1860,11 @@ specified as surface geometries from *.STL files. [Author:] Georg Ganzenmuller (Fraunhofer-Institute for High-Speed Dynamics, Ernst Mach Institute, Germany). -[Install or un-install:] +[Install:] -Before building LAMMPS with this package, you must first download the -Eigen library. Eigen is a template library, so you do not need to -build it, just download it. You can do this manually if you prefer; -follow the instructions in lib/smd/README. You can also do it in one -step from the lammps/src dir, using a command like these, which simply -invoke the lib/smd/Install.py script with the specified args: - -make lib-smd # print help message -make lib-smd args="-b" # download and build in default lib/smd/eigen-eigen-... -make lib-smd args="-p /usr/include/eigen3" # use existing Eigen installation in /usr/include/eigen3 :pre - -Note that a symbolic (soft) link named "includelink" is created in -lib/smd to point to the Eigen dir. When LAMMPS builds it will use -this link. You should not need to edit the lib/smd/Makefile.lammps file. - -You can then install/un-install the package and build LAMMPS in the -usual manner: - -make yes-user-smd -make machine :pre - -make no-user-smd -make machine :pre +This package has "specific installation +instructions"_Build_extras.html#gpu on the "Build +extras"_Build_extras.html doc page. [Supporting info:] @@ -2778,7 +1876,7 @@ http://lammps.sandia.gov/movies.html#smd :ul :line -USER-SMTBQ package :link(USER-SMTBQ),h4 +USER-SMTBQ package :link(PKG-USER-SMTBQ),h4 [Contents:] @@ -2789,14 +1887,6 @@ ionocovalent bonds in oxides. [Authors:] Nicolas Salles, Emile Maras, Olivier Politano, and Robert Tetot (LAAS-CNRS, France). -[Install or un-install:] - -make yes-user-smtbq -make machine :pre - -make no-user-smtbq -make machine :pre - [Supporting info:] src/USER-SMTBQ: filenames -> commands @@ -2806,13 +1896,13 @@ examples/USER/smtbq :ul :line -USER-SPH package :link(USER-SPH),h4 +USER-SPH package :link(PKG-USER-SPH),h4 [Contents:] An atom style, fixes, computes, and several pair styles which implements smoothed particle hydrodynamics (SPH) for liquids. See the -related "USER-SMD package"_#USER-SMD package for smooth Mach dynamics +related "USER-SMD package"_#PKG-USER-SMD package for smooth Mach dynamics (SMD) for solids. This package contains ideal gas, Lennard-Jones equation of states, @@ -2828,14 +1918,6 @@ property/atom"_compute_property_atom.html command. [Author:] Georg Ganzenmuller (Fraunhofer-Institute for High-Speed Dynamics, Ernst Mach Institute, Germany). -[Install or un-install:] - -make yes-user-sph -make machine :pre - -make no-user-sph -make machine :pre - [Supporting info:] src/USER-SPH: filenames -> commands @@ -2846,7 +1928,7 @@ http://lammps.sandia.gov/movies.html#sph :ul :line -USER-TALLY package :link(USER-TALLY),h4 +USER-TALLY package :link(PKG-USER-TALLY),h4 [Contents:] @@ -2856,14 +1938,6 @@ stress, etc) about individual interactions. [Author:] Axel Kohlmeyer (Temple U). -[Install or un-install:] - -make yes-user-tally -make machine :pre - -make no-user-tally -make machine :pre - [Supporting info:] src/USER-TALLY: filenames -> commands @@ -2873,7 +1947,7 @@ examples/USER/tally :ul :line -USER-UEF package :link(USER-UEF),h4 +USER-UEF package :link(PKG-USER-UEF),h4 [Contents:] @@ -2883,14 +1957,6 @@ supporting compute styles and an output option. [Author:] David Nicholson (MIT). -[Install or un-install:] - -make yes-user-uef -make machine :pre - -make no-user-uef -make machine :pre - [Supporting info:] src/USER-UEF: filenames -> commands @@ -2904,7 +1970,7 @@ examples/uef :ul :line -USER-VTK package :link(USER-VTK),h4 +USER-VTK package :link(PKG-USER-VTK),h4 [Contents:] @@ -2920,23 +1986,11 @@ system. [Authors:] Richard Berger (JKU) and Daniel Queteschiner (DCS Computing). -[Install or un-install:] +[Install:] -The lib/vtk/Makefile.lammps file has settings for accessing VTK files -and its library, which are required for LAMMPS to build and link with -this package. If the settings are not valid for your system, check if -one of the other lib/vtk/Makefile.lammps.* files is compatible and -copy it to Makefile.lammps. If none of the provided files work, you -will need to edit the Makefile.lammps file. - -You can then install/un-install the package and build LAMMPS in the -usual manner: - -make yes-user-vtk -make machine :pre - -make no-user-vtk -make machine :pre +This package has "specific installation +instructions"_Build_extras.html#gpu on the "Build +extras"_Build_extras.html doc page. [Supporting info:] From a9fb8636adc555486d4ed3080d2a5766436539d5 Mon Sep 17 00:00:00 2001 From: "Steven J. Plimpton" Date: Wed, 22 Aug 2018 09:52:44 -0600 Subject: [PATCH 110/302] doc page updates and changed domain->remap() call --- doc/src/Build_extras.txt | 40 ++++++++++++++++++++++++++++++++++ doc/src/Build_package.txt | 1 + doc/src/Packages_details.txt | 36 ++++++++++++++++++++++++++++++ doc/src/Packages_user.txt | 1 + doc/src/kspace_style.txt | 4 ++-- src/USER-SCAFACOS/scafacos.cpp | 12 +++++++++- 6 files changed, 91 insertions(+), 3 deletions(-) diff --git a/doc/src/Build_extras.txt b/doc/src/Build_extras.txt index 5c33a0a4d4..2fc0785227 100644 --- a/doc/src/Build_extras.txt +++ b/doc/src/Build_extras.txt @@ -47,6 +47,7 @@ This is the list of packages that may require additional steps. "USER-OMP"_#user-omp, "USER-QMMM"_#user-qmmm, "USER-QUIP"_#user-quip, +"USER-SCAFACOS"_#user-scafacos, "USER-SMD"_#user-smd, "USER-VTK"_#user-vtk :tb(c=6,ea=c,a=l) @@ -894,6 +895,45 @@ successfully build on your system. :line +USER-SCAFACOS package :h4,link(user-scafacos) + +To build with this package, you must download and build the "ScaFaCoS +Coulomb solver library"_scafacos_home + +:link(scafacos_home,http://www.scafacos.de) + +[CMake build]: + +-D DOWNLOAD_SCAFACOS=value # download ScaFaCoS for build, value = no (default) or yes +-D SCAFACOS_LIBRARY=path # ScaFaCos library file (only needed if at custom location) +-D SCAFACOS_INCLUDE_DIR=path # ScaFaCoS include directory (only needed if at custom location) :pre + +If DOWNLOAD_SCAFACOS is set, the ScaFaCoS library will be downloaded +and built inside the CMake build directory. If the ScaFaCoS library +is already on your system (in a location CMake cannot find it), +SCAFACOS_LIBRARY is the filename (plus path) of the ScaFaCoS library +file, not the directory the library file is in. SCAFACOS_INCLUDE_DIR +is the directory the ScaFaCoS include file is in. + +[Traditional make]: + +You can download and build the ScaFaCoS library manually if you +prefer; follow the instructions in lib/scafacos/README. You can also +do it in one step from the lammps/src dir, using a command like these, +which simply invoke the lib/scafacos/Install.py script with the +specified args: + +make lib-scafacos # print help message +make lib-scafacos args="-b" # download and build in lib/scafacos/scafacos- +make lib-scafacos args="-p $HOME/scafacos # use existing ScaFaCoS installation in $HOME/scafacos + +Note that 2 symbolic (soft) links, "includelink" and "liblink", are +created in lib/scafacos to point to the ScaFaCoS src dir. When LAMMPS +builds in src it will use these links. You should not need to edit +the lib/scafacos/Makefile.lammps file. + +:line + USER-SMD package :h4,link(user-smd) To build with this package, you must download the Eigen3 library. diff --git a/doc/src/Build_package.txt b/doc/src/Build_package.txt index 4f71e9eb18..fab987ea0d 100644 --- a/doc/src/Build_package.txt +++ b/doc/src/Build_package.txt @@ -58,6 +58,7 @@ packages: "USER-OMP"_Build_extras.html#user-omp, "USER-QMMM"_Build_extras.html#user-qmmm, "USER-QUIP"_Build_extras.html#user-quip, +"USER-SCAFACOS"_#Build_extras.html#user-scafacos, "USER-SMD"_Build_extras.html#user-smd, "USER-VTK"_Build_extras.html#user-vtk :tb(c=6,ea=c,a=l) diff --git a/doc/src/Packages_details.txt b/doc/src/Packages_details.txt index 892774be38..c4c9043908 100644 --- a/doc/src/Packages_details.txt +++ b/doc/src/Packages_details.txt @@ -92,6 +92,7 @@ as contained in the file name. "USER-QTB"_#PKG-USER-QTB, "USER-QUIP"_#PKG-USER-QUIP, "USER-REAXC"_#PKG-USER-REAXC, +"USER-SCAFACOS"_#USER-SCAFACOS, "USER-SMD"_#PKG-USER-SMD, "USER-SMTBQ"_#PKG-USER-SMTBQ, "USER-SPH"_#PKG-USER-SPH, @@ -1839,6 +1840,41 @@ examples/reax :ul :line +USER-SCAFACOS package :link(USER-SCAFACOS),h4 + +[Contents:] + +A KSpace style which wraps the "ScaFaCoS Coulomb solver +library"_http://www.scafacos.de to compute long-range Coulombic +interactions. + +To use this package you must have the ScaFaCoS library available on +your system. + +[Author:] Rene Halver (JSC) wrote the scafacos LAMMPS command. + +ScaFaCoS itself was developed by a consortium of German research +facilities with a BMBF (German Ministry of Science and Education) +funded project in 2009-2012. Participants of the consortium were the +Universities of Bonn, Chemnitz, Stuttgart, and Wuppertal as well as +the Forschungszentrum Juelich. + +[Install:] + +This package has "specific installation +instructions"_Build_extras.html#user-scafacos on the "Build +extras"_Build_extras.html doc page. + +[Supporting info:] + +src/USER-SCAFACOS: filenames -> commands +src/USER-SCAFACOS/README +"kspace_style scafacos"_kspace_style.html +"kspace_modify"_kspace_modify.html +examples/USER/scafacos :ul + +:line + USER-SMD package :link(PKG-USER-SMD),h4 [Contents:] diff --git a/doc/src/Packages_user.txt b/doc/src/Packages_user.txt index c1a52fd0d0..5ed5c6f6d3 100644 --- a/doc/src/Packages_user.txt +++ b/doc/src/Packages_user.txt @@ -66,6 +66,7 @@ Package, Description, Doc page, Example, Library "USER-QTB"_Packages_details.html#PKG-USER-QTB, quantum nuclear effects,"fix qtb"_fix_qtb.html "fix qbmsst"_fix_qbmsst.html, qtb, no "USER-QUIP"_Packages_details.html#PKG-USER-QUIP, QUIP/libatoms interface,"pair_style quip"_pair_quip.html, USER/quip, ext "USER-REAXC"_Packages_details.html#PKG-USER-REAXC, ReaxFF potential (C/C++) ,"pair_style reaxc"_pair_reaxc.html, reax, no +"USER-SCAFACOS"_Packages_details.html#PKG-USER-SCAFACOS, wrapper on ScaFaCoS solver,"kspace_style scafacos"_kspace_style.html, USER/scafacos, ext "USER-SMD"_Packages_details.html#PKG-USER-SMD, smoothed Mach dynamics,"SMD User Guide"_PDF/SMD_LAMMPS_userguide.pdf, USER/smd, ext "USER-SMTBQ"_Packages_details.html#PKG-USER-SMTBQ, second moment tight binding QEq potential,"pair_style smtbq"_pair_smtbq.html, USER/smtbq, no "USER-SPH"_Packages_details.html#PKG-USER-SPH, smoothed particle hydrodynamics,"SPH User Guide"_PDF/SPH_LAMMPS_userguide.pdf, USER/sph, no diff --git a/doc/src/kspace_style.txt b/doc/src/kspace_style.txt index deb8d8ab51..ddf4e15703 100644 --- a/doc/src/kspace_style.txt +++ b/doc/src/kspace_style.txt @@ -252,7 +252,7 @@ These are the ScaFaCoS methods currently available from LAMMPS: {p2nfft} = FFT-based Coulomb solver {ewald} = Ewald summation {direct} = direct O(N^2) summation -{p3m} = PPPM +{p3m} = PPPM :ul We plan to support additional ScaFaCoS solvers from LAMMPS in the future. For an overview of the included solvers, refer to @@ -268,7 +268,7 @@ energy or the total Columic energy. To select from these options, see the "kspace_modify scafacos accuracy"_kspace_modify.html doc page. The "kspace_modify scafacos"_kspace_modify.html command also explains -all the ScaFaCoS options currently exposed to LAMMPS. +other ScaFaCoS options currently exposed to LAMMPS. :line diff --git a/src/USER-SCAFACOS/scafacos.cpp b/src/USER-SCAFACOS/scafacos.cpp index f3e8ce64f7..d047853b55 100644 --- a/src/USER-SCAFACOS/scafacos.cpp +++ b/src/USER-SCAFACOS/scafacos.cpp @@ -199,7 +199,6 @@ void Scafacos::compute(int eflag, int vflag) eflag_atom = 0; vflag_global = 0; } - // grow xpbc, epot, efield if necessary @@ -223,6 +222,8 @@ void Scafacos::compute(int eflag, int vflag) // pack coords into xpbc and apply PBC memcpy(xpbc,&x[0][0],3*nlocal*sizeof(double)); + // RENE: remove this section (see RENE below) + //int j = 0; for (int i = 0; i < nlocal; i++) { if (domain->xperiodic) domain->remap(&xpbc[3*i]); @@ -231,6 +232,15 @@ void Scafacos::compute(int eflag, int vflag) //j += 3; } + // RENE: I think the call to domain->remap needs to be this way + // b/c the remap() method checks for PBC and does all 3 dims at once + + int j = 0; + for (int i = 0; i < nlocal; i++) { + domain->remap(&xpbc[j]); + j += 3; + } + // if simulation box has changed, call fcs_tune() if (box_has_changed()) { From cb8482b0e6e9ac007ca79eb96a38dd86f5ce4673 Mon Sep 17 00:00:00 2001 From: "Steven J. Plimpton" Date: Wed, 22 Aug 2018 10:22:51 -0600 Subject: [PATCH 111/302] another doc change --- doc/src/Commands_kspace.txt | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/doc/src/Commands_kspace.txt b/doc/src/Commands_kspace.txt index a126344505..d56b7fa767 100644 --- a/doc/src/Commands_kspace.txt +++ b/doc/src/Commands_kspace.txt @@ -33,4 +33,5 @@ OPT. "pppm/disp (i)"_kspace_style.html, "pppm/disp/tip4p"_kspace_style.html, "pppm/stagger"_kspace_style.html, -"pppm/tip4p (o)"_kspace_style.html :tb(c=4,ea=c) +"pppm/tip4p (o)"_kspace_style.html, +"scafacos"_kspace_style.html :tb(c=4,ea=c) From fd56124a94288635c942ac33a8c4aacd60231d74 Mon Sep 17 00:00:00 2001 From: Rene Halver Date: Wed, 22 Aug 2018 14:17:21 -0600 Subject: [PATCH 112/302] corrected remap call and logic for check if correct solver / tolerance combinations are set --- src/USER-SCAFACOS/scafacos.cpp | 27 ++++++++------------------- 1 file changed, 8 insertions(+), 19 deletions(-) diff --git a/src/USER-SCAFACOS/scafacos.cpp b/src/USER-SCAFACOS/scafacos.cpp index d047853b55..7c2dd0b68d 100644 --- a/src/USER-SCAFACOS/scafacos.cpp +++ b/src/USER-SCAFACOS/scafacos.cpp @@ -222,25 +222,14 @@ void Scafacos::compute(int eflag, int vflag) // pack coords into xpbc and apply PBC memcpy(xpbc,&x[0][0],3*nlocal*sizeof(double)); - // RENE: remove this section (see RENE below) - - //int j = 0; - for (int i = 0; i < nlocal; i++) { - if (domain->xperiodic) domain->remap(&xpbc[3*i]); - if (domain->yperiodic) domain->remap(&xpbc[3*i+1]); - if (domain->zperiodic) domain->remap(&xpbc[3*i+2]); - //j += 3; - } - - // RENE: I think the call to domain->remap needs to be this way - // b/c the remap() method checks for PBC and does all 3 dims at once int j = 0; - for (int i = 0; i < nlocal; i++) { - domain->remap(&xpbc[j]); - j += 3; + if (domain->xperiodic || domain -> yperiodic || domain -> zperiodic){ + for (int i = 0; i < nlocal; i++) { + domain->remap(&xpbc[j]); + j += 3; + } } - // if simulation box has changed, call fcs_tune() if (box_has_changed()) { @@ -328,20 +317,20 @@ int Scafacos::modify_param(int narg, char **arg) tolerance_type != FCS_TOLERANCE_TYPE_ENERGY && tolerance_type != FCS_TOLERANCE_TYPE_ENERGY_REL ) - ) && + ) || ( strcmp(method,"p2nfft") == 0 && ( tolerance_type != FCS_TOLERANCE_TYPE_FIELD && tolerance_type != FCS_TOLERANCE_TYPE_POTENTIAL ) - ) && + ) || ( strcmp(method,"p3m") == 0 && ( tolerance_type != FCS_TOLERANCE_TYPE_FIELD ) - ) && + ) || ( strcmp(method,"ewald") == 0 && ( From 01fe3569041f5f8c19b9f46ebf4600e110bcfeae Mon Sep 17 00:00:00 2001 From: Rene Halver Date: Wed, 22 Aug 2018 17:18:36 -0600 Subject: [PATCH 113/302] first version of scafacos.h without the inclusion of the ScaFaCoS header --- src/USER-SCAFACOS/scafacos.cpp | 83 +++++++++++++++++++--------------- src/USER-SCAFACOS/scafacos.h | 19 ++++---- 2 files changed, 55 insertions(+), 47 deletions(-) diff --git a/src/USER-SCAFACOS/scafacos.cpp b/src/USER-SCAFACOS/scafacos.cpp index 7c2dd0b68d..92d0612947 100644 --- a/src/USER-SCAFACOS/scafacos.cpp +++ b/src/USER-SCAFACOS/scafacos.cpp @@ -90,7 +90,7 @@ Scafacos::~Scafacos() memory->destroy(efield); // clean up of the ScaFaCoS handle and internal arrays - fcs_destroy(fcs); + fcs_destroy((FCS)fcs); } /* ---------------------------------------------------------------------- */ @@ -112,20 +112,24 @@ void Scafacos::init() if (domain->triclinic) error->all(FLERR,"Cannot use ScaFaCoS with triclinic domain yet"); - if (atom->natoms > INT_MAX && sizeof(fcs_int) != 8) + if (atom->natoms > INT_MAX && sizeof(int) != 8) error->all(FLERR,"Scafacos atom count exceeds 2B"); if (atom->molecular > 0) error->all(FLERR, "Cannot use Scafacos with molecular charged systems yet"); + FCSResult result; + // one-time initialization of ScaFaCoS qqrd2e = force->qqrd2e; if (!initialized) { - result = fcs_init(&fcs,method,world); - check_result(result); + printf("DEBUG: %p\n",&fcs); + result = fcs_init((FCS*)&fcs,method,world); + check_result((void*)&result); + printf("DEBUG: %p\n",&fcs); setup_handle(); @@ -136,8 +140,8 @@ void Scafacos::init() strcmp(method,"p2nfft") == 0 || strcmp(method,"ewald") == 0) { - result = fcs_set_tolerance(fcs,tolerance_type,tolerance); - check_result(result); + result = fcs_set_tolerance((FCS)fcs,tolerance_type,tolerance); + check_result((void*)&result); } double **x = atom->x; @@ -147,9 +151,9 @@ void Scafacos::init() if (strcmp(method,"fmm") == 0) { if (fmm_tuning_flag == 1) - fcs_fmm_set_internal_tuning(fcs,FCS_FMM_INHOMOGENOUS_SYSTEM); + fcs_fmm_set_internal_tuning((FCS)fcs,FCS_FMM_INHOMOGENOUS_SYSTEM); else - fcs_fmm_set_internal_tuning(fcs,FCS_FMM_HOMOGENOUS_SYSTEM); + fcs_fmm_set_internal_tuning((FCS)fcs,FCS_FMM_HOMOGENOUS_SYSTEM); } // for the FMM at least one particle is required per process @@ -158,15 +162,15 @@ void Scafacos::init() int empty = (nlocal==0)?1:0; MPI_Allreduce(MPI_IN_PLACE,&empty,1,MPI_INT,MPI_SUM,world); if (empty > 0) - fcs_set_redistribute(fcs,1); + fcs_set_redistribute((FCS)fcs,1); else - fcs_set_redistribute(fcs,0); + fcs_set_redistribute((FCS)fcs,0); } - result = fcs_tune(fcs,nlocal,&x[0][0],q); - check_result(result); + result = fcs_tune((FCS)fcs,nlocal,&x[0][0],q); + check_result((void*)&result); // more useful here, since the parameters should be tuned now - if (me == 0) fcs_print_parameters(fcs); + if (me == 0) fcs_print_parameters((FCS)fcs); } initialized = 1; @@ -181,6 +185,7 @@ void Scafacos::compute(int eflag, int vflag) int nlocal = atom->nlocal; const double qscale = qqrd2e; + FCSResult result; // for the FMM at least one particle is required per process if (strcmp(method,"fmm")) @@ -188,9 +193,9 @@ void Scafacos::compute(int eflag, int vflag) int empty = (nlocal==0)?1:0; MPI_Allreduce(MPI_IN_PLACE,&empty,1,MPI_INT,MPI_SUM,world); if (empty > 0) - fcs_set_redistribute(fcs,1); + fcs_set_redistribute((FCS)fcs,1); else - fcs_set_redistribute(fcs,0); + fcs_set_redistribute((FCS)fcs,0); } if (eflag || vflag) ev_setup(eflag,vflag); @@ -214,7 +219,7 @@ void Scafacos::compute(int eflag, int vflag) if (vflag_global) { - fcs_set_compute_virial(fcs,1); + fcs_set_compute_virial((FCS)fcs,1); //if (strcmp(method,"p3m") == 0) // error->all(FLERR,"ScaFaCoS p3m does not support computation of virial"); } @@ -223,8 +228,8 @@ void Scafacos::compute(int eflag, int vflag) memcpy(xpbc,&x[0][0],3*nlocal*sizeof(double)); - int j = 0; if (domain->xperiodic || domain -> yperiodic || domain -> zperiodic){ + int j = 0; for (int i = 0; i < nlocal; i++) { domain->remap(&xpbc[j]); j += 3; @@ -234,20 +239,20 @@ void Scafacos::compute(int eflag, int vflag) if (box_has_changed()) { setup_handle(); - result = fcs_tune(fcs,nlocal,xpbc,q); - check_result(result); + result = fcs_tune((FCS)fcs,nlocal,xpbc,q); + check_result((void*)&result); } // invoke ScaFaCoS solver - result = fcs_run(fcs,nlocal,xpbc,q,&efield[0][0],epot); - check_result(result); + result = fcs_run((FCS)fcs,nlocal,xpbc,q,&efield[0][0],epot); + check_result((void*)&result); // extract virial if (vflag_global) { - fcs_get_virial(fcs,virial_int); + fcs_get_virial((FCS)fcs,virial_int); virial[0] = virial_int[0]; virial[1] = virial_int[1]; virial[2] = virial_int[2]; @@ -380,6 +385,8 @@ double Scafacos::memory_usage() void Scafacos::setup_handle() { + FCSResult result; + // store simulation box params // setup periodicity @@ -404,23 +411,23 @@ void Scafacos::setup_handle() old_natoms = atom->natoms; // store parameters to ScaFaCoS handle - result = fcs_set_box_a(fcs,old_box_x); - check_result(result); + result = fcs_set_box_a((FCS)fcs,old_box_x); + check_result((void*)&result); - result = fcs_set_box_b(fcs,old_box_y); - check_result(result); + result = fcs_set_box_b((FCS)fcs,old_box_y); + check_result((void*)&result); - result = fcs_set_box_c(fcs,old_box_z); - check_result(result); + result = fcs_set_box_c((FCS)fcs,old_box_z); + check_result((void*)&result); - result = fcs_set_box_origin(fcs,old_origin); - check_result(result); + result = fcs_set_box_origin((FCS)fcs,old_origin); + check_result((void*)&result); - result = fcs_set_periodicity(fcs,old_periodicity); - check_result(result); + result = fcs_set_periodicity((FCS)fcs,old_periodicity); + check_result((void*)&result); - result = fcs_set_total_particles(fcs,old_natoms); - check_result(result); + result = fcs_set_total_particles((FCS)fcs,old_natoms); + check_result((void*)&result); // allow ScaFaCoS to calculate the near field computations for now // TODO: allow the delegation of the near field computations @@ -428,8 +435,8 @@ void Scafacos::setup_handle() // (near_field_flag = 1 -> enables the internal near field calcs // 0 -> disables the internal near field calcs int near_field_flag = 1; - result = fcs_set_near_field_flag(fcs,near_field_flag); - check_result(result); + result = fcs_set_near_field_flag((FCS)fcs,near_field_flag); + check_result((void*)&result); } /* ---------------------------------------------------------------------- @@ -460,8 +467,10 @@ bool Scafacos::box_has_changed() check ScaFaCoS result for error condition ------------------------------------------------------------------------- */ -void Scafacos::check_result(FCSResult result) +void Scafacos::check_result(void* result_p) { + FCSResult result = *(FCSResult*)result_p; + if (!result) return; std::stringstream ss; diff --git a/src/USER-SCAFACOS/scafacos.h b/src/USER-SCAFACOS/scafacos.h index bf07b3b45a..fdf15739a6 100644 --- a/src/USER-SCAFACOS/scafacos.h +++ b/src/USER-SCAFACOS/scafacos.h @@ -21,7 +21,7 @@ KSpaceStyle(scafacos,Scafacos) #define LMP_SCAFACOS_H #include "kspace.h" -#include "fcs.h" +//#include "fcs.h" namespace LAMMPS_NS { @@ -35,7 +35,7 @@ class Scafacos : public KSpace { int modify_param(int, char **); double memory_usage(); - private: + private: int me; char *method; @@ -46,20 +46,19 @@ class Scafacos : public KSpace { int fmm_tuning_flag; - FCS fcs; // ScaFaCoS handle - FCSResult result; // result for each ScaFaCoS call + void* fcs; // ScaFaCoS handle // simulation state: box, natoms // so ScaFaCoS can detect if changes, e.g. for NPT - fcs_float old_box_x[3],old_box_y[3],old_box_z[3]; - fcs_float old_origin[3]; - fcs_int old_periodicity[3]; - fcs_int old_natoms; + double old_box_x[3],old_box_y[3],old_box_z[3]; + double old_origin[3]; + int old_periodicity[3]; + int old_natoms; - fcs_float virial_int[9]; + double virial_int[9]; - void check_result(FCSResult); + void check_result(void*); void setup_handle(); bool box_has_changed(); }; From 2eeb8cecb2e658efa9adebe8db17e9634fcc743a Mon Sep 17 00:00:00 2001 From: Rene Halver Date: Thu, 23 Aug 2018 10:08:31 -0600 Subject: [PATCH 114/302] removed left-over debug messages --- src/USER-SCAFACOS/scafacos.cpp | 2 -- 1 file changed, 2 deletions(-) diff --git a/src/USER-SCAFACOS/scafacos.cpp b/src/USER-SCAFACOS/scafacos.cpp index 92d0612947..52bb0e46c4 100644 --- a/src/USER-SCAFACOS/scafacos.cpp +++ b/src/USER-SCAFACOS/scafacos.cpp @@ -126,10 +126,8 @@ void Scafacos::init() qqrd2e = force->qqrd2e; if (!initialized) { - printf("DEBUG: %p\n",&fcs); result = fcs_init((FCS*)&fcs,method,world); check_result((void*)&result); - printf("DEBUG: %p\n",&fcs); setup_handle(); From c4c5f9a32eb556ad78be55bdf188d9eae8c4e56b Mon Sep 17 00:00:00 2001 From: "Steven J. Plimpton" Date: Fri, 31 Aug 2018 13:44:49 -0600 Subject: [PATCH 115/302] 2 new computes: chunk/spread/atom and reduce/chunk --- doc/src/Commands_compute.txt | 2 + doc/src/Howto_chunk.txt | 45 ++- doc/src/compute.txt | 2 + doc/src/compute_chunk_atom.txt | 11 +- doc/src/compute_chunk_spread_atom.txt | 173 +++++++++ doc/src/compute_reduce.txt | 6 +- doc/src/compute_reduce_chunk.txt | 177 +++++++++ doc/src/computes.txt | 2 + doc/src/lammps.book | 2 + src/compute_chunk_spread_atom.cpp | 352 ++++++++++++++++++ src/compute_chunk_spread_atom.h | 61 +++ src/compute_reduce.cpp | 1 + src/compute_reduce_chunk.cpp | 512 ++++++++++++++++++++++++++ src/compute_reduce_chunk.h | 77 ++++ 14 files changed, 1407 insertions(+), 16 deletions(-) create mode 100644 doc/src/compute_chunk_spread_atom.txt create mode 100644 doc/src/compute_reduce_chunk.txt create mode 100644 src/compute_chunk_spread_atom.cpp create mode 100644 src/compute_chunk_spread_atom.h create mode 100644 src/compute_reduce_chunk.cpp create mode 100644 src/compute_reduce_chunk.h diff --git a/doc/src/Commands_compute.txt b/doc/src/Commands_compute.txt index 028e274c9b..6185634187 100644 --- a/doc/src/Commands_compute.txt +++ b/doc/src/Commands_compute.txt @@ -35,6 +35,7 @@ KOKKOS, o = USER-OMP, t = OPT. "bond/local"_compute_bond_local.html, "centro/atom"_compute_centro_atom.html, "chunk/atom"_compute_chunk_atom.html, +"chunk/spread/atom"_compute_chunk_spread_atom.html, "cluster/atom"_compute_cluster_atom.html, "cna/atom"_compute_cna_atom.html, "cnp/atom"_compute_cnp_atom.html, @@ -97,6 +98,7 @@ KOKKOS, o = USER-OMP, t = OPT. "property/local"_compute_property_local.html, "rdf"_compute_rdf.html, "reduce"_compute_reduce.html, +"reduce/chunk"_compute_reduce_chunk.html, "reduce/region"_compute_reduce.html, "rigid/local"_compute_rigid_local.html, "saed"_compute_saed.html, diff --git a/doc/src/Howto_chunk.txt b/doc/src/Howto_chunk.txt index 8e52acf4b8..611b71dac7 100644 --- a/doc/src/Howto_chunk.txt +++ b/doc/src/Howto_chunk.txt @@ -22,7 +22,7 @@ commands, to calculate various properties of a system: "fix ave/chunk"_fix_ave_chunk.html any of the "compute */chunk"_compute.html commands :ul -Here, each of the 3 kinds of chunk-related commands is briefly +Here, each of the 4 kinds of chunk-related commands is briefly overviewed. Then some examples are given of how to compute different properties with chunk commands. @@ -83,8 +83,9 @@ chunk. Compute */chunk commands: :h4 -Currently the following computes operate on chunks of atoms to produce -per-chunk values. +The following computes operate on chunks of atoms to produce per-chunk +values. Any compute whose style name ends in "/chunk" is in this +category: "compute com/chunk"_compute_com_chunk.html "compute gyration/chunk"_compute_gyration_chunk.html @@ -111,8 +112,8 @@ of a center of mass, which requires summing mass*position over the atoms and then dividing by summed mass. All of these computes produce a global vector or global array as -output, wih one or more values per chunk. They can be used -in various ways: +output, wih one or more values per chunk. The output can be used in +various ways: As input to the "fix ave/time"_fix_ave_time.html command, which can write the values to a file and optionally time average them. :ulb,l @@ -122,9 +123,27 @@ histogram values across chunks. E.g. a histogram of cluster sizes or molecule diffusion rates. :l As input to special functions of "equal-style -variables"_variable.html, like sum() and max(). E.g. to find the -largest cluster or fastest diffusing molecule. :l -:ule +variables"_variable.html, like sum() and max() and ave(). E.g. to +find the largest cluster or fastest diffusing molecule or average +radius-of-gyration of a set of molecules (chunks). :l :ule + +Other chunk commands: :h4 + +"compute chunk/spread/atom"_compute_chunk_spread_atom.html +"compute reduce/chunk"_compute_reduce_chunk.html :ul + +The "compute chunk/spread/atom"_compute_chunk_spread_atom.html command +spreads per-chunk values to each atom in the chunk, producing per-atom +values as its output. This can be useful for outputting per-chunk +values to a per-atom "dump file"_dump.html. Or for using an atom's +associated chunk value in an "atom-style variable"_variable.html. + +The "compute reduce/chunk"_compute_reduce_chunk.html command reduces a +peratom value across the atoms in each chunk to produce a value per +chunk. When used with the "compute +chunk/spread/atom"_compute_chunk_spread_atom.html command it can +create peratom values that induce a new set of chunks with a second +"compute chunk/atom"_compute_chunk_atom.html command. Example calculations with chunks :h4 @@ -164,3 +183,13 @@ compute cluster all cluster/atom 1.0 compute cc1 all chunk/atom c_cluster compress yes compute size all property/chunk cc1 count fix 1 all ave/histo 100 1 100 0 20 20 c_size mode vector ave running beyond ignore file tmp.histo :pre + +(6) An example of using a per-chunk value to apply per-atom forces to +compress individual polymer chains (molecules) in a mixture, is +explained on the "compute +chunk/spread/atom"_compute_chunk_spread_atom.html command doc page. + +(7) An example of using one set of per-chunk values for molecule +chunks, to create a 2nd set of micelle-scale chunks (clustered +molecules, due to hydrophobicity), is explained on the "compute +chunk/reduce"_compute_reduce_chunk.html command doc page. diff --git a/doc/src/compute.txt b/doc/src/compute.txt index 8facb4de63..72ea1c1930 100644 --- a/doc/src/compute.txt +++ b/doc/src/compute.txt @@ -183,6 +183,7 @@ compute"_Commands_compute.html doc page are followed by one or more of "bond/local"_compute_bond_local.html - distance and energy of each bond "centro/atom"_compute_centro_atom.html - centro-symmetry parameter for each atom "chunk/atom"_compute_chunk_atom.html - assign chunk IDs to each atom +"chunk/spread/atom"_compute_chunk_spread_atom.html - spreads chunk values to each atom in chunk "cluster/atom"_compute_cluster_atom.html - cluster ID for each atom "cna/atom"_compute_cna_atom.html - common neighbor analysis (CNA) for each atom "com"_compute_com.html - center-of-mass of group of atoms @@ -225,6 +226,7 @@ compute"_Commands_compute.html doc page are followed by one or more of "property/chunk"_compute_property_chunk.html - extract various per-chunk attributes "rdf"_compute_rdf.html - radial distribution function g(r) histogram of group of atoms "reduce"_compute_reduce.html - combine per-atom quantities into a single global value +"reduce/chunk"_compute_reduce_chunk.html - reduce per-atom quantities within each chunk "reduce/region"_compute_reduce.html - same as compute reduce, within a region "rigid/local"_compute_rigid_local.html - extract rigid body attributes "slice"_compute_slice.html - extract values from global vector or array diff --git a/doc/src/compute_chunk_atom.txt b/doc/src/compute_chunk_atom.txt index e76b51e6ec..c29a5600a9 100644 --- a/doc/src/compute_chunk_atom.txt +++ b/doc/src/compute_chunk_atom.txt @@ -14,7 +14,7 @@ compute ID group-ID chunk/atom style args keyword values ... :pre ID, group-ID are documented in "compute"_compute.html command :ulb,l chunk/atom = style name of this compute command :l -style = {bin/1d} or {bin/2d} or {bin/3d} or {bin/sphere} or {type} or {molecule} or {compute/fix/variable} +style = {bin/1d} or {bin/2d} or {bin/3d} or {bin/sphere} or {type} or {molecule} or c_ID, c_ID\[I\], f_ID, f_ID\[I\], v_name {bin/1d} args = dim origin delta dim = {x} or {y} or {z} origin = {lower} or {center} or {upper} or coordinate value (distance units) @@ -40,7 +40,7 @@ style = {bin/1d} or {bin/2d} or {bin/3d} or {bin/sphere} or {type} or {molecule} ncbin = # of concentric circle bins between rmin and rmax {type} args = none {molecule} args = none - {compute/fix/variable} = c_ID, c_ID\[I\], f_ID, f_ID\[I\], v_name with no args + c_ID, c_ID\[I\], f_ID, f_ID\[I\], v_name args = none c_ID = per-atom vector calculated by a compute with ID c_ID\[I\] = Ith column of per-atom array calculated by a compute with ID f_ID = per-atom vector calculated by a fix with ID @@ -85,7 +85,8 @@ compute 1 all chunk/atom bin/1d z lower 0.02 units reduced compute 1 all chunk/atom bin/2d z lower 1.0 y 0.0 2.5 compute 1 all chunk/atom molecule region sphere nchunk once ids once compress yes compute 1 all chunk/atom bin/sphere 5 5 5 2.0 5.0 5 discard yes -compute 1 all chunk/atom bin/cylinder z lower 2 10 10 2.0 5.0 3 discard yes :pre +compute 1 all chunk/atom bin/cylinder z lower 2 10 10 2.0 5.0 3 discard yes +compute 1 all chunk/atom c_cluster :pre [Description:] @@ -386,8 +387,8 @@ described below, which resets {Nchunk}. The {limit} keyword is then applied to the new {Nchunk} value, exactly as described in the preceding paragraph. Note that in this case, all atoms will end up with chunk IDs <= {Nc}, but their original values (e.g. molecule ID or -compute/fix/variable value) may have been > {Nc}, because of the -compression operation. +compute/fix/variable) may have been > {Nc}, because of the compression +operation. If {compress yes} is set, and the {compress} keyword comes after the {limit} keyword, then the {limit} value of {Nc} is applied first to diff --git a/doc/src/compute_chunk_spread_atom.txt b/doc/src/compute_chunk_spread_atom.txt new file mode 100644 index 0000000000..59662035e5 --- /dev/null +++ b/doc/src/compute_chunk_spread_atom.txt @@ -0,0 +1,173 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +compute chunk/spread/atom command :h3 + +[Syntax:] + +compute ID group-ID chunk/spread/atom chunkID input1 input2 ... :pre + +ID, group-ID are documented in "compute"_compute.html command :ulb,l +chunk/spread/atom = style name of this compute command :l +chunkID = ID of "compute chunk/atom"_compute_chunk_atom.html command :l +one or more inputs can be listed :l +input = c_ID, c_ID\[N\], f_ID, f_ID\[N\] :l + c_ID = global vector calculated by a compute with ID + c_ID\[I\] = Ith column of global array calculated by a compute with ID, I can include wildcard (see below) + f_ID = global vector calculated by a fix with ID + f_ID\[I\] = Ith column of global array calculated by a fix with ID, I can include wildcard (see below) :pre +:ule + +[Examples:] + +compute 1 all chunk/spread/atom mychunk c_com[*] c_gyration :pre + +[Description:] + +Define a calculation that "spreads" one or more per-chunk values to +each atom in the chunk. This can be useful for creating a "dump +file"_dump.html where each atom lists info about the chunk it is in, +e.g. for post-processing purposes. It can also be used in "atom-style +variables"_variable.html that need info about the chunk each atom is +in. Examples are given below. + +In LAMMPS, chunks are collections of atoms defined by a "compute +chunk/atom"_compute_chunk_atom.html command, which assigns each atom +to a single chunk (or no chunk). The ID for this command is specified +as chunkID. For example, a single chunk could be the atoms in a +molecule or atoms in a spatial bin. See the "compute +chunk/atom"_compute_chunk_atom.html and "Howto chunk"_Howto_chunk.html +doc pages for details of how chunks can be defined and examples of how +they can be used to measure properties of a system. + +For inputs that are computes, they must be a compute that calculates +per-chunk values. These are computes whose style names end in +"/chunk". + +For inputs that are fixes, they should be a a fix that calculates +per-chunk values. For example, "fix ave/chunk"_fix_ave_chunk.html or +"fix ave/time"_fix_ave_time.html (assuming it is time-averaging +per-chunk data). + +For each atom, this compute accesses its chunk ID from the specified +{chunkID} compute, then accesses the per-chunk value in each input. +Those values are copied to this compute to become the output for that +atom. + +The values generated by this compute will be 0.0 for atoms not in the +specified compute group {group-ID}. They will also be 0.0 if the atom +is not in a chunk, as assigned by the {chunkID} compute. They will +also be 0.0 if the current chunk ID for the atom is out-of-bounds with +respect to the number of chunks stored by a particular input compute +or fix. + +NOTE: LAMMPS does not check that a compute or fix which calculates +per-chunk values uses the same definition of chunks as this compute. +It's up to you to be consistent. Likewise, for a fix input, LAMMPS +does not check that it is per-chunk data. It only checks that the fix +produces a global vector or array. + +:line + +Each listed input is operated on independently. + +If a bracketed index I is used, it can be specified using a wildcard +asterisk with the index to effectively specify multiple values. This +takes the form "*" or "*n" or "n*" or "m*n". If N = the number of +columns in the array, then an asterisk with no numeric values means +all indices from 1 to N. A leading asterisk means all indices from 1 +to n (inclusive). A trailing asterisk means all indices from n to N +(inclusive). A middle asterisk means all indices from m to n +(inclusive). + +Using a wildcard is the same as if the individual columns of the array +had been listed one by one. E.g. these 2 compute chunk/spread/atom +commands are equivalent, since the "compute +com/chunk"_compute_com_chunk.html command creates a per-atom array +with 3 columns: + +compute com all com/chunk mychunk +compute 10 all chunk/spread/atom mychunk c_com\[*\] +compute 10 all chunk/spread/atom mychunk c_com\[1\] c_com\[2\] c_com\[3\] :pre + +:line + +Here is an example of writing a dump file the with the center-of-mass +(COM) for the chunk each atom is in: + +compute cmol all chunk/atom molecule +compute com all com/chunk cmol +compute comchunk all chunk/spread/atom cmol c_com[*] +dump 1 all custom 50 tmp.dump id mol type x y z c_comchunk[*] +dump_modify 1 sort id :pre + +The same per-chunk data for each atom could be used to define per-atom +forces for the "fix addforce"_fix_addforce.html command. In this +example the forces act to pull atoms of an extended polymer chain +towards its COM in an attractive manner. + +compute prop all property/atom xu yu zu +variable k equal 0.1 +variable fx atom v_k*(c_comchunk\[1\]-c_prop\[1\]) +variable fy atom v_k*(c_comchunk\[2\]-c_prop\[2\]) +variable fz atom v_k*(c_comchunk\[3\]-c_prop\[3\]) +fix 3 all addforce v_fx v_fy v_fz :pre + +Note that "compute property/atom"_compute_property_atom.html is used +to generate unwrapped coordinates for use in the per-atom force +calculation, so that the effect of periodic boundaries is accounted +for properly. + +Over time this applied force could shrink each polymer chain's radius +of gyration in a polymer mixture simulation. Here is output after +adding the above lines to the bench/in.chain script. The thermo +output is shown for 1000 steps, where the last column is the average +radius of gyration over all 320 chains in the 32000 atom system: + +compute gyr all gyration/chunk cmol +variable ave equal ave(c_gyr) +thermo_style custom step etotal press v_ave :pre + + 0 22.394765 4.6721833 5.128278 + 100 22.445002 4.8166709 5.0348372 + 200 22.500128 4.8790392 4.9364875 + 300 22.534686 4.9183766 4.8590693 + 400 22.557196 4.9492211 4.7937849 + 500 22.571017 4.9161853 4.7412008 + 600 22.573944 5.0229708 4.6931243 + 700 22.581804 5.0541301 4.6440647 + 800 22.584683 4.9691734 4.6000016 + 900 22.59128 5.0247538 4.5611513 + 1000 22.586832 4.94697 4.5238362 :pre + +:line + +[Output info:] + +This compute calculates a per-atom vector or array, which can be +accessed by any command that uses per-atom values from a compute as +input. See the "Howto output"_Howto_output.html doc page for an +overview of LAMMPS output options. + +The output is a per-atom vector if a single input value is specified, +otherwise a per-atom array is output. The number of columns in the +array is the number of inputs provided. The per-atom values for the +vector or each column of the array will be in whatever +"units"_units.html the corresponding input value is in. + +The vector or array values are "intensive". + +[Restrictions:] none + +[Related commands:] + +"compute chunk/atom"_compute_chunk_atom.html, "fix +ave/chunk"_fix_ave_chunk.html, "compute +reduce/chunk"_compute_reduce_chunk.html + +[Default:] none diff --git a/doc/src/compute_reduce.txt b/doc/src/compute_reduce.txt index ef3c7c6489..0bd2accf3c 100644 --- a/doc/src/compute_reduce.txt +++ b/doc/src/compute_reduce.txt @@ -97,9 +97,9 @@ equivalent, since the "compute stress/atom"_compute_stress_atom.html command creates a per-atom array with 6 columns: compute myPress all stress/atom NULL -compute 2 all reduce min myPress\[*\] -compute 2 all reduce min myPress\[1\] myPress\[2\] myPress\[3\] & - myPress\[4\] myPress\[5\] myPress\[6\] :pre +compute 2 all reduce min c_myPress\[*\] +compute 2 all reduce min c_myPress\[1\] c_myPress\[2\] c_myPress\[3\] & + c_myPress\[4\] c_myPress\[5\] c_myPress\[6\] :pre :line diff --git a/doc/src/compute_reduce_chunk.txt b/doc/src/compute_reduce_chunk.txt new file mode 100644 index 0000000000..3628c0f1ad --- /dev/null +++ b/doc/src/compute_reduce_chunk.txt @@ -0,0 +1,177 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +compute reduce/chunk command :h3 + +[Syntax:] + +compute ID group-ID reduce/chunk chunkID mode input1 input2 ... :pre + +ID, group-ID are documented in "compute"_compute.html command :ulb,l +reduce/chunk = style name of this compute command :l +chunkID = ID of "compute chunk/atom"_compute_chunk_atom.html command :l +mode = {sum} or {min} or {max} :l +one or more inputs can be listed :l +input = c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_ID :l + c_ID = per-atom vector calculated by a compute with ID + c_ID\[I\] = Ith column of per-atom array calculated by a compute with ID, I can include wildcard (see below) + f_ID = per-atom vector calculated by a fix with ID + f_ID\[I\] = Ith column of per-atom array calculated by a fix with ID, I can include wildcard (see below) + v_name = per-atom vector calculated by an atom-style variable with name :pre +:ule + +[Examples:] + +compute 1 all reduce/chunk/atom mychunk min c_cluster :pre + +[Description:] + +Define a calculation that reduces one or more per-atom vectors into +per-chunk values. This can be useful for diagnostic output. Or when +used in conjunction with the "compute +chunk/spread/atom"_compute_chunk_spread_atom.html command it can be +used ot create per-atom values that induce a new set of chunks with a +second "compute chunk/atom"_compute_chunk_atom.html command. An +example is given below. + +In LAMMPS, chunks are collections of atoms defined by a "compute +chunk/atom"_compute_chunk_atom.html command, which assigns each atom +to a single chunk (or no chunk). The ID for this command is specified +as chunkID. For example, a single chunk could be the atoms in a +molecule or atoms in a spatial bin. See the "compute +chunk/atom"_compute_chunk_atom.html and "Howto chunk"_Howto_chunk.html +doc pages for details of how chunks can be defined and examples of how +they can be used to measure properties of a system. + +For each atom, this compute accesses its chunk ID from the specified +{chunkID} compute. The per-atom value from an input contributes +to a per-chunk value corresponding the the chunk ID. + +The reduction operation is specified by the {mode} setting and is +performed over all the per-atom values from the atoms in each chunk. +The {sum} option adds the pre-atom values to a per-chunk total. The +{min} or {max} options find the minimum or maximum value of the +per-atom values for each chunk. + +Note that only atoms in the specified group contribute to the +reduction operation. If the {chunkID} compute returns a 0 for the +chunk ID of an atom (i.e. the atom is not in a chunk defined by the +"compute chunk/atom"_compute_chunk_atom.html command), that atom will +also not contribute to the reduction operation. An input that is a +compute or fix may define its own group which affects the quantities +it returns. For example, a compute with return a zero value for atoms +that are not in the group specified for that compute. + +Each listed input is operated on independently. Each input can be the +result of a "compute"_compute.html or "fix"_fix.html or the evaluation +of an atom-style "variable"_variable.html. + +Note that for values from a compute or fix, the bracketed index I can +be specified using a wildcard asterisk with the index to effectively +specify multiple values. This takes the form "*" or "*n" or "n*" or +"m*n". If N = the size of the vector (for {mode} = scalar) or the +number of columns in the array (for {mode} = vector), then an asterisk +with no numeric values means all indices from 1 to N. A leading +asterisk means all indices from 1 to n (inclusive). A trailing +asterisk means all indices from n to N (inclusive). A middle asterisk +means all indices from m to n (inclusive). + +Using a wildcard is the same as if the individual columns of the array +had been listed one by one. E.g. these 2 compute reduce/chunk +commands are equivalent, since the "compute +property/chunk"_compute_property_chunk.html command creates a per-atom +array with 3 columns: + +compute prop all property/atom vx vy vz +compute 10 all reduce/chunk mychunk max c_prop\[*\] +compute 10 all reduce/chunk mychunk max c_prop\[1\] c_prop\[2\] c_prop\[3\] :pre + +:line + +Here is an example of using this compute, in conjunction with the +compute chunk/spread/atom command to identify self-assembled micelles. +The commands below can be added to the examples/in.micelle script. + +Imagine a collection of polymer chains or small molecules with +hydrophobic end groups. All the hydrophobic (HP) atoms are assigned +to a group called "phobic". + +These commands will assign a unique cluster ID to all HP atoms within +a specified distance of each other. A cluster will contain all HP +atoms in a single molecule, but also the HP atoms in nearby molecules, +e.g. molecules that have clumped to form a micelle due to the +attraction induced by the hydrophobicity. The output of the +chunk/reduce command will be a cluster ID per chunk (molecule). +Molecules with the same cluster ID are in the same micelle. + +group phobic type 4 # specific to in.micelle model +compute cluster phobic cluster/atom 2.0 +compute cmol all chunk/atom molecule +compute reduce phobic reduce/chunk cmol min c_cluster :pre + +This per-chunk info could be output in at least two ways: + +fix 10 all ave/time 1000 1 1000 c_reduce file tmp.phobic mode vector :pre + +compute spread all chunk/spread/atom cmol c_reduce +dump 1 all custom 1000 tmp.dump id type mol x y z c_cluster c_spread +dump_modify 1 sort id :pre + +In the first case, each snapshot in the tmp.phobic file will contain +one line per molecule. Molecules with the same value are in the same +micelle. In the second case each dump snapshot contains all atoms, +each with a final field with the cluster ID of the micelle that the HP +atoms of that atom's molecule belong to. + +The result from compute chunk/spread/atom can be used to define a new +set of chunks, where all the atoms in all the molecules in the same +micelle are assigned to the same chunk, i.e. one chunk per micelle. + +compute micelle all chunk/atom c_spread compress yes :pre + +Further analysis on a per-micelle basis can now be performed using any +of the per-chunk computes listed on the "Howto chunk"_Howto_chunk.html +doc page. E.g. count the number of atoms in each micelle, calculate +its center or mass, shape (moments of intertia), radius of gyration, +etc. + +compute prop all property/chunk micelle count +fix 20 all ave/time 1000 1 1000 c_prop file tmp.micelle mode vector :pre + +Each snapshot in the tmp.micelle file will have one line per micelle +with its count of atoms, plus a first line for a chunk with all the +solvent atoms. By the time 50000 steps have elapsed there are a +handful of large micelles. + +:line + +[Output info:] + +This compute calculates a global vector if a single input value is +specified, otherwise a global array is output. The number of columns +in the array is the number of inputs provided. The length of the +vector or the number of vector elements or array rows = the number of +chunks {Nchunk} as calculated by the specified "compute +chunk/atom"_compute_chunk_atom.html command. The vector or array can +be accessed by any command that uses global values from a compute as +input. See the "Howto output"_Howto_output.html doc page for an +overview of LAMMPS output options. + +The per-atom values for the vector or each column of the array will be +in whatever "units"_units.html the corresponding input value is in. +The vector or array values are "intensive". + +[Restrictions:] none + +[Related commands:] + +"compute chunk/atom"_compute_chunk_atom.html, "compute +reduce"_compute_reduce.html, "compute +chunk/spread/atom"_compute_chunk_spread_atom.html + +[Default:] none diff --git a/doc/src/computes.txt b/doc/src/computes.txt index 46dd30f757..6528f78e40 100644 --- a/doc/src/computes.txt +++ b/doc/src/computes.txt @@ -15,6 +15,7 @@ Computes :h1 compute_bond_local compute_centro_atom compute_chunk_atom + compute_chunk_spread_atom compute_cluster_atom compute_cna_atom compute_cnp_atom @@ -72,6 +73,7 @@ Computes :h1 compute_property_local compute_rdf compute_reduce + compute_reduce_chunk compute_rigid_local compute_saed compute_slice diff --git a/doc/src/lammps.book b/doc/src/lammps.book index c296ff4039..c7f0b2fddd 100644 --- a/doc/src/lammps.book +++ b/doc/src/lammps.book @@ -406,6 +406,7 @@ compute_bond.html compute_bond_local.html compute_centro_atom.html compute_chunk_atom.html +compute_chunk_spread_atom.html compute_cluster_atom.html compute_cna_atom.html compute_cnp_atom.html @@ -463,6 +464,7 @@ compute_property_chunk.html compute_property_local.html compute_rdf.html compute_reduce.html +compute_reduce_chunk.html compute_rigid_local.html compute_saed.html compute_slice.html diff --git a/src/compute_chunk_spread_atom.cpp b/src/compute_chunk_spread_atom.cpp new file mode 100644 index 0000000000..93a4d30a2e --- /dev/null +++ b/src/compute_chunk_spread_atom.cpp @@ -0,0 +1,352 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include +#include +#include "compute_chunk_spread_atom.h" +#include "atom.h" +#include "update.h" +#include "modify.h" +#include "fix.h" +#include "compute.h" +#include "compute_chunk_atom.h" +#include "input.h" +#include "memory.h" +#include "error.h" + +using namespace LAMMPS_NS; + +enum{COMPUTE,FIX}; + +#define INVOKED_VECTOR 2 +#define INVOKED_ARRAY 4 +#define INVOKED_PERATOM 8 + +/* ---------------------------------------------------------------------- */ + +ComputeChunkSpreadAtom:: +ComputeChunkSpreadAtom(LAMMPS *lmp, int narg, char **arg) : + Compute(lmp, narg, arg), + which(NULL), argindex(NULL), ids(NULL), value2index(NULL), idchunk(NULL) +{ + if (narg < 5) error->all(FLERR,"Illegal compute chunk/spread/atom command"); + + // ID of compute chunk/atom + + int n = strlen(arg[3]) + 1; + idchunk = new char[n]; + strcpy(idchunk,arg[3]); + init_chunk(); + + // expand args if any have wildcard character "*" + + int iarg = 4; + int expand = 0; + char **earg; + int nargnew = input->expand_args(narg-iarg,&arg[iarg],1,earg); + + if (earg != &arg[iarg]) expand = 1; + arg = earg; + + // parse values + + which = new int[nargnew]; + argindex = new int[nargnew]; + ids = new char*[nargnew]; + value2index = new int[nargnew]; + nvalues = 0; + + iarg = 0; + while (iarg < nargnew) { + ids[nvalues] = NULL; + + if (strncmp(arg[iarg],"c_",2) == 0 || + strncmp(arg[iarg],"f_",2) == 0) { + if (arg[iarg][0] == 'c') which[nvalues] = COMPUTE; + else if (arg[iarg][0] == 'f') which[nvalues] = FIX; + + int n = strlen(arg[iarg]); + char *suffix = new char[n]; + strcpy(suffix,&arg[iarg][2]); + + char *ptr = strchr(suffix,'['); + if (ptr) { + if (suffix[strlen(suffix)-1] != ']') + error->all(FLERR,"Illegal compute chunk/spread/atom command"); + argindex[nvalues] = atoi(ptr+1); + *ptr = '\0'; + } else argindex[nvalues] = 0; + + n = strlen(suffix) + 1; + ids[nvalues] = new char[n]; + strcpy(ids[nvalues],suffix); + nvalues++; + delete [] suffix; + + } else error->all(FLERR,"Illegal compute chunk/spread/atom command"); + + iarg++; + } + + // if wildcard expansion occurred, free earg memory from expand_args() + + if (expand) { + for (int i = 0; i < nargnew; i++) delete [] earg[i]; + memory->sfree(earg); + } + + // setup and error check + // for compute, must calculate per-chunk values, i.e. style ends in "/chunk" + // for fix, assume a global vector or array is per-chunk data + + for (int i = 0; i < nvalues; i++) { + if (which[i] == COMPUTE) { + int icompute = modify->find_compute(ids[i]); + if (icompute < 0) + error->all(FLERR,"Compute ID for compute chunk/spread/atom " + "does not exist"); + + char *ptr = strstr(modify->compute[icompute]->style,"/chunk"); + if (!ptr || (ptr != modify->compute[icompute]->style + + strlen(modify->compute[icompute]->style) - strlen("/chunk"))) + error->all(FLERR,"Compute for compute chunk/spread/atom " + "does not calculate per-chunk values"); + + if (argindex[i] == 0) { + if (!modify->compute[icompute]->vector_flag) + error->all(FLERR,"Compute chunk/spread/atom compute " + "does not calculate global vector"); + } else { + if (!modify->compute[icompute]->array_flag) + error->all(FLERR,"Compute chunk/spread/atom compute " + "does not calculate global array"); + if (argindex[i] > modify->compute[icompute]->size_array_cols) + error->all(FLERR,"Compute chunk/spread/atom compute array " + "is accessed out-of-range"); + } + + } else if (which[i] == FIX) { + int ifix = modify->find_fix(ids[i]); + if (ifix < 0) + error->all(FLERR,"Fix ID for compute chunk/spread/atom does not exist"); + if (argindex[i] == 0) { + if (!modify->fix[ifix]->vector_flag) + error->all(FLERR,"Compute chunk/spread/atom fix " + "does not calculate global vector"); + } else { + if (!modify->fix[ifix]->array_flag) + error->all(FLERR,"Compute chunk/spread/atom fix " + "does not calculate global array"); + if (argindex[i] > modify->fix[ifix]->size_array_cols) + error->all(FLERR,"Compute chunk/spread/atom fix array " + "is accessed out-of-range"); + } + } + } + + // this compute produces a peratom vector or array + + peratom_flag = 1; + if (nvalues == 1) size_peratom_cols = 0; + else size_peratom_cols = nvalues; + + // per-atom vector or array + + nmax = 0; + vector_atom = NULL; + array_atom = NULL; +} + +/* ---------------------------------------------------------------------- */ + +ComputeChunkSpreadAtom::~ComputeChunkSpreadAtom() +{ + delete [] idchunk; + + delete [] which; + delete [] argindex; + for (int i = 0; i < nvalues; i++) delete [] ids[i]; + delete [] ids; + delete [] value2index; + + memory->destroy(vector_atom); + memory->destroy(array_atom); +} + +/* ---------------------------------------------------------------------- */ + +void ComputeChunkSpreadAtom::init() +{ + init_chunk(); + + // set indices of all computes,fixes,variables + + for (int m = 0; m < nvalues; m++) { + if (which[m] == COMPUTE) { + int icompute = modify->find_compute(ids[m]); + if (icompute < 0) + error->all(FLERR,"Compute ID for compute chunk/spread/atom " + "does not exist"); + value2index[m] = icompute; + + } else if (which[m] == FIX) { + int ifix = modify->find_fix(ids[m]); + if (ifix < 0) + error->all(FLERR,"Fix ID for compute chunk/spread/atom does not exist"); + value2index[m] = ifix; + } + } +} + +/* ---------------------------------------------------------------------- */ + +void ComputeChunkSpreadAtom::init_chunk() +{ + int icompute = modify->find_compute(idchunk); + if (icompute < 0) + error->all(FLERR,"Chunk/atom compute does not exist for compute chunk/spread/atom"); + cchunk = (ComputeChunkAtom *) modify->compute[icompute]; + if (strcmp(cchunk->style,"chunk/atom") != 0) + error->all(FLERR,"Compute chunk/spread/atom does not use chunk/atom compute"); +} + +/* ---------------------------------------------------------------------- */ + +void ComputeChunkSpreadAtom::compute_peratom() +{ + invoked_peratom = update->ntimestep; + + // grow local vector_atom or array_atom if necessary + + if (atom->nmax > nmax) { + if (nvalues == 1) { + memory->destroy(vector_atom); + nmax = atom->nmax; + memory->create(vector_atom,nmax,"chunk/spread/atom:vector_atom"); + } else { + memory->destroy(array_atom); + nmax = atom->nmax; + memory->create(array_atom,nmax,nvalues,"chunk/spread/atom:array_atom"); + } + } + + // compute chunk/atom assigns atoms to chunk IDs + // extract ichunk index vector from compute + // ichunk = 1 to Nchunk for included atoms, 0 for excluded atoms + + int nchunk = cchunk->setup_chunks(); + cchunk->compute_ichunk(); + int *ichunk = cchunk->ichunk; + + // loop over values, access compute or fix + // loop over atoms, use chunk ID of each atom to store value from compute/fix + + int *mask = atom->mask; + int nlocal = atom->nlocal; + + int i,m,n,index,nstride; + double *ptr; + + for (m = 0; m < nvalues; m++) { + n = value2index[m]; + + // copy compute/fix values into vector_atom or array_atom + // nstride between values for each atom + + if (nvalues == 1) { + ptr = vector_atom; + nstride = 1; + } else { + ptr = &array_atom[0][m]; + nstride = nvalues; + } + + // invoke compute if not previously invoked + + if (which[m] == COMPUTE) { + Compute *compute = modify->compute[n]; + + if (argindex[m] == 0) { + if (!(compute->invoked_flag & INVOKED_VECTOR)) { + compute->compute_vector(); + compute->invoked_flag |= INVOKED_VECTOR; + } + double *cvector = compute->vector; + for (i = 0; i < nlocal; i++, ptr += nstride) { + *ptr = 0.0; + if (!(mask[i] & groupbit)) continue; + index = ichunk[i]-1; + if (index < 0 || index >= nchunk) continue; + *ptr = cvector[index]; + } + + } else { + if (!(compute->invoked_flag & INVOKED_ARRAY)) { + compute->compute_array(); + compute->invoked_flag |= INVOKED_ARRAY; + } + int icol = argindex[m]-1; + double **carray = compute->array; + for (i = 0; i < nlocal; i++, ptr += nstride) { + *ptr = 0.0; + if (!(mask[i] & groupbit)) continue; + index = ichunk[i]-1; + if (index < 0 || index >= nchunk) continue; + *ptr = carray[index][icol]; + } + } + + // access fix data, check if fix frequency is a match + // are assuming the fix global vector/array is per-chunk data + // check if index exceeds fix output length/rows + + } else if (which[m] == FIX) { + Fix *fix = modify->fix[n]; + if (update->ntimestep % fix->global_freq) + error->all(FLERR,"Fix used in compute chunk/spread/atom not " + "computed at compatible time"); + + if (argindex[m] == 0) { + int nfix = fix->size_vector; + for (i = 0; i < nlocal; i++, ptr += nstride) { + *ptr = 0.0; + if (!(mask[i] & groupbit)) continue; + index = ichunk[i]-1; + if (index < 0 || index >= nchunk || index >= nfix) continue; + *ptr = fix->compute_vector(index); + } + + } else { + int icol = argindex[m]-1; + int nfix = fix->size_array_rows; + for (i = 0; i < nlocal; i++, ptr += nstride) { + *ptr = 0.0; + if (!(mask[i] & groupbit)) continue; + index = ichunk[i]-1; + if (index < 0 || index >= nchunk || index >= nfix) continue; + *ptr = fix->compute_array(index,icol); + } + } + } + } +} + +/* ---------------------------------------------------------------------- + memory usage of local atom-based array +------------------------------------------------------------------------- */ + +double ComputeChunkSpreadAtom::memory_usage() +{ + double bytes = nmax*nvalues * sizeof(double); + return bytes; +} diff --git a/src/compute_chunk_spread_atom.h b/src/compute_chunk_spread_atom.h new file mode 100644 index 0000000000..9a4df080ca --- /dev/null +++ b/src/compute_chunk_spread_atom.h @@ -0,0 +1,61 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef COMPUTE_CLASS + +ComputeStyle(chunk/spread/atom,ComputeChunkSpreadAtom) + +#else + +#ifndef LMP_COMPUTE_CHUNK_SPREAD_ATOM_H +#define LMP_COMPUTE_CHUNK_SPREAD_ATOM_H + +#include "compute.h" + +namespace LAMMPS_NS { + +class ComputeChunkSpreadAtom : public Compute { + public: + ComputeChunkSpreadAtom(class LAMMPS *, int, char **); + ~ComputeChunkSpreadAtom(); + void init(); + void compute_peratom(); + double memory_usage(); + + protected: + int mode,nvalues; + char *idchunk; + + int *which,*argindex,*value2index; + char **ids; + + int nmax; + class ComputeChunkAtom *cchunk; + + void init_chunk(); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +*/ diff --git a/src/compute_reduce.cpp b/src/compute_reduce.cpp index 7c61d666b2..e3c3c5b70a 100644 --- a/src/compute_reduce.cpp +++ b/src/compute_reduce.cpp @@ -11,6 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include #include #include #include "compute_reduce.h" diff --git a/src/compute_reduce_chunk.cpp b/src/compute_reduce_chunk.cpp new file mode 100644 index 0000000000..40e9dad8dd --- /dev/null +++ b/src/compute_reduce_chunk.cpp @@ -0,0 +1,512 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include +#include +#include "compute_reduce_chunk.h" +#include "atom.h" +#include "update.h" +#include "modify.h" +#include "fix.h" +#include "compute.h" +#include "compute_chunk_atom.h" +#include "input.h" +#include "variable.h" +#include "memory.h" +#include "error.h" + +using namespace LAMMPS_NS; + +enum{SUM,MINN,MAXX}; +enum{COMPUTE,FIX,VARIABLE}; + +#define INVOKED_PERATOM 8 + +#define BIG 1.0e20 + +/* ---------------------------------------------------------------------- */ + +ComputeReduceChunk::ComputeReduceChunk(LAMMPS *lmp, int narg, char **arg) : + Compute(lmp, narg, arg), + vlocal(NULL), vglobal(NULL), alocal(NULL), aglobal(NULL), varatom(NULL), + which(NULL), argindex(NULL), value2index(NULL), idchunk(NULL), ids(NULL) +{ + if (narg < 6) error->all(FLERR,"Illegal compute reduce/chunk command"); + + // ID of compute chunk/atom + + int n = strlen(arg[3]) + 1; + idchunk = new char[n]; + strcpy(idchunk,arg[3]); + init_chunk(); + + // mode + + if (strcmp(arg[4],"sum") == 0) mode = SUM; + else if (strcmp(arg[4],"min") == 0) mode = MINN; + else if (strcmp(arg[4],"max") == 0) mode = MAXX; + else error->all(FLERR,"Illegal compute reduce/chunk command"); + + int iarg = 5; + + // expand args if any have wildcard character "*" + + int expand = 0; + char **earg; + int nargnew = input->expand_args(narg-iarg,&arg[iarg],1,earg); + + if (earg != &arg[iarg]) expand = 1; + arg = earg; + + // parse values until one isn't recognized + + which = new int[nargnew]; + argindex = new int[nargnew]; + ids = new char*[nargnew]; + value2index = new int[nargnew]; + nvalues = 0; + + iarg = 0; + while (iarg < nargnew) { + ids[nvalues] = NULL; + + if (strncmp(arg[iarg],"c_",2) == 0 || + strncmp(arg[iarg],"f_",2) == 0 || + strncmp(arg[iarg],"v_",2) == 0) { + if (arg[iarg][0] == 'c') which[nvalues] = COMPUTE; + else if (arg[iarg][0] == 'f') which[nvalues] = FIX; + else if (arg[iarg][0] == 'v') which[nvalues] = VARIABLE; + + int n = strlen(arg[iarg]); + char *suffix = new char[n]; + strcpy(suffix,&arg[iarg][2]); + + char *ptr = strchr(suffix,'['); + if (ptr) { + if (suffix[strlen(suffix)-1] != ']') + error->all(FLERR,"Illegal compute reduce/chunk command"); + argindex[nvalues] = atoi(ptr+1); + *ptr = '\0'; + } else argindex[nvalues] = 0; + + n = strlen(suffix) + 1; + ids[nvalues] = new char[n]; + strcpy(ids[nvalues],suffix); + nvalues++; + delete [] suffix; + + } else error->all(FLERR,"Illegal compute reduce/chunk command"); + + iarg++; + } + + // if wildcard expansion occurred, free earg memory from expand_args() + + if (expand) { + for (int i = 0; i < nargnew; i++) delete [] earg[i]; + memory->sfree(earg); + } + + // error check + + for (int i = 0; i < nvalues; i++) { + if (which[i] == COMPUTE) { + int icompute = modify->find_compute(ids[i]); + if (icompute < 0) + error->all(FLERR,"Compute ID for compute reduce/chunk does not exist"); + if (!modify->compute[icompute]->peratom_flag) + error->all(FLERR,"Compute reduce/chunk compute does not " + "calculate per-atom values"); + if (argindex[i] == 0 && + modify->compute[icompute]->size_peratom_cols != 0) + error->all(FLERR,"Compute reduce/chunk compute does not " + "calculate a per-atom vector"); + if (argindex[i] && modify->compute[icompute]->size_peratom_cols == 0) + error->all(FLERR,"Compute reduce/chunk compute does not " + "calculate a per-atom array"); + if (argindex[i] && + argindex[i] > modify->compute[icompute]->size_peratom_cols) + error->all(FLERR, + "Compute reduce/chunk compute array is accessed out-of-range"); + + } else if (which[i] == FIX) { + int ifix = modify->find_fix(ids[i]); + if (ifix < 0) + error->all(FLERR,"Fix ID for compute reduce/chunk does not exist"); + if (!modify->fix[ifix]->peratom_flag) + error->all(FLERR,"Compute reduce/chunk fix does not " + "calculate per-atom values"); + if (argindex[i] == 0 && + modify->fix[ifix]->size_peratom_cols != 0) + error->all(FLERR,"Compute reduce/chunk fix does not " + "calculate a per-atom vector"); + if (argindex[i] && modify->fix[ifix]->size_peratom_cols == 0) + error->all(FLERR,"Compute reduce/chunk fix does not " + "calculate a per-atom array"); + if (argindex[i] && argindex[i] > modify->fix[ifix]->size_peratom_cols) + error->all(FLERR,"Compute reduce/chunk fix array is " + "accessed out-of-range"); + + } else if (which[i] == VARIABLE) { + int ivariable = input->variable->find(ids[i]); + if (ivariable < 0) + error->all(FLERR,"Variable name for compute reduce/chunk does not exist"); + if (input->variable->atomstyle(ivariable) == 0) + error->all(FLERR,"Compute reduce/chunk variable is " + "not atom-style variable"); + } + } + + // this compute produces either a vector or array + + if (nvalues == 1) { + vector_flag = 1; + size_vector_variable = 1; + extvector = 0; + } else { + array_flag = 1; + size_array_rows_variable = 1; + size_array_cols = nvalues; + extarray = 0; + } + + // setup + + if (mode == SUM) initvalue = 0.0; + else if (mode == MINN) initvalue = BIG; + else if (mode == MAXX) initvalue = -BIG; + + maxchunk = 0; + vlocal = vglobal = NULL; + alocal = aglobal = NULL; + + maxatom = 0; + varatom = NULL; +} + +/* ---------------------------------------------------------------------- */ + +ComputeReduceChunk::~ComputeReduceChunk() +{ + delete [] idchunk; + + delete [] which; + delete [] argindex; + for (int m = 0; m < nvalues; m++) delete [] ids[m]; + delete [] ids; + delete [] value2index; + + memory->destroy(vlocal); + memory->destroy(vglobal); + memory->destroy(alocal); + memory->destroy(aglobal); + + memory->destroy(varatom); +} + +/* ---------------------------------------------------------------------- */ + +void ComputeReduceChunk::init() +{ + init_chunk(); + + // set indices of all computes,fixes,variables + + for (int m = 0; m < nvalues; m++) { + if (which[m] == COMPUTE) { + int icompute = modify->find_compute(ids[m]); + if (icompute < 0) + error->all(FLERR,"Compute ID for compute reduce/chunk does not exist"); + value2index[m] = icompute; + + } else if (which[m] == FIX) { + int ifix = modify->find_fix(ids[m]); + if (ifix < 0) + error->all(FLERR,"Fix ID for compute reduce/chunk does not exist"); + value2index[m] = ifix; + + } else if (which[m] == VARIABLE) { + int ivariable = input->variable->find(ids[m]); + if (ivariable < 0) + error->all(FLERR,"Variable name for compute reduce/chunk does not exist"); + value2index[m] = ivariable; + } + } +} + +/* ---------------------------------------------------------------------- */ + +void ComputeReduceChunk::init_chunk() +{ + int icompute = modify->find_compute(idchunk); + if (icompute < 0) + error->all(FLERR,"Chunk/atom compute does not exist for " + "compute reduce/chunk"); + cchunk = (ComputeChunkAtom *) modify->compute[icompute]; + if (strcmp(cchunk->style,"chunk/atom") != 0) + error->all(FLERR,"Compute reduce/chunk does not use chunk/atom compute"); +} + +/* ---------------------------------------------------------------------- */ + +void ComputeReduceChunk::compute_vector() +{ + invoked_vector = update->ntimestep; + + // compute chunk/atom assigns atoms to chunk IDs + // extract ichunk index vector from compute + // ichunk = 1 to Nchunk for included atoms, 0 for excluded atoms + + nchunk = cchunk->setup_chunks(); + cchunk->compute_ichunk(); + ichunk = cchunk->ichunk; + if (!nchunk) return; + + size_vector = nchunk; + + if (nchunk > maxchunk) { + memory->destroy(vlocal); + memory->destroy(vglobal); + maxchunk = nchunk; + memory->create(vlocal,maxchunk,"reduce/chunk:vlocal"); + memory->create(vglobal,maxchunk,"reduce/chunk:vglobal"); + vector = vglobal; + } + + // perform local reduction of single peratom value + + compute_one(0,vlocal,1); + + // reduce the per-chunk values across all procs + + if (mode == SUM) + MPI_Allreduce(vlocal,vglobal,nchunk,MPI_DOUBLE,MPI_SUM,world); + else if (mode == MINN) + MPI_Allreduce(vlocal,vglobal,nchunk,MPI_DOUBLE,MPI_MIN,world); + else if (mode == MAXX) + MPI_Allreduce(vlocal,vglobal,nchunk,MPI_DOUBLE,MPI_MAX,world); +} + +/* ---------------------------------------------------------------------- */ + +void ComputeReduceChunk::compute_array() +{ + invoked_array = update->ntimestep; + + // compute chunk/atom assigns atoms to chunk IDs + // extract ichunk index vector from compute + // ichunk = 1 to Nchunk for included atoms, 0 for excluded atoms + + nchunk = cchunk->setup_chunks(); + cchunk->compute_ichunk(); + ichunk = cchunk->ichunk; + if (!nchunk) return; + + size_array_rows = nchunk; + + if (nchunk > maxchunk) { + memory->destroy(alocal); + memory->destroy(aglobal); + maxchunk = nchunk; + memory->create(alocal,maxchunk,nvalues,"reduce/chunk:alocal"); + memory->create(aglobal,maxchunk,nvalues,"reduce/chunk:aglobal"); + array = aglobal; + } + + // perform local reduction of all peratom values + + for (int m = 0; m < nvalues; m++) compute_one(m,&alocal[0][m],nvalues); + + // reduce the per-chunk values across all procs + + if (mode == SUM) + MPI_Allreduce(&alocal[0][0],&aglobal[0][0],nchunk*nvalues, + MPI_DOUBLE,MPI_SUM,world); + else if (mode == MINN) + MPI_Allreduce(&alocal[0][0],&aglobal[0][0],nchunk*nvalues, + MPI_DOUBLE,MPI_MIN,world); + else if (mode == MAXX) + MPI_Allreduce(&alocal[0][0],&aglobal[0][0],nchunk*nvalues, + MPI_DOUBLE,MPI_MAX,world); +} + +/* ---------------------------------------------------------------------- */ + +void ComputeReduceChunk::compute_one(int m, double *vchunk, int nstride) +{ + // initialize per-chunk values in accumulation vector + + for (int i = 0; i < nchunk; i += nstride) vchunk[i] = initvalue; + + // loop over my atoms + // use peratom input and chunk ID of each atom to update vector + + int *mask = atom->mask; + int nlocal = atom->nlocal; + + int index; + + if (which[m] == COMPUTE) { + Compute *compute = modify->compute[value2index[m]]; + + if (!(compute->invoked_flag & INVOKED_PERATOM)) { + compute->compute_peratom(); + compute->invoked_flag |= INVOKED_PERATOM; + } + + if (argindex[m] == 0) { + double *vcompute = compute->vector_atom; + for (int i = 0; i < nlocal; i++) { + if (!(mask[i] & groupbit)) continue; + index = ichunk[i]-1; + if (index < 0) continue; + combine(vchunk[index*nstride],vcompute[i]); + } + } else { + double **acompute = compute->array_atom; + int argindexm1 = argindex[m] - 1; + for (int i = 0; i < nlocal; i++) { + if (!(mask[i] & groupbit)) continue; + index = ichunk[i]-1; + if (index < 0) continue; + combine(vchunk[index*nstride],acompute[i][argindexm1]); + } + } + + // access fix fields, check if fix frequency is a match + + } else if (which[m] == FIX) { + Fix *fix = modify->fix[value2index[m]]; + if (update->ntimestep % fix->peratom_freq) + error->all(FLERR,"Fix used in compute reduce/chunk not " + "computed at compatible time"); + + if (argindex[m] == 0) { + double *vfix = fix->vector_atom; + for (int i = 0; i < nlocal; i++) { + if (!(mask[i] & groupbit)) continue; + index = ichunk[i]-1; + if (index < 0) continue; + combine(vchunk[index*nstride],vfix[i]); + } + } else { + double **afix = fix->array_atom; + int argindexm1 = argindex[m] - 1; + for (int i = 0; i < nlocal; i++) { + if (!(mask[i] & groupbit)) continue; + index = ichunk[i]-1; + if (index < 0) continue; + combine(vchunk[index*nstride],afix[i][argindexm1]); + } + } + + // evaluate atom-style variable + + } else if (which[m] == VARIABLE) { + if (atom->nmax > maxatom) { + memory->destroy(varatom); + maxatom = atom->nmax; + memory->create(varatom,maxatom,"reduce/chunk:varatom"); + } + + input->variable->compute_atom(value2index[m],igroup,varatom,1,0); + for (int i = 0; i < nlocal; i++) { + if (!(mask[i] & groupbit)) continue; + index = ichunk[i]-1; + if (index < 0) continue; + combine(vchunk[index*nstride],varatom[i]); + } + } +} + +/* ---------------------------------------------------------------------- + combine two values according to reduction mode +------------------------------------------------------------------------- */ + +void ComputeReduceChunk::combine(double &one, double two) +{ + if (mode == SUM) one += two; + else if (mode == MINN) { + if (two < one) one = two; + } else if (mode == MAXX) { + if (two > one) one = two; + } +} + +/* ---------------------------------------------------------------------- + lock methods: called by fix ave/time + these methods insure vector/array size is locked for Nfreq epoch + by passing lock info along to compute chunk/atom +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + increment lock counter +------------------------------------------------------------------------- */ + +void ComputeReduceChunk::lock_enable() +{ + cchunk->lockcount++; +} + +/* ---------------------------------------------------------------------- + decrement lock counter in compute chunk/atom, if it still exists +------------------------------------------------------------------------- */ + +void ComputeReduceChunk::lock_disable() +{ + int icompute = modify->find_compute(idchunk); + if (icompute >= 0) { + cchunk = (ComputeChunkAtom *) modify->compute[icompute]; + cchunk->lockcount--; + } +} + +/* ---------------------------------------------------------------------- + calculate and return # of chunks = length of vector/array +------------------------------------------------------------------------- */ + +int ComputeReduceChunk::lock_length() +{ + nchunk = cchunk->setup_chunks(); + return nchunk; +} + +/* ---------------------------------------------------------------------- + set the lock from startstep to stopstep +------------------------------------------------------------------------- */ + +void ComputeReduceChunk::lock(Fix *fixptr, bigint startstep, bigint stopstep) +{ + cchunk->lock(fixptr,startstep,stopstep); +} + +/* ---------------------------------------------------------------------- + unset the lock +------------------------------------------------------------------------- */ + +void ComputeReduceChunk::unlock(Fix *fixptr) +{ + cchunk->unlock(fixptr); +} + +/* ---------------------------------------------------------------------- + memory usage of local data +------------------------------------------------------------------------- */ + +double ComputeReduceChunk::memory_usage() +{ + double bytes = (bigint) maxatom * sizeof(double); + if (nvalues == 1) bytes += (bigint) maxchunk * 2 * sizeof(double); + else bytes += (bigint) maxchunk * nvalues * 2 * sizeof(double); + return bytes; +} diff --git a/src/compute_reduce_chunk.h b/src/compute_reduce_chunk.h new file mode 100644 index 0000000000..ac556907b7 --- /dev/null +++ b/src/compute_reduce_chunk.h @@ -0,0 +1,77 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef COMPUTE_CLASS + +ComputeStyle(reduce/chunk,ComputeReduceChunk) + +#else + +#ifndef LMP_COMPUTE_REDUCE_CHUNK_H +#define LMP_COMPUTE_REDUCE_CHUNK_H + +#include "compute.h" + +namespace LAMMPS_NS { + +class ComputeReduceChunk : public Compute { + public: + ComputeReduceChunk(class LAMMPS *, int, char **); + ~ComputeReduceChunk(); + void init(); + void compute_vector(); + void compute_array(); + + void lock_enable(); + void lock_disable(); + int lock_length(); + void lock(class Fix *, bigint, bigint); + void unlock(class Fix *); + + double memory_usage(); + + private: + int mode,nvalues; + int *which,*argindex,*value2index; + char *idchunk; + char **ids; + + int nchunk; + int maxchunk,maxatom; + double initvalue; + double *vlocal,*vglobal; + double **alocal,**aglobal; + double *varatom; + + class ComputeChunkAtom *cchunk; + int *ichunk; + + void init_chunk(); + void compute_one(int, double *, int); + void combine(double &, double); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +*/ From e3ce702eec1c6d8b2d875827de642c68e6b4e77d Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Fri, 31 Aug 2018 13:53:02 -0600 Subject: [PATCH 116/302] doc adjust --- doc/src/compute_chunk_spread_atom.txt | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/doc/src/compute_chunk_spread_atom.txt b/doc/src/compute_chunk_spread_atom.txt index 59662035e5..f84ef67974 100644 --- a/doc/src/compute_chunk_spread_atom.txt +++ b/doc/src/compute_chunk_spread_atom.txt @@ -98,7 +98,8 @@ compute 10 all chunk/spread/atom mychunk c_com\[1\] c_com\[2\] c_com\[3\] :pre :line Here is an example of writing a dump file the with the center-of-mass -(COM) for the chunk each atom is in: +(COM) for the chunk each atom is in. The commands below can be added +to the bench/in.chain script. compute cmol all chunk/atom molecule compute com all com/chunk cmol @@ -124,10 +125,10 @@ calculation, so that the effect of periodic boundaries is accounted for properly. Over time this applied force could shrink each polymer chain's radius -of gyration in a polymer mixture simulation. Here is output after -adding the above lines to the bench/in.chain script. The thermo -output is shown for 1000 steps, where the last column is the average -radius of gyration over all 320 chains in the 32000 atom system: +of gyration in a polymer mixture simulation. Here is output from the +bench/in.chain script. Thermo output is shown for 1000 steps, where +the last column is the average radius of gyration over all 320 chains +in the 32000 atom system: compute gyr all gyration/chunk cmol variable ave equal ave(c_gyr) From a989d04d09025e41770b2f71e9e8571c7ded95c0 Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Fri, 31 Aug 2018 14:17:36 -0600 Subject: [PATCH 117/302] think this flag should not be set by this fix --- src/fix_ave_chunk.cpp | 1 - 1 file changed, 1 deletion(-) diff --git a/src/fix_ave_chunk.cpp b/src/fix_ave_chunk.cpp index 1aead70644..fc3ef6ed6e 100644 --- a/src/fix_ave_chunk.cpp +++ b/src/fix_ave_chunk.cpp @@ -63,7 +63,6 @@ FixAveChunk::FixAveChunk(LAMMPS *lmp, int narg, char **arg) : strcpy(idchunk,arg[6]); global_freq = nfreq; - peratom_freq = nfreq; no_change_box = 1; // expand args if any have wildcard character "*" From ba4ff7744b5209a5164228673b58785b1acda63c Mon Sep 17 00:00:00 2001 From: RomainVermorel Date: Mon, 3 Sep 2018 16:26:36 +0200 Subject: [PATCH 118/302] new USER-MOP package submitted --- src/USER-MOP/README | 35 ++ src/USER-MOP/compute_mop.cpp | 424 +++++++++++++++++++++++ src/USER-MOP/compute_mop.example | 62 ++++ src/USER-MOP/compute_mop.h | 74 ++++ src/USER-MOP/compute_mop.txt | 71 ++++ src/USER-MOP/compute_mop_profile.cpp | 490 +++++++++++++++++++++++++++ src/USER-MOP/compute_mop_profile.h | 81 +++++ src/USER-MOP/compute_mop_profile.txt | 72 ++++ 8 files changed, 1309 insertions(+) create mode 100644 src/USER-MOP/README create mode 100755 src/USER-MOP/compute_mop.cpp create mode 100755 src/USER-MOP/compute_mop.example create mode 100755 src/USER-MOP/compute_mop.h create mode 100755 src/USER-MOP/compute_mop.txt create mode 100755 src/USER-MOP/compute_mop_profile.cpp create mode 100755 src/USER-MOP/compute_mop_profile.h create mode 100755 src/USER-MOP/compute_mop_profile.txt diff --git a/src/USER-MOP/README b/src/USER-MOP/README new file mode 100644 index 0000000000..d8e7d2f732 --- /dev/null +++ b/src/USER-MOP/README @@ -0,0 +1,35 @@ +USER-MOP +============ + +This package provides the mop and mop/profile compute styles. +See the doc page for compute mop or compute mop/profile command for how to use +them. + +PACKAGE DESCRIPTION +------------------- + +This is a LAMMPS (http://lammps.sandia.gov/) compute style that calculates +components of the local stress tensor using the method of planes as described in +the paper by Todd et al. (B. D. Todd, Denis J. Evans, and Peter J. Daivis: "Pressure +tensor for inhomogeneous fluids", Phys. Rev. E 52, 1627 (1995)). + +This package contains the source files of two compute styles: +* compute mop calculates components of the local stress tensor using the method of planes, applied on one plane. +* compute mop/profile calculates profiles of components of the local stress tensor using the method of planes, applied on an array of regularly spaced planes. + +The persons who created these files are Laurent Joly at University of Lyon 1 and Romain Vermorel at University of Pau and Pays de l'Adour. +Contact them directly if you have questions. + +Laurent Joly +Institut Lumière Matière +Université Lyon 1 et CNRS +43 boulevard du 11 novembre 1918 +69622 Villeurbanne Cedex +e-mail: laurent.joly@univ-lyon1.fr + +Romain Vermorel +Laboratory of Complex Fluids and their Reservoirs (LFCR) +Université de Pau et des Pays de l'Adour +Avenue de l'Université +64012 Pau +e-mail: romain.vermorel@univ-pau.fr diff --git a/src/USER-MOP/compute_mop.cpp b/src/USER-MOP/compute_mop.cpp new file mode 100755 index 0000000000..42639d73ab --- /dev/null +++ b/src/USER-MOP/compute_mop.cpp @@ -0,0 +1,424 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. + ------------------------------------------------------------------------- */ + +/*------------------------------------------------------------------------ + Contributing Authors : Romain Vermorel (LFCR), Laurent Joly (ULyon) + --------------------------------------------------------------------------*/ + +#include "math.h" +#include "mpi.h" +#include "string.h" +#include "stdlib.h" +#include "compute_mop.h" +#include "atom.h" +#include "update.h" +#include "domain.h" +#include "group.h" +#include "modify.h" +#include "fix.h" +#include "neighbor.h" +#include "force.h" +#include "pair.h" +#include "neigh_request.h" +#include "neigh_list.h" +#include "error.h" +#include "memory.h" + +#include + +using namespace LAMMPS_NS; + +enum{X,Y,Z}; +enum{TOTAL,CONF,KIN}; + +#define BIG 1000000000 + +/* ---------------------------------------------------------------------- */ + +ComputeMop::ComputeMop(LAMMPS *lmp, int narg, char **arg) : + Compute(lmp, narg, arg) +{ + if (narg < 6) error->all(FLERR,"Illegal compute mop command"); + + MPI_Comm_rank(world,&me); + + //set compute mode and direction of plane(s) for pressure calculation + + if (strcmp(arg[3],"x")==0){ + dir = X; + } + else if (strcmp(arg[3],"y")==0){ + dir = Y; + } + else if (strcmp(arg[3],"z")==0){ + dir = Z; + } + else error->all(FLERR,"Illegal compute mop command"); + + //Position of the plane + if (strcmp(arg[4],"lower")==0){ + pos = domain->boxlo[dir]; + } + else if (strcmp(arg[4],"upper")==0){ + pos = domain->boxhi[dir]; + } + else if (strcmp(arg[4],"center")==0){ + pos = 0.5*(domain->boxlo[dir]+domain->boxhi[dir]); + } + else pos = force->numeric(FLERR,arg[4]); + + if ( pos < (domain->boxlo[dir]+domain->prd_half[dir]) ) { + pos1 = pos + domain->prd[dir]; + } else { + pos1 = pos - domain->prd[dir]; + } + + // parse values until one isn't recognized + + which = new int[3*(narg-5)]; + nvalues = 0; + int i; + + int iarg=5; + while (iarg < narg) { + if (strcmp(arg[iarg],"conf") == 0) { + for (i=0; i<3; i++) { + which[nvalues] = CONF; + nvalues++; + } + } else if (strcmp(arg[iarg],"kin") == 0) { + for (i=0; i<3; i++) { + which[nvalues] = KIN; + nvalues++; + } + } else if (strcmp(arg[iarg],"total") == 0) { + for (i=0; i<3; i++) { + which[nvalues] = TOTAL; + nvalues++; + } + } else error->all(FLERR, "Illegal compute mop command"); //break; + + iarg++; + } + + //Error check + // 3D only + if (domain->dimension<3) + error->all(FLERR, "Compute mop incompatible with simulation dimension"); + // orthogonal simulation box + if (domain->triclinic != 0) + error->all(FLERR, "Compute mop incompatible with triclinic simulation box"); + // plane inside the box + if (pos >domain->boxhi[dir] || pos boxlo[dir]) + error->all(FLERR, "Plane for compute mop is out of bounds"); + + + // Initialize some variables + values_local = values_global = vector = NULL; + + // this fix produces a global vector + + memory->create(vector,nvalues,"mop:vector"); + memory->create(values_local,nvalues,"mop/spatial:values_local"); + memory->create(values_global,nvalues,"mop/spatial:values_global"); + size_vector = nvalues; + + vector_flag = 1; + extvector = 0; + +} + +/* ---------------------------------------------------------------------- */ + +ComputeMop::~ComputeMop() +{ + + delete [] which; + + memory->destroy(values_local); + memory->destroy(values_global); + memory->destroy(vector); +} + +/* ---------------------------------------------------------------------- */ + +void ComputeMop::init() +{ + + //Conversion constants + nktv2p = force->nktv2p; + ftm2v = force->ftm2v; + + //Plane area + area = 1; + int i; + for (i=0; i<3; i++){ + if (i!=dir) area = area*domain->prd[i]; + } + + //Timestep Value + dt = update->dt; + +// Error check + +// Compute mop requires fixed simulation box +if (domain->box_change_size || domain->box_change_shape || domain->deform_flag) + error->all(FLERR, "Compute mop requires a fixed simulation box"); + +//This compute requires a pair style with pair_single method implemented +if (force->pair == NULL) + error->all(FLERR,"No pair style is defined for compute mop"); +if (force->pair->single_enable == 0) + error->all(FLERR,"Pair style does not support compute mop"); + +// Warnings +if (me==0){ + //Compute mop only accounts for pair interactions. + // issue a warning if any intramolecular potential or Kspace is defined. + if (force->bond!=NULL) + error->warning(FLERR,"compute mop does not account for bond potentials"); + if (force->angle!=NULL) + error->warning(FLERR,"compute mop does not account for angle potentials"); + if (force->dihedral!=NULL) + error->warning(FLERR,"compute mop does not account for dihedral potentials"); + if (force->improper!=NULL) + error->warning(FLERR,"compute mop does not account for improper potentials"); + if (force->kspace!=NULL) + error->warning(FLERR,"compute mop does not account for kspace contributions"); + } + + // need an occasional half neighbor list + int irequest = neighbor->request((void *) this); + neighbor->requests[irequest]->pair = 0; + neighbor->requests[irequest]->compute = 1; + neighbor->requests[irequest]->occasional = 1; + +} + +/* ---------------------------------------------------------------------- */ + +void ComputeMop::init_list(int id, NeighList *ptr) +{ + list = ptr; +} + + +/* ---------------------------------------------------------------------- + compute output vector + ------------------------------------------------------------------------- */ + +void ComputeMop::compute_vector() +{ + + invoked_array = update->ntimestep; + + //Compute pressures on separate procs + compute_pairs(); + + // sum pressure contributions over all procs + MPI_Allreduce(values_local,values_global,nvalues, + MPI_DOUBLE,MPI_SUM,world); + + int m; + for (m=0; mmass; + int *type = atom->type; + int *mask = atom->mask; + int nlocal = atom->nlocal; + double *special_coul = force->special_coul; + double *special_lj = force->special_lj; + int newton_pair = force->newton_pair; + + + // zero out arrays for one sample + for (i = 0; i < nvalues; i++) values_local[i] = 0.0; + + // invoke half neighbor list (will copy or build if necessary) + neighbor->build_one(list); + + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + // loop over neighbors of my atoms + + Pair *pair = force->pair; + double **cutsq = force->pair->cutsq; + + //Parse values + double xi[3]; + double vi[3]; + double fi[3]; + double xj[3]; + + m = 0; + while (mx[i][0]; + xi[1] = atom->x[i][1]; + xi[2] = atom->x[i][2]; + itype = type[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + factor_lj = special_lj[sbmask(j)]; + factor_coul = special_coul[sbmask(j)]; + j &= NEIGHMASK; + + // skip if neither I nor J are in group + if (!(mask[i] & groupbit || mask[j] & groupbit)) continue; + + xj[0] = atom->x[j][0]; + xj[1] = atom->x[j][1]; + xj[2] = atom->x[j][2]; + delx = xi[0] - xj[0]; + dely = xi[1] - xj[1]; + delz = xi[2] - xj[2]; + rsq = delx*delx + dely*dely + delz*delz; + jtype = type[j]; + if (rsq >= cutsq[itype][jtype]) continue; + + if (newton_pair || j < nlocal) { + + //check if ij pair is accross plane, add contribution to pressure + if ( ((xi[dir]>pos) && (xj[dir]pos1) && (xj[dir]single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair); + + values_local[m] += fpair*(xi[0]-xj[0])/area*nktv2p; + values_local[m+1] += fpair*(xi[1]-xj[1])/area*nktv2p; + values_local[m+2] += fpair*(xi[2]-xj[2])/area*nktv2p; + } + else if ( ((xi[dir]pos)) || ((xi[dir]pos1)) ){ + + pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair); + + values_local[m] -= fpair*(xi[0]-xj[0])/area*nktv2p; + values_local[m+1] -= fpair*(xi[1]-xj[1])/area*nktv2p; + values_local[m+2] -= fpair*(xi[2]-xj[2])/area*nktv2p; + } + + } else { + + if ( ((xi[dir]>pos) && (xj[dir]pos1) && (xj[dir]single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair); + + values_local[m] += fpair*(xi[0]-xj[0])/area*nktv2p; + values_local[m+1] += fpair*(xi[1]-xj[1])/area*nktv2p; + values_local[m+2] += fpair*(xi[2]-xj[2])/area*nktv2p; + } + + } + + } + + } + + } + + + if (which[m] == KIN || which[m] == TOTAL){ + //Compute kinetic contribution to pressure + // counts local particles transfers across the plane + + double vcm[3]; + double masstotal,sgn; + + //Velocity of the center of mass + //int ivcm,vcmbit; + //ivcm = igroup; + //vcmbit = groupbit; + //masstotal = group->mass(ivcm); + //group->vcm(ivcm,masstotal,vcm); + + for (int i = 0; i < nlocal; i++){ + + // skip if I is not in group + if (mask[i] & groupbit){ + + itype = type[i]; + + //coordinates at t + xi[0] = atom->x[i][0]; + xi[1] = atom->x[i][1]; + xi[2] = atom->x[i][2]; + + //velocities at t + vi[0] = atom->v[i][0]; + vi[1] = atom->v[i][1]; + vi[2] = atom->v[i][2]; + + //forces at t + fi[0] = atom->f[i][0]; + fi[1] = atom->f[i][1]; + fi[2] = atom->f[i][2]; + + //coordinates at t-dt (based on Velocity-Verlet alg.) + xj[0] = xi[0]-vi[0]*dt+fi[0]/2/mass[itype]*dt*dt*ftm2v; + xj[1] = xi[1]-vi[1]*dt+fi[1]/2/mass[itype]*dt*dt*ftm2v; + xj[2] = xi[2]-vi[2]*dt+fi[2]/2/mass[itype]*dt*dt*ftm2v; + + //because LAMMPS does not put atoms back in the box at each timestep, must check + //atoms going through the image of the plane that is closest to the box + double pos_temp = pos+copysign(1,domain->prd_half[dir]-pos)*domain->prd[dir]; + if (fabs(xi[dir]-pos)single() to be implemented. In particular, it does not work with more than two-body pair interactions, intra-molecular interactions, and long range (kspace) interactions. + +[Related commands:] + +"compute mop/profile"_compute_mop_profile.html, "compute stress/atom"_compute_stress_atom.html + +[Default:] none + +:line + +:link(mop-todd) +[(Todd)] B. D. Todd, Denis J. Evans, and Peter J. Daivis: "Pressure tensor for inhomogeneous fluids", +Phys. Rev. E 52, 1627 (1995). diff --git a/src/USER-MOP/compute_mop_profile.cpp b/src/USER-MOP/compute_mop_profile.cpp new file mode 100755 index 0000000000..8c9e9041c4 --- /dev/null +++ b/src/USER-MOP/compute_mop_profile.cpp @@ -0,0 +1,490 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. + ------------------------------------------------------------------------- */ + +/*------------------------------------------------------------------------ + Contributing Authors : Romain Vermorel (LFCR), Laurent Joly (ULyon) + --------------------------------------------------------------------------*/ + +#include "math.h" +#include "mpi.h" +#include "string.h" +#include "stdlib.h" +#include "compute_mop_profile.h" +#include "atom.h" +#include "update.h" +#include "domain.h" +#include "group.h" +#include "modify.h" +#include "fix.h" +#include "neighbor.h" +#include "force.h" +#include "pair.h" +#include "neigh_request.h" +#include "neigh_list.h" +#include "error.h" +#include "memory.h" + +#include + +using namespace LAMMPS_NS; + +enum{X,Y,Z}; +enum{LOWER,CENTER,UPPER,COORD}; +enum{TOTAL,CONF,KIN}; + +#define BIG 1000000000 + +/* ---------------------------------------------------------------------- */ + +ComputeMopProfile::ComputeMopProfile(LAMMPS *lmp, int narg, char **arg) : + Compute(lmp, narg, arg) +{ + if (narg < 7) error->all(FLERR,"Illegal compute mop/profile command"); + + MPI_Comm_rank(world,&me); + + //set compute mode and direction of plane(s) for pressure calculation + + if (strcmp(arg[3],"x")==0){ + dir = X; + } + else if (strcmp(arg[3],"y")==0){ + dir = Y; + } + else if (strcmp(arg[3],"z")==0){ + dir = Z; + } + else error->all(FLERR,"Illegal compute mop/profile command"); + + //Bin parameters + if (strcmp(arg[4],"lower") == 0) originflag = LOWER; + else if (strcmp(arg[4],"center") == 0) originflag = CENTER; + else if (strcmp(arg[4],"upper") == 0) originflag = UPPER; + else originflag = COORD; + if (originflag == COORD) + origin = force->numeric(FLERR,arg[4]); + delta = force->numeric(FLERR,arg[5]); + invdelta = 1.0/delta; + + // parse values until one isn't recognized + + which = new int[3*(narg-6)]; + nvalues = 0; + int i; + + int iarg=6; + while (iarg < narg) { + if (strcmp(arg[iarg],"conf") == 0) { + for (i=0; i<3; i++) { + which[nvalues] = CONF; + nvalues++; + } + } else if (strcmp(arg[iarg],"kin") == 0) { + for (i=0; i<3; i++) { + which[nvalues] = KIN; + nvalues++; + } + } else if (strcmp(arg[iarg],"total") == 0) { + for (i=0; i<3; i++) { + which[nvalues] = TOTAL; + nvalues++; + } + } else error->all(FLERR, "Illegal compute mop/profile command"); //break; + + iarg++; + } + + //Check domain relared errors + // 3D only + if (domain->dimension<3) + error->all(FLERR, "Compute mop/profile incompatible with simulation dimension"); + // orthogonal simulation box + if (domain->triclinic != 0) + error->all(FLERR, "Compute mop/profile incompatible with triclinic simulation box"); + + // Initialize some variables + nbins = 0; + coord = coordp = NULL; + values_local = values_global = array = NULL; + + //Bin setup + setup_bins(); + + // this fix produces a global array + + memory->create(array,nbins,1+nvalues,"mop/profile:array"); + size_array_rows = nbins; + size_array_cols = 1 + nvalues; + + array_flag = 1; + extarray = 0; + +} + +/* ---------------------------------------------------------------------- */ + +ComputeMopProfile::~ComputeMopProfile() +{ + + delete [] which; + + memory->destroy(coord); + memory->destroy(coordp); + memory->destroy(values_local); + memory->destroy(values_global); + memory->destroy(array); +} + +/* ---------------------------------------------------------------------- */ + +void ComputeMopProfile::init() +{ + + //Conversion constants + nktv2p = force->nktv2p; + ftm2v = force->ftm2v; + + //Plane area + area = 1; + int i; + for (i=0; i<3; i++){ + if (i!=dir) area = area*domain->prd[i]; + } + + //Timestep Value + dt = update->dt; + + // Error check + // Compute mop/profile requires fixed simulation box + if (domain->box_change_size || domain->box_change_shape || domain->deform_flag) + error->all(FLERR, "Compute mop/profile requires a fixed simulation box"); + + //This compute requires a pair style with pair_single method implemented + if (force->pair == NULL) + error->all(FLERR,"No pair style is defined for compute mop/profile"); + if (force->pair->single_enable == 0) + error->all(FLERR,"Pair style does not support compute mop/profile"); + + // Warnings + if (me==0){ + //Compute mop/profile only accounts for pair interactions. + // issue a warning if any intramolecular potential or Kspace is defined. + if (force->bond!=NULL) + error->warning(FLERR,"compute mop/profile does not account for bond potentials"); + if (force->angle!=NULL) + error->warning(FLERR,"compute mop/profile does not account for angle potentials"); + if (force->dihedral!=NULL) + error->warning(FLERR,"compute mop/profile does not account for dihedral potentials"); + if (force->improper!=NULL) + error->warning(FLERR,"compute mop/profile does not account for improper potentials"); + if (force->kspace!=NULL) + error->warning(FLERR,"compute mop/profile does not account for kspace contributions"); + } + + // need an occasional half neighbor list + + int irequest = neighbor->request((void *) this); + neighbor->requests[irequest]->pair = 0; + neighbor->requests[irequest]->compute = 1; + neighbor->requests[irequest]->occasional = 1; + +} + +/* ---------------------------------------------------------------------- */ + +void ComputeMopProfile::init_list(int id, NeighList *ptr) +{ + list = ptr; +} + + +/* ---------------------------------------------------------------------- + compute output array + ------------------------------------------------------------------------- */ + +void ComputeMopProfile::compute_array() +{ + + invoked_array = update->ntimestep; + + //Compute pressures on separate procs + compute_pairs(); + + // sum pressure contributions over all procs + MPI_Allreduce(&values_local[0][0],&values_global[0][0],nbins*nvalues, + MPI_DOUBLE,MPI_SUM,world); + + int ibin,m,mo; + for (ibin=0; ibinmass; + int *type = atom->type; + int *mask = atom->mask; + int nlocal = atom->nlocal; + double *special_coul = force->special_coul; + double *special_lj = force->special_lj; + int newton_pair = force->newton_pair; + + + // zero out arrays for one sample + for (m = 0; m < nbins; m++) { + for (i = 0; i < nvalues; i++) values_local[m][i] = 0.0; + } + + // invoke half neighbor list (will copy or build if necessary) + neighbor->build_one(list); + + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + // loop over neighbors of my atoms + + Pair *pair = force->pair; + double **cutsq = force->pair->cutsq; + + //Parse values + double xi[3]; + double vi[3]; + double fi[3]; + double xj[3]; + + m = 0; + while (mx[i][0]; + xi[1] = atom->x[i][1]; + xi[2] = atom->x[i][2]; + itype = type[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + factor_lj = special_lj[sbmask(j)]; + factor_coul = special_coul[sbmask(j)]; + j &= NEIGHMASK; + + // skip if neither I nor J are in group + if (!(mask[i] & groupbit || mask[j] & groupbit)) continue; + + xj[0] = atom->x[j][0]; + xj[1] = atom->x[j][1]; + xj[2] = atom->x[j][2]; + delx = xi[0] - xj[0]; + dely = xi[1] - xj[1]; + delz = xi[2] - xj[2]; + rsq = delx*delx + dely*dely + delz*delz; + jtype = type[j]; + if (rsq >= cutsq[itype][jtype]) continue; + + if (newton_pair || j < nlocal) { + + for (ibin=0;ibinpos) && (xj[dir]pos1) && (xj[dir]single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair); + + values_local[ibin][m] += fpair*(xi[0]-xj[0])/area*nktv2p; + values_local[ibin][m+1] += fpair*(xi[1]-xj[1])/area*nktv2p; + values_local[ibin][m+2] += fpair*(xi[2]-xj[2])/area*nktv2p; + } + else if ( ((xi[dir]pos)) || ((xi[dir]pos1)) ){ + + pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair); + + values_local[ibin][m] -= fpair*(xi[0]-xj[0])/area*nktv2p; + values_local[ibin][m+1] -= fpair*(xi[1]-xj[1])/area*nktv2p; + values_local[ibin][m+2] -= fpair*(xi[2]-xj[2])/area*nktv2p; + } + + } + + } else { + + for (ibin=0;ibinpos) && (xj[dir]pos1) && (xj[dir]single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair); + + values_local[ibin][m] += fpair*(xi[0]-xj[0])/area*nktv2p; + values_local[ibin][m+1] += fpair*(xi[1]-xj[1])/area*nktv2p; + values_local[ibin][m+2] += fpair*(xi[2]-xj[2])/area*nktv2p; + } + + } + + } + + } + + } + + } + + + if (which[m] == KIN || which[m] == TOTAL){ + //Compute kinetic contribution to pressure + // counts local particles transfers across the plane + + double vcm[3]; + double masstotal,sgn; + + for (int i = 0; i < nlocal; i++){ + + // skip if I is not in group + if (mask[i] & groupbit){ + + itype = type[i]; + + //coordinates at t + xi[0] = atom->x[i][0]; + xi[1] = atom->x[i][1]; + xi[2] = atom->x[i][2]; + + //velocities at t + vi[0] = atom->v[i][0]; + vi[1] = atom->v[i][1]; + vi[2] = atom->v[i][2]; + + //forces at t + fi[0] = atom->f[i][0]; + fi[1] = atom->f[i][1]; + fi[2] = atom->f[i][2]; + + //coordinates at t-dt (based on Velocity-Verlet alg.) + xj[0] = xi[0]-vi[0]*dt+fi[0]/2/mass[itype]*dt*dt*ftm2v; + xj[1] = xi[1]-vi[1]*dt+fi[1]/2/mass[itype]*dt*dt*ftm2v; + xj[2] = xi[2]-vi[2]*dt+fi[2]/2/mass[itype]*dt*dt*ftm2v; + + for (ibin=0;ibinboxlo; + boxhi = domain->boxhi; + prd = domain->prd; + + if (originflag == LOWER) origin = boxlo[dir]; + else if (originflag == UPPER) origin = boxhi[dir]; + else if (originflag == CENTER) + origin = 0.5 * (boxlo[dir] + boxhi[dir]); + + if (origin < boxlo[dir]) { + error->all(FLERR,"Origin of bins for compute mop/profile is out of bounds" ); + } else { + n = static_cast ((origin - boxlo[dir]) * invdelta); + lo = origin - n*delta; + } + if (origin < boxhi[dir]) { + n = static_cast ((boxhi[dir] - origin) * invdelta); + hi = origin + n*delta; + } else { + error->all(FLERR,"Origin of bins for compute mop/profile is out of bounds" ); + } + + offset = lo; + nbins = static_cast ((hi-lo) * invdelta + 1.5); + + //allocate bin arrays + memory->create(coord,nbins,1,"mop/profile:coord"); + memory->create(coordp,nbins,1,"mop/profile:coordp"); + memory->create(values_local,nbins,nvalues,"mop/profile:values_local"); + memory->create(values_global,nbins,nvalues,"mop/profile:values_global"); + + // set bin coordinates + for (i = 0; i < nbins; i++) { + coord[i][0] = offset + i*delta; + if ( coord[i][0] < (domain->boxlo[dir]+domain->prd_half[dir]) ) { + coordp[i][0] = coord[i][0] + domain->prd[dir]; + } else { + coordp[i][0] = coord[i][0] - domain->prd[dir]; + } + } + +} diff --git a/src/USER-MOP/compute_mop_profile.h b/src/USER-MOP/compute_mop_profile.h new file mode 100755 index 0000000000..3cb46087ae --- /dev/null +++ b/src/USER-MOP/compute_mop_profile.h @@ -0,0 +1,81 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. + ------------------------------------------------------------------------- */ + +/*------------------------------------------------------------------------ + Contributing Authors : Romain Vermorel (LFCR), Laurent Joly (ULyon) + --------------------------------------------------------------------------*/ + +#ifdef COMPUTE_CLASS + +ComputeStyle(mop/profile,ComputeMopProfile) + +#else + +#ifndef LMP_COMPUTE_MOP_PROFILE_H +#define LMP_COMPUTE_MOP_PROFILE_H + +#include "compute.h" + +namespace LAMMPS_NS { + + class ComputeMopProfile : public Compute { + public: + ComputeMopProfile(class LAMMPS *, int, char **); + virtual ~ComputeMopProfile(); + void init(); + void init_list(int, class NeighList *); + void compute_array(); + + private: + + void compute_pairs(); + void setup_bins(); + + int me,nvalues,dir; + int *which; + + int originflag; + double origin,delta,offset,invdelta; + int nbins; + double **coord,**coordp; + double **values_local,**values_global; + + int ndim; + double dt,nktv2p,ftm2v; + double area; + class NeighList *list; + + }; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + + E: Illegal ... command + + Self-explanatory. Check the input script syntax and compare to the + documentation for the command. You can use -echo screen as a + command-line option when running LAMMPS to see the offending line. + + E: Pair style does not support compute mop/profile + + The pair style does not have a single() function, so it can + not be invoked by compute mop/profile. + + + +*/ + diff --git a/src/USER-MOP/compute_mop_profile.txt b/src/USER-MOP/compute_mop_profile.txt new file mode 100755 index 0000000000..24b624a144 --- /dev/null +++ b/src/USER-MOP/compute_mop_profile.txt @@ -0,0 +1,72 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +compute mop/profile command :h3 + +[Syntax:] + +compute ID group-ID mop/profile dir origin delta keyword ... :pre + +ID, group-ID are documented in "compute"_compute.html command +mop/profile = style name of this compute command +dir = {x} or {y} or {z} is the direction normal to the planes +origin = {lower} or {center} or {upper} or coordinate value (distance units) is the position of the first plane +delta = value (distance units) is the distance between planes +between one and three keywords can be appended +keyword = {kin} or {conf} or {total} :ul + +[Examples:] +:link(mop-examples) + +compute 1 all mop/profile x lower 0.1 total +compute 1 liquid mop/profile z 0.0 0.25 kin conf +fix 1 all ave/time 500 20 10000 c_1\[*\] ave running overwrite file mopp.time mode vector :pre + + +[Description:] + +Define a computation that calculates profiles of components of the local stress tensor using the method of planes "(Todd)"_#mop-todd, applied on an array of regularly spaced planes. +Specifically 3 components are computed in directions {dir},{x}; {dir},{y}; and {dir},{z}; where {dir} is the direction normal to the planes. + +Contrary to methods based on histograms of atomic stress (i.e. using "compute stress/atom"_compute_stress_atom.html), the method of planes is compatible with mechanical balance in heterogeneous systems and at interfaces "(Todd)"_#mop-todd. + +The stress tensor is the sum of a kinetic term and a configurational term, which are given respectively by Eq. (21) and Eq. (16) in "(Todd)"_#mop-todd. For the kinetic part, the algorithm considers that atoms have crossed the plane if their positions at times t-dt and t are one on either side of the plane, and uses the velocity at time t-dt/2 given by the velocity-Verlet algorithm. + +Between one and three keywords can be used to indicate which contributions to the stress must be computed: kinetic stress (kin), configurational stress (conf), and/or total stress (total). + +NOTE 1: The configurational stress is computed considering all pairs of atoms where at least one atom belongs to group group-ID. + +NOTE 2: The local stress does not include any Lennard-Jones tail +corrections to the pressure added by the "pair_modify tail +yes"_pair_modify.html command, since those are contributions to the global system pressure. + +[Output info:] + +This compute calculates a global array, with 1 column giving the position of the planes where the stress tensor was computed, and with 3 columns of values for each declared keyword (in the order the keywords have been declared). For each keyword, the profiles of stress tensor components are ordered as follows: stress_dir,x; stress_dir,y; and stress_dir,z. + +The values are in pressure "units"_units.html. + +The values produced by this compute can be accessed by various "output commands"_Section_howto.html#howto_15. For instance, the results can be written to a file using the "fix ave/time"_fix_ave_time.html command, see "Examples"_#mop-examples above. + +[Restrictions:] + +The method is only implemented for 3d orthogonal simulation boxes whose size does not change in time, and axis-aligned planes. + +The method only works with two-body pair interactions, because it requires the class method pair->single() to be implemented. In particular, it does not work with more than two-body pair interactions, intra-molecular interactions, and long range (kspace) interactions. + +[Related commands:] + +"compute mop"_compute_mop.html, "compute stress/atom"_compute_stress_atom.html + +[Default:] none + +:line + +:link(mop-todd) +[(Todd)] B. D. Todd, Denis J. Evans, and Peter J. Daivis: "Pressure tensor for inhomogeneous fluids", +Phys. Rev. E 52, 1627 (1995). From 7b423c6d4b2ad482c7c1466f34e31a244dd402dd Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 3 Sep 2018 23:37:25 -0400 Subject: [PATCH 119/302] integrate USER-MOP package into build and documentat system. apply latest LAMMPS programming style conventions --- cmake/CMakeLists.txt | 4 +- doc/src/Packages_details.txt | 24 ++ doc/src/Packages_user.txt | 1 + doc/src/compute_mop.txt | 111 +++++++++ doc/src/computes.txt | 1 + doc/src/lammps.book | 1 + .../USER/mop/in.compute_mop | 4 +- .../USER/mop/log.31Aug18.compute_mop.g++.1 | 186 ++++++++++++++ examples/USER/mop/moppz.time.reference | 226 +++++++++++++++++ examples/USER/mop/mopz0.time.reference | 6 + examples/USER/mop/profile.z.reference | 227 ++++++++++++++++++ src/.gitignore | 4 + src/Makefile | 2 +- src/USER-MOP/compute_mop.cpp | 134 +++++------ src/USER-MOP/compute_mop.h | 0 src/USER-MOP/compute_mop.txt | 71 ------ src/USER-MOP/compute_mop_profile.cpp | 154 ++++++------ src/USER-MOP/compute_mop_profile.h | 0 src/USER-MOP/compute_mop_profile.txt | 72 ------ 19 files changed, 939 insertions(+), 289 deletions(-) create mode 100644 doc/src/compute_mop.txt rename src/USER-MOP/compute_mop.example => examples/USER/mop/in.compute_mop (94%) mode change 100755 => 100644 create mode 100644 examples/USER/mop/log.31Aug18.compute_mop.g++.1 create mode 100644 examples/USER/mop/moppz.time.reference create mode 100644 examples/USER/mop/mopz0.time.reference create mode 100644 examples/USER/mop/profile.z.reference mode change 100755 => 100644 src/USER-MOP/compute_mop.cpp mode change 100755 => 100644 src/USER-MOP/compute_mop.h delete mode 100755 src/USER-MOP/compute_mop.txt mode change 100755 => 100644 src/USER-MOP/compute_mop_profile.cpp mode change 100755 => 100644 src/USER-MOP/compute_mop_profile.h delete mode 100755 src/USER-MOP/compute_mop_profile.txt diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index 53ac20f5d9..190ef3b2e0 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -215,8 +215,8 @@ set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE GRANULAR SRD KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-MESO USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD USER-LB USER-MANIFOLD USER-MEAMC USER-MGPT USER-MISC - USER-MOFFF USER-MOLFILE USER-NETCDF USER-PHONON USER-QTB USER-REAXC USER-SMD - USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM) + USER-MOP USER-MOFFF USER-MOLFILE USER-NETCDF USER-PHONON USER-QTB USER-REAXC + USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM) set(ACCEL_PACKAGES USER-OMP KOKKOS OPT USER-INTEL GPU) set(OTHER_PACKAGES CORESHELL QEQ) foreach(PKG ${DEFAULT_PACKAGES}) diff --git a/doc/src/Packages_details.txt b/doc/src/Packages_details.txt index 381dc2e995..16f867b7c0 100644 --- a/doc/src/Packages_details.txt +++ b/doc/src/Packages_details.txt @@ -84,6 +84,7 @@ as contained in the file name. "USER-MGPT"_#PKG-USER-MGPT, "USER-MISC"_#PKG-USER-MISC, "USER-MOFFF"_#PKG-USER-MOFFF, +"USER-MOP"_#PKG-USER-MOP, "USER-MOLFILE"_#PKG-USER-MOLFILE, "USER-NETCDF"_#PKG-USER-NETCDF, "USER-OMP"_#PKG-USER-OMP, @@ -1572,6 +1573,29 @@ examples/USER/mofff :ul :line +USER-MOP package :link(PKG-USER-MOP),h4 + +[Contents:] + +This package contains two compute styles: compute mop and compute mop/profile. + +compute mop calculates components of the local stress tensor using the method of planes, applied on one plane. + +compute mop/profile calculates profiles of components of the local stress tensor using the method of planes, applied on an array of regularly spaced planes. + +[Author:] Laurent Joly (University of Lyon 1) +Romain Vermorel at (University of Pau and Pays de l'Adour) + +[Supporting info:] + +src/USER-MOP: filenames -> commands +src/USER-MOP/README +"compute mop"_compute_mop.html +"compute mop/profile"_compute_mop.html +examples/USER/mop :ul + +:line + USER-MOLFILE package :link(PKG-USER-MOLFILE),h4 [Contents:] diff --git a/doc/src/Packages_user.txt b/doc/src/Packages_user.txt index 7db2fa895c..731cf7ff10 100644 --- a/doc/src/Packages_user.txt +++ b/doc/src/Packages_user.txt @@ -57,6 +57,7 @@ Package, Description, Doc page, Example, Library "USER-MESO"_Packages_details.html#PKG-USER-MESO, mesoscale DPD models, "pair_style edpd"_pair_meso.html, USER/meso, no "USER-MGPT"_Packages_details.html#PKG-USER-MGPT, fast MGPT multi-ion potentials, "pair_style mgpt"_pair_mgpt.html, USER/mgpt, no "USER-MISC"_Packages_details.html#PKG-USER-MISC, single-file contributions, USER-MISC/README, USER/misc, no +"USER-MOP"_Packages_details.html#PKG-USER-MOP, compute stress via method-of-planes, "compute_style mop"_compute_mop.html, USER/mop, no "USER-MOFFF"_Packages_details.html#PKG-USER-MOFFF, styles for "MOF-FF"_MOFplus force field, "pair_style buck6d/coul/gauss"_pair_buck6d_coul_gauss.html, USER/mofff, no "USER-MOLFILE"_Packages_details.html#PKG-USER-MOLFILE, "VMD"_https://www.ks.uiuc.edu/Research/vmd/ molfile plug-ins,"dump molfile"_dump_molfile.html, n/a, ext "USER-NETCDF"_Packages_details.html#PKG-USER-NETCDF, dump output via NetCDF,"dump netcdf"_dump_netcdf.html, n/a, ext diff --git a/doc/src/compute_mop.txt b/doc/src/compute_mop.txt new file mode 100644 index 0000000000..732f55657a --- /dev/null +++ b/doc/src/compute_mop.txt @@ -0,0 +1,111 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +compute mop command :h3 +compute mop/profile command :h3 + + +[Syntax:] + +compute ID group-ID style dir args keywords ... :pre + +ID, group-ID are documented in "compute"_compute.html command +style = {mop} or {mop/profile} +dir = {x} or {y} or {z} is the direction normal to the plane +args = argument specific to the compute style +keywords = {kin} or {conf} or {total} (one of more can be specified) :ul + {mop} args = pos + pos = {lower} or {center} or {upper} or coordinate value (distance units) is the position of the plane + {mop/profile} args = origin delta + origin = {lower} or {center} or {upper} or coordinate value (distance units) is the position of the first plane + delta = value (distance units) is the distance between planes :pre + +compute 1 all mop x lower total +compute 1 liquid mop z 0.0 kin conf +fix 1 all ave/time 10 1000 10000 c_1\[*\] file mop.time +fix 1 all ave/time 10 1000 10000 c_1\[2\] file mop.time :pre + +compute 1 all mop/profile x lower 0.1 total +compute 1 liquid mop/profile z 0.0 0.25 kin conf +fix 1 all ave/time 500 20 10000 c_1\[*\] ave running overwrite file mopp.time mode vector :pre + + +[Description:] + +Compute {mop} and compute {mop/profile} define computations that +calculate components of the local stress tensor using the method of +planes "(Todd)"_#mop-todd. Specifically in compute {mop} calculates 3 +components are computed in directions {dir},{x}; {dir},{y}; and +{dir},{z}; where {dir} is the direction normal to the plane, while +in compute {mop/profile} the profile of the stress is computed. + +Contrary to methods based on histograms of atomic stress (i.e. using +"compute stress/atom"_compute_stress_atom.html), the method of planes is +compatible with mechanical balance in heterogeneous systems and at +interfaces "(Todd)"_#mop-todd. + +The stress tensor is the sum of a kinetic term and a configurational +term, which are given respectively by Eq. (21) and Eq. (16) in +"(Todd)"_#mop-todd. For the kinetic part, the algorithm considers that +atoms have crossed the plane if their positions at times t-dt and t are +one on either side of the plane, and uses the velocity at time t-dt/2 +given by the velocity-Verlet algorithm. + +Between one and three keywords can be used to indicate which +contributions to the stress must be computed: kinetic stress (kin), +configurational stress (conf), and/or total stress (total). + +NOTE 1: The configurational stress is computed considering all pairs of atoms where at least one atom belongs to group group-ID. + +NOTE 2: The local stress does not include any Lennard-Jones tail +corrections to the pressure added by the "pair_modify tail +yes"_pair_modify.html command, since those are contributions to the global system pressure. + +[Output info:] + +Compute {mop} calculates a global vector (indices starting at 1), with 3 +values for each declared keyword (in the order the keywords have been +declared). For each keyword, the stress tensor components are ordered as +follows: stress_dir,x, stress_dir,y, and stress_dir,z. + +Compute {mop/profile} instead calculates a global array, with 1 column +giving the position of the planes where the stress tensor was computed, +and with 3 columns of values for each declared keyword (in the order the +keywords have been declared). For each keyword, the profiles of stress +tensor components are ordered as follows: stress_dir,x; stress_dir,y; +and stress_dir,z. + +The values are in pressure "units"_units.html. + +The values produced by this compute can be accessed by various "output commands"_Howto_output.html. For instance, the results can be written to a file using the "fix ave/time"_fix_ave_time.html command. Please see the example in the examples/USER/mop folder. + +[Restrictions:] + +This style is part of the USER-MOP package. It is only enabled if LAMMPS +is built with that package. See the "Build package"_Build_package.html +doc page on for more info. + +The method is only implemented for 3d orthogonal simulation boxes whose +size does not change in time, and axis-aligned planes. + +The method only works with two-body pair interactions, because it +requires the class method pair->single() to be implemented. In +particular, it does not work with more than two-body pair interactions, +intra-molecular interactions, and long range (kspace) interactions. + +[Related commands:] + +"compute stress/atom"_compute_stress_atom.html + +[Default:] none + +:line + +:link(mop-todd) +[(Todd)] B. D. Todd, Denis J. Evans, and Peter J. Daivis: "Pressure tensor for inhomogeneous fluids", +Phys. Rev. E 52, 1627 (1995). diff --git a/doc/src/computes.txt b/doc/src/computes.txt index 46dd30f757..c431f1c184 100644 --- a/doc/src/computes.txt +++ b/doc/src/computes.txt @@ -55,6 +55,7 @@ Computes :h1 compute_meso_e_atom compute_meso_rho_atom compute_meso_t_atom + compute_mop compute_msd compute_msd_chunk compute_msd_nongauss diff --git a/doc/src/lammps.book b/doc/src/lammps.book index c296ff4039..0aa382ae39 100644 --- a/doc/src/lammps.book +++ b/doc/src/lammps.book @@ -446,6 +446,7 @@ compute_ke_rigid.html compute_meso_e_atom.html compute_meso_rho_atom.html compute_meso_t_atom.html +compute_mop.html compute_msd.html compute_msd_chunk.html compute_msd_nongauss.html diff --git a/src/USER-MOP/compute_mop.example b/examples/USER/mop/in.compute_mop old mode 100755 new mode 100644 similarity index 94% rename from src/USER-MOP/compute_mop.example rename to examples/USER/mop/in.compute_mop index 8dea9aecbd..ab9552796f --- a/src/USER-MOP/compute_mop.example +++ b/examples/USER/mop/in.compute_mop @@ -38,12 +38,12 @@ fix_modify nvtliq temp Tliq thermo 10000 thermo_modify flush yes temp Tliq -dump 1 all atom 10000 dump.lammpstrj +# dump 1 all atom 10000 dump.lammpstrj fix fxbal all balance 1000 1.05 shift z 10 1.05 velocity liquid create $T 47298 dist gaussian rot yes run 50000 -undump 1 +# undump 1 reset_timestep 0 compute bin_z liquid chunk/atom bin/1d z 0.0 0.1 units box diff --git a/examples/USER/mop/log.31Aug18.compute_mop.g++.1 b/examples/USER/mop/log.31Aug18.compute_mop.g++.1 new file mode 100644 index 0000000000..98b403b444 --- /dev/null +++ b/examples/USER/mop/log.31Aug18.compute_mop.g++.1 @@ -0,0 +1,186 @@ +LAMMPS (31 Aug 2018) +variable T equal 0.8 +variable p_solid equal 0.05 + +lattice fcc 1.0 +Lattice spacing in x,y,z = 1.5874 1.5874 1.5874 +region box block 0.0 6.0 0.0 6.0 -2.0 12.0 +create_box 2 box +Created orthogonal box = (0 0 -3.1748) to (9.52441 9.52441 19.0488) + 1 by 1 by 1 MPI processor grid + +mass * 1.0 +pair_style lj/cut 2.5 +pair_coeff * * 1.0 1.0 +pair_coeff 1 2 0.5 1.0 +pair_coeff 2 2 0.0 0.0 +neigh_modify delay 0 + +region solid_bottom block INF INF INF INF -1.1 0.1 +region liquid block INF INF INF INF 1.1 8.9 +region solid_up block INF INF INF INF 9.9 11.1 + +create_atoms 1 region liquid +Created 1080 atoms + Time spent = 0.000631094 secs +delete_atoms porosity liquid 0.26 88765 +Deleted 257 atoms, new total = 823 +group liquid region liquid +823 atoms in group liquid + +create_atoms 2 region solid_bottom +Created 216 atoms + Time spent = 0.000221014 secs +group solid_bottom region solid_bottom +216 atoms in group solid_bottom +create_atoms 2 region solid_up +Created 216 atoms + Time spent = 0.000169039 secs +group solid_up region solid_up +216 atoms in group solid_up +group solid union solid_bottom solid_up +432 atoms in group solid + +variable faSolid equal ${p_solid}*lx*ly/count(solid_up) +variable faSolid equal 0.05*lx*ly/count(solid_up) +fix piston_up solid_up aveforce NULL NULL -${faSolid} +fix piston_up solid_up aveforce NULL NULL -0.0209986841649146 +fix freeze_up solid_up setforce 0.0 0.0 NULL +fix freeze_bottom solid_bottom setforce 0.0 0.0 0.0 +fix nvesol solid nve +compute Tliq liquid temp +fix nvtliq liquid nvt temp $T $T 0.5 +fix nvtliq liquid nvt temp 0.8 $T 0.5 +fix nvtliq liquid nvt temp 0.8 0.8 0.5 +fix_modify nvtliq temp Tliq +WARNING: Temperature for fix modify is not for group all (../fix_nh.cpp:1404) + +thermo 10000 +thermo_modify flush yes temp Tliq +WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:488) + +# dump 1 all atom 10000 dump.lammpstrj + +fix fxbal all balance 1000 1.05 shift z 10 1.05 +velocity liquid create $T 47298 dist gaussian rot yes +velocity liquid create 0.8 47298 dist gaussian rot yes +run 50000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 7 7 16 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.187 | 3.187 | 3.187 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 0.8 -3.7188573 0 -2.9328812 -0.65673631 2016 + 10000 0.80645968 -3.2160592 0 -2.4237366 -0.17266146 2016 + 20000 0.85787011 -3.2087113 0 -2.3658796 0.032152534 2016 + 30000 0.76357074 -3.1761807 0 -2.4259953 -0.034009443 2016 + 40000 0.8116632 -3.1965608 0 -2.399126 -0.030033303 2016 + 50000 0.83600463 -3.1878245 0 -2.3664749 0.054158845 2016 +Loop time of 40.6472 on 1 procs for 50000 steps with 1255 atoms + +Performance: 531401.825 tau/day, 1230.097 timesteps/s +99.7% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 28.102 | 28.102 | 28.102 | 0.0 | 69.14 +Neigh | 9.8377 | 9.8377 | 9.8377 | 0.0 | 24.20 +Comm | 0.91642 | 0.91642 | 0.91642 | 0.0 | 2.25 +Output | 0.00024581 | 0.00024581 | 0.00024581 | 0.0 | 0.00 +Modify | 1.4027 | 1.4027 | 1.4027 | 0.0 | 3.45 +Other | | 0.3879 | | | 0.95 + +Nlocal: 1255 ave 1255 max 1255 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 2268 ave 2268 max 2268 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 40149 ave 40149 max 40149 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 40149 +Ave neighs/atom = 31.9912 +Neighbor list builds = 5714 +Dangerous builds = 0 +# undump 1 +reset_timestep 0 + +compute bin_z liquid chunk/atom bin/1d z 0.0 0.1 units box + +compute liquidStress_ke liquid stress/atom NULL ke +compute liquidStress_vir liquid stress/atom NULL virial +fix profile_z liquid ave/chunk 10 1000 10000 bin_z density/number temp c_liquidStress_ke[1] c_liquidStress_ke[2] c_liquidStress_ke[3] c_liquidStress_ke[4] c_liquidStress_ke[5] c_liquidStress_ke[6] c_liquidStress_vir[1] c_liquidStress_vir[2] c_liquidStress_vir[3] c_liquidStress_vir[4] c_liquidStress_vir[5] c_liquidStress_vir[6] ave running overwrite file profile.z + +compute mopz0 all mop z center kin conf +fix mopz0t all ave/time 10 1000 10000 c_mopz0[*] file mopz0.time + +compute moppz liquid mop/profile z 0.0 0.1 kin conf +fix moppzt all ave/time 100 100 10000 c_moppz[*] ave running overwrite file moppz.time mode vector + +run 40000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 7 7 16 + 3 neighbor lists, perpetual/occasional/extra = 1 2 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard + (2) compute mop, occasional, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (3) compute mop/profile, occasional, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 4.186 | 4.186 | 4.186 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 0.83600463 -3.1878245 0 -2.3664749 0.054158845 2016 + 10000 0.80600425 -3.1900933 0 -2.3982182 -0.042750667 2016 + 20000 0.78117978 -3.2121798 0 -2.444694 0.0092285451 2016 + 30000 0.81008494 -3.1728363 0 -2.376952 0.053347807 2016 + 40000 0.80440016 -3.1768915 0 -2.3865924 -0.0075214347 2016 +Loop time of 45.4499 on 1 procs for 40000 steps with 1255 atoms + +Performance: 380198.462 tau/day, 880.089 timesteps/s +99.8% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 25.456 | 25.456 | 25.456 | 0.0 | 56.01 +Neigh | 7.9422 | 7.9422 | 7.9422 | 0.0 | 17.47 +Comm | 0.73477 | 0.73477 | 0.73477 | 0.0 | 1.62 +Output | 0.00010562 | 0.00010562 | 0.00010562 | 0.0 | 0.00 +Modify | 11.004 | 11.004 | 11.004 | 0.0 | 24.21 +Other | | 0.3131 | | | 0.69 + +Nlocal: 1255 ave 1255 max 1255 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 2269 ave 2269 max 2269 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 40325 ave 40325 max 40325 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 40325 +Ave neighs/atom = 32.1315 +Neighbor list builds = 4587 +Dangerous builds = 0 + +Total wall time: 0:01:26 diff --git a/examples/USER/mop/moppz.time.reference b/examples/USER/mop/moppz.time.reference new file mode 100644 index 0000000000..f8d4b532ea --- /dev/null +++ b/examples/USER/mop/moppz.time.reference @@ -0,0 +1,226 @@ +# Time-averaged data for fix moppzt +# TimeStep Number-of-rows +# Row c_moppz[1] c_moppz[2] c_moppz[3] c_moppz[4] c_moppz[5] c_moppz[6] c_moppz[7] +40000 222 +1 -3.1 0 0 0 0 0 0 +2 -3 0 0 0 0 0 0 +3 -2.9 0 0 0 0 0 0 +4 -2.8 0 0 0 0 0 0 +5 -2.7 0 0 0 0 0 0 +6 -2.6 0 0 0 0 0 0 +7 -2.5 0 0 0 0 0 0 +8 -2.4 0 0 0 0 0 0 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-0.00486842 0.0289193 +34 0.2 0 0 0 -0.00643877 -0.00486842 0.0289193 +35 0.3 0 0 0 -0.00643877 -0.00486842 0.0289193 +36 0.4 0 0 0 -0.00643877 -0.00486842 0.0289193 +37 0.5 0 0 0 -0.00643877 -0.00486842 0.0289193 +38 0.6 -0.00279194 0.0093508 0.013353 -0.00639358 -0.00380391 0.021025 +39 0.7 -0.00373537 0.0122501 0.0840939 -0.00503616 -0.0112127 -0.132562 +40 0.8 0.061158 -0.0280862 0.636594 0.00453591 -0.00214426 -0.557591 +41 0.9 -0.000266217 -0.0385723 0.969803 -0.0100643 0.00387732 -0.972644 +42 1 -0.0667633 -0.0208723 0.846848 0.0121337 -0.000646173 -0.936078 +43 1.1 -0.0479918 0.0444386 0.783228 0.0206387 -0.00229641 -0.640358 +44 1.2 0.0907347 -0.00458127 0.508479 0.0271462 -0.0136805 -0.427689 +45 1.3 0.0346947 -0.015182 0.397443 0.0162624 -0.0165167 -0.323227 +46 1.4 0.0576422 -0.00277706 0.359744 0.0291978 -0.0156949 -0.265795 +47 1.5 0.0596081 -0.00318334 0.238852 0.0157713 -0.0150214 -0.273303 +48 1.6 0.016955 0.0183139 0.459661 0.00421857 -0.0129777 -0.340127 +49 1.7 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0 0 0 0 +211 17.9 0 0 0 0 0 0 +212 18 0 0 0 0 0 0 +213 18.1 0 0 0 0 0 0 +214 18.2 0 0 0 0 0 0 +215 18.3 0 0 0 0 0 0 +216 18.4 0 0 0 0 0 0 +217 18.5 0 0 0 0 0 0 +218 18.6 0 0 0 0 0 0 +219 18.7 0 0 0 0 0 0 +220 18.8 0 0 0 0 0 0 +221 18.9 0 0 0 0 0 0 +222 19 0 0 0 0 0 0 diff --git a/examples/USER/mop/mopz0.time.reference b/examples/USER/mop/mopz0.time.reference new file mode 100644 index 0000000000..6341d22906 --- /dev/null +++ b/examples/USER/mop/mopz0.time.reference @@ -0,0 +1,6 @@ +# Time-averaged data for fix mopz0t +# TimeStep c_mopz0[1] c_mopz0[2] c_mopz0[3] c_mopz0[4] c_mopz0[5] c_mopz0[6] +10000 -0.0267908 -0.0366912 0.634417 0.00702203 0.00200985 -0.552264 +20000 0.0202912 -0.0217482 0.597513 -0.00157669 -0.00587006 -0.537147 +30000 -0.00244239 -0.02829 0.616384 0.00640645 0.00932437 -0.561132 +40000 0.00541112 -0.0764546 0.613812 -0.00450554 -0.0038376 -0.537305 diff --git a/examples/USER/mop/profile.z.reference b/examples/USER/mop/profile.z.reference new file mode 100644 index 0000000000..1e0d1bf26b --- /dev/null +++ b/examples/USER/mop/profile.z.reference @@ -0,0 +1,227 @@ +# Chunk-averaged data for fix profile_z and group temp +# Timestep Number-of-chunks Total-count +# Chunk Coord1 Ncount density/number temp c_liquidStress_ke[1] c_liquidStress_ke[2] c_liquidStress_ke[3] c_liquidStress_ke[4] c_liquidStress_ke[5] c_liquidStress_ke[6] c_liquidStress_vir[1] c_liquidStress_vir[2] c_liquidStress_vir[3] c_liquidStress_vir[4] c_liquidStress_vir[5] c_liquidStress_vir[6] +40000 223 3292 + 1 -3.15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + 2 -3.05 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + 3 -2.95 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + 4 -2.85 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + 5 -2.75 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + 6 -2.65 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + 7 -2.55 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + 8 -2.45 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + 9 -2.35 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + 10 -2.25 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + 11 -2.15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + 12 -2.05 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + 13 -1.95 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + 14 -1.85 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + 15 -1.75 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + 16 -1.65 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + 17 -1.55 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + 18 -1.45 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + 19 -1.35 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + 20 -1.25 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + 21 -1.15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + 22 -1.05 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + 23 -0.95 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + 24 -0.85 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + 25 -0.75 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + 26 -0.65 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + 27 -0.55 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + 28 -0.45 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + 29 -0.35 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + 30 -0.25 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + 31 -0.15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + 32 -0.05 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + 33 0.05 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + 34 0.15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + 35 0.25 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + 36 0.35 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + 37 0.45 0 0 0 0 0 0 0 0 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19.05 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 diff --git a/src/.gitignore b/src/.gitignore index df3a22a5cd..c7aaa8ab64 100644 --- a/src/.gitignore +++ b/src/.gitignore @@ -288,6 +288,10 @@ /compute_meso_rho_atom.h /compute_meso_t_atom.cpp /compute_meso_t_atom.h +/compute_mop.cpp +/compute_mop.h +/compute_mop_profile.cpp +/compute_mop_profile.h /compute_msd_nongauss.cpp /compute_msd_nongauss.h /compute_pe_tally.cpp diff --git a/src/Makefile b/src/Makefile index 948d203cfe..6b1a2bdb98 100644 --- a/src/Makefile +++ b/src/Makefile @@ -60,7 +60,7 @@ PACKAGE = asphere body class2 colloid compress coreshell dipole gpu \ PACKUSER = user-atc user-awpmd user-bocs user-cgdna user-cgsdk user-colvars \ user-diffraction user-dpd user-drude user-eff user-fep user-h5md \ user-intel user-lb user-manifold user-meamc user-meso \ - user-mgpt user-misc user-mofff user-molfile \ + user-mgpt user-misc user-mop user-mofff user-molfile \ user-netcdf user-omp user-phonon user-qmmm user-qtb \ user-quip user-reaxc user-smd user-smtbq user-sph user-tally \ user-uef user-vtk diff --git a/src/USER-MOP/compute_mop.cpp b/src/USER-MOP/compute_mop.cpp old mode 100755 new mode 100644 index 42639d73ab..ba6b458172 --- a/src/USER-MOP/compute_mop.cpp +++ b/src/USER-MOP/compute_mop.cpp @@ -15,10 +15,11 @@ Contributing Authors : Romain Vermorel (LFCR), Laurent Joly (ULyon) --------------------------------------------------------------------------*/ -#include "math.h" -#include "mpi.h" -#include "string.h" -#include "stdlib.h" +#include +#include +#include +#include + #include "compute_mop.h" #include "atom.h" #include "update.h" @@ -34,8 +35,6 @@ #include "error.h" #include "memory.h" -#include - using namespace LAMMPS_NS; enum{X,Y,Z}; @@ -52,30 +51,25 @@ ComputeMop::ComputeMop(LAMMPS *lmp, int narg, char **arg) : MPI_Comm_rank(world,&me); - //set compute mode and direction of plane(s) for pressure calculation + // set compute mode and direction of plane(s) for pressure calculation - if (strcmp(arg[3],"x")==0){ + if (strcmp(arg[3],"x")==0) { dir = X; - } - else if (strcmp(arg[3],"y")==0){ + } else if (strcmp(arg[3],"y")==0) { dir = Y; - } - else if (strcmp(arg[3],"z")==0){ + } else if (strcmp(arg[3],"z")==0) { dir = Z; - } - else error->all(FLERR,"Illegal compute mop command"); + } else error->all(FLERR,"Illegal compute mop command"); - //Position of the plane - if (strcmp(arg[4],"lower")==0){ + // Position of the plane + + if (strcmp(arg[4],"lower")==0) { pos = domain->boxlo[dir]; - } - else if (strcmp(arg[4],"upper")==0){ + } else if (strcmp(arg[4],"upper")==0) { pos = domain->boxhi[dir]; - } - else if (strcmp(arg[4],"center")==0){ + } else if (strcmp(arg[4],"center")==0) { pos = 0.5*(domain->boxlo[dir]+domain->boxhi[dir]); - } - else pos = force->numeric(FLERR,arg[4]); + } else pos = force->numeric(FLERR,arg[4]); if ( pos < (domain->boxlo[dir]+domain->prd_half[dir]) ) { pos1 = pos + domain->prd[dir]; @@ -111,19 +105,22 @@ ComputeMop::ComputeMop(LAMMPS *lmp, int narg, char **arg) : iarg++; } - //Error check - // 3D only - if (domain->dimension<3) - error->all(FLERR, "Compute mop incompatible with simulation dimension"); - // orthogonal simulation box - if (domain->triclinic != 0) - error->all(FLERR, "Compute mop incompatible with triclinic simulation box"); - // plane inside the box - if (pos >domain->boxhi[dir] || pos boxlo[dir]) - error->all(FLERR, "Plane for compute mop is out of bounds"); + // Error check + // 3D only + + if (domain->dimension < 3) + error->all(FLERR, "Compute mop incompatible with simulation dimension"); + + // orthogonal simulation box + if (domain->triclinic != 0) + error->all(FLERR, "Compute mop incompatible with triclinic simulation box"); + // plane inside the box + if (pos >domain->boxhi[dir] || pos boxlo[dir]) + error->all(FLERR, "Plane for compute mop is out of bounds"); // Initialize some variables + values_local = values_global = vector = NULL; // this fix produces a global vector @@ -155,54 +152,60 @@ ComputeMop::~ComputeMop() void ComputeMop::init() { - //Conversion constants + // Conversion constants + nktv2p = force->nktv2p; ftm2v = force->ftm2v; - //Plane area + // Plane area + area = 1; int i; for (i=0; i<3; i++){ if (i!=dir) area = area*domain->prd[i]; } - //Timestep Value + // Timestep Value + dt = update->dt; -// Error check + // Error check -// Compute mop requires fixed simulation box -if (domain->box_change_size || domain->box_change_shape || domain->deform_flag) + // Compute mop requires fixed simulation box + if (domain->box_change_size || domain->box_change_shape || domain->deform_flag) error->all(FLERR, "Compute mop requires a fixed simulation box"); -//This compute requires a pair style with pair_single method implemented -if (force->pair == NULL) + // This compute requires a pair style with pair_single method implemented + + if (force->pair == NULL) error->all(FLERR,"No pair style is defined for compute mop"); -if (force->pair->single_enable == 0) + if (force->pair->single_enable == 0) error->all(FLERR,"Pair style does not support compute mop"); -// Warnings -if (me==0){ - //Compute mop only accounts for pair interactions. - // issue a warning if any intramolecular potential or Kspace is defined. - if (force->bond!=NULL) + // Warnings + + if (me==0){ + + //Compute mop only accounts for pair interactions. + // issue a warning if any intramolecular potential or Kspace is defined. + + if (force->bond!=NULL) error->warning(FLERR,"compute mop does not account for bond potentials"); - if (force->angle!=NULL) + if (force->angle!=NULL) error->warning(FLERR,"compute mop does not account for angle potentials"); - if (force->dihedral!=NULL) + if (force->dihedral!=NULL) error->warning(FLERR,"compute mop does not account for dihedral potentials"); - if (force->improper!=NULL) + if (force->improper!=NULL) error->warning(FLERR,"compute mop does not account for improper potentials"); - if (force->kspace!=NULL) - error->warning(FLERR,"compute mop does not account for kspace contributions"); - } + if (force->kspace!=NULL) + error->warning(FLERR,"compute mop does not account for kspace contributions"); + } // need an occasional half neighbor list int irequest = neighbor->request((void *) this); neighbor->requests[irequest]->pair = 0; neighbor->requests[irequest]->compute = 1; neighbor->requests[irequest]->occasional = 1; - } /* ---------------------------------------------------------------------- */ @@ -219,7 +222,6 @@ void ComputeMop::init_list(int id, NeighList *ptr) void ComputeMop::compute_vector() { - invoked_array = update->ntimestep; //Compute pressures on separate procs @@ -259,9 +261,11 @@ void ComputeMop::compute_pairs() // zero out arrays for one sample + for (i = 0; i < nvalues; i++) values_local[i] = 0.0; // invoke half neighbor list (will copy or build if necessary) + neighbor->build_one(list); inum = list->inum; @@ -274,7 +278,8 @@ void ComputeMop::compute_pairs() Pair *pair = force->pair; double **cutsq = force->pair->cutsq; - //Parse values + // Parse values + double xi[3]; double vi[3]; double fi[3]; @@ -354,20 +359,13 @@ void ComputeMop::compute_pairs() } - if (which[m] == KIN || which[m] == TOTAL){ - //Compute kinetic contribution to pressure - // counts local particles transfers across the plane + // Compute kinetic contribution to pressure + // counts local particles transfers across the plane + if (which[m] == KIN || which[m] == TOTAL){ double vcm[3]; double masstotal,sgn; - //Velocity of the center of mass - //int ivcm,vcmbit; - //ivcm = igroup; - //vcmbit = groupbit; - //masstotal = group->mass(ivcm); - //group->vcm(ivcm,masstotal,vcm); - for (int i = 0; i < nlocal; i++){ // skip if I is not in group @@ -395,8 +393,10 @@ void ComputeMop::compute_pairs() xj[1] = xi[1]-vi[1]*dt+fi[1]/2/mass[itype]*dt*dt*ftm2v; xj[2] = xi[2]-vi[2]*dt+fi[2]/2/mass[itype]*dt*dt*ftm2v; - //because LAMMPS does not put atoms back in the box at each timestep, must check - //atoms going through the image of the plane that is closest to the box + // because LAMMPS does not put atoms back in the box + // at each timestep, must check atoms going through the + // image of the plane that is closest to the box + double pos_temp = pos+copysign(1,domain->prd_half[dir]-pos)*domain->prd[dir]; if (fabs(xi[dir]-pos)single() to be implemented. In particular, it does not work with more than two-body pair interactions, intra-molecular interactions, and long range (kspace) interactions. - -[Related commands:] - -"compute mop/profile"_compute_mop_profile.html, "compute stress/atom"_compute_stress_atom.html - -[Default:] none - -:line - -:link(mop-todd) -[(Todd)] B. D. Todd, Denis J. Evans, and Peter J. Daivis: "Pressure tensor for inhomogeneous fluids", -Phys. Rev. E 52, 1627 (1995). diff --git a/src/USER-MOP/compute_mop_profile.cpp b/src/USER-MOP/compute_mop_profile.cpp old mode 100755 new mode 100644 index 8c9e9041c4..df62518c53 --- a/src/USER-MOP/compute_mop_profile.cpp +++ b/src/USER-MOP/compute_mop_profile.cpp @@ -15,10 +15,11 @@ Contributing Authors : Romain Vermorel (LFCR), Laurent Joly (ULyon) --------------------------------------------------------------------------*/ -#include "math.h" -#include "mpi.h" -#include "string.h" -#include "stdlib.h" +#include +#include +#include +#include + #include "compute_mop_profile.h" #include "atom.h" #include "update.h" @@ -34,8 +35,6 @@ #include "error.h" #include "memory.h" -#include - using namespace LAMMPS_NS; enum{X,Y,Z}; @@ -53,20 +52,18 @@ ComputeMopProfile::ComputeMopProfile(LAMMPS *lmp, int narg, char **arg) : MPI_Comm_rank(world,&me); - //set compute mode and direction of plane(s) for pressure calculation + // set compute mode and direction of plane(s) for pressure calculation - if (strcmp(arg[3],"x")==0){ + if (strcmp(arg[3],"x")==0) { dir = X; - } - else if (strcmp(arg[3],"y")==0){ + } else if (strcmp(arg[3],"y")==0) { dir = Y; - } - else if (strcmp(arg[3],"z")==0){ + } else if (strcmp(arg[3],"z")==0) { dir = Z; - } - else error->all(FLERR,"Illegal compute mop/profile command"); + } else error->all(FLERR,"Illegal compute mop/profile command"); + + // bin parameters - //Bin parameters if (strcmp(arg[4],"lower") == 0) originflag = LOWER; else if (strcmp(arg[4],"center") == 0) originflag = CENTER; else if (strcmp(arg[4],"upper") == 0) originflag = UPPER; @@ -104,20 +101,26 @@ ComputeMopProfile::ComputeMopProfile(LAMMPS *lmp, int narg, char **arg) : iarg++; } - //Check domain relared errors - // 3D only - if (domain->dimension<3) - error->all(FLERR, "Compute mop/profile incompatible with simulation dimension"); - // orthogonal simulation box - if (domain->triclinic != 0) - error->all(FLERR, "Compute mop/profile incompatible with triclinic simulation box"); + // check domain related errors + + // 3D only + + if (domain->dimension < 3) + error->all(FLERR, "Compute mop/profile incompatible with simulation dimension"); + + // orthogonal simulation box + + if (domain->triclinic != 0) + error->all(FLERR, "Compute mop/profile incompatible with triclinic simulation box"); + + // initialize some variables - // Initialize some variables nbins = 0; coord = coordp = NULL; values_local = values_global = array = NULL; - //Bin setup + // bin setup + setup_bins(); // this fix produces a global array @@ -128,7 +131,6 @@ ComputeMopProfile::ComputeMopProfile(LAMMPS *lmp, int narg, char **arg) : array_flag = 1; extarray = 0; - } /* ---------------------------------------------------------------------- */ @@ -150,46 +152,54 @@ ComputeMopProfile::~ComputeMopProfile() void ComputeMopProfile::init() { - //Conversion constants + // conversion constants + nktv2p = force->nktv2p; ftm2v = force->ftm2v; - //Plane area + // plane area + area = 1; int i; - for (i=0; i<3; i++){ + for (i=0; i<3; i++) { if (i!=dir) area = area*domain->prd[i]; } - //Timestep Value + // timestep Value + dt = update->dt; // Error check - // Compute mop/profile requires fixed simulation box - if (domain->box_change_size || domain->box_change_shape || domain->deform_flag) - error->all(FLERR, "Compute mop/profile requires a fixed simulation box"); + // Compute mop/profile requires fixed simulation box + + if (domain->box_change_size || domain->box_change_shape || domain->deform_flag) + error->all(FLERR, "Compute mop/profile requires a fixed simulation box"); - //This compute requires a pair style with pair_single method implemented - if (force->pair == NULL) - error->all(FLERR,"No pair style is defined for compute mop/profile"); - if (force->pair->single_enable == 0) - error->all(FLERR,"Pair style does not support compute mop/profile"); + //This compute requires a pair style with pair_single method implemented + + if (force->pair == NULL) + error->all(FLERR,"No pair style is defined for compute mop/profile"); + if (force->pair->single_enable == 0) + error->all(FLERR,"Pair style does not support compute mop/profile"); - // Warnings - if (me==0){ - //Compute mop/profile only accounts for pair interactions. - // issue a warning if any intramolecular potential or Kspace is defined. - if (force->bond!=NULL) - error->warning(FLERR,"compute mop/profile does not account for bond potentials"); - if (force->angle!=NULL) - error->warning(FLERR,"compute mop/profile does not account for angle potentials"); - if (force->dihedral!=NULL) - error->warning(FLERR,"compute mop/profile does not account for dihedral potentials"); - if (force->improper!=NULL) - error->warning(FLERR,"compute mop/profile does not account for improper potentials"); - if (force->kspace!=NULL) - error->warning(FLERR,"compute mop/profile does not account for kspace contributions"); - } + // Warnings + + if (me==0){ + + //Compute mop/profile only accounts for pair interactions. + // issue a warning if any intramolecular potential or Kspace is defined. + + if (force->bond!=NULL) + error->warning(FLERR,"compute mop/profile does not account for bond potentials"); + if (force->angle!=NULL) + error->warning(FLERR,"compute mop/profile does not account for angle potentials"); + if (force->dihedral!=NULL) + error->warning(FLERR,"compute mop/profile does not account for dihedral potentials"); + if (force->improper!=NULL) + error->warning(FLERR,"compute mop/profile does not account for improper potentials"); + if (force->kspace!=NULL) + error->warning(FLERR,"compute mop/profile does not account for kspace contributions"); + } // need an occasional half neighbor list @@ -197,7 +207,6 @@ void ComputeMopProfile::init() neighbor->requests[irequest]->pair = 0; neighbor->requests[irequest]->compute = 1; neighbor->requests[irequest]->occasional = 1; - } /* ---------------------------------------------------------------------- */ @@ -214,7 +223,6 @@ void ComputeMopProfile::init_list(int id, NeighList *ptr) void ComputeMopProfile::compute_array() { - invoked_array = update->ntimestep; //Compute pressures on separate procs @@ -235,7 +243,6 @@ void ComputeMopProfile::compute_array() m++; } } - } @@ -267,6 +274,7 @@ void ComputeMopProfile::compute_pairs() } // invoke half neighbor list (will copy or build if necessary) + neighbor->build_one(list); inum = list->inum; @@ -279,7 +287,8 @@ void ComputeMopProfile::compute_pairs() Pair *pair = force->pair; double **cutsq = force->pair->cutsq; - //Parse values + // parse values + double xi[3]; double vi[3]; double fi[3]; @@ -289,7 +298,8 @@ void ComputeMopProfile::compute_pairs() while (mx[j][0]; @@ -326,15 +337,18 @@ void ComputeMopProfile::compute_pairs() pos1 = coordp[ibin][0]; //check if ij pair is accross plane, add contribution to pressure - if ( ((xi[dir]>pos) && (xj[dir]pos1) && (xj[dir]pos) && (xj[dir]pos1) && (xj[dir]single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair); values_local[ibin][m] += fpair*(xi[0]-xj[0])/area*nktv2p; values_local[ibin][m+1] += fpair*(xi[1]-xj[1])/area*nktv2p; values_local[ibin][m+2] += fpair*(xi[2]-xj[2])/area*nktv2p; - } - else if ( ((xi[dir]pos)) || ((xi[dir]pos1)) ){ + + } else if ( ((xi[dir]pos)) + || ((xi[dir]pos1)) ) { pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair); @@ -342,9 +356,7 @@ void ComputeMopProfile::compute_pairs() values_local[ibin][m+1] -= fpair*(xi[1]-xj[1])/area*nktv2p; values_local[ibin][m+2] -= fpair*(xi[2]-xj[2])/area*nktv2p; } - } - } else { for (ibin=0;ibinpos) && (xj[dir]pos1) && (xj[dir]pos) && (xj[dir]pos1) && (xj[dir]single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair); @@ -360,21 +374,16 @@ void ComputeMopProfile::compute_pairs() values_local[ibin][m+1] += fpair*(xi[1]-xj[1])/area*nktv2p; values_local[ibin][m+2] += fpair*(xi[2]-xj[2])/area*nktv2p; } - } - } - } - } - } + // compute kinetic contribution to pressure + // counts local particles transfers across the plane if (which[m] == KIN || which[m] == TOTAL){ - //Compute kinetic contribution to pressure - // counts local particles transfers across the plane double vcm[3]; double masstotal,sgn; @@ -382,6 +391,7 @@ void ComputeMopProfile::compute_pairs() for (int i = 0; i < nlocal; i++){ // skip if I is not in group + if (mask[i] & groupbit){ itype = type[i]; @@ -424,9 +434,7 @@ void ComputeMopProfile::compute_pairs() values_local[ibin][m+1] += mass[itype]*vcross[1]*sgn/dt/area*nktv2p/ftm2v; values_local[ibin][m+2] += mass[itype]*vcross[2]*sgn/dt/area*nktv2p/ftm2v; } - } - } } } @@ -434,7 +442,6 @@ void ComputeMopProfile::compute_pairs() } } - /* ---------------------------------------------------------------------- setup 1d bins and their extent and coordinates called at init() @@ -486,5 +493,4 @@ void ComputeMopProfile::setup_bins() coordp[i][0] = coord[i][0] - domain->prd[dir]; } } - } diff --git a/src/USER-MOP/compute_mop_profile.h b/src/USER-MOP/compute_mop_profile.h old mode 100755 new mode 100644 diff --git a/src/USER-MOP/compute_mop_profile.txt b/src/USER-MOP/compute_mop_profile.txt deleted file mode 100755 index 24b624a144..0000000000 --- a/src/USER-MOP/compute_mop_profile.txt +++ /dev/null @@ -1,72 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Section_commands.html#comm) - -:line - -compute mop/profile command :h3 - -[Syntax:] - -compute ID group-ID mop/profile dir origin delta keyword ... :pre - -ID, group-ID are documented in "compute"_compute.html command -mop/profile = style name of this compute command -dir = {x} or {y} or {z} is the direction normal to the planes -origin = {lower} or {center} or {upper} or coordinate value (distance units) is the position of the first plane -delta = value (distance units) is the distance between planes -between one and three keywords can be appended -keyword = {kin} or {conf} or {total} :ul - -[Examples:] -:link(mop-examples) - -compute 1 all mop/profile x lower 0.1 total -compute 1 liquid mop/profile z 0.0 0.25 kin conf -fix 1 all ave/time 500 20 10000 c_1\[*\] ave running overwrite file mopp.time mode vector :pre - - -[Description:] - -Define a computation that calculates profiles of components of the local stress tensor using the method of planes "(Todd)"_#mop-todd, applied on an array of regularly spaced planes. -Specifically 3 components are computed in directions {dir},{x}; {dir},{y}; and {dir},{z}; where {dir} is the direction normal to the planes. - -Contrary to methods based on histograms of atomic stress (i.e. using "compute stress/atom"_compute_stress_atom.html), the method of planes is compatible with mechanical balance in heterogeneous systems and at interfaces "(Todd)"_#mop-todd. - -The stress tensor is the sum of a kinetic term and a configurational term, which are given respectively by Eq. (21) and Eq. (16) in "(Todd)"_#mop-todd. For the kinetic part, the algorithm considers that atoms have crossed the plane if their positions at times t-dt and t are one on either side of the plane, and uses the velocity at time t-dt/2 given by the velocity-Verlet algorithm. - -Between one and three keywords can be used to indicate which contributions to the stress must be computed: kinetic stress (kin), configurational stress (conf), and/or total stress (total). - -NOTE 1: The configurational stress is computed considering all pairs of atoms where at least one atom belongs to group group-ID. - -NOTE 2: The local stress does not include any Lennard-Jones tail -corrections to the pressure added by the "pair_modify tail -yes"_pair_modify.html command, since those are contributions to the global system pressure. - -[Output info:] - -This compute calculates a global array, with 1 column giving the position of the planes where the stress tensor was computed, and with 3 columns of values for each declared keyword (in the order the keywords have been declared). For each keyword, the profiles of stress tensor components are ordered as follows: stress_dir,x; stress_dir,y; and stress_dir,z. - -The values are in pressure "units"_units.html. - -The values produced by this compute can be accessed by various "output commands"_Section_howto.html#howto_15. For instance, the results can be written to a file using the "fix ave/time"_fix_ave_time.html command, see "Examples"_#mop-examples above. - -[Restrictions:] - -The method is only implemented for 3d orthogonal simulation boxes whose size does not change in time, and axis-aligned planes. - -The method only works with two-body pair interactions, because it requires the class method pair->single() to be implemented. In particular, it does not work with more than two-body pair interactions, intra-molecular interactions, and long range (kspace) interactions. - -[Related commands:] - -"compute mop"_compute_mop.html, "compute stress/atom"_compute_stress_atom.html - -[Default:] none - -:line - -:link(mop-todd) -[(Todd)] B. D. Todd, Denis J. Evans, and Peter J. Daivis: "Pressure tensor for inhomogeneous fluids", -Phys. Rev. E 52, 1627 (1995). From f6f4b58167cb4ef78cae3b0fa2cb6a3ae266f1ee Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 3 Sep 2018 23:42:52 -0400 Subject: [PATCH 120/302] add parallel reference output --- .../USER/mop/log.31Aug18.compute_mop.g++.4 | 188 ++++++++++++++++++ 1 file changed, 188 insertions(+) create mode 100644 examples/USER/mop/log.31Aug18.compute_mop.g++.4 diff --git a/examples/USER/mop/log.31Aug18.compute_mop.g++.4 b/examples/USER/mop/log.31Aug18.compute_mop.g++.4 new file mode 100644 index 0000000000..16ef8a2ce1 --- /dev/null +++ b/examples/USER/mop/log.31Aug18.compute_mop.g++.4 @@ -0,0 +1,188 @@ +LAMMPS (31 Aug 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +variable T equal 0.8 +variable p_solid equal 0.05 + +lattice fcc 1.0 +Lattice spacing in x,y,z = 1.5874 1.5874 1.5874 +region box block 0.0 6.0 0.0 6.0 -2.0 12.0 +create_box 2 box +Created orthogonal box = (0 0 -3.1748) to (9.52441 9.52441 19.0488) + 1 by 1 by 4 MPI processor grid + +mass * 1.0 +pair_style lj/cut 2.5 +pair_coeff * * 1.0 1.0 +pair_coeff 1 2 0.5 1.0 +pair_coeff 2 2 0.0 0.0 +neigh_modify delay 0 + +region solid_bottom block INF INF INF INF -1.1 0.1 +region liquid block INF INF INF INF 1.1 8.9 +region solid_up block INF INF INF INF 9.9 11.1 + +create_atoms 1 region liquid +Created 1080 atoms + Time spent = 0.000378132 secs +delete_atoms porosity liquid 0.26 88765 +Deleted 288 atoms, new total = 792 +group liquid region liquid +792 atoms in group liquid + +create_atoms 2 region solid_bottom +Created 216 atoms + Time spent = 0.000345945 secs +group solid_bottom region solid_bottom +216 atoms in group solid_bottom +create_atoms 2 region solid_up +Created 216 atoms + Time spent = 0.000124454 secs +group solid_up region solid_up +216 atoms in group solid_up +group solid union solid_bottom solid_up +432 atoms in group solid + +variable faSolid equal ${p_solid}*lx*ly/count(solid_up) +variable faSolid equal 0.05*lx*ly/count(solid_up) +fix piston_up solid_up aveforce NULL NULL -${faSolid} +fix piston_up solid_up aveforce NULL NULL -0.0209986841649146 +fix freeze_up solid_up setforce 0.0 0.0 NULL +fix freeze_bottom solid_bottom setforce 0.0 0.0 0.0 +fix nvesol solid nve +compute Tliq liquid temp +fix nvtliq liquid nvt temp $T $T 0.5 +fix nvtliq liquid nvt temp 0.8 $T 0.5 +fix nvtliq liquid nvt temp 0.8 0.8 0.5 +fix_modify nvtliq temp Tliq +WARNING: Temperature for fix modify is not for group all (src/fix_nh.cpp:1404) + +thermo 10000 +thermo_modify flush yes temp Tliq +WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488) + +# dump 1 all atom 10000 dump.lammpstrj + +fix fxbal all balance 1000 1.05 shift z 10 1.05 +velocity liquid create $T 47298 dist gaussian rot yes +velocity liquid create 0.8 47298 dist gaussian rot yes +run 50000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 7 7 16 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.122 | 3.135 | 3.147 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 0.8 -3.4905808 0 -2.7150906 -0.59565852 2016 + 10000 0.82075861 -3.1822235 0 -2.3866107 0.013840263 2016 + 20000 0.76467575 -3.0955084 0 -2.3542602 -0.076868925 2016 + 30000 0.75803557 -3.1011543 0 -2.3663428 -0.052887049 2016 + 40000 0.81732724 -3.064259 0 -2.2719724 0.070708808 2016 + 50000 0.75874551 -3.1070261 0 -2.3715265 -0.074970431 2016 +Loop time of 22.1566 on 4 procs for 50000 steps with 1224 atoms + +Performance: 974879.887 tau/day, 2256.666 timesteps/s +98.5% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 10.732 | 13.012 | 14.39 | 38.0 | 58.73 +Neigh | 2.47 | 3.7351 | 4.3661 | 38.4 | 16.86 +Comm | 1.881 | 3.4383 | 5.8722 | 79.7 | 15.52 +Output | 0.00014567 | 0.0003581 | 0.0009892 | 0.0 | 0.00 +Modify | 1.1006 | 1.5188 | 2.6121 | 51.3 | 6.85 +Other | | 0.4521 | | | 2.04 + +Nlocal: 306 ave 312 max 295 min +Histogram: 1 0 0 0 0 0 0 1 1 1 +Nghost: 1242.75 ave 1373 max 944 min +Histogram: 1 0 0 0 0 0 0 0 1 2 +Neighs: 9770.25 ave 10807 max 8736 min +Histogram: 1 0 0 1 0 0 1 0 0 1 + +Total # of neighbors = 39081 +Ave neighs/atom = 31.9289 +Neighbor list builds = 5704 +Dangerous builds = 0 +# undump 1 +reset_timestep 0 + +compute bin_z liquid chunk/atom bin/1d z 0.0 0.1 units box + +compute liquidStress_ke liquid stress/atom NULL ke +compute liquidStress_vir liquid stress/atom NULL virial +fix profile_z liquid ave/chunk 10 1000 10000 bin_z density/number temp c_liquidStress_ke[1] c_liquidStress_ke[2] c_liquidStress_ke[3] c_liquidStress_ke[4] c_liquidStress_ke[5] c_liquidStress_ke[6] c_liquidStress_vir[1] c_liquidStress_vir[2] c_liquidStress_vir[3] c_liquidStress_vir[4] c_liquidStress_vir[5] c_liquidStress_vir[6] ave running overwrite file profile.z + +compute mopz0 all mop z center kin conf +fix mopz0t all ave/time 10 1000 10000 c_mopz0[*] file mopz0.time + +compute moppz liquid mop/profile z 0.0 0.1 kin conf +fix moppzt all ave/time 100 100 10000 c_moppz[*] ave running overwrite file moppz.time mode vector + +run 40000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 7 7 16 + 3 neighbor lists, perpetual/occasional/extra = 1 2 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard + (2) compute mop, occasional, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (3) compute mop/profile, occasional, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 4.139 | 4.147 | 4.15 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 0.75874551 -3.1070261 0 -2.3715265 -0.074970431 2016 + 10000 0.82372476 -3.1299329 0 -2.3314448 -0.14706101 2016 + 20000 0.80692892 -3.1278896 0 -2.3456828 -0.085123604 2016 + 30000 0.78458951 -3.0966006 0 -2.3360488 0.13637007 2016 + 40000 0.80106495 -3.1135836 0 -2.3370611 -0.14404185 2016 +Loop time of 31.4145 on 4 procs for 40000 steps with 1224 atoms + +Performance: 550065.249 tau/day, 1273.299 timesteps/s +92.6% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 10.199 | 12.307 | 13.428 | 35.4 | 39.18 +Neigh | 2.1261 | 3.1416 | 3.6373 | 33.5 | 10.00 +Comm | 3.5381 | 4.476 | 6.229 | 48.9 | 14.25 +Output | 0.00062943 | 0.0031546 | 0.0040004 | 2.6 | 0.01 +Modify | 10.186 | 10.862 | 12.26 | 24.8 | 34.58 +Other | | 0.6247 | | | 1.99 + +Nlocal: 306 ave 315 max 299 min +Histogram: 1 0 0 1 1 0 0 0 0 1 +Nghost: 1221.5 ave 1347 max 912 min +Histogram: 1 0 0 0 0 0 0 0 1 2 +Neighs: 9710.25 ave 10301 max 8980 min +Histogram: 1 0 0 0 0 1 1 0 0 1 + +Total # of neighbors = 38841 +Ave neighs/atom = 31.7328 +Neighbor list builds = 4573 +Dangerous builds = 0 + +Total wall time: 0:00:53 From a797a0d193cacfad1ca0329927ddb52f19799f58 Mon Sep 17 00:00:00 2001 From: RomainVermorel Date: Tue, 4 Sep 2018 14:02:19 +0200 Subject: [PATCH 121/302] changed computes names to stress/mop and stress/mop/profile --- doc/src/compute_stress_mop.txt | 111 +++++ examples/USER/mop/in.compute_stress_mop | 62 +++ src/USER-MOP/README | 10 +- src/USER-MOP/compute_stress_mop.cpp | 424 +++++++++++++++++ src/USER-MOP/compute_stress_mop.h | 102 ++++ src/USER-MOP/compute_stress_mop_profile.cpp | 496 ++++++++++++++++++++ src/USER-MOP/compute_stress_mop_profile.h | 113 +++++ 7 files changed, 1313 insertions(+), 5 deletions(-) create mode 100644 doc/src/compute_stress_mop.txt create mode 100755 examples/USER/mop/in.compute_stress_mop create mode 100644 src/USER-MOP/compute_stress_mop.cpp create mode 100644 src/USER-MOP/compute_stress_mop.h create mode 100644 src/USER-MOP/compute_stress_mop_profile.cpp create mode 100644 src/USER-MOP/compute_stress_mop_profile.h diff --git a/doc/src/compute_stress_mop.txt b/doc/src/compute_stress_mop.txt new file mode 100644 index 0000000000..8d95ef42e2 --- /dev/null +++ b/doc/src/compute_stress_mop.txt @@ -0,0 +1,111 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +compute stress/mop command :h3 +compute stress/mop/profile command :h3 + + +[Syntax:] + +compute ID group-ID style dir args keywords ... :pre + +ID, group-ID are documented in "compute"_compute.html command +style = {stress/mop} or {stress/mop/profile} +dir = {x} or {y} or {z} is the direction normal to the plane +args = argument specific to the compute style +keywords = {kin} or {conf} or {total} (one of more can be specified) :ul + {stress/mop} args = pos + pos = {lower} or {center} or {upper} or coordinate value (distance units) is the position of the plane + {stress/mop/profile} args = origin delta + origin = {lower} or {center} or {upper} or coordinate value (distance units) is the position of the first plane + delta = value (distance units) is the distance between planes :pre + +compute 1 all stress/mop x lower total +compute 1 liquid stress/mop z 0.0 kin conf +fix 1 all ave/time 10 1000 10000 c_1\[*\] file mop.time +fix 1 all ave/time 10 1000 10000 c_1\[2\] file mop.time :pre + +compute 1 all stress/mop/profile x lower 0.1 total +compute 1 liquid stress/mop/profile z 0.0 0.25 kin conf +fix 1 all ave/time 500 20 10000 c_1\[*\] ave running overwrite file mopp.time mode vector :pre + + +[Description:] + +Compute {stress/mop} and compute {stress/mop/profile} define computations that +calculate components of the local stress tensor using the method of +planes "(Todd)"_#mop-todd. Specifically in compute {stress/mop} calculates 3 +components are computed in directions {dir},{x}; {dir},{y}; and +{dir},{z}; where {dir} is the direction normal to the plane, while +in compute {stress/mop/profile} the profile of the stress is computed. + +Contrary to methods based on histograms of atomic stress (i.e. using +"compute stress/atom"_compute_stress_atom.html), the method of planes is +compatible with mechanical balance in heterogeneous systems and at +interfaces "(Todd)"_#mop-todd. + +The stress tensor is the sum of a kinetic term and a configurational +term, which are given respectively by Eq. (21) and Eq. (16) in +"(Todd)"_#mop-todd. For the kinetic part, the algorithm considers that +atoms have crossed the plane if their positions at times t-dt and t are +one on either side of the plane, and uses the velocity at time t-dt/2 +given by the velocity-Verlet algorithm. + +Between one and three keywords can be used to indicate which +contributions to the stress must be computed: kinetic stress (kin), +configurational stress (conf), and/or total stress (total). + +NOTE 1: The configurational stress is computed considering all pairs of atoms where at least one atom belongs to group group-ID. + +NOTE 2: The local stress does not include any Lennard-Jones tail +corrections to the pressure added by the "pair_modify tail +yes"_pair_modify.html command, since those are contributions to the global system pressure. + +[Output info:] + +Compute {stress/mop} calculates a global vector (indices starting at 1), with 3 +values for each declared keyword (in the order the keywords have been +declared). For each keyword, the stress tensor components are ordered as +follows: stress_dir,x, stress_dir,y, and stress_dir,z. + +Compute {stress/mop/profile} instead calculates a global array, with 1 column +giving the position of the planes where the stress tensor was computed, +and with 3 columns of values for each declared keyword (in the order the +keywords have been declared). For each keyword, the profiles of stress +tensor components are ordered as follows: stress_dir,x; stress_dir,y; +and stress_dir,z. + +The values are in pressure "units"_units.html. + +The values produced by this compute can be accessed by various "output commands"_Howto_output.html. For instance, the results can be written to a file using the "fix ave/time"_fix_ave_time.html command. Please see the example in the examples/USER/mop folder. + +[Restrictions:] + +This style is part of the USER-MOP package. It is only enabled if LAMMPS +is built with that package. See the "Build package"_Build_package.html +doc page on for more info. + +The method is only implemented for 3d orthogonal simulation boxes whose +size does not change in time, and axis-aligned planes. + +The method only works with two-body pair interactions, because it +requires the class method pair->single() to be implemented. In +particular, it does not work with more than two-body pair interactions, +intra-molecular interactions, and long range (kspace) interactions. + +[Related commands:] + +"compute stress/atom"_compute_stress_atom.html + +[Default:] none + +:line + +:link(mop-todd) +[(Todd)] B. D. Todd, Denis J. Evans, and Peter J. Daivis: "Pressure tensor for inhomogeneous fluids", +Phys. Rev. E 52, 1627 (1995). diff --git a/examples/USER/mop/in.compute_stress_mop b/examples/USER/mop/in.compute_stress_mop new file mode 100755 index 0000000000..cfa97f5dfe --- /dev/null +++ b/examples/USER/mop/in.compute_stress_mop @@ -0,0 +1,62 @@ +variable T equal 0.8 +variable p_solid equal 0.05 + +lattice fcc 1.0 +region box block 0.0 6.0 0.0 6.0 -2.0 12.0 +create_box 2 box + +mass * 1.0 +pair_style lj/cut 2.5 +pair_coeff * * 1.0 1.0 +pair_coeff 1 2 0.5 1.0 +pair_coeff 2 2 0.0 0.0 +neigh_modify delay 0 + +region solid_bottom block INF INF INF INF -1.1 0.1 +region liquid block INF INF INF INF 1.1 8.9 +region solid_up block INF INF INF INF 9.9 11.1 + +create_atoms 1 region liquid +delete_atoms porosity liquid 0.26 88765 +group liquid region liquid + +create_atoms 2 region solid_bottom +group solid_bottom region solid_bottom +create_atoms 2 region solid_up +group solid_up region solid_up +group solid union solid_bottom solid_up + +variable faSolid equal ${p_solid}*lx*ly/count(solid_up) +fix piston_up solid_up aveforce NULL NULL -${faSolid} +fix freeze_up solid_up setforce 0.0 0.0 NULL +fix freeze_bottom solid_bottom setforce 0.0 0.0 0.0 +fix nvesol solid nve +compute Tliq liquid temp +fix nvtliq liquid nvt temp $T $T 0.5 +fix_modify nvtliq temp Tliq + +thermo 10000 +thermo_modify flush yes temp Tliq + +dump 1 all atom 10000 dump.lammpstrj + +fix fxbal all balance 1000 1.05 shift z 10 1.05 +velocity liquid create $T 47298 dist gaussian rot yes +run 50000 +undump 1 +reset_timestep 0 + +compute bin_z liquid chunk/atom bin/1d z 0.0 0.1 units box + +compute liquidStress_ke liquid stress/atom NULL ke +compute liquidStress_vir liquid stress/atom NULL virial +fix profile_z liquid ave/chunk 10 1000 10000 bin_z density/number temp c_liquidStress_ke[1] c_liquidStress_ke[2] c_liquidStress_ke[3] c_liquidStress_ke[4] c_liquidStress_ke[5] c_liquidStress_ke[6] c_liquidStress_vir[1] c_liquidStress_vir[2] c_liquidStress_vir[3] c_liquidStress_vir[4] c_liquidStress_vir[5] c_liquidStress_vir[6] ave running overwrite file profile.z + +compute mopz0 all stress/mop z center kin conf +fix mopz0t all ave/time 10 1000 10000 c_mopz0[*] file mopz0.time + +compute moppz liquid stress/mop/profile z 0.0 0.1 kin conf +fix moppzt all ave/time 100 100 10000 c_moppz[*] ave running overwrite file moppz.time mode vector + +run 40000 + diff --git a/src/USER-MOP/README b/src/USER-MOP/README index d8e7d2f732..15fcb3701a 100644 --- a/src/USER-MOP/README +++ b/src/USER-MOP/README @@ -1,21 +1,21 @@ USER-MOP ============ -This package provides the mop and mop/profile compute styles. -See the doc page for compute mop or compute mop/profile command for how to use +This package provides the stress/mop and stress/mop/profile compute styles. +See the doc page for compute stress/mop or compute stress/mop/profile command for how to use them. PACKAGE DESCRIPTION ------------------- -This is a LAMMPS (http://lammps.sandia.gov/) compute style that calculates +These are LAMMPS (http://lammps.sandia.gov/) compute styles that calculate components of the local stress tensor using the method of planes as described in the paper by Todd et al. (B. D. Todd, Denis J. Evans, and Peter J. Daivis: "Pressure tensor for inhomogeneous fluids", Phys. Rev. E 52, 1627 (1995)). This package contains the source files of two compute styles: -* compute mop calculates components of the local stress tensor using the method of planes, applied on one plane. -* compute mop/profile calculates profiles of components of the local stress tensor using the method of planes, applied on an array of regularly spaced planes. +* compute stress/mop calculates components of the local stress tensor using the method of planes, applied on one plane. +* compute stress/mop/profile calculates profiles of components of the local stress tensor using the method of planes, applied on an array of regularly spaced planes. The persons who created these files are Laurent Joly at University of Lyon 1 and Romain Vermorel at University of Pau and Pays de l'Adour. Contact them directly if you have questions. diff --git a/src/USER-MOP/compute_stress_mop.cpp b/src/USER-MOP/compute_stress_mop.cpp new file mode 100644 index 0000000000..f764e0ee7e --- /dev/null +++ b/src/USER-MOP/compute_stress_mop.cpp @@ -0,0 +1,424 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. + ------------------------------------------------------------------------- */ + +/*------------------------------------------------------------------------ + Contributing Authors : Romain Vermorel (LFCR), Laurent Joly (ULyon) + --------------------------------------------------------------------------*/ + +#include +#include +#include +#include + +#include "compute_stress_mop.h" +#include "atom.h" +#include "update.h" +#include "domain.h" +#include "group.h" +#include "modify.h" +#include "fix.h" +#include "neighbor.h" +#include "force.h" +#include "pair.h" +#include "neigh_request.h" +#include "neigh_list.h" +#include "error.h" +#include "memory.h" + +using namespace LAMMPS_NS; + +enum{X,Y,Z}; +enum{TOTAL,CONF,KIN}; + +#define BIG 1000000000 + +/* ---------------------------------------------------------------------- */ + +ComputeStressMop::ComputeStressMop(LAMMPS *lmp, int narg, char **arg) : + Compute(lmp, narg, arg) +{ + if (narg < 6) error->all(FLERR,"Illegal compute stress/mop command"); + + MPI_Comm_rank(world,&me); + + // set compute mode and direction of plane(s) for pressure calculation + + if (strcmp(arg[3],"x")==0) { + dir = X; + } else if (strcmp(arg[3],"y")==0) { + dir = Y; + } else if (strcmp(arg[3],"z")==0) { + dir = Z; + } else error->all(FLERR,"Illegal compute stress/mop command"); + + // Position of the plane + + if (strcmp(arg[4],"lower")==0) { + pos = domain->boxlo[dir]; + } else if (strcmp(arg[4],"upper")==0) { + pos = domain->boxhi[dir]; + } else if (strcmp(arg[4],"center")==0) { + pos = 0.5*(domain->boxlo[dir]+domain->boxhi[dir]); + } else pos = force->numeric(FLERR,arg[4]); + + if ( pos < (domain->boxlo[dir]+domain->prd_half[dir]) ) { + pos1 = pos + domain->prd[dir]; + } else { + pos1 = pos - domain->prd[dir]; + } + + // parse values until one isn't recognized + + which = new int[3*(narg-5)]; + nvalues = 0; + int i; + + int iarg=5; + while (iarg < narg) { + if (strcmp(arg[iarg],"conf") == 0) { + for (i=0; i<3; i++) { + which[nvalues] = CONF; + nvalues++; + } + } else if (strcmp(arg[iarg],"kin") == 0) { + for (i=0; i<3; i++) { + which[nvalues] = KIN; + nvalues++; + } + } else if (strcmp(arg[iarg],"total") == 0) { + for (i=0; i<3; i++) { + which[nvalues] = TOTAL; + nvalues++; + } + } else error->all(FLERR, "Illegal compute stress/mop command"); //break; + + iarg++; + } + + // Error check + // 3D only + + if (domain->dimension < 3) + error->all(FLERR, "Compute stress/mop incompatible with simulation dimension"); + + // orthogonal simulation box + if (domain->triclinic != 0) + error->all(FLERR, "Compute stress/mop incompatible with triclinic simulation box"); + // plane inside the box + if (pos >domain->boxhi[dir] || pos boxlo[dir]) + error->all(FLERR, "Plane for compute stress/mop is out of bounds"); + + + // Initialize some variables + + values_local = values_global = vector = NULL; + + // this fix produces a global vector + + memory->create(vector,nvalues,"stress/mop:vector"); + memory->create(values_local,nvalues,"stress/mop/spatial:values_local"); + memory->create(values_global,nvalues,"stress/mop/spatial:values_global"); + size_vector = nvalues; + + vector_flag = 1; + extvector = 0; + +} + +/* ---------------------------------------------------------------------- */ + +ComputeStressMop::~ComputeStressMop() +{ + + delete [] which; + + memory->destroy(values_local); + memory->destroy(values_global); + memory->destroy(vector); +} + +/* ---------------------------------------------------------------------- */ + +void ComputeStressMop::init() +{ + + // Conversion constants + + nktv2p = force->nktv2p; + ftm2v = force->ftm2v; + + // Plane area + + area = 1; + int i; + for (i=0; i<3; i++){ + if (i!=dir) area = area*domain->prd[i]; + } + + // Timestep Value + + dt = update->dt; + + // Error check + + // Compute stress/mop requires fixed simulation box + if (domain->box_change_size || domain->box_change_shape || domain->deform_flag) + error->all(FLERR, "Compute stress/mop requires a fixed simulation box"); + + // This compute requires a pair style with pair_single method implemented + + if (force->pair == NULL) + error->all(FLERR,"No pair style is defined for compute stress/mop"); + if (force->pair->single_enable == 0) + error->all(FLERR,"Pair style does not support compute stress/mop"); + + // Warnings + + if (me==0){ + + //Compute stress/mop only accounts for pair interactions. + // issue a warning if any intramolecular potential or Kspace is defined. + + if (force->bond!=NULL) + error->warning(FLERR,"compute stress/mop does not account for bond potentials"); + if (force->angle!=NULL) + error->warning(FLERR,"compute stress/mop does not account for angle potentials"); + if (force->dihedral!=NULL) + error->warning(FLERR,"compute stress/mop does not account for dihedral potentials"); + if (force->improper!=NULL) + error->warning(FLERR,"compute stress/mop does not account for improper potentials"); + if (force->kspace!=NULL) + error->warning(FLERR,"compute stress/mop does not account for kspace contributions"); + } + + // need an occasional half neighbor list + int irequest = neighbor->request((void *) this); + neighbor->requests[irequest]->pair = 0; + neighbor->requests[irequest]->compute = 1; + neighbor->requests[irequest]->occasional = 1; +} + +/* ---------------------------------------------------------------------- */ + +void ComputeStressMop::init_list(int id, NeighList *ptr) +{ + list = ptr; +} + + +/* ---------------------------------------------------------------------- + compute output vector + ------------------------------------------------------------------------- */ + +void ComputeStressMop::compute_vector() +{ + invoked_array = update->ntimestep; + + //Compute pressures on separate procs + compute_pairs(); + + // sum pressure contributions over all procs + MPI_Allreduce(values_local,values_global,nvalues, + MPI_DOUBLE,MPI_SUM,world); + + int m; + for (m=0; mmass; + int *type = atom->type; + int *mask = atom->mask; + int nlocal = atom->nlocal; + double *special_coul = force->special_coul; + double *special_lj = force->special_lj; + int newton_pair = force->newton_pair; + + + // zero out arrays for one sample + + for (i = 0; i < nvalues; i++) values_local[i] = 0.0; + + // invoke half neighbor list (will copy or build if necessary) + + neighbor->build_one(list); + + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + // loop over neighbors of my atoms + + Pair *pair = force->pair; + double **cutsq = force->pair->cutsq; + + // Parse values + + double xi[3]; + double vi[3]; + double fi[3]; + double xj[3]; + + m = 0; + while (mx[i][0]; + xi[1] = atom->x[i][1]; + xi[2] = atom->x[i][2]; + itype = type[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + factor_lj = special_lj[sbmask(j)]; + factor_coul = special_coul[sbmask(j)]; + j &= NEIGHMASK; + + // skip if neither I nor J are in group + if (!(mask[i] & groupbit || mask[j] & groupbit)) continue; + + xj[0] = atom->x[j][0]; + xj[1] = atom->x[j][1]; + xj[2] = atom->x[j][2]; + delx = xi[0] - xj[0]; + dely = xi[1] - xj[1]; + delz = xi[2] - xj[2]; + rsq = delx*delx + dely*dely + delz*delz; + jtype = type[j]; + if (rsq >= cutsq[itype][jtype]) continue; + + if (newton_pair || j < nlocal) { + + //check if ij pair is accross plane, add contribution to pressure + if ( ((xi[dir]>pos) && (xj[dir]pos1) && (xj[dir]single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair); + + values_local[m] += fpair*(xi[0]-xj[0])/area*nktv2p; + values_local[m+1] += fpair*(xi[1]-xj[1])/area*nktv2p; + values_local[m+2] += fpair*(xi[2]-xj[2])/area*nktv2p; + } + else if ( ((xi[dir]pos)) || ((xi[dir]pos1)) ){ + + pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair); + + values_local[m] -= fpair*(xi[0]-xj[0])/area*nktv2p; + values_local[m+1] -= fpair*(xi[1]-xj[1])/area*nktv2p; + values_local[m+2] -= fpair*(xi[2]-xj[2])/area*nktv2p; + } + + } else { + + if ( ((xi[dir]>pos) && (xj[dir]pos1) && (xj[dir]single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair); + + values_local[m] += fpair*(xi[0]-xj[0])/area*nktv2p; + values_local[m+1] += fpair*(xi[1]-xj[1])/area*nktv2p; + values_local[m+2] += fpair*(xi[2]-xj[2])/area*nktv2p; + } + + } + + } + + } + + } + + + // Compute kinetic contribution to pressure + // counts local particles transfers across the plane + + if (which[m] == KIN || which[m] == TOTAL){ + double vcm[3]; + double masstotal,sgn; + + for (int i = 0; i < nlocal; i++){ + + // skip if I is not in group + if (mask[i] & groupbit){ + + itype = type[i]; + + //coordinates at t + xi[0] = atom->x[i][0]; + xi[1] = atom->x[i][1]; + xi[2] = atom->x[i][2]; + + //velocities at t + vi[0] = atom->v[i][0]; + vi[1] = atom->v[i][1]; + vi[2] = atom->v[i][2]; + + //forces at t + fi[0] = atom->f[i][0]; + fi[1] = atom->f[i][1]; + fi[2] = atom->f[i][2]; + + //coordinates at t-dt (based on Velocity-Verlet alg.) + xj[0] = xi[0]-vi[0]*dt+fi[0]/2/mass[itype]*dt*dt*ftm2v; + xj[1] = xi[1]-vi[1]*dt+fi[1]/2/mass[itype]*dt*dt*ftm2v; + xj[2] = xi[2]-vi[2]*dt+fi[2]/2/mass[itype]*dt*dt*ftm2v; + + // because LAMMPS does not put atoms back in the box + // at each timestep, must check atoms going through the + // image of the plane that is closest to the box + + double pos_temp = pos+copysign(1,domain->prd_half[dir]-pos)*domain->prd[dir]; + if (fabs(xi[dir]-pos) +#include +#include +#include + +#include "compute_stress_mop_profile.h" +#include "atom.h" +#include "update.h" +#include "domain.h" +#include "group.h" +#include "modify.h" +#include "fix.h" +#include "neighbor.h" +#include "force.h" +#include "pair.h" +#include "neigh_request.h" +#include "neigh_list.h" +#include "error.h" +#include "memory.h" + +using namespace LAMMPS_NS; + +enum{X,Y,Z}; +enum{LOWER,CENTER,UPPER,COORD}; +enum{TOTAL,CONF,KIN}; + +#define BIG 1000000000 + +/* ---------------------------------------------------------------------- */ + +ComputeStressMopProfile::ComputeStressMopProfile(LAMMPS *lmp, int narg, char **arg) : + Compute(lmp, narg, arg) +{ + if (narg < 7) error->all(FLERR,"Illegal compute stress/mop/profile command"); + + MPI_Comm_rank(world,&me); + + // set compute mode and direction of plane(s) for pressure calculation + + if (strcmp(arg[3],"x")==0) { + dir = X; + } else if (strcmp(arg[3],"y")==0) { + dir = Y; + } else if (strcmp(arg[3],"z")==0) { + dir = Z; + } else error->all(FLERR,"Illegal compute stress/mop/profile command"); + + // bin parameters + + if (strcmp(arg[4],"lower") == 0) originflag = LOWER; + else if (strcmp(arg[4],"center") == 0) originflag = CENTER; + else if (strcmp(arg[4],"upper") == 0) originflag = UPPER; + else originflag = COORD; + if (originflag == COORD) + origin = force->numeric(FLERR,arg[4]); + delta = force->numeric(FLERR,arg[5]); + invdelta = 1.0/delta; + + // parse values until one isn't recognized + + which = new int[3*(narg-6)]; + nvalues = 0; + int i; + + int iarg=6; + while (iarg < narg) { + if (strcmp(arg[iarg],"conf") == 0) { + for (i=0; i<3; i++) { + which[nvalues] = CONF; + nvalues++; + } + } else if (strcmp(arg[iarg],"kin") == 0) { + for (i=0; i<3; i++) { + which[nvalues] = KIN; + nvalues++; + } + } else if (strcmp(arg[iarg],"total") == 0) { + for (i=0; i<3; i++) { + which[nvalues] = TOTAL; + nvalues++; + } + } else error->all(FLERR, "Illegal compute stress/mop/profile command"); //break; + + iarg++; + } + + // check domain related errors + + // 3D only + + if (domain->dimension < 3) + error->all(FLERR, "Compute stress/mop/profile incompatible with simulation dimension"); + + // orthogonal simulation box + + if (domain->triclinic != 0) + error->all(FLERR, "Compute stress/mop/profile incompatible with triclinic simulation box"); + + // initialize some variables + + nbins = 0; + coord = coordp = NULL; + values_local = values_global = array = NULL; + + // bin setup + + setup_bins(); + + // this fix produces a global array + + memory->create(array,nbins,1+nvalues,"stress/mop/profile:array"); + size_array_rows = nbins; + size_array_cols = 1 + nvalues; + + array_flag = 1; + extarray = 0; +} + +/* ---------------------------------------------------------------------- */ + +ComputeStressMopProfile::~ComputeStressMopProfile() +{ + + delete [] which; + + memory->destroy(coord); + memory->destroy(coordp); + memory->destroy(values_local); + memory->destroy(values_global); + memory->destroy(array); +} + +/* ---------------------------------------------------------------------- */ + +void ComputeStressMopProfile::init() +{ + + // conversion constants + + nktv2p = force->nktv2p; + ftm2v = force->ftm2v; + + // plane area + + area = 1; + int i; + for (i=0; i<3; i++) { + if (i!=dir) area = area*domain->prd[i]; + } + + // timestep Value + + dt = update->dt; + + // Error check + // Compute stress/mop/profile requires fixed simulation box + + if (domain->box_change_size || domain->box_change_shape || domain->deform_flag) + error->all(FLERR, "Compute stress/mop/profile requires a fixed simulation box"); + + //This compute requires a pair style with pair_single method implemented + + if (force->pair == NULL) + error->all(FLERR,"No pair style is defined for compute stress/mop/profile"); + if (force->pair->single_enable == 0) + error->all(FLERR,"Pair style does not support compute stress/mop/profile"); + + // Warnings + + if (me==0){ + + //Compute stress/mop/profile only accounts for pair interactions. + // issue a warning if any intramolecular potential or Kspace is defined. + + if (force->bond!=NULL) + error->warning(FLERR,"compute stress/mop/profile does not account for bond potentials"); + if (force->angle!=NULL) + error->warning(FLERR,"compute stress/mop/profile does not account for angle potentials"); + if (force->dihedral!=NULL) + error->warning(FLERR,"compute stress/mop/profile does not account for dihedral potentials"); + if (force->improper!=NULL) + error->warning(FLERR,"compute stress/mop/profile does not account for improper potentials"); + if (force->kspace!=NULL) + error->warning(FLERR,"compute stress/mop/profile does not account for kspace contributions"); + } + + // need an occasional half neighbor list + + int irequest = neighbor->request((void *) this); + neighbor->requests[irequest]->pair = 0; + neighbor->requests[irequest]->compute = 1; + neighbor->requests[irequest]->occasional = 1; +} + +/* ---------------------------------------------------------------------- */ + +void ComputeStressMopProfile::init_list(int id, NeighList *ptr) +{ + list = ptr; +} + + +/* ---------------------------------------------------------------------- + compute output array + ------------------------------------------------------------------------- */ + +void ComputeStressMopProfile::compute_array() +{ + invoked_array = update->ntimestep; + + //Compute pressures on separate procs + compute_pairs(); + + // sum pressure contributions over all procs + MPI_Allreduce(&values_local[0][0],&values_global[0][0],nbins*nvalues, + MPI_DOUBLE,MPI_SUM,world); + + int ibin,m,mo; + for (ibin=0; ibinmass; + int *type = atom->type; + int *mask = atom->mask; + int nlocal = atom->nlocal; + double *special_coul = force->special_coul; + double *special_lj = force->special_lj; + int newton_pair = force->newton_pair; + + + // zero out arrays for one sample + for (m = 0; m < nbins; m++) { + for (i = 0; i < nvalues; i++) values_local[m][i] = 0.0; + } + + // invoke half neighbor list (will copy or build if necessary) + + neighbor->build_one(list); + + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + // loop over neighbors of my atoms + + Pair *pair = force->pair; + double **cutsq = force->pair->cutsq; + + // parse values + + double xi[3]; + double vi[3]; + double fi[3]; + double xj[3]; + + m = 0; + while (mx[i][0]; + xi[1] = atom->x[i][1]; + xi[2] = atom->x[i][2]; + itype = type[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + factor_lj = special_lj[sbmask(j)]; + factor_coul = special_coul[sbmask(j)]; + j &= NEIGHMASK; + + // skip if neither I nor J are in group + + if (!(mask[i] & groupbit || mask[j] & groupbit)) continue; + + xj[0] = atom->x[j][0]; + xj[1] = atom->x[j][1]; + xj[2] = atom->x[j][2]; + delx = xi[0] - xj[0]; + dely = xi[1] - xj[1]; + delz = xi[2] - xj[2]; + rsq = delx*delx + dely*dely + delz*delz; + jtype = type[j]; + if (rsq >= cutsq[itype][jtype]) continue; + + if (newton_pair || j < nlocal) { + + for (ibin=0;ibinpos) && (xj[dir]pos1) && (xj[dir]single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair); + + values_local[ibin][m] += fpair*(xi[0]-xj[0])/area*nktv2p; + values_local[ibin][m+1] += fpair*(xi[1]-xj[1])/area*nktv2p; + values_local[ibin][m+2] += fpair*(xi[2]-xj[2])/area*nktv2p; + + } else if ( ((xi[dir]pos)) + || ((xi[dir]pos1)) ) { + + pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair); + + values_local[ibin][m] -= fpair*(xi[0]-xj[0])/area*nktv2p; + values_local[ibin][m+1] -= fpair*(xi[1]-xj[1])/area*nktv2p; + values_local[ibin][m+2] -= fpair*(xi[2]-xj[2])/area*nktv2p; + } + } + } else { + + for (ibin=0;ibinpos) && (xj[dir]pos1) && (xj[dir]single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair); + + values_local[ibin][m] += fpair*(xi[0]-xj[0])/area*nktv2p; + values_local[ibin][m+1] += fpair*(xi[1]-xj[1])/area*nktv2p; + values_local[ibin][m+2] += fpair*(xi[2]-xj[2])/area*nktv2p; + } + } + } + } + } + } + + // compute kinetic contribution to pressure + // counts local particles transfers across the plane + + if (which[m] == KIN || which[m] == TOTAL){ + + double vcm[3]; + double masstotal,sgn; + + for (int i = 0; i < nlocal; i++){ + + // skip if I is not in group + + if (mask[i] & groupbit){ + + itype = type[i]; + + //coordinates at t + xi[0] = atom->x[i][0]; + xi[1] = atom->x[i][1]; + xi[2] = atom->x[i][2]; + + //velocities at t + vi[0] = atom->v[i][0]; + vi[1] = atom->v[i][1]; + vi[2] = atom->v[i][2]; + + //forces at t + fi[0] = atom->f[i][0]; + fi[1] = atom->f[i][1]; + fi[2] = atom->f[i][2]; + + //coordinates at t-dt (based on Velocity-Verlet alg.) + xj[0] = xi[0]-vi[0]*dt+fi[0]/2/mass[itype]*dt*dt*ftm2v; + xj[1] = xi[1]-vi[1]*dt+fi[1]/2/mass[itype]*dt*dt*ftm2v; + xj[2] = xi[2]-vi[2]*dt+fi[2]/2/mass[itype]*dt*dt*ftm2v; + + for (ibin=0;ibinboxlo; + boxhi = domain->boxhi; + prd = domain->prd; + + if (originflag == LOWER) origin = boxlo[dir]; + else if (originflag == UPPER) origin = boxhi[dir]; + else if (originflag == CENTER) + origin = 0.5 * (boxlo[dir] + boxhi[dir]); + + if (origin < boxlo[dir]) { + error->all(FLERR,"Origin of bins for compute stress/mop/profile is out of bounds" ); + } else { + n = static_cast ((origin - boxlo[dir]) * invdelta); + lo = origin - n*delta; + } + if (origin < boxhi[dir]) { + n = static_cast ((boxhi[dir] - origin) * invdelta); + hi = origin + n*delta; + } else { + error->all(FLERR,"Origin of bins for compute stress/mop/profile is out of bounds" ); + } + + offset = lo; + nbins = static_cast ((hi-lo) * invdelta + 1.5); + + //allocate bin arrays + memory->create(coord,nbins,1,"stress/mop/profile:coord"); + memory->create(coordp,nbins,1,"stress/mop/profile:coordp"); + memory->create(values_local,nbins,nvalues,"stress/mop/profile:values_local"); + memory->create(values_global,nbins,nvalues,"stress/mop/profile:values_global"); + + // set bin coordinates + for (i = 0; i < nbins; i++) { + coord[i][0] = offset + i*delta; + if ( coord[i][0] < (domain->boxlo[dir]+domain->prd_half[dir]) ) { + coordp[i][0] = coord[i][0] + domain->prd[dir]; + } else { + coordp[i][0] = coord[i][0] - domain->prd[dir]; + } + } +} diff --git a/src/USER-MOP/compute_stress_mop_profile.h b/src/USER-MOP/compute_stress_mop_profile.h new file mode 100644 index 0000000000..648d86cc7f --- /dev/null +++ b/src/USER-MOP/compute_stress_mop_profile.h @@ -0,0 +1,113 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. + ------------------------------------------------------------------------- */ + +/*------------------------------------------------------------------------ + Contributing Authors : Romain Vermorel (LFCR), Laurent Joly (ULyon) + --------------------------------------------------------------------------*/ + +#ifdef COMPUTE_CLASS + +ComputeStyle(stress/mop/profile,ComputeStressMopProfile) + +#else + +#ifndef LMP_COMPUTE_STRESS_MOP_PROFILE_H +#define LMP_COMPUTE_STRESS_MOP_PROFILE_H + +#include "compute.h" + +namespace LAMMPS_NS { + + class ComputeStressMopProfile : public Compute { + public: + ComputeStressMopProfile(class LAMMPS *, int, char **); + virtual ~ComputeStressMopProfile(); + void init(); + void init_list(int, class NeighList *); + void compute_array(); + + private: + + void compute_pairs(); + void setup_bins(); + + int me,nvalues,dir; + int *which; + + int originflag; + double origin,delta,offset,invdelta; + int nbins; + double **coord,**coordp; + double **values_local,**values_global; + + int ndim; + double dt,nktv2p,ftm2v; + double area; + class NeighList *list; + + }; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + + E: Illegal ... command + + Self-explanatory. Check the input script syntax and compare to the + documentation for the command. You can use -echo screen as a + command-line option when running LAMMPS to see the offending line. + + E: Compute stress/mop/profile incompatible with simulation dimension + + Compute stress/mop/profile only works with 3D simulations. + + E: Compute stress/mop/profile incompatible with triclinic simulation box + + Self-explanatory. + + E: Compute stress/mop/profile requires a fixed simulation box + + Compute stress/mop/profile is not compatible with any change of volume or shape + or boundary conditions of the simulation box. + + E: No pair style is defined for compute stress/mop/profile + + Self-explanatory. Compute stress/mop/profile requires the definition of a pair style. + + E: Pair style does not support compute stress/mop/profile + + The pair style does not have a single() function, so it can + not be invoked by compute stress/mop/profile. + + E: Origin of bins for compute stress/mop/profile is out of bounds + + Self-explanatory. + + W: compute stress/mop/profile does not account for bond potentials + + W: compute stress/mop/profile does not account for angle potentials + + W: compute stress/mop/profile does not account for dihedral potentials + + W: compute stress/mop/profile does not account for improper potentials + + W: compute stress/mop/profile does not account for kspace contributions + + Compute stress/mop/profile only accounts for pairwise additive interactions for + the computation of local stress tensor components. + +*/ + From cb4ffaf95c7de455a2a15e8c3f0bbe4c50b2b5e7 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 4 Sep 2018 08:42:32 -0400 Subject: [PATCH 122/302] update docs and references for name changes in USER-MOP package, remove obsoleted files --- doc/src/Packages_details.txt | 10 +- doc/src/Packages_user.txt | 2 +- doc/src/compute_mop.txt | 111 ---- doc/src/computes.txt | 2 +- doc/src/lammps.book | 2 +- examples/USER/mop/in.compute_mop | 62 --- examples/USER/mop/in.compute_stress_mop | 0 .../USER/mop/log.31Aug18.compute_mop.g++.1 | 186 ------- .../USER/mop/log.31Aug18.compute_mop.g++.4 | 188 ------- src/.gitignore | 8 +- src/USER-MOP/compute_mop.cpp | 424 --------------- src/USER-MOP/compute_mop.h | 74 --- src/USER-MOP/compute_mop_profile.cpp | 496 ------------------ src/USER-MOP/compute_mop_profile.h | 81 --- 14 files changed, 12 insertions(+), 1634 deletions(-) delete mode 100644 doc/src/compute_mop.txt delete mode 100644 examples/USER/mop/in.compute_mop mode change 100755 => 100644 examples/USER/mop/in.compute_stress_mop delete mode 100644 examples/USER/mop/log.31Aug18.compute_mop.g++.1 delete mode 100644 examples/USER/mop/log.31Aug18.compute_mop.g++.4 delete mode 100644 src/USER-MOP/compute_mop.cpp delete mode 100644 src/USER-MOP/compute_mop.h delete mode 100644 src/USER-MOP/compute_mop_profile.cpp delete mode 100644 src/USER-MOP/compute_mop_profile.h diff --git a/doc/src/Packages_details.txt b/doc/src/Packages_details.txt index 16f867b7c0..36071064c0 100644 --- a/doc/src/Packages_details.txt +++ b/doc/src/Packages_details.txt @@ -1577,11 +1577,11 @@ USER-MOP package :link(PKG-USER-MOP),h4 [Contents:] -This package contains two compute styles: compute mop and compute mop/profile. +This package contains two compute styles: compute stress/mop and compute stress/mop/profile. -compute mop calculates components of the local stress tensor using the method of planes, applied on one plane. +compute stress/mop calculates components of the local stress tensor using the method of planes, applied on one plane. -compute mop/profile calculates profiles of components of the local stress tensor using the method of planes, applied on an array of regularly spaced planes. +compute stress/mop/profile calculates profiles of components of the local stress tensor using the method of planes, applied on an array of regularly spaced planes. [Author:] Laurent Joly (University of Lyon 1) Romain Vermorel at (University of Pau and Pays de l'Adour) @@ -1590,8 +1590,8 @@ Romain Vermorel at (University of Pau and Pays de l'Adour) src/USER-MOP: filenames -> commands src/USER-MOP/README -"compute mop"_compute_mop.html -"compute mop/profile"_compute_mop.html +"compute stress/mop"_compute_stress_mop.html +"compute stress/mop/profile"_compute_stress_mop.html examples/USER/mop :ul :line diff --git a/doc/src/Packages_user.txt b/doc/src/Packages_user.txt index 731cf7ff10..5b9b8734b3 100644 --- a/doc/src/Packages_user.txt +++ b/doc/src/Packages_user.txt @@ -57,7 +57,7 @@ Package, Description, Doc page, Example, Library "USER-MESO"_Packages_details.html#PKG-USER-MESO, mesoscale DPD models, "pair_style edpd"_pair_meso.html, USER/meso, no "USER-MGPT"_Packages_details.html#PKG-USER-MGPT, fast MGPT multi-ion potentials, "pair_style mgpt"_pair_mgpt.html, USER/mgpt, no "USER-MISC"_Packages_details.html#PKG-USER-MISC, single-file contributions, USER-MISC/README, USER/misc, no -"USER-MOP"_Packages_details.html#PKG-USER-MOP, compute stress via method-of-planes, "compute_style mop"_compute_mop.html, USER/mop, no +"USER-MOP"_Packages_details.html#PKG-USER-MOP, compute stress via method-of-planes, "compute_style stress/mop"_compute_stress_mop.html, USER/mop, no "USER-MOFFF"_Packages_details.html#PKG-USER-MOFFF, styles for "MOF-FF"_MOFplus force field, "pair_style buck6d/coul/gauss"_pair_buck6d_coul_gauss.html, USER/mofff, no "USER-MOLFILE"_Packages_details.html#PKG-USER-MOLFILE, "VMD"_https://www.ks.uiuc.edu/Research/vmd/ molfile plug-ins,"dump molfile"_dump_molfile.html, n/a, ext "USER-NETCDF"_Packages_details.html#PKG-USER-NETCDF, dump output via NetCDF,"dump netcdf"_dump_netcdf.html, n/a, ext diff --git a/doc/src/compute_mop.txt b/doc/src/compute_mop.txt deleted file mode 100644 index 732f55657a..0000000000 --- a/doc/src/compute_mop.txt +++ /dev/null @@ -1,111 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Section_commands.html#comm) - -:line - -compute mop command :h3 -compute mop/profile command :h3 - - -[Syntax:] - -compute ID group-ID style dir args keywords ... :pre - -ID, group-ID are documented in "compute"_compute.html command -style = {mop} or {mop/profile} -dir = {x} or {y} or {z} is the direction normal to the plane -args = argument specific to the compute style -keywords = {kin} or {conf} or {total} (one of more can be specified) :ul - {mop} args = pos - pos = {lower} or {center} or {upper} or coordinate value (distance units) is the position of the plane - {mop/profile} args = origin delta - origin = {lower} or {center} or {upper} or coordinate value (distance units) is the position of the first plane - delta = value (distance units) is the distance between planes :pre - -compute 1 all mop x lower total -compute 1 liquid mop z 0.0 kin conf -fix 1 all ave/time 10 1000 10000 c_1\[*\] file mop.time -fix 1 all ave/time 10 1000 10000 c_1\[2\] file mop.time :pre - -compute 1 all mop/profile x lower 0.1 total -compute 1 liquid mop/profile z 0.0 0.25 kin conf -fix 1 all ave/time 500 20 10000 c_1\[*\] ave running overwrite file mopp.time mode vector :pre - - -[Description:] - -Compute {mop} and compute {mop/profile} define computations that -calculate components of the local stress tensor using the method of -planes "(Todd)"_#mop-todd. Specifically in compute {mop} calculates 3 -components are computed in directions {dir},{x}; {dir},{y}; and -{dir},{z}; where {dir} is the direction normal to the plane, while -in compute {mop/profile} the profile of the stress is computed. - -Contrary to methods based on histograms of atomic stress (i.e. using -"compute stress/atom"_compute_stress_atom.html), the method of planes is -compatible with mechanical balance in heterogeneous systems and at -interfaces "(Todd)"_#mop-todd. - -The stress tensor is the sum of a kinetic term and a configurational -term, which are given respectively by Eq. (21) and Eq. (16) in -"(Todd)"_#mop-todd. For the kinetic part, the algorithm considers that -atoms have crossed the plane if their positions at times t-dt and t are -one on either side of the plane, and uses the velocity at time t-dt/2 -given by the velocity-Verlet algorithm. - -Between one and three keywords can be used to indicate which -contributions to the stress must be computed: kinetic stress (kin), -configurational stress (conf), and/or total stress (total). - -NOTE 1: The configurational stress is computed considering all pairs of atoms where at least one atom belongs to group group-ID. - -NOTE 2: The local stress does not include any Lennard-Jones tail -corrections to the pressure added by the "pair_modify tail -yes"_pair_modify.html command, since those are contributions to the global system pressure. - -[Output info:] - -Compute {mop} calculates a global vector (indices starting at 1), with 3 -values for each declared keyword (in the order the keywords have been -declared). For each keyword, the stress tensor components are ordered as -follows: stress_dir,x, stress_dir,y, and stress_dir,z. - -Compute {mop/profile} instead calculates a global array, with 1 column -giving the position of the planes where the stress tensor was computed, -and with 3 columns of values for each declared keyword (in the order the -keywords have been declared). For each keyword, the profiles of stress -tensor components are ordered as follows: stress_dir,x; stress_dir,y; -and stress_dir,z. - -The values are in pressure "units"_units.html. - -The values produced by this compute can be accessed by various "output commands"_Howto_output.html. For instance, the results can be written to a file using the "fix ave/time"_fix_ave_time.html command. Please see the example in the examples/USER/mop folder. - -[Restrictions:] - -This style is part of the USER-MOP package. It is only enabled if LAMMPS -is built with that package. See the "Build package"_Build_package.html -doc page on for more info. - -The method is only implemented for 3d orthogonal simulation boxes whose -size does not change in time, and axis-aligned planes. - -The method only works with two-body pair interactions, because it -requires the class method pair->single() to be implemented. In -particular, it does not work with more than two-body pair interactions, -intra-molecular interactions, and long range (kspace) interactions. - -[Related commands:] - -"compute stress/atom"_compute_stress_atom.html - -[Default:] none - -:line - -:link(mop-todd) -[(Todd)] B. D. Todd, Denis J. Evans, and Peter J. Daivis: "Pressure tensor for inhomogeneous fluids", -Phys. Rev. E 52, 1627 (1995). diff --git a/doc/src/computes.txt b/doc/src/computes.txt index c431f1c184..158389bda9 100644 --- a/doc/src/computes.txt +++ b/doc/src/computes.txt @@ -55,7 +55,6 @@ Computes :h1 compute_meso_e_atom compute_meso_rho_atom compute_meso_t_atom - compute_mop compute_msd compute_msd_chunk compute_msd_nongauss @@ -99,6 +98,7 @@ Computes :h1 compute_sna_atom compute_spin compute_stress_atom + compute_stress_mop compute_tally compute_tdpd_cc_atom compute_temp diff --git a/doc/src/lammps.book b/doc/src/lammps.book index 0aa382ae39..c177757695 100644 --- a/doc/src/lammps.book +++ b/doc/src/lammps.book @@ -446,7 +446,6 @@ compute_ke_rigid.html compute_meso_e_atom.html compute_meso_rho_atom.html compute_meso_t_atom.html -compute_mop.html compute_msd.html compute_msd_chunk.html compute_msd_nongauss.html @@ -490,6 +489,7 @@ compute_smd_vol.html compute_sna_atom.html compute_spin.html compute_stress_atom.html +compute_stress_mop.html compute_tally.html compute_tdpd_cc_atom.html compute_temp.html diff --git a/examples/USER/mop/in.compute_mop b/examples/USER/mop/in.compute_mop deleted file mode 100644 index ab9552796f..0000000000 --- a/examples/USER/mop/in.compute_mop +++ /dev/null @@ -1,62 +0,0 @@ -variable T equal 0.8 -variable p_solid equal 0.05 - -lattice fcc 1.0 -region box block 0.0 6.0 0.0 6.0 -2.0 12.0 -create_box 2 box - -mass * 1.0 -pair_style lj/cut 2.5 -pair_coeff * * 1.0 1.0 -pair_coeff 1 2 0.5 1.0 -pair_coeff 2 2 0.0 0.0 -neigh_modify delay 0 - -region solid_bottom block INF INF INF INF -1.1 0.1 -region liquid block INF INF INF INF 1.1 8.9 -region solid_up block INF INF INF INF 9.9 11.1 - -create_atoms 1 region liquid -delete_atoms porosity liquid 0.26 88765 -group liquid region liquid - -create_atoms 2 region solid_bottom -group solid_bottom region solid_bottom -create_atoms 2 region solid_up -group solid_up region solid_up -group solid union solid_bottom solid_up - -variable faSolid equal ${p_solid}*lx*ly/count(solid_up) -fix piston_up solid_up aveforce NULL NULL -${faSolid} -fix freeze_up solid_up setforce 0.0 0.0 NULL -fix freeze_bottom solid_bottom setforce 0.0 0.0 0.0 -fix nvesol solid nve -compute Tliq liquid temp -fix nvtliq liquid nvt temp $T $T 0.5 -fix_modify nvtliq temp Tliq - -thermo 10000 -thermo_modify flush yes temp Tliq - -# dump 1 all atom 10000 dump.lammpstrj - -fix fxbal all balance 1000 1.05 shift z 10 1.05 -velocity liquid create $T 47298 dist gaussian rot yes -run 50000 -# undump 1 -reset_timestep 0 - -compute bin_z liquid chunk/atom bin/1d z 0.0 0.1 units box - -compute liquidStress_ke liquid stress/atom NULL ke -compute liquidStress_vir liquid stress/atom NULL virial -fix profile_z liquid ave/chunk 10 1000 10000 bin_z density/number temp c_liquidStress_ke[1] c_liquidStress_ke[2] c_liquidStress_ke[3] c_liquidStress_ke[4] c_liquidStress_ke[5] c_liquidStress_ke[6] c_liquidStress_vir[1] c_liquidStress_vir[2] c_liquidStress_vir[3] c_liquidStress_vir[4] c_liquidStress_vir[5] c_liquidStress_vir[6] ave running overwrite file profile.z - -compute mopz0 all mop z center kin conf -fix mopz0t all ave/time 10 1000 10000 c_mopz0[*] file mopz0.time - -compute moppz liquid mop/profile z 0.0 0.1 kin conf -fix moppzt all ave/time 100 100 10000 c_moppz[*] ave running overwrite file moppz.time mode vector - -run 40000 - diff --git a/examples/USER/mop/in.compute_stress_mop b/examples/USER/mop/in.compute_stress_mop old mode 100755 new mode 100644 diff --git a/examples/USER/mop/log.31Aug18.compute_mop.g++.1 b/examples/USER/mop/log.31Aug18.compute_mop.g++.1 deleted file mode 100644 index 98b403b444..0000000000 --- a/examples/USER/mop/log.31Aug18.compute_mop.g++.1 +++ /dev/null @@ -1,186 +0,0 @@ -LAMMPS (31 Aug 2018) -variable T equal 0.8 -variable p_solid equal 0.05 - -lattice fcc 1.0 -Lattice spacing in x,y,z = 1.5874 1.5874 1.5874 -region box block 0.0 6.0 0.0 6.0 -2.0 12.0 -create_box 2 box -Created orthogonal box = (0 0 -3.1748) to (9.52441 9.52441 19.0488) - 1 by 1 by 1 MPI processor grid - -mass * 1.0 -pair_style lj/cut 2.5 -pair_coeff * * 1.0 1.0 -pair_coeff 1 2 0.5 1.0 -pair_coeff 2 2 0.0 0.0 -neigh_modify delay 0 - -region solid_bottom block INF INF INF INF -1.1 0.1 -region liquid block INF INF INF INF 1.1 8.9 -region solid_up block INF INF INF INF 9.9 11.1 - -create_atoms 1 region liquid -Created 1080 atoms - Time spent = 0.000631094 secs -delete_atoms porosity liquid 0.26 88765 -Deleted 257 atoms, new total = 823 -group liquid region liquid -823 atoms in group liquid - -create_atoms 2 region solid_bottom -Created 216 atoms - Time spent = 0.000221014 secs -group solid_bottom region solid_bottom -216 atoms in group solid_bottom -create_atoms 2 region solid_up -Created 216 atoms - Time spent = 0.000169039 secs -group solid_up region solid_up -216 atoms in group solid_up -group solid union solid_bottom solid_up -432 atoms in group solid - -variable faSolid equal ${p_solid}*lx*ly/count(solid_up) -variable faSolid equal 0.05*lx*ly/count(solid_up) -fix piston_up solid_up aveforce NULL NULL -${faSolid} -fix piston_up solid_up aveforce NULL NULL -0.0209986841649146 -fix freeze_up solid_up setforce 0.0 0.0 NULL -fix freeze_bottom solid_bottom setforce 0.0 0.0 0.0 -fix nvesol solid nve -compute Tliq liquid temp -fix nvtliq liquid nvt temp $T $T 0.5 -fix nvtliq liquid nvt temp 0.8 $T 0.5 -fix nvtliq liquid nvt temp 0.8 0.8 0.5 -fix_modify nvtliq temp Tliq -WARNING: Temperature for fix modify is not for group all (../fix_nh.cpp:1404) - -thermo 10000 -thermo_modify flush yes temp Tliq -WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:488) - -# dump 1 all atom 10000 dump.lammpstrj - -fix fxbal all balance 1000 1.05 shift z 10 1.05 -velocity liquid create $T 47298 dist gaussian rot yes -velocity liquid create 0.8 47298 dist gaussian rot yes -run 50000 -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 7 7 16 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.187 | 3.187 | 3.187 Mbytes -Step Temp E_pair E_mol TotEng Press Volume - 0 0.8 -3.7188573 0 -2.9328812 -0.65673631 2016 - 10000 0.80645968 -3.2160592 0 -2.4237366 -0.17266146 2016 - 20000 0.85787011 -3.2087113 0 -2.3658796 0.032152534 2016 - 30000 0.76357074 -3.1761807 0 -2.4259953 -0.034009443 2016 - 40000 0.8116632 -3.1965608 0 -2.399126 -0.030033303 2016 - 50000 0.83600463 -3.1878245 0 -2.3664749 0.054158845 2016 -Loop time of 40.6472 on 1 procs for 50000 steps with 1255 atoms - -Performance: 531401.825 tau/day, 1230.097 timesteps/s -99.7% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 28.102 | 28.102 | 28.102 | 0.0 | 69.14 -Neigh | 9.8377 | 9.8377 | 9.8377 | 0.0 | 24.20 -Comm | 0.91642 | 0.91642 | 0.91642 | 0.0 | 2.25 -Output | 0.00024581 | 0.00024581 | 0.00024581 | 0.0 | 0.00 -Modify | 1.4027 | 1.4027 | 1.4027 | 0.0 | 3.45 -Other | | 0.3879 | | | 0.95 - -Nlocal: 1255 ave 1255 max 1255 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 2268 ave 2268 max 2268 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 40149 ave 40149 max 40149 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 40149 -Ave neighs/atom = 31.9912 -Neighbor list builds = 5714 -Dangerous builds = 0 -# undump 1 -reset_timestep 0 - -compute bin_z liquid chunk/atom bin/1d z 0.0 0.1 units box - -compute liquidStress_ke liquid stress/atom NULL ke -compute liquidStress_vir liquid stress/atom NULL virial -fix profile_z liquid ave/chunk 10 1000 10000 bin_z density/number temp c_liquidStress_ke[1] c_liquidStress_ke[2] c_liquidStress_ke[3] c_liquidStress_ke[4] c_liquidStress_ke[5] c_liquidStress_ke[6] c_liquidStress_vir[1] c_liquidStress_vir[2] c_liquidStress_vir[3] c_liquidStress_vir[4] c_liquidStress_vir[5] c_liquidStress_vir[6] ave running overwrite file profile.z - -compute mopz0 all mop z center kin conf -fix mopz0t all ave/time 10 1000 10000 c_mopz0[*] file mopz0.time - -compute moppz liquid mop/profile z 0.0 0.1 kin conf -fix moppzt all ave/time 100 100 10000 c_moppz[*] ave running overwrite file moppz.time mode vector - -run 40000 -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 7 7 16 - 3 neighbor lists, perpetual/occasional/extra = 1 2 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard - (2) compute mop, occasional, copy from (1) - attributes: half, newton on - pair build: copy - stencil: none - bin: none - (3) compute mop/profile, occasional, copy from (1) - attributes: half, newton on - pair build: copy - stencil: none - bin: none -Per MPI rank memory allocation (min/avg/max) = 4.186 | 4.186 | 4.186 Mbytes -Step Temp E_pair E_mol TotEng Press Volume - 0 0.83600463 -3.1878245 0 -2.3664749 0.054158845 2016 - 10000 0.80600425 -3.1900933 0 -2.3982182 -0.042750667 2016 - 20000 0.78117978 -3.2121798 0 -2.444694 0.0092285451 2016 - 30000 0.81008494 -3.1728363 0 -2.376952 0.053347807 2016 - 40000 0.80440016 -3.1768915 0 -2.3865924 -0.0075214347 2016 -Loop time of 45.4499 on 1 procs for 40000 steps with 1255 atoms - -Performance: 380198.462 tau/day, 880.089 timesteps/s -99.8% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 25.456 | 25.456 | 25.456 | 0.0 | 56.01 -Neigh | 7.9422 | 7.9422 | 7.9422 | 0.0 | 17.47 -Comm | 0.73477 | 0.73477 | 0.73477 | 0.0 | 1.62 -Output | 0.00010562 | 0.00010562 | 0.00010562 | 0.0 | 0.00 -Modify | 11.004 | 11.004 | 11.004 | 0.0 | 24.21 -Other | | 0.3131 | | | 0.69 - -Nlocal: 1255 ave 1255 max 1255 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 2269 ave 2269 max 2269 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 40325 ave 40325 max 40325 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 40325 -Ave neighs/atom = 32.1315 -Neighbor list builds = 4587 -Dangerous builds = 0 - -Total wall time: 0:01:26 diff --git a/examples/USER/mop/log.31Aug18.compute_mop.g++.4 b/examples/USER/mop/log.31Aug18.compute_mop.g++.4 deleted file mode 100644 index 16ef8a2ce1..0000000000 --- a/examples/USER/mop/log.31Aug18.compute_mop.g++.4 +++ /dev/null @@ -1,188 +0,0 @@ -LAMMPS (31 Aug 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) - using 1 OpenMP thread(s) per MPI task -variable T equal 0.8 -variable p_solid equal 0.05 - -lattice fcc 1.0 -Lattice spacing in x,y,z = 1.5874 1.5874 1.5874 -region box block 0.0 6.0 0.0 6.0 -2.0 12.0 -create_box 2 box -Created orthogonal box = (0 0 -3.1748) to (9.52441 9.52441 19.0488) - 1 by 1 by 4 MPI processor grid - -mass * 1.0 -pair_style lj/cut 2.5 -pair_coeff * * 1.0 1.0 -pair_coeff 1 2 0.5 1.0 -pair_coeff 2 2 0.0 0.0 -neigh_modify delay 0 - -region solid_bottom block INF INF INF INF -1.1 0.1 -region liquid block INF INF INF INF 1.1 8.9 -region solid_up block INF INF INF INF 9.9 11.1 - -create_atoms 1 region liquid -Created 1080 atoms - Time spent = 0.000378132 secs -delete_atoms porosity liquid 0.26 88765 -Deleted 288 atoms, new total = 792 -group liquid region liquid -792 atoms in group liquid - -create_atoms 2 region solid_bottom -Created 216 atoms - Time spent = 0.000345945 secs -group solid_bottom region solid_bottom -216 atoms in group solid_bottom -create_atoms 2 region solid_up -Created 216 atoms - Time spent = 0.000124454 secs -group solid_up region solid_up -216 atoms in group solid_up -group solid union solid_bottom solid_up -432 atoms in group solid - -variable faSolid equal ${p_solid}*lx*ly/count(solid_up) -variable faSolid equal 0.05*lx*ly/count(solid_up) -fix piston_up solid_up aveforce NULL NULL -${faSolid} -fix piston_up solid_up aveforce NULL NULL -0.0209986841649146 -fix freeze_up solid_up setforce 0.0 0.0 NULL -fix freeze_bottom solid_bottom setforce 0.0 0.0 0.0 -fix nvesol solid nve -compute Tliq liquid temp -fix nvtliq liquid nvt temp $T $T 0.5 -fix nvtliq liquid nvt temp 0.8 $T 0.5 -fix nvtliq liquid nvt temp 0.8 0.8 0.5 -fix_modify nvtliq temp Tliq -WARNING: Temperature for fix modify is not for group all (src/fix_nh.cpp:1404) - -thermo 10000 -thermo_modify flush yes temp Tliq -WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488) - -# dump 1 all atom 10000 dump.lammpstrj - -fix fxbal all balance 1000 1.05 shift z 10 1.05 -velocity liquid create $T 47298 dist gaussian rot yes -velocity liquid create 0.8 47298 dist gaussian rot yes -run 50000 -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 7 7 16 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.122 | 3.135 | 3.147 Mbytes -Step Temp E_pair E_mol TotEng Press Volume - 0 0.8 -3.4905808 0 -2.7150906 -0.59565852 2016 - 10000 0.82075861 -3.1822235 0 -2.3866107 0.013840263 2016 - 20000 0.76467575 -3.0955084 0 -2.3542602 -0.076868925 2016 - 30000 0.75803557 -3.1011543 0 -2.3663428 -0.052887049 2016 - 40000 0.81732724 -3.064259 0 -2.2719724 0.070708808 2016 - 50000 0.75874551 -3.1070261 0 -2.3715265 -0.074970431 2016 -Loop time of 22.1566 on 4 procs for 50000 steps with 1224 atoms - -Performance: 974879.887 tau/day, 2256.666 timesteps/s -98.5% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 10.732 | 13.012 | 14.39 | 38.0 | 58.73 -Neigh | 2.47 | 3.7351 | 4.3661 | 38.4 | 16.86 -Comm | 1.881 | 3.4383 | 5.8722 | 79.7 | 15.52 -Output | 0.00014567 | 0.0003581 | 0.0009892 | 0.0 | 0.00 -Modify | 1.1006 | 1.5188 | 2.6121 | 51.3 | 6.85 -Other | | 0.4521 | | | 2.04 - -Nlocal: 306 ave 312 max 295 min -Histogram: 1 0 0 0 0 0 0 1 1 1 -Nghost: 1242.75 ave 1373 max 944 min -Histogram: 1 0 0 0 0 0 0 0 1 2 -Neighs: 9770.25 ave 10807 max 8736 min -Histogram: 1 0 0 1 0 0 1 0 0 1 - -Total # of neighbors = 39081 -Ave neighs/atom = 31.9289 -Neighbor list builds = 5704 -Dangerous builds = 0 -# undump 1 -reset_timestep 0 - -compute bin_z liquid chunk/atom bin/1d z 0.0 0.1 units box - -compute liquidStress_ke liquid stress/atom NULL ke -compute liquidStress_vir liquid stress/atom NULL virial -fix profile_z liquid ave/chunk 10 1000 10000 bin_z density/number temp c_liquidStress_ke[1] c_liquidStress_ke[2] c_liquidStress_ke[3] c_liquidStress_ke[4] c_liquidStress_ke[5] c_liquidStress_ke[6] c_liquidStress_vir[1] c_liquidStress_vir[2] c_liquidStress_vir[3] c_liquidStress_vir[4] c_liquidStress_vir[5] c_liquidStress_vir[6] ave running overwrite file profile.z - -compute mopz0 all mop z center kin conf -fix mopz0t all ave/time 10 1000 10000 c_mopz0[*] file mopz0.time - -compute moppz liquid mop/profile z 0.0 0.1 kin conf -fix moppzt all ave/time 100 100 10000 c_moppz[*] ave running overwrite file moppz.time mode vector - -run 40000 -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 7 7 16 - 3 neighbor lists, perpetual/occasional/extra = 1 2 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard - (2) compute mop, occasional, copy from (1) - attributes: half, newton on - pair build: copy - stencil: none - bin: none - (3) compute mop/profile, occasional, copy from (1) - attributes: half, newton on - pair build: copy - stencil: none - bin: none -Per MPI rank memory allocation (min/avg/max) = 4.139 | 4.147 | 4.15 Mbytes -Step Temp E_pair E_mol TotEng Press Volume - 0 0.75874551 -3.1070261 0 -2.3715265 -0.074970431 2016 - 10000 0.82372476 -3.1299329 0 -2.3314448 -0.14706101 2016 - 20000 0.80692892 -3.1278896 0 -2.3456828 -0.085123604 2016 - 30000 0.78458951 -3.0966006 0 -2.3360488 0.13637007 2016 - 40000 0.80106495 -3.1135836 0 -2.3370611 -0.14404185 2016 -Loop time of 31.4145 on 4 procs for 40000 steps with 1224 atoms - -Performance: 550065.249 tau/day, 1273.299 timesteps/s -92.6% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 10.199 | 12.307 | 13.428 | 35.4 | 39.18 -Neigh | 2.1261 | 3.1416 | 3.6373 | 33.5 | 10.00 -Comm | 3.5381 | 4.476 | 6.229 | 48.9 | 14.25 -Output | 0.00062943 | 0.0031546 | 0.0040004 | 2.6 | 0.01 -Modify | 10.186 | 10.862 | 12.26 | 24.8 | 34.58 -Other | | 0.6247 | | | 1.99 - -Nlocal: 306 ave 315 max 299 min -Histogram: 1 0 0 1 1 0 0 0 0 1 -Nghost: 1221.5 ave 1347 max 912 min -Histogram: 1 0 0 0 0 0 0 0 1 2 -Neighs: 9710.25 ave 10301 max 8980 min -Histogram: 1 0 0 0 0 1 1 0 0 1 - -Total # of neighbors = 38841 -Ave neighs/atom = 31.7328 -Neighbor list builds = 4573 -Dangerous builds = 0 - -Total wall time: 0:00:53 diff --git a/src/.gitignore b/src/.gitignore index c7aaa8ab64..3a6ba21426 100644 --- a/src/.gitignore +++ b/src/.gitignore @@ -288,10 +288,6 @@ /compute_meso_rho_atom.h /compute_meso_t_atom.cpp /compute_meso_t_atom.h -/compute_mop.cpp -/compute_mop.h -/compute_mop_profile.cpp -/compute_mop_profile.h /compute_msd_nongauss.cpp /compute_msd_nongauss.h /compute_pe_tally.cpp @@ -306,6 +302,10 @@ /compute_rigid_local.h /compute_spec_atom.cpp /compute_spec_atom.h +/compute_stress_mop.cpp +/compute_stress_mop.h +/compute_stress_mop.profile.cpp +/compute_stress_mop.profile.h /compute_stress_tally.cpp /compute_stress_tally.h /compute_temp_asphere.cpp diff --git a/src/USER-MOP/compute_mop.cpp b/src/USER-MOP/compute_mop.cpp deleted file mode 100644 index ba6b458172..0000000000 --- a/src/USER-MOP/compute_mop.cpp +++ /dev/null @@ -1,424 +0,0 @@ -/* ---------------------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. - ------------------------------------------------------------------------- */ - -/*------------------------------------------------------------------------ - Contributing Authors : Romain Vermorel (LFCR), Laurent Joly (ULyon) - --------------------------------------------------------------------------*/ - -#include -#include -#include -#include - -#include "compute_mop.h" -#include "atom.h" -#include "update.h" -#include "domain.h" -#include "group.h" -#include "modify.h" -#include "fix.h" -#include "neighbor.h" -#include "force.h" -#include "pair.h" -#include "neigh_request.h" -#include "neigh_list.h" -#include "error.h" -#include "memory.h" - -using namespace LAMMPS_NS; - -enum{X,Y,Z}; -enum{TOTAL,CONF,KIN}; - -#define BIG 1000000000 - -/* ---------------------------------------------------------------------- */ - -ComputeMop::ComputeMop(LAMMPS *lmp, int narg, char **arg) : - Compute(lmp, narg, arg) -{ - if (narg < 6) error->all(FLERR,"Illegal compute mop command"); - - MPI_Comm_rank(world,&me); - - // set compute mode and direction of plane(s) for pressure calculation - - if (strcmp(arg[3],"x")==0) { - dir = X; - } else if (strcmp(arg[3],"y")==0) { - dir = Y; - } else if (strcmp(arg[3],"z")==0) { - dir = Z; - } else error->all(FLERR,"Illegal compute mop command"); - - // Position of the plane - - if (strcmp(arg[4],"lower")==0) { - pos = domain->boxlo[dir]; - } else if (strcmp(arg[4],"upper")==0) { - pos = domain->boxhi[dir]; - } else if (strcmp(arg[4],"center")==0) { - pos = 0.5*(domain->boxlo[dir]+domain->boxhi[dir]); - } else pos = force->numeric(FLERR,arg[4]); - - if ( pos < (domain->boxlo[dir]+domain->prd_half[dir]) ) { - pos1 = pos + domain->prd[dir]; - } else { - pos1 = pos - domain->prd[dir]; - } - - // parse values until one isn't recognized - - which = new int[3*(narg-5)]; - nvalues = 0; - int i; - - int iarg=5; - while (iarg < narg) { - if (strcmp(arg[iarg],"conf") == 0) { - for (i=0; i<3; i++) { - which[nvalues] = CONF; - nvalues++; - } - } else if (strcmp(arg[iarg],"kin") == 0) { - for (i=0; i<3; i++) { - which[nvalues] = KIN; - nvalues++; - } - } else if (strcmp(arg[iarg],"total") == 0) { - for (i=0; i<3; i++) { - which[nvalues] = TOTAL; - nvalues++; - } - } else error->all(FLERR, "Illegal compute mop command"); //break; - - iarg++; - } - - // Error check - // 3D only - - if (domain->dimension < 3) - error->all(FLERR, "Compute mop incompatible with simulation dimension"); - - // orthogonal simulation box - if (domain->triclinic != 0) - error->all(FLERR, "Compute mop incompatible with triclinic simulation box"); - // plane inside the box - if (pos >domain->boxhi[dir] || pos boxlo[dir]) - error->all(FLERR, "Plane for compute mop is out of bounds"); - - - // Initialize some variables - - values_local = values_global = vector = NULL; - - // this fix produces a global vector - - memory->create(vector,nvalues,"mop:vector"); - memory->create(values_local,nvalues,"mop/spatial:values_local"); - memory->create(values_global,nvalues,"mop/spatial:values_global"); - size_vector = nvalues; - - vector_flag = 1; - extvector = 0; - -} - -/* ---------------------------------------------------------------------- */ - -ComputeMop::~ComputeMop() -{ - - delete [] which; - - memory->destroy(values_local); - memory->destroy(values_global); - memory->destroy(vector); -} - -/* ---------------------------------------------------------------------- */ - -void ComputeMop::init() -{ - - // Conversion constants - - nktv2p = force->nktv2p; - ftm2v = force->ftm2v; - - // Plane area - - area = 1; - int i; - for (i=0; i<3; i++){ - if (i!=dir) area = area*domain->prd[i]; - } - - // Timestep Value - - dt = update->dt; - - // Error check - - // Compute mop requires fixed simulation box - if (domain->box_change_size || domain->box_change_shape || domain->deform_flag) - error->all(FLERR, "Compute mop requires a fixed simulation box"); - - // This compute requires a pair style with pair_single method implemented - - if (force->pair == NULL) - error->all(FLERR,"No pair style is defined for compute mop"); - if (force->pair->single_enable == 0) - error->all(FLERR,"Pair style does not support compute mop"); - - // Warnings - - if (me==0){ - - //Compute mop only accounts for pair interactions. - // issue a warning if any intramolecular potential or Kspace is defined. - - if (force->bond!=NULL) - error->warning(FLERR,"compute mop does not account for bond potentials"); - if (force->angle!=NULL) - error->warning(FLERR,"compute mop does not account for angle potentials"); - if (force->dihedral!=NULL) - error->warning(FLERR,"compute mop does not account for dihedral potentials"); - if (force->improper!=NULL) - error->warning(FLERR,"compute mop does not account for improper potentials"); - if (force->kspace!=NULL) - error->warning(FLERR,"compute mop does not account for kspace contributions"); - } - - // need an occasional half neighbor list - int irequest = neighbor->request((void *) this); - neighbor->requests[irequest]->pair = 0; - neighbor->requests[irequest]->compute = 1; - neighbor->requests[irequest]->occasional = 1; -} - -/* ---------------------------------------------------------------------- */ - -void ComputeMop::init_list(int id, NeighList *ptr) -{ - list = ptr; -} - - -/* ---------------------------------------------------------------------- - compute output vector - ------------------------------------------------------------------------- */ - -void ComputeMop::compute_vector() -{ - invoked_array = update->ntimestep; - - //Compute pressures on separate procs - compute_pairs(); - - // sum pressure contributions over all procs - MPI_Allreduce(values_local,values_global,nvalues, - MPI_DOUBLE,MPI_SUM,world); - - int m; - for (m=0; mmass; - int *type = atom->type; - int *mask = atom->mask; - int nlocal = atom->nlocal; - double *special_coul = force->special_coul; - double *special_lj = force->special_lj; - int newton_pair = force->newton_pair; - - - // zero out arrays for one sample - - for (i = 0; i < nvalues; i++) values_local[i] = 0.0; - - // invoke half neighbor list (will copy or build if necessary) - - neighbor->build_one(list); - - inum = list->inum; - ilist = list->ilist; - numneigh = list->numneigh; - firstneigh = list->firstneigh; - - // loop over neighbors of my atoms - - Pair *pair = force->pair; - double **cutsq = force->pair->cutsq; - - // Parse values - - double xi[3]; - double vi[3]; - double fi[3]; - double xj[3]; - - m = 0; - while (mx[i][0]; - xi[1] = atom->x[i][1]; - xi[2] = atom->x[i][2]; - itype = type[i]; - jlist = firstneigh[i]; - jnum = numneigh[i]; - - for (jj = 0; jj < jnum; jj++) { - j = jlist[jj]; - factor_lj = special_lj[sbmask(j)]; - factor_coul = special_coul[sbmask(j)]; - j &= NEIGHMASK; - - // skip if neither I nor J are in group - if (!(mask[i] & groupbit || mask[j] & groupbit)) continue; - - xj[0] = atom->x[j][0]; - xj[1] = atom->x[j][1]; - xj[2] = atom->x[j][2]; - delx = xi[0] - xj[0]; - dely = xi[1] - xj[1]; - delz = xi[2] - xj[2]; - rsq = delx*delx + dely*dely + delz*delz; - jtype = type[j]; - if (rsq >= cutsq[itype][jtype]) continue; - - if (newton_pair || j < nlocal) { - - //check if ij pair is accross plane, add contribution to pressure - if ( ((xi[dir]>pos) && (xj[dir]pos1) && (xj[dir]single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair); - - values_local[m] += fpair*(xi[0]-xj[0])/area*nktv2p; - values_local[m+1] += fpair*(xi[1]-xj[1])/area*nktv2p; - values_local[m+2] += fpair*(xi[2]-xj[2])/area*nktv2p; - } - else if ( ((xi[dir]pos)) || ((xi[dir]pos1)) ){ - - pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair); - - values_local[m] -= fpair*(xi[0]-xj[0])/area*nktv2p; - values_local[m+1] -= fpair*(xi[1]-xj[1])/area*nktv2p; - values_local[m+2] -= fpair*(xi[2]-xj[2])/area*nktv2p; - } - - } else { - - if ( ((xi[dir]>pos) && (xj[dir]pos1) && (xj[dir]single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair); - - values_local[m] += fpair*(xi[0]-xj[0])/area*nktv2p; - values_local[m+1] += fpair*(xi[1]-xj[1])/area*nktv2p; - values_local[m+2] += fpair*(xi[2]-xj[2])/area*nktv2p; - } - - } - - } - - } - - } - - - // Compute kinetic contribution to pressure - // counts local particles transfers across the plane - - if (which[m] == KIN || which[m] == TOTAL){ - double vcm[3]; - double masstotal,sgn; - - for (int i = 0; i < nlocal; i++){ - - // skip if I is not in group - if (mask[i] & groupbit){ - - itype = type[i]; - - //coordinates at t - xi[0] = atom->x[i][0]; - xi[1] = atom->x[i][1]; - xi[2] = atom->x[i][2]; - - //velocities at t - vi[0] = atom->v[i][0]; - vi[1] = atom->v[i][1]; - vi[2] = atom->v[i][2]; - - //forces at t - fi[0] = atom->f[i][0]; - fi[1] = atom->f[i][1]; - fi[2] = atom->f[i][2]; - - //coordinates at t-dt (based on Velocity-Verlet alg.) - xj[0] = xi[0]-vi[0]*dt+fi[0]/2/mass[itype]*dt*dt*ftm2v; - xj[1] = xi[1]-vi[1]*dt+fi[1]/2/mass[itype]*dt*dt*ftm2v; - xj[2] = xi[2]-vi[2]*dt+fi[2]/2/mass[itype]*dt*dt*ftm2v; - - // because LAMMPS does not put atoms back in the box - // at each timestep, must check atoms going through the - // image of the plane that is closest to the box - - double pos_temp = pos+copysign(1,domain->prd_half[dir]-pos)*domain->prd[dir]; - if (fabs(xi[dir]-pos) -#include -#include -#include - -#include "compute_mop_profile.h" -#include "atom.h" -#include "update.h" -#include "domain.h" -#include "group.h" -#include "modify.h" -#include "fix.h" -#include "neighbor.h" -#include "force.h" -#include "pair.h" -#include "neigh_request.h" -#include "neigh_list.h" -#include "error.h" -#include "memory.h" - -using namespace LAMMPS_NS; - -enum{X,Y,Z}; -enum{LOWER,CENTER,UPPER,COORD}; -enum{TOTAL,CONF,KIN}; - -#define BIG 1000000000 - -/* ---------------------------------------------------------------------- */ - -ComputeMopProfile::ComputeMopProfile(LAMMPS *lmp, int narg, char **arg) : - Compute(lmp, narg, arg) -{ - if (narg < 7) error->all(FLERR,"Illegal compute mop/profile command"); - - MPI_Comm_rank(world,&me); - - // set compute mode and direction of plane(s) for pressure calculation - - if (strcmp(arg[3],"x")==0) { - dir = X; - } else if (strcmp(arg[3],"y")==0) { - dir = Y; - } else if (strcmp(arg[3],"z")==0) { - dir = Z; - } else error->all(FLERR,"Illegal compute mop/profile command"); - - // bin parameters - - if (strcmp(arg[4],"lower") == 0) originflag = LOWER; - else if (strcmp(arg[4],"center") == 0) originflag = CENTER; - else if (strcmp(arg[4],"upper") == 0) originflag = UPPER; - else originflag = COORD; - if (originflag == COORD) - origin = force->numeric(FLERR,arg[4]); - delta = force->numeric(FLERR,arg[5]); - invdelta = 1.0/delta; - - // parse values until one isn't recognized - - which = new int[3*(narg-6)]; - nvalues = 0; - int i; - - int iarg=6; - while (iarg < narg) { - if (strcmp(arg[iarg],"conf") == 0) { - for (i=0; i<3; i++) { - which[nvalues] = CONF; - nvalues++; - } - } else if (strcmp(arg[iarg],"kin") == 0) { - for (i=0; i<3; i++) { - which[nvalues] = KIN; - nvalues++; - } - } else if (strcmp(arg[iarg],"total") == 0) { - for (i=0; i<3; i++) { - which[nvalues] = TOTAL; - nvalues++; - } - } else error->all(FLERR, "Illegal compute mop/profile command"); //break; - - iarg++; - } - - // check domain related errors - - // 3D only - - if (domain->dimension < 3) - error->all(FLERR, "Compute mop/profile incompatible with simulation dimension"); - - // orthogonal simulation box - - if (domain->triclinic != 0) - error->all(FLERR, "Compute mop/profile incompatible with triclinic simulation box"); - - // initialize some variables - - nbins = 0; - coord = coordp = NULL; - values_local = values_global = array = NULL; - - // bin setup - - setup_bins(); - - // this fix produces a global array - - memory->create(array,nbins,1+nvalues,"mop/profile:array"); - size_array_rows = nbins; - size_array_cols = 1 + nvalues; - - array_flag = 1; - extarray = 0; -} - -/* ---------------------------------------------------------------------- */ - -ComputeMopProfile::~ComputeMopProfile() -{ - - delete [] which; - - memory->destroy(coord); - memory->destroy(coordp); - memory->destroy(values_local); - memory->destroy(values_global); - memory->destroy(array); -} - -/* ---------------------------------------------------------------------- */ - -void ComputeMopProfile::init() -{ - - // conversion constants - - nktv2p = force->nktv2p; - ftm2v = force->ftm2v; - - // plane area - - area = 1; - int i; - for (i=0; i<3; i++) { - if (i!=dir) area = area*domain->prd[i]; - } - - // timestep Value - - dt = update->dt; - - // Error check - // Compute mop/profile requires fixed simulation box - - if (domain->box_change_size || domain->box_change_shape || domain->deform_flag) - error->all(FLERR, "Compute mop/profile requires a fixed simulation box"); - - //This compute requires a pair style with pair_single method implemented - - if (force->pair == NULL) - error->all(FLERR,"No pair style is defined for compute mop/profile"); - if (force->pair->single_enable == 0) - error->all(FLERR,"Pair style does not support compute mop/profile"); - - // Warnings - - if (me==0){ - - //Compute mop/profile only accounts for pair interactions. - // issue a warning if any intramolecular potential or Kspace is defined. - - if (force->bond!=NULL) - error->warning(FLERR,"compute mop/profile does not account for bond potentials"); - if (force->angle!=NULL) - error->warning(FLERR,"compute mop/profile does not account for angle potentials"); - if (force->dihedral!=NULL) - error->warning(FLERR,"compute mop/profile does not account for dihedral potentials"); - if (force->improper!=NULL) - error->warning(FLERR,"compute mop/profile does not account for improper potentials"); - if (force->kspace!=NULL) - error->warning(FLERR,"compute mop/profile does not account for kspace contributions"); - } - - // need an occasional half neighbor list - - int irequest = neighbor->request((void *) this); - neighbor->requests[irequest]->pair = 0; - neighbor->requests[irequest]->compute = 1; - neighbor->requests[irequest]->occasional = 1; -} - -/* ---------------------------------------------------------------------- */ - -void ComputeMopProfile::init_list(int id, NeighList *ptr) -{ - list = ptr; -} - - -/* ---------------------------------------------------------------------- - compute output array - ------------------------------------------------------------------------- */ - -void ComputeMopProfile::compute_array() -{ - invoked_array = update->ntimestep; - - //Compute pressures on separate procs - compute_pairs(); - - // sum pressure contributions over all procs - MPI_Allreduce(&values_local[0][0],&values_global[0][0],nbins*nvalues, - MPI_DOUBLE,MPI_SUM,world); - - int ibin,m,mo; - for (ibin=0; ibinmass; - int *type = atom->type; - int *mask = atom->mask; - int nlocal = atom->nlocal; - double *special_coul = force->special_coul; - double *special_lj = force->special_lj; - int newton_pair = force->newton_pair; - - - // zero out arrays for one sample - for (m = 0; m < nbins; m++) { - for (i = 0; i < nvalues; i++) values_local[m][i] = 0.0; - } - - // invoke half neighbor list (will copy or build if necessary) - - neighbor->build_one(list); - - inum = list->inum; - ilist = list->ilist; - numneigh = list->numneigh; - firstneigh = list->firstneigh; - - // loop over neighbors of my atoms - - Pair *pair = force->pair; - double **cutsq = force->pair->cutsq; - - // parse values - - double xi[3]; - double vi[3]; - double fi[3]; - double xj[3]; - - m = 0; - while (mx[i][0]; - xi[1] = atom->x[i][1]; - xi[2] = atom->x[i][2]; - itype = type[i]; - jlist = firstneigh[i]; - jnum = numneigh[i]; - - for (jj = 0; jj < jnum; jj++) { - j = jlist[jj]; - factor_lj = special_lj[sbmask(j)]; - factor_coul = special_coul[sbmask(j)]; - j &= NEIGHMASK; - - // skip if neither I nor J are in group - - if (!(mask[i] & groupbit || mask[j] & groupbit)) continue; - - xj[0] = atom->x[j][0]; - xj[1] = atom->x[j][1]; - xj[2] = atom->x[j][2]; - delx = xi[0] - xj[0]; - dely = xi[1] - xj[1]; - delz = xi[2] - xj[2]; - rsq = delx*delx + dely*dely + delz*delz; - jtype = type[j]; - if (rsq >= cutsq[itype][jtype]) continue; - - if (newton_pair || j < nlocal) { - - for (ibin=0;ibinpos) && (xj[dir]pos1) && (xj[dir]single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair); - - values_local[ibin][m] += fpair*(xi[0]-xj[0])/area*nktv2p; - values_local[ibin][m+1] += fpair*(xi[1]-xj[1])/area*nktv2p; - values_local[ibin][m+2] += fpair*(xi[2]-xj[2])/area*nktv2p; - - } else if ( ((xi[dir]pos)) - || ((xi[dir]pos1)) ) { - - pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair); - - values_local[ibin][m] -= fpair*(xi[0]-xj[0])/area*nktv2p; - values_local[ibin][m+1] -= fpair*(xi[1]-xj[1])/area*nktv2p; - values_local[ibin][m+2] -= fpair*(xi[2]-xj[2])/area*nktv2p; - } - } - } else { - - for (ibin=0;ibinpos) && (xj[dir]pos1) && (xj[dir]single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair); - - values_local[ibin][m] += fpair*(xi[0]-xj[0])/area*nktv2p; - values_local[ibin][m+1] += fpair*(xi[1]-xj[1])/area*nktv2p; - values_local[ibin][m+2] += fpair*(xi[2]-xj[2])/area*nktv2p; - } - } - } - } - } - } - - // compute kinetic contribution to pressure - // counts local particles transfers across the plane - - if (which[m] == KIN || which[m] == TOTAL){ - - double vcm[3]; - double masstotal,sgn; - - for (int i = 0; i < nlocal; i++){ - - // skip if I is not in group - - if (mask[i] & groupbit){ - - itype = type[i]; - - //coordinates at t - xi[0] = atom->x[i][0]; - xi[1] = atom->x[i][1]; - xi[2] = atom->x[i][2]; - - //velocities at t - vi[0] = atom->v[i][0]; - vi[1] = atom->v[i][1]; - vi[2] = atom->v[i][2]; - - //forces at t - fi[0] = atom->f[i][0]; - fi[1] = atom->f[i][1]; - fi[2] = atom->f[i][2]; - - //coordinates at t-dt (based on Velocity-Verlet alg.) - xj[0] = xi[0]-vi[0]*dt+fi[0]/2/mass[itype]*dt*dt*ftm2v; - xj[1] = xi[1]-vi[1]*dt+fi[1]/2/mass[itype]*dt*dt*ftm2v; - xj[2] = xi[2]-vi[2]*dt+fi[2]/2/mass[itype]*dt*dt*ftm2v; - - for (ibin=0;ibinboxlo; - boxhi = domain->boxhi; - prd = domain->prd; - - if (originflag == LOWER) origin = boxlo[dir]; - else if (originflag == UPPER) origin = boxhi[dir]; - else if (originflag == CENTER) - origin = 0.5 * (boxlo[dir] + boxhi[dir]); - - if (origin < boxlo[dir]) { - error->all(FLERR,"Origin of bins for compute mop/profile is out of bounds" ); - } else { - n = static_cast ((origin - boxlo[dir]) * invdelta); - lo = origin - n*delta; - } - if (origin < boxhi[dir]) { - n = static_cast ((boxhi[dir] - origin) * invdelta); - hi = origin + n*delta; - } else { - error->all(FLERR,"Origin of bins for compute mop/profile is out of bounds" ); - } - - offset = lo; - nbins = static_cast ((hi-lo) * invdelta + 1.5); - - //allocate bin arrays - memory->create(coord,nbins,1,"mop/profile:coord"); - memory->create(coordp,nbins,1,"mop/profile:coordp"); - memory->create(values_local,nbins,nvalues,"mop/profile:values_local"); - memory->create(values_global,nbins,nvalues,"mop/profile:values_global"); - - // set bin coordinates - for (i = 0; i < nbins; i++) { - coord[i][0] = offset + i*delta; - if ( coord[i][0] < (domain->boxlo[dir]+domain->prd_half[dir]) ) { - coordp[i][0] = coord[i][0] + domain->prd[dir]; - } else { - coordp[i][0] = coord[i][0] - domain->prd[dir]; - } - } -} diff --git a/src/USER-MOP/compute_mop_profile.h b/src/USER-MOP/compute_mop_profile.h deleted file mode 100644 index 3cb46087ae..0000000000 --- a/src/USER-MOP/compute_mop_profile.h +++ /dev/null @@ -1,81 +0,0 @@ -/* ---------------------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. - ------------------------------------------------------------------------- */ - -/*------------------------------------------------------------------------ - Contributing Authors : Romain Vermorel (LFCR), Laurent Joly (ULyon) - --------------------------------------------------------------------------*/ - -#ifdef COMPUTE_CLASS - -ComputeStyle(mop/profile,ComputeMopProfile) - -#else - -#ifndef LMP_COMPUTE_MOP_PROFILE_H -#define LMP_COMPUTE_MOP_PROFILE_H - -#include "compute.h" - -namespace LAMMPS_NS { - - class ComputeMopProfile : public Compute { - public: - ComputeMopProfile(class LAMMPS *, int, char **); - virtual ~ComputeMopProfile(); - void init(); - void init_list(int, class NeighList *); - void compute_array(); - - private: - - void compute_pairs(); - void setup_bins(); - - int me,nvalues,dir; - int *which; - - int originflag; - double origin,delta,offset,invdelta; - int nbins; - double **coord,**coordp; - double **values_local,**values_global; - - int ndim; - double dt,nktv2p,ftm2v; - double area; - class NeighList *list; - - }; - -} - -#endif -#endif - -/* ERROR/WARNING messages: - - E: Illegal ... command - - Self-explanatory. Check the input script syntax and compare to the - documentation for the command. You can use -echo screen as a - command-line option when running LAMMPS to see the offending line. - - E: Pair style does not support compute mop/profile - - The pair style does not have a single() function, so it can - not be invoked by compute mop/profile. - - - -*/ - From f18f12d1a6ab2a7cba28ff3eaed16f726d6b9d53 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Tue, 4 Sep 2018 09:14:42 -0400 Subject: [PATCH 123/302] Fix NETCDF include and libs in CMake --- cmake/CMakeLists.txt | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index 0d4bab29f1..f1124fc127 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -435,8 +435,8 @@ endif() if(PKG_USER-NETCDF) find_package(NetCDF REQUIRED) - include_directories(NETCDF_INCLUDE_DIR) - list(APPEND LAMMPS_LINK_LIBS ${NETCDF_LIBRARY}) + include_directories(${NETCDF_INCLUDE_DIRS}) + list(APPEND LAMMPS_LINK_LIBS ${NETCDF_LIBRARIES}) add_definitions(-DLMP_HAS_NETCDF -DNC_64BIT_DATA=0x0020) endif() From 842136afc841e90720abae1fa32ef84bf73f8e52 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Tue, 4 Sep 2018 12:12:49 -0400 Subject: [PATCH 124/302] Add core tests to CMake --- cmake/CMakeLists.txt | 39 ++++++++++++++++++++++++++++++++++++--- 1 file changed, 36 insertions(+), 3 deletions(-) diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index 0d4bab29f1..47a4075bcc 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -136,6 +136,7 @@ if(BUILD_EXE) if(LAMMPS_MACHINE) set(LAMMPS_MACHINE "_${LAMMPS_MACHINE}") endif() + set(LAMMPS_BINARY lmp${LAMMPS_MACHINE}) endif() option(BUILD_LIB "Build LAMMPS library" OFF) @@ -208,6 +209,38 @@ option(CMAKE_VERBOSE_MAKEFILE "Verbose makefile" OFF) option(ENABLE_TESTING "Enable testing" OFF) if(ENABLE_TESTING) enable_testing() + + if (CMAKE_VERSION VERSION_GREATER "3.10.3") # due to FetchContent + include(FetchContent) + + + FetchContent_Declare(lammps-testing + GIT_REPOSITORY https://github.com/lammps/lammps-testing.git + GIT_TAG master + ) + + FetchContent_GetProperties(lammps-testing) + if(NOT lammps-testing_POPULATED) + message(STATUS "Downloading tests...") + FetchContent_Populate(lammps-testing) + endif() + message(STATUS "Running test discovery...") + + file(GLOB_RECURSE TEST_SCRIPTS ${lammps-testing_SOURCE_DIR}/tests/core/*/in.*) + foreach(script_path ${TEST_SCRIPTS}) + get_filename_component(TEST_NAME ${script_path} EXT) + get_filename_component(SCRIPT_NAME ${script_path} NAME) + get_filename_component(PARENT_DIR ${script_path} DIRECTORY) + string(SUBSTRING ${TEST_NAME} 1 -1 TEST_NAME) + string(REPLACE "-" "_" TEST_NAME ${TEST_NAME}) + string(REPLACE "+" "_" TEST_NAME ${TEST_NAME}) + set(TEST_NAME "test_core_${TEST_NAME}_serial") + add_test(${TEST_NAME} ${CMAKE_BINARY_DIR}/${LAMMPS_BINARY} -in ${SCRIPT_NAME}) + set_tests_properties(${TEST_NAME} PROPERTIES WORKING_DIRECTORY ${PARENT_DIR}) + endforeach() + else() + message(WARNING "Full test-suite requires CMake >= 3.11") + endif() endif(ENABLE_TESTING) set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE GRANULAR @@ -1119,11 +1152,11 @@ if(BUILD_EXE) endif() endif() - set_target_properties(lmp PROPERTIES OUTPUT_NAME lmp${LAMMPS_MACHINE}) + set_target_properties(lmp PROPERTIES OUTPUT_NAME ${LAMMPS_BINARY}) install(TARGETS lmp DESTINATION ${CMAKE_INSTALL_BINDIR}) - install(FILES ${LAMMPS_DOC_DIR}/lammps.1 DESTINATION ${CMAKE_INSTALL_MANDIR}/man1 RENAME lmp${LAMMPS_MACHINE}.1) + install(FILES ${LAMMPS_DOC_DIR}/lammps.1 DESTINATION ${CMAKE_INSTALL_MANDIR}/man1 RENAME ${LAMMPS_BINARY}.1) if(ENABLE_TESTING) - add_test(ShowHelp lmp${LAMMPS_MACHINE} -help) + add_test(ShowHelp ${LAMMPS_BINARY} -help) endif() endif() From af4b2b935428b4e7738b17e78bcca96463e212eb Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Tue, 4 Sep 2018 15:37:32 -0400 Subject: [PATCH 125/302] Add LAMMPS_TESTING_SOURCE_DIR and LAMMPS_TESTING_GIT_TAG options --- cmake/CMakeLists.txt | 23 +++++++++++++++++------ 1 file changed, 17 insertions(+), 6 deletions(-) diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index 47a4075bcc..0d8da8409d 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -209,14 +209,16 @@ option(CMAKE_VERBOSE_MAKEFILE "Verbose makefile" OFF) option(ENABLE_TESTING "Enable testing" OFF) if(ENABLE_TESTING) enable_testing() + option(LAMMPS_TESTING_SOURCE_DIR "Location of lammps-testing source directory" "") + option(LAMMPS_TESTING_GIT_TAG "Git tag of lammps-testing" "master") + mark_as_advanced(LAMMPS_TESTING_SOURCE_DIR LAMMPS_TESTING_GIT_TAG) - if (CMAKE_VERSION VERSION_GREATER "3.10.3") # due to FetchContent + if (CMAKE_VERSION VERSION_GREATER "3.10.3" AND NOT LAMMPS_TESTING_SOURCE_DIR) include(FetchContent) - FetchContent_Declare(lammps-testing GIT_REPOSITORY https://github.com/lammps/lammps-testing.git - GIT_TAG master + GIT_TAG ${LAMMPS_TESTING_GIT_TAG} ) FetchContent_GetProperties(lammps-testing) @@ -224,9 +226,17 @@ if(ENABLE_TESTING) message(STATUS "Downloading tests...") FetchContent_Populate(lammps-testing) endif() + + set(LAMMPS_TESTING_SOURCE_DIR ${lammps-testing_SOURCE_DIR}) + elseif(NOT LAMMPS_TESTING_SOURCE_DIR) + message(WARNING "Full test-suite requires CMake >= 3.11 or copy of\n" + "https://github.com/lammps/lammps-testing in LAMMPS_TESTING_SOURCE_DIR") + endif() + + if(EXISTS ${LAMMPS_TESTING_SOURCE_DIR}) message(STATUS "Running test discovery...") - file(GLOB_RECURSE TEST_SCRIPTS ${lammps-testing_SOURCE_DIR}/tests/core/*/in.*) + file(GLOB_RECURSE TEST_SCRIPTS ${LAMMPS_TESTING_SOURCE_DIR}/tests/core/*/in.*) foreach(script_path ${TEST_SCRIPTS}) get_filename_component(TEST_NAME ${script_path} EXT) get_filename_component(SCRIPT_NAME ${script_path} NAME) @@ -238,8 +248,9 @@ if(ENABLE_TESTING) add_test(${TEST_NAME} ${CMAKE_BINARY_DIR}/${LAMMPS_BINARY} -in ${SCRIPT_NAME}) set_tests_properties(${TEST_NAME} PROPERTIES WORKING_DIRECTORY ${PARENT_DIR}) endforeach() - else() - message(WARNING "Full test-suite requires CMake >= 3.11") + list(LENGTH TEST_SCRIPTS NUM_TESTS) + + message(STATUS "Found ${NUM_TESTS} tests.") endif() endif(ENABLE_TESTING) From bcecc0389e0607223383a8fa0713d73045d41ad9 Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Tue, 4 Sep 2018 14:48:44 -0600 Subject: [PATCH 126/302] add variable option to compute bond/angle/dihedral local --- doc/src/compute_angle_local.txt | 66 +++++++-- doc/src/compute_bond_local.txt | 69 +++++++-- doc/src/compute_dihedral_local.txt | 64 +++++++-- src/compute_angle_local.cpp | 203 +++++++++++++++++++------- src/compute_angle_local.h | 8 +- src/compute_bond_local.cpp | 111 +++++++++++++-- src/compute_bond_local.h | 9 +- src/compute_dihedral_local.cpp | 220 +++++++++++++++++++++-------- src/compute_dihedral_local.h | 8 +- 9 files changed, 601 insertions(+), 157 deletions(-) diff --git a/doc/src/compute_angle_local.txt b/doc/src/compute_angle_local.txt index 3a321965ef..8acaec94d5 100644 --- a/doc/src/compute_angle_local.txt +++ b/doc/src/compute_angle_local.txt @@ -10,20 +10,27 @@ compute angle/local command :h3 [Syntax:] -compute ID group-ID angle/local value1 value2 ... :pre +compute ID group-ID angle/local value1 value2 ... keyword args ... :pre ID, group-ID are documented in "compute"_compute.html command :ulb,l angle/local = style name of this compute command :l one or more values may be appended :l -value = {theta} or {eng} :l +value = {theta} or {eng} or {v_name} :l {theta} = tabulate angles - {eng} = tabulate angle energies :pre + {eng} = tabulate angle energies + {v_name} = equal-style variable with name (see below) :pre +zero or more keyword/args pairs may be appended :l +keyword = {set} :l + {set} args = theta name + theta = only currently allowed arg + name = name of variable to set with theta :pre :ule [Examples:] compute 1 all angle/local theta -compute 1 all angle/local eng theta :pre +compute 1 all angle/local eng theta +compute 1 all angle/local theta v_cos set theta t :pre [Description:] @@ -36,6 +43,47 @@ The value {theta} is the angle for the 3 atoms in the interaction. The value {eng} is the interaction energy for the angle. +The value {v_name} can be used together with the {set} keyword to +compute a user-specified function of the angle theta. The {name} +specified for the {v_name} value is the name of an "equal-style +variable"_variable.html which should evaluate a formula based on a +variable which will store the angle theta. This other variable must +be an "internal-style variable"_variable.html defined in the input +script; its initial numeric value can be anything. It must be an +internal-style variable, because this command resets its value +directly. The {set} keyword is used to identify the name of this +other variable associated with theta. + +Note that the value of theta for each angle which stored in the +internal variable is in radians, not degrees. + +As an example, these commands can be added to the bench/in.rhodo +script to compute the cosine and cosine^2 of every angle in the system +and output the statistics in various ways: + +variable t internal 0.0 +variable cos equal cos(v_t) +variable cossq equal cos(v_t)*cos(v_t) :pre + +compute 1 all property/local aatom1 aatom2 aatom3 atype +compute 2 all angle/local eng theta v_cos v_cossq set theta t +dump 1 all local 100 tmp.dump c_1[*] c_2[*] :pre + +compute 3 all reduce ave c_2[*] +thermo_style custom step temp press c_3[*] :pre + +fix 10 all ave/histo 10 10 100 -1 1 20 c_2[3] mode vector file tmp.histo :pre + +The "dump local"_dump.html command will output the energy, angle, +cosine(angle), cosine^2(angle) for every angle in the system. The +"thermo_style"_thermo_style.html command will print the average of +those quantities via the "compute reduce"_compute_reduce.html command +with thermo output. And the "fix ave/histo"_fix_ave_histo.html +command will histogram the cosine(angle) values and write them to a +file. + +:line + The local data stored by this command is generated by looping over all the atoms owned on a processor and their angles. An angle will only be included if all 3 atoms in the angle are in the specified compute @@ -65,12 +113,12 @@ dump 1 all local 1000 tmp.dump index c_1\[1\] c_1\[2\] c_1\[3\] c_1\[4\] c_2\[1\ [Output info:] This compute calculates a local vector or local array depending on the -number of keywords. The length of the vector or number of rows in the -array is the number of angles. If a single keyword is specified, a -local vector is produced. If two or more keywords are specified, a +number of values. The length of the vector or number of rows in the +array is the number of angles. If a single value is specified, a +local vector is produced. If two or more values are specified, a local array is produced where the number of columns = the number of -keywords. The vector or array can be accessed by any command that -uses local values from a compute as input. See the "Howto +values. The vector or array can be accessed by any command that uses +local values from a compute as input. See the "Howto output"_Howto_output.html doc page for an overview of LAMMPS output options. diff --git a/doc/src/compute_bond_local.txt b/doc/src/compute_bond_local.txt index c3dc1cc4af..4afd1aec40 100644 --- a/doc/src/compute_bond_local.txt +++ b/doc/src/compute_bond_local.txt @@ -10,12 +10,12 @@ compute bond/local command :h3 [Syntax:] -compute ID group-ID bond/local value1 value2 ... :pre +compute ID group-ID bond/local value1 value2 ... keyword args ... :pre ID, group-ID are documented in "compute"_compute.html command :ulb,l bond/local = style name of this compute command :l one or more values may be appended :l -value = {dist} or {engpot} or {force} or {engvib} or {engrot} or {engtrans} or {omega} or {velvib} :l +value = {dist} or {engpot} or {force} or {engvib} or {engrot} or {engtrans} or {omega} or {velvib} or {v_name} :l {dist} = bond distance {engpot} = bond potential energy {force} = bond force :pre @@ -23,13 +23,22 @@ value = {dist} or {engpot} or {force} or {engvib} or {engrot} or {engtrans} or { {engrot} = bond kinetic energy of rotation {engtrans} = bond kinetic energy of translation {omega} = magnitude of bond angular velocity - {velvib} = vibrational velocity along the bond length :pre + {velvib} = vibrational velocity along the bond length + {v_name} = equal-style variable with name (see below) :pre +zero or more keyword/args pairs may be appended :l +keyword = {set} :l + {set} args = dist name + dist = only currently allowed arg + name = name of variable to set with distance (dist) :pre +:ule + :ule [Examples:] compute 1 all bond/local engpot compute 1 all bond/local dist engpot force :pre +compute 1 all angle/local dist v_distsq set dist d :pre [Description:] @@ -38,6 +47,10 @@ interactions. The number of datums generated, aggregated across all processors, equals the number of bonds in the system, modified by the group parameter as explained below. +All these properties are computed for the pair of atoms in a bond, +whether the 2 atoms represent a simple diatomic molecule, or are part +of some larger molecule. + The value {dist} is the current length of the bond. The value {engpot} is the potential energy for the bond, @@ -79,9 +92,41 @@ two atoms in the bond towards each other. A negative value means the 2 atoms are moving toward each other; a positive value means they are moving apart. -Note that all these properties are computed for the pair of atoms in a -bond, whether the 2 atoms represent a simple diatomic molecule, or are -part of some larger molecule. +The value {v_name} can be used together with the {set} keyword to +compute a user-specified function of the bond distance. The {name} +specified for the {v_name} value is the name of an "equal-style +variable"_variable.html which should evaluate a formula based on a +variable which will store the bond distance. This other variable must +be an "internal-style variable"_variable.html defined in the input +script; its initial numeric value can be anything. It must be an +internal-style variable, because this command resets its value +directly. The {set} keyword is used to identify the name of this +other variable associated with theta. + +As an example, these commands can be added to the bench/in.rhodo +script to compute the distance^2 of every bond in the system and +output the statistics in various ways: + +variable d internal 0.0 +variable dsq equal v_d*v_d :pre + +compute 1 all property/local batom1 batom2 btype +compute 2 all bond/local engpot dist v_dsq set dist d +dump 1 all local 100 tmp.dump c_1[*] c_2[*] :pre + +compute 3 all reduce ave c_2[*] +thermo_style custom step temp press c_3[*] :pre + +fix 10 all ave/histo 10 10 100 0 6 20 c_2[3] mode vector file tmp.histo :pre + +The "dump local"_dump.html command will output the energy, distance, +distance^2 for every bond in the system. The +"thermo_style"_thermo_style.html command will print the average of +those quantities via the "compute reduce"_compute_reduce.html command +with thermo output. And the "fix ave/histo"_fix_ave_histo.html +command will histogram the distance^2 values and write them to a file. + +:line The local data stored by this command is generated by looping over all the atoms owned on a processor and their bonds. A bond will only be @@ -111,12 +156,12 @@ dump 1 all local 1000 tmp.dump index c_1\[*\] c_2\[*\] :pre [Output info:] This compute calculates a local vector or local array depending on the -number of keywords. The length of the vector or number of rows in the -array is the number of bonds. If a single keyword is specified, a -local vector is produced. If two or more keywords are specified, a -local array is produced where the number of columns = the number of -keywords. The vector or array can be accessed by any command that -uses local values from a compute as input. See the "Howto +number of values. The length of the vector or number of rows in the +array is the number of bonds. If a single value is specified, a local +vector is produced. If two or more values are specified, a local +array is produced where the number of columns = the number of values. +The vector or array can be accessed by any command that uses local +values from a compute as input. See the "Howto output"_Howto_output.html doc page for an overview of LAMMPS output options. diff --git a/doc/src/compute_dihedral_local.txt b/doc/src/compute_dihedral_local.txt index 77812699d3..951b360f19 100644 --- a/doc/src/compute_dihedral_local.txt +++ b/doc/src/compute_dihedral_local.txt @@ -10,18 +10,25 @@ compute dihedral/local command :h3 [Syntax:] -compute ID group-ID dihedral/local value1 value2 ... :pre +compute ID group-ID dihedral/local value1 value2 ... keyword args ... :pre ID, group-ID are documented in "compute"_compute.html command :ulb,l dihedral/local = style name of this compute command :l one or more values may be appended :l -value = {phi} :l - {phi} = tabulate dihedral angles :pre +value = {phi} or {v_name} :l + {phi} = tabulate dihedral angles + {v_name} = equal-style variable with name (see below) :pre +zero or more keyword/args pairs may be appended :l +keyword = {set} :l + {set} args = phi name + phi = only currently allowed arg + name = name of variable to set with phi :pre :ule [Examples:] compute 1 all dihedral/local phi :pre +compute 1 all dihedral/local phi v_cos set phi p :pre [Description:] @@ -33,6 +40,47 @@ by the group parameter as explained below. The value {phi} is the dihedral angle, as defined in the diagram on the "dihedral_style"_dihedral_style.html doc page. +The value {v_name} can be used together with the {set} keyword to +compute a user-specified function of the dihedral angle phi. The +{name} specified for the {v_name} value is the name of an "equal-style +variable"_variable.html which should evaluate a formula based on a +variable which will store the angle phi. This other variable must +be an "internal-style variable"_variable.html defined in the input +script; its initial numeric value can be anything. It must be an +internal-style variable, because this command resets its value +directly. The {set} keyword is used to identify the name of this +other variable associated with phi. + +Note that the value of phi for each angle which stored in the internal +variable is in radians, not degrees. + +As an example, these commands can be added to the bench/in.rhodo +script to compute the cosine and cosine^2 of every dihedral angle in +the system and output the statistics in various ways: + +variable p internal 0.0 +variable cos equal cos(v_p) +variable cossq equal cos(v_p)*cos(v_p) :pre + +compute 1 all property/local datom1 datom2 datom3 datom4 dtype +compute 2 all dihedral/local phi v_cos v_cossq set phi p +dump 1 all local 100 tmp.dump c_1[*] c_2[*] :pre + +compute 3 all reduce ave c_2[*] +thermo_style custom step temp press c_3[*] :pre + +fix 10 all ave/histo 10 10 100 -1 1 20 c_2[2] mode vector file tmp.histo :pre + +The "dump local"_dump.html command will output the angle, +cosine(angle), cosine^2(angle) for every dihedral in the system. The +"thermo_style"_thermo_style.html command will print the average of +those quantities via the "compute reduce"_compute_reduce.html command +with thermo output. And the "fix ave/histo"_fix_ave_histo.html +command will histogram the cosine(angle) values and write them to a +file. + +:line + The local data stored by this command is generated by looping over all the atoms owned on a processor and their dihedrals. A dihedral will only be included if all 4 atoms in the dihedral are in the specified @@ -57,12 +105,12 @@ dump 1 all local 1000 tmp.dump index c_1\[1\] c_1\[2\] c_1\[3\] c_1\[4\] c_1\[5\ [Output info:] This compute calculates a local vector or local array depending on the -number of keywords. The length of the vector or number of rows in the -array is the number of dihedrals. If a single keyword is specified, a -local vector is produced. If two or more keywords are specified, a +number of values. The length of the vector or number of rows in the +array is the number of dihedrals. If a single value is specified, a +local vector is produced. If two or more values are specified, a local array is produced where the number of columns = the number of -keywords. The vector or array can be accessed by any command that -uses local values from a compute as input. See the "Howto +values. The vector or array can be accessed by any command that uses +local values from a compute as input. See the "Howto output"_Howto_output.html doc page for an overview of LAMMPS output options. diff --git a/src/compute_angle_local.cpp b/src/compute_angle_local.cpp index 7137077158..95faad54ad 100644 --- a/src/compute_angle_local.cpp +++ b/src/compute_angle_local.cpp @@ -21,6 +21,8 @@ #include "domain.h" #include "force.h" #include "angle.h" +#include "input.h" +#include "variable.h" #include "math_const.h" #include "memory.h" #include "error.h" @@ -30,11 +32,13 @@ using namespace MathConst; #define DELTA 10000 +enum{THETA,ENG,VARIABLE}; + /* ---------------------------------------------------------------------- */ ComputeAngleLocal::ComputeAngleLocal(LAMMPS *lmp, int narg, char **arg) : Compute(lmp, narg, arg), - vlocal(NULL), alocal(NULL) + bstyle(NULL), vstr(NULL), vvar(NULL), tstr(NULL), vlocal(NULL), alocal(NULL) { if (narg < 4) error->all(FLERR,"Illegal compute angle/local command"); @@ -42,19 +46,82 @@ ComputeAngleLocal::ComputeAngleLocal(LAMMPS *lmp, int narg, char **arg) : error->all(FLERR,"Compute angle/local used when angles are not allowed"); local_flag = 1; + + // style args + nvalues = narg - 3; + bstyle = new int[nvalues]; + vstr = new char*[nvalues]; + vvar = new int[nvalues]; + + nvalues = 0; + tflag = 0; + nvar = 0; + + int iarg; + for (iarg = 3; iarg < narg; iarg++) { + if (strcmp(arg[iarg],"theta") == 0) { + bstyle[nvalues++] = THETA; + tflag = 1; + } else if (strcmp(arg[iarg],"eng") == 0) { + bstyle[nvalues++] = ENG; + } else if (strncmp(arg[iarg],"v_",2) == 0) { + bstyle[nvalues++] = VARIABLE; + int n = strlen(arg[iarg]); + vstr[nvar] = new char[n]; + strcpy(vstr[nvar],&arg[iarg][2]); + nvar++; + } else break; + } + + // optional args + + setflag = 0; + tstr = NULL; + + while (iarg < narg) { + if (strcmp(arg[iarg],"set") == 0) { + setflag = 1; + if (iarg+3 > narg) error->all(FLERR,"Illegal compute angle/local command"); + if (strcmp(arg[iarg+1],"theta") == 0) { + delete [] tstr; + int n = strlen(arg[iarg+2]) + 1; + tstr = new char[n]; + strcpy(tstr,arg[iarg+2]); + tflag = 1; + } else error->all(FLERR,"Illegal compute angle/local command"); + iarg += 3; + } else error->all(FLERR,"Illegal compute angle/local command"); + } + + // error check + + if (nvar) { + if (!setflag) + error->all(FLERR,"Compute angle/local variable requires a set variable"); + for (int i = 0; i < nvar; i++) { + vvar[i] = input->variable->find(vstr[i]); + if (vvar[i] < 0) + error->all(FLERR,"Variable name for copute angle/local does not exist"); + if (!input->variable->equalstyle(vvar[i])) + error->all(FLERR,"Variable for compute angle/local is invalid style"); + } + + if (tstr) { + tvar = input->variable->find(tstr); + if (tvar < 0) + error->all(FLERR,"Variable name for compute angle/local does not exist"); + if (!input->variable->internalstyle(tvar)) + error->all(FLERR,"Variable for compute angle/local is invalid style"); + } + } else if (setflag) + error->all(FLERR,"Compute angle/local set with no variable"); + + // initialize output + if (nvalues == 1) size_local_cols = 0; else size_local_cols = nvalues; - tflag = eflag = -1; - nvalues = 0; - - for (int iarg = 3; iarg < narg; iarg++) { - if (strcmp(arg[iarg],"theta") == 0) tflag = nvalues++; - else if (strcmp(arg[iarg],"eng") == 0) eflag = nvalues++; - else error->all(FLERR,"Invalid keyword in compute angle/local command"); - } - nmax = 0; vlocal = NULL; alocal = NULL; @@ -64,6 +131,13 @@ ComputeAngleLocal::ComputeAngleLocal(LAMMPS *lmp, int narg, char **arg) : ComputeAngleLocal::~ComputeAngleLocal() { + delete [] bstyle; + for (int i = 0; i < nvar; i++) delete [] vstr[i]; + delete [] vstr; + delete [] vvar; + + delete [] tstr; + memory->destroy(vlocal); memory->destroy(alocal); } @@ -75,6 +149,20 @@ void ComputeAngleLocal::init() if (force->angle == NULL) error->all(FLERR,"No angle style is defined for compute angle/local"); + if (nvar) { + for (int i = 0; i < nvar; i++) { + vvar[i] = input->variable->find(vstr[i]); + if (vvar[i] < 0) + error->all(FLERR,"Variable name for compute angle/local does not exist"); + } + + if (tstr) { + tvar = input->variable->find(tstr); + if (tvar < 0) + error->all(FLERR,"Variable name for compute angle/local does not exist"); + } + } + // do initial memory allocation so that memory_usage() is correct ncount = compute_angles(0); @@ -109,11 +197,11 @@ void ComputeAngleLocal::compute_local() int ComputeAngleLocal::compute_angles(int flag) { - int i,m,n,na,atom1,atom2,atom3,imol,iatom,atype; + int i,m,n,na,atom1,atom2,atom3,imol,iatom,atype,ivar; tagint tagprev; double delx1,dely1,delz1,delx2,dely2,delz2; - double rsq1,rsq2,r1,r2,c; - double *tbuf,*ebuf; + double rsq1,rsq2,r1,r2,c,theta; + double *ptr; double **x = atom->x; tagint *tag = atom->tag; @@ -131,17 +219,7 @@ int ComputeAngleLocal::compute_angles(int flag) int nlocal = atom->nlocal; int molecular = atom->molecular; - if (flag) { - if (nvalues == 1) { - if (tflag >= 0) tbuf = vlocal; - if (eflag >= 0) ebuf = vlocal; - } else { - if (tflag >= 0 && alocal) tbuf = &alocal[0][tflag]; - else tbuf = NULL; - if (eflag >= 0 && alocal) ebuf = &alocal[0][eflag]; - else ebuf = NULL; - } - } + // loop over all atoms and their angles Angle *angle = force->angle; @@ -175,39 +253,62 @@ int ComputeAngleLocal::compute_angles(int flag) if (atom3 < 0 || !(mask[atom3] & groupbit)) continue; if (atype == 0) continue; - if (flag) { - if (tflag >= 0) { - delx1 = x[atom1][0] - x[atom2][0]; - dely1 = x[atom1][1] - x[atom2][1]; - delz1 = x[atom1][2] - x[atom2][2]; - domain->minimum_image(delx1,dely1,delz1); + if (!flag) { + m++; + continue; + } - rsq1 = delx1*delx1 + dely1*dely1 + delz1*delz1; - r1 = sqrt(rsq1); + // theta needed by one or more outputs - delx2 = x[atom3][0] - x[atom2][0]; - dely2 = x[atom3][1] - x[atom2][1]; - delz2 = x[atom3][2] - x[atom2][2]; - domain->minimum_image(delx2,dely2,delz2); + if (tflag) { + delx1 = x[atom1][0] - x[atom2][0]; + dely1 = x[atom1][1] - x[atom2][1]; + delz1 = x[atom1][2] - x[atom2][2]; + domain->minimum_image(delx1,dely1,delz1); - rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2; - r2 = sqrt(rsq2); + rsq1 = delx1*delx1 + dely1*dely1 + delz1*delz1; + r1 = sqrt(rsq1); + + delx2 = x[atom3][0] - x[atom2][0]; + dely2 = x[atom3][1] - x[atom2][1]; + delz2 = x[atom3][2] - x[atom2][2]; + domain->minimum_image(delx2,dely2,delz2); - // c = cosine of angle + rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2; + r2 = sqrt(rsq2); - c = delx1*delx2 + dely1*dely2 + delz1*delz2; - c /= r1*r2; - if (c > 1.0) c = 1.0; - if (c < -1.0) c = -1.0; - tbuf[n] = 180.0*acos(c)/MY_PI; + // c = cosine of angle + // theta = angle in radians + + c = delx1*delx2 + dely1*dely2 + delz1*delz2; + c /= r1*r2; + if (c > 1.0) c = 1.0; + if (c < -1.0) c = -1.0; + theta = acos(c); + } + + if (nvalues == 1) ptr = &vlocal[m]; + else ptr = alocal[m]; + + if (nvar) { + ivar = 0; + if (tstr) input->variable->internal_set(tvar,theta); + } + + for (n = 0; n < nvalues; n++) { + switch (bstyle[n]) { + case THETA: + ptr[n] = 180.0*theta/MY_PI; + break; + case ENG: + if (atype > 0) ptr[n] = angle->single(atype,atom1,atom2,atom3); + else ptr[n] = 0.0; + break; + case VARIABLE: + ptr[n] = input->variable->compute_equal(vvar[ivar]); + ivar++; + break; } - - if (eflag >= 0) { - if (atype > 0) - ebuf[n] = angle->single(atype,atom1,atom2,atom3); - else ebuf[n] = 0.0; - } - n += nvalues; } m++; diff --git a/src/compute_angle_local.h b/src/compute_angle_local.h index 6f59d7f097..a95e23206d 100644 --- a/src/compute_angle_local.h +++ b/src/compute_angle_local.h @@ -33,8 +33,12 @@ class ComputeAngleLocal : public Compute { double memory_usage(); private: - int nvalues,tflag,eflag; - int ncount; + int nvalues,nvar,ncount,setflag,tflag; + + int tvar; + int *bstyle,*vvar; + char *tstr; + char **vstr; int nmax; double *vlocal; diff --git a/src/compute_bond_local.cpp b/src/compute_bond_local.cpp index 56abb9b071..6a179cf1b4 100644 --- a/src/compute_bond_local.cpp +++ b/src/compute_bond_local.cpp @@ -21,8 +21,10 @@ #include "domain.h" #include "force.h" #include "bond.h" -#include "math_extra.h" #include "comm.h" +#include "input.h" +#include "variable.h" +#include "math_extra.h" #include "memory.h" #include "error.h" @@ -31,13 +33,13 @@ using namespace LAMMPS_NS; #define DELTA 10000 #define EPSILON 1.0e-12 -enum{DIST,VELVIB,OMEGA,ENGTRANS,ENGVIB,ENGROT,ENGPOT,FORCE}; +enum{DIST,VELVIB,OMEGA,ENGTRANS,ENGVIB,ENGROT,ENGPOT,FORCE,VARIABLE}; /* ---------------------------------------------------------------------- */ ComputeBondLocal::ComputeBondLocal(LAMMPS *lmp, int narg, char **arg) : Compute(lmp, narg, arg), - bstyle(NULL), vlocal(NULL), alocal(NULL) + bstyle(NULL), vstr(NULL), vvar(NULL), dstr(NULL), vlocal(NULL), alocal(NULL) { if (narg < 4) error->all(FLERR,"Illegal compute bond/local command"); @@ -47,14 +49,18 @@ ComputeBondLocal::ComputeBondLocal(LAMMPS *lmp, int narg, char **arg) : local_flag = 1; comm_forward = 3; + // style args + nvalues = narg - 3; - if (nvalues == 1) size_local_cols = 0; - else size_local_cols = nvalues; - bstyle = new int[nvalues]; - + vstr = new char*[nvalues]; + vvar = new int[nvalues]; + nvalues = 0; - for (int iarg = 3; iarg < narg; iarg++) { + nvar = 0; + + int iarg; + for (iarg = 3; iarg < narg; iarg++) { if (strcmp(arg[iarg],"dist") == 0) bstyle[nvalues++] = DIST; else if (strcmp(arg[iarg],"engpot") == 0) bstyle[nvalues++] = ENGPOT; else if (strcmp(arg[iarg],"force") == 0) bstyle[nvalues++] = FORCE; @@ -63,9 +69,58 @@ ComputeBondLocal::ComputeBondLocal(LAMMPS *lmp, int narg, char **arg) : else if (strcmp(arg[iarg],"engtrans") == 0) bstyle[nvalues++] = ENGTRANS; else if (strcmp(arg[iarg],"omega") == 0) bstyle[nvalues++] = OMEGA; else if (strcmp(arg[iarg],"velvib") == 0) bstyle[nvalues++] = VELVIB; - else error->all(FLERR,"Invalid keyword in compute bond/local command"); + else if (strncmp(arg[iarg],"v_",2) == 0) { + bstyle[nvalues++] = VARIABLE; + int n = strlen(arg[iarg]); + vstr[nvar] = new char[n]; + strcpy(vstr[nvar],&arg[iarg][2]); + nvar++; + } else break; } + // optional args + + setflag = 0; + dstr = NULL; + + while (iarg < narg) { + if (strcmp(arg[iarg],"set") == 0) { + setflag = 1; + if (iarg+3 > narg) error->all(FLERR,"Illegal compute bond/local command"); + if (strcmp(arg[iarg+1],"dist") == 0) { + delete [] dstr; + int n = strlen(arg[iarg+2]) + 1; + dstr = new char[n]; + strcpy(dstr,arg[iarg+2]); + } else error->all(FLERR,"Illegal compute bond/local command"); + iarg += 3; + } else error->all(FLERR,"Illegal compute bond/local command"); + } + + // error check + + if (nvar) { + if (!setflag) + error->all(FLERR,"Compute bond/local variable requires a set variable"); + for (int i = 0; i < nvar; i++) { + vvar[i] = input->variable->find(vstr[i]); + if (vvar[i] < 0) + error->all(FLERR,"Variable name for copute bond/local does not exist"); + if (!input->variable->equalstyle(vvar[i])) + error->all(FLERR,"Variable for compute bond/local is invalid style"); + } + + if (dstr) { + dvar = input->variable->find(dstr); + if (dvar < 0) + error->all(FLERR,"Variable name for compute bond/local does not exist"); + if (!input->variable->internalstyle(dvar)) + error->all(FLERR,"Variable for compute bond/local is invalid style"); + } + } else if (setflag) + error->all(FLERR,"Compute bond/local set with no variable"); + + // set singleflag if need to call bond->single() // set velflag if compute any quantities based on velocities @@ -77,6 +132,11 @@ ComputeBondLocal::ComputeBondLocal(LAMMPS *lmp, int narg, char **arg) : bstyle[i] == ENGVIB || bstyle[i] == ENGROT) velflag = 1; } + // initialize output + + if (nvalues == 1) size_local_cols = 0; + else size_local_cols = nvalues; + nmax = 0; vlocal = NULL; alocal = NULL; @@ -86,9 +146,15 @@ ComputeBondLocal::ComputeBondLocal(LAMMPS *lmp, int narg, char **arg) : ComputeBondLocal::~ComputeBondLocal() { + delete [] bstyle; + for (int i = 0; i < nvar; i++) delete [] vstr[i]; + delete [] vstr; + delete [] vvar; + + delete [] dstr; + memory->destroy(vlocal); memory->destroy(alocal); - delete [] bstyle; } /* ---------------------------------------------------------------------- */ @@ -98,6 +164,20 @@ void ComputeBondLocal::init() if (force->bond == NULL) error->all(FLERR,"No bond style is defined for compute bond/local"); + if (nvar) { + for (int i = 0; i < nvar; i++) { + vvar[i] = input->variable->find(vstr[i]); + if (vvar[i] < 0) + error->all(FLERR,"Variable name for compute bond/local does not exist"); + } + + if (dstr) { + dvar = input->variable->find(dstr); + if (dvar < 0) + error->all(FLERR,"Variable name for compute bond/local does not exist"); + } + } + // set ghostvelflag if need to acquire ghost atom velocities if (velflag && !comm->ghost_velocity) ghostvelflag = 1; @@ -140,7 +220,7 @@ void ComputeBondLocal::compute_local() int ComputeBondLocal::compute_bonds(int flag) { - int i,m,n,nb,atom1,atom2,imol,iatom,btype; + int i,m,n,nb,atom1,atom2,imol,iatom,btype,ivar; tagint tagprev; double dx,dy,dz,rsq; double mass1,mass2,masstotal,invmasstotal; @@ -297,6 +377,11 @@ int ComputeBondLocal::compute_bonds(int flag) if (nvalues == 1) ptr = &vlocal[m]; else ptr = alocal[m]; + if (nvar) { + ivar = 0; + if (dstr) input->variable->internal_set(dvar,sqrt(rsq)); + } + for (n = 0; n < nvalues; n++) { switch (bstyle[n]) { case DIST: @@ -323,6 +408,10 @@ int ComputeBondLocal::compute_bonds(int flag) case VELVIB: ptr[n] = vvib; break; + case VARIABLE: + ptr[n] = input->variable->compute_equal(vvar[ivar]); + ivar++; + break; } } } diff --git a/src/compute_bond_local.h b/src/compute_bond_local.h index b3e99fc61b..17111a941c 100644 --- a/src/compute_bond_local.h +++ b/src/compute_bond_local.h @@ -35,10 +35,13 @@ class ComputeBondLocal : public Compute { double memory_usage(); private: - int nvalues; - int ncount; - int *bstyle; + int nvalues,nvar,ncount,setflag; + int singleflag,velflag,ghostvelflag,initflag; + int dvar; + int *bstyle,*vvar; + char *dstr; + char **vstr; int nmax; double *vlocal; diff --git a/src/compute_dihedral_local.cpp b/src/compute_dihedral_local.cpp index 42d1476ad2..7444630090 100644 --- a/src/compute_dihedral_local.cpp +++ b/src/compute_dihedral_local.cpp @@ -21,6 +21,9 @@ #include "domain.h" #include "force.h" #include "dihedral.h" +#include "input.h" +#include "variable.h" + #include "math_const.h" #include "memory.h" #include "error.h" @@ -31,11 +34,13 @@ using namespace MathConst; #define DELTA 10000 #define SMALL 0.001 +enum{PHI,VARIABLE}; + /* ---------------------------------------------------------------------- */ ComputeDihedralLocal::ComputeDihedralLocal(LAMMPS *lmp, int narg, char **arg) : Compute(lmp, narg, arg), - vlocal(NULL), alocal(NULL) + bstyle(NULL), vstr(NULL), vvar(NULL), pstr(NULL), vlocal(NULL), alocal(NULL) { if (narg < 4) error->all(FLERR,"Illegal compute dihedral/local command"); @@ -44,18 +49,80 @@ ComputeDihedralLocal::ComputeDihedralLocal(LAMMPS *lmp, int narg, char **arg) : "Compute dihedral/local used when dihedrals are not allowed"); local_flag = 1; + + // style args + nvalues = narg - 3; + bstyle = new int[nvalues]; + vstr = new char*[nvalues]; + vvar = new int[nvalues]; + + nvalues = 0; + nvar = 0; + + int iarg; + for (iarg = 3; iarg < narg; iarg++) { + if (strcmp(arg[iarg],"phi") == 0) { + bstyle[nvalues++] = PHI; + } else if (strncmp(arg[iarg],"v_",2) == 0) { + bstyle[nvalues++] = VARIABLE; + int n = strlen(arg[iarg]); + vstr[nvar] = new char[n]; + strcpy(vstr[nvar],&arg[iarg][2]); + nvar++; + } else break; + } + + // optional args + + setflag = 0; + pstr = NULL; + + while (iarg < narg) { + if (strcmp(arg[iarg],"set") == 0) { + setflag = 1; + if (iarg+3 > narg) + error->all(FLERR,"Illegal compute dihedral/local command"); + if (strcmp(arg[iarg+1],"phi") == 0) { + delete [] pstr; + int n = strlen(arg[iarg+2]) + 1; + pstr = new char[n]; + strcpy(pstr,arg[iarg+2]); + } else error->all(FLERR,"Illegal compute dihedral/local command"); + iarg += 3; + } else error->all(FLERR,"Illegal compute dihedral/local command"); + } + + // error check + + if (nvar) { + if (!setflag) + error->all(FLERR,"Compute dihedral/local variable requires a set variable"); + for (int i = 0; i < nvar; i++) { + vvar[i] = input->variable->find(vstr[i]); + if (vvar[i] < 0) + error->all(FLERR, + "Variable name for copute dihedral/local does not exist"); + if (!input->variable->equalstyle(vvar[i])) + error->all(FLERR,"Variable for compute dihedral/local is invalid style"); + } + + if (pstr) { + pvar = input->variable->find(pstr); + if (pvar < 0) + error->all(FLERR, + "Variable name for compute dihedral/local does not exist"); + if (!input->variable->internalstyle(pvar)) + error->all(FLERR,"Variable for compute dihedral/local is invalid style"); + } + } else if (setflag) + error->all(FLERR,"Compute dihedral/local set with no variable"); + + // initialize output + if (nvalues == 1) size_local_cols = 0; else size_local_cols = nvalues; - pflag = -1; - nvalues = 0; - - for (int iarg = 3; iarg < narg; iarg++) { - if (strcmp(arg[iarg],"phi") == 0) pflag = nvalues++; - else error->all(FLERR,"Invalid keyword in compute dihedral/local command"); - } - nmax = 0; vlocal = NULL; alocal = NULL; @@ -65,6 +132,13 @@ ComputeDihedralLocal::ComputeDihedralLocal(LAMMPS *lmp, int narg, char **arg) : ComputeDihedralLocal::~ComputeDihedralLocal() { + delete [] bstyle; + for (int i = 0; i < nvar; i++) delete [] vstr[i]; + delete [] vstr; + delete [] vvar; + + delete [] pstr; + memory->destroy(vlocal); memory->destroy(alocal); } @@ -76,6 +150,22 @@ void ComputeDihedralLocal::init() if (force->dihedral == NULL) error->all(FLERR,"No dihedral style is defined for compute dihedral/local"); + if (nvar) { + for (int i = 0; i < nvar; i++) { + vvar[i] = input->variable->find(vstr[i]); + if (vvar[i] < 0) + error->all(FLERR, + "Variable name for compute dihedral/local does not exist"); + } + + if (pstr) { + pvar = input->variable->find(pstr); + if (pvar < 0) + error->all(FLERR, + "Variable name for compute dihedral/local does not exist"); + } + } + // do initial memory allocation so that memory_usage() is correct ncount = compute_dihedrals(0); @@ -107,12 +197,12 @@ void ComputeDihedralLocal::compute_local() int ComputeDihedralLocal::compute_dihedrals(int flag) { - int i,m,n,nd,atom1,atom2,atom3,atom4,imol,iatom; + int i,m,n,nd,atom1,atom2,atom3,atom4,imol,iatom,ivar; tagint tagprev; double vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,vb2xm,vb2ym,vb2zm; double ax,ay,az,bx,by,bz,rasq,rbsq,rgsq,rg,ra2inv,rb2inv,rabinv; - double s,c; - double *pbuf; + double s,c,phi; + double *ptr; double **x = atom->x; tagint *tag = atom->tag; @@ -130,14 +220,7 @@ int ComputeDihedralLocal::compute_dihedrals(int flag) int nlocal = atom->nlocal; int molecular = atom->molecular; - if (flag) { - if (nvalues == 1) { - if (pflag >= 0) pbuf = vlocal; - } else { - if (pflag >= 0 && alocal) pbuf = &alocal[0][pflag]; - else pbuf = NULL; - } - } + // loop over all atoms and their dihedrals m = n = 0; for (atom2 = 0; atom2 < nlocal; atom2++) { @@ -169,56 +252,75 @@ int ComputeDihedralLocal::compute_dihedrals(int flag) if (atom3 < 0 || !(mask[atom3] & groupbit)) continue; if (atom4 < 0 || !(mask[atom4] & groupbit)) continue; - if (flag) { + if (!flag) { + m++; + continue; + } - // phi calculation from dihedral style harmonic + // phi calculation from dihedral style harmonic - if (pflag >= 0) { - vb1x = x[atom1][0] - x[atom2][0]; - vb1y = x[atom1][1] - x[atom2][1]; - vb1z = x[atom1][2] - x[atom2][2]; - domain->minimum_image(vb1x,vb1y,vb1z); + vb1x = x[atom1][0] - x[atom2][0]; + vb1y = x[atom1][1] - x[atom2][1]; + vb1z = x[atom1][2] - x[atom2][2]; + domain->minimum_image(vb1x,vb1y,vb1z); - vb2x = x[atom3][0] - x[atom2][0]; - vb2y = x[atom3][1] - x[atom2][1]; - vb2z = x[atom3][2] - x[atom2][2]; - domain->minimum_image(vb2x,vb2y,vb2z); + vb2x = x[atom3][0] - x[atom2][0]; + vb2y = x[atom3][1] - x[atom2][1]; + vb2z = x[atom3][2] - x[atom2][2]; + domain->minimum_image(vb2x,vb2y,vb2z); - vb2xm = -vb2x; - vb2ym = -vb2y; - vb2zm = -vb2z; - domain->minimum_image(vb2xm,vb2ym,vb2zm); + vb2xm = -vb2x; + vb2ym = -vb2y; + vb2zm = -vb2z; + domain->minimum_image(vb2xm,vb2ym,vb2zm); - vb3x = x[atom4][0] - x[atom3][0]; - vb3y = x[atom4][1] - x[atom3][1]; - vb3z = x[atom4][2] - x[atom3][2]; - domain->minimum_image(vb3x,vb3y,vb3z); + vb3x = x[atom4][0] - x[atom3][0]; + vb3y = x[atom4][1] - x[atom3][1]; + vb3z = x[atom4][2] - x[atom3][2]; + domain->minimum_image(vb3x,vb3y,vb3z); - ax = vb1y*vb2zm - vb1z*vb2ym; - ay = vb1z*vb2xm - vb1x*vb2zm; - az = vb1x*vb2ym - vb1y*vb2xm; - bx = vb3y*vb2zm - vb3z*vb2ym; - by = vb3z*vb2xm - vb3x*vb2zm; - bz = vb3x*vb2ym - vb3y*vb2xm; + ax = vb1y*vb2zm - vb1z*vb2ym; + ay = vb1z*vb2xm - vb1x*vb2zm; + az = vb1x*vb2ym - vb1y*vb2xm; + bx = vb3y*vb2zm - vb3z*vb2ym; + by = vb3z*vb2xm - vb3x*vb2zm; + bz = vb3x*vb2ym - vb3y*vb2xm; - rasq = ax*ax + ay*ay + az*az; - rbsq = bx*bx + by*by + bz*bz; - rgsq = vb2xm*vb2xm + vb2ym*vb2ym + vb2zm*vb2zm; - rg = sqrt(rgsq); + rasq = ax*ax + ay*ay + az*az; + rbsq = bx*bx + by*by + bz*bz; + rgsq = vb2xm*vb2xm + vb2ym*vb2ym + vb2zm*vb2zm; + rg = sqrt(rgsq); - ra2inv = rb2inv = 0.0; - if (rasq > 0) ra2inv = 1.0/rasq; - if (rbsq > 0) rb2inv = 1.0/rbsq; - rabinv = sqrt(ra2inv*rb2inv); + ra2inv = rb2inv = 0.0; + if (rasq > 0) ra2inv = 1.0/rasq; + if (rbsq > 0) rb2inv = 1.0/rbsq; + rabinv = sqrt(ra2inv*rb2inv); + + c = (ax*bx + ay*by + az*bz)*rabinv; + s = rg*rabinv*(ax*vb3x + ay*vb3y + az*vb3z); + + if (c > 1.0) c = 1.0; + if (c < -1.0) c = -1.0; + phi = atan2(s,c); - c = (ax*bx + ay*by + az*bz)*rabinv; - s = rg*rabinv*(ax*vb3x + ay*vb3y + az*vb3z); + if (nvalues == 1) ptr = &vlocal[m]; + else ptr = alocal[m]; + + if (nvar) { + ivar = 0; + if (pstr) input->variable->internal_set(pvar,phi); + } - if (c > 1.0) c = 1.0; - if (c < -1.0) c = -1.0; - pbuf[n] = 180.0*atan2(s,c)/MY_PI; + for (n = 0; n < nvalues; n++) { + switch (bstyle[n]) { + case PHI: + ptr[n] = 180.0*phi/MY_PI; + break; + case VARIABLE: + ptr[n] = input->variable->compute_equal(vvar[ivar]); + ivar++; + break; } - n += nvalues; } m++; diff --git a/src/compute_dihedral_local.h b/src/compute_dihedral_local.h index c077e52dbd..d5f6a64183 100644 --- a/src/compute_dihedral_local.h +++ b/src/compute_dihedral_local.h @@ -33,8 +33,12 @@ class ComputeDihedralLocal : public Compute { double memory_usage(); private: - int nvalues,pflag; - int ncount; + int nvalues,nvar,ncount,setflag,tflag; + + int pvar; + int *bstyle,*vvar; + char *pstr; + char **vstr; int nmax; double *vlocal; From 037420b611979f5fca9a1aeb360824294cb8ae64 Mon Sep 17 00:00:00 2001 From: Christoph Junghans Date: Tue, 4 Sep 2018 14:59:30 -0600 Subject: [PATCH 127/302] cmake: only add tests if exe is build --- cmake/CMakeLists.txt | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index 0d8da8409d..d4701102f7 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -207,7 +207,7 @@ endif() option(CMAKE_VERBOSE_MAKEFILE "Verbose makefile" OFF) option(ENABLE_TESTING "Enable testing" OFF) -if(ENABLE_TESTING) +if(ENABLE_TESTING AND BUILD_EXE) enable_testing() option(LAMMPS_TESTING_SOURCE_DIR "Location of lammps-testing source directory" "") option(LAMMPS_TESTING_GIT_TAG "Git tag of lammps-testing" "master") @@ -252,7 +252,7 @@ if(ENABLE_TESTING) message(STATUS "Found ${NUM_TESTS} tests.") endif() -endif(ENABLE_TESTING) +endif() set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE GRANULAR KSPACE MANYBODY MC MEAM MESSAGE MISC MOLECULE PERI REAX REPLICA RIGID SHOCK SPIN SNAP From db7c2549d064c61c6f8b6a62acea5f04aa33e470 Mon Sep 17 00:00:00 2001 From: Christoph Junghans Date: Tue, 4 Sep 2018 17:05:59 -0600 Subject: [PATCH 128/302] cmake: inject with-pic into Scafacos --- cmake/CMakeLists.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index b7bbd6e1ba..fcc547c5b1 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -416,6 +416,7 @@ if(PKG_USER-SCAFACOS) --with-internal-fftw --with-internal-pfft --with-internal-pnfft + $<$:--with-pic> FC=${CMAKE_MPI_Fortran_COMPILER} CXX=${CMAKE_MPI_CXX_COMPILER} CC=${CMAKE_MPI_C_COMPILER} From 8608b4f93c8e66d3e518c2ba783b775d978d6034 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Tue, 4 Sep 2018 21:31:08 -0400 Subject: [PATCH 129/302] Remove extra libm in LAMMPS_LINK_LIBS --- cmake/CMakeLists.txt | 1 - 1 file changed, 1 deletion(-) diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index fcc547c5b1..e0f8d08a25 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -434,7 +434,6 @@ if(PKG_USER-SCAFACOS) list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_p2nfft.a) list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_p3m.a) list(APPEND LAMMPS_LINK_LIBS ${GSL_LIBRARIES}) - list(APPEND LAMMPS_LINK_LIBS m) list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_near.a) list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_gridsort.a) list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_resort.a) From a5f7b418dea73439d6cb4a56ccec4f312b582263 Mon Sep 17 00:00:00 2001 From: jrgissing Date: Tue, 4 Sep 2018 22:06:49 -0600 Subject: [PATCH 130/302] bond/react: efficient competing reactions --- src/USER-MISC/fix_bond_react.cpp | 25 ++++++++++++++++++------- src/comm.h | 3 +++ src/comm_brick.cpp | 31 ++++++++++++++++++++++++++++++- src/comm_brick.h | 2 ++ 4 files changed, 53 insertions(+), 8 deletions(-) diff --git a/src/USER-MISC/fix_bond_react.cpp b/src/USER-MISC/fix_bond_react.cpp index 5ce1f11475..f369a9a10f 100644 --- a/src/USER-MISC/fix_bond_react.cpp +++ b/src/USER-MISC/fix_bond_react.cpp @@ -1858,16 +1858,27 @@ if so, flag for broadcasting for perusal by all processors void FixBondReact::glove_ghostcheck() { - // it appears this little loop was deemed important enough for its own function! - // noteworthy: it's only relevant for parallel - // here we add glove to either local_mega_glove or ghostly_mega_glove + // ghostly_mega_glove includes atoms that are ghosts, either of this proc or another + // 'ghosts of another' indication taken from comm->sendlist + int ghostly = 0; - for (int i = 0; i < onemol->natoms; i++) { - if (atom->map(glove[i][1]) >= atom->nlocal) { - ghostly = 1; - break; + if (comm->style == 0) { + int tmp; + int *localsendlist = (int *) comm->extract("localsendlist",tmp); + + // create an indexed sendlist + for (int i = 0; i < onemol->natoms; i++) { + int ilocal = atom->map(glove[i][1]); + if (ilocal >= atom->nlocal || localsendlist[ilocal] == 1) { + ghostly = 1; + break; + } } + } else { + #if !defined(MPI_STUBS) + ghostly = 1; + #endif } if (ghostly == 1) { diff --git a/src/comm.h b/src/comm.h index 298f435c3d..2579f9b283 100644 --- a/src/comm.h +++ b/src/comm.h @@ -112,6 +112,9 @@ class Comm : protected Pointers { int read_lines_from_file(FILE *, int, int, char *); int read_lines_from_file_universe(FILE *, int, int, char *); + // extract data useful to other classes + virtual void *extract(const char *, int &) {return NULL;} + protected: int bordergroup; // only communicate this group in borders diff --git a/src/comm_brick.cpp b/src/comm_brick.cpp index 3aa6d7748c..d179475345 100644 --- a/src/comm_brick.cpp +++ b/src/comm_brick.cpp @@ -55,7 +55,8 @@ CommBrick::CommBrick(LAMMPS *lmp) : size_reverse_send(NULL), size_reverse_recv(NULL), slablo(NULL), slabhi(NULL), multilo(NULL), multihi(NULL), cutghostmulti(NULL), pbc_flag(NULL), pbc(NULL), firstrecv(NULL), - sendlist(NULL), maxsendlist(NULL), buf_send(NULL), buf_recv(NULL) + sendlist(NULL), localsendlist(NULL), maxsendlist(NULL), + buf_send(NULL), buf_recv(NULL) { style = 0; layout = Comm::LAYOUT_UNIFORM; @@ -74,6 +75,7 @@ CommBrick::~CommBrick() } if (sendlist) for (int i = 0; i < maxswap; i++) memory->destroy(sendlist[i]); + if (localsendlist) memory->destroy(localsendlist); memory->sfree(sendlist); memory->destroy(maxsendlist); @@ -1469,6 +1471,33 @@ void CommBrick::free_multi() multilo = multihi = NULL; } +/* ---------------------------------------------------------------------- + extract data potentially useful to other classes +------------------------------------------------------------------------- */ + +void *CommBrick::extract(const char *str, int &dim) +{ + if (strcmp(str,"localsendlist") == 0) { + int i, iswap, isend; + if (!localsendlist) + memory->create(localsendlist,atom->nlocal,"comm:localsendlist"); + else + memory->grow(localsendlist,atom->nlocal,"comm:localsendlist"); + + for (i = 0; i < atom->nlocal; i++) + localsendlist[i] = 0; + + for (iswap = 0; iswap < nswap; iswap++) + for (isend = 0; isend < sendnum[iswap]; isend++) + if (sendlist[iswap][isend] < atom->nlocal) + localsendlist[sendlist[iswap][isend]] = 1; + + return (void *) localsendlist; + } + + return NULL; +} + /* ---------------------------------------------------------------------- return # of bytes of allocated memory ------------------------------------------------------------------------- */ diff --git a/src/comm_brick.h b/src/comm_brick.h index 461ee84b40..b3a3a7e094 100644 --- a/src/comm_brick.h +++ b/src/comm_brick.h @@ -46,6 +46,7 @@ class CommBrick : public Comm { void forward_comm_array(int, double **); // forward comm of array int exchange_variable(int, double *, double *&); // exchange on neigh stencil + void *extract(const char *,int &); virtual bigint memory_usage(); protected: @@ -67,6 +68,7 @@ class CommBrick : public Comm { int *firstrecv; // where to put 1st recv atom in each swap int **sendlist; // list of atoms to send in each swap + int *localsendlist; // indexed list of local sendlist atoms int *maxsendlist; // max size of send list for each swap double *buf_send; // send buffer for all comm From ae7b18fb772c17c6df105ba7f1f76fac420e998d Mon Sep 17 00:00:00 2001 From: jrgissing Date: Wed, 5 Sep 2018 00:11:50 -0600 Subject: [PATCH 131/302] only one call to extract needed --- src/USER-MISC/fix_bond_react.cpp | 8 ++++---- src/USER-MISC/fix_bond_react.h | 1 + 2 files changed, 5 insertions(+), 4 deletions(-) diff --git a/src/USER-MISC/fix_bond_react.cpp b/src/USER-MISC/fix_bond_react.cpp index 469e1d6347..a6f08a7376 100644 --- a/src/USER-MISC/fix_bond_react.cpp +++ b/src/USER-MISC/fix_bond_react.cpp @@ -961,6 +961,10 @@ void FixBondReact::superimpose_algorithm() local_num_mega = 0; ghostly_num_mega = 0; + // indicates local ghosts of other procs + int tmp; + localsendlist = (int *) comm->extract("localsendlist",tmp); + // quick description of important global indices you'll see floating about: // 'pion' is the pioneer loop index // 'neigh' in the first neighbor index @@ -1863,10 +1867,6 @@ void FixBondReact::glove_ghostcheck() int ghostly = 0; if (comm->style == 0) { - int tmp; - int *localsendlist = (int *) comm->extract("localsendlist",tmp); - - // create an indexed sendlist for (int i = 0; i < onemol->natoms; i++) { int ilocal = atom->map(glove[i][1]); if (ilocal >= atom->nlocal || localsendlist[ilocal] == 1) { diff --git a/src/USER-MISC/fix_bond_react.h b/src/USER-MISC/fix_bond_react.h index 8ff71141f8..08756f8131 100644 --- a/src/USER-MISC/fix_bond_react.h +++ b/src/USER-MISC/fix_bond_react.h @@ -122,6 +122,7 @@ class FixBondReact : public Fix { tagint **local_mega_glove; // consolidation local of reaction instances tagint **ghostly_mega_glove; // consolidation nonlocal of reaction instances tagint **global_mega_glove; // consolidation (inter-processor) of gloves containing nonlocal atoms + int *localsendlist; // indicates ghosts of other procs int local_num_mega; // num of local reaction instances int ghostly_num_mega; // num of ghostly reaction instances int global_megasize; // num of reaction instances in global_mega_glove From d3d16882ca562b51476e7037949c6fdbfc260da5 Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Wed, 5 Sep 2018 08:12:19 -0600 Subject: [PATCH 132/302] remove note for Rene --- examples/USER/scafacos/README | 10 ---------- 1 file changed, 10 deletions(-) delete mode 100644 examples/USER/scafacos/README diff --git a/examples/USER/scafacos/README b/examples/USER/scafacos/README deleted file mode 100644 index 0ddd19d3ee..0000000000 --- a/examples/USER/scafacos/README +++ /dev/null @@ -1,10 +0,0 @@ -RENE: this dir needs a few short-running examples, -for both 1 and 4 procs, of using different Scafacos methods. -with sample log file outputs - so users can verify -they are running it correctly - -For each input script, there should be files like - -in.scafacos.fmm -log.20Jul18.scafacos.fmm.g++.1 -log.20Jul18.scafacos.fmm.g++.4 From 4a5e28af81ff62f33ca603fda26ebf609f3c4a2e Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 5 Sep 2018 10:32:11 -0400 Subject: [PATCH 133/302] Avoid unnecessary sorting in print_columns std::map is a sorted associative container. We don't need to first copy it into a vector and sort that one. print_columns has been refactored as a template function and makes use of this property. --- src/info.cpp | 156 ++++++++++----------------------------------------- 1 file changed, 30 insertions(+), 126 deletions(-) diff --git a/src/info.cpp b/src/info.cpp index 748354e878..672ce72b74 100644 --- a/src/info.cpp +++ b/src/info.cpp @@ -44,7 +44,7 @@ #include "error.h" #include -#include +#include #include #include @@ -117,7 +117,8 @@ static const char bstyles[] = "pfsm"; using namespace LAMMPS_NS; using namespace std; -static void print_columns(FILE* fp, vector & styles); +template +static void print_columns(FILE* fp, map * styles); /* ---------------------------------------------------------------------- */ @@ -686,196 +687,98 @@ void Info::available_styles(FILE * out, int flags) void Info::atom_styles(FILE * out) { fprintf(out, "\nAtom styles:\n"); - - vector styles; - - for(Atom::AtomVecCreatorMap::iterator it = atom->avec_map->begin(); it != atom->avec_map->end(); ++it) { - styles.push_back(it->first); - } - - print_columns(out, styles); + print_columns(out, atom->avec_map); fprintf(out, "\n\n\n"); } void Info::integrate_styles(FILE * out) { fprintf(out, "\nIntegrate styles:\n"); - - vector styles; - - for(Update::IntegrateCreatorMap::iterator it = update->integrate_map->begin(); it != update->integrate_map->end(); ++it) { - styles.push_back(it->first); - } - - print_columns(out, styles); + print_columns(out, update->integrate_map); fprintf(out, "\n\n\n"); } void Info::minimize_styles(FILE * out) { fprintf(out, "\nMinimize styles:\n"); - - vector styles; - - for(Update::MinimizeCreatorMap::iterator it = update->minimize_map->begin(); it != update->minimize_map->end(); ++it) { - styles.push_back(it->first); - } - - print_columns(out, styles); + print_columns(out, update->minimize_map); fprintf(out, "\n\n\n"); } void Info::pair_styles(FILE * out) { fprintf(out, "\nPair styles:\n"); - - vector styles; - - for(Force::PairCreatorMap::iterator it = force->pair_map->begin(); it != force->pair_map->end(); ++it) { - styles.push_back(it->first); - } - - print_columns(out, styles); + print_columns(out, force->pair_map); fprintf(out, "\n\n\n"); } void Info::bond_styles(FILE * out) { fprintf(out, "\nBond styles:\n"); - - vector styles; - - for(Force::BondCreatorMap::iterator it = force->bond_map->begin(); it != force->bond_map->end(); ++it) { - styles.push_back(it->first); - } - - print_columns(out, styles); + print_columns(out, force->bond_map); fprintf(out, "\n\n\n"); } void Info::angle_styles(FILE * out) { fprintf(out, "\nAngle styles:\n"); - - vector styles; - - for(Force::AngleCreatorMap::iterator it = force->angle_map->begin(); it != force->angle_map->end(); ++it) { - styles.push_back(it->first); - } - - print_columns(out, styles); + print_columns(out, force->angle_map); fprintf(out, "\n\n\n"); } void Info::dihedral_styles(FILE * out) { fprintf(out, "\nDihedral styles:\n"); - - vector styles; - - for(Force::DihedralCreatorMap::iterator it = force->dihedral_map->begin(); it != force->dihedral_map->end(); ++it) { - styles.push_back(it->first); - } - - print_columns(out, styles); + print_columns(out, force->dihedral_map); fprintf(out, "\n\n\n"); } void Info::improper_styles(FILE * out) { fprintf(out, "\nImproper styles:\n"); - - vector styles; - - for(Force::ImproperCreatorMap::iterator it = force->improper_map->begin(); it != force->improper_map->end(); ++it) { - styles.push_back(it->first); - } - - print_columns(out, styles); + print_columns(out, force->improper_map); fprintf(out, "\n\n\n"); } void Info::kspace_styles(FILE * out) { fprintf(out, "\nKSpace styles:\n"); - - vector styles; - - for(Force::KSpaceCreatorMap::iterator it = force->kspace_map->begin(); it != force->kspace_map->end(); ++it) { - styles.push_back(it->first); - } - - print_columns(out, styles); + print_columns(out, force->kspace_map); fprintf(out, "\n\n\n"); } void Info::fix_styles(FILE * out) { fprintf(out, "\nFix styles:\n"); - - vector styles; - - for(Modify::FixCreatorMap::iterator it = modify->fix_map->begin(); it != modify->fix_map->end(); ++it) { - styles.push_back(it->first); - } - - print_columns(out, styles); + print_columns(out, modify->fix_map); fprintf(out, "\n\n\n"); } void Info::compute_styles(FILE * out) { fprintf(out, "\nCompute styles:\n"); - - vector styles; - - for(Modify::ComputeCreatorMap::iterator it = modify->compute_map->begin(); it != modify->compute_map->end(); ++it) { - styles.push_back(it->first); - } - - print_columns(out, styles); + print_columns(out, modify->compute_map); fprintf(out, "\n\n\n"); } void Info::region_styles(FILE * out) { fprintf(out, "\nRegion styles:\n"); - - vector styles; - - for(Domain::RegionCreatorMap::iterator it = domain->region_map->begin(); it != domain->region_map->end(); ++it) { - styles.push_back(it->first); - } - - print_columns(out, styles); + print_columns(out, domain->region_map); fprintf(out, "\n\n\n"); } void Info::dump_styles(FILE * out) { fprintf(out, "\nDump styles:\n"); - - vector styles; - - for(Output::DumpCreatorMap::iterator it = output->dump_map->begin(); it != output->dump_map->end(); ++it) { - styles.push_back(it->first); - } - - print_columns(out, styles); + print_columns(out, output->dump_map); fprintf(out, "\n\n\n"); } void Info::command_styles(FILE * out) { fprintf(out, "\nCommand styles (add-on input script commands):\n"); - - vector styles; - - for(Input::CommandCreatorMap::iterator it = input->command_map->begin(); it != input->command_map->end(); ++it) { - styles.push_back(it->first); - } - - print_columns(out, styles); + print_columns(out, input->command_map); fprintf(out, "\n\n\n"); } @@ -1110,41 +1013,42 @@ bool Info::is_defined(const char *category, const char *name) return false; } -static void print_columns(FILE* fp, vector & styles) +template +static void print_columns(FILE* fp, map * styles) { - if (styles.size() == 0) { + if (styles->empty()) { fprintf(fp, "\nNone"); return; } - std::sort(styles.begin(), styles.end()); - + // std::map keys are already sorted int pos = 80; - for (int i = 0; i < styles.size(); ++i) { + for(typename map::iterator it = styles->begin(); it != styles->end(); ++it) { + const string & style_name = it->first; // skip "secret" styles - if (isupper(styles[i][0])) continue; + if (isupper(style_name[0])) continue; - int len = styles[i].length(); + int len = style_name.length(); if (pos + len > 80) { fprintf(fp,"\n"); pos = 0; } if (len < 16) { - fprintf(fp,"%-16s",styles[i].c_str()); + fprintf(fp,"%-16s", style_name.c_str()); pos += 16; } else if (len < 32) { - fprintf(fp,"%-32s",styles[i].c_str()); + fprintf(fp,"%-32s", style_name.c_str()); pos += 32; } else if (len < 48) { - fprintf(fp,"%-48s",styles[i].c_str()); + fprintf(fp,"%-48s", style_name.c_str()); pos += 48; } else if (len < 64) { - fprintf(fp,"%-64s",styles[i].c_str()); + fprintf(fp,"%-64s", style_name.c_str()); pos += 64; } else { - fprintf(fp,"%-80s",styles[i].c_str()); + fprintf(fp,"%-80s", style_name.c_str()); pos += 80; } } From 0c92c22755c8b101022e7f5907ff10bacee3076d Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 5 Sep 2018 10:56:12 -0400 Subject: [PATCH 134/302] moved contents of USER-MOP package to USER-MISC as suggested by @sjplimp --- cmake/CMakeLists.txt | 2 +- doc/src/Packages_details.txt | 24 ------------- doc/src/Packages_user.txt | 1 - doc/src/compute_stress_mop.txt | 4 +-- .../USER/{ => misc}/mop/in.compute_stress_mop | 0 .../USER/{ => misc}/mop/moppz.time.reference | 0 .../USER/{ => misc}/mop/mopz0.time.reference | 0 .../USER/{ => misc}/mop/profile.z.reference | 0 src/Makefile | 2 +- src/USER-MISC/README | 2 ++ .../compute_stress_mop.cpp | 0 .../compute_stress_mop.h | 0 .../compute_stress_mop_profile.cpp | 0 .../compute_stress_mop_profile.h | 0 src/USER-MOP/README | 35 ------------------- 15 files changed, 6 insertions(+), 64 deletions(-) rename examples/USER/{ => misc}/mop/in.compute_stress_mop (100%) rename examples/USER/{ => misc}/mop/moppz.time.reference (100%) rename examples/USER/{ => misc}/mop/mopz0.time.reference (100%) rename examples/USER/{ => misc}/mop/profile.z.reference (100%) rename src/{USER-MOP => USER-MISC}/compute_stress_mop.cpp (100%) rename src/{USER-MOP => USER-MISC}/compute_stress_mop.h (100%) rename src/{USER-MOP => USER-MISC}/compute_stress_mop_profile.cpp (100%) rename src/{USER-MOP => USER-MISC}/compute_stress_mop_profile.h (100%) delete mode 100644 src/USER-MOP/README diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index 190ef3b2e0..eecdc6d132 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -215,7 +215,7 @@ set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE GRANULAR SRD KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-MESO USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD USER-LB USER-MANIFOLD USER-MEAMC USER-MGPT USER-MISC - USER-MOP USER-MOFFF USER-MOLFILE USER-NETCDF USER-PHONON USER-QTB USER-REAXC + USER-MOFFF USER-MOLFILE USER-NETCDF USER-PHONON USER-QTB USER-REAXC USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM) set(ACCEL_PACKAGES USER-OMP KOKKOS OPT USER-INTEL GPU) set(OTHER_PACKAGES CORESHELL QEQ) diff --git a/doc/src/Packages_details.txt b/doc/src/Packages_details.txt index 36071064c0..381dc2e995 100644 --- a/doc/src/Packages_details.txt +++ b/doc/src/Packages_details.txt @@ -84,7 +84,6 @@ as contained in the file name. "USER-MGPT"_#PKG-USER-MGPT, "USER-MISC"_#PKG-USER-MISC, "USER-MOFFF"_#PKG-USER-MOFFF, -"USER-MOP"_#PKG-USER-MOP, "USER-MOLFILE"_#PKG-USER-MOLFILE, "USER-NETCDF"_#PKG-USER-NETCDF, "USER-OMP"_#PKG-USER-OMP, @@ -1573,29 +1572,6 @@ examples/USER/mofff :ul :line -USER-MOP package :link(PKG-USER-MOP),h4 - -[Contents:] - -This package contains two compute styles: compute stress/mop and compute stress/mop/profile. - -compute stress/mop calculates components of the local stress tensor using the method of planes, applied on one plane. - -compute stress/mop/profile calculates profiles of components of the local stress tensor using the method of planes, applied on an array of regularly spaced planes. - -[Author:] Laurent Joly (University of Lyon 1) -Romain Vermorel at (University of Pau and Pays de l'Adour) - -[Supporting info:] - -src/USER-MOP: filenames -> commands -src/USER-MOP/README -"compute stress/mop"_compute_stress_mop.html -"compute stress/mop/profile"_compute_stress_mop.html -examples/USER/mop :ul - -:line - USER-MOLFILE package :link(PKG-USER-MOLFILE),h4 [Contents:] diff --git a/doc/src/Packages_user.txt b/doc/src/Packages_user.txt index 5b9b8734b3..7db2fa895c 100644 --- a/doc/src/Packages_user.txt +++ b/doc/src/Packages_user.txt @@ -57,7 +57,6 @@ Package, Description, Doc page, Example, Library "USER-MESO"_Packages_details.html#PKG-USER-MESO, mesoscale DPD models, "pair_style edpd"_pair_meso.html, USER/meso, no "USER-MGPT"_Packages_details.html#PKG-USER-MGPT, fast MGPT multi-ion potentials, "pair_style mgpt"_pair_mgpt.html, USER/mgpt, no "USER-MISC"_Packages_details.html#PKG-USER-MISC, single-file contributions, USER-MISC/README, USER/misc, no -"USER-MOP"_Packages_details.html#PKG-USER-MOP, compute stress via method-of-planes, "compute_style stress/mop"_compute_stress_mop.html, USER/mop, no "USER-MOFFF"_Packages_details.html#PKG-USER-MOFFF, styles for "MOF-FF"_MOFplus force field, "pair_style buck6d/coul/gauss"_pair_buck6d_coul_gauss.html, USER/mofff, no "USER-MOLFILE"_Packages_details.html#PKG-USER-MOLFILE, "VMD"_https://www.ks.uiuc.edu/Research/vmd/ molfile plug-ins,"dump molfile"_dump_molfile.html, n/a, ext "USER-NETCDF"_Packages_details.html#PKG-USER-NETCDF, dump output via NetCDF,"dump netcdf"_dump_netcdf.html, n/a, ext diff --git a/doc/src/compute_stress_mop.txt b/doc/src/compute_stress_mop.txt index 8d95ef42e2..1006463179 100644 --- a/doc/src/compute_stress_mop.txt +++ b/doc/src/compute_stress_mop.txt @@ -86,8 +86,8 @@ The values produced by this compute can be accessed by various "output commands" [Restrictions:] -This style is part of the USER-MOP package. It is only enabled if LAMMPS -is built with that package. See the "Build package"_Build_package.html +These styles are part of the USER-MISC package. They are only enabled if +LAMMPS is built with that package. See the "Build package"_Build_package.html doc page on for more info. The method is only implemented for 3d orthogonal simulation boxes whose diff --git a/examples/USER/mop/in.compute_stress_mop b/examples/USER/misc/mop/in.compute_stress_mop similarity index 100% rename from examples/USER/mop/in.compute_stress_mop rename to examples/USER/misc/mop/in.compute_stress_mop diff --git a/examples/USER/mop/moppz.time.reference b/examples/USER/misc/mop/moppz.time.reference similarity index 100% rename from examples/USER/mop/moppz.time.reference rename to examples/USER/misc/mop/moppz.time.reference diff --git a/examples/USER/mop/mopz0.time.reference b/examples/USER/misc/mop/mopz0.time.reference similarity index 100% rename from examples/USER/mop/mopz0.time.reference rename to examples/USER/misc/mop/mopz0.time.reference diff --git a/examples/USER/mop/profile.z.reference b/examples/USER/misc/mop/profile.z.reference similarity index 100% rename from examples/USER/mop/profile.z.reference rename to examples/USER/misc/mop/profile.z.reference diff --git a/src/Makefile b/src/Makefile index 6b1a2bdb98..948d203cfe 100644 --- a/src/Makefile +++ b/src/Makefile @@ -60,7 +60,7 @@ PACKAGE = asphere body class2 colloid compress coreshell dipole gpu \ PACKUSER = user-atc user-awpmd user-bocs user-cgdna user-cgsdk user-colvars \ user-diffraction user-dpd user-drude user-eff user-fep user-h5md \ user-intel user-lb user-manifold user-meamc user-meso \ - user-mgpt user-misc user-mop user-mofff user-molfile \ + user-mgpt user-misc user-mofff user-molfile \ user-netcdf user-omp user-phonon user-qmmm user-qtb \ user-quip user-reaxc user-smd user-smtbq user-sph user-tally \ user-uef user-vtk diff --git a/src/USER-MISC/README b/src/USER-MISC/README index 0f9e7bf383..eb221c07db 100644 --- a/src/USER-MISC/README +++ b/src/USER-MISC/README @@ -30,6 +30,8 @@ compute ackland/atom, Gerolf Ziegenhain, gerolf at ziegenhain.com, 4 Oct 2007 compute basal/atom, Christopher Barrett, cdb333 at cavs.msstate.edu, 3 Mar 2013 compute cnp/atom, Paulo Branicio (USC), branicio at usc.edu, 31 May 2017 compute entropy/atom, Pablo Piaggi (EPFL), pablo.piaggi at epfl.ch, 15 June 2018 +compute stress/mop, Romain Vermorel (U Pau) & Laurent Joly (U Lyon), romain.vermorel at univ-pau.fr & ljoly.ulyon at gmail.com, 5 Sep 18 +compute stress/mop/profile, Romain Vermorel (U Pau) & Laurent Joly (U Lyon), romain.vermorel at univ-pau.fr & ljoly.ulyon at gmail.com, 5 Sep 18 compute temp/rotate, Laurent Joly (U Lyon), ljoly.ulyon at gmail.com, 8 Aug 11 compute PRESSURE/GREM, David Stelter, dstelter@bu.edu, 22 Nov 16 dihedral_style cosine/shift/exp, Carsten Svaneborg, science at zqex.dk, 8 Aug 11 diff --git a/src/USER-MOP/compute_stress_mop.cpp b/src/USER-MISC/compute_stress_mop.cpp similarity index 100% rename from src/USER-MOP/compute_stress_mop.cpp rename to src/USER-MISC/compute_stress_mop.cpp diff --git a/src/USER-MOP/compute_stress_mop.h b/src/USER-MISC/compute_stress_mop.h similarity index 100% rename from src/USER-MOP/compute_stress_mop.h rename to src/USER-MISC/compute_stress_mop.h diff --git a/src/USER-MOP/compute_stress_mop_profile.cpp b/src/USER-MISC/compute_stress_mop_profile.cpp similarity index 100% rename from src/USER-MOP/compute_stress_mop_profile.cpp rename to src/USER-MISC/compute_stress_mop_profile.cpp diff --git a/src/USER-MOP/compute_stress_mop_profile.h b/src/USER-MISC/compute_stress_mop_profile.h similarity index 100% rename from src/USER-MOP/compute_stress_mop_profile.h rename to src/USER-MISC/compute_stress_mop_profile.h diff --git a/src/USER-MOP/README b/src/USER-MOP/README deleted file mode 100644 index 15fcb3701a..0000000000 --- a/src/USER-MOP/README +++ /dev/null @@ -1,35 +0,0 @@ -USER-MOP -============ - -This package provides the stress/mop and stress/mop/profile compute styles. -See the doc page for compute stress/mop or compute stress/mop/profile command for how to use -them. - -PACKAGE DESCRIPTION -------------------- - -These are LAMMPS (http://lammps.sandia.gov/) compute styles that calculate -components of the local stress tensor using the method of planes as described in -the paper by Todd et al. (B. D. Todd, Denis J. Evans, and Peter J. Daivis: "Pressure -tensor for inhomogeneous fluids", Phys. Rev. E 52, 1627 (1995)). - -This package contains the source files of two compute styles: -* compute stress/mop calculates components of the local stress tensor using the method of planes, applied on one plane. -* compute stress/mop/profile calculates profiles of components of the local stress tensor using the method of planes, applied on an array of regularly spaced planes. - -The persons who created these files are Laurent Joly at University of Lyon 1 and Romain Vermorel at University of Pau and Pays de l'Adour. -Contact them directly if you have questions. - -Laurent Joly -Institut Lumière Matière -Université Lyon 1 et CNRS -43 boulevard du 11 novembre 1918 -69622 Villeurbanne Cedex -e-mail: laurent.joly@univ-lyon1.fr - -Romain Vermorel -Laboratory of Complex Fluids and their Reservoirs (LFCR) -Université de Pau et des Pays de l'Adour -Avenue de l'Université -64012 Pau -e-mail: romain.vermorel@univ-pau.fr From 779f1bd0b1c45d622982759c578446694b8e2872 Mon Sep 17 00:00:00 2001 From: Stefan Paquay Date: Wed, 5 Sep 2018 11:27:10 -0400 Subject: [PATCH 135/302] Fixes a bug in pair_morse_smooth_linear where the cutoff was not properly initialized. --- cmake/CMakeLists.txt | 84 +- cmake/FindLAMMPS.cmake.in | 48 + cmake/Modules/FindZMQ.cmake | 8 + cmake/pkgconfig/liblammps.pc.in | 6 +- doc/src/Build_extras.txt | 34 + doc/src/Build_package.txt | 1 + doc/src/Commands_all.txt | 2 + doc/src/Howto.txt | 4 +- doc/src/Howto_client_server.txt | 131 + doc/src/Howto_couple.txt | 14 +- doc/src/Manual.txt | 4 +- doc/src/Packages_details.txt | 29 +- doc/src/Packages_standard.txt | 1 + doc/src/Run_options.txt | 25 + doc/src/commands_list.txt | 2 + doc/src/fix_client_md.txt | 106 + doc/src/lammps.book | 5 + doc/src/message.txt | 162 + doc/src/server.txt | 71 + doc/src/server_mc.txt | 116 + doc/src/server_md.txt | 147 + examples/COUPLE/README | 5 + examples/COUPLE/lammps_mc/Makefile | 33 + examples/COUPLE/lammps_mc/README | 128 + examples/COUPLE/lammps_mc/in.mc | 7 + examples/COUPLE/lammps_mc/in.mc.server | 36 + .../COUPLE/lammps_mc/log.28Aug18.file.g++.1 | 254 + .../COUPLE/lammps_mc/log.28Aug18.file.g++.4 | 254 + .../COUPLE/lammps_mc/log.28Aug18.zmq.g++.1 | 254 + .../COUPLE/lammps_mc/log.28Aug18.zmq.g++.4 | 254 + examples/COUPLE/lammps_mc/mc.cpp | 263 + examples/COUPLE/lammps_mc/mc.h | 40 + examples/COUPLE/lammps_mc/random_park.cpp | 72 + examples/COUPLE/lammps_mc/random_park.h | 28 + examples/COUPLE/lammps_vasp/INCAR | 53 + examples/COUPLE/lammps_vasp/KPOINTS | 6 + examples/COUPLE/lammps_vasp/POSCAR_W | 11 + examples/COUPLE/lammps_vasp/README | 149 + examples/COUPLE/lammps_vasp/data.W | 15 + examples/COUPLE/lammps_vasp/in.client.W | 34 + examples/COUPLE/lammps_vasp/log.client.output | 76 + examples/COUPLE/lammps_vasp/vasp_wrap.py | 300 + examples/COUPLE/lammps_vasp/vasprun.xml | 12329 ++++++++++++++++ examples/README | 1 + examples/USER/diffraction/BulkNi.in | 5 +- examples/USER/diffraction/Output/BulkNi.in | 35 - examples/message/README | 117 + examples/message/Script.sh | 55 + examples/message/in.message | 29 + examples/message/in.message.client | 41 + examples/message/in.message.server | 29 + examples/message/in.message.tilt | 30 + examples/message/in.message.tilt.client | 42 + examples/message/in.message.tilt.server | 31 + .../log.28Aug18.message.client.file.g++.1 | 79 + .../log.28Aug18.message.client.file.g++.2 | 79 + .../log.28Aug18.message.client.mpione.g++.1 | 79 + .../log.28Aug18.message.client.mpione.g++.2 | 79 + .../log.28Aug18.message.client.mpitwo.g++.1 | 79 + .../log.28Aug18.message.client.mpitwo.g++.2 | 79 + .../log.28Aug18.message.client.zmq.g++.1 | 79 + .../log.28Aug18.message.client.zmq.g++.2 | 79 + examples/message/log.28Aug18.message.g++.1 | 85 + examples/message/log.28Aug18.message.g++.4 | 85 + .../log.28Aug18.message.server.file.g++.1 | 44 + .../log.28Aug18.message.server.file.g++.4 | 44 + .../log.28Aug18.message.server.mpione.g++.1 | 44 + .../log.28Aug18.message.server.mpione.g++.4 | 44 + .../log.28Aug18.message.server.mpitwo.g++.1 | 44 + .../log.28Aug18.message.server.mpitwo.g++.4 | 44 + .../log.28Aug18.message.server.zmq.g++.1 | 44 + .../log.28Aug18.message.server.zmq.g++.4 | 44 + ...g.28Aug18.message.tilt.client.mpione.g++.1 | 130 + ...g.28Aug18.message.tilt.client.mpione.g++.2 | 130 + ...g.28Aug18.message.tilt.client.mpitwo.g++.1 | 130 + ...g.28Aug18.message.tilt.client.mpitwo.g++.2 | 130 + .../log.28Aug18.message.tilt.client.zmq.g++.1 | 130 + .../log.28Aug18.message.tilt.client.zmq.g++.2 | 130 + .../message/log.28Aug18.message.tilt.g++.1 | 129 + .../message/log.28Aug18.message.tilt.g++.4 | 129 + ...g.28Aug18.message.tilt.server.mpione.g++.1 | 48 + ...g.28Aug18.message.tilt.server.mpione.g++.4 | 48 + ...g.28Aug18.message.tilt.server.mpitwo.g++.1 | 48 + ...g.28Aug18.message.tilt.server.mpitwo.g++.4 | 48 + .../log.28Aug18.message.tilt.server.zmq.g++.1 | 48 + .../log.28Aug18.message.tilt.server.zmq.g++.4 | 48 + lib/README | 2 + lib/message/Install.py | 118 + lib/message/Makefile.lammps.nozmq | 5 + lib/message/Makefile.lammps.zmq | 5 + lib/message/README | 51 + lib/message/cslib/LICENSE | 32 + lib/message/cslib/README | 23 + lib/message/cslib/src/Makefile | 107 + lib/message/cslib/src/STUBS_MPI/mpi.h | 96 + lib/message/cslib/src/STUBS_ZMQ/zmq.h | 36 + lib/message/cslib/src/cslib.cpp | 768 + lib/message/cslib/src/cslib.h | 87 + lib/message/cslib/src/cslib.py | 362 + lib/message/cslib/src/cslib_wrap.cpp | 239 + lib/message/cslib/src/cslib_wrap.f90 | 147 + lib/message/cslib/src/cslib_wrap.h | 54 + lib/message/cslib/src/msg.cpp | 110 + lib/message/cslib/src/msg.h | 52 + lib/message/cslib/src/msg_file.cpp | 143 + lib/message/cslib/src/msg_file.h | 40 + lib/message/cslib/src/msg_mpi_one.cpp | 82 + lib/message/cslib/src/msg_mpi_one.h | 38 + lib/message/cslib/src/msg_mpi_two.cpp | 81 + lib/message/cslib/src/msg_mpi_two.h | 35 + lib/message/cslib/src/msg_zmq.cpp | 140 + lib/message/cslib/src/msg_zmq.h | 38 + src/MESSAGE/Install.sh | 67 + src/MESSAGE/fix_client_md.cpp | 325 + src/MESSAGE/fix_client_md.h | 65 + src/MESSAGE/message.cpp | 90 + src/MESSAGE/message.h | 40 + src/MESSAGE/server.cpp | 50 + src/MESSAGE/server.h | 40 + src/MESSAGE/server_mc.cpp | 148 + src/MESSAGE/server_mc.h | 29 + src/MESSAGE/server_md.cpp | 389 + src/MESSAGE/server_md.h | 38 + src/Makefile | 6 +- src/USER-MISC/pair_morse_smooth_linear.cpp | 17 +- src/atom.cpp | 3 +- src/domain.cpp | 13 +- src/domain.h | 5 +- src/fix_tmd.cpp | 2 +- src/lammps.cpp | 231 +- src/lammps.h | 4 + src/library.cpp | 3 +- src/version.h | 2 +- 133 files changed, 22782 insertions(+), 172 deletions(-) create mode 100644 cmake/FindLAMMPS.cmake.in create mode 100644 cmake/Modules/FindZMQ.cmake create mode 100644 doc/src/Howto_client_server.txt create mode 100644 doc/src/fix_client_md.txt create mode 100644 doc/src/message.txt create mode 100644 doc/src/server.txt create mode 100644 doc/src/server_mc.txt create mode 100644 doc/src/server_md.txt create mode 100644 examples/COUPLE/lammps_mc/Makefile create mode 100644 examples/COUPLE/lammps_mc/README create mode 100644 examples/COUPLE/lammps_mc/in.mc create mode 100644 examples/COUPLE/lammps_mc/in.mc.server create mode 100644 examples/COUPLE/lammps_mc/log.28Aug18.file.g++.1 create mode 100644 examples/COUPLE/lammps_mc/log.28Aug18.file.g++.4 create mode 100644 examples/COUPLE/lammps_mc/log.28Aug18.zmq.g++.1 create mode 100644 examples/COUPLE/lammps_mc/log.28Aug18.zmq.g++.4 create mode 100644 examples/COUPLE/lammps_mc/mc.cpp create mode 100644 examples/COUPLE/lammps_mc/mc.h create mode 100644 examples/COUPLE/lammps_mc/random_park.cpp create mode 100644 examples/COUPLE/lammps_mc/random_park.h create mode 100644 examples/COUPLE/lammps_vasp/INCAR create mode 100644 examples/COUPLE/lammps_vasp/KPOINTS create mode 100644 examples/COUPLE/lammps_vasp/POSCAR_W create mode 100644 examples/COUPLE/lammps_vasp/README create mode 100644 examples/COUPLE/lammps_vasp/data.W create mode 100644 examples/COUPLE/lammps_vasp/in.client.W create mode 100644 examples/COUPLE/lammps_vasp/log.client.output create mode 100644 examples/COUPLE/lammps_vasp/vasp_wrap.py create mode 100644 examples/COUPLE/lammps_vasp/vasprun.xml delete mode 100644 examples/USER/diffraction/Output/BulkNi.in create mode 100644 examples/message/README create mode 100644 examples/message/Script.sh create mode 100644 examples/message/in.message create mode 100644 examples/message/in.message.client create mode 100644 examples/message/in.message.server create mode 100644 examples/message/in.message.tilt create mode 100644 examples/message/in.message.tilt.client create mode 100644 examples/message/in.message.tilt.server create mode 100644 examples/message/log.28Aug18.message.client.file.g++.1 create mode 100644 examples/message/log.28Aug18.message.client.file.g++.2 create mode 100644 examples/message/log.28Aug18.message.client.mpione.g++.1 create mode 100644 examples/message/log.28Aug18.message.client.mpione.g++.2 create mode 100644 examples/message/log.28Aug18.message.client.mpitwo.g++.1 create mode 100644 examples/message/log.28Aug18.message.client.mpitwo.g++.2 create mode 100644 examples/message/log.28Aug18.message.client.zmq.g++.1 create mode 100644 examples/message/log.28Aug18.message.client.zmq.g++.2 create mode 100644 examples/message/log.28Aug18.message.g++.1 create mode 100644 examples/message/log.28Aug18.message.g++.4 create mode 100644 examples/message/log.28Aug18.message.server.file.g++.1 create mode 100644 examples/message/log.28Aug18.message.server.file.g++.4 create mode 100644 examples/message/log.28Aug18.message.server.mpione.g++.1 create mode 100644 examples/message/log.28Aug18.message.server.mpione.g++.4 create mode 100644 examples/message/log.28Aug18.message.server.mpitwo.g++.1 create mode 100644 examples/message/log.28Aug18.message.server.mpitwo.g++.4 create mode 100644 examples/message/log.28Aug18.message.server.zmq.g++.1 create mode 100644 examples/message/log.28Aug18.message.server.zmq.g++.4 create mode 100644 examples/message/log.28Aug18.message.tilt.client.mpione.g++.1 create mode 100644 examples/message/log.28Aug18.message.tilt.client.mpione.g++.2 create mode 100644 examples/message/log.28Aug18.message.tilt.client.mpitwo.g++.1 create mode 100644 examples/message/log.28Aug18.message.tilt.client.mpitwo.g++.2 create mode 100644 examples/message/log.28Aug18.message.tilt.client.zmq.g++.1 create mode 100644 examples/message/log.28Aug18.message.tilt.client.zmq.g++.2 create mode 100644 examples/message/log.28Aug18.message.tilt.g++.1 create mode 100644 examples/message/log.28Aug18.message.tilt.g++.4 create mode 100644 examples/message/log.28Aug18.message.tilt.server.mpione.g++.1 create mode 100644 examples/message/log.28Aug18.message.tilt.server.mpione.g++.4 create mode 100644 examples/message/log.28Aug18.message.tilt.server.mpitwo.g++.1 create mode 100644 examples/message/log.28Aug18.message.tilt.server.mpitwo.g++.4 create mode 100644 examples/message/log.28Aug18.message.tilt.server.zmq.g++.1 create mode 100644 examples/message/log.28Aug18.message.tilt.server.zmq.g++.4 create mode 100644 lib/message/Install.py create mode 100644 lib/message/Makefile.lammps.nozmq create mode 100644 lib/message/Makefile.lammps.zmq create mode 100644 lib/message/README create mode 100644 lib/message/cslib/LICENSE create mode 100644 lib/message/cslib/README create mode 100644 lib/message/cslib/src/Makefile create mode 100644 lib/message/cslib/src/STUBS_MPI/mpi.h create mode 100644 lib/message/cslib/src/STUBS_ZMQ/zmq.h create mode 100644 lib/message/cslib/src/cslib.cpp create mode 100644 lib/message/cslib/src/cslib.h create mode 100644 lib/message/cslib/src/cslib.py create mode 100644 lib/message/cslib/src/cslib_wrap.cpp create mode 100644 lib/message/cslib/src/cslib_wrap.f90 create mode 100644 lib/message/cslib/src/cslib_wrap.h create mode 100644 lib/message/cslib/src/msg.cpp create mode 100644 lib/message/cslib/src/msg.h create mode 100644 lib/message/cslib/src/msg_file.cpp create mode 100644 lib/message/cslib/src/msg_file.h create mode 100644 lib/message/cslib/src/msg_mpi_one.cpp create mode 100644 lib/message/cslib/src/msg_mpi_one.h create mode 100644 lib/message/cslib/src/msg_mpi_two.cpp create mode 100644 lib/message/cslib/src/msg_mpi_two.h create mode 100644 lib/message/cslib/src/msg_zmq.cpp create mode 100644 lib/message/cslib/src/msg_zmq.h create mode 100644 src/MESSAGE/Install.sh create mode 100644 src/MESSAGE/fix_client_md.cpp create mode 100644 src/MESSAGE/fix_client_md.h create mode 100644 src/MESSAGE/message.cpp create mode 100644 src/MESSAGE/message.h create mode 100644 src/MESSAGE/server.cpp create mode 100644 src/MESSAGE/server.h create mode 100644 src/MESSAGE/server_mc.cpp create mode 100644 src/MESSAGE/server_mc.h create mode 100644 src/MESSAGE/server_md.cpp create mode 100644 src/MESSAGE/server_md.h diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index 3ef3e8d7f4..0d4bab29f1 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -43,6 +43,29 @@ function(validate_option name values) endif() endfunction(validate_option) +function(get_lammps_version version_header variable) + file(READ ${version_header} line) + set(MONTHS x Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec) + string(REGEX REPLACE "#define LAMMPS_VERSION \"([0-9]+) ([A-Za-z]+) ([0-9]+)\"" "\\1" day "${line}") + string(REGEX REPLACE "#define LAMMPS_VERSION \"([0-9]+) ([A-Za-z]+) ([0-9]+)\"" "\\2" month "${line}") + string(REGEX REPLACE "#define LAMMPS_VERSION \"([0-9]+) ([A-Za-z]+) ([0-9]+)\"" "\\3" year "${line}") + string(STRIP ${day} day) + string(STRIP ${month} month) + string(STRIP ${year} year) + list(FIND MONTHS "${month}" month) + string(LENGTH ${day} day_length) + string(LENGTH ${month} month_length) + if(day_length EQUAL 1) + set(day "0${day}") + endif() + if(month_length EQUAL 1) + set(month "0${month}") + endif() + set(${variable} "${year}${month}${day}" PARENT_SCOPE) +endfunction() + +get_lammps_version(${LAMMPS_SOURCE_DIR}/version.h LAMMPS_VERSION) + # Cmake modules/macros are in a subdirectory to keep this file cleaner set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/Modules) @@ -121,10 +144,10 @@ if(BUILD_LIB) if(BUILD_SHARED_LIBS) # for all pkg libs, mpi_stubs and linalg set(CMAKE_POSITION_INDEPENDENT_CODE ON) endif() - set(LIB_SUFFIX "" CACHE STRING "Suffix to append to liblammps and pkg-config file") - mark_as_advanced(LIB_SUFFIX) - if(LIB_SUFFIX) - set(LIB_SUFFIX "_${LIB_SUFFIX}") + set(LAMMPS_LIB_SUFFIX "" CACHE STRING "Suffix to append to liblammps and pkg-config file") + mark_as_advanced(LAMMPS_LIB_SUFFIX) + if(LAMMPS_LIB_SUFFIX) + set(LAMMPS_LIB_SUFFIX "_${LAMMPS_LIB_SUFFIX}") endif() endif() @@ -188,7 +211,7 @@ if(ENABLE_TESTING) endif(ENABLE_TESTING) set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE GRANULAR - KSPACE MANYBODY MC MEAM MISC MOLECULE PERI REAX REPLICA RIGID SHOCK SPIN SNAP + KSPACE MANYBODY MC MEAM MESSAGE MISC MOLECULE PERI REAX REPLICA RIGID SHOCK SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-MESO USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD USER-LB USER-MANIFOLD USER-MEAMC USER-MGPT USER-MISC @@ -481,6 +504,39 @@ if(PKG_KIM) include_directories(${KIM_INCLUDE_DIRS}) endif() +if(PKG_MESSAGE) + option(MESSAGE_ZMQ "Use ZeroMQ in MESSAGE package" OFF) + file(GLOB_RECURSE cslib_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/*.F + ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/*.c ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/*.cpp) + + if(BUILD_SHARED_LIBS) + add_library(cslib SHARED ${cslib_SOURCES}) + else() + add_library(cslib STATIC ${cslib_SOURCES}) + endif() + + if(BUILD_MPI) + target_compile_definitions(cslib PRIVATE -DMPI_YES) + set_target_properties(cslib PROPERTIES OUTPUT_NAME "csmpi") + else() + target_compile_definitions(cslib PRIVATE -DMPI_NO) + set_target_properties(cslib PROPERTIES OUTPUT_NAME "csnompi") + endif() + + if(MESSAGE_ZMQ) + target_compile_definitions(cslib PRIVATE -DZMQ_YES) + find_package(ZMQ REQUIRED) + target_include_directories(cslib PRIVATE ${ZMQ_INCLUDE_DIRS}) + target_link_libraries(cslib PUBLIC ${ZMQ_LIBRARIES}) + else() + target_compile_definitions(cslib PRIVATE -DZMQ_NO) + target_include_directories(cslib PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/src/STUBS_ZMQ) + endif() + + list(APPEND LAMMPS_LINK_LIBS cslib) + include_directories(${LAMMPS_LIB_SOURCE_DIR}/message/cslib/src) +endif() + if(PKG_MSCG) find_package(GSL REQUIRED) option(DOWNLOAD_MSCG "Download latte (instead of using the system's one)" OFF) @@ -1040,14 +1096,14 @@ if(BUILD_LIB) if(LAMMPS_DEPS) add_dependencies(lammps ${LAMMPS_DEPS}) endif() - set_target_properties(lammps PROPERTIES OUTPUT_NAME lammps${LIB_SUFFIX}) - if(BUILD_SHARED_LIBS) - set_target_properties(lammps PROPERTIES SOVERSION ${SOVERSION}) - install(TARGETS lammps LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}) - install(FILES ${LAMMPS_SOURCE_DIR}/library.h DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps) - configure_file(pkgconfig/liblammps.pc.in ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LIB_SUFFIX}.pc @ONLY) - install(FILES ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LIB_SUFFIX}.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig) - endif() + set_target_properties(lammps PROPERTIES OUTPUT_NAME lammps${LAMMPS_LIB_SUFFIX}) + set_target_properties(lammps PROPERTIES SOVERSION ${SOVERSION}) + install(TARGETS lammps LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}) + install(FILES ${LAMMPS_SOURCE_DIR}/library.h DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps) + configure_file(pkgconfig/liblammps.pc.in ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_LIB_SUFFIX}.pc @ONLY) + install(FILES ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_LIB_SUFFIX}.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig) + configure_file(FindLAMMPS.cmake.in ${CMAKE_CURRENT_BINARY_DIR}/FindLAMMPS${LAMMPS_LIB_SUFFIX}.cmake @ONLY) + install(FILES ${CMAKE_CURRENT_BINARY_DIR}/FindLAMMPS${LAMMPS_LIB_SUFFIX}.cmake DESTINATION ${CMAKE_INSTALL_DATADIR}/cmake/Module) else() list(APPEND LMP_SOURCES ${LIB_SOURCES}) endif() @@ -1177,7 +1233,7 @@ endif() ############################################################################### # Print package summary ############################################################################### -foreach(PKG ${DEFAULT_PACKAGES} ${ACCEL_PACKAGES}) +foreach(PKG ${DEFAULT_PACKAGES} ${ACCEL_PACKAGES} ${OTHER_PACKAGES}) if(PKG_${PKG}) message(STATUS "Building package: ${PKG}") endif() diff --git a/cmake/FindLAMMPS.cmake.in b/cmake/FindLAMMPS.cmake.in new file mode 100644 index 0000000000..586df83c2d --- /dev/null +++ b/cmake/FindLAMMPS.cmake.in @@ -0,0 +1,48 @@ +# - Find liblammps +# Find the native liblammps headers and libraries. +# +# The following variables will set: +# LAMMPS_INCLUDE_DIRS - where to find lammps/library.h, etc. +# LAMMPS_LIBRARIES - List of libraries when using lammps. +# LAMMPS_API_DEFINES - lammps library api defines +# LAMMPS_VERSION - lammps library version +# LAMMPS_FOUND - True if liblammps found. +# +# In addition a LAMMPS::LAMMPS imported target is getting created. +# +# LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator +# http://lammps.sandia.gov, Sandia National Laboratories +# Steve Plimpton, sjplimp@sandia.gov +# +# Copyright (2003) Sandia Corporation. Under the terms of Contract +# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains +# certain rights in this software. This software is distributed under +# the GNU General Public License. +# +# See the README file in the top-level LAMMPS directory. +# + +find_package(PkgConfig) + +pkg_check_modules(PC_LAMMPS liblammps@LAMMPS_LIB_SUFFIX@) +find_path(LAMMPS_INCLUDE_DIR lammps/library.h HINTS ${PC_LAMMPS_INCLUDE_DIRS} @CMAKE_INSTALL_FULL_INCLUDEDIR@) + +set(LAMMPS_VERSION @LAMMPS_VERSION@) +set(LAMMPS_API_DEFINES @LAMMPS_API_DEFINES@) + +find_library(LAMMPS_LIBRARY NAMES lammps@LAMMPS_LIB_SUFFIX@ HINTS ${PC_LAMMPS_LIBRARY_DIRS} @CMAKE_INSTALL_FULL_LIBDIR@) + +set(LAMMPS_INCLUDE_DIRS "${LAMMPS_INCLUDE_DIR}") +set(LAMMPS_LIBRARIES "${LAMMPS_LIBRARY}") + +include(FindPackageHandleStandardArgs) +# handle the QUIETLY and REQUIRED arguments and set LAMMPS_FOUND to TRUE +# if all listed variables are TRUE +find_package_handle_standard_args(LAMMPS REQUIRED_VARS LAMMPS_LIBRARY LAMMPS_INCLUDE_DIR VERSION_VAR LAMMPS_VERSION) + +mark_as_advanced(LAMMPS_INCLUDE_DIR LAMMPS_LIBRARY) + +if(LAMMPS_FOUND AND NOT TARGET LAMMPS::LAMMPS) + add_library(LAMMPS::LAMMPS UNKNOWN IMPORTED) + set_target_properties(LAMMPS::LAMMPS PROPERTIES IMPORTED_LOCATION "${LAMMPS_LIBRARY}" INTERFACE_INCLUDE_DIRECTORIES "${LAMMPS_INCLUDE_DIR}" INTERFACE_COMPILE_DEFINITIONS "${LAMMPS_API_DEFINES}") +endif() diff --git a/cmake/Modules/FindZMQ.cmake b/cmake/Modules/FindZMQ.cmake new file mode 100644 index 0000000000..608ccda777 --- /dev/null +++ b/cmake/Modules/FindZMQ.cmake @@ -0,0 +1,8 @@ +find_path(ZMQ_INCLUDE_DIR zmq.h) +find_library(ZMQ_LIBRARY NAMES zmq) + +set(ZMQ_LIBRARIES ${ZMQ_LIBRARY}) +set(ZMQ_INCLUDE_DIRS ${ZMQ_INCLUDE_DIR}) + +include(FindPackageHandleStandardArgs) +find_package_handle_standard_args(ZMQ DEFAULT_MSG ZMQ_LIBRARY ZMQ_INCLUDE_DIR) diff --git a/cmake/pkgconfig/liblammps.pc.in b/cmake/pkgconfig/liblammps.pc.in index 400b7593cf..7850972f3b 100644 --- a/cmake/pkgconfig/liblammps.pc.in +++ b/cmake/pkgconfig/liblammps.pc.in @@ -4,15 +4,15 @@ # after you added @CMAKE_INSTALL_FULL_LIBDIR@/pkg-config to PKG_CONFIG_PATH, # e.g. export PKG_CONFIG_PATH=@CMAKE_INSTALL_FULL_LIBDIR@/pkgconfig -prefix=@CMAKE_INSTALL_FULL_PREFIX@ +prefix=@CMAKE_INSTALL_PREFIX@ libdir=@CMAKE_INSTALL_FULL_LIBDIR@ includedir=@CMAKE_INSTALL_FULL_INCLUDEDIR@ Name: liblammps@LAMMPS_MACHINE@ Description: Large-scale Atomic/Molecular Massively Parallel Simulator Library URL: http://lammps.sandia.gov -Version: +Version: @LAMMPS_VERSION@ Requires: -Libs: -L${libdir} -llammps@LIB_SUFFIX@@ +Libs: -L${libdir} -llammps@LAMMPS_LIB_SUFFIX@ Libs.private: -lm Cflags: -I${includedir} @LAMMPS_API_DEFINES@ diff --git a/doc/src/Build_extras.txt b/doc/src/Build_extras.txt index 088ffd8972..1e3744b7fb 100644 --- a/doc/src/Build_extras.txt +++ b/doc/src/Build_extras.txt @@ -31,6 +31,7 @@ This is the list of packages that may require additional steps. "KOKKOS"_#kokkos, "LATTE"_#latte, "MEAM"_#meam, +"MESSAGE"_#message, "MSCG"_#mscg, "OPT"_#opt, "POEMS"_#poems, @@ -361,6 +362,10 @@ make lib-meam args="-m mpi" # build with default Fortran compiler compatible make lib-meam args="-m serial" # build with compiler compatible with "make serial" (GNU Fortran) make lib-meam args="-m ifort" # build with Intel Fortran compiler using Makefile.ifort :pre +NOTE: You should test building the MEAM library with both the Intel +and GNU compilers to see if a simulation runs faster with one versus +the other on your system. + The build should produce two files: lib/meam/libmeam.a and lib/meam/Makefile.lammps. The latter is copied from an existing Makefile.lammps.* and has settings needed to link C++ (LAMMPS) with @@ -373,6 +378,35 @@ file. :line +MESSAGE package :h4,link(message) + +This package can optionally include support for messaging via sockets, +using the open-source "ZeroMQ library"_http://zeromq.org, which must +be installed on your system. + +[CMake build]: + +-D MESSAGE_ZMQ=value # build with ZeroMQ support, value = no (default) or yes + +[Traditional make]: + +Before building LAMMPS, you must build the CSlib library in +lib/message. You can build the CSlib library manually if you prefer; +follow the instructions in lib/message/README. You can also do it in +one step from the lammps/src dir, using a command like these, which +simply invoke the lib/message/Install.py script with the specified args: + +make lib-message # print help message +make lib-message args="-m -z" # build with MPI and socket (ZMQ) support +make lib-message args="-s" # build as serial lib with no ZMQ support + +The build should produce two files: lib/message/cslib/src/libmessage.a +and lib/message/Makefile.lammps. The latter is copied from an +existing Makefile.lammps.* and has settings to link with the ZeroMQ +library if requested in the build. + +:line + MSCG package :h4,link(mscg) To build with this package, you must download and build the MS-CG diff --git a/doc/src/Build_package.txt b/doc/src/Build_package.txt index 4f71e9eb18..aaa340f302 100644 --- a/doc/src/Build_package.txt +++ b/doc/src/Build_package.txt @@ -42,6 +42,7 @@ packages: "KOKKOS"_Build_extras.html#kokkos, "LATTE"_Build_extras.html#latte, "MEAM"_Build_extras.html#meam, +"MESSAGE"_#Build_extras.html#message, "MSCG"_Build_extras.html#mscg, "OPT"_Build_extras.html#opt, "POEMS"_Build_extras.html#poems, diff --git a/doc/src/Commands_all.txt b/doc/src/Commands_all.txt index aec5a9db8b..6f54681342 100644 --- a/doc/src/Commands_all.txt +++ b/doc/src/Commands_all.txt @@ -71,6 +71,7 @@ An alphabetic list of all LAMMPS commands. "lattice"_lattice.html, "log"_log.html, "mass"_mass.html, +"message"_message.html, "minimize"_minimize.html, "min_modify"_min_modify.html, "min_style"_min_style.html, @@ -103,6 +104,7 @@ An alphabetic list of all LAMMPS commands. "restart"_restart.html, "run"_run.html, "run_style"_run_style.html, +"server"_server.html, "set"_set.html, "shell"_shell.html, "special_bonds"_special_bonds.html, diff --git a/doc/src/Howto.txt b/doc/src/Howto.txt index 438ea561a1..730b492699 100644 --- a/doc/src/Howto.txt +++ b/doc/src/Howto.txt @@ -54,6 +54,7 @@ General howto :h3 Howto_replica Howto_library Howto_couple + Howto_client_server END_RST --> @@ -64,7 +65,8 @@ END_RST --> "Run multiple simulations from one input script"_Howto_multiple.html "Multi-replica simulations"_Howto_replica.html "Library interface to LAMMPS"_Howto_library.html -"Couple LAMMPS to other codes"_Howto_couple.html :all(b) +"Couple LAMMPS to other codes"_Howto_couple.html +"Using LAMMPS in client/server mode"_Howto_client_server.html :all(b) diff --git a/doc/src/Howto_client_server.txt b/doc/src/Howto_client_server.txt new file mode 100644 index 0000000000..714c23f066 --- /dev/null +++ b/doc/src/Howto_client_server.txt @@ -0,0 +1,131 @@ +"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Using LAMMPS in client/server mode + +Client/server coupling of two codes is where one code is the "client" +and sends request messages to a "server" code. The server responds to +each request with a reply message. This enables the two codes to work +in tandem to perform a simulation. LAMMPS can act as either a client +or server code. + +Some advantages of client/server coupling are that the two codes run +as stand-alone executables; they are not linked together. Thus +neither code needs to have a library interface. This often makes it +easier to run the two codes on different numbers of processors. If a +message protocol (format and content) is defined for a particular kind +of simulation, then in principle any code that implements the +client-side protocol can be used in tandem with any code that +implements the server-side protocol, without the two codes needing to +know anything more specific about each other. + +A simple example of client/server coupling is where LAMMPS is the +client code performing MD timestepping. Each timestep it sends a +message to a server quantum code containing current coords of all the +atoms. The quantum code computes energy and forces based on the +coords. It returns them as a message to LAMMPS, which completes the +timestep. + +Alternate methods for code coupling with LAMMPS are described on +the "Howto couple"_Howto_couple.html doc page. + +LAMMPS support for client/server coupling is in its "MESSAGE +package"_Packages_details.html#PKG-MESSAGE which implements several +commands that enable LAMMPS to act as a client or server, as discussed +below. The MESSAGE package also wraps a client/server library called +CSlib which enables two codes to exchange messages in different ways, +either via files, sockets, or MPI. The CSlib is provided with LAMMPS +in the lib/message dir. The CSlib has its own +"website"_http://cslib.sandia.gov with documentation and test +programs. + +NOTE: For client/server coupling to work between LAMMPS and another +code, the other code also has to use the CSlib. This can sometimes be +done without any modifications to the other code by simply wrapping it +with a Python script that exchanges CSlib messages with LAMMPS and +prepares input for or processes output from the other code. The other +code also has to implement a matching protocol for the format and +content of messages that LAMMPS exchanges with it. + +These are the commands currently in the MESSAGE package for two +protocols, MD and MC (Monte Carlo). New protocols can easily be +defined and added to this directory, where LAMMPS acts as either the +client or server. + +"message"_message.html +"fix client md"_fix_client_md.html = LAMMPS is a client for running MD +"server md"_server_md.html = LAMMPS is a server for computing MD forces +"server mc"_server_mc.html = LAMMPS is a server for computing a Monte Carlo energy + +The server doc files give details of the message protocols +for data that is exchanged bewteen the client and server. + +These example directories illustrate how to use LAMMPS as either a +client or server code: + +examples/message +examples/COUPLE/README +examples/COUPLE/lammps_mc +examples/COUPLE/lammps_vasp :ul + +The examples/message dir couples a client instance of LAMMPS to a +server instance of LAMMPS. + +The lammps_mc dir shows how to couple LAMMPS as a server to a simple +Monte Carlo client code as the driver. + +The lammps_vasp dir shows how to couple LAMMPS as a client code +running MD timestepping to VASP acting as a server providing quantum +DFT forces, thru a Python wrapper script on VASP. + +Here is how to launch a client and server code together for any of the +4 modes of message exchange that the "message"_message.html command +and the CSlib support. Here LAMMPS is used as both the client and +server code. Another code could be subsitituted for either. + +The examples below show launching both codes from the same window (or +batch script), using the "&" character to launch the first code in the +background. For all modes except {mpi/one}, you could also launch the +codes in separate windows on your desktop machine. It does not +matter whether you launch the client or server first. + +In these examples either code can be run on one or more processors. +If running in a non-MPI mode (file or zmq) you can launch a code on a +single processor without using mpirun. + +IMPORTANT: If you run in mpi/two mode, you must launch both codes via +mpirun, even if one or both of them runs on a single processor. This +is so that MPI can figure out how to connect both MPI processes +together to exchange MPI messages between them. + +For message exchange in {file}, {zmq}, or {mpi/two} modes: + +% mpirun -np 1 lmp_mpi -log log.client < in.client & +% mpirun -np 2 lmp_mpi -log log.server < in.server :pre + +% mpirun -np 4 lmp_mpi -log log.client < in.client & +% mpirun -np 1 lmp_mpi -log log.server < in.server :pre + +% mpirun -np 2 lmp_mpi -log log.client < in.client & +% mpirun -np 4 lmp_mpi -log log.server < in.server :pre + +For message exchange in {mpi/one} mode: + +Launch both codes in a single mpirun command: + +mpirun -np 2 lmp_mpi -mpicolor 0 -in in.message.client -log log.client : -np 4 lmp_mpi -mpicolor 1 -in in.message.server -log log.server + +The two -np values determine how many procs the client and the server +run on. + +A LAMMPS executable run in this manner must use the -mpicolor color +command-line option as their its option, where color is an integer +label that will be used to distinguish one executable from another in +the multiple executables that the mpirun command launches. In this +example the client was colored with a 0, and the server with a 1. diff --git a/doc/src/Howto_couple.txt b/doc/src/Howto_couple.txt index d7b4924d8c..0214db1ece 100644 --- a/doc/src/Howto_couple.txt +++ b/doc/src/Howto_couple.txt @@ -16,10 +16,12 @@ atoms and pass those forces to LAMMPS. Or a continuum finite element nodal points, compute a FE solution, and return interpolated forces on MD atoms. -LAMMPS can be coupled to other codes in at least 3 ways. Each has +LAMMPS can be coupled to other codes in at least 4 ways. Each has advantages and disadvantages, which you'll have to think about in the context of your application. +:line + (1) Define a new "fix"_fix.html command that calls the other code. In this scenario, LAMMPS is the driver code. During its timestepping, the fix is invoked, and can make library calls to the other code, @@ -32,6 +34,8 @@ LAMMPS. :link(poems,http://www.rpi.edu/~anderk5/lab) +:line + (2) Define a new LAMMPS command that calls the other code. This is conceptually similar to method (1), but in this case LAMMPS and the other code are on a more equal footing. Note that now the other code @@ -52,6 +56,8 @@ command writes and reads. See the "Modify command"_Modify_command.html doc page for info on how to add a new command to LAMMPS. +:line + (3) Use LAMMPS as a library called by another code. In this case the other code is the driver and calls LAMMPS as needed. Or a wrapper code could link and call both LAMMPS and another code as libraries. @@ -102,3 +108,9 @@ on all the processors. Or it might allocate half the processors to LAMMPS and half to the other code and run both codes simultaneously before syncing them up periodically. Or it might instantiate multiple instances of LAMMPS to perform different calculations. + +:line + +(4) Couple LAMMPS with another code in a client/server mode. This is +described on the "Howto client/server"_Howto_client_server.html doc +page. diff --git a/doc/src/Manual.txt b/doc/src/Manual.txt index ad3e66a4b2..e442aa1808 100644 --- a/doc/src/Manual.txt +++ b/doc/src/Manual.txt @@ -1,7 +1,7 @@ LAMMPS Users Manual - + @@ -21,7 +21,7 @@ :line LAMMPS Documentation :c,h1 -22 Aug 2018 version :c,h2 +31 Aug 2018 version :c,h2 "What is a LAMMPS version?"_Manual_version.html diff --git a/doc/src/Packages_details.txt b/doc/src/Packages_details.txt index 381dc2e995..a4ed1e3ff4 100644 --- a/doc/src/Packages_details.txt +++ b/doc/src/Packages_details.txt @@ -549,10 +549,6 @@ This package has "specific installation instructions"_Build_extras.html#gpu on the "Build extras"_Build_extras.html doc page. -NOTE: You should test building the MEAM library with both the Intel -and GNU compilers to see if a simulation runs faster with one versus -the other on your system. - [Supporting info:] src/MEAM: filenames -> commands @@ -563,6 +559,31 @@ examples/meam :ul :line +MESSAGE package :link(PKG-MESSAGE),h4 + +[Contents:] + +Commands to use LAMMPS as either a client or server and couple it to +another application. + +[Install:] + +This package has "specific installation +instructions"_Build_extras.html#message on the "Build +extras"_Build_extras.html doc page. + +[Supporting info:] + +src/MESSAGE: filenames -> commands +lib/message/README +"message"_message.html +"fix client/md"_fix_client_md.html +"server md"_server_md.html +"server mc"_server_mc.html +examples/message :ul + +:line + MISC package :link(PKG-MISC),h4 [Contents:] diff --git a/doc/src/Packages_standard.txt b/doc/src/Packages_standard.txt index 2feb4e142d..583ecf39fe 100644 --- a/doc/src/Packages_standard.txt +++ b/doc/src/Packages_standard.txt @@ -47,6 +47,7 @@ Package, Description, Doc page, Example, Library "MANYBODY"_Packages_details.html#PKG-MANYBODY, many-body potentials, "pair_style tersoff"_pair_tersoff.html, shear, no "MC"_Packages_details.html#PKG-MC, Monte Carlo options, "fix gcmc"_fix_gcmc.html, n/a, no "MEAM"_Packages_details.html#PKG-MEAM, modified EAM potential, "pair_style meam"_pair_meam.html, meam, int +"MESSAGE"_Packages_details.html#PKG-MESSAGE, client/server messaging, "message"_message.html, message, int "MISC"_Packages_details.html#PKG-MISC, miscellaneous single-file commands, n/a, no, no "MOLECULE"_Packages_details.html#PKG-MOLECULE, molecular system force fields, "Howto bioFF"_Howto_bioFF.html, peptide, no "MPIIO"_Packages_details.html#PKG-MPIIO, MPI parallel I/O dump and restart, "dump"_dump.html, n/a, no diff --git a/doc/src/Run_options.txt b/doc/src/Run_options.txt index 9c862d7b8e..27f436ed55 100644 --- a/doc/src/Run_options.txt +++ b/doc/src/Run_options.txt @@ -18,6 +18,7 @@ letter abbreviation can be used: "-i or -in"_#file "-k or -kokkos"_#run-kokkos "-l or -log"_#log +"-m or -mpicolor"_#mpicolor "-nc or -nocite"_#nocite "-pk or -package"_#package "-p or -partition"_#partition @@ -175,6 +176,30 @@ Option -plog will override the name of the partition log files file.N. :line +[-mpicolor] color :link(mpi) + +If used, this must be the first command-line argument after the LAMMPS +executable name. It is only used when LAMMPS is launched by an mpirun +command which also launches another executable(s) at the same time. +(The other executable could be LAMMPS as well.) The color is an +integer value which should be different for each executable (another +application may set this value in a different way). LAMMPS and the +other executable(s) perform an MPI_Comm_split() with their own colors +to shrink the MPI_COMM_WORLD communication to be the subset of +processors they are actually running on. + +Currently, this is only used in LAMMPS to perform client/server +messaging with another application. LAMMPS can act as either a client +or server (or both). More details are given on the "Howto +client/server"_Howto_client_server.html doc page. + +Specifically, this refers to the "mpi/one" mode of messaging provided +by the "message"_message.html command and the CSlib library LAMMPS +links with from the lib/message directory. See the +"message"_message.html command for more details. + +:line + [-nocite] :link(nocite) Disable writing the log.cite file which is normally written to list diff --git a/doc/src/commands_list.txt b/doc/src/commands_list.txt index 62b973e3a4..8fae57a718 100644 --- a/doc/src/commands_list.txt +++ b/doc/src/commands_list.txt @@ -56,6 +56,7 @@ Commands :h1 lattice log mass + message min_modify min_style minimize @@ -87,6 +88,7 @@ Commands :h1 restart run run_style + server set shell special_bonds diff --git a/doc/src/fix_client_md.txt b/doc/src/fix_client_md.txt new file mode 100644 index 0000000000..5b62d5617d --- /dev/null +++ b/doc/src/fix_client_md.txt @@ -0,0 +1,106 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +fix client/md command :h3 + +[Syntax:] + +fix ID group-ID client/md :pre + +ID, group-ID are documented in "fix"_fix.html command +client/md = style name of this fix command :ul + +[Examples:] + +fix 1 all client/md :pre + +[Description:] + +This fix style enables LAMMPS to run as a "client" code and +communicate each timestep with a separate "server" code to perform an +MD simulation together. + +The "Howto client/server"_Howto_client_server.html doc page gives an +overview of client/server coupling of LAMMPS with another code where +one code is the "client" and sends request messages to a "server" +code. The server responds to each request with a reply message. This +enables the two codes to work in tandem to perform a simulation. + +When using this fix, LAMMPS (as the client code) passes the current +coordinates of all particles to the server code each timestep, which +computes their interaction, and returns the energy, forces, and virial +for the interacting particles to LAMMPS, so it can complete the +timestep. + +The server code could be a quantum code, or another classical MD code +which encodes a force field (pair_style in LAMMPS lingo) which LAMMPS +does not have. In the quantum case, this fix is a mechanism for +running {ab initio} MD with quantum forces. + +The group associated with this fix is ignored. + +The protocol and "units"_units.html for message format and content +that LAMMPS exchanges with the server code is defined on the "server +md"_server_md.html doc page. + +Note that when using LAMMPS as an MD client, your LAMMPS input script +should not normally contain force field commands, like a +"pair_style"_doc/pair_style.html, "bond_style"_doc/bond_style.html, or +"kspace_style"_kspace_style.html commmand. However it is possible for +a server code to only compute a portion of the full force-field, while +LAMMPS computes the remaining part. Your LAMMPS script can also +specify boundary conditions or force constraints in the usual way, +which will be added to the per-atom forces returned by the server +code. + +See the examples/message dir for example scripts where LAMMPS is both +the "client" and/or "server" code for this kind of client/server MD +simulation. The examples/message/README file explains how to launch +LAMMPS and another code in tandem to perform a coupled simulation. + +:line + +[Restart, fix_modify, output, run start/stop, minimize info:] + +No information about this fix is written to "binary restart +files"_restart.html. + +The "fix_modify"_fix_modify.html {energy} option is supported by this +fix to add the potential energy computed by the server application to +the system's potential energy as part of "thermodynamic +output"_thermo_style.html. + +The "fix_modify"_fix_modify.html {virial} option is supported by this +fix to add the server application's contribution to the system's +virial as part of "thermodynamic output"_thermo_style.html. The +default is {virial yes} + +This fix computes a global scalar which can be accessed by various +"output commands"_Howto_output.html. The scalar is the potential +energy discussed above. The scalar value calculated by this fix is +"extensive". + +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. + +[Restrictions:] + +This fix is part of the MESSAGE package. It is only enabled if LAMMPS +was built with that package. See the "Build +package"_Build_package.html doc page for more info. + +A script that uses this command must also use the +"message"_message.html command to setup the messaging protocol with +the other server code. + +[Related commands:] + +"message"_message.html, "server"_server.html + +[Default:] none diff --git a/doc/src/lammps.book b/doc/src/lammps.book index c296ff4039..72a07945e7 100644 --- a/doc/src/lammps.book +++ b/doc/src/lammps.book @@ -167,6 +167,7 @@ label.html lattice.html log.html mass.html +message.html min_modify.html min_style.html minimize.html @@ -194,6 +195,9 @@ reset_timestep.html restart.html run.html run_style.html +server.html +server_mc.html +server_md.html set.html shell.html special_bonds.html @@ -241,6 +245,7 @@ fix_bond_create.html fix_bond_react.html fix_bond_swap.html fix_box_relax.html +fix_client_md.html fix_cmap.html fix_colvars.html fix_controller.html diff --git a/doc/src/message.txt b/doc/src/message.txt new file mode 100644 index 0000000000..cca1a5b369 --- /dev/null +++ b/doc/src/message.txt @@ -0,0 +1,162 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Command_all.html) + +:line + +message command :h3 + +[Syntax:] + +message which protocol mode arg :pre + +which = {client} or {server} :ulb,l +protocol = {md} or {mc} :l +mode = {file} or {zmq} or {mpi/one} or {mpi/two} :l + {file} arg = filename + filename = file used for message exchanges + {zmq} arg = socket-ID + socket-ID for client = localhost:5555, see description below + socket-ID for server = *:5555, see description below + {mpi/one} arg = none + {mpi/two} arg = filename + filename = file used to establish communication bewteen 2 MPI jobs :pre +:ule + +[Examples:] + +message client md file tmp.couple +message server md file tmp.couple :pre + +message client md zmq localhost:5555 +message server md zmq *:5555 :pre + +message client md mpi/one +message server md mpi/one :pre + +message client md mpi/two tmp.couple +message server md mpi/two tmp.couple :pre + +[Description:] + +Establish a messaging protocol between LAMMPS and another code for the +purpose of client/server coupling. + +The "Howto client/server"_Howto_client_server.html doc page gives an +overview of client/server coupling of LAMMPS with another code where +one code is the "client" and sends request messages to a "server" +code. The server responds to each request with a reply message. This +enables the two codes to work in tandem to perform a simulation. + +:line + +The {which} argument defines LAMMPS to be the client or the server. + +:line + +The {protocol} argument defines the format and content of messages +that will be exchanged between the two codes. The current options +are: + +md = run dynamics with another code +mc = perform Monte Carlo moves with another code :ul + +For protocol {md}, LAMMPS can be either a client or server. See the +"server md"_server_md.html doc page for details on the protocol. + +For protocol {mc}, LAMMPS can be the server. See the "server +mc"_server_mc.html doc page for details on the protocol. + +:line + +The {mode} argument specifies how messages are exchanged between the +client and server codes. Both codes must use the same mode and use +consistent parameters. + +For mode {file}, the 2 codes communicate via binary files. They must +use the same filename, which is actually a file prefix. Several files +with that prefix will be created and deleted as a simulation runs. +The filename can include a path. Both codes must be able to access +the path/file in a common filesystem. + +For mode {zmq}, the 2 codes communicate via a socket on the server +code's machine. Support for socket messaging is provided by the +open-source "ZeroMQ library"_http://zeromq.org, which must be +installed on your system. The client specifies an IP address (IPv4 +format) or the DNS name of the machine the server code is running on, +followed by a 4-digit port ID for the socket, separated by a colon. +E.g. + +localhost:5555 # client and server running on same machine +192.168.1.1:5555 # server is 192.168.1.1 +deptbox.uni.edu:5555 # server is deptbox.uni.edu :pre + +The server specifes "*:5555" where "*" represents all available +interfaces on the server's machine, and the port ID must match +what the client specifies. + +NOTE: What are allowed port IDs? + +NOTE: Additional explanation is needed here about how to use the {zmq} +mode on a parallel machine, e.g. a cluster with many nodes. + +For mode {mpi/one}, the 2 codes communicate via MPI and are launched +by the same mpirun command, e.g. with this syntax for OpenMPI: + +mpirun -np 2 lmp_mpi -mpicolor 0 -in in.client -log log.client : -np 4 othercode args # LAMMPS is client +mpirun -np 2 othercode args : -np 4 lmp_mpi -mpicolor 1 -in in.server # LAMMPS is server :pre + +Note the use of the "-mpicolor color" command-line argument with +LAMMPS. See the "command-line args"_Run_options.html doc page for +further explanation. + +For mode {mpi/two}, the 2 codes communicate via MPI, but are launched +be 2 separate mpirun commands. The specified {filename} argument is a +file the 2 MPI processes will use to exchange info so that an MPI +inter-communicator can be established to enable the 2 codes to send +MPI messages to each other. Both codes must be able to access the +path/file in a common filesystem. + +:line + +Normally, the message command should be used at the top of a LAMMPS +input script. It performs an initial handshake with the other code to +setup messaging and to verify that both codes are using the same +message protocol and mode. Assuming both codes are launched at +(nearly) the same time, the other code should perform the same kind of +initialization. + +If LAMMPS is the client code, it will begin sending messages when a +LAMMPS client command begins its operation. E.g. for the "fix +client/md"_fix_client_md.html command, it is when a "run"_run.html +command is executed. + +If LAMMPS is the server code, it will begin receiving messages when +the "server"_server.html command is invoked. + +A fix client command will terminate its messaging with the server when +LAMMPS ends, or the fix is deleted via the "unfix"_unfix command. The +server command will terminate its messaging with the client when the +client signals it. Then the remainder of the LAMMPS input script will +be processed. + +If both codes do something similar, this means a new round of +client/server messaging can be initiated after termination by re-using +a 2nd message command in your LAMMPS input script, followed by a new +fix client or server command. + +:line + +[Restrictions:] + +This command is part of the MESSAGE package. It is only enabled if +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. + +[Related commands:] + +"server"_server.html, "fix client/md"_fix_client_md.html + +[Default:] none diff --git a/doc/src/server.txt b/doc/src/server.txt new file mode 100644 index 0000000000..86fb68d012 --- /dev/null +++ b/doc/src/server.txt @@ -0,0 +1,71 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +server command :h3 + +[Syntax:] + +server protocol :pre + +protocol = {md} or {mc} :ul + +[Examples:] + +server md :pre + +[Description:] + +This command starts LAMMPS running in "server" mode, where it receives +messages from a separate "client" code and responds by sending a reply +message back to the client. The specified {protocol} determines the +format and content of messages LAMMPS expects to receive and how it +responds. + +The "Howto client/server"_Howto_client_server.html doc page gives an +overview of client/server coupling of LAMMPS with another code where +one code is the "client" and sends request messages to a "server" +code. The server responds to each request with a reply message. This +enables the two codes to work in tandem to perform a simulation. + +When this command is invoked, LAMMPS will run in server mode in an +endless loop, waiting for messages from the client code. The client +signals when it is done sending messages to LAMMPS, at which point the +loop will exit, and the remainder of the LAMMPS script will be +processed. + +The {protocol} argument defines the format and content of messages +that will be exchanged between the two codes. The current options +are: + +"md"_server_md.html = run dynamics with another code +"mc"_server_mc.html = perform Monte Carlo moves with another code :ul + +For protocol {md}, LAMMPS can be either a client (via the "fix +client/md"_fix_client_md.html command) or server. See the "server +md"_server_md.html doc page for details on the protocol. + +For protocol {mc}, LAMMPS can be the server. See the "server +mc"_server_mc.html doc page for details on the protocol. + +:line + +[Restrictions:] + +This command is part of the MESSAGE package. It is only enabled if +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. + +A script that uses this command must also use the +"message"_message.html command to setup the messaging protocol with +the other client code. + +[Related commands:] + +"message"_message.html, "fix client/md"_fix_client_md.html + +[Default:] none diff --git a/doc/src/server_mc.txt b/doc/src/server_mc.txt new file mode 100644 index 0000000000..53ccfc8ecd --- /dev/null +++ b/doc/src/server_mc.txt @@ -0,0 +1,116 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +server mc command :h3 + +[Syntax:] + +server mc :pre + +mc = the protocol argument to the "server"_server.html command + +[Examples:] + +server mc :pre + +[Description:] + +This command starts LAMMPS running in "server" mode, where it will +expect messages from a separate "client" code that match the {mc} +protocol for format and content explained below. For each message +LAMMPS receives it will send a message back to the client. + +The "Howto client/server"_Howto_client_server.html doc page gives an +overview of client/server coupling of LAMMPS with another code where +one code is the "client" and sends request messages to a "server" +code. The server responds to each request with a reply message. This +enables the two codes to work in tandem to perform a simulation. + +When this command is invoked, LAMMPS will run in server mode in an +endless loop, waiting for messages from the client code. The client +signals when it is done sending messages to LAMMPS, at which point the +loop will exit, and the remainder of the LAMMPS script will be +processed. + +The "server"_server.html doc page gives other options for using LAMMPS +See an example of how this command is used in +examples/COUPLE/lammps_mc/in.server. + +:line + +When using this command, LAMMPS (as the server code) receives +instructions from a Monte Carlo (MC) driver to displace random atoms, +compute the energy before and after displacement, and run dynamics to +equilibrate the system. + +The MC driver performs the random displacements on random atoms, +accepts or rejects the move in an MC sense, and orchestrates the MD +runs. + +The format and content of the exchanged messages are explained here in +a conceptual sense. Python-style pseudo code for the library calls to +the CSlib is shown, which performs the actual message exchange between +the two codes. See the "CSlib website"_http://cslib.sandia.gov doc +pages for more details on the actual library syntax. The "cs" object +in this pseudo code is a pointer to an instance of the CSlib. + +See the src/MESSAGE/server_mc.cpp file for details on how LAMMPS uses +these messages. See the examples/COUPLE/lammmps_mc/mc.cpp file for an +example of how an MC driver code can use these messages. + +Let NATOMS=1, EINIT=2, DISPLACE=3, ACCEPT=4, RUN=5. + +[Client sends one of these kinds of message]: + +cs->send(NATOMS,0) # msgID = 1 with no fields :pre + +cs->send(EINIT,0) # msgID = 2 with no fields :pre + +cs->send(DISPLACE,2) # msgID = 3 with 2 fields +cs->pack_int(1,ID) # 1st field = ID of atom to displace +cs->pack(2,3,xnew) # 2nd field = new xyz coords of displaced atom :pre + +cs->send(ACCEPT,1) # msgID = 4 with 1 field +cs->pack_int(1,flag) # 1st field = accept/reject flag :pre + +cs->send(RUN,1) # msgID = 5 with 1 field +cs->pack_int(1,nsteps) # 1st field = # of timesteps to run MD :pre + +[Server replies]: + +cs->send(NATOMS,1) # msgID = 1 with 1 field +cs->pack_int(1,natoms) # 1st field = number of atoms :pre + +cs->send(EINIT,2) # msgID = 2 with 2 fields +cs->pack_double(1,poteng) # 1st field = potential energy of system +cs->pack(2,3*natoms,x) # 2nd field = 3N coords of Natoms :pre + +cs->send(DISPLACE,1) # msgID = 3 with 1 field +cs->pack_double(1,poteng) # 1st field = new potential energy of system :pre + +cs->send(ACCEPT,0) # msgID = 4 with no fields + +cs->send(RUN,0) # msgID = 5 with no fields + +:line + +[Restrictions:] + +This command is part of the MESSAGE package. It is only enabled if +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. + +A script that uses this command must also use the +"message"_message.html command to setup the messaging protocol with +the other client code. + +[Related commands:] + +"message"_message.html + +[Default:] none diff --git a/doc/src/server_md.txt b/doc/src/server_md.txt new file mode 100644 index 0000000000..0db7bbe16b --- /dev/null +++ b/doc/src/server_md.txt @@ -0,0 +1,147 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +server md command :h3 + +[Syntax:] + +server md :pre + +md = the protocol argument to the "server"_server.html command + +[Examples:] + +server md :pre + +[Description:] + +This command starts LAMMPS running in "server" mode, where it will +expect messages from a separate "client" code that match the {md} +protocol for format and content explained below. For each message +LAMMPS receives it will send a message back to the client. + +The "Howto client/server"_Howto_client_server.html doc page gives an +overview of client/server coupling of LAMMPS with another code where +one code is the "client" and sends request messages to a "server" +code. The server responds to each request with a reply message. This +enables the two codes to work in tandem to perform a simulation. + +When this command is invoked, LAMMPS will run in server mode in an +endless loop, waiting for messages from the client code. The client +signals when it is done sending messages to LAMMPS, at which point the +loop will exit, and the remainder of the LAMMPS script will be +processed. + +The "server"_server.html doc page gives other options for using LAMMPS +in server mode. See an example of how this command is used in +examples/message/in.message.server. + +:line + +When using this command, LAMMPS (as the server code) receives the +current coordinates of all particles from the client code each +timestep, computes their interaction, and returns the energy, forces, +and pressure for the interacting particles to the client code, so it +can complete the timestep. This command could also be used with a +client code that performs energy minimization, using the server to +compute forces and energy each iteration of its minimizer. + +When using the "fix client/md" command, LAMMPS (as the client code) +does the timestepping and receives needed energy, forces, and pressure +values from the server code. + +The format and content of the exchanged messages are explained here in +a conceptual sense. Python-style pseudo code for the library calls to +the CSlib is shown, which performs the actual message exchange between +the two codes. See the "CSlib website"_http://cslib.sandia.gov doc +pages for more details on the actual library syntax. The "cs" object +in this pseudo code is a pointer to an instance of the CSlib. + +See the src/MESSAGE/server_md.cpp and src/MESSAGE/fix_client_md.cpp +files for details on how LAMMPS uses these messages. See the +examples/COUPLE/lammps_vasp/vasp_wrapper.py file for an example of how +a quantum code (VASP) can use use these messages. + +The following pseudo-code uses these values, defined as enums. + +enum{SETUP=1,STEP}; +enum{DIM=1,PERIODICITY,ORIGIN,BOX,NATOMS,NTYPES,TYPES,COORDS,UNITS,CHARGE}; +enum{FORCES=1,ENERGY,PRESSURE,ERROR}; :pre + +[Client sends 2 kinds of messages]: + +# required fields: DIM, PERIODICTY, ORIGIN, BOX, NATOMS, NTYPES, TYPES, COORDS +# optional fields: UNITS, CHARGE :pre + +cs->send(SETUP,nfields) # msgID with nfields :pre + +cs->pack_int(DIM,dim) # dimension (2,3) of simulation +cs->pack(PERIODICITY,3,xyz) # periodicity flags in 3 dims +cs->pack(ORIGIN,3,origin) # lower-left corner of simulation box +cs->pack(BOX,9,box) # 3 edge vectors of simulation box +cs->pack_int(NATOMS,natoms) # total number of atoms +cs->pack_int(NTYPES,ntypes) # number of atom types +cs->pack(TYPES,natoms,type) # vector of per-atom types +cs->pack(COORDS,3*natoms,x) # vector of 3N atom coords +cs->pack_string(UNITS,units) # units = "lj", "real", "metal", etc +cs->pack(CHARGE,natoms,q) # vector of per-atom charge :pre + +# required fields: COORDS +# optional fields: ORIGIN, BOX :pre + +cs->send(STEP,nfields) # msgID with nfields :pre + +cs->pack(COORDS,3*natoms,x) # vector of 3N atom coords +cs->pack(ORIGIN,3,origin) # lower-left corner of simulation box +cs->pack(BOX,9,box) # 3 edge vectors of simulation box + +[Server replies to either kind of message]: + +# required fields: FORCES, ENERGY, PRESSURE +# optional fields: ERROR :pre + +cs->send(msgID,nfields) # msgID with nfields +cs->pack(FORCES,3*Natoms,f) # vector of 3N forces on atoms +cs->pack(ENERGY,1,poteng) # total potential energy of system +cs->pack(PRESSURE,6,press) # global pressure tensor (6-vector) +cs->pack_int(ERROR,flag) # server had an error (e.g. DFT non-convergence) :pre + +:line + +The units for various quantities that are sent and received iva +messages are defined for atomic-scale simulations in the table below. +The client and server codes (including LAMMPS) can use internal units +different than these (e.g. "real units"_units.html in LAMMPS), so long +as they convert to these units for meesaging. + +COORDS, ORIGIN, BOX = Angstroms +CHARGE = multiple of electron charge (1.0 is a proton) +ENERGY = eV +FORCES = eV/Angstrom +PRESSURE = bars :ul + +Note that these are "metal units"_units.html in LAMMPS. + +If you wish to run LAMMPS in another its non-atomic units, e.g. "lj +units"_units.html, then the client and server should exchange a UNITS +message as indicated above, and both the client and server should +agree on the units for the data they exchange. + +:line + +[Restrictions:] + +This command is part of the MESSAGE package. It is only enabled if +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. + +[Related commands:] + +"message"_message.html, "fix client/md"_fix_client_md.html + +[Default:] none diff --git a/examples/COUPLE/README b/examples/COUPLE/README index 83e7463531..0e611befbd 100644 --- a/examples/COUPLE/README +++ b/examples/COUPLE/README @@ -10,6 +10,7 @@ See these sections of the LAMMPS manaul for details: 2.5 Building LAMMPS as a library (doc/Section_start.html#start_5) 6.10 Coupling LAMMPS to other codes (doc/Section_howto.html#howto_10) +6.29 Using LAMMPS in client/server mode (doc/Section_howto.html#howto_29) In all of the examples included here, LAMMPS must first be built as a library. Basically, in the src dir you type one of @@ -33,9 +34,13 @@ These are the sub-directories included in this directory: simple simple example of driver code calling LAMMPS as a lib multiple example of driver code calling multiple instances of LAMMPS +lammps_mc client/server coupling of Monte Carlo client + with LAMMPS server for energy evaluation lammps_quest MD with quantum forces, coupling to Quest DFT code lammps_spparks grain-growth Monte Carlo with strain via MD, coupling to SPPARKS kinetic MC code +lammps_vasp client/server coupling of LAMMPS client with + VASP quantum DFT as server for quantum forces library collection of useful inter-code communication routines fortran a simple wrapper on the LAMMPS library API that can be called from Fortran diff --git a/examples/COUPLE/lammps_mc/Makefile b/examples/COUPLE/lammps_mc/Makefile new file mode 100644 index 0000000000..c75bd08c73 --- /dev/null +++ b/examples/COUPLE/lammps_mc/Makefile @@ -0,0 +1,33 @@ +# Makefile for MC + +SHELL = /bin/sh + +SRC = mc.cpp random_park.cpp +OBJ = $(SRC:.cpp=.o) + +# change this line for your machine to path for CSlib src dir + +CSLIB = /home/sjplimp/lammps/lib/message/cslib/src + +# compiler/linker settings + +CC = g++ +CCFLAGS = -g -O3 -I$(CSLIB) +LINK = g++ +LINKFLAGS = -g -O -L$(CSLIB) + +# targets + +mc: $(OBJ) +# first line if built the CSlib within lib/message with ZMQ support +# second line if built the CSlib without ZMQ support + $(LINK) $(LINKFLAGS) $(OBJ) -lcsnompi -lzmq -o mc +# $(LINK) $(LINKFLAGS) $(OBJ) -lcsnompi -o mc + +clean: + @rm -f *.o mc + +# rules + +%.o:%.cpp + $(CC) $(CCFLAGS) -c $< diff --git a/examples/COUPLE/lammps_mc/README b/examples/COUPLE/lammps_mc/README new file mode 100644 index 0000000000..c201a6351c --- /dev/null +++ b/examples/COUPLE/lammps_mc/README @@ -0,0 +1,128 @@ +Sample Monte Carlo (MC) wrapper on LAMMPS via client/server coupling + +See the MESSAGE package (doc/Section_messages.html#MESSAGE) +and Section_howto.html#howto10 for more details on how +client/server coupling works in LAMMPS. + +In this dir, the mc.cpp/h files are a standalone "client" MC code. It +should be run on a single processor, though it could become a parallel +program at some point. LAMMPS is also run as a standalone executable +as a "server" on as many processors as desired using its "server mc" +command; see it's doc page for details. + +Messages are exchanged between MC and LAMMPS via a client/server +library (CSlib), which is included in the LAMMPS distribution in +lib/message. As explained below you can choose to exchange data +between the two programs either via files or sockets (ZMQ). If the MC +program became parallel, data could also be exchanged via MPI. + +The MC code makes simple MC moves, by displacing a single random atom +by a small random amount. It uses LAMMPS to calculate the energy +change, and to run dynamics between MC moves. + +---------------- + +Build LAMMPS with its MESSAGE package installed: + +See the Build extras doc page and its MESSAGE package +section for details. + +CMake: + +-D PKG_MESSAGE=yes # include the MESSAGE package +-D MESSAGE_ZMQ=value # build with ZeroMQ support, value = no (default) or yes + +Traditional make: + +% cd lammps/lib/message +% python Install.py -m -z # build CSlib with MPI and ZMQ support +% cd lammps/src +% make yes-message +% make mpi + +You can leave off the -z if you do not have ZMQ on your system. + +---------------- + +Build the MC client code + +The source files for the MC code are in this dir. It links with the +CSlib library in lib/message/cslib. + +You must first build the CSlib in serial mode, e.g. + +% cd lammps/lib/message/cslib/src +% make lib # build serial and parallel lib with ZMQ support +% make lib zmq=no # build serial and parallel lib without ZMQ support + +Then edit the Makefile in this dir. The CSLIB variable should be the +path to where the LAMMPS lib/message/cslib/src dir is on your system. +If you built the CSlib without ZMQ support you will also need to +comment/uncomment one line. Then you can just type + +% make + +and you should get an "mc" executable. + +---------------- + +To run in client/server mode: + +Both the client (MC) and server (LAMMPS) must use the same messaging +mode, namely file or zmq. This is an argument to the MC code; it can +be selected by setting the "mode" variable when you run LAMMPS. The +default mode = file. + +Here we assume LAMMPS was built to run in parallel, and the MESSAGE +package was installed with socket (ZMQ) support. This means either of +the messaging modes can be used and LAMMPS can be run in serial or +parallel. The MC code is always run in serial. + +When you run, the server should print out thermodynamic info +for every MD run it performs (between MC moves). The client +will print nothing until the simulation ends, then it will +print stats about the accepted MC moves. + +The examples below are commands you should use in two different +terminal windows. The order of the two commands (client or server +launch) does not matter. You can run them both in the same window if +you append a "&" character to the first one to run it in the +background. + +-------------- + +File mode of messaging: + +% mpirun -np 1 mc in.mc file tmp.couple +% mpirun -np 1 lmp_mpi -v mode file < in.mc.server + +% mpirun -np 1 mc in.mc file tmp.couple +% mpirun -np 4 lmp_mpi -v mode file < in.mc.server + +ZMQ mode of messaging: + +% mpirun -np 1 mc in.mc zmq localhost:5555 +% mpirun -np 1 lmp_mpi -v mode zmq < in.mc.server + +% mpirun -np 1 mc in.mc zmq localhost:5555 +% mpirun -np 4 lmp_mpi -v mode zmq < in.mc.server + +-------------- + +The input script for the MC program is in.mc. You can edit it to run +longer simulations. + +500 nsteps = total # of steps of MD +100 ndynamics = # of MD steps between MC moves +0.1 delta = displacement size of MC move +1.0 temperature = used in MC Boltzman factor +12345 seed = random number seed + +-------------- + +The problem size that LAMMPS is computing the MC energy for and +running dynamics on is set by the x,y,z variables in the LAMMPS +in.mc.server script. The default size is 500 particles. You can +adjust the size as follows: + +lmp_mpi -v x 10 -v y 10 -v z 20 # 8000 particles diff --git a/examples/COUPLE/lammps_mc/in.mc b/examples/COUPLE/lammps_mc/in.mc new file mode 100644 index 0000000000..85052d09f1 --- /dev/null +++ b/examples/COUPLE/lammps_mc/in.mc @@ -0,0 +1,7 @@ +# MC params + +500 nsteps +100 ndynamics +0.1 delta +1.0 temperature +12345 seed diff --git a/examples/COUPLE/lammps_mc/in.mc.server b/examples/COUPLE/lammps_mc/in.mc.server new file mode 100644 index 0000000000..8b10bb0f7b --- /dev/null +++ b/examples/COUPLE/lammps_mc/in.mc.server @@ -0,0 +1,36 @@ +# 3d Lennard-Jones Monte Carlo server script + +variable mode index file + +if "${mode} == file" then & + "message server mc file tmp.couple" & +elif "${mode} == zmq" & + "message server mc zmq *:5555" & + +variable x index 5 +variable y index 5 +variable z index 5 + +units lj +atom_style atomic +atom_modify map yes + +lattice fcc 0.8442 +region box block 0 $x 0 $y 0 $z +create_box 1 box +create_atoms 1 box +mass 1 1.0 + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 20 check no + +velocity all create 1.44 87287 loop geom + +fix 1 all nve + +thermo 50 + +server mc diff --git a/examples/COUPLE/lammps_mc/log.28Aug18.file.g++.1 b/examples/COUPLE/lammps_mc/log.28Aug18.file.g++.1 new file mode 100644 index 0000000000..0d67c89cf1 --- /dev/null +++ b/examples/COUPLE/lammps_mc/log.28Aug18.file.g++.1 @@ -0,0 +1,254 @@ +LAMMPS (22 Aug 2018) +# 3d Lennard-Jones Monte Carlo server script + +variable mode index file + +if "${mode} == file" then "message server mc file tmp.couple" elif "${mode} == zmq" "message server mc zmq *:5555" +message server mc file tmp.couple +variable x index 5 +variable y index 5 +variable z index 5 + +units lj +atom_style atomic +atom_modify map yes + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 +region box block 0 $x 0 $y 0 $z +region box block 0 5 0 $y 0 $z +region box block 0 5 0 5 0 $z +region box block 0 5 0 5 0 5 +create_box 1 box +Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 500 atoms + Time spent = 0.000649929 secs +mass 1 1.0 + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 20 check no + +velocity all create 1.44 87287 loop geom + +fix 1 all nve + +thermo 50 + +server mc +run 0 +Neighbor list info ... + update every 20 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.44 -6.7733681 0 -4.6176881 -5.0221006 +Loop time of 2.14577e-06 on 1 procs for 0 steps with 500 atoms + +93.2% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 2.146e-06 | | |100.00 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1956 ave 1956 max 1956 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 19500 ave 19500 max 19500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 19500 +Ave neighs/atom = 39 +Neighbor list builds = 0 +Dangerous builds not checked +run 0 +Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.44 -6.7723127 0 -4.6166327 -5.015531 +Loop time of 2.14577e-06 on 1 procs for 0 steps with 500 atoms + +93.2% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 2.146e-06 | | |100.00 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1956 ave 1956 max 1956 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 19501 ave 19501 max 19501 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 19501 +Ave neighs/atom = 39.002 +Neighbor list builds = 0 +Dangerous builds not checked +Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.44 -6.7723127 0 -4.6166327 -5.015531 + 50 0.70239211 -5.6763152 0 -4.6248342 0.59544428 + 100 0.7565013 -5.757431 0 -4.6249485 0.21982657 +run 0 +Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes +Step Temp E_pair E_mol TotEng Press + 100 0.7565013 -5.7565768 0 -4.6240944 0.22436405 +Loop time of 1.90735e-06 on 1 procs for 0 steps with 500 atoms + +157.3% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 1.907e-06 | | |100.00 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1939 ave 1939 max 1939 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 18757 ave 18757 max 18757 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 18757 +Ave neighs/atom = 37.514 +Neighbor list builds = 0 +Dangerous builds not checked +Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes +Step Temp E_pair E_mol TotEng Press + 100 0.7565013 -5.757431 0 -4.6249485 0.21982657 + 150 0.76110797 -5.7664315 0 -4.6270529 0.16005254 + 200 0.73505651 -5.7266069 0 -4.6262273 0.34189744 +run 0 +Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes +Step Temp E_pair E_mol TotEng Press + 200 0.73505651 -5.7181381 0 -4.6177585 0.37629943 +Loop time of 2.14577e-06 on 1 procs for 0 steps with 500 atoms + +139.8% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 2.146e-06 | | |100.00 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1899 ave 1899 max 1899 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 18699 ave 18699 max 18699 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 18699 +Ave neighs/atom = 37.398 +Neighbor list builds = 0 +Dangerous builds not checked +Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes +Step Temp E_pair E_mol TotEng Press + 200 0.73505651 -5.7266069 0 -4.6262273 0.34189744 + 250 0.73052476 -5.7206316 0 -4.627036 0.39287516 + 300 0.76300831 -5.7675007 0 -4.6252773 0.16312925 +run 0 +Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes +Step Temp E_pair E_mol TotEng Press + 300 0.76300831 -5.768304 0 -4.6260806 0.15954325 +Loop time of 2.14577e-06 on 1 procs for 0 steps with 500 atoms + +139.8% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 2.146e-06 | | |100.00 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1903 ave 1903 max 1903 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 18715 ave 18715 max 18715 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 18715 +Ave neighs/atom = 37.43 +Neighbor list builds = 0 +Dangerous builds not checked +Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes +Step Temp E_pair E_mol TotEng Press + 300 0.76300831 -5.768304 0 -4.6260806 0.15954325 + 350 0.72993309 -5.7193261 0 -4.6266162 0.3358374 + 400 0.72469448 -5.713463 0 -4.6285954 0.44859547 +run 0 +Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes +Step Temp E_pair E_mol TotEng Press + 400 0.72469448 -5.7077332 0 -4.6228655 0.47669832 +Loop time of 1.90735e-06 on 1 procs for 0 steps with 500 atoms + +157.3% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 1.907e-06 | | |100.00 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1899 ave 1899 max 1899 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 18683 ave 18683 max 18683 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 18683 +Ave neighs/atom = 37.366 +Neighbor list builds = 0 +Dangerous builds not checked +Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes +Step Temp E_pair E_mol TotEng Press + 400 0.72469448 -5.713463 0 -4.6285954 0.44859547 + 450 0.75305735 -5.7518283 0 -4.6245015 0.34658587 + 500 0.73092571 -5.7206337 0 -4.6264379 0.43715809 +Total wall time: 0:00:02 diff --git a/examples/COUPLE/lammps_mc/log.28Aug18.file.g++.4 b/examples/COUPLE/lammps_mc/log.28Aug18.file.g++.4 new file mode 100644 index 0000000000..2ae51d2461 --- /dev/null +++ b/examples/COUPLE/lammps_mc/log.28Aug18.file.g++.4 @@ -0,0 +1,254 @@ +LAMMPS (22 Aug 2018) +# 3d Lennard-Jones Monte Carlo server script + +variable mode index file + +if "${mode} == file" then "message server mc file tmp.couple" elif "${mode} == zmq" "message server mc zmq *:5555" +message server mc file tmp.couple +variable x index 5 +variable y index 5 +variable z index 5 + +units lj +atom_style atomic +atom_modify map yes + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 +region box block 0 $x 0 $y 0 $z +region box block 0 5 0 $y 0 $z +region box block 0 5 0 5 0 $z +region box block 0 5 0 5 0 5 +create_box 1 box +Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 500 atoms + Time spent = 0.000592947 secs +mass 1 1.0 + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 20 check no + +velocity all create 1.44 87287 loop geom + +fix 1 all nve + +thermo 50 + +server mc +run 0 +Neighbor list info ... + update every 20 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.44 -6.7733681 0 -4.6176881 -5.0221006 +Loop time of 3.8147e-06 on 4 procs for 0 steps with 500 atoms + +59.0% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 3.815e-06 | | |100.00 + +Nlocal: 125 ave 125 max 125 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 1099 ave 1099 max 1099 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 4875 ave 4875 max 4875 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 19500 +Ave neighs/atom = 39 +Neighbor list builds = 0 +Dangerous builds not checked +run 0 +Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.44 -6.7723127 0 -4.6166327 -5.015531 +Loop time of 3.03984e-06 on 4 procs for 0 steps with 500 atoms + +106.9% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 3.04e-06 | | |100.00 + +Nlocal: 125 ave 125 max 125 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 1099 ave 1099 max 1099 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 4875.25 ave 4885 max 4866 min +Histogram: 1 0 0 0 2 0 0 0 0 1 + +Total # of neighbors = 19501 +Ave neighs/atom = 39.002 +Neighbor list builds = 0 +Dangerous builds not checked +Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.44 -6.7723127 0 -4.6166327 -5.015531 + 50 0.70210225 -5.6759068 0 -4.6248598 0.59609192 + 100 0.75891559 -5.7611234 0 -4.6250267 0.20841608 +run 0 +Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes +Step Temp E_pair E_mol TotEng Press + 100 0.75891559 -5.7609392 0 -4.6248426 0.20981291 +Loop time of 3.75509e-06 on 4 procs for 0 steps with 500 atoms + +113.2% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 3.755e-06 | | |100.00 + +Nlocal: 125 ave 126 max 124 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 1085.25 ave 1089 max 1079 min +Histogram: 1 0 0 0 0 1 0 0 0 2 +Neighs: 4690.25 ave 4996 max 4401 min +Histogram: 1 0 0 1 0 1 0 0 0 1 + +Total # of neighbors = 18761 +Ave neighs/atom = 37.522 +Neighbor list builds = 0 +Dangerous builds not checked +Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes +Step Temp E_pair E_mol TotEng Press + 100 0.75891559 -5.7609392 0 -4.6248426 0.20981291 + 150 0.75437991 -5.7558622 0 -4.6265555 0.20681722 + 200 0.73111257 -5.7193748 0 -4.6248993 0.35230715 +run 0 +Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes +Step Temp E_pair E_mol TotEng Press + 200 0.73111257 -5.7143906 0 -4.6199151 0.37126023 +Loop time of 2.563e-06 on 4 procs for 0 steps with 500 atoms + +117.1% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 2.563e-06 | | |100.00 + +Nlocal: 125 ave 126 max 123 min +Histogram: 1 0 0 0 0 0 1 0 0 2 +Nghost: 1068.5 ave 1076 max 1063 min +Histogram: 2 0 0 0 0 0 1 0 0 1 +Neighs: 4674.75 ave 4938 max 4419 min +Histogram: 1 0 0 0 1 1 0 0 0 1 + +Total # of neighbors = 18699 +Ave neighs/atom = 37.398 +Neighbor list builds = 0 +Dangerous builds not checked +Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes +Step Temp E_pair E_mol TotEng Press + 200 0.73111257 -5.7193748 0 -4.6248993 0.35230715 + 250 0.73873144 -5.7312505 0 -4.6253696 0.33061033 + 300 0.76392796 -5.7719207 0 -4.6283206 0.18197874 +run 0 +Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes +Step Temp E_pair E_mol TotEng Press + 300 0.76392796 -5.7725589 0 -4.6289588 0.17994628 +Loop time of 3.99351e-06 on 4 procs for 0 steps with 500 atoms + +93.9% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 3.994e-06 | | |100.00 + +Nlocal: 125 ave 128 max 121 min +Histogram: 1 0 0 0 0 1 0 1 0 1 +Nghost: 1069 ave 1080 max 1055 min +Histogram: 1 0 0 0 0 0 2 0 0 1 +Neighs: 4672 ave 4803 max 4600 min +Histogram: 2 0 0 1 0 0 0 0 0 1 + +Total # of neighbors = 18688 +Ave neighs/atom = 37.376 +Neighbor list builds = 0 +Dangerous builds not checked +Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes +Step Temp E_pair E_mol TotEng Press + 300 0.76392796 -5.7725589 0 -4.6289588 0.17994628 + 350 0.71953041 -5.7041632 0 -4.6270261 0.44866153 + 400 0.7319047 -5.7216051 0 -4.6259438 0.46321355 +run 0 +Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes +Step Temp E_pair E_mol TotEng Press + 400 0.7319047 -5.7158168 0 -4.6201554 0.49192039 +Loop time of 3.57628e-06 on 4 procs for 0 steps with 500 atoms + +111.8% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 3.576e-06 | | |100.00 + +Nlocal: 125 ave 132 max 118 min +Histogram: 1 0 0 0 0 2 0 0 0 1 +Nghost: 1057.5 ave 1068 max 1049 min +Histogram: 1 0 0 1 1 0 0 0 0 1 +Neighs: 4685.75 ave 5045 max 4229 min +Histogram: 1 0 0 1 0 0 0 0 0 2 + +Total # of neighbors = 18743 +Ave neighs/atom = 37.486 +Neighbor list builds = 0 +Dangerous builds not checked +Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes +Step Temp E_pair E_mol TotEng Press + 400 0.7319047 -5.7216051 0 -4.6259438 0.46321355 + 450 0.74503154 -5.7405318 0 -4.6252196 0.33211879 + 500 0.70570501 -5.6824439 0 -4.6260035 0.62020788 +Total wall time: 0:00:02 diff --git a/examples/COUPLE/lammps_mc/log.28Aug18.zmq.g++.1 b/examples/COUPLE/lammps_mc/log.28Aug18.zmq.g++.1 new file mode 100644 index 0000000000..0565487bc6 --- /dev/null +++ b/examples/COUPLE/lammps_mc/log.28Aug18.zmq.g++.1 @@ -0,0 +1,254 @@ +LAMMPS (22 Aug 2018) +# 3d Lennard-Jones Monte Carlo server script + +variable mode index file + +if "${mode} == file" then "message server mc file tmp.couple" elif "${mode} == zmq" "message server mc zmq *:5555" +message server mc zmq *:5555 +variable x index 5 +variable y index 5 +variable z index 5 + +units lj +atom_style atomic +atom_modify map yes + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 +region box block 0 $x 0 $y 0 $z +region box block 0 5 0 $y 0 $z +region box block 0 5 0 5 0 $z +region box block 0 5 0 5 0 5 +create_box 1 box +Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 500 atoms + Time spent = 0.000741005 secs +mass 1 1.0 + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 20 check no + +velocity all create 1.44 87287 loop geom + +fix 1 all nve + +thermo 50 + +server mc +run 0 +Neighbor list info ... + update every 20 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.44 -6.7733681 0 -4.6176881 -5.0221006 +Loop time of 1.90735e-06 on 1 procs for 0 steps with 500 atoms + +52.4% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 1.907e-06 | | |100.00 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1956 ave 1956 max 1956 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 19500 ave 19500 max 19500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 19500 +Ave neighs/atom = 39 +Neighbor list builds = 0 +Dangerous builds not checked +run 0 +Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.44 -6.7723127 0 -4.6166327 -5.015531 +Loop time of 1.90735e-06 on 1 procs for 0 steps with 500 atoms + +52.4% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 1.907e-06 | | |100.00 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1956 ave 1956 max 1956 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 19501 ave 19501 max 19501 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 19501 +Ave neighs/atom = 39.002 +Neighbor list builds = 0 +Dangerous builds not checked +Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.44 -6.7723127 0 -4.6166327 -5.015531 + 50 0.70239211 -5.6763152 0 -4.6248342 0.59544428 + 100 0.7565013 -5.757431 0 -4.6249485 0.21982657 +run 0 +Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes +Step Temp E_pair E_mol TotEng Press + 100 0.7565013 -5.7565768 0 -4.6240944 0.22436405 +Loop time of 1.19209e-06 on 1 procs for 0 steps with 500 atoms + +83.9% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 1.192e-06 | | |100.00 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1939 ave 1939 max 1939 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 18757 ave 18757 max 18757 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 18757 +Ave neighs/atom = 37.514 +Neighbor list builds = 0 +Dangerous builds not checked +Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes +Step Temp E_pair E_mol TotEng Press + 100 0.7565013 -5.757431 0 -4.6249485 0.21982657 + 150 0.76110797 -5.7664315 0 -4.6270529 0.16005254 + 200 0.73505651 -5.7266069 0 -4.6262273 0.34189744 +run 0 +Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes +Step Temp E_pair E_mol TotEng Press + 200 0.73505651 -5.7181381 0 -4.6177585 0.37629943 +Loop time of 9.53674e-07 on 1 procs for 0 steps with 500 atoms + +209.7% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 9.537e-07 | | |100.00 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1899 ave 1899 max 1899 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 18699 ave 18699 max 18699 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 18699 +Ave neighs/atom = 37.398 +Neighbor list builds = 0 +Dangerous builds not checked +Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes +Step Temp E_pair E_mol TotEng Press + 200 0.73505651 -5.7266069 0 -4.6262273 0.34189744 + 250 0.73052476 -5.7206316 0 -4.627036 0.39287516 + 300 0.76300831 -5.7675007 0 -4.6252773 0.16312925 +run 0 +Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes +Step Temp E_pair E_mol TotEng Press + 300 0.76300831 -5.768304 0 -4.6260806 0.15954325 +Loop time of 9.53674e-07 on 1 procs for 0 steps with 500 atoms + +104.9% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 9.537e-07 | | |100.00 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1903 ave 1903 max 1903 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 18715 ave 18715 max 18715 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 18715 +Ave neighs/atom = 37.43 +Neighbor list builds = 0 +Dangerous builds not checked +Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes +Step Temp E_pair E_mol TotEng Press + 300 0.76300831 -5.768304 0 -4.6260806 0.15954325 + 350 0.72993309 -5.7193261 0 -4.6266162 0.3358374 + 400 0.72469448 -5.713463 0 -4.6285954 0.44859547 +run 0 +Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes +Step Temp E_pair E_mol TotEng Press + 400 0.72469448 -5.7077332 0 -4.6228655 0.47669832 +Loop time of 9.53674e-07 on 1 procs for 0 steps with 500 atoms + +209.7% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 9.537e-07 | | |100.00 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1899 ave 1899 max 1899 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 18683 ave 18683 max 18683 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 18683 +Ave neighs/atom = 37.366 +Neighbor list builds = 0 +Dangerous builds not checked +Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes +Step Temp E_pair E_mol TotEng Press + 400 0.72469448 -5.713463 0 -4.6285954 0.44859547 + 450 0.75305735 -5.7518283 0 -4.6245015 0.34658587 + 500 0.73092571 -5.7206337 0 -4.6264379 0.43715809 +Total wall time: 0:00:00 diff --git a/examples/COUPLE/lammps_mc/log.28Aug18.zmq.g++.4 b/examples/COUPLE/lammps_mc/log.28Aug18.zmq.g++.4 new file mode 100644 index 0000000000..e74d03235d --- /dev/null +++ b/examples/COUPLE/lammps_mc/log.28Aug18.zmq.g++.4 @@ -0,0 +1,254 @@ +LAMMPS (22 Aug 2018) +# 3d Lennard-Jones Monte Carlo server script + +variable mode index file + +if "${mode} == file" then "message server mc file tmp.couple" elif "${mode} == zmq" "message server mc zmq *:5555" +message server mc zmq *:5555 +variable x index 5 +variable y index 5 +variable z index 5 + +units lj +atom_style atomic +atom_modify map yes + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 +region box block 0 $x 0 $y 0 $z +region box block 0 5 0 $y 0 $z +region box block 0 5 0 5 0 $z +region box block 0 5 0 5 0 5 +create_box 1 box +Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 500 atoms + Time spent = 0.000576019 secs +mass 1 1.0 + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 20 check no + +velocity all create 1.44 87287 loop geom + +fix 1 all nve + +thermo 50 + +server mc +run 0 +Neighbor list info ... + update every 20 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.44 -6.7733681 0 -4.6176881 -5.0221006 +Loop time of 4.76837e-06 on 4 procs for 0 steps with 500 atoms + +89.1% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 4.768e-06 | | |100.00 + +Nlocal: 125 ave 125 max 125 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 1099 ave 1099 max 1099 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 4875 ave 4875 max 4875 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 19500 +Ave neighs/atom = 39 +Neighbor list builds = 0 +Dangerous builds not checked +run 0 +Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.44 -6.7723127 0 -4.6166327 -5.015531 +Loop time of 3.45707e-06 on 4 procs for 0 steps with 500 atoms + +94.0% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 3.457e-06 | | |100.00 + +Nlocal: 125 ave 125 max 125 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 1099 ave 1099 max 1099 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 4875.25 ave 4885 max 4866 min +Histogram: 1 0 0 0 2 0 0 0 0 1 + +Total # of neighbors = 19501 +Ave neighs/atom = 39.002 +Neighbor list builds = 0 +Dangerous builds not checked +Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.44 -6.7723127 0 -4.6166327 -5.015531 + 50 0.70210225 -5.6759068 0 -4.6248598 0.59609192 + 100 0.75891559 -5.7611234 0 -4.6250267 0.20841608 +run 0 +Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes +Step Temp E_pair E_mol TotEng Press + 100 0.75891559 -5.7609392 0 -4.6248426 0.20981291 +Loop time of 3.03984e-06 on 4 procs for 0 steps with 500 atoms + +115.1% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 3.04e-06 | | |100.00 + +Nlocal: 125 ave 126 max 124 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 1085.25 ave 1089 max 1079 min +Histogram: 1 0 0 0 0 1 0 0 0 2 +Neighs: 4690.25 ave 4996 max 4401 min +Histogram: 1 0 0 1 0 1 0 0 0 1 + +Total # of neighbors = 18761 +Ave neighs/atom = 37.522 +Neighbor list builds = 0 +Dangerous builds not checked +Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes +Step Temp E_pair E_mol TotEng Press + 100 0.75891559 -5.7609392 0 -4.6248426 0.20981291 + 150 0.75437991 -5.7558622 0 -4.6265555 0.20681722 + 200 0.73111257 -5.7193748 0 -4.6248993 0.35230715 +run 0 +Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes +Step Temp E_pair E_mol TotEng Press + 200 0.73111257 -5.7143906 0 -4.6199151 0.37126023 +Loop time of 2.38419e-06 on 4 procs for 0 steps with 500 atoms + +125.8% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 2.384e-06 | | |100.00 + +Nlocal: 125 ave 126 max 123 min +Histogram: 1 0 0 0 0 0 1 0 0 2 +Nghost: 1068.5 ave 1076 max 1063 min +Histogram: 2 0 0 0 0 0 1 0 0 1 +Neighs: 4674.75 ave 4938 max 4419 min +Histogram: 1 0 0 0 1 1 0 0 0 1 + +Total # of neighbors = 18699 +Ave neighs/atom = 37.398 +Neighbor list builds = 0 +Dangerous builds not checked +Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes +Step Temp E_pair E_mol TotEng Press + 200 0.73111257 -5.7193748 0 -4.6248993 0.35230715 + 250 0.73873144 -5.7312505 0 -4.6253696 0.33061033 + 300 0.76392796 -5.7719207 0 -4.6283206 0.18197874 +run 0 +Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes +Step Temp E_pair E_mol TotEng Press + 300 0.76392796 -5.7725589 0 -4.6289588 0.17994628 +Loop time of 2.44379e-06 on 4 procs for 0 steps with 500 atoms + +112.5% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 2.444e-06 | | |100.00 + +Nlocal: 125 ave 128 max 121 min +Histogram: 1 0 0 0 0 1 0 1 0 1 +Nghost: 1069 ave 1080 max 1055 min +Histogram: 1 0 0 0 0 0 2 0 0 1 +Neighs: 4672 ave 4803 max 4600 min +Histogram: 2 0 0 1 0 0 0 0 0 1 + +Total # of neighbors = 18688 +Ave neighs/atom = 37.376 +Neighbor list builds = 0 +Dangerous builds not checked +Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes +Step Temp E_pair E_mol TotEng Press + 300 0.76392796 -5.7725589 0 -4.6289588 0.17994628 + 350 0.71953041 -5.7041632 0 -4.6270261 0.44866153 + 400 0.7319047 -5.7216051 0 -4.6259438 0.46321355 +run 0 +Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes +Step Temp E_pair E_mol TotEng Press + 400 0.7319047 -5.7158168 0 -4.6201554 0.49192039 +Loop time of 2.14577e-06 on 4 procs for 0 steps with 500 atoms + +139.8% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 2.146e-06 | | |100.00 + +Nlocal: 125 ave 132 max 118 min +Histogram: 1 0 0 0 0 2 0 0 0 1 +Nghost: 1057.5 ave 1068 max 1049 min +Histogram: 1 0 0 1 1 0 0 0 0 1 +Neighs: 4685.75 ave 5045 max 4229 min +Histogram: 1 0 0 1 0 0 0 0 0 2 + +Total # of neighbors = 18743 +Ave neighs/atom = 37.486 +Neighbor list builds = 0 +Dangerous builds not checked +Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes +Step Temp E_pair E_mol TotEng Press + 400 0.7319047 -5.7216051 0 -4.6259438 0.46321355 + 450 0.74503154 -5.7405318 0 -4.6252196 0.33211879 + 500 0.70570501 -5.6824439 0 -4.6260035 0.62020788 +Total wall time: 0:00:00 diff --git a/examples/COUPLE/lammps_mc/mc.cpp b/examples/COUPLE/lammps_mc/mc.cpp new file mode 100644 index 0000000000..7c2e2ce039 --- /dev/null +++ b/examples/COUPLE/lammps_mc/mc.cpp @@ -0,0 +1,263 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov +------------------------------------------------------------------------- */ + +// MC code used with LAMMPS in client/server mode +// MC is the client, LAMMPS is the server + +// Syntax: mc infile mode modearg +// mode = file, zmq +// modearg = filename for file, localhost:5555 for zmq + +#include +#include +#include +#include +#include "mc.h" +#include "random_park.h" + +#include "cslib.h" +using namespace CSLIB_NS; + +void error(const char *); +CSlib *cs_create(char *, char *); + +#define MAXLINE 256 + +/* ---------------------------------------------------------------------- */ + +// main program + +int main(int narg, char **arg) +{ + if (narg != 4) { + error("Syntax: mc infile mode modearg"); + exit(1); + } + + // initialize CSlib + + CSlib *cs = cs_create(arg[2],arg[3]); + + // create MC class and perform run + + MC *mc = new MC(arg[1],cs); + mc->run(); + + // final MC stats + + int naccept = mc->naccept; + int nattempt = mc->nattempt; + + printf("------ MC stats ------\n"); + printf("MC attempts = %d\n",nattempt); + printf("MC accepts = %d\n",naccept); + printf("Acceptance ratio = %g\n",1.0*naccept/nattempt); + + // clean up + + delete cs; + delete mc; +} + +/* ---------------------------------------------------------------------- */ + +void error(const char *str) +{ + printf("ERROR: %s\n",str); + exit(1); +} + +/* ---------------------------------------------------------------------- */ + +CSlib *cs_create(char *mode, char *arg) +{ + CSlib *cs = new CSlib(0,mode,arg,NULL); + + // initial handshake to agree on protocol + + cs->send(0,1); + cs->pack_string(1,(char *) "mc"); + + int msgID,nfield; + int *fieldID,*fieldtype,*fieldlen; + msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen); + + return cs; +} + +// ---------------------------------------------------------------------- +// MC class +// ---------------------------------------------------------------------- + +MC::MC(char *mcfile, void *cs_caller) +//MC::MC(char *mcfile, CSlib *cs_caller) +{ + cs_void = cs_caller; + + // setup MC params + + options(mcfile); + + // random # generator + + random = new RanPark(seed); +} + +/* ---------------------------------------------------------------------- */ + +MC::~MC() +{ + free(x); + delete random; +} + +/* ---------------------------------------------------------------------- */ + +void MC::run() +{ + int iatom,accept,msgID,nfield; + double pe_initial,pe_final,edelta; + double dx,dy,dz; + double xold[3],xnew[3]; + int *fieldID,*fieldtype,*fieldlen; + + enum{NATOMS=1,EINIT,DISPLACE,ACCEPT,RUN}; + + CSlib *cs = (CSlib *) cs_void; + + // one-time request for atom count from MD + // allocate 1d coord buffer + + cs->send(NATOMS,0); + + msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen); + natoms = cs->unpack_int(1); + + x = (double *) malloc(3*natoms*sizeof(double)); + + // loop over MC moves + + naccept = nattempt = 0; + + for (int iloop = 0; iloop < nloop; iloop++) { + + // request current energy from MD + // recv energy, coords from MD + + cs->send(EINIT,0); + + msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen); + pe_initial = cs->unpack_double(1); + double *x = (double *) cs->unpack(2); + + // perform simple MC event + // displace a single atom by random amount + + iatom = (int) natoms*random->uniform(); + xold[0] = x[3*iatom+0]; + xold[1] = x[3*iatom+1]; + xold[2] = x[3*iatom+2]; + + dx = 2.0*delta*random->uniform() - delta; + dy = 2.0*delta*random->uniform() - delta; + dz = 2.0*delta*random->uniform() - delta; + + xnew[0] = xold[0] + dx; + xnew[1] = xold[1] + dx; + xnew[2] = xold[2] + dx; + + // send atom ID and its new coords to MD + // recv new energy + + cs->send(DISPLACE,2); + cs->pack_int(1,iatom+1); + cs->pack(2,4,3,xnew); + + msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen); + pe_final = cs->unpack_double(1); + + // decide whether to accept/reject MC event + + if (pe_final <= pe_initial) accept = 1; + else if (temperature == 0.0) accept = 0; + else if (random->uniform() > + exp(natoms*(pe_initial-pe_final)/temperature)) accept = 0; + else accept = 1; + + nattempt++; + if (accept) naccept++; + + // send accept (1) or reject (0) flag to MD + + cs->send(ACCEPT,1); + cs->pack_int(1,accept); + + msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen); + + // send dynamics timesteps + + cs->send(RUN,1); + cs->pack_int(1,ndynamics); + + msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen); + } + + // send exit message to MD + + cs->send(-1,0); + msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen); +} + +/* ---------------------------------------------------------------------- */ + +void MC::options(char *filename) +{ + // default params + + nsteps = 0; + ndynamics = 100; + delta = 0.1; + temperature = 1.0; + seed = 12345; + + // read and parse file + + FILE *fp = fopen(filename,"r"); + if (fp == NULL) error("Could not open MC file"); + + char line[MAXLINE]; + char *keyword,*value; + char *eof = fgets(line,MAXLINE,fp); + + while (eof) { + if (line[0] == '#') { // comment line + eof = fgets(line,MAXLINE,fp); + continue; + } + + value = strtok(line," \t\n\r\f"); + if (value == NULL) { // blank line + eof = fgets(line,MAXLINE,fp); + continue; + } + + keyword = strtok(NULL," \t\n\r\f"); + if (keyword == NULL) error("Missing keyword in MC file"); + + if (strcmp(keyword,"nsteps") == 0) nsteps = atoi(value); + else if (strcmp(keyword,"ndynamics") == 0) ndynamics = atoi(value); + else if (strcmp(keyword,"delta") == 0) delta = atof(value); + else if (strcmp(keyword,"temperature") == 0) temperature = atof(value); + else if (strcmp(keyword,"seed") == 0) seed = atoi(value); + else error("Unknown param in MC file"); + + eof = fgets(line,MAXLINE,fp); + } + + // derived params + + nloop = nsteps/ndynamics; +} diff --git a/examples/COUPLE/lammps_mc/mc.h b/examples/COUPLE/lammps_mc/mc.h new file mode 100644 index 0000000000..e9d88523fc --- /dev/null +++ b/examples/COUPLE/lammps_mc/mc.h @@ -0,0 +1,40 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov +------------------------------------------------------------------------- */ + +#ifndef MC_H +#define MC_H + +/* ---------------------------------------------------------------------- */ + +class MC { + public: + int naccept; // # of accepted MC events + int nattempt; // # of attempted MC events + + MC(char *, void *); + ~MC(); + void run(); + + private: + int nsteps; // total # of MD steps + int ndynamics; // steps in one short dynamics run + int nloop; // nsteps/ndynamics + int natoms; // # of MD atoms + + double delta; // MC displacement distance + double temperature; // MC temperature for Boltzmann criterion + double *x; // atom coords as 3N 1d vector + double energy; // global potential energy + + int seed; // RNG seed + class RanPark *random; + + void *cs_void; // messaging library + + void options(char *); +}; + +#endif diff --git a/examples/COUPLE/lammps_mc/random_park.cpp b/examples/COUPLE/lammps_mc/random_park.cpp new file mode 100644 index 0000000000..61ac18c6c0 --- /dev/null +++ b/examples/COUPLE/lammps_mc/random_park.cpp @@ -0,0 +1,72 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +// Park/Miller RNG + +#include +#include "random_park.h" +//#include "error.h" + +#define IA 16807 +#define IM 2147483647 +#define AM (1.0/IM) +#define IQ 127773 +#define IR 2836 + +/* ---------------------------------------------------------------------- */ + +RanPark::RanPark(int seed_init) +{ + //if (seed_init <= 0) + // error->one(FLERR,"Invalid seed for Park random # generator"); + seed = seed_init; + save = 0; +} + +/* ---------------------------------------------------------------------- + uniform RN +------------------------------------------------------------------------- */ + +double RanPark::uniform() +{ + int k = seed/IQ; + seed = IA*(seed-k*IQ) - IR*k; + if (seed < 0) seed += IM; + double ans = AM*seed; + return ans; +} + +/* ---------------------------------------------------------------------- + gaussian RN +------------------------------------------------------------------------- */ + +double RanPark::gaussian() +{ + double first,v1,v2,rsq,fac; + + if (!save) { + do { + v1 = 2.0*uniform()-1.0; + v2 = 2.0*uniform()-1.0; + rsq = v1*v1 + v2*v2; + } while ((rsq >= 1.0) || (rsq == 0.0)); + fac = sqrt(-2.0*log(rsq)/rsq); + second = v1*fac; + first = v2*fac; + save = 1; + } else { + first = second; + save = 0; + } + return first; +} diff --git a/examples/COUPLE/lammps_mc/random_park.h b/examples/COUPLE/lammps_mc/random_park.h new file mode 100644 index 0000000000..0dc2081768 --- /dev/null +++ b/examples/COUPLE/lammps_mc/random_park.h @@ -0,0 +1,28 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifndef RANPARK_H +#define RANPARK_H + +class RanPark { + public: + RanPark(int); + double uniform(); + double gaussian(); + + private: + int seed,save; + double second; +}; + +#endif diff --git a/examples/COUPLE/lammps_vasp/INCAR b/examples/COUPLE/lammps_vasp/INCAR new file mode 100644 index 0000000000..ac2358e5fb --- /dev/null +++ b/examples/COUPLE/lammps_vasp/INCAR @@ -0,0 +1,53 @@ +# Startparameter for this run: + NWRITE = 2 write-flag & timer + PREC = normal normal or accurate (medium, high low for compatibility) + ISTART = 0 job : 0-new 1-cont 2-samecut + ICHARG = 2 charge: 1-file 2-atom 10-const + ISPIN = 1 spin polarized calculation? + LSORBIT = F spin-orbit coupling + INIWAV = 1 electr: 0-lowe 1-rand 2-diag + +# Electronic Relaxation 1 + ENCUT = 600.0 eV #Plane wave energy cutoff + ENINI = 600.0 initial cutoff + NELM = 100; NELMIN= 2; NELMDL= -5 # of ELM steps + EDIFF = 0.1E-05 stopping-criterion for ELM +# Ionic relaxation + EDIFFG = 0.1E-02 stopping-criterion for IOM + NSW = 0 number of steps for IOM + NBLOCK = 1; KBLOCK = 1 inner block; outer block + IBRION = -1 ionic relax: 0-MD 1-quasi-New 2-CG #No ion relaxation with -1 + NFREE = 0 steps in history (QN), initial steepest desc. (CG) + ISIF = 2 stress and relaxation # 2: F-yes Sts-yes RlxIon-yes cellshape-no cellvol-no + IWAVPR = 10 prediction: 0-non 1-charg 2-wave 3-comb # 10: TMPCAR stored in memory rather than file + + POTIM = 0.5000 time-step for ionic-motion + TEBEG = 3500.0; TEEND = 3500.0 temperature during run # Finite Temperature variables if AI-MD is on + SMASS = -3.00 Nose mass-parameter (am) + estimated Nose-frequenzy (Omega) = 0.10E-29 period in steps =****** mass= -0.366E-27a.u. + PSTRESS= 0.0 pullay stress + +# DOS related values: + EMIN = 10.00; EMAX =-10.00 energy-range for DOS + EFERMI = 0.00 + ISMEAR = 0; SIGMA = 0.10 broadening in eV -4-tet -1-fermi 0-gaus + +# Electronic relaxation 2 (details) + IALGO = 48 algorithm + +# Write flags + LWAVE = T write WAVECAR + LCHARG = T write CHGCAR + LVTOT = F write LOCPOT, total local potential + LVHAR = F write LOCPOT, Hartree potential only + LELF = F write electronic localiz. function (ELF) + +# Dipole corrections + LMONO = F monopole corrections only (constant potential shift) + LDIPOL = F correct potential (dipole corrections) + IDIPOL = 0 1-x, 2-y, 3-z, 4-all directions + EPSILON= 1.0000000 bulk dielectric constant + +# Exchange correlation treatment: + GGA = -- GGA type + diff --git a/examples/COUPLE/lammps_vasp/KPOINTS b/examples/COUPLE/lammps_vasp/KPOINTS new file mode 100644 index 0000000000..322509da30 --- /dev/null +++ b/examples/COUPLE/lammps_vasp/KPOINTS @@ -0,0 +1,6 @@ +K-Points + 0 +Monkhorst Pack + 15 15 15 + 0 0 0 + diff --git a/examples/COUPLE/lammps_vasp/POSCAR_W b/examples/COUPLE/lammps_vasp/POSCAR_W new file mode 100644 index 0000000000..aba5df54a0 --- /dev/null +++ b/examples/COUPLE/lammps_vasp/POSCAR_W @@ -0,0 +1,11 @@ +W unit cell +1.0 +3.16 0.00000000 0.00000000 +0.00000000 3.16 0.00000000 +0.00000000 0.00000000 3.16 +W +2 +Direct + 0.00000000 0.00000000 0.00000000 + 0.50000000 0.50000000 0.50000000 + diff --git a/examples/COUPLE/lammps_vasp/README b/examples/COUPLE/lammps_vasp/README new file mode 100644 index 0000000000..e942d52535 --- /dev/null +++ b/examples/COUPLE/lammps_vasp/README @@ -0,0 +1,149 @@ +Sample LAMMPS MD wrapper on VASP quantum DFT via client/server +coupling + +See the MESSAGE package (doc/Section_messages.html#MESSAGE) and +Section_howto.html#howto10 for more details on how client/server +coupling works in LAMMPS. + +In this dir, the vasp_wrap.py is a wrapper on the VASP quantum DFT +code so it can work as a "server" code which LAMMPS drives as a +"client" code to perform ab initio MD. LAMMPS performs the MD +timestepping, sends VASP a current set of coordinates each timestep, +VASP computes forces and energy and virial and returns that info to +LAMMPS. + +Messages are exchanged between MC and LAMMPS via a client/server +library (CSlib), which is included in the LAMMPS distribution in +lib/message. As explained below you can choose to exchange data +between the two programs either via files or sockets (ZMQ). If the +vasp_wrap.py program became parallel, or the CSlib library calls were +integrated into VASP directly, then data could also be exchanged via +MPI. + +---------------- + +Build LAMMPS with its MESSAGE package installed: + +See the Build extras doc page and its MESSAGE package +section for details. + +CMake: + +-D PKG_MESSAGE=yes # include the MESSAGE package +-D MESSAGE_ZMQ=value # build with ZeroMQ support, value = no (default) or yes + +Traditional make: + +cd lammps/lib/message +python Install.py -m -z # build CSlib with MPI and ZMQ support +cd lammps/src +make yes-message +make mpi + +You can leave off the -z if you do not have ZMQ on your system. + +---------------- + +Build the CSlib in a form usable by the vasp_wrapper.py script: + +% cd lammps/lib/message/cslib/src +% make shlib # build serial and parallel shared lib with ZMQ support +% make shlib zmq=no # build serial and parallel shared lib w/out ZMQ support + +This will make a shared library versions of the CSlib, which Python +requires. Python must be able to find both the cslib.py script and +the libcsnompi.so library in your lammps/lib/message/cslib/src +directory. If it is not able to do this, you will get an error when +you run vasp_wrapper.py. + +You can do this by augmenting two environment variables, either +from the command line, or in your shell start-up script. +Here is the sample syntax for the csh or tcsh shells: + +setenv PYTHONPATH ${PYTHONPATH}:/home/sjplimp/lammps/lib/message/cslib/src +setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/home/sjplimp/lammps/lib/message/cslib/src + +---------------- + +Prepare to use VASP and the vasp_wrapper.py script + +You can run the vasp_wrap.py script as-is to test that the coupling +between it and LAMMPS is functional. This will use the included +vasprun.xml file output by a previous VASP run. + +But note that the as-is version of vasp_wrap.py will not attempt to +run VASP. + +To do this, you must edit the 1st vaspcmd line at the top of +vasp_wrapper.py to be the launch command needed to run VASP on your +system. It can be a command to run VASP in serial or in parallel, +e.g. an mpirun command. Then comment out the 2nd vaspcmd line +immediately following it. + +Insure you have the necessary VASP input files in this +directory, suitable for the VASP calculation you want to perform: + +INCAR +KPOINTS +POSCAR_template +POTCAR + +Examples of all but the POTCAR file are provided. As explained below, +POSCAR_W is an input file for a 2-atom unit cell of tungsten and can +be used to test the LAMMPS/VASP coupling. The POTCAR file is a +proprietary VASP file, so use one from your VASP installation. + +Note that the POSCAR_template file should be matched to the LAMMPS +input script (# of atoms and atom types, box size, etc). The provided +POSCAR_W matches in.client.W. + +Once you run VASP yourself, the vasprun.xml file will be overwritten. + +---------------- + +To run in client/server mode: + +NOTE: The vasp_wrap.py script must be run with Python version 2, not +3. This is because it used the CSlib python wrapper, which only +supports version 2. We plan to upgrade CSlib to support Python 3. + +Both the client (LAMMPS) and server (vasp_wrap.py) must use the same +messaging mode, namely file or zmq. This is an argument to the +vasp_wrap.py code; it can be selected by setting the "mode" variable +when you run LAMMPS. The default mode = file. + +Here we assume LAMMPS was built to run in parallel, and the MESSAGE +package was installed with socket (ZMQ) support. This means either of +the messaging modes can be used and LAMMPS can be run in serial or +parallel. The vasp_wrap.py code is always run in serial, but it +launches VASP from Python via an mpirun command which can run VASP +itself in parallel. + +When you run, the server should print out thermodynamic info every +timestep which corresponds to the forces and virial computed by VASP. +VASP will also generate output files each timestep. The vasp_wrapper.py +script could be generalized to archive these. + +The examples below are commands you should use in two different +terminal windows. The order of the two commands (client or server +launch) does not matter. You can run them both in the same window if +you append a "&" character to the first one to run it in the +background. + +-------------- + +File mode of messaging: + +% mpirun -np 1 lmp_mpi -v mode file < in.client.W +% python vasp_wrap.py file POSCAR_W + +% mpirun -np 2 lmp_mpi -v mode file < in.client.W +% python vasp_wrap.py file POSCAR_W + +ZMQ mode of messaging: + +% mpirun -np 1 lmp_mpi -v mode zmq < in.client.W +% python vasp_wrap.py zmq POSCAR_W + +% mpirun -np 2 lmp_mpi -v mode zmq < in.client.W +% python vasp_wrap.py zmq POSCAR_W diff --git a/examples/COUPLE/lammps_vasp/data.W b/examples/COUPLE/lammps_vasp/data.W new file mode 100644 index 0000000000..8accd9ca79 --- /dev/null +++ b/examples/COUPLE/lammps_vasp/data.W @@ -0,0 +1,15 @@ +LAMMPS W data file + +2 atoms + +1 atom types + +0.0 3.16 xlo xhi +0.0 3.16 ylo yhi +0.0 3.16 zlo zhi + +Atoms + +1 1 0.000 0.000 0.000 +2 1 1.58 1.58 1.58 + diff --git a/examples/COUPLE/lammps_vasp/in.client.W b/examples/COUPLE/lammps_vasp/in.client.W new file mode 100644 index 0000000000..3eaf99dcbb --- /dev/null +++ b/examples/COUPLE/lammps_vasp/in.client.W @@ -0,0 +1,34 @@ +# small W unit cell for use with VASP + +variable mode index file + +if "${mode} == file" then & + "message client md file tmp.couple" & +elif "${mode} == zmq" & + "message client md zmq localhost:5555" & + +variable x index 1 +variable y index 1 +variable z index 1 + +units metal +atom_style atomic +atom_modify sort 0 0.0 map yes + +read_data data.W +mass 1 183.85 + +replicate $x $y $z + +velocity all create 300.0 87287 loop geom + +neighbor 0.3 bin +neigh_modify delay 0 every 10 check no + +fix 1 all nve +fix 2 all client/md +fix_modify 2 energy yes + +thermo 1 +run 3 + diff --git a/examples/COUPLE/lammps_vasp/log.client.output b/examples/COUPLE/lammps_vasp/log.client.output new file mode 100644 index 0000000000..fa8f4f920a --- /dev/null +++ b/examples/COUPLE/lammps_vasp/log.client.output @@ -0,0 +1,76 @@ +LAMMPS (22 Aug 2018) +# small W unit cell for use with VASP + +variable mode index file + +if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" +message client md zmq localhost:5555 +variable x index 1 +variable y index 1 +variable z index 1 + +units metal +atom_style atomic +atom_modify sort 0 0.0 map yes + +read_data data.W + orthogonal box = (0 0 0) to (3.16 3.16 3.16) + 1 by 1 by 2 MPI processor grid + reading atoms ... + 2 atoms +mass 1 183.85 + +replicate $x $y $z +replicate 1 $y $z +replicate 1 1 $z +replicate 1 1 1 + orthogonal box = (0 0 0) to (3.16 3.16 3.16) + 1 by 1 by 2 MPI processor grid + 2 atoms + Time spent = 0.000148058 secs + +velocity all create 300.0 87287 loop geom + +neighbor 0.3 bin +neigh_modify delay 0 every 10 check no + +fix 1 all nve +fix 2 all client/md +fix_modify 2 energy yes + +thermo 1 +run 3 +Per MPI rank memory allocation (min/avg/max) = 1.8 | 1.8 | 1.8 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 300 0 0 -48.030793 -78159.503 + 1 298.24318 0 0 -48.03102 -78167.19 + 2 296.85584 0 0 -48.031199 -78173.26 + 3 295.83795 0 0 -48.031331 -78177.714 +Loop time of 0.457491 on 2 procs for 3 steps with 2 atoms + +Performance: 0.567 ns/day, 42.360 hours/ns, 6.558 timesteps/s +50.1% CPU use with 2 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 1.3828e-05 | 2.9922e-05 | 4.6015e-05 | 0.0 | 0.01 +Output | 7.5817e-05 | 9.3937e-05 | 0.00011206 | 0.0 | 0.02 +Modify | 0.45735 | 0.45736 | 0.45736 | 0.0 | 99.97 +Other | | 1.204e-05 | | | 0.00 + +Nlocal: 1 ave 1 max 1 min +Histogram: 2 0 0 0 0 0 0 0 0 0 +Nghost: 4 ave 4 max 4 min +Histogram: 2 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds not checked + +Total wall time: 0:01:21 diff --git a/examples/COUPLE/lammps_vasp/vasp_wrap.py b/examples/COUPLE/lammps_vasp/vasp_wrap.py new file mode 100644 index 0000000000..1e2c52aa46 --- /dev/null +++ b/examples/COUPLE/lammps_vasp/vasp_wrap.py @@ -0,0 +1,300 @@ +#!/usr/bin/env python + +# ---------------------------------------------------------------------- +# LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator +# http://lammps.sandia.gov, Sandia National Laboratories +# Steve Plimpton, sjplimp@sandia.gov +# ---------------------------------------------------------------------- + +# Syntax: vasp_wrap.py file/zmq POSCARfile + +# wrapper on VASP to act as server program using CSlib +# receives message with list of coords from client +# creates VASP inputs +# invokes VASP to calculate self-consistent energy of that config +# reads VASP outputs +# sends message with energy, forces, pressure to client + +# NOTES: +# check to insure basic VASP input files are in place? +# could archive VASP input/output in special filenames or dirs? +# need to check that POTCAR file is consistent with atom ordering? +# could make syntax for launching VASP more flexible +# e.g. command-line arg for # of procs +# detect if VASP had an error and return ERROR field, e.g. non-convergence ?? + +from __future__ import print_function +import sys + +version = sys.version_info[0] +if version == 3: + sys.exit("The CSlib python wrapper does not yet support python 3") + +import subprocess +import xml.etree.ElementTree as ET +from cslib import CSlib + +# comment out 2nd line once 1st line is correct for your system + +vaspcmd = "srun -N 1 --ntasks-per-node=4 " + \ + "-n 4 /projects/vasp/2017-build/cts1/vasp5.4.4/vasp_tfermi/bin/vasp_std" +vaspcmd = "touch tmp" + +# enums matching FixClientMD class in LAMMPS + +SETUP,STEP = range(1,2+1) +DIM,PERIODICITY,ORIGIN,BOX,NATOMS,NTYPES,TYPES,COORDS,UNITS,CHARGE = range(1,10+1) +FORCES,ENERGY,VIRIAL,ERROR = range(1,4+1) + +# ------------------------------------- +# functions + +# error message and exit + +def error(txt): + print("ERROR:",txt) + sys.exit(1) + +# ------------------------------------- +# read initial VASP POSCAR file to setup problem +# return natoms,ntypes,box + +def vasp_setup(poscar): + + ps = open(poscar,'r').readlines() + + # box size + + words = ps[2].split() + xbox = float(words[0]) + words = ps[3].split() + ybox = float(words[1]) + words = ps[4].split() + zbox = float(words[2]) + box = [xbox,ybox,zbox] + + ntypes = 0 + natoms = 0 + words = ps[6].split() + for word in words: + if word == '#': break + ntypes += 1 + natoms += int(word) + + return natoms,ntypes,box + +# ------------------------------------- +# write a new POSCAR file for VASP + +def poscar_write(poscar,natoms,ntypes,types,coords,box): + + psold = open(poscar,'r').readlines() + psnew = open("POSCAR",'w') + + # header, including box size + + psnew.write(psold[0]) + psnew.write(psold[1]) + psnew.write("%g %g %g\n" % (box[0],box[1],box[2])) + psnew.write("%g %g %g\n" % (box[3],box[4],box[5])) + psnew.write("%g %g %g\n" % (box[6],box[7],box[8])) + psnew.write(psold[5]) + psnew.write(psold[6]) + + # per-atom coords + # grouped by types + + psnew.write("Cartesian\n") + + for itype in range(1,ntypes+1): + for i in range(natoms): + if types[i] != itype: continue + x = coords[3*i+0] + y = coords[3*i+1] + z = coords[3*i+2] + aline = " %g %g %g\n" % (x,y,z) + psnew.write(aline) + + psnew.close() + +# ------------------------------------- +# read a VASP output vasprun.xml file +# uses ElementTree module +# see https://docs.python.org/2/library/xml.etree.elementtree.html + +def vasprun_read(): + tree = ET.parse('vasprun.xml') + root = tree.getroot() + + #fp = open("vasprun.xml","r") + #root = ET.parse(fp) + + scsteps = root.findall('calculation/scstep') + energy = scsteps[-1].find('energy') + for child in energy: + if child.attrib["name"] == "e_0_energy": + eout = float(child.text) + + fout = [] + sout = [] + + varrays = root.findall('calculation/varray') + for varray in varrays: + if varray.attrib["name"] == "forces": + forces = varray.findall("v") + for line in forces: + fxyz = line.text.split() + fxyz = [float(value) for value in fxyz] + fout += fxyz + if varray.attrib["name"] == "stress": + tensor = varray.findall("v") + stensor = [] + for line in tensor: + sxyz = line.text.split() + sxyz = [float(value) for value in sxyz] + stensor.append(sxyz) + sxx = stensor[0][0] + syy = stensor[1][1] + szz = stensor[2][2] + # symmetrize off-diagonal components + sxy = 0.5 * (stensor[0][1] + stensor[1][0]) + sxz = 0.5 * (stensor[0][2] + stensor[2][0]) + syz = 0.5 * (stensor[1][2] + stensor[2][1]) + sout = [sxx,syy,szz,sxy,sxz,syz] + + #fp.close() + + return eout,fout,sout + +# ------------------------------------- +# main program + +# command-line args + +if len(sys.argv) != 3: + print("Syntax: python vasp_wrap.py file/zmq POSCARfile") + sys.exit(1) + +mode = sys.argv[1] +poscar_template = sys.argv[2] + +if mode == "file": cs = CSlib(1,mode,"tmp.couple",None) +elif mode == "zmq": cs = CSlib(1,mode,"*:5555",None) +else: + print("Syntax: python vasp_wrap.py file/zmq POSCARfile") + sys.exit(1) + +natoms,ntypes,box = vasp_setup(poscar_template) + +# initial message for MD protocol + +msgID,nfield,fieldID,fieldtype,fieldlen = cs.recv() +if msgID != 0: error("Bad initial client/server handshake") +protocol = cs.unpack_string(1) +if protocol != "md": error("Mismatch in client/server protocol") +cs.send(0,0) + +# endless server loop + +while 1: + + # recv message from client + # msgID = 0 = all-done message + + msgID,nfield,fieldID,fieldtype,fieldlen = cs.recv() + if msgID < 0: break + + # SETUP receive at beginning of each run + # required fields: DIM, PERIODICTY, ORIGIN, BOX, + # NATOMS, NTYPES, TYPES, COORDS + # optional fields: others in enum above, but VASP ignores them + + if msgID == SETUP: + + origin = [] + box = [] + natoms_recv = ntypes_recv = 0 + types = [] + coords = [] + + for field in fieldID: + if field == DIM: + dim = cs.unpack_int(DIM) + if dim != 3: error("VASP only performs 3d simulations") + elif field == PERIODICITY: + periodicity = cs.unpack(PERIODICITY,1) + if not periodicity[0] or not periodicity[1] or not periodicity[2]: + error("VASP wrapper only currently supports fully periodic systems") + elif field == ORIGIN: + origin = cs.unpack(ORIGIN,1) + elif field == BOX: + box = cs.unpack(BOX,1) + elif field == NATOMS: + natoms_recv = cs.unpack_int(NATOMS) + if natoms != natoms_recv: + error("VASP wrapper mis-match in number of atoms") + elif field == NTYPES: + ntypes_recv = cs.unpack_int(NTYPES) + if ntypes != ntypes_recv: + error("VASP wrapper mis-match in number of atom types") + elif field == TYPES: + types = cs.unpack(TYPES,1) + elif field == COORDS: + coords = cs.unpack(COORDS,1) + + if not origin or not box or not natoms or not ntypes or \ + not types or not coords: + error("Required VASP wrapper setup field not received"); + + # STEP receive at each timestep of run or minimization + # required fields: COORDS + # optional fields: ORIGIN, BOX + + elif msgID == STEP: + + coords = [] + + for field in fieldID: + if field == COORDS: + coords = cs.unpack(COORDS,1) + elif field == ORIGIN: + origin = cs.unpack(ORIGIN,1) + elif field == BOX: + box = cs.unpack(BOX,1) + + if not coords: error("Required VASP wrapper step field not received"); + + else: error("VASP wrapper received unrecognized message") + + # create POSCAR file + + poscar_write(poscar_template,natoms,ntypes,types,coords,box) + + # invoke VASP + + print("\nLaunching VASP ...") + print(vaspcmd) + subprocess.check_output(vaspcmd,stderr=subprocess.STDOUT,shell=True) + + # process VASP output + + energy,forces,virial = vasprun_read() + + # convert VASP kilobars to bars + + for i,value in enumerate(virial): virial[i] *= 1000.0 + + # return forces, energy, pressure to client + + cs.send(msgID,3); + cs.pack(FORCES,4,3*natoms,forces) + cs.pack_double(ENERGY,energy) + cs.pack(VIRIAL,4,6,virial) + +# final reply to client + +cs.send(0,0) + +# clean-up + +del cs diff --git a/examples/COUPLE/lammps_vasp/vasprun.xml b/examples/COUPLE/lammps_vasp/vasprun.xml new file mode 100644 index 0000000000..0f15c871b4 --- /dev/null +++ b/examples/COUPLE/lammps_vasp/vasprun.xml @@ -0,0 +1,12329 @@ + + + + vasp + 5.4.4.18Apr17-6-g9f103f2a35 + (build Aug 01 2017 10:32:50) complex parallel + LinuxIFC + 2017 12 19 + 15:22:45 + + + 0 + normal normal or accurate (medium, h + 48 + F + 1 + 2 + 1 + 100 + -5 + 2 + -1 + 0 + 0.00000100 + 0.00100000 + 0 + 2 + 10 + 1 + 1 + 600.00000000 + 600.00000000 + 0.50000000 + 3500.00000000 + 3500.00000000 + -3.00000000 + 10.00000000 + -10.00000000 + 0.00000000 + 0 + 0.10000000 + 2 + 0.00000000 + T + T + F + F + F + -1 0 0 0 + 100 + -- GGA type + F + F + 0 + 1.00000000 + + + + + 3.66961100 0.00000000 0.00000000 + 0.00000000 3.55744000 0.00000000 + 0.00000000 0.00000000 3.17678100 + + 41.47103646 + + 0.27250845 0.00000000 0.00000000 + 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0.00000000 0.00000000 + 0.00000000 0.28110102 0.00000000 + 0.00000000 0.00000000 0.31478405 + + + + 0.00000000 0.00000000 0.00000000 + 0.00000000 0.50000000 0.50000000 + 0.50000000 0.00000000 0.50000000 + 0.50000000 0.50000000 0.00000000 + + + diff --git a/examples/README b/examples/README index d6c946725f..3c9c299819 100644 --- a/examples/README +++ b/examples/README @@ -83,6 +83,7 @@ kim: use of potentials in Knowledge Base for Interatomic Models (KIM) latte: use of LATTE density-functional tight-binding quantum code meam: MEAM test for SiC and shear (same as shear examples) melt: rapid melt of 3d LJ system +message: client/server coupling of 2 codes micelle: self-assembly of small lipid-like molecules into 2d bilayers min: energy minimization of 2d LJ melt mscg: parameterize a multi-scale coarse-graining (MSCG) model diff --git a/examples/USER/diffraction/BulkNi.in b/examples/USER/diffraction/BulkNi.in index 0fa9c1b74c..8315e57750 100644 --- a/examples/USER/diffraction/BulkNi.in +++ b/examples/USER/diffraction/BulkNi.in @@ -17,8 +17,9 @@ atom_modify sort 0 0 compute XRD all xrd 1.541838 Ni 2Theta 40 80 c 2 2 2 LP 1 echo -compute SAED all saed 0.0251 Ni Kmax 0.85 Zone 1 0 0 c 0.025 0.025 0.025 & - dR_Ewald 0.05 echo manual +compute SAED all saed 0.0251 Ni Kmax 0.85 & + Zone 0 0 0 c 0.025 0.025 0.025 & + dR_Ewald 0.01 echo manual fix 1 all ave/histo/weight 1 1 1 40 80 200 c_XRD[1] c_XRD[2] & mode vector file $A.hist.xrd diff --git a/examples/USER/diffraction/Output/BulkNi.in b/examples/USER/diffraction/Output/BulkNi.in deleted file mode 100644 index 8315e57750..0000000000 --- a/examples/USER/diffraction/Output/BulkNi.in +++ /dev/null @@ -1,35 +0,0 @@ -variable A string bulkNi -log $A.log - -boundary p p p - -units metal -timestep 0.001 - -lattice fcc 3.52 -region box block 0 20 0 20 0 20 -create_box 1 box -create_atoms 1 box - -pair_style none -mass * 58.71 -atom_modify sort 0 0 - -compute XRD all xrd 1.541838 Ni 2Theta 40 80 c 2 2 2 LP 1 echo - -compute SAED all saed 0.0251 Ni Kmax 0.85 & - Zone 0 0 0 c 0.025 0.025 0.025 & - dR_Ewald 0.01 echo manual - -fix 1 all ave/histo/weight 1 1 1 40 80 200 c_XRD[1] c_XRD[2] & - mode vector file $A.hist.xrd - -fix 2 all saed/vtk 1 1 1 c_SAED file $A_001.saed - -dump 1 all custom 1 $A.dump id x y z -run 0 - -unfix 1 -unfix 2 -uncompute XRD -uncompute SAED diff --git a/examples/message/README b/examples/message/README new file mode 100644 index 0000000000..6cd99d5c09 --- /dev/null +++ b/examples/message/README @@ -0,0 +1,117 @@ +This dir contains scripts that demonstrate how to use LAMMPS as both a +client and server code to run a simple MD simulation. LAMMPS as a +client performs the MD timestepping. LAMMPS as a server provides the +energy and forces between interacting particles. Every timestep the +LAMMPS client sends a message to the LAMMPS server and receives a +response message in return. + +Another code could replace LAMMPS as the client, e.g. another MD code +which wants to use a LAMMPS potential. Another code could replace +LAMMPS as the server, e.g. a quantum code computing quantum forces, so +that ab initio MD could be performed. See an example of the latter in +examples/COUPLE/lammps_vasp. + +See the doc pages for the "MESSAGE package" +(Package_details.html#PKG-MESSAGE) and "Howto client/server" +(Howto_client_server.html) for more details on how client/server +coupling works in LAMMPS. + +-------------- + +Note that you can adjust the problem size run by these scripts by +setting "x,y,z" variables when you run LAMMPS. The default problem size +is x = y = z = 5, which is 500 particles. + +lmp_mpi -v x 10 -v y 10 -v z 20 # 8000 particles + +This applies to either in.message or in.message.client + +You can also run the in.message scripts with an NPT integrator +instead of NVE, if you comment/uncomment the correct lines. + +The client and server script define a "mode" variable +which can be set to file, zmq, mpi/one, or mpi/two, +as illustrated below. + +-------------- + +To run this problem in the traditional way (no client/server coupling) +do one of these: + +% lmp_serial < in.message +% mpirun -np 4 lmp_mpi < in.message + +Or run with in.message.tilt. + +-------------- + +To run in client/server mode: + +Both the client and server script must use the same messaging mode. +This can be selected by setting the "mode" variable when you run +LAMMPS. The default mode = file. The other options for the mode +variable are zmq, mpione, mpitwo. + +Here we assume LAMMPS was built to run in parallel, and the MESSAGE +package was installed with socket (ZMQ) support. This means any of +the 4 messaging modes can be used. + +The next sections illustrate how to launch LAMMPS twice, once as a +client, once as a server, for each of the messaging modes. + +In all cases, the client should print out thermodynamic info for 50 +steps. The server should print out setup info, print nothing until +the client exits, at which point the server should also exit. + +The examples below show launching LAMMPS twice from the same window +(or batch script), using the "&" character to launch the first time in +the background. For all modes except {mpi/one}, you could also launch +twice in separate windows on your desktop machine. It does not matter +whether you launch the client or server first. + +In these examples either the client or server can be run on one or +more processors. If running in a non-MPI mode (file or zmq) you can +launch LAMMPS on a single processor without using mpirun. + +IMPORTANT: If you run in mpi/two mode, you must launch LAMMPS both +times via mpirun, even if one or both of them runs on a single +processor. This is so that MPI can figure out how to connect both MPI +processes together to exchange MPI messages between them. + +-------------- + +NOTE: the Script.sh file has comands to perform all the +runs listed below. + +-------------- + +File or ZMQ or mpi/two modes of messaging: + +% mpirun -np 1 lmp_mpi -v mode file -log log.client < in.message.client & +% mpirun -np 2 lmp_mpi -v mode file -log log.server < in.message.server + +% mpirun -np 4 lmp_mpi -v mode zmq -log log.client < in.message.client & +% mpirun -np 1 lmp_mpi -v mode zmq -log log.server < in.message.server + +% mpirun -np 2 lmp_mpi -v mode mpitwo -log log.client < in.message.client & +% mpirun -np 4 lmp_mpi -v mode mpitwo -log log.server < in.message.server + +Or run with in.message.tilt.client/server. +Don't run the tilt files with the "file" mode; they run too slow. + +-------------- + +Mpi/one mode of messaging: + +Launch LAMMPS twice in a single mpirun command: + +% mpirun -np 2 lmp_mpi -mpicolor 0 -in in.message.client -v mode mpione -log log.client : -np 4 lmp_mpi -mpicolor 1 -in in.message.server -v mode mpione -log log.server + +Or run with in.message.tilt.client/server. + +The two -np values determine how many procs the client and the server +run on. + +A LAMMPS executable run in this manner must use the -mpicolor color +command-line option as its first option, where color is set to one +integer value for the 1st app, and another value for the 2nd app. diff --git a/examples/message/Script.sh b/examples/message/Script.sh new file mode 100644 index 0000000000..fdcd6f1188 --- /dev/null +++ b/examples/message/Script.sh @@ -0,0 +1,55 @@ +# sample launch script + +# message on 1 proc each + +mpirun -np 1 lmp_mpi -log log.message.g++.1 < in.message + +mpirun -np 1 lmp_mpi -v mode file -log log.message.client.file.g++.1 < in.message.client & +mpirun -np 1 lmp_mpi -v mode file -log log.message.server.file.g++.1 < in.message.server + +mpirun -np 1 lmp_mpi -v mode zmq -log log.message.client.zmq.g++.1 < in.message.client & +mpirun -np 1 lmp_mpi -v mode zmq -log log.message.server.zmq.g++.1 < in.message.server + +mpirun -np 1 lmp_mpi -v mode mpitwo -log log.message.client.mpitwo.g++.1 < in.message.client & +mpirun -np 1 lmp_mpi -v mode mpitwo -log log.message.server.mpitwo.g++.1 < in.message.server + +mpirun -np 1 lmp_mpi -m 0 -in in.message.client -v mode mpione -log log.message.client.mpione.g++.1 : -np 1 lmp_mpi -m 1 -in in.message.server -v mode mpione -log log.message.server.mpione.g++.1 + +# message on 2/4 procs each + +mpirun -np 4 lmp_mpi -log log.message.g++.4 < in.message + +mpirun -np 2 lmp_mpi -v mode file -log log.message.client.file.g++.2 < in.message.client & +mpirun -np 4 lmp_mpi -v mode file -log log.message.server.file.g++.4 < in.message.server + +mpirun -np 2 lmp_mpi -v mode zmq -log log.message.client.zmq.g++.2 < in.message.client & +mpirun -np 4 lmp_mpi -v mode zmq -log log.message.server.zmq.g++.4 < in.message.server + +mpirun -np 2 lmp_mpi -v mode mpitwo -log log.message.client.mpitwo.g++.2 < in.message.client & +mpirun -np 4 lmp_mpi -v mode mpitwo -log log.message.server.mpitwo.g++.4 < in.message.server + +mpirun -np 2 lmp_mpi -m 0 -in in.message.client -v mode mpione -log log.message.client.mpione.g++.2 : -np 4 lmp_mpi -m 1 -in in.message.server -v mode mpione -log log.message.server.mpione.g++.4 + +# message.tilt on 1 proc each + +mpirun -np 1 lmp_mpi -log log.message.tilt.g++.1 < in.message.tilt + +mpirun -np 1 lmp_mpi -v mode zmq -log log.message.tilt.client.zmq.g++.1 < in.message.tilt.client & +mpirun -np 1 lmp_mpi -v mode zmq -log log.message.tilt.server.zmq.g++.1 < in.message.tilt.server + +mpirun -np 1 lmp_mpi -v mode mpitwo -log log.message.tilt.client.mpitwo.g++.1 < in.message.tilt.client & +mpirun -np 1 lmp_mpi -v mode mpitwo -log log.message.tilt.server.mpitwo.g++.1 < in.message.tilt.server + +mpirun -np 1 lmp_mpi -m 0 -in in.message.tilt.client -v mode mpione -log log.message.tilt.client.mpione.g++.1 : -np 1 lmp_mpi -m 1 -in in.message.tilt.server -v mode mpione -log log.message.tilt.server.mpione.g++.1 + +# message.tilt on 2/4 procs each + +mpirun -np 1 lmp_mpi -log log.message.tilt.g++.4 < in.message.tilt + +mpirun -np 2 lmp_mpi -v mode zmq -log log.message.tilt.client.zmq.g++.2 < in.message.tilt.client & +mpirun -np 4 lmp_mpi -v mode zmq -log log.message.tilt.server.zmq.g++.4 < in.message.tilt.server + +mpirun -np 2 lmp_mpi -v mode mpitwo -log log.message.tilt.client.mpitwo.g++.2 < in.message.tilt.client & +mpirun -np 4 lmp_mpi -v mode mpitwo -log log.message.tilt.server.mpitwo.g++.4 < in.message.tilt.server + +mpirun -np 2 lmp_mpi -m 0 -in in.message.tilt.client -v mode mpione -log log.message.tilt.client.mpione.g++.2 : -np 4 lmp_mpi -m 1 -in in.message.tilt.server -v mode mpione -log log.message.tilt.server.mpione.g++.4 diff --git a/examples/message/in.message b/examples/message/in.message new file mode 100644 index 0000000000..7fbbffc355 --- /dev/null +++ b/examples/message/in.message @@ -0,0 +1,29 @@ +# 3d Lennard-Jones melt - no client/server mode + +variable x index 5 +variable y index 5 +variable z index 5 + +units lj +atom_style atomic + +lattice fcc 0.8442 +region box block 0 $x 0 $y 0 $z +create_box 1 box +create_atoms 1 box +mass 1 1.0 + +velocity all create 1.44 87287 loop geom + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nve +# same with NPT +#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0 + +thermo 10 +run 50 diff --git a/examples/message/in.message.client b/examples/message/in.message.client new file mode 100644 index 0000000000..f1ec644a80 --- /dev/null +++ b/examples/message/in.message.client @@ -0,0 +1,41 @@ +# 3d Lennard-Jones melt - client script + +variable mode index file + +if "${mode} == file" then & + "message client md file tmp.couple" & +elif "${mode} == zmq" & + "message client md zmq localhost:5555" & +elif "${mode} == mpione" & + "message client md mpi/one" & +elif "${mode} == mpitwo" & + "message client md mpi/two tmp.couple" + +variable x index 5 +variable y index 5 +variable z index 5 + +units lj +atom_style atomic +atom_modify sort 0 0.0 map yes + +lattice fcc 0.8442 +region box block 0 $x 0 $y 0 $z +create_box 1 box +create_atoms 1 box +mass 1 1.0 + +velocity all create 1.44 87287 loop geom + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nve +# same with NPT +#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0 + +fix 2 all client/md +fix_modify 2 energy yes + +thermo 10 +run 50 diff --git a/examples/message/in.message.server b/examples/message/in.message.server new file mode 100644 index 0000000000..2fedd2ae00 --- /dev/null +++ b/examples/message/in.message.server @@ -0,0 +1,29 @@ +# 3d Lennard-Jones melt - server script + +variable mode index file + +if "${mode} == file" then & + "message server md file tmp.couple" & +elif "${mode} == zmq" & + "message server md zmq *:5555" & +elif "${mode} == mpione" & + "message server md mpi/one" & +elif "${mode} == mpitwo" & + "message server md mpi/two tmp.couple" + +units lj +atom_style atomic +atom_modify map yes + +lattice fcc 0.8442 +region box block 0 1 0 1 0 1 +create_box 1 box +mass * 1.0 # masses not used by server + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +server md diff --git a/examples/message/in.message.tilt b/examples/message/in.message.tilt new file mode 100644 index 0000000000..51126eae1e --- /dev/null +++ b/examples/message/in.message.tilt @@ -0,0 +1,30 @@ +# 2d NEMD simulation - no client/server mode + +units lj +atom_style atomic +dimension 2 + +lattice sq2 0.8442 +region box prism 0 10 0 8 -0.5 0.5 0 0 0 +create_box 2 box +create_atoms 1 box +mass * 1.0 + +velocity all create 1.44 87287 loop geom + +region slice block 4 6 INF INF INF INF +set region slice type 2 + +pair_style lj/cut 2.5 +pair_coeff * * 1.0 1.0 1.0 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1 +fix 2 all deform 1 xy erate 0.01 remap v + +thermo_style custom step temp epair etotal press xy + +thermo 1000 +run 50000 diff --git a/examples/message/in.message.tilt.client b/examples/message/in.message.tilt.client new file mode 100644 index 0000000000..b55bc6585b --- /dev/null +++ b/examples/message/in.message.tilt.client @@ -0,0 +1,42 @@ +# 2d NEMD simulation - client script + +variable mode index file + +if "${mode} == file" then & + "message client md file tmp.couple" & +elif "${mode} == zmq" & + "message client md zmq localhost:5555" & +elif "${mode} == mpione" & + "message client md mpi/one" & +elif "${mode} == mpitwo" & + "message client md mpi/two tmp.couple" + +units lj +atom_style atomic +dimension 2 +atom_modify sort 0 0.0 map yes + +lattice sq2 0.8442 +region box prism 0 10 0 8 -0.5 0.5 0 0 0 +create_box 2 box +create_atoms 1 box +mass * 1.0 + +velocity all create 1.44 87287 loop geom + +region slice block 4 6 INF INF INF INF +set region slice type 2 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1 +fix 2 all deform 1 xy erate 0.01 remap v + +fix 3 all client/md +fix_modify 3 energy yes + +thermo_style custom step temp epair etotal press xy + +thermo 1000 +run 50000 diff --git a/examples/message/in.message.tilt.server b/examples/message/in.message.tilt.server new file mode 100644 index 0000000000..ba211ed15f --- /dev/null +++ b/examples/message/in.message.tilt.server @@ -0,0 +1,31 @@ +# 3d Lennard-Jones melt - server script + +variable mode index file + +if "${mode} == file" then & + "message server md file tmp.couple" & +elif "${mode} == zmq" & + "message server md zmq *:5555" & +elif "${mode} == mpione" & + "message server md mpi/one" & +elif "${mode} == mpitwo" & + "message server md mpi/two tmp.couple" + +units lj +atom_style atomic +dimension 2 +atom_modify map yes + +lattice sq2 0.8442 +region box prism 0 10 0 8 -0.5 0.5 0 0 0 +create_box 2 box +create_atoms 1 box +mass * 1.0 # masses not used by server + +pair_style lj/cut 2.5 +pair_coeff * * 1.0 1.0 1.0 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +server md diff --git a/examples/message/log.28Aug18.message.client.file.g++.1 b/examples/message/log.28Aug18.message.client.file.g++.1 new file mode 100644 index 0000000000..bca1d37dd5 --- /dev/null +++ b/examples/message/log.28Aug18.message.client.file.g++.1 @@ -0,0 +1,79 @@ +LAMMPS (22 Aug 2018) +# 3d Lennard-Jones melt - client script + +variable mode index file + +if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple" +message client md file tmp.couple + +variable x index 5 +variable y index 5 +variable z index 5 + +units lj +atom_style atomic +atom_modify sort 0 0.0 map yes + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 +region box block 0 $x 0 $y 0 $z +region box block 0 5 0 $y 0 $z +region box block 0 5 0 5 0 $z +region box block 0 5 0 5 0 5 +create_box 1 box +Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 500 atoms + Time spent = 0.000752926 secs +mass 1 1.0 + +velocity all create 1.44 87287 loop geom + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nve +# same with NPT +#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0 + +fix 2 all client/md +fix_modify 2 energy yes + +thermo 10 +run 50 +Per MPI rank memory allocation (min/avg/max) = 2.303 | 2.303 | 2.303 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.44 0 0 -4.6176881 -5.0221006 + 10 1.1347688 0 0 -4.6166043 -2.6072847 + 20 0.628166 0 0 -4.62213 1.0186262 + 30 0.73767593 0 0 -4.6254647 0.49629637 + 40 0.69517962 0 0 -4.6253506 0.69303877 + 50 0.70150496 0 0 -4.6259832 0.59551518 +Loop time of 5.0251 on 1 procs for 50 steps with 500 atoms + +Performance: 4298.421 tau/day, 9.950 timesteps/s +0.1% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 9.7752e-06 | 9.7752e-06 | 9.7752e-06 | 0.0 | 0.00 +Comm | 0.00014925 | 0.00014925 | 0.00014925 | 0.0 | 0.00 +Output | 0.00023127 | 0.00023127 | 0.00023127 | 0.0 | 0.00 +Modify | 5.0242 | 5.0242 | 5.0242 | 0.0 | 99.98 +Other | | 0.0004668 | | | 0.01 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 4 +Dangerous builds = 0 +Total wall time: 0:00:05 diff --git a/examples/message/log.28Aug18.message.client.file.g++.2 b/examples/message/log.28Aug18.message.client.file.g++.2 new file mode 100644 index 0000000000..1c868dde37 --- /dev/null +++ b/examples/message/log.28Aug18.message.client.file.g++.2 @@ -0,0 +1,79 @@ +LAMMPS (22 Aug 2018) +# 3d Lennard-Jones melt - client script + +variable mode index file + +if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple" +message client md file tmp.couple + +variable x index 5 +variable y index 5 +variable z index 5 + +units lj +atom_style atomic +atom_modify sort 0 0.0 map yes + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 +region box block 0 $x 0 $y 0 $z +region box block 0 5 0 $y 0 $z +region box block 0 5 0 5 0 $z +region box block 0 5 0 5 0 5 +create_box 1 box +Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798) + 1 by 1 by 2 MPI processor grid +create_atoms 1 box +Created 500 atoms + Time spent = 0.000613928 secs +mass 1 1.0 + +velocity all create 1.44 87287 loop geom + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nve +# same with NPT +#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0 + +fix 2 all client/md +fix_modify 2 energy yes + +thermo 10 +run 50 +Per MPI rank memory allocation (min/avg/max) = 2.302 | 2.302 | 2.302 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.44 0 0 -4.6176881 -5.0221006 + 10 1.1347688 0 0 -4.6166043 -2.6072847 + 20 0.628166 0 0 -4.62213 1.0186262 + 30 0.73767593 0 0 -4.6254647 0.49629637 + 40 0.69517962 0 0 -4.6253506 0.69303877 + 50 0.70150496 0 0 -4.6259832 0.59551518 +Loop time of 5.02384 on 2 procs for 50 steps with 500 atoms + +Performance: 4299.499 tau/day, 9.953 timesteps/s +50.1% CPU use with 2 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 1.9073e-06 | 3.3379e-06 | 4.7684e-06 | 0.0 | 0.00 +Comm | 0.00020742 | 0.00021136 | 0.00021529 | 0.0 | 0.00 +Output | 0.00026989 | 0.00048053 | 0.00069118 | 0.0 | 0.01 +Modify | 5.0171 | 5.0199 | 5.0228 | 0.1 | 99.92 +Other | | 0.003203 | | | 0.06 + +Nlocal: 250 ave 255 max 245 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Nghost: 0 ave 0 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 4 +Dangerous builds = 0 +Total wall time: 0:00:05 diff --git a/examples/message/log.28Aug18.message.client.mpione.g++.1 b/examples/message/log.28Aug18.message.client.mpione.g++.1 new file mode 100644 index 0000000000..78bee72fdf --- /dev/null +++ b/examples/message/log.28Aug18.message.client.mpione.g++.1 @@ -0,0 +1,79 @@ +LAMMPS (22 Aug 2018) +# 3d Lennard-Jones melt - client script + +variable mode index file + +if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple" +message client md mpi/one + +variable x index 5 +variable y index 5 +variable z index 5 + +units lj +atom_style atomic +atom_modify sort 0 0.0 map yes + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 +region box block 0 $x 0 $y 0 $z +region box block 0 5 0 $y 0 $z +region box block 0 5 0 5 0 $z +region box block 0 5 0 5 0 5 +create_box 1 box +Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 500 atoms + Time spent = 0.000540018 secs +mass 1 1.0 + +velocity all create 1.44 87287 loop geom + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nve +# same with NPT +#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0 + +fix 2 all client/md +fix_modify 2 energy yes + +thermo 10 +run 50 +Per MPI rank memory allocation (min/avg/max) = 2.303 | 2.303 | 2.303 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.44 0 0 -4.6176881 -5.0221006 + 10 1.1347688 0 0 -4.6166043 -2.6072847 + 20 0.628166 0 0 -4.62213 1.0186262 + 30 0.73767593 0 0 -4.6254647 0.49629637 + 40 0.69517962 0 0 -4.6253506 0.69303877 + 50 0.70150496 0 0 -4.6259832 0.59551518 +Loop time of 0.0403891 on 1 procs for 50 steps with 500 atoms + +Performance: 534798.272 tau/day, 1237.959 timesteps/s +99.9% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 4.7684e-06 | 4.7684e-06 | 4.7684e-06 | 0.0 | 0.01 +Comm | 6.3181e-05 | 6.3181e-05 | 6.3181e-05 | 0.0 | 0.16 +Output | 9.5367e-05 | 9.5367e-05 | 9.5367e-05 | 0.0 | 0.24 +Modify | 0.040053 | 0.040053 | 0.040053 | 0.0 | 99.17 +Other | | 0.0001726 | | | 0.43 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 4 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/message/log.28Aug18.message.client.mpione.g++.2 b/examples/message/log.28Aug18.message.client.mpione.g++.2 new file mode 100644 index 0000000000..7d7af866e3 --- /dev/null +++ b/examples/message/log.28Aug18.message.client.mpione.g++.2 @@ -0,0 +1,79 @@ +LAMMPS (22 Aug 2018) +# 3d Lennard-Jones melt - client script + +variable mode index file + +if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple" +message client md mpi/one + +variable x index 5 +variable y index 5 +variable z index 5 + +units lj +atom_style atomic +atom_modify sort 0 0.0 map yes + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 +region box block 0 $x 0 $y 0 $z +region box block 0 5 0 $y 0 $z +region box block 0 5 0 5 0 $z +region box block 0 5 0 5 0 5 +create_box 1 box +Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798) + 1 by 1 by 2 MPI processor grid +create_atoms 1 box +Created 500 atoms + Time spent = 0.000475883 secs +mass 1 1.0 + +velocity all create 1.44 87287 loop geom + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nve +# same with NPT +#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0 + +fix 2 all client/md +fix_modify 2 energy yes + +thermo 10 +run 50 +Per MPI rank memory allocation (min/avg/max) = 2.302 | 2.302 | 2.302 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.44 0 0 -4.6176881 -5.0221006 + 10 1.1347688 0 0 -4.6166043 -2.6072847 + 20 0.628166 0 0 -4.62213 1.0186262 + 30 0.73767593 0 0 -4.6254647 0.49629637 + 40 0.69517962 0 0 -4.6253506 0.69303877 + 50 0.70150496 0 0 -4.6259832 0.59551518 +Loop time of 0.0208495 on 2 procs for 50 steps with 500 atoms + +Performance: 1035997.740 tau/day, 2398.143 timesteps/s +99.1% CPU use with 2 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 3.0994e-06 | 4.53e-06 | 5.9605e-06 | 0.0 | 0.02 +Comm | 0.00012422 | 0.00012457 | 0.00012493 | 0.0 | 0.60 +Output | 5.7697e-05 | 7.987e-05 | 0.00010204 | 0.0 | 0.38 +Modify | 0.020463 | 0.020464 | 0.020466 | 0.0 | 98.15 +Other | | 0.0001761 | | | 0.84 + +Nlocal: 250 ave 255 max 245 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Nghost: 0 ave 0 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 4 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/message/log.28Aug18.message.client.mpitwo.g++.1 b/examples/message/log.28Aug18.message.client.mpitwo.g++.1 new file mode 100644 index 0000000000..ee97e7bd1a --- /dev/null +++ b/examples/message/log.28Aug18.message.client.mpitwo.g++.1 @@ -0,0 +1,79 @@ +LAMMPS (22 Aug 2018) +# 3d Lennard-Jones melt - client script + +variable mode index file + +if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple" +message client md mpi/two tmp.couple + +variable x index 5 +variable y index 5 +variable z index 5 + +units lj +atom_style atomic +atom_modify sort 0 0.0 map yes + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 +region box block 0 $x 0 $y 0 $z +region box block 0 5 0 $y 0 $z +region box block 0 5 0 5 0 $z +region box block 0 5 0 5 0 5 +create_box 1 box +Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 500 atoms + Time spent = 0.000603914 secs +mass 1 1.0 + +velocity all create 1.44 87287 loop geom + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nve +# same with NPT +#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0 + +fix 2 all client/md +fix_modify 2 energy yes + +thermo 10 +run 50 +Per MPI rank memory allocation (min/avg/max) = 2.303 | 2.303 | 2.303 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.44 0 0 -4.6176881 -5.0221006 + 10 1.1347688 0 0 -4.6166043 -2.6072847 + 20 0.628166 0 0 -4.62213 1.0186262 + 30 0.73767593 0 0 -4.6254647 0.49629637 + 40 0.69517962 0 0 -4.6253506 0.69303877 + 50 0.70150496 0 0 -4.6259832 0.59551518 +Loop time of 0.069119 on 1 procs for 50 steps with 500 atoms + +Performance: 312504.627 tau/day, 723.390 timesteps/s +42.0% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 7.1526e-06 | 7.1526e-06 | 7.1526e-06 | 0.0 | 0.01 +Comm | 0.0001049 | 0.0001049 | 0.0001049 | 0.0 | 0.15 +Output | 0.00014019 | 0.00014019 | 0.00014019 | 0.0 | 0.20 +Modify | 0.068602 | 0.068602 | 0.068602 | 0.0 | 99.25 +Other | | 0.0002651 | | | 0.38 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 4 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/message/log.28Aug18.message.client.mpitwo.g++.2 b/examples/message/log.28Aug18.message.client.mpitwo.g++.2 new file mode 100644 index 0000000000..72db0198d5 --- /dev/null +++ b/examples/message/log.28Aug18.message.client.mpitwo.g++.2 @@ -0,0 +1,79 @@ +LAMMPS (22 Aug 2018) +# 3d Lennard-Jones melt - client script + +variable mode index file + +if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple" +message client md mpi/two tmp.couple + +variable x index 5 +variable y index 5 +variable z index 5 + +units lj +atom_style atomic +atom_modify sort 0 0.0 map yes + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 +region box block 0 $x 0 $y 0 $z +region box block 0 5 0 $y 0 $z +region box block 0 5 0 5 0 $z +region box block 0 5 0 5 0 5 +create_box 1 box +Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798) + 1 by 1 by 2 MPI processor grid +create_atoms 1 box +Created 500 atoms + Time spent = 0.000667095 secs +mass 1 1.0 + +velocity all create 1.44 87287 loop geom + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nve +# same with NPT +#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0 + +fix 2 all client/md +fix_modify 2 energy yes + +thermo 10 +run 50 +Per MPI rank memory allocation (min/avg/max) = 2.302 | 2.302 | 2.302 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.44 0 0 -4.6176881 -5.0221006 + 10 1.1347688 0 0 -4.6166043 -2.6072847 + 20 0.628166 0 0 -4.62213 1.0186262 + 30 0.73767593 0 0 -4.6254647 0.49629637 + 40 0.69517962 0 0 -4.6253506 0.69303877 + 50 0.70150496 0 0 -4.6259832 0.59551518 +Loop time of 0.0190214 on 2 procs for 50 steps with 500 atoms + +Performance: 1135563.588 tau/day, 2628.619 timesteps/s +58.5% CPU use with 2 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 1.9073e-06 | 2.861e-06 | 3.8147e-06 | 0.0 | 0.02 +Comm | 0.00017238 | 0.00017989 | 0.0001874 | 0.0 | 0.95 +Output | 0.00012803 | 0.00015497 | 0.00018191 | 0.0 | 0.81 +Modify | 0.018065 | 0.018181 | 0.018297 | 0.1 | 95.58 +Other | | 0.0005029 | | | 2.64 + +Nlocal: 250 ave 255 max 245 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Nghost: 0 ave 0 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 4 +Dangerous builds = 0 +Total wall time: 0:00:01 diff --git a/examples/message/log.28Aug18.message.client.zmq.g++.1 b/examples/message/log.28Aug18.message.client.zmq.g++.1 new file mode 100644 index 0000000000..23fa70c1be --- /dev/null +++ b/examples/message/log.28Aug18.message.client.zmq.g++.1 @@ -0,0 +1,79 @@ +LAMMPS (22 Aug 2018) +# 3d Lennard-Jones melt - client script + +variable mode index file + +if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple" +message client md zmq localhost:5555 + +variable x index 5 +variable y index 5 +variable z index 5 + +units lj +atom_style atomic +atom_modify sort 0 0.0 map yes + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 +region box block 0 $x 0 $y 0 $z +region box block 0 5 0 $y 0 $z +region box block 0 5 0 5 0 $z +region box block 0 5 0 5 0 5 +create_box 1 box +Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 500 atoms + Time spent = 0.000734091 secs +mass 1 1.0 + +velocity all create 1.44 87287 loop geom + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nve +# same with NPT +#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0 + +fix 2 all client/md +fix_modify 2 energy yes + +thermo 10 +run 50 +Per MPI rank memory allocation (min/avg/max) = 2.303 | 2.303 | 2.303 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.44 0 0 -4.6176881 -5.0221006 + 10 1.1347688 0 0 -4.6166043 -2.6072847 + 20 0.628166 0 0 -4.62213 1.0186262 + 30 0.73767593 0 0 -4.6254647 0.49629637 + 40 0.69517962 0 0 -4.6253506 0.69303877 + 50 0.70150496 0 0 -4.6259832 0.59551518 +Loop time of 0.0778341 on 1 procs for 50 steps with 500 atoms + +Performance: 277513.222 tau/day, 642.392 timesteps/s +11.4% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 7.8678e-06 | 7.8678e-06 | 7.8678e-06 | 0.0 | 0.01 +Comm | 8.3685e-05 | 8.3685e-05 | 8.3685e-05 | 0.0 | 0.11 +Output | 0.00011373 | 0.00011373 | 0.00011373 | 0.0 | 0.15 +Modify | 0.07734 | 0.07734 | 0.07734 | 0.0 | 99.37 +Other | | 0.0002885 | | | 0.37 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 4 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/message/log.28Aug18.message.client.zmq.g++.2 b/examples/message/log.28Aug18.message.client.zmq.g++.2 new file mode 100644 index 0000000000..7833befd21 --- /dev/null +++ b/examples/message/log.28Aug18.message.client.zmq.g++.2 @@ -0,0 +1,79 @@ +LAMMPS (22 Aug 2018) +# 3d Lennard-Jones melt - client script + +variable mode index file + +if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple" +message client md zmq localhost:5555 + +variable x index 5 +variable y index 5 +variable z index 5 + +units lj +atom_style atomic +atom_modify sort 0 0.0 map yes + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 +region box block 0 $x 0 $y 0 $z +region box block 0 5 0 $y 0 $z +region box block 0 5 0 5 0 $z +region box block 0 5 0 5 0 5 +create_box 1 box +Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798) + 1 by 1 by 2 MPI processor grid +create_atoms 1 box +Created 500 atoms + Time spent = 0.000570059 secs +mass 1 1.0 + +velocity all create 1.44 87287 loop geom + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nve +# same with NPT +#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0 + +fix 2 all client/md +fix_modify 2 energy yes + +thermo 10 +run 50 +Per MPI rank memory allocation (min/avg/max) = 2.302 | 2.302 | 2.302 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.44 0 0 -4.6176881 -5.0221006 + 10 1.1347688 0 0 -4.6166043 -2.6072847 + 20 0.628166 0 0 -4.62213 1.0186262 + 30 0.73767593 0 0 -4.6254647 0.49629637 + 40 0.69517962 0 0 -4.6253506 0.69303877 + 50 0.70150496 0 0 -4.6259832 0.59551518 +Loop time of 0.0416595 on 2 procs for 50 steps with 500 atoms + +Performance: 518489.499 tau/day, 1200.207 timesteps/s +56.5% CPU use with 2 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 2.861e-06 | 3.3379e-06 | 3.8147e-06 | 0.0 | 0.01 +Comm | 0.00013399 | 0.00013685 | 0.00013971 | 0.0 | 0.33 +Output | 8.6784e-05 | 0.00011206 | 0.00013733 | 0.0 | 0.27 +Modify | 0.040948 | 0.04103 | 0.041112 | 0.0 | 98.49 +Other | | 0.0003769 | | | 0.90 + +Nlocal: 250 ave 255 max 245 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Nghost: 0 ave 0 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 4 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/message/log.28Aug18.message.g++.1 b/examples/message/log.28Aug18.message.g++.1 new file mode 100644 index 0000000000..c06af4e0d1 --- /dev/null +++ b/examples/message/log.28Aug18.message.g++.1 @@ -0,0 +1,85 @@ +LAMMPS (22 Aug 2018) +# 3d Lennard-Jones melt - no client/server mode + +variable x index 5 +variable y index 5 +variable z index 5 + +units lj +atom_style atomic + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 +region box block 0 $x 0 $y 0 $z +region box block 0 5 0 $y 0 $z +region box block 0 5 0 5 0 $z +region box block 0 5 0 5 0 5 +create_box 1 box +Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 500 atoms + Time spent = 0.000682831 secs +mass 1 1.0 + +velocity all create 1.44 87287 loop geom + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nve +# same with NPT +#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0 + +thermo 10 +run 50 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.143 | 3.143 | 3.143 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.44 -6.7733681 0 -4.6176881 -5.0221006 + 10 1.1347688 -6.3153532 0 -4.6166043 -2.6072847 + 20 0.628166 -5.5624945 0 -4.62213 1.0186262 + 30 0.73767593 -5.7297655 0 -4.6254647 0.49629637 + 40 0.69517962 -5.6660345 0 -4.6253506 0.69303877 + 50 0.70150496 -5.6761362 0 -4.6259832 0.59551518 +Loop time of 0.039681 on 1 procs for 50 steps with 500 atoms + +Performance: 544341.699 tau/day, 1260.050 timesteps/s +99.2% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.029993 | 0.029993 | 0.029993 | 0.0 | 75.59 +Neigh | 0.0073051 | 0.0073051 | 0.0073051 | 0.0 | 18.41 +Comm | 0.0012736 | 0.0012736 | 0.0012736 | 0.0 | 3.21 +Output | 0.00012803 | 0.00012803 | 0.00012803 | 0.0 | 0.32 +Modify | 0.00053287 | 0.00053287 | 0.00053287 | 0.0 | 1.34 +Other | | 0.000448 | | | 1.13 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1946 ave 1946 max 1946 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 18820 ave 18820 max 18820 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 18820 +Ave neighs/atom = 37.64 +Neighbor list builds = 4 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/message/log.28Aug18.message.g++.4 b/examples/message/log.28Aug18.message.g++.4 new file mode 100644 index 0000000000..695b51f166 --- /dev/null +++ b/examples/message/log.28Aug18.message.g++.4 @@ -0,0 +1,85 @@ +LAMMPS (22 Aug 2018) +# 3d Lennard-Jones melt - no client/server mode + +variable x index 5 +variable y index 5 +variable z index 5 + +units lj +atom_style atomic + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 +region box block 0 $x 0 $y 0 $z +region box block 0 5 0 $y 0 $z +region box block 0 5 0 5 0 $z +region box block 0 5 0 5 0 5 +create_box 1 box +Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 500 atoms + Time spent = 0.000656843 secs +mass 1 1.0 + +velocity all create 1.44 87287 loop geom + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nve +# same with NPT +#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0 + +thermo 10 +run 50 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.109 | 3.109 | 3.109 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.44 -6.7733681 0 -4.6176881 -5.0221006 + 10 1.1347688 -6.3153532 0 -4.6166043 -2.6072847 + 20 0.628166 -5.5624945 0 -4.62213 1.0186262 + 30 0.73767593 -5.7297655 0 -4.6254647 0.49629637 + 40 0.69517962 -5.6660345 0 -4.6253506 0.69303877 + 50 0.70150496 -5.6761362 0 -4.6259832 0.59551518 +Loop time of 0.0131519 on 4 procs for 50 steps with 500 atoms + +Performance: 1642350.242 tau/day, 3801.737 timesteps/s +97.9% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.006074 | 0.0065379 | 0.0072589 | 0.6 | 49.71 +Neigh | 0.0014219 | 0.0015552 | 0.0017018 | 0.3 | 11.82 +Comm | 0.003546 | 0.0043943 | 0.0049584 | 0.8 | 33.41 +Output | 0.000108 | 0.00012845 | 0.00016999 | 0.0 | 0.98 +Modify | 0.00014353 | 0.00014949 | 0.00015569 | 0.0 | 1.14 +Other | | 0.0003865 | | | 2.94 + +Nlocal: 125 ave 128 max 121 min +Histogram: 1 0 0 0 1 0 0 0 1 1 +Nghost: 1091 ave 1094 max 1089 min +Histogram: 1 0 1 0 1 0 0 0 0 1 +Neighs: 4705 ave 4849 max 4648 min +Histogram: 2 1 0 0 0 0 0 0 0 1 + +Total # of neighbors = 18820 +Ave neighs/atom = 37.64 +Neighbor list builds = 4 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/message/log.28Aug18.message.server.file.g++.1 b/examples/message/log.28Aug18.message.server.file.g++.1 new file mode 100644 index 0000000000..cf1418d3c5 --- /dev/null +++ b/examples/message/log.28Aug18.message.server.file.g++.1 @@ -0,0 +1,44 @@ +LAMMPS (22 Aug 2018) +# 3d Lennard-Jones melt - server script + +variable mode index file + +if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple" +message server md file tmp.couple + +units lj +atom_style atomic +atom_modify map yes + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 +region box block 0 1 0 1 0 1 +create_box 1 box +Created orthogonal box = (0 0 0) to (1.6796 1.6796 1.6796) + 1 by 1 by 1 MPI processor grid +mass * 1.0 # masses not used by server + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +server md + 1 by 1 by 1 MPI processor grid +WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Server MD calls = 51 +Server MD reneighborings 5 +Total wall time: 0:00:05 diff --git a/examples/message/log.28Aug18.message.server.file.g++.4 b/examples/message/log.28Aug18.message.server.file.g++.4 new file mode 100644 index 0000000000..c233bad692 --- /dev/null +++ b/examples/message/log.28Aug18.message.server.file.g++.4 @@ -0,0 +1,44 @@ +LAMMPS (22 Aug 2018) +# 3d Lennard-Jones melt - server script + +variable mode index file + +if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple" +message server md file tmp.couple + +units lj +atom_style atomic +atom_modify map yes + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 +region box block 0 1 0 1 0 1 +create_box 1 box +Created orthogonal box = (0 0 0) to (1.6796 1.6796 1.6796) + 1 by 2 by 2 MPI processor grid +mass * 1.0 # masses not used by server + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +server md + 1 by 2 by 2 MPI processor grid +WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Server MD calls = 51 +Server MD reneighborings 5 +Total wall time: 0:00:05 diff --git a/examples/message/log.28Aug18.message.server.mpione.g++.1 b/examples/message/log.28Aug18.message.server.mpione.g++.1 new file mode 100644 index 0000000000..81e04aa923 --- /dev/null +++ b/examples/message/log.28Aug18.message.server.mpione.g++.1 @@ -0,0 +1,44 @@ +LAMMPS (22 Aug 2018) +# 3d Lennard-Jones melt - server script + +variable mode index file + +if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple" +message server md mpi/one + +units lj +atom_style atomic +atom_modify map yes + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 +region box block 0 1 0 1 0 1 +create_box 1 box +Created orthogonal box = (0 0 0) to (1.6796 1.6796 1.6796) + 1 by 1 by 1 MPI processor grid +mass * 1.0 # masses not used by server + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +server md + 1 by 1 by 1 MPI processor grid +WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Server MD calls = 51 +Server MD reneighborings 5 +Total wall time: 0:00:00 diff --git a/examples/message/log.28Aug18.message.server.mpione.g++.4 b/examples/message/log.28Aug18.message.server.mpione.g++.4 new file mode 100644 index 0000000000..a185cb1c29 --- /dev/null +++ b/examples/message/log.28Aug18.message.server.mpione.g++.4 @@ -0,0 +1,44 @@ +LAMMPS (22 Aug 2018) +# 3d Lennard-Jones melt - server script + +variable mode index file + +if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple" +message server md mpi/one + +units lj +atom_style atomic +atom_modify map yes + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 +region box block 0 1 0 1 0 1 +create_box 1 box +Created orthogonal box = (0 0 0) to (1.6796 1.6796 1.6796) + 1 by 2 by 2 MPI processor grid +mass * 1.0 # masses not used by server + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +server md + 1 by 2 by 2 MPI processor grid +WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Server MD calls = 51 +Server MD reneighborings 5 +Total wall time: 0:00:00 diff --git a/examples/message/log.28Aug18.message.server.mpitwo.g++.1 b/examples/message/log.28Aug18.message.server.mpitwo.g++.1 new file mode 100644 index 0000000000..973a08eb6a --- /dev/null +++ b/examples/message/log.28Aug18.message.server.mpitwo.g++.1 @@ -0,0 +1,44 @@ +LAMMPS (22 Aug 2018) +# 3d Lennard-Jones melt - server script + +variable mode index file + +if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple" +message server md mpi/two tmp.couple + +units lj +atom_style atomic +atom_modify map yes + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 +region box block 0 1 0 1 0 1 +create_box 1 box +Created orthogonal box = (0 0 0) to (1.6796 1.6796 1.6796) + 1 by 1 by 1 MPI processor grid +mass * 1.0 # masses not used by server + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +server md + 1 by 1 by 1 MPI processor grid +WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Server MD calls = 51 +Server MD reneighborings 5 +Total wall time: 0:00:00 diff --git a/examples/message/log.28Aug18.message.server.mpitwo.g++.4 b/examples/message/log.28Aug18.message.server.mpitwo.g++.4 new file mode 100644 index 0000000000..9e76e52d90 --- /dev/null +++ b/examples/message/log.28Aug18.message.server.mpitwo.g++.4 @@ -0,0 +1,44 @@ +LAMMPS (22 Aug 2018) +# 3d Lennard-Jones melt - server script + +variable mode index file + +if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple" +message server md mpi/two tmp.couple + +units lj +atom_style atomic +atom_modify map yes + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 +region box block 0 1 0 1 0 1 +create_box 1 box +Created orthogonal box = (0 0 0) to (1.6796 1.6796 1.6796) + 1 by 2 by 2 MPI processor grid +mass * 1.0 # masses not used by server + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +server md + 1 by 2 by 2 MPI processor grid +WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Server MD calls = 51 +Server MD reneighborings 5 +Total wall time: 0:00:00 diff --git a/examples/message/log.28Aug18.message.server.zmq.g++.1 b/examples/message/log.28Aug18.message.server.zmq.g++.1 new file mode 100644 index 0000000000..ce5729878b --- /dev/null +++ b/examples/message/log.28Aug18.message.server.zmq.g++.1 @@ -0,0 +1,44 @@ +LAMMPS (22 Aug 2018) +# 3d Lennard-Jones melt - server script + +variable mode index file + +if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple" +message server md zmq *:5555 + +units lj +atom_style atomic +atom_modify map yes + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 +region box block 0 1 0 1 0 1 +create_box 1 box +Created orthogonal box = (0 0 0) to (1.6796 1.6796 1.6796) + 1 by 1 by 1 MPI processor grid +mass * 1.0 # masses not used by server + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +server md + 1 by 1 by 1 MPI processor grid +WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Server MD calls = 51 +Server MD reneighborings 5 +Total wall time: 0:00:00 diff --git a/examples/message/log.28Aug18.message.server.zmq.g++.4 b/examples/message/log.28Aug18.message.server.zmq.g++.4 new file mode 100644 index 0000000000..b3201da4da --- /dev/null +++ b/examples/message/log.28Aug18.message.server.zmq.g++.4 @@ -0,0 +1,44 @@ +LAMMPS (22 Aug 2018) +# 3d Lennard-Jones melt - server script + +variable mode index file + +if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple" +message server md zmq *:5555 + +units lj +atom_style atomic +atom_modify map yes + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 +region box block 0 1 0 1 0 1 +create_box 1 box +Created orthogonal box = (0 0 0) to (1.6796 1.6796 1.6796) + 1 by 2 by 2 MPI processor grid +mass * 1.0 # masses not used by server + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +server md + 1 by 2 by 2 MPI processor grid +WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Server MD calls = 51 +Server MD reneighborings 5 +Total wall time: 0:00:00 diff --git a/examples/message/log.28Aug18.message.tilt.client.mpione.g++.1 b/examples/message/log.28Aug18.message.tilt.client.mpione.g++.1 new file mode 100644 index 0000000000..a290ec307b --- /dev/null +++ b/examples/message/log.28Aug18.message.tilt.client.mpione.g++.1 @@ -0,0 +1,130 @@ +LAMMPS (22 Aug 2018) +# 2d NEMD simulation - client script + +variable mode index file + +if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple" +message client md mpi/one + +units lj +atom_style atomic +dimension 2 +atom_modify sort 0 0.0 map yes + +lattice sq2 0.8442 +Lattice spacing in x,y,z = 1.53919 1.53919 1.53919 +region box prism 0 10 0 8 -0.5 0.5 0 0 0 +create_box 2 box +Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 160 atoms + Time spent = 0.000485897 secs +mass * 1.0 + +velocity all create 1.44 87287 loop geom + +region slice block 4 6 INF INF INF INF +set region slice type 2 + 40 settings made for type + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1 +fix 2 all deform 1 xy erate 0.01 remap v + +fix 3 all client/md +fix_modify 3 energy yes + +thermo_style custom step temp epair etotal press xy + +thermo 1000 +run 50000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 0 + ghost atom cutoff = 0 + binsize = 15.3919, bins = 1 1 1 + 0 neighbor lists, perpetual/occasional/extra = 0 0 0 +Per MPI rank memory allocation (min/avg/max) = 2.308 | 2.308 | 2.308 Mbytes +Step Temp E_pair TotEng Press Xy + 0 1.44 0 1.431 1.2080502 0 + 1000 1.0086399 0 1.3760711 6.8772078 0.61567613 + 2000 1.0707188 0 1.3744107 6.628097 1.2313523 + 3000 1.0627515 0 1.310096 6.1647179 1.8470284 + 4000 0.94091054 0 1.268976 6.4723215 2.4627045 + 5000 1.0218949 0 1.2430242 5.6945977 3.0783806 + 6000 0.98649481 0 1.1997565 5.2870413 3.6940568 + 7000 0.9047957 0 1.1461262 5.9291636 4.3097329 + 8000 0.85697614 0 1.0437412 5.0652097 4.925409 + 9000 0.84208329 0 1.109218 6.1749808 5.5410852 + 10000 0.86418108 0 1.1594773 6.2581867 6.1567613 + 11000 0.95136356 0 1.1650901 5.8389085 6.7724374 + 12000 0.94571583 0 1.2210342 6.2498816 7.3881135 + 13000 0.95994288 0 1.2172042 5.9608165 -7.3881135 + 14000 0.99053999 0 1.2925597 6.9994446 -6.7724374 + 15000 1.0316726 0 1.3346023 6.6902672 -6.1567613 + 16000 0.99537481 0 1.3227696 7.0301123 -5.5410852 + 17000 1.0306843 0 1.3101457 6.4750102 -4.925409 + 18000 1.071154 0 1.2947547 5.695888 -4.3097329 + 19000 0.97120752 0 1.3035465 7.3945362 -3.6940568 + 20000 0.97198994 0 1.2244663 6.0047605 -3.0783806 + 21000 0.97943545 0 1.2393394 6.3871012 -2.4627045 + 22000 0.98550707 0 1.1768148 5.019967 -1.8470284 + 23000 0.96920052 0 1.1730698 5.7944947 -1.2313523 + 24000 0.94069959 0 1.184119 5.8434876 -0.61567613 + 25000 0.91569312 0 1.1642118 5.668997 0 + 26000 0.98882932 0 1.1999248 5.0115507 0.61567613 + 27000 0.8972608 0 1.2556546 7.0837158 1.2313523 + 28000 0.93554756 0 1.2221911 5.9302841 1.8470284 + 29000 0.97894608 0 1.2168736 5.5766766 2.4627045 + 30000 0.97877055 0 1.2575839 6.4308887 3.0783806 + 31000 1.0002387 0 1.2338069 5.3873124 3.6940568 + 32000 0.89608618 0 1.2382021 6.7892204 4.3097329 + 33000 0.87439302 0 1.2252635 7.078134 4.925409 + 34000 1.076102 0 1.2991393 5.5556892 5.5410852 + 35000 1.0018689 0 1.272105 6.1320483 6.1567613 + 36000 0.93327214 0 1.2428039 7.0030867 6.7724374 + 37000 1.0770236 0 1.3002931 5.4996076 7.3881135 + 38000 0.98715132 0 1.215562 5.5958335 -7.3881135 + 39000 0.95028417 0 1.2566706 6.4133713 -6.7724374 + 40000 1.0445585 0 1.241151 5.3589806 -6.1567613 + 41000 0.93799713 0 1.2109086 6.4957845 -5.5410852 + 42000 0.99231038 0 1.2228781 5.9363471 -4.925409 + 43000 0.97913815 0 1.1854842 5.8837987 -4.3097329 + 44000 0.86748838 0 1.1616201 6.8991278 -3.6940568 + 45000 0.96284421 0 1.1549383 5.1226785 -3.0783806 + 46000 0.98701623 0 1.170581 4.9719567 -2.4627045 + 47000 0.92618683 0 1.2146576 6.7100075 -1.8470284 + 48000 1.0092593 0 1.2523988 5.7067864 -1.2313523 + 49000 1.0187472 0 1.271608 5.3355092 -0.61567613 + 50000 1.0194881 0 1.2831094 6.2449759 0 +Loop time of 1.74559 on 1 procs for 50000 steps with 160 atoms + +Performance: 12374053.445 tau/day, 28643.642 timesteps/s +100.0% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0.0020533 | 0.0020533 | 0.0020533 | 0.0 | 0.12 +Comm | 0.015517 | 0.015517 | 0.015517 | 0.0 | 0.89 +Output | 0.00052404 | 0.00052404 | 0.00052404 | 0.0 | 0.03 +Modify | 1.6784 | 1.6784 | 1.6784 | 0.0 | 96.15 +Other | | 0.04905 | | | 2.81 + +Nlocal: 160 ave 160 max 160 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 5270 +Dangerous builds = 0 +Total wall time: 0:00:01 diff --git a/examples/message/log.28Aug18.message.tilt.client.mpione.g++.2 b/examples/message/log.28Aug18.message.tilt.client.mpione.g++.2 new file mode 100644 index 0000000000..0089732355 --- /dev/null +++ b/examples/message/log.28Aug18.message.tilt.client.mpione.g++.2 @@ -0,0 +1,130 @@ +LAMMPS (22 Aug 2018) +# 2d NEMD simulation - client script + +variable mode index file + +if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple" +message client md mpi/one + +units lj +atom_style atomic +dimension 2 +atom_modify sort 0 0.0 map yes + +lattice sq2 0.8442 +Lattice spacing in x,y,z = 1.53919 1.53919 1.53919 +region box prism 0 10 0 8 -0.5 0.5 0 0 0 +create_box 2 box +Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0) + 2 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 160 atoms + Time spent = 0.000453949 secs +mass * 1.0 + +velocity all create 1.44 87287 loop geom + +region slice block 4 6 INF INF INF INF +set region slice type 2 + 40 settings made for type + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1 +fix 2 all deform 1 xy erate 0.01 remap v + +fix 3 all client/md +fix_modify 3 energy yes + +thermo_style custom step temp epair etotal press xy + +thermo 1000 +run 50000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 0 + ghost atom cutoff = 0 + binsize = 15.3919, bins = 1 1 1 + 0 neighbor lists, perpetual/occasional/extra = 0 0 0 +Per MPI rank memory allocation (min/avg/max) = 2.308 | 2.308 | 2.308 Mbytes +Step Temp E_pair TotEng Press Xy + 0 1.44 0 1.431 1.2080502 0 + 1000 1.0876599 0 1.3637783 6.063363 0.61567613 + 2000 1.0722996 0 1.4108622 7.0518942 1.2313523 + 3000 1.0580774 0 1.3845895 6.0395275 1.8470284 + 4000 1.0068006 0 1.3804387 7.0944598 2.4627045 + 5000 0.95391814 0 1.2578438 6.1878831 3.0783806 + 6000 0.93492945 0 1.2711287 7.0440517 3.6940568 + 7000 0.94107853 0 1.2384371 6.1438077 4.3097329 + 8000 0.89711744 0 1.145748 6.3558305 4.925409 + 9000 0.90190304 0 1.0860684 4.957098 5.5410852 + 10000 0.84255749 0 1.0376892 5.2351795 6.1567613 + 11000 0.90250882 0 1.0497695 4.3844838 6.7724374 + 12000 0.83461274 0 1.0281949 5.1534361 7.3881135 + 13000 0.80315331 0 1.0226333 5.757222 -7.3881135 + 14000 0.81820939 0 0.99276466 4.6943725 -6.7724374 + 15000 0.8239631 0 1.0408289 5.1669006 -6.1567613 + 16000 0.88908894 0 1.1554855 6.3510278 -5.5410852 + 17000 0.98268136 0 1.2086981 5.6302847 -4.925409 + 18000 1.0098162 0 1.3687676 7.5243587 -4.3097329 + 19000 1.0795086 0 1.4562691 7.639418 -3.6940568 + 20000 1.1932155 0 1.5278988 7.0668432 -3.0783806 + 21000 1.2424296 0 1.6048792 7.959585 -2.4627045 + 22000 1.297169 0 1.7421262 8.9432388 -1.8470284 + 23000 1.2863494 0 1.7236774 8.3584973 -1.2313523 + 24000 1.4084347 0 1.7370339 7.2729078 -0.61567613 + 25000 1.3339728 0 1.6883255 7.529098 0 + 26000 1.1483243 0 1.5155578 7.3869994 0.61567613 + 27000 1.1372606 0 1.4368323 7.0580136 1.2313523 + 28000 1.0518579 0 1.355311 6.478857 1.8470284 + 29000 1.0581145 0 1.2535509 5.3697479 2.4627045 + 30000 0.93612564 0 1.185532 5.5520142 3.0783806 + 31000 0.94387516 0 1.1716454 5.8655485 3.6940568 + 32000 0.83953515 0 1.0737746 5.5551953 4.3097329 + 33000 0.84862926 0 1.0564042 5.7795428 4.925409 + 34000 0.83621877 0 1.079387 5.7514243 5.5410852 + 35000 0.86938506 0 1.031783 4.5897825 6.1567613 + 36000 0.88990609 0 1.0807597 5.3751744 6.7724374 + 37000 0.89534631 0 1.1238882 5.2400355 7.3881135 + 38000 0.98545003 0 1.2121125 5.7783854 -7.3881135 + 39000 0.96737778 0 1.2472934 6.1139 -6.7724374 + 40000 1.0664194 0 1.2956811 5.7353661 -6.1567613 + 41000 1.0681494 0 1.3269435 6.3102722 -5.5410852 + 42000 1.0875422 0 1.3963739 7.1208066 -4.925409 + 43000 1.0968173 0 1.3388062 6.1704339 -4.3097329 + 44000 1.1182109 0 1.3773214 7.0872686 -3.6940568 + 45000 1.1243261 0 1.432186 6.884782 -3.0783806 + 46000 1.039713 0 1.4389721 7.5585257 -2.4627045 + 47000 1.0816108 0 1.4100361 6.4611126 -1.8470284 + 48000 0.97637127 0 1.3605389 7.3992744 -1.2313523 + 49000 1.0361978 0 1.2721873 5.8166109 -0.61567613 + 50000 0.92367087 0 1.1875669 6.4685214 0 +Loop time of 2.82785 on 2 procs for 50000 steps with 160 atoms + +Performance: 7638300.565 tau/day, 17681.251 timesteps/s +100.0% CPU use with 2 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0.0011888 | 0.0012611 | 0.0013335 | 0.2 | 0.04 +Comm | 0.024838 | 0.025075 | 0.025312 | 0.1 | 0.89 +Output | 0.0003581 | 0.00052559 | 0.00069308 | 0.0 | 0.02 +Modify | 2.7209 | 2.7263 | 2.7318 | 0.3 | 96.41 +Other | | 0.07465 | | | 2.64 + +Nlocal: 80 ave 80 max 80 min +Histogram: 2 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 5257 +Dangerous builds = 0 +Total wall time: 0:00:02 diff --git a/examples/message/log.28Aug18.message.tilt.client.mpitwo.g++.1 b/examples/message/log.28Aug18.message.tilt.client.mpitwo.g++.1 new file mode 100644 index 0000000000..814b3df1aa --- /dev/null +++ b/examples/message/log.28Aug18.message.tilt.client.mpitwo.g++.1 @@ -0,0 +1,130 @@ +LAMMPS (22 Aug 2018) +# 2d NEMD simulation - client script + +variable mode index file + +if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple" +message client md mpi/two tmp.couple + +units lj +atom_style atomic +dimension 2 +atom_modify sort 0 0.0 map yes + +lattice sq2 0.8442 +Lattice spacing in x,y,z = 1.53919 1.53919 1.53919 +region box prism 0 10 0 8 -0.5 0.5 0 0 0 +create_box 2 box +Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 160 atoms + Time spent = 0.000543118 secs +mass * 1.0 + +velocity all create 1.44 87287 loop geom + +region slice block 4 6 INF INF INF INF +set region slice type 2 + 40 settings made for type + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1 +fix 2 all deform 1 xy erate 0.01 remap v + +fix 3 all client/md +fix_modify 3 energy yes + +thermo_style custom step temp epair etotal press xy + +thermo 1000 +run 50000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 0 + ghost atom cutoff = 0 + binsize = 15.3919, bins = 1 1 1 + 0 neighbor lists, perpetual/occasional/extra = 0 0 0 +Per MPI rank memory allocation (min/avg/max) = 2.308 | 2.308 | 2.308 Mbytes +Step Temp E_pair TotEng Press Xy + 0 1.44 0 1.431 1.2080502 0 + 1000 1.0086399 0 1.3760711 6.8772078 0.61567613 + 2000 1.0707188 0 1.3744107 6.628097 1.2313523 + 3000 1.0627515 0 1.310096 6.1647179 1.8470284 + 4000 0.94091054 0 1.268976 6.4723215 2.4627045 + 5000 1.0218949 0 1.2430242 5.6945977 3.0783806 + 6000 0.98649481 0 1.1997565 5.2870413 3.6940568 + 7000 0.9047957 0 1.1461262 5.9291636 4.3097329 + 8000 0.85697614 0 1.0437412 5.0652097 4.925409 + 9000 0.84208329 0 1.109218 6.1749808 5.5410852 + 10000 0.86418108 0 1.1594773 6.2581867 6.1567613 + 11000 0.95136356 0 1.1650901 5.8389085 6.7724374 + 12000 0.94571583 0 1.2210342 6.2498816 7.3881135 + 13000 0.95994288 0 1.2172042 5.9608165 -7.3881135 + 14000 0.99053999 0 1.2925597 6.9994446 -6.7724374 + 15000 1.0316726 0 1.3346023 6.6902672 -6.1567613 + 16000 0.99537481 0 1.3227696 7.0301123 -5.5410852 + 17000 1.0306843 0 1.3101457 6.4750102 -4.925409 + 18000 1.071154 0 1.2947547 5.695888 -4.3097329 + 19000 0.97120752 0 1.3035465 7.3945362 -3.6940568 + 20000 0.97198994 0 1.2244663 6.0047605 -3.0783806 + 21000 0.97943545 0 1.2393394 6.3871012 -2.4627045 + 22000 0.98550707 0 1.1768148 5.019967 -1.8470284 + 23000 0.96920052 0 1.1730698 5.7944947 -1.2313523 + 24000 0.94069959 0 1.184119 5.8434876 -0.61567613 + 25000 0.91569312 0 1.1642118 5.668997 0 + 26000 0.98882932 0 1.1999248 5.0115507 0.61567613 + 27000 0.8972608 0 1.2556546 7.0837158 1.2313523 + 28000 0.93554756 0 1.2221911 5.9302841 1.8470284 + 29000 0.97894608 0 1.2168736 5.5766766 2.4627045 + 30000 0.97877055 0 1.2575839 6.4308887 3.0783806 + 31000 1.0002387 0 1.2338069 5.3873124 3.6940568 + 32000 0.89608618 0 1.2382021 6.7892204 4.3097329 + 33000 0.87439302 0 1.2252635 7.078134 4.925409 + 34000 1.076102 0 1.2991393 5.5556892 5.5410852 + 35000 1.0018689 0 1.272105 6.1320483 6.1567613 + 36000 0.93327214 0 1.2428039 7.0030867 6.7724374 + 37000 1.0770236 0 1.3002931 5.4996076 7.3881135 + 38000 0.98715132 0 1.215562 5.5958335 -7.3881135 + 39000 0.95028417 0 1.2566706 6.4133713 -6.7724374 + 40000 1.0445585 0 1.241151 5.3589806 -6.1567613 + 41000 0.93799713 0 1.2109086 6.4957845 -5.5410852 + 42000 0.99231038 0 1.2228781 5.9363471 -4.925409 + 43000 0.97913815 0 1.1854842 5.8837987 -4.3097329 + 44000 0.86748838 0 1.1616201 6.8991278 -3.6940568 + 45000 0.96284421 0 1.1549383 5.1226785 -3.0783806 + 46000 0.98701623 0 1.170581 4.9719567 -2.4627045 + 47000 0.92618683 0 1.2146576 6.7100075 -1.8470284 + 48000 1.0092593 0 1.2523988 5.7067864 -1.2313523 + 49000 1.0187472 0 1.271608 5.3355092 -0.61567613 + 50000 1.0194881 0 1.2831094 6.2449759 0 +Loop time of 4.80282 on 1 procs for 50000 steps with 160 atoms + +Performance: 4497356.047 tau/day, 10410.546 timesteps/s +50.2% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0.0032325 | 0.0032325 | 0.0032325 | 0.0 | 0.07 +Comm | 0.033613 | 0.033613 | 0.033613 | 0.0 | 0.70 +Output | 0.00089812 | 0.00089812 | 0.00089812 | 0.0 | 0.02 +Modify | 4.6706 | 4.6706 | 4.6706 | 0.0 | 97.25 +Other | | 0.09449 | | | 1.97 + +Nlocal: 160 ave 160 max 160 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 5270 +Dangerous builds = 0 +Total wall time: 0:00:04 diff --git a/examples/message/log.28Aug18.message.tilt.client.mpitwo.g++.2 b/examples/message/log.28Aug18.message.tilt.client.mpitwo.g++.2 new file mode 100644 index 0000000000..7c172d3727 --- /dev/null +++ b/examples/message/log.28Aug18.message.tilt.client.mpitwo.g++.2 @@ -0,0 +1,130 @@ +LAMMPS (22 Aug 2018) +# 2d NEMD simulation - client script + +variable mode index file + +if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple" +message client md mpi/two tmp.couple + +units lj +atom_style atomic +dimension 2 +atom_modify sort 0 0.0 map yes + +lattice sq2 0.8442 +Lattice spacing in x,y,z = 1.53919 1.53919 1.53919 +region box prism 0 10 0 8 -0.5 0.5 0 0 0 +create_box 2 box +Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0) + 2 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 160 atoms + Time spent = 0.000574827 secs +mass * 1.0 + +velocity all create 1.44 87287 loop geom + +region slice block 4 6 INF INF INF INF +set region slice type 2 + 40 settings made for type + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1 +fix 2 all deform 1 xy erate 0.01 remap v + +fix 3 all client/md +fix_modify 3 energy yes + +thermo_style custom step temp epair etotal press xy + +thermo 1000 +run 50000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 0 + ghost atom cutoff = 0 + binsize = 15.3919, bins = 1 1 1 + 0 neighbor lists, perpetual/occasional/extra = 0 0 0 +Per MPI rank memory allocation (min/avg/max) = 2.308 | 2.308 | 2.308 Mbytes +Step Temp E_pair TotEng Press Xy + 0 1.44 0 1.431 1.2080502 0 + 1000 1.0876599 0 1.3637783 6.063363 0.61567613 + 2000 1.0722996 0 1.4108622 7.0518942 1.2313523 + 3000 1.0580774 0 1.3845895 6.0395275 1.8470284 + 4000 1.0068006 0 1.3804387 7.0944598 2.4627045 + 5000 0.95391814 0 1.2578438 6.1878831 3.0783806 + 6000 0.93492945 0 1.2711287 7.0440517 3.6940568 + 7000 0.94107853 0 1.2384371 6.1438077 4.3097329 + 8000 0.89711744 0 1.145748 6.3558305 4.925409 + 9000 0.90190304 0 1.0860684 4.957098 5.5410852 + 10000 0.84255749 0 1.0376892 5.2351795 6.1567613 + 11000 0.90250882 0 1.0497695 4.3844838 6.7724374 + 12000 0.83461274 0 1.0281949 5.1534361 7.3881135 + 13000 0.80315331 0 1.0226333 5.757222 -7.3881135 + 14000 0.81820939 0 0.99276466 4.6943725 -6.7724374 + 15000 0.8239631 0 1.0408289 5.1669006 -6.1567613 + 16000 0.88908894 0 1.1554855 6.3510278 -5.5410852 + 17000 0.98268136 0 1.2086981 5.6302847 -4.925409 + 18000 1.0098162 0 1.3687676 7.5243587 -4.3097329 + 19000 1.0795086 0 1.4562691 7.639418 -3.6940568 + 20000 1.1932155 0 1.5278988 7.0668432 -3.0783806 + 21000 1.2424296 0 1.6048792 7.959585 -2.4627045 + 22000 1.297169 0 1.7421262 8.9432388 -1.8470284 + 23000 1.2863494 0 1.7236774 8.3584973 -1.2313523 + 24000 1.4084347 0 1.7370339 7.2729078 -0.61567613 + 25000 1.3339728 0 1.6883255 7.529098 0 + 26000 1.1483243 0 1.5155578 7.3869994 0.61567613 + 27000 1.1372606 0 1.4368323 7.0580136 1.2313523 + 28000 1.0518579 0 1.355311 6.478857 1.8470284 + 29000 1.0581145 0 1.2535509 5.3697479 2.4627045 + 30000 0.93612564 0 1.185532 5.5520142 3.0783806 + 31000 0.94387516 0 1.1716454 5.8655485 3.6940568 + 32000 0.83953515 0 1.0737746 5.5551953 4.3097329 + 33000 0.84862926 0 1.0564042 5.7795428 4.925409 + 34000 0.83621877 0 1.079387 5.7514243 5.5410852 + 35000 0.86938506 0 1.031783 4.5897825 6.1567613 + 36000 0.88990609 0 1.0807597 5.3751744 6.7724374 + 37000 0.89534631 0 1.1238882 5.2400355 7.3881135 + 38000 0.98545003 0 1.2121125 5.7783854 -7.3881135 + 39000 0.96737778 0 1.2472934 6.1139 -6.7724374 + 40000 1.0664194 0 1.2956811 5.7353661 -6.1567613 + 41000 1.0681494 0 1.3269435 6.3102722 -5.5410852 + 42000 1.0875422 0 1.3963739 7.1208066 -4.925409 + 43000 1.0968173 0 1.3388062 6.1704339 -4.3097329 + 44000 1.1182109 0 1.3773214 7.0872686 -3.6940568 + 45000 1.1243261 0 1.432186 6.884782 -3.0783806 + 46000 1.039713 0 1.4389721 7.5585257 -2.4627045 + 47000 1.0816108 0 1.4100361 6.4611126 -1.8470284 + 48000 0.97637127 0 1.3605389 7.3992744 -1.2313523 + 49000 1.0361978 0 1.2721873 5.8166109 -0.61567613 + 50000 0.92367087 0 1.1875669 6.4685214 0 +Loop time of 5.66536 on 2 procs for 50000 steps with 160 atoms + +Performance: 3812643.232 tau/day, 8825.563 timesteps/s +48.1% CPU use with 2 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0.0012836 | 0.0015377 | 0.0017917 | 0.6 | 0.03 +Comm | 0.037211 | 0.037922 | 0.038633 | 0.4 | 0.67 +Output | 0.00052023 | 0.00073683 | 0.00095344 | 0.0 | 0.01 +Modify | 5.5101 | 5.5105 | 5.511 | 0.0 | 97.27 +Other | | 0.1146 | | | 2.02 + +Nlocal: 80 ave 80 max 80 min +Histogram: 2 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 5257 +Dangerous builds = 0 +Total wall time: 0:00:06 diff --git a/examples/message/log.28Aug18.message.tilt.client.zmq.g++.1 b/examples/message/log.28Aug18.message.tilt.client.zmq.g++.1 new file mode 100644 index 0000000000..f5e2f220cd --- /dev/null +++ b/examples/message/log.28Aug18.message.tilt.client.zmq.g++.1 @@ -0,0 +1,130 @@ +LAMMPS (22 Aug 2018) +# 2d NEMD simulation - client script + +variable mode index file + +if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple" +message client md zmq localhost:5555 + +units lj +atom_style atomic +dimension 2 +atom_modify sort 0 0.0 map yes + +lattice sq2 0.8442 +Lattice spacing in x,y,z = 1.53919 1.53919 1.53919 +region box prism 0 10 0 8 -0.5 0.5 0 0 0 +create_box 2 box +Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 160 atoms + Time spent = 0.000530005 secs +mass * 1.0 + +velocity all create 1.44 87287 loop geom + +region slice block 4 6 INF INF INF INF +set region slice type 2 + 40 settings made for type + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1 +fix 2 all deform 1 xy erate 0.01 remap v + +fix 3 all client/md +fix_modify 3 energy yes + +thermo_style custom step temp epair etotal press xy + +thermo 1000 +run 50000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 0 + ghost atom cutoff = 0 + binsize = 15.3919, bins = 1 1 1 + 0 neighbor lists, perpetual/occasional/extra = 0 0 0 +Per MPI rank memory allocation (min/avg/max) = 2.308 | 2.308 | 2.308 Mbytes +Step Temp E_pair TotEng Press Xy + 0 1.44 0 1.431 1.2080502 0 + 1000 1.0086399 0 1.3760711 6.8772078 0.61567613 + 2000 1.0707188 0 1.3744107 6.628097 1.2313523 + 3000 1.0627515 0 1.310096 6.1647179 1.8470284 + 4000 0.94091054 0 1.268976 6.4723215 2.4627045 + 5000 1.0218949 0 1.2430242 5.6945977 3.0783806 + 6000 0.98649481 0 1.1997565 5.2870413 3.6940568 + 7000 0.9047957 0 1.1461262 5.9291636 4.3097329 + 8000 0.85697614 0 1.0437412 5.0652097 4.925409 + 9000 0.84208329 0 1.109218 6.1749808 5.5410852 + 10000 0.86418108 0 1.1594773 6.2581867 6.1567613 + 11000 0.95136356 0 1.1650901 5.8389085 6.7724374 + 12000 0.94571583 0 1.2210342 6.2498816 7.3881135 + 13000 0.95994288 0 1.2172042 5.9608165 -7.3881135 + 14000 0.99053999 0 1.2925597 6.9994446 -6.7724374 + 15000 1.0316726 0 1.3346023 6.6902672 -6.1567613 + 16000 0.99537481 0 1.3227696 7.0301123 -5.5410852 + 17000 1.0306843 0 1.3101457 6.4750102 -4.925409 + 18000 1.071154 0 1.2947547 5.695888 -4.3097329 + 19000 0.97120752 0 1.3035465 7.3945362 -3.6940568 + 20000 0.97198994 0 1.2244663 6.0047605 -3.0783806 + 21000 0.97943545 0 1.2393394 6.3871012 -2.4627045 + 22000 0.98550707 0 1.1768148 5.019967 -1.8470284 + 23000 0.96920052 0 1.1730698 5.7944947 -1.2313523 + 24000 0.94069959 0 1.184119 5.8434876 -0.61567613 + 25000 0.91569312 0 1.1642118 5.668997 0 + 26000 0.98882932 0 1.1999248 5.0115507 0.61567613 + 27000 0.8972608 0 1.2556546 7.0837158 1.2313523 + 28000 0.93554756 0 1.2221911 5.9302841 1.8470284 + 29000 0.97894608 0 1.2168736 5.5766766 2.4627045 + 30000 0.97877055 0 1.2575839 6.4308887 3.0783806 + 31000 1.0002387 0 1.2338069 5.3873124 3.6940568 + 32000 0.89608618 0 1.2382021 6.7892204 4.3097329 + 33000 0.87439302 0 1.2252635 7.078134 4.925409 + 34000 1.076102 0 1.2991393 5.5556892 5.5410852 + 35000 1.0018689 0 1.272105 6.1320483 6.1567613 + 36000 0.93327214 0 1.2428039 7.0030867 6.7724374 + 37000 1.0770236 0 1.3002931 5.4996076 7.3881135 + 38000 0.98715132 0 1.215562 5.5958335 -7.3881135 + 39000 0.95028417 0 1.2566706 6.4133713 -6.7724374 + 40000 1.0445585 0 1.241151 5.3589806 -6.1567613 + 41000 0.93799713 0 1.2109086 6.4957845 -5.5410852 + 42000 0.99231038 0 1.2228781 5.9363471 -4.925409 + 43000 0.97913815 0 1.1854842 5.8837987 -4.3097329 + 44000 0.86748838 0 1.1616201 6.8991278 -3.6940568 + 45000 0.96284421 0 1.1549383 5.1226785 -3.0783806 + 46000 0.98701623 0 1.170581 4.9719567 -2.4627045 + 47000 0.92618683 0 1.2146576 6.7100075 -1.8470284 + 48000 1.0092593 0 1.2523988 5.7067864 -1.2313523 + 49000 1.0187472 0 1.271608 5.3355092 -0.61567613 + 50000 1.0194881 0 1.2831094 6.2449759 0 +Loop time of 12.9652 on 1 procs for 50000 steps with 160 atoms + +Performance: 1666000.147 tau/day, 3856.482 timesteps/s +23.2% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0.0018659 | 0.0018659 | 0.0018659 | 0.0 | 0.01 +Comm | 0.020679 | 0.020679 | 0.020679 | 0.0 | 0.16 +Output | 0.00052547 | 0.00052547 | 0.00052547 | 0.0 | 0.00 +Modify | 12.871 | 12.871 | 12.871 | 0.0 | 99.28 +Other | | 0.07062 | | | 0.54 + +Nlocal: 160 ave 160 max 160 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 5270 +Dangerous builds = 0 +Total wall time: 0:00:12 diff --git a/examples/message/log.28Aug18.message.tilt.client.zmq.g++.2 b/examples/message/log.28Aug18.message.tilt.client.zmq.g++.2 new file mode 100644 index 0000000000..8fc570f5da --- /dev/null +++ b/examples/message/log.28Aug18.message.tilt.client.zmq.g++.2 @@ -0,0 +1,130 @@ +LAMMPS (22 Aug 2018) +# 2d NEMD simulation - client script + +variable mode index file + +if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple" +message client md zmq localhost:5555 + +units lj +atom_style atomic +dimension 2 +atom_modify sort 0 0.0 map yes + +lattice sq2 0.8442 +Lattice spacing in x,y,z = 1.53919 1.53919 1.53919 +region box prism 0 10 0 8 -0.5 0.5 0 0 0 +create_box 2 box +Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0) + 2 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 160 atoms + Time spent = 0.000673056 secs +mass * 1.0 + +velocity all create 1.44 87287 loop geom + +region slice block 4 6 INF INF INF INF +set region slice type 2 + 40 settings made for type + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1 +fix 2 all deform 1 xy erate 0.01 remap v + +fix 3 all client/md +fix_modify 3 energy yes + +thermo_style custom step temp epair etotal press xy + +thermo 1000 +run 50000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 0 + ghost atom cutoff = 0 + binsize = 15.3919, bins = 1 1 1 + 0 neighbor lists, perpetual/occasional/extra = 0 0 0 +Per MPI rank memory allocation (min/avg/max) = 2.308 | 2.308 | 2.308 Mbytes +Step Temp E_pair TotEng Press Xy + 0 1.44 0 1.431 1.2080502 0 + 1000 1.0876599 0 1.3637783 6.063363 0.61567613 + 2000 1.0722996 0 1.4108622 7.0518942 1.2313523 + 3000 1.0580774 0 1.3845895 6.0395275 1.8470284 + 4000 1.0068006 0 1.3804387 7.0944598 2.4627045 + 5000 0.95391814 0 1.2578438 6.1878831 3.0783806 + 6000 0.93492945 0 1.2711287 7.0440517 3.6940568 + 7000 0.94107853 0 1.2384371 6.1438077 4.3097329 + 8000 0.89711744 0 1.145748 6.3558305 4.925409 + 9000 0.90190304 0 1.0860684 4.957098 5.5410852 + 10000 0.84255749 0 1.0376892 5.2351795 6.1567613 + 11000 0.90250882 0 1.0497695 4.3844838 6.7724374 + 12000 0.83461274 0 1.0281949 5.1534361 7.3881135 + 13000 0.80315331 0 1.0226333 5.757222 -7.3881135 + 14000 0.81820939 0 0.99276466 4.6943725 -6.7724374 + 15000 0.8239631 0 1.0408289 5.1669006 -6.1567613 + 16000 0.88908894 0 1.1554855 6.3510278 -5.5410852 + 17000 0.98268136 0 1.2086981 5.6302847 -4.925409 + 18000 1.0098162 0 1.3687676 7.5243587 -4.3097329 + 19000 1.0795086 0 1.4562691 7.639418 -3.6940568 + 20000 1.1932155 0 1.5278988 7.0668432 -3.0783806 + 21000 1.2424296 0 1.6048792 7.959585 -2.4627045 + 22000 1.297169 0 1.7421262 8.9432388 -1.8470284 + 23000 1.2863494 0 1.7236774 8.3584973 -1.2313523 + 24000 1.4084347 0 1.7370339 7.2729078 -0.61567613 + 25000 1.3339728 0 1.6883255 7.529098 0 + 26000 1.1483243 0 1.5155578 7.3869994 0.61567613 + 27000 1.1372606 0 1.4368323 7.0580136 1.2313523 + 28000 1.0518579 0 1.355311 6.478857 1.8470284 + 29000 1.0581145 0 1.2535509 5.3697479 2.4627045 + 30000 0.93612564 0 1.185532 5.5520142 3.0783806 + 31000 0.94387516 0 1.1716454 5.8655485 3.6940568 + 32000 0.83953515 0 1.0737746 5.5551953 4.3097329 + 33000 0.84862926 0 1.0564042 5.7795428 4.925409 + 34000 0.83621877 0 1.079387 5.7514243 5.5410852 + 35000 0.86938506 0 1.031783 4.5897825 6.1567613 + 36000 0.88990609 0 1.0807597 5.3751744 6.7724374 + 37000 0.89534631 0 1.1238882 5.2400355 7.3881135 + 38000 0.98545003 0 1.2121125 5.7783854 -7.3881135 + 39000 0.96737778 0 1.2472934 6.1139 -6.7724374 + 40000 1.0664194 0 1.2956811 5.7353661 -6.1567613 + 41000 1.0681494 0 1.3269435 6.3102722 -5.5410852 + 42000 1.0875422 0 1.3963739 7.1208066 -4.925409 + 43000 1.0968173 0 1.3388062 6.1704339 -4.3097329 + 44000 1.1182109 0 1.3773214 7.0872686 -3.6940568 + 45000 1.1243261 0 1.432186 6.884782 -3.0783806 + 46000 1.039713 0 1.4389721 7.5585257 -2.4627045 + 47000 1.0816108 0 1.4100361 6.4611126 -1.8470284 + 48000 0.97637127 0 1.3605389 7.3992744 -1.2313523 + 49000 1.0361978 0 1.2721873 5.8166109 -0.61567613 + 50000 0.92367087 0 1.1875669 6.4685214 0 +Loop time of 13.6129 on 2 procs for 50000 steps with 160 atoms + +Performance: 1586733.497 tau/day, 3672.994 timesteps/s +59.3% CPU use with 2 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0.0015125 | 0.0015551 | 0.0015976 | 0.1 | 0.01 +Comm | 0.026598 | 0.028413 | 0.030227 | 1.1 | 0.21 +Output | 0.00046492 | 0.00063884 | 0.00081277 | 0.0 | 0.00 +Modify | 13.465 | 13.483 | 13.501 | 0.5 | 99.04 +Other | | 0.0994 | | | 0.73 + +Nlocal: 80 ave 80 max 80 min +Histogram: 2 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 5257 +Dangerous builds = 0 +Total wall time: 0:00:13 diff --git a/examples/message/log.28Aug18.message.tilt.g++.1 b/examples/message/log.28Aug18.message.tilt.g++.1 new file mode 100644 index 0000000000..3f7cfc9da0 --- /dev/null +++ b/examples/message/log.28Aug18.message.tilt.g++.1 @@ -0,0 +1,129 @@ +LAMMPS (22 Aug 2018) +# 2d NEMD simulation - no client/server mode + +units lj +atom_style atomic +dimension 2 + +lattice sq2 0.8442 +Lattice spacing in x,y,z = 1.53919 1.53919 1.53919 +region box prism 0 10 0 8 -0.5 0.5 0 0 0 +create_box 2 box +Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 160 atoms + Time spent = 0.000437021 secs +mass * 1.0 + +velocity all create 1.44 87287 loop geom + +region slice block 4 6 INF INF INF INF +set region slice type 2 + 40 settings made for type + +pair_style lj/cut 2.5 +pair_coeff * * 1.0 1.0 1.0 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1 +fix 2 all deform 1 xy erate 0.01 remap v + +thermo_style custom step temp epair etotal press xy + +thermo 1000 +run 50000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.3 + ghost atom cutoff = 1.3 + binsize = 0.65, bins = 24 19 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton/tri + stencil: half/bin/2d/newton/tri + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.065 | 3.065 | 3.065 Mbytes +Step Temp E_pair TotEng Press Xy + 0 1.44 0 1.431 1.2080502 0 + 1000 1.1326992 0.25863754 1.3842573 6.0588079 0.61567613 + 2000 1.0158438 0.33502643 1.3445212 7.2638652 1.2313523 + 3000 1.0968167 0.3149227 1.4048843 7.0653223 1.8470284 + 4000 1.0070993 0.40611915 1.4069241 7.7283521 2.4627045 + 5000 1.1153133 0.2674828 1.3758254 6.2949171 3.0783806 + 6000 1.0170665 0.25843673 1.2691466 6.049412 3.6940568 + 7000 1.0224605 0.20974914 1.2258193 5.5104976 4.3097329 + 8000 0.96149374 0.24035439 1.1958388 5.4179146 4.925409 + 9000 0.87759014 0.2590493 1.1311545 5.8711239 5.5410852 + 10000 0.83791968 0.23477897 1.0674617 5.666904 6.1567613 + 11000 0.87702487 0.22958877 1.1011322 5.9068062 6.7724374 + 12000 0.81507294 0.26375817 1.0737369 5.9166925 7.3881135 + 13000 0.85655284 0.24676491 1.0979643 5.6918734 -7.3881135 + 14000 0.84369293 0.27818471 1.1166046 6.4146184 -6.7724374 + 15000 0.90052173 0.19836095 1.0932544 5.2690913 -6.1567613 + 16000 0.83836874 0.26921637 1.1023453 5.9579526 -5.5410852 + 17000 0.90492897 0.21933098 1.1186041 5.6042194 -4.925409 + 18000 0.90113412 0.24880908 1.1443111 6.0634846 -4.3097329 + 19000 1.0160445 0.17252962 1.1822239 5.3149334 -3.6940568 + 20000 0.96217234 0.2414377 1.1975965 5.476653 -3.0783806 + 21000 0.98229664 0.27569118 1.2518485 5.9340174 -2.4627045 + 22000 1.0551763 0.26997615 1.3185576 6.2094112 -1.8470284 + 23000 1.051999 0.34076639 1.3861904 7.082385 -1.2313523 + 24000 1.1350071 0.23701844 1.3649317 6.1829742 -0.61567613 + 25000 1.0946409 0.33366032 1.4214597 7.1907559 0 + 26000 1.1511799 0.24626808 1.3902531 5.8469984 0.61567613 + 27000 1.1009203 0.25653085 1.3505704 6.1504287 1.2313523 + 28000 1.0521302 0.2876798 1.3332342 5.9906187 1.8470284 + 29000 1.0518465 0.21853 1.2638025 5.6577549 2.4627045 + 30000 0.97264625 0.28758145 1.2541487 6.5769804 3.0783806 + 31000 1.0133579 0.31575837 1.3227828 6.6650893 3.6940568 + 32000 1.0714324 0.28757036 1.3523063 6.2682059 4.3097329 + 33000 1.0739451 0.28062459 1.3478575 6.6862746 4.925409 + 34000 1.0056867 0.38289586 1.382297 7.1120131 5.5410852 + 35000 1.0911349 0.26370939 1.3480247 6.1476048 6.1567613 + 36000 1.0618618 0.28269593 1.3379211 6.9414608 6.7724374 + 37000 1.0704991 0.29974994 1.3635585 7.0834346 7.3881135 + 38000 1.1087507 0.2682201 1.3700411 5.8506019 -7.3881135 + 39000 1.1303733 0.22362416 1.3469326 5.2500269 -6.7724374 + 40000 1.0174248 0.28956571 1.3006316 6.4491571 -6.1567613 + 41000 0.95981887 0.29162143 1.2454414 6.4658646 -5.5410852 + 42000 0.88302144 0.30432252 1.1818251 6.7401923 -4.925409 + 43000 0.93164419 0.25110308 1.1769245 5.9067383 -4.3097329 + 44000 0.98352598 0.23322873 1.2106077 5.5606585 -3.6940568 + 45000 1.0247245 0.26503082 1.2833508 6.533394 -3.0783806 + 46000 0.93004532 0.32277782 1.2470104 6.4689179 -2.4627045 + 47000 1.0653176 0.29185413 1.3505135 6.9534569 -1.8470284 + 48000 1.0401524 0.3420245 1.3756759 6.8016042 -1.2313523 + 49000 1.0023407 0.31833091 1.314407 6.7385662 -0.61567613 + 50000 1.0566272 0.28657142 1.3365947 6.261203 0 +Loop time of 1.15672 on 1 procs for 50000 steps with 160 atoms + +Performance: 18673426.371 tau/day, 43225.524 timesteps/s +99.8% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.19267 | 0.19267 | 0.19267 | 0.0 | 16.66 +Neigh | 0.15156 | 0.15156 | 0.15156 | 0.0 | 13.10 +Comm | 0.044569 | 0.044569 | 0.044569 | 0.0 | 3.85 +Output | 0.00057936 | 0.00057936 | 0.00057936 | 0.0 | 0.05 +Modify | 0.71051 | 0.71051 | 0.71051 | 0.0 | 61.42 +Other | | 0.05684 | | | 4.91 + +Nlocal: 160 ave 160 max 160 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 71 ave 71 max 71 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 362 ave 362 max 362 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 362 +Ave neighs/atom = 2.2625 +Neighbor list builds = 5256 +Dangerous builds = 0 +Total wall time: 0:00:01 diff --git a/examples/message/log.28Aug18.message.tilt.g++.4 b/examples/message/log.28Aug18.message.tilt.g++.4 new file mode 100644 index 0000000000..74061463f6 --- /dev/null +++ b/examples/message/log.28Aug18.message.tilt.g++.4 @@ -0,0 +1,129 @@ +LAMMPS (22 Aug 2018) +# 2d NEMD simulation - no client/server mode + +units lj +atom_style atomic +dimension 2 + +lattice sq2 0.8442 +Lattice spacing in x,y,z = 1.53919 1.53919 1.53919 +region box prism 0 10 0 8 -0.5 0.5 0 0 0 +create_box 2 box +Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 160 atoms + Time spent = 0.000396967 secs +mass * 1.0 + +velocity all create 1.44 87287 loop geom + +region slice block 4 6 INF INF INF INF +set region slice type 2 + 40 settings made for type + +pair_style lj/cut 2.5 +pair_coeff * * 1.0 1.0 1.0 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1 +fix 2 all deform 1 xy erate 0.01 remap v + +thermo_style custom step temp epair etotal press xy + +thermo 1000 +run 50000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.3 + ghost atom cutoff = 1.3 + binsize = 0.65, bins = 24 19 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton/tri + stencil: half/bin/2d/newton/tri + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.065 | 3.065 | 3.065 Mbytes +Step Temp E_pair TotEng Press Xy + 0 1.44 0 1.431 1.2080502 0 + 1000 1.1326992 0.25863754 1.3842573 6.0588079 0.61567613 + 2000 1.0158438 0.33502643 1.3445212 7.2638652 1.2313523 + 3000 1.0968167 0.3149227 1.4048843 7.0653223 1.8470284 + 4000 1.0070993 0.40611915 1.4069241 7.7283521 2.4627045 + 5000 1.1153133 0.2674828 1.3758254 6.2949171 3.0783806 + 6000 1.0170665 0.25843673 1.2691466 6.049412 3.6940568 + 7000 1.0224605 0.20974914 1.2258193 5.5104976 4.3097329 + 8000 0.96149374 0.24035439 1.1958388 5.4179146 4.925409 + 9000 0.87759014 0.2590493 1.1311545 5.8711239 5.5410852 + 10000 0.83791968 0.23477897 1.0674617 5.666904 6.1567613 + 11000 0.87702487 0.22958877 1.1011322 5.9068062 6.7724374 + 12000 0.81507294 0.26375817 1.0737369 5.9166925 7.3881135 + 13000 0.85655284 0.24676491 1.0979643 5.6918734 -7.3881135 + 14000 0.84369293 0.27818471 1.1166046 6.4146184 -6.7724374 + 15000 0.90052173 0.19836095 1.0932544 5.2690913 -6.1567613 + 16000 0.83836874 0.26921637 1.1023453 5.9579526 -5.5410852 + 17000 0.90492897 0.21933098 1.1186041 5.6042194 -4.925409 + 18000 0.90113412 0.24880908 1.1443111 6.0634846 -4.3097329 + 19000 1.0160445 0.17252962 1.1822239 5.3149334 -3.6940568 + 20000 0.96217234 0.2414377 1.1975965 5.476653 -3.0783806 + 21000 0.98229664 0.27569118 1.2518485 5.9340174 -2.4627045 + 22000 1.0551763 0.26997615 1.3185576 6.2094112 -1.8470284 + 23000 1.051999 0.34076639 1.3861904 7.082385 -1.2313523 + 24000 1.1350071 0.23701844 1.3649317 6.1829742 -0.61567613 + 25000 1.0946409 0.33366032 1.4214597 7.1907559 0 + 26000 1.1511799 0.24626808 1.3902531 5.8469984 0.61567613 + 27000 1.1009203 0.25653085 1.3505704 6.1504287 1.2313523 + 28000 1.0521302 0.2876798 1.3332342 5.9906187 1.8470284 + 29000 1.0518465 0.21853 1.2638025 5.6577549 2.4627045 + 30000 0.97264625 0.28758145 1.2541487 6.5769804 3.0783806 + 31000 1.0133579 0.31575837 1.3227828 6.6650893 3.6940568 + 32000 1.0714324 0.28757036 1.3523063 6.2682059 4.3097329 + 33000 1.0739451 0.28062459 1.3478575 6.6862746 4.925409 + 34000 1.0056867 0.38289586 1.382297 7.1120131 5.5410852 + 35000 1.0911349 0.26370939 1.3480247 6.1476048 6.1567613 + 36000 1.0618618 0.28269593 1.3379211 6.9414608 6.7724374 + 37000 1.0704991 0.29974994 1.3635585 7.0834346 7.3881135 + 38000 1.1087507 0.2682201 1.3700411 5.8506019 -7.3881135 + 39000 1.1303733 0.22362416 1.3469326 5.2500269 -6.7724374 + 40000 1.0174248 0.28956571 1.3006316 6.4491571 -6.1567613 + 41000 0.95981887 0.29162143 1.2454414 6.4658646 -5.5410852 + 42000 0.88302144 0.30432252 1.1818251 6.7401923 -4.925409 + 43000 0.93164419 0.25110308 1.1769245 5.9067383 -4.3097329 + 44000 0.98352598 0.23322873 1.2106077 5.5606585 -3.6940568 + 45000 1.0247245 0.26503082 1.2833508 6.533394 -3.0783806 + 46000 0.93004532 0.32277782 1.2470104 6.4689179 -2.4627045 + 47000 1.0653176 0.29185413 1.3505135 6.9534569 -1.8470284 + 48000 1.0401524 0.3420245 1.3756759 6.8016042 -1.2313523 + 49000 1.0023407 0.31833091 1.314407 6.7385662 -0.61567613 + 50000 1.0566272 0.28657142 1.3365947 6.261203 0 +Loop time of 0.92653 on 1 procs for 50000 steps with 160 atoms + +Performance: 23312793.646 tau/day, 53964.800 timesteps/s +100.0% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.15063 | 0.15063 | 0.15063 | 0.0 | 16.26 +Neigh | 0.11869 | 0.11869 | 0.11869 | 0.0 | 12.81 +Comm | 0.035839 | 0.035839 | 0.035839 | 0.0 | 3.87 +Output | 0.00064468 | 0.00064468 | 0.00064468 | 0.0 | 0.07 +Modify | 0.57422 | 0.57422 | 0.57422 | 0.0 | 61.98 +Other | | 0.0465 | | | 5.02 + +Nlocal: 160 ave 160 max 160 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 71 ave 71 max 71 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 362 ave 362 max 362 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 362 +Ave neighs/atom = 2.2625 +Neighbor list builds = 5256 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/message/log.28Aug18.message.tilt.server.mpione.g++.1 b/examples/message/log.28Aug18.message.tilt.server.mpione.g++.1 new file mode 100644 index 0000000000..428ff346ad --- /dev/null +++ b/examples/message/log.28Aug18.message.tilt.server.mpione.g++.1 @@ -0,0 +1,48 @@ +LAMMPS (22 Aug 2018) +# 3d Lennard-Jones melt - server script + +variable mode index file + +if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple" +message server md mpi/one + +units lj +atom_style atomic +dimension 2 +atom_modify map yes + +lattice sq2 0.8442 +Lattice spacing in x,y,z = 1.53919 1.53919 1.53919 +region box prism 0 10 0 8 -0.5 0.5 0 0 0 +create_box 2 box +Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 160 atoms + Time spent = 0.000438929 secs +mass * 1.0 # masses not used by server + +pair_style lj/cut 2.5 +pair_coeff * * 1.0 1.0 1.0 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +server md + 1 by 1 by 1 MPI processor grid +WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.3 + ghost atom cutoff = 1.3 + binsize = 0.65, bins = 24 19 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton/tri + stencil: half/bin/2d/newton/tri + bin: standard +Server MD calls = 50001 +Server MD reneighborings 5073 +Total wall time: 0:00:01 diff --git a/examples/message/log.28Aug18.message.tilt.server.mpione.g++.4 b/examples/message/log.28Aug18.message.tilt.server.mpione.g++.4 new file mode 100644 index 0000000000..3da50163ed --- /dev/null +++ b/examples/message/log.28Aug18.message.tilt.server.mpione.g++.4 @@ -0,0 +1,48 @@ +LAMMPS (22 Aug 2018) +# 3d Lennard-Jones melt - server script + +variable mode index file + +if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple" +message server md mpi/one + +units lj +atom_style atomic +dimension 2 +atom_modify map yes + +lattice sq2 0.8442 +Lattice spacing in x,y,z = 1.53919 1.53919 1.53919 +region box prism 0 10 0 8 -0.5 0.5 0 0 0 +create_box 2 box +Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0) + 2 by 2 by 1 MPI processor grid +create_atoms 1 box +Created 160 atoms + Time spent = 0.000455141 secs +mass * 1.0 # masses not used by server + +pair_style lj/cut 2.5 +pair_coeff * * 1.0 1.0 1.0 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +server md + 2 by 2 by 1 MPI processor grid +WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.3 + ghost atom cutoff = 1.3 + binsize = 0.65, bins = 24 19 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton/tri + stencil: half/bin/2d/newton/tri + bin: standard +Server MD calls = 50001 +Server MD reneighborings 5066 +Total wall time: 0:00:02 diff --git a/examples/message/log.28Aug18.message.tilt.server.mpitwo.g++.1 b/examples/message/log.28Aug18.message.tilt.server.mpitwo.g++.1 new file mode 100644 index 0000000000..fc29a6da63 --- /dev/null +++ b/examples/message/log.28Aug18.message.tilt.server.mpitwo.g++.1 @@ -0,0 +1,48 @@ +LAMMPS (22 Aug 2018) +# 3d Lennard-Jones melt - server script + +variable mode index file + +if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple" +message server md mpi/two tmp.couple + +units lj +atom_style atomic +dimension 2 +atom_modify map yes + +lattice sq2 0.8442 +Lattice spacing in x,y,z = 1.53919 1.53919 1.53919 +region box prism 0 10 0 8 -0.5 0.5 0 0 0 +create_box 2 box +Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 160 atoms + Time spent = 0.000521898 secs +mass * 1.0 # masses not used by server + +pair_style lj/cut 2.5 +pair_coeff * * 1.0 1.0 1.0 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +server md + 1 by 1 by 1 MPI processor grid +WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.3 + ghost atom cutoff = 1.3 + binsize = 0.65, bins = 24 19 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton/tri + stencil: half/bin/2d/newton/tri + bin: standard +Server MD calls = 50001 +Server MD reneighborings 5073 +Total wall time: 0:00:04 diff --git a/examples/message/log.28Aug18.message.tilt.server.mpitwo.g++.4 b/examples/message/log.28Aug18.message.tilt.server.mpitwo.g++.4 new file mode 100644 index 0000000000..758b84fe9d --- /dev/null +++ b/examples/message/log.28Aug18.message.tilt.server.mpitwo.g++.4 @@ -0,0 +1,48 @@ +LAMMPS (22 Aug 2018) +# 3d Lennard-Jones melt - server script + +variable mode index file + +if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple" +message server md mpi/two tmp.couple + +units lj +atom_style atomic +dimension 2 +atom_modify map yes + +lattice sq2 0.8442 +Lattice spacing in x,y,z = 1.53919 1.53919 1.53919 +region box prism 0 10 0 8 -0.5 0.5 0 0 0 +create_box 2 box +Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0) + 2 by 2 by 1 MPI processor grid +create_atoms 1 box +Created 160 atoms + Time spent = 0.000378847 secs +mass * 1.0 # masses not used by server + +pair_style lj/cut 2.5 +pair_coeff * * 1.0 1.0 1.0 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +server md + 2 by 2 by 1 MPI processor grid +WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.3 + ghost atom cutoff = 1.3 + binsize = 0.65, bins = 24 19 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton/tri + stencil: half/bin/2d/newton/tri + bin: standard +Server MD calls = 50001 +Server MD reneighborings 5066 +Total wall time: 0:00:06 diff --git a/examples/message/log.28Aug18.message.tilt.server.zmq.g++.1 b/examples/message/log.28Aug18.message.tilt.server.zmq.g++.1 new file mode 100644 index 0000000000..78526ba748 --- /dev/null +++ b/examples/message/log.28Aug18.message.tilt.server.zmq.g++.1 @@ -0,0 +1,48 @@ +LAMMPS (22 Aug 2018) +# 3d Lennard-Jones melt - server script + +variable mode index file + +if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple" +message server md zmq *:5555 + +units lj +atom_style atomic +dimension 2 +atom_modify map yes + +lattice sq2 0.8442 +Lattice spacing in x,y,z = 1.53919 1.53919 1.53919 +region box prism 0 10 0 8 -0.5 0.5 0 0 0 +create_box 2 box +Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 160 atoms + Time spent = 0.000557184 secs +mass * 1.0 # masses not used by server + +pair_style lj/cut 2.5 +pair_coeff * * 1.0 1.0 1.0 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +server md + 1 by 1 by 1 MPI processor grid +WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.3 + ghost atom cutoff = 1.3 + binsize = 0.65, bins = 24 19 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton/tri + stencil: half/bin/2d/newton/tri + bin: standard +Server MD calls = 50001 +Server MD reneighborings 5073 +Total wall time: 0:00:12 diff --git a/examples/message/log.28Aug18.message.tilt.server.zmq.g++.4 b/examples/message/log.28Aug18.message.tilt.server.zmq.g++.4 new file mode 100644 index 0000000000..b1ad768470 --- /dev/null +++ b/examples/message/log.28Aug18.message.tilt.server.zmq.g++.4 @@ -0,0 +1,48 @@ +LAMMPS (22 Aug 2018) +# 3d Lennard-Jones melt - server script + +variable mode index file + +if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple" +message server md zmq *:5555 + +units lj +atom_style atomic +dimension 2 +atom_modify map yes + +lattice sq2 0.8442 +Lattice spacing in x,y,z = 1.53919 1.53919 1.53919 +region box prism 0 10 0 8 -0.5 0.5 0 0 0 +create_box 2 box +Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0) + 2 by 2 by 1 MPI processor grid +create_atoms 1 box +Created 160 atoms + Time spent = 0.000586987 secs +mass * 1.0 # masses not used by server + +pair_style lj/cut 2.5 +pair_coeff * * 1.0 1.0 1.0 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +server md + 2 by 2 by 1 MPI processor grid +WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.3 + ghost atom cutoff = 1.3 + binsize = 0.65, bins = 24 19 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton/tri + stencil: half/bin/2d/newton/tri + bin: standard +Server MD calls = 50001 +Server MD reneighborings 5066 +Total wall time: 0:00:13 diff --git a/lib/README b/lib/README index 3c8f46dd0a..12c27b2a39 100644 --- a/lib/README +++ b/lib/README @@ -35,6 +35,8 @@ linalg set of BLAS and LAPACK routines needed by USER-ATC package from Axel Kohlmeyer (Temple U) meam modified embedded atom method (MEAM) potential, MEAM package from Greg Wagner (Sandia) +message client/server communication library via MPI, sockets, files + from Steve Plimpton (Sandia) molfile hooks to VMD molfile plugins, used by the USER-MOLFILE package from Axel Kohlmeyer (Temple U) and the VMD development team mscg hooks to the MSCG library, used by fix_mscg command diff --git a/lib/message/Install.py b/lib/message/Install.py new file mode 100644 index 0000000000..d3f31c986f --- /dev/null +++ b/lib/message/Install.py @@ -0,0 +1,118 @@ +#!/usr/bin/env python + +# Install.py tool to build the CSlib library +# used to automate the steps described in the README file in this dir + +from __future__ import print_function +import sys,os,re,subprocess + +# help message + +help = """ +Syntax from src dir: make lib-message args="-m" + or: make lib-message args="-s -z" +Syntax from lib dir: python Install.py -m + or: python Install.py -s -z + +specify zero or more options, order does not matter + + -m = parallel build of CSlib library + -s = serial build of CSlib library + -z = build CSlib library with ZMQ socket support, default = no ZMQ support + +Example: + +make lib-message args="-m -z" # build parallel CSlib with ZMQ support +make lib-message args="-s" # build serial CSlib with no ZMQ support +""" + +# print error message or help + +def error(str=None): + if not str: print(help) + else: print("ERROR",str) + sys.exit() + +# expand to full path name +# process leading '~' or relative path + +def fullpath(path): + return os.path.abspath(os.path.expanduser(path)) + +def which(program): + def is_exe(fpath): + return os.path.isfile(fpath) and os.access(fpath, os.X_OK) + + fpath, fname = os.path.split(program) + if fpath: + if is_exe(program): + return program + else: + for path in os.environ["PATH"].split(os.pathsep): + path = path.strip('"') + exe_file = os.path.join(path, program) + if is_exe(exe_file): + return exe_file + + return None + +# parse args + +args = sys.argv[1:] +nargs = len(args) +if nargs == 0: error() + +mpiflag = False +serialflag = False +zmqflag = False + +iarg = 0 +while iarg < nargs: + if args[iarg] == "-m": + mpiflag = True + iarg += 1 + elif args[iarg] == "-s": + serialflag = True + iarg += 1 + elif args[iarg] == "-z": + zmqflag = True + iarg += 1 + else: error() + +if (not mpiflag and not serialflag): + error("Must use either -m or -s flag") + +if (mpiflag and serialflag): + error("Cannot use -m and -s flag at the same time") + +# build CSlib +# copy resulting lib to cslib/src/libmessage.a +# copy appropriate Makefile.lammps.* to Makefile.lammps + +print("Building CSlib ...") +srcdir = fullpath("./cslib/src") + +if mpiflag and zmqflag: + cmd = "cd %s; make lib_parallel" % srcdir +elif mpiflag and not zmqflag: + cmd = "cd %s; make lib_parallel zmq=no" % srcdir +elif not mpiflag and zmqflag: + cmd = "cd %s; make lib_serial" % srcdir +elif not mpiflag and not zmqflag: + cmd = "cd %s; make lib_serial zmq=no" % srcdir + +print(cmd) +txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) +print(txt.decode('UTF-8')) + +if mpiflag: cmd = "cd %s; cp libcsmpi.a libmessage.a" % srcdir +else: cmd = "cd %s; cp libcsnompi.a libmessage.a" % srcdir +print(cmd) +txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) +print(txt.decode('UTF-8')) + +if zmqflag: cmd = "cp Makefile.lammps.zmq Makefile.lammps" +else: cmd = "cp Makefile.lammps.nozmq Makefile.lammps" +print(cmd) +txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) +print(txt.decode('UTF-8')) diff --git a/lib/message/Makefile.lammps.nozmq b/lib/message/Makefile.lammps.nozmq new file mode 100644 index 0000000000..1bb10cc988 --- /dev/null +++ b/lib/message/Makefile.lammps.nozmq @@ -0,0 +1,5 @@ +# Settings that the LAMMPS build will import when this package library is used + +message_SYSINC = +message_SYSLIB = +message_SYSPATH = diff --git a/lib/message/Makefile.lammps.zmq b/lib/message/Makefile.lammps.zmq new file mode 100644 index 0000000000..759f2ce04b --- /dev/null +++ b/lib/message/Makefile.lammps.zmq @@ -0,0 +1,5 @@ +# Settings that the LAMMPS build will import when this package library is used + +message_SYSINC = +message_SYSLIB = -lzmq +message_SYSPATH = diff --git a/lib/message/README b/lib/message/README new file mode 100644 index 0000000000..dafb94e9ef --- /dev/null +++ b/lib/message/README @@ -0,0 +1,51 @@ +This directory contains the CSlib library which is required +to use the MESSAGE package and its client/server commands +in a LAMMPS input script. + +The CSlib libary is included in the LAMMPS distribution. A fuller +version including documentation and test programs is available at +http://cslib.sandia.gov. It was developed by Steve Plimpton at Sandia +National Laboratories. + +You can type "make lib-message" from the src directory to see help on +how to build this library via make commands, or you can do the same +thing by typing "python Install.py" from within this directory, or you +can do it manually by following the instructions below. + +The CSlib can be optionally built with support for sockets using +the open-source ZeroMQ (ZMQ) library. If it is not installed +on your system, it is easy to download and install. + +Go to the ZMQ website for details: http://zeromq.org + +----------------- + +Instructions: + +1. Compile CSlib from within cslib/src with one of the following: + % make lib_parallel # build parallel library with ZMQ socket support + % make lib_serial # build serial library with ZMQ support + % make lib_parallel zmq=no # build parallel lib with no ZMQ support + % make lib_serial zmq=no # build serial lib with no ZMQ support + +2. Copy the produced cslib/src/libcsmpi.a or libscnompi.a file to + cslib/src/libmessage.a + +3. Copy either lib/message/Makefile.lammps.zmq or Makefile.lammps.nozmq + to lib/message/Makefile.lammps, depending on whether you + build the library with ZMQ support or not. + If your ZMQ library is not in a place your shell path finds, + you can set the INCLUDE and PATH variables in Makefile.lammps + to point to the dirs where the ZMQ include and library files are. + +----------------- + +When these steps are complete you can build LAMMPS +with the MESSAGAE package installed: + +% cd lammps/src +% make yes-message +% make mpi (or whatever target you wish) + +Note that if you download and unpack a new LAMMPS tarball, you will +need to re-build the CSlib in this dir. diff --git a/lib/message/cslib/LICENSE b/lib/message/cslib/LICENSE new file mode 100644 index 0000000000..7a36e21daf --- /dev/null +++ b/lib/message/cslib/LICENSE @@ -0,0 +1,32 @@ +Program: CSlib client/server coupling library + +Copyright 2018 National Technology & Engineering Solutions of Sandia, +LLC (NTESS). Under the terms of Contract DE-NA0003525 with NTESS, the +U.S. Government retains certain rights in this software. This +software is distributed under the modified Berkeley Software +Distribution (BSD) License. + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + +* Redistributions of source code must retain the above copyright notice, + this list of conditions and the following disclaimer. + +* Redistributions in binary form must reproduce the above copyright notice, + this list of conditions and the following disclaimer in the documentation + and/or other materials provided with the distribution. + +* Neither the name of Sandia Corporation nor the names of contributors + to this software may be used to endorse or promote products derived + from this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' +AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHORS OR CONTRIBUTORS BE LIABLE FOR +ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, +OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. diff --git a/lib/message/cslib/README b/lib/message/cslib/README new file mode 100644 index 0000000000..37f4a97d54 --- /dev/null +++ b/lib/message/cslib/README @@ -0,0 +1,23 @@ +This is the the Client/Server messaging library (CSlib). + +Only the source directory and license file are included here as part +of the LAMMPS distribution. The full CSlib distribution, including +documentation and test codes, can be found at the website: +http://cslib.sandia.gov (as of Aug 2018). + +The contact author is + +Steve Plimpton +Sandia National Laboratories +sjplimp@sandia.gov +http://www.sandia.gov/~sjplimp + +The CSlib is distributed as open-source code under the modified +Berkeley Software Distribution (BSD) License. See the accompanying +LICENSE file. + +This directory contains the following: + +README this file +LICENSE GNU LGPL license +src source files for library diff --git a/lib/message/cslib/src/Makefile b/lib/message/cslib/src/Makefile new file mode 100644 index 0000000000..83cf902220 --- /dev/null +++ b/lib/message/cslib/src/Makefile @@ -0,0 +1,107 @@ +# Makefile for CSlib = client/server messaging library +# type "make help" for options + +SHELL = /bin/sh + +# ---------------------------------------- +# should only need to change this section +# compiler/linker settings +# ---------------------------------------- + +CC = g++ +CCFLAGS = -g -O3 -DZMQ_$(ZMQ) -DMPI_$(MPI) +SHFLAGS = -fPIC +ARCHIVE = ar +ARCHFLAGS = -rc +SHLIBFLAGS = -shared + +# files + +LIB = libcsmpi.a +SHLIB = libcsmpi.so +SRC = $(wildcard *.cpp) +INC = $(wildcard *.h) +OBJ = $(SRC:.cpp=.o) + +# build with ZMQ support or not + +zmq = yes +ZMQ = $(shell echo $(zmq) | tr a-z A-Z) + +ifeq ($(ZMQ),YES) + ZMQLIB = -lzmq +else + CCFLAGS += -I./STUBS_ZMQ +endif + +# build with MPI support or not + +mpi = yes +MPI = $(shell echo $(mpi) | tr a-z A-Z) + +ifeq ($(MPI),YES) + CC = mpicxx +else + CCFLAGS += -I./STUBS_MPI + LIB = libcsnompi.a + SHLIB = libcsnompi.so +endif + +# targets + +shlib: shlib_parallel shlib_serial + +lib: lib_parallel lib_serial + +all: shlib lib + +help: + @echo 'make default = shlib' + @echo 'make shlib build 2 shared CSlibs: parallel & serial' + @echo 'make lib build 2 static CSlibs: parallel & serial' + @echo 'make all build 4 CSlibs: shlib and lib' + @echo 'make shlib_parallel build shared parallel CSlib' + @echo 'make shlib_serial build shared serial CSlib' + @echo 'make lib_parallel build static parallel CSlib' + @echo 'make lib_serial build static serial CSlib' + @echo 'make ... zmq=no build w/out ZMQ support' + @echo 'make clean remove all *.o files' + @echo 'make clean-all remove *.o and lib files' + @echo 'make tar create a tarball, 2 levels up' + +shlib_parallel: + $(MAKE) clean + $(MAKE) shared zmq=$(zmq) mpi=yes + +shlib_serial: + $(MAKE) clean + $(MAKE) shared zmq=$(zmq) mpi=no + +lib_parallel: + $(MAKE) clean + $(MAKE) static zmq=$(zmq) mpi=yes + +lib_serial: + $(MAKE) clean + $(MAKE) static zmq=$(zmq) mpi=no + +static: $(OBJ) + $(ARCHIVE) $(ARCHFLAGS) $(LIB) $(OBJ) + +shared: $(OBJ) + $(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) -o $(SHLIB) $(OBJ) $(ZMQLIB) + +clean: + @rm -f *.o *.pyc + +clean-all: + @rm -f *.o *.pyc lib*.a lib*.so + +tar: + cd ../..; tar cvf cslib.tar cslib/README cslib/LICENSE \ + cslib/doc cslib/src cslib/test + +# rules + +%.o:%.cpp + $(CC) $(CCFLAGS) $(SHFLAGS) -c $< diff --git a/lib/message/cslib/src/STUBS_MPI/mpi.h b/lib/message/cslib/src/STUBS_MPI/mpi.h new file mode 100644 index 0000000000..2919e4c3a2 --- /dev/null +++ b/lib/message/cslib/src/STUBS_MPI/mpi.h @@ -0,0 +1,96 @@ +/* ---------------------------------------------------------------------- + CSlib - Client/server library for code coupling + http://cslib.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright 2018 National Technology & Engineering Solutions of + Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with + NTESS, the U.S. Government retains certain rights in this software. + This software is distributed under the modified Berkeley Software + Distribution (BSD) License. + + See the README file in the top-level CSlib directory. +------------------------------------------------------------------------- */ + +// MPI constants and dummy functions + +#ifndef MPI_DUMMY_H +#define MPI_DUMMY_H + +#include +#include +#include + +namespace CSLIB_NS { + +typedef int MPI_Comm; +typedef int MPI_Fint; +typedef int MPI_Datatype; +typedef int MPI_Status; +typedef int MPI_Op; +typedef int MPI_Info; + +#define MPI_COMM_WORLD 0 +#define MPI_MAX_PORT_NAME 0 +#define MPI_INFO_NULL 0 +#define MPI_INT 1 +#define MPI_LONG_LONG 2 +#define MPI_FLOAT 3 +#define MPI_DOUBLE 4 +#define MPI_CHAR 5 +#define MPI_SUM 0 + +static void MPI_Init(int *, char ***) {} +static MPI_Comm MPI_Comm_f2c(MPI_Comm world) {return world;} +static void MPI_Comm_rank(MPI_Comm, int *) {} +static void MPI_Comm_size(MPI_Comm, int *) {} + +static void MPI_Open_port(MPI_Info, char *) {} +static void MPI_Close_port(const char *) {} +static void MPI_Comm_accept(const char *, MPI_Info, int, + MPI_Comm, MPI_Comm *) {} +static void MPI_Comm_connect(const char *, MPI_Info, int, + MPI_Comm, MPI_Comm *) {} + +static void MPI_Comm_split(MPI_Comm, int, int, MPI_Comm *) {} +static void MPI_Comm_free(MPI_Comm *) {} + +static void MPI_Send(const void *, int, MPI_Datatype, int, int, MPI_Comm) {} +static void MPI_Recv(void *, int, MPI_Datatype, int, int, + MPI_Comm, MPI_Status *) {} + +static void MPI_Allreduce(const void *in, void *out, int, MPI_Datatype type, + MPI_Op op, MPI_Comm) +{ + if (type == MPI_INT) *((int *) out) = *((int *) in); +} +static void MPI_Scan(const void *in, void *out, int, MPI_Datatype intype, + MPI_Op op,MPI_Comm) +{ + if (intype == MPI_INT) *((int *) out) = *((int *) in); +} + +static void MPI_Bcast(void *, int, MPI_Datatype, int, MPI_Comm) {} +static void MPI_Allgather(const void *in, int incount, MPI_Datatype intype, + void *out, int, MPI_Datatype, MPI_Comm) +{ + // assuming incount = 1 + if (intype == MPI_INT) *((int *) out) = *((int *) in); +} +static void MPI_Allgatherv(const void *in, int incount, MPI_Datatype intype, + void *out, const int *, const int *, + MPI_Datatype, MPI_Comm) +{ + if (intype == MPI_INT) memcpy(out,in,incount*sizeof(int)); + else if (intype == MPI_LONG_LONG) memcpy(out,in,incount*sizeof(int64_t)); + else if (intype == MPI_FLOAT) memcpy(out,in,incount*sizeof(float)); + else if (intype == MPI_DOUBLE) memcpy(out,in,incount*sizeof(double)); + else if (intype == MPI_CHAR) memcpy(out,in,incount*sizeof(char)); +} + +static void MPI_Abort(MPI_Comm, int) {exit(1);} +static void MPI_Finalize() {} + +} + +#endif diff --git a/lib/message/cslib/src/STUBS_ZMQ/zmq.h b/lib/message/cslib/src/STUBS_ZMQ/zmq.h new file mode 100644 index 0000000000..2f02eb4035 --- /dev/null +++ b/lib/message/cslib/src/STUBS_ZMQ/zmq.h @@ -0,0 +1,36 @@ +/* ---------------------------------------------------------------------- + CSlib - Client/server library for code coupling + http://cslib.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright 2018 National Technology & Engineering Solutions of + Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with + NTESS, the U.S. Government retains certain rights in this software. + This software is distributed under the modified Berkeley Software + Distribution (BSD) License. + + See the README file in the top-level CSlib directory. +------------------------------------------------------------------------- */ + +// ZMQ constants and dummy functions + +#ifndef ZMQ_DUMMY_H +#define ZMQ_DUMMY_H + +namespace CSLIB_NS { + +#define ZMQ_REQ 0 +#define ZMQ_REP 0 + +static void *zmq_ctx_new() {return NULL;} +static void *zmq_connect(void *, char *) {return NULL;} +static int zmq_bind(void *, char *) {return 0;} +static void *zmq_socket(void *,int) {return NULL;} +static void zmq_close(void *) {} +static void zmq_ctx_destroy(void *) {} +static void zmq_send(void *, void *, int, int) {} +static void zmq_recv(void *, void *, int, int) {} + +}; + +#endif diff --git a/lib/message/cslib/src/cslib.cpp b/lib/message/cslib/src/cslib.cpp new file mode 100644 index 0000000000..874333607e --- /dev/null +++ b/lib/message/cslib/src/cslib.cpp @@ -0,0 +1,768 @@ +/* ---------------------------------------------------------------------- + CSlib - Client/server library for code coupling + http://cslib.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright 2018 National Technology & Engineering Solutions of + Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with + NTESS, the U.S. Government retains certain rights in this software. + This software is distributed under the modified Berkeley Software + Distribution (BSD) License. + + See the README file in the top-level CSlib directory. +------------------------------------------------------------------------- */ + +#include +#include +#include +#include +#include + +#include "cslib.h" +#include "msg_file.h" +#include "msg_zmq.h" +#include "msg_mpi_one.h" +#include "msg_mpi_two.h" + +using namespace CSLIB_NS; + +#define MAXTYPE 5 // # of defined field data types + +/* ---------------------------------------------------------------------- */ + +CSlib::CSlib(int csflag, const char *mode, const void *ptr, const void *pcomm) +{ + if (pcomm) myworld = (uint64_t) *((MPI_Comm *) pcomm); + else myworld = 0; + +#ifdef MPI_NO + if (pcomm) + error_all("constructor(): CSlib invoked with MPI_Comm " + "but built w/out MPI support"); +#endif +#ifdef MPI_YES // NOTE: this could be OK to allow ?? + // would allow a parallel app to invoke CSlib + // in parallel and/or in serial + if (!pcomm) + error_all("constructor(): CSlib invoked w/out MPI_Comm " + "but built with MPI support"); +#endif + + client = server = 0; + if (csflag == 0) client = 1; + else if (csflag == 1) server = 1; + else error_all("constructor(): Invalid client/server arg"); + + if (pcomm == NULL) { + me = 0; + nprocs = 1; + + if (strcmp(mode,"file") == 0) msg = new MsgFile(csflag,ptr); + else if (strcmp(mode,"zmq") == 0) msg = new MsgZMQ(csflag,ptr); + else if (strcmp(mode,"mpi/one") == 0) + error_all("constructor(): No mpi/one mode for serial lib usage"); + else if (strcmp(mode,"mpi/two") == 0) + error_all("constructor(): No mpi/two mode for serial lib usage"); + else error_all("constructor(): Unknown mode"); + + } else if (pcomm) { + MPI_Comm world = (MPI_Comm) myworld; + MPI_Comm_rank(world,&me); + MPI_Comm_size(world,&nprocs); + + if (strcmp(mode,"file") == 0) msg = new MsgFile(csflag,ptr,world); + else if (strcmp(mode,"zmq") == 0) msg = new MsgZMQ(csflag,ptr,world); + else if (strcmp(mode,"mpi/one") == 0) msg = new MsgMPIOne(csflag,ptr,world); + else if (strcmp(mode,"mpi/two") == 0) msg = new MsgMPITwo(csflag,ptr,world); + else error_all("constructor(): Unknown mode"); + } + + maxfield = 0; + fieldID = fieldtype = fieldlen = fieldoffset = NULL; + maxheader = 0; + header = NULL; + maxbuf = 0; + buf = NULL; + + recvcounts = displs = NULL; + maxglobal = 0; + allids = NULL; + maxfieldbytes = 0; + fielddata = NULL; + + pad = "\0\0\0\0\0\0\0"; // just length 7 since will have trailing NULL + + nsend = nrecv = 0; +} + +/* ---------------------------------------------------------------------- */ + +CSlib::~CSlib() +{ + deallocate_fields(); + sfree(header); + sfree(buf); + + sfree(recvcounts); + sfree(displs); + sfree(allids); + sfree(fielddata); + + delete msg; +} + +/* ---------------------------------------------------------------------- */ + +void CSlib::send(int msgID_caller, int nfield_caller) +{ + if (nfield_caller < 0) error_all("send(): Invalid nfield"); + + msgID = msgID_caller; + nfield = nfield_caller; + allocate_fields(); + + fieldcount = 0; + nbuf = 0; + + if (fieldcount == nfield) send_message(); +} + +/* ---------------------------------------------------------------------- */ + +void CSlib::pack_int(int id, int value) +{ + pack(id,1,1,&value); +} + +/* ---------------------------------------------------------------------- */ + +void CSlib::pack_int64(int id, int64_t value) +{ + pack(id,2,1,&value); +} + +/* ---------------------------------------------------------------------- */ + +void CSlib::pack_float(int id, float value) +{ + pack(id,3,1,&value); +} + +/* ---------------------------------------------------------------------- */ + +void CSlib::pack_double(int id, double value) +{ + pack(id,4,1,&value); +} + +/* ---------------------------------------------------------------------- */ + +void CSlib::pack_string(int id, char *value) +{ + pack(id,5,strlen(value)+1,value); +} + +/* ---------------------------------------------------------------------- */ + +void CSlib::pack(int id, int ftype, int flen, void *data) +{ + if (find_field(id,fieldcount) >= 0) + error_all("pack(): Reuse of field ID"); + if (ftype < 1 || ftype > MAXTYPE) error_all("pack(): Invalid ftype"); + if (flen < 0) error_all("pack(): Invalid flen"); + + fieldID[fieldcount] = id; + fieldtype[fieldcount] = ftype; + fieldlen[fieldcount] = flen; + + int nbytes,nbytesround; + onefield(ftype,flen,nbytes,nbytesround); + + memcpy(&buf[nbuf],data,nbytes); + memcpy(&buf[nbuf+nbytes],pad,nbytesround-nbytes); + nbuf += nbytesround; + + fieldcount++; + if (fieldcount == nfield) send_message(); +} + +/* ---------------------------------------------------------------------- */ + +void CSlib::pack_parallel(int id, int ftype, + int nlocal, int *ids, int nper, void *data) +{ + int i,j,k,m; + + if (find_field(id,fieldcount) >= 0) + error_all("pack_parallel(): Reuse of field ID"); + if (ftype < 1 || ftype > MAXTYPE) error_all("pack_parallel(): Invalid ftype"); + if (nlocal < 0) error_all("pack_parallel(): Invalid nlocal"); + if (nper < 1) error_all("pack_parallel(): Invalid nper"); + + MPI_Comm world = (MPI_Comm) myworld; + + // NOTE: check for overflow of maxglobal and flen + + int nglobal; + MPI_Allreduce(&nlocal,&nglobal,1,MPI_INT,MPI_SUM,world); + int flen = nper*nglobal; + + fieldID[fieldcount] = id; + fieldtype[fieldcount] = ftype; + fieldlen[fieldcount] = flen; + + // nlocal datums, each of nper length, from all procs + // final data in buf = datums for all natoms, ordered by ids + + if (recvcounts == NULL) { + recvcounts = (int *) smalloc(nprocs*sizeof(int)); + displs = (int *) smalloc(nprocs*sizeof(int)); + } + + MPI_Allgather(&nlocal,1,MPI_INT,recvcounts,1,MPI_INT,world); + + displs[0] = 0; + for (int iproc = 1; iproc < nprocs; iproc++) + displs[iproc] = displs[iproc-1] + recvcounts[iproc-1]; + + if (ids && nglobal > maxglobal) { + sfree(allids); + maxglobal = nglobal; + // NOTE: maxglobal*sizeof(int) could overflow int + allids = (int *) smalloc(maxglobal*sizeof(int)); + } + + MPI_Allgatherv(ids,nlocal,MPI_INT,allids, + recvcounts,displs,MPI_INT,world); + + int nlocalsize = nper*nlocal; + MPI_Allgather(&nlocalsize,1,MPI_INT,recvcounts,1,MPI_INT,world); + + displs[0] = 0; + for (int iproc = 1; iproc < nprocs; iproc++) + displs[iproc] = displs[iproc-1] + recvcounts[iproc-1]; + + int nbytes,nbytesround; + onefield(ftype,flen,nbytes,nbytesround); + + if (ftype == 1) { + int *alldata; + if (ids) { + if (nbytes > maxfieldbytes) { + sfree(fielddata); + maxfieldbytes = nbytes; + fielddata = (char *) smalloc(maxfieldbytes); + } + alldata = (int *) fielddata; + } else alldata = (int *) &buf[nbuf]; + MPI_Allgatherv(data,nlocalsize,MPI_INT,alldata, + recvcounts,displs,MPI_INT,world); + if (ids) { + int *bufptr = (int *) &buf[nbuf]; + m = 0; + for (i = 0; i < nglobal; i++) { + j = (allids[i]-1) * nper; + if (nper == 1) bufptr[j] = alldata[m++]; + else + for (k = 0; k < nper; k++) + bufptr[j++] = alldata[m++]; + } + } + + } else if (ftype == 2) { + int64_t *alldata; + if (ids) { + if (nbytes > maxfieldbytes) { + sfree(fielddata); + maxfieldbytes = nbytes; + fielddata = (char *) smalloc(maxfieldbytes); + } + alldata = (int64_t *) fielddata; + } else alldata = (int64_t *) &buf[nbuf]; + // NOTE: may be just MPI_LONG on some machines + MPI_Allgatherv(data,nlocalsize,MPI_LONG_LONG,alldata, + recvcounts,displs,MPI_LONG_LONG,world); + if (ids) { + int64_t *bufptr = (int64_t *) &buf[nbuf]; + m = 0; + for (i = 0; i < nglobal; i++) { + j = (allids[i]-1) * nper; + if (nper == 1) bufptr[j] = alldata[m++]; + else + for (k = 0; k < nper; k++) + bufptr[j++] = alldata[m++]; + } + } + + } else if (ftype == 3) { + float *alldata; + if (ids) { + if (nbytes > maxfieldbytes) { + sfree(fielddata); + maxfieldbytes = nbytes; + fielddata = (char *) smalloc(maxfieldbytes); + } + alldata = (float *) fielddata; + } else alldata = (float *) &buf[nbuf]; + MPI_Allgatherv(data,nlocalsize,MPI_FLOAT,alldata, + recvcounts,displs,MPI_FLOAT,world); + if (ids) { + float *bufptr = (float *) &buf[nbuf]; + m = 0; + for (i = 0; i < nglobal; i++) { + j = (allids[i]-1) * nper; + if (nper == 1) bufptr[j] = alldata[m++]; + else + for (k = 0; k < nper; k++) + bufptr[j++] = alldata[m++]; + } + } + + } else if (ftype == 4) { + double *alldata; + if (ids) { + if (nbytes > maxfieldbytes) { + sfree(fielddata); + maxfieldbytes = nbytes; + fielddata = (char *) smalloc(maxfieldbytes); + } + alldata = (double *) fielddata; + } else alldata = (double *) &buf[nbuf]; + MPI_Allgatherv(data,nlocalsize,MPI_DOUBLE,alldata, + recvcounts,displs,MPI_DOUBLE,world); + if (ids) { + double *bufptr = (double *) &buf[nbuf]; + m = 0; + for (i = 0; i < nglobal; i++) { + j = (allids[i]-1) * nper; + if (nper == 1) bufptr[j] = alldata[m++]; + else + for (k = 0; k < nper; k++) + bufptr[j++] = alldata[m++]; + } + } + + /* eventually ftype = BYTE, but not yet + } else if (ftype == 5) { + char *alldata; + if (ids) { + if (nbytes > maxfieldbytes) { + sfree(fielddata); + maxfieldbytes = nbytes; + fielddata = (char *) smalloc(maxfieldbytes); + } + alldata = (char *) fielddata; + } else alldata = (char *) &buf[nbuf]; + MPI_Allgatherv(data,nlocalsize,MPI_CHAR,alldata, + recvcounts,displs,MPI_CHAR,world); + if (ids) { + char *bufptr = (char *) &buf[nbuf]; + m = 0; + for (i = 0; i < nglobal; i++) { + j = (allids[i]-1) * nper; + memcpy(&bufptr[j],&alldata[m],nper); + m += nper; + } + } + */ + } + + memcpy(&buf[nbuf+nbytes],pad,nbytesround-nbytes); + nbuf += nbytesround; + + fieldcount++; + if (fieldcount == nfield) send_message(); +} + +/* ---------------------------------------------------------------------- */ + +void CSlib::send_message() +{ + // setup header message + + int m = 0; + header[m++] = msgID; + header[m++] = nfield; + for (int ifield = 0; ifield < nfield; ifield++) { + header[m++] = fieldID[ifield]; + header[m++] = fieldtype[ifield]; + header[m++] = fieldlen[ifield]; + } + + msg->send(nheader,header,nbuf,buf); + nsend++; +} + +/* ---------------------------------------------------------------------- */ + +int CSlib::recv(int &nfield_caller, int *&fieldID_caller, + int *&fieldtype_caller, int *&fieldlen_caller) +{ + msg->recv(maxheader,header,maxbuf,buf); + nrecv++; + + // unpack header message + + int m = 0; + msgID = header[m++]; + nfield = header[m++]; + allocate_fields(); + + int nbytes,nbytesround; + + nbuf = 0; + for (int ifield = 0; ifield < nfield; ifield++) { + fieldID[ifield] = header[m++]; + fieldtype[ifield] = header[m++]; + fieldlen[ifield] = header[m++]; + fieldoffset[ifield] = nbuf; + onefield(fieldtype[ifield],fieldlen[ifield],nbytes,nbytesround); + nbuf += nbytesround; + } + + // return message parameters + + nfield_caller = nfield; + fieldID_caller = fieldID; + fieldtype_caller = fieldtype; + fieldlen_caller = fieldlen; + + return msgID; +} + +/* ---------------------------------------------------------------------- */ + +int CSlib::unpack_int(int id) +{ + int ifield = find_field(id,nfield); + if (ifield < 0) error_all("unpack_int(): Unknown field ID"); + if (fieldtype[ifield] != 1) error_all("unpack_int(): Mis-match of ftype"); + if (fieldlen[ifield] != 1) error_all("unpack_int(): Flen is not 1"); + + int *ptr = (int *) unpack(id); + return *ptr; +} + +/* ---------------------------------------------------------------------- */ + +int64_t CSlib::unpack_int64(int id) +{ + int ifield = find_field(id,nfield); + if (ifield < 0) error_all("unpack_int64(): Unknown field ID"); + if (fieldtype[ifield] != 2) error_all("unpack_int64(): Mis-match of ftype"); + if (fieldlen[ifield] != 1) error_all("unpack_int64(): Flen is not 1"); + + int64_t *ptr = (int64_t *) unpack(id); + return *ptr; +} + +/* ---------------------------------------------------------------------- */ + +float CSlib::unpack_float(int id) +{ + int ifield = find_field(id,nfield); + if (ifield < 0) error_all("unpack_float(): Unknown field ID"); + if (fieldtype[ifield] != 3) error_all("unpack_float(): Mis-match of ftype"); + if (fieldlen[ifield] != 1) error_all("unpack_float(): Flen is not 1"); + + float *ptr = (float *) unpack(id); + return *ptr; +} + +/* ---------------------------------------------------------------------- */ + +double CSlib::unpack_double(int id) +{ + int ifield = find_field(id,nfield); + if (ifield < 0) error_all("unpack_double(): Unknown field ID"); + if (fieldtype[ifield] != 4) error_all("unpack_double(): Mis-match of ftype"); + if (fieldlen[ifield] != 1) error_all("unpack_double(): Flen is not 1"); + + double *ptr = (double *) unpack(id); + return *ptr; +} + +/* ---------------------------------------------------------------------- */ + +char *CSlib::unpack_string(int id) +{ + int ifield = find_field(id,nfield); + if (ifield < 0) error_all("unpack_string(): Unknown field ID"); + if (fieldtype[ifield] != 5) error_all("unpack_string(): Mis-match of ftype"); + + char *ptr = (char *) unpack(id); + return ptr; +} + +/* ---------------------------------------------------------------------- */ + +void *CSlib::unpack(int id) +{ + int ifield = find_field(id,nfield); + if (ifield < 0) error_all("unpack(): Unknown field ID"); + return &buf[fieldoffset[ifield]]; +} + +/* ---------------------------------------------------------------------- */ + +void CSlib::unpack(int id, void *data) +{ + int ifield = find_field(id,nfield); + if (ifield < 0) error_all("unpack(): Unknown field ID"); + + int ftype = fieldtype[ifield]; + int nbytes = fieldlen[ifield]; + if (ftype == 1) nbytes *= sizeof(int); + else if (ftype == 2) nbytes *= sizeof(int64_t); + else if (ftype == 3) nbytes *= sizeof(float); + else if (ftype == 4) nbytes *= sizeof(double); + memcpy(data,&buf[fieldoffset[ifield]],nbytes); +} + +/* ---------------------------------------------------------------------- */ + +void CSlib::unpack_parallel(int id, int nlocal, int *ids, int nper, void *data) +{ + int i,j,k,m; + + int ifield = find_field(id,nfield); + if (ifield < 0) error_all("unpack_parallel(): Unknown field ID"); + if (nlocal < 0) error_all("unpack_parallel(): Invalid nlocal"); + if (nper < 1) error_all("pack_parallel(): Invalid nper"); + + MPI_Comm world = (MPI_Comm) myworld; + + int upto; + if (!ids) { + MPI_Scan(&nlocal,&upto,1,MPI_INT,MPI_SUM,world); + upto -= nlocal; + } + + if (fieldtype[ifield] == 1) { + int *local = (int *) data; + int *global = (int *) &buf[fieldoffset[ifield]]; + if (!ids) memcpy(local,&global[nper*upto],nper*nlocal*sizeof(int)); + else { + m = 0; + for (i = 0; i < nlocal; i++) { + j = (ids[i]-1) * nper; + if (nper == 1) local[m++] = global[j]; + else + for (k = 0; k < nper; k++) + local[m++] = global[j++]; + } + } + + } else if (fieldtype[ifield] == 2) { + int64_t *local = (int64_t *) data; + int64_t *global = (int64_t *) &buf[fieldoffset[ifield]]; + if (!ids) memcpy(local,&global[nper*upto],nper*nlocal*sizeof(int64_t)); + else { + m = 0; + for (i = 0; i < nlocal; i++) { + j = (ids[i]-1) * nper; + if (nper == 1) local[m++] = global[j]; + else + for (k = 0; k < nper; k++) + local[m++] = global[j++]; + } + } + + } else if (fieldtype[ifield] == 3) { + float *local = (float *) data; + float *global = (float *) &buf[fieldoffset[ifield]]; + if (!ids) memcpy(local,&global[nper*upto],nper*nlocal*sizeof(float)); + else { + m = 0; + for (i = 0; i < nlocal; i++) { + j = (ids[i]-1) * nper; + if (nper == 1) local[m++] = global[j]; + else + for (k = 0; k < nper; k++) + local[m++] = global[j++]; + } + } + + } else if (fieldtype[ifield] == 4) { + double *local = (double *) data; + double *global = (double *) &buf[fieldoffset[ifield]]; + if (!ids) memcpy(local,&global[nper*upto],nper*nlocal*sizeof(double)); + else { + m = 0; + for (i = 0; i < nlocal; i++) { + j = (ids[i]-1) * nper; + if (nper == 1) local[m++] = global[j]; + else + for (k = 0; k < nper; k++) + local[m++] = global[j++]; + } + } + + /* eventually ftype = BYTE, but not yet + } else if (fieldtype[ifield] == 5) { + char *local = (char *) data; + char *global = (char *) &buf[fieldoffset[ifield]]; + if (!ids) memcpy(local,&global[nper*upto],nper*nlocal*sizeof(char)); + else { + m = 0; + for (i = 0; i < nlocal; i++) { + j = (ids[i]-1) * nper; + memcpy(&local[m],&global[j],nper); + m += nper; + } + } + */ + } +} + +/* ---------------------------------------------------------------------- */ + +int CSlib::extract(int flag) +{ + if (flag == 1) return nsend; + if (flag == 2) return nrecv; + error_all("extract(): Invalid flag"); + return 0; +} + +/* ---------------------------------------------------------------------- */ + +void CSlib::onefield(int ftype, int flen, int &nbytes, int &nbytesround) +{ + int64_t bigbytes,bigbytesround; + int64_t biglen = flen; + + if (ftype == 1) bigbytes = biglen * sizeof(int); + else if (ftype == 2) bigbytes = biglen * sizeof(int64_t); + else if (ftype == 3) bigbytes = biglen * sizeof(float); + else if (ftype == 4) bigbytes = biglen * sizeof(double); + else if (ftype == 5) bigbytes = biglen * sizeof(char); + bigbytesround = roundup(bigbytes,8); + + if (nbuf + bigbytesround > INT_MAX) + error_all("pack(): Message size exceeds 32-bit integer limit"); + + nbytes = (int) bigbytes; + nbytesround = (int) bigbytesround; + if (nbuf + nbytesround > maxbuf) { + maxbuf = nbuf + nbytesround; + buf = (char *) srealloc(buf,maxbuf); + } +} + +/* ---------------------------------------------------------------------- */ + +int CSlib::find_field(int id, int n) +{ + int ifield; + for (ifield = 0; ifield < n; ifield++) + if (id == fieldID[ifield]) return ifield; + return -1; +} + +/* ---------------------------------------------------------------------- */ + +void CSlib::allocate_fields() +{ + int64_t bigbytes = (2 + 3*((int64_t) nfield)) * sizeof(int); + if (bigbytes > INT_MAX) + error_all("send(): Message header size exceeds 32-bit integer limit"); + + nheader = 2; + nheader += 3 * nfield; + + if (nfield > maxfield) { + deallocate_fields(); + maxfield = nfield; + fieldID = new int[maxfield]; + fieldtype = new int[maxfield]; + fieldlen = new int[maxfield]; + fieldoffset = new int[maxfield]; + } + + if (nheader > maxheader) { + sfree(header); + maxheader = nheader; + header = (int *) smalloc(maxheader*sizeof(int)); + } +} + +/* ---------------------------------------------------------------------- */ + +void CSlib::deallocate_fields() +{ + delete [] fieldID; + delete [] fieldtype; + delete [] fieldlen; + delete [] fieldoffset; +} + +/* ---------------------------------------------------------------------- */ + +void *CSlib::smalloc(int nbytes) +{ + if (nbytes == 0) return NULL; + void *ptr = malloc(nbytes); + if (ptr == NULL) { + char str[128]; + sprintf(str,"malloc(): Failed to allocate %d bytes",nbytes); + error_one(str); + } + return ptr; +} + +/* ---------------------------------------------------------------------- */ + +void *CSlib::srealloc(void *ptr, int nbytes) +{ + if (nbytes == 0) { + sfree(ptr); + return NULL; + } + + ptr = realloc(ptr,nbytes); + if (ptr == NULL) { + char str[128]; + sprintf(str,"realloc(): Failed to reallocate %d bytes",nbytes); + error_one(str); + } + return ptr; +} + +/* ---------------------------------------------------------------------- */ + +void CSlib::sfree(void *ptr) +{ + if (ptr == NULL) return; + free(ptr); +} + +/* ---------------------------------------------------------------------- */ + +void CSlib::error_all(const char *str) +{ + if (me == 0) printf("CSlib ERROR: %s\n",str); + MPI_Comm world = (MPI_Comm) myworld; + MPI_Abort(world,1); +} + +/* ---------------------------------------------------------------------- */ + +void CSlib::error_one(const char *str) +{ + printf("CSlib ERROR: %s\n",str); + MPI_Comm world = (MPI_Comm) myworld; + MPI_Abort(world,1); +} + +/* ---------------------------------------------------------------------- + round N up to multiple of nalign and return it + NOTE: see mapreduce/src/keyvalue.cpp for doing this as uint64_t +------------------------------------------------------------------------- */ + +int64_t CSlib::roundup(int64_t n, int nalign) +{ + if (n % nalign == 0) return n; + n = (n/nalign + 1) * nalign; + return n; +} diff --git a/lib/message/cslib/src/cslib.h b/lib/message/cslib/src/cslib.h new file mode 100644 index 0000000000..b4da968026 --- /dev/null +++ b/lib/message/cslib/src/cslib.h @@ -0,0 +1,87 @@ +/* ---------------------------------------------------------------------- + CSlib - Client/server library for code coupling + http://cslib.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright 2018 National Technology & Engineering Solutions of + Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with + NTESS, the U.S. Government retains certain rights in this software. + This software is distributed under the modified Berkeley Software + Distribution (BSD) License. + + See the README file in the top-level CSlib directory. +------------------------------------------------------------------------- */ + +#ifndef CSLIB_H +#define CSLIB_H + +#include + +namespace CSLIB_NS { + +class CSlib { + public: + int nsend,nrecv; + + CSlib(int, const char *, const void *, const void *); + ~CSlib(); + + void send(int, int); + + void pack_int(int, int); + void pack_int64(int, int64_t); + void pack_float(int, float); + void pack_double(int, double); + void pack_string(int, char *); + void pack(int, int, int, void *); + void pack_parallel(int, int, int, int *, int, void *); + + int recv(int &, int *&, int *&, int *&); + + int unpack_int(int); + int64_t unpack_int64(int); + float unpack_float(int); + double unpack_double(int); + char *unpack_string(int); + void *unpack(int); + void unpack(int, void *); + void unpack_parallel(int, int, int *, int, void *); + + int extract(int); + + private: + uint64_t myworld; // really MPI_Comm, but avoids use of mpi.h in this file + // so apps can include this file w/ no MPI on system + int me,nprocs; + int client,server; + int nfield,maxfield; + int msgID,fieldcount; + int nheader,maxheader; + int nbuf,maxbuf; + int maxglobal,maxfieldbytes; + int *fieldID,*fieldtype,*fieldlen,*fieldoffset; + int *header; + int *recvcounts,*displs; // nprocs size for Allgathers + int *allids; // nglobal size for pack_parallel() + char *buf; // maxbuf size for msg with all fields + char *fielddata; // maxfieldbytes size for one global field + const char *pad; + + class Msg *msg; + + void send_message(); + void onefield(int, int, int &, int &); + int find_field(int, int); + void allocate_fields(); + void deallocate_fields(); + int64_t roundup(int64_t, int); + void *smalloc(int); + void *srealloc(void *, int); + void sfree(void *); + void error_all(const char *); + void error_one(const char *); +}; + +} + +#endif diff --git a/lib/message/cslib/src/cslib.py b/lib/message/cslib/src/cslib.py new file mode 100644 index 0000000000..0ba3516255 --- /dev/null +++ b/lib/message/cslib/src/cslib.py @@ -0,0 +1,362 @@ +# ------------------------------------------------------------------------ +# CSlib - Client/server library for code coupling +# http://cslib.sandia.gov, Sandia National Laboratories +# Steve Plimpton, sjplimp@sandia.gov +# +# Copyright 2018 National Technology & Engineering Solutions of +# Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with +# NTESS, the U.S. Government retains certain rights in this software. +# This software is distributed under the modified Berkeley Software +# Distribution (BSD) License. +# +# See the README file in the top-level CSlib directory. +# ------------------------------------------------------------------------- + +# Python wrapper on CSlib library via ctypes + +# ctypes and Numpy data types: +# 32-bit int = c_int = np.intc = np.int32 +# 64-bit int = c_longlong = np.int64 +# 32-bit floating point = c_float = np.float32 +# 64-bit floating point = c_double = np.float = np.float64 + +import sys,traceback +from ctypes import * + +# Numpy and mpi4py packages may not exist + +try: + import numpy as np + numpyflag = 1 +except: + numpyflag = 0 + +try: + from mpi4py import MPI + mpi4pyflag = 1 +except: + mpi4pyflag = 0 + +# wrapper class + +class CSlib: + + # instantiate CSlib thru its C-interface + + def __init__(self,csflag,mode,ptr,comm): + + # load libcslib.so + + try: + if comm: self.lib = CDLL("libcsmpi.so",RTLD_GLOBAL) + else: self.lib = CDLL("libcsnompi.so",RTLD_GLOBAL) + except: + etype,value,tb = sys.exc_info() + traceback.print_exception(etype,value,tb) + raise OSError,"Could not load CSlib dynamic library" + + # define ctypes API for each library method + + self.lib.cslib_open.argtypes = [c_int,c_char_p,c_void_p,c_void_p, + POINTER(c_void_p)] + self.lib.cslib_open.restype = None + + self.lib.cslib_close.argtypes = [c_void_p] + self.lib.cslib_close.restype = None + + self.lib.cslib_send.argtypes = [c_void_p,c_int,c_int] + self.lib.cslib_send.restype = None + + self.lib.cslib_pack_int.argtypes = [c_void_p,c_int,c_int] + self.lib.cslib_pack_int.restype = None + + self.lib.cslib_pack_int64.argtypes = [c_void_p,c_int,c_longlong] + self.lib.cslib_pack_int64.restype = None + + self.lib.cslib_pack_float.argtypes = [c_void_p,c_int,c_float] + self.lib.cslib_pack_float.restype = None + + self.lib.cslib_pack_double.argtypes = [c_void_p,c_int,c_double] + self.lib.cslib_pack_double.restype = None + + self.lib.cslib_pack_string.argtypes = [c_void_p,c_int,c_char_p] + self.lib.cslib_pack_string.restype = None + + self.lib.cslib_pack.argtypes = [c_void_p,c_int,c_int,c_int,c_void_p] + self.lib.cslib_pack.restype = None + + self.lib.cslib_pack_parallel.argtypes = [c_void_p,c_int,c_int,c_int, + POINTER(c_int),c_int,c_void_p] + self.lib.cslib_pack_parallel.restype = None + + self.lib.cslib_recv.argtypes = [c_void_p,POINTER(c_int), + POINTER(POINTER(c_int)), + POINTER(POINTER(c_int)), + POINTER(POINTER(c_int))] + self.lib.cslib_recv.restype = c_int + + self.lib.cslib_unpack_int.argtypes = [c_void_p,c_int] + self.lib.cslib_unpack_int.restype = c_int + + self.lib.cslib_unpack_int64.argtypes = [c_void_p,c_int] + self.lib.cslib_unpack_int64.restype = c_longlong + + self.lib.cslib_unpack_float.argtypes = [c_void_p,c_int] + self.lib.cslib_unpack_float.restype = c_float + + self.lib.cslib_unpack_double.argtypes = [c_void_p,c_int] + self.lib.cslib_unpack_double.restype = c_double + + self.lib.cslib_unpack_string.argtypes = [c_void_p,c_int] + self.lib.cslib_unpack_string.restype = c_char_p + + # override return in unpack() + self.lib.cslib_unpack.argtypes = [c_void_p,c_int] + self.lib.cslib_unpack.restype = c_void_p + + self.lib.cslib_unpack_data.argtypes = [c_void_p,c_int,c_void_p] + self.lib.cslib_unpack_data.restype = None + + # override last arg in unpack_parallel() + self.lib.cslib_unpack_parallel.argtypes = [c_void_p,c_int,c_int, + POINTER(c_int),c_int,c_void_p] + self.lib.cslib_unpack_parallel.restype = None + + self.lib.cslib_extract.argtypes = [c_void_p,c_int] + self.lib.cslib_extract.restype = c_int + + # create an instance of CSlib with or w/out MPI communicator + + self.cs = c_void_p() + + if not comm: + self.lib.cslib_open(csflag,mode,ptr,None,byref(self.cs)) + elif not mpi4pyflag: + print "Cannot pass MPI communicator to CSlib w/out mpi4py package" + sys.exit() + else: + address = MPI._addressof(comm) + comm_ptr = c_void_p(address) + if mode == "mpi/one": + address = MPI._addressof(ptr) + ptrcopy = c_void_p(address) + else: ptrcopy = ptr + self.lib.cslib_open(csflag,mode,ptrcopy,comm_ptr,byref(self.cs)) + + # destroy instance of CSlib + + def __del__(self): + if self.cs: self.lib.cslib_close(self.cs) + + def close(self): + self.lib.cslib_close(self.cs) + self.lib = None + + # send a message + + def send(self,msgID,nfield): + self.nfield = nfield + self.lib.cslib_send(self.cs,msgID,nfield) + + # pack one field of message + + def pack_int(self,id,value): + self.lib.cslib_pack_int(self.cs,id,value) + + def pack_int64(self,id,value): + self.lib.cslib_pack_int64(self.cs,id,value) + + def pack_float(self,id,value): + self.lib.cslib_pack_float(self.cs,id,value) + + def pack_double(self,id,value): + self.lib.cslib_pack_double(self.cs,id,value) + + def pack_string(self,id,value): + self.lib.cslib_pack_string(self.cs,id,value) + + def pack(self,id,ftype,flen,data): + cdata = self.data_convert(ftype,flen,data) + self.lib.cslib_pack(self.cs,id,ftype,flen,cdata) + + def pack_parallel(self,id,ftype,nlocal,ids,nper,data): + cids = self.data_convert(1,nlocal,ids) + cdata = self.data_convert(ftype,nper*nlocal,data) + self.lib.cslib_pack_parallel(self.cs,id,ftype,nlocal,cids,nper,cdata) + + # convert input data to a ctypes vector to pass to CSlib + + def data_convert(self,ftype,flen,data): + + # tflag = type of data + # tflag = 1 if data is list or tuple + # tflag = 2 if data is Numpy array + # tflag = 3 if data is ctypes vector + # same usage of tflag as in unpack function + + txttype = str(type(data)) + if "numpy" in txttype: tflag = 2 + elif "c_" in txttype: tflag = 3 + else: tflag = 1 + + # create ctypes vector out of data to pass to lib + # cdata = ctypes vector to return + # NOTE: error check on ftype and tflag everywhere, also flen + + if ftype == 1: + if tflag == 1: cdata = (flen * c_int)(*data) + elif tflag == 2: cdata = data.ctypes.data_as(POINTER(c_int)) + elif tflag == 3: cdata = data + elif ftype == 2: + if tflag == 1: cdata = (flen * c_longlong)(*data) + elif tflag == 2: cdata = data.ctypes.data_as(POINTER(c_longlong)) + elif tflag == 3: cdata = data + elif ftype == 3: + if tflag == 1: cdata = (flen * c_float)(*data) + elif tflag == 2: cdata = data.ctypes.data_as(POINTER(c_float)) + elif tflag == 3: cdata = data + elif ftype == 4: + if tflag == 1: cdata = (flen * c_double)(*data) + elif tflag == 2: cdata = data.ctypes.data_as(POINTER(c_double)) + elif tflag == 3: cdata = data + + return cdata + + # receive a message + + def recv(self): + self.lib.cslib_recv.restype = c_int + nfield = c_int() + fieldID = POINTER(c_int)() + fieldtype = POINTER(c_int)() + fieldlen = POINTER(c_int)() + msgID = self.lib.cslib_recv(self.cs,byref(nfield), + byref(fieldID),byref(fieldtype),byref(fieldlen)) + + # copy returned C args to native Python int and lists + # store them in class so unpack() methods can access the info + + self.nfield = nfield = nfield.value + self.fieldID = fieldID[:nfield] + self.fieldtype = fieldtype[:nfield] + self.fieldlen = fieldlen[:nfield] + + return msgID,self.nfield,self.fieldID,self.fieldtype,self.fieldlen + + # unpack one field of message + # tflag = type of data to return + # 3 = ctypes vector is default, since no conversion required + + def unpack_int(self,id): + return self.lib.cslib_unpack_int(self.cs,id) + + def unpack_int64(self,id): + return self.lib.cslib_unpack_int64(self.cs,id) + + def unpack_float(self,id): + return self.lib.cslib_unpack_float(self.cs,id) + + def unpack_double(self,id): + return self.lib.cslib_unpack_double(self.cs,id) + + def unpack_string(self,id): + return self.lib.cslib_unpack_string(self.cs,id) + + def unpack(self,id,tflag=3): + index = self.fieldID.index(id) + + # reset data type of return so can morph by tflag + # cannot do this for the generic c_void_p returned by CSlib + + if self.fieldtype[index] == 1: + self.lib.cslib_unpack.restype = POINTER(c_int) + elif self.fieldtype[index] == 2: + self.lib.cslib_unpack.restype = POINTER(c_longlong) + elif self.fieldtype[index] == 3: + self.lib.cslib_unpack.restype = POINTER(c_float) + elif self.fieldtype[index] == 4: + self.lib.cslib_unpack.restype = POINTER(c_double) + #elif self.fieldtype[index] == 5: + # self.lib.cslib_unpack.restype = POINTER(c_char) + + cdata = self.lib.cslib_unpack(self.cs,id) + + # tflag = user-requested type of data to return + # tflag = 1 to return data as list + # tflag = 2 to return data as Numpy array + # tflag = 3 to return data as ctypes vector + # same usage of tflag as in pack functions + # tflag = 2,3 should NOT perform a data copy + + if tflag == 1: + data = cdata[:self.fieldlen[index]] + elif tflag == 2: + if numpyflag == 0: + print "Cannot return Numpy array w/out numpy package" + sys.exit() + data = np.ctypeslib.as_array(cdata,shape=(self.fieldlen[index],)) + elif tflag == 3: + data = cdata + + return data + + # handle data array like pack() or unpack_parallel() ?? + + def unpack_data(self,id,tflag=3): + index = self.fieldID.index(id) + + # unpack one field of message in parallel + # tflag = type of data to return + # 3 = ctypes vector is default, since no conversion required + # NOTE: allow direct use of user array (e.g. Numpy), if user provides data arg? + # as opposed to creating this cdata + # does that make any performance difference ? + # e.g. should we allow CSlib to populate an existing Numpy array's memory + + def unpack_parallel(self,id,nlocal,ids,nper,tflag=3): + cids = self.data_convert(1,nlocal,ids) + + # allocate memory for the returned data + # pass cdata ptr to the memory to CSlib unpack_parallel() + # this resets data type of last unpack_parallel() arg + + index = self.fieldID.index(id) + if self.fieldtype[index] == 1: cdata = (nper*nlocal * c_int)() + elif self.fieldtype[index] == 2: cdata = (nlocal*nper * c_longlong)() + elif self.fieldtype[index] == 3: cdata = (nlocal*nper * c_float)() + elif self.fieldtype[index] == 4: cdata = (nlocal*nper * c_double)() + #elif self.fieldtype[index] == 5: cdata = (nlocal*nper * c_char)() + + self.lib.cslib_unpack_parallel(self.cs,id,nlocal,cids,nper,cdata) + + # tflag = user-requested type of data to return + # tflag = 1 to return data as list + # tflag = 2 to return data as Numpy array + # tflag = 3 to return data as ctypes vector + # same usage of tflag as in pack functions + + if tflag == 1: + data = cdata[:nper*nlocal] + elif tflag == 2: + if numpyflag == 0: + print "Cannot return Numpy array w/out numpy package" + sys.exit() + # NOTE: next line gives ctypes warning for fieldtype = 2 = 64-bit int + # not sure why, reported as bug between ctypes and Numpy here: + # https://stackoverflow.com/questions/4964101/pep-3118- + # warning-when-using-ctypes-array-as-numpy-array + # but why not same warning when just using unpack() ?? + # in Python these lines give same warning: + # >>> import ctypes,numpy + # >>> a = (10 * ctypes.c_longlong)() + # >>> b = numpy.ctypeslib.as_array(a) + data = np.ctypeslib.as_array(cdata,shape=(nlocal*nper,)) + elif tflag == 3: + data = cdata + + return data + + # extract a library value + + def extract(self,flag): + return self.lib.cslib_extract(self.cs,flag) diff --git a/lib/message/cslib/src/cslib_wrap.cpp b/lib/message/cslib/src/cslib_wrap.cpp new file mode 100644 index 0000000000..c2d69eaf0d --- /dev/null +++ b/lib/message/cslib/src/cslib_wrap.cpp @@ -0,0 +1,239 @@ +/* ---------------------------------------------------------------------- + CSlib - Client/server library for code coupling + http://cslib.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright 2018 National Technology & Engineering Solutions of + Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with + NTESS, the U.S. Government retains certain rights in this software. + This software is distributed under the modified Berkeley Software + Distribution (BSD) License. + + See the README file in the top-level CSlib directory. +------------------------------------------------------------------------- */ + +// C style library interface to CSlib class + +#include +#include +#include +#include +#include + +#include "cslib_wrap.h" +#include "cslib.h" + +using namespace CSLIB_NS; + +// ---------------------------------------------------------------------- + +void cslib_open(int csflag, const char *mode, const void *ptr, + const void *pcomm, void **csptr) +{ + CSlib *cs = new CSlib(csflag,mode,ptr,pcomm); + *csptr = (void *) cs; +} + +// ---------------------------------------------------------------------- + +void cslib_open_fortran(int csflag, const char *mode, const char *str, + const void *pcomm, void **csptr) +{ + MPI_Comm ccomm; + void *pccomm = NULL; + + if (pcomm) { + MPI_Fint *fcomm = (MPI_Fint *) pcomm; + ccomm = MPI_Comm_f2c(*fcomm); + pccomm = &ccomm; + } + + CSlib *cs = new CSlib(csflag,mode,str,pccomm); + *csptr = (void *) cs; +} + +// ---------------------------------------------------------------------- + +void cslib_open_fortran_mpi_one(int csflag, const char *mode, + const void *pboth, const void *pcomm, + void **csptr) +{ + MPI_Comm ccomm,cboth; + void *pccomm,*pcboth; + + MPI_Fint *fcomm = (MPI_Fint *) pcomm; + ccomm = MPI_Comm_f2c(*fcomm); + pccomm = &ccomm; + + MPI_Fint *fboth = (MPI_Fint *) pboth; + cboth = MPI_Comm_f2c(*fboth); + pcboth = &cboth; + + CSlib *cs = new CSlib(csflag,mode,pcboth,pccomm); + *csptr = (void *) cs; +} + +// ---------------------------------------------------------------------- + +void cslib_close(void *ptr) +{ + CSlib *cs = (CSlib *) ptr; + delete cs; +} + +// ---------------------------------------------------------------------- + +void cslib_send(void *ptr, int msgID, int nfield) +{ + CSlib *cs = (CSlib *) ptr; + cs->send(msgID,nfield); +} + +// ---------------------------------------------------------------------- + +void cslib_pack_int(void *ptr, int id, int value) +{ + CSlib *cs = (CSlib *) ptr; + cs->pack_int(id,value); +} + +// ---------------------------------------------------------------------- + +void cslib_pack_int64(void *ptr, int id, int64_t value) +{ + CSlib *cs = (CSlib *) ptr; + cs->pack_int64(id,value); +} + +// ---------------------------------------------------------------------- + +void cslib_pack_float(void *ptr, int id, float value) +{ + CSlib *cs = (CSlib *) ptr; + cs->pack_float(id,value); +} + +// ---------------------------------------------------------------------- + +void cslib_pack_double(void *ptr, int id, double value) +{ + CSlib *cs = (CSlib *) ptr; + cs->pack_double(id,value); +} + +// ---------------------------------------------------------------------- + +void cslib_pack_string(void *ptr, int id, char *value) +{ + CSlib *cs = (CSlib *) ptr; + cs->pack_string(id,value); +} + +// ---------------------------------------------------------------------- + +void cslib_pack(void *ptr, int id, int ftype, int flen, void *data) +{ + CSlib *cs = (CSlib *) ptr; + cs->pack(id,ftype,flen,data); +} + +// ---------------------------------------------------------------------- + +void cslib_pack_parallel(void *ptr, int id, int ftype, + int nlocal, int *ids, int nper, void *data) +{ + CSlib *cs = (CSlib *) ptr; + cs->pack_parallel(id,ftype,nlocal,ids,nper,data); +} + +// ---------------------------------------------------------------------- + +int cslib_recv(void *ptr, int *nfield_caller, + int **fieldID_caller, int **fieldtype_caller, + int **fieldlen_caller) +{ + CSlib *cs = (CSlib *) ptr; + + int nfield; + int *fieldID,*fieldtype,*fieldlen; + int msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen); + + *nfield_caller = nfield; + *fieldID_caller = fieldID; + *fieldtype_caller = fieldtype; + *fieldlen_caller = fieldlen; + + return msgID; +} + +// ---------------------------------------------------------------------- + +int cslib_unpack_int(void *ptr, int id) +{ + CSlib *cs = (CSlib *) ptr; + return cs->unpack_int(id); +} +// ---------------------------------------------------------------------- + +int64_t cslib_unpack_int64(void *ptr, int id) +{ + CSlib *cs = (CSlib *) ptr; + return cs->unpack_int64(id); +} + +// ---------------------------------------------------------------------- + +float cslib_unpack_float(void *ptr, int id) +{ + CSlib *cs = (CSlib *) ptr; + return cs->unpack_float(id); +} + +// ---------------------------------------------------------------------- + +double cslib_unpack_double(void *ptr, int id) +{ + CSlib *cs = (CSlib *) ptr; + return cs->unpack_double(id); +} + +// ---------------------------------------------------------------------- + +char *cslib_unpack_string(void *ptr, int id) +{ + CSlib *cs = (CSlib *) ptr; + return cs->unpack_string(id); +} + +// ---------------------------------------------------------------------- + +void *cslib_unpack(void *ptr, int id) +{ + CSlib *cs = (CSlib *) ptr; + return cs->unpack(id); +} + +// ---------------------------------------------------------------------- + +void cslib_unpack_data(void *ptr, int id, void *data) +{ + CSlib *cs = (CSlib *) ptr; + cs->unpack(id,data); +} + +// ---------------------------------------------------------------------- + +void cslib_unpack_parallel(void *ptr, int id, int nlocal, int *ids, + int nper, void *data) +{ + CSlib *cs = (CSlib *) ptr; + cs->unpack_parallel(id,nlocal,ids,nper,data); +} + +// ---------------------------------------------------------------------- + +int cslib_extract(void *ptr, int flag) +{ + CSlib *cs = (CSlib *) ptr; + return cs->extract(flag); +} diff --git a/lib/message/cslib/src/cslib_wrap.f90 b/lib/message/cslib/src/cslib_wrap.f90 new file mode 100644 index 0000000000..cd2e058b78 --- /dev/null +++ b/lib/message/cslib/src/cslib_wrap.f90 @@ -0,0 +1,147 @@ +! ISO_C_binding wrapper on CSlib C interface + +module cslib_wrap + +interface + subroutine cslib_open_fortran(csflag,mode,str,pcomm,ptr) bind(c) + use iso_c_binding + integer(c_int), value :: csflag + character(c_char) :: mode(*),str(*) + type(c_ptr), value :: pcomm + type(c_ptr) :: ptr + end subroutine cslib_open_fortran + + subroutine cslib_open_fortran_mpi_one(csflag,mode,pboth,pcomm,ptr) bind(c) + use iso_c_binding + integer(c_int), value :: csflag + character(c_char) :: mode(*) + type(c_ptr), value :: pboth,pcomm + type(c_ptr) :: ptr + end subroutine cslib_open_fortran_mpi_one + + subroutine cslib_close(ptr) bind(c) + use iso_c_binding + type(c_ptr), value :: ptr + end subroutine cslib_close + + subroutine cslib_send(ptr,msgID,nfield) bind(c) + use iso_c_binding + type(c_ptr), value :: ptr + integer(c_int), value :: msgID,nfield + end subroutine cslib_send + + subroutine cslib_pack_int(ptr,id,value) bind(c) + use iso_c_binding + type(c_ptr), value :: ptr + integer(c_int), value :: id + integer(c_int), value :: value + end subroutine cslib_pack_int + + subroutine cslib_pack_int64(ptr,id,value) bind(c) + use iso_c_binding + type(c_ptr), value :: ptr + integer(c_int), value :: id + integer(c_int64_t), value :: value + end subroutine cslib_pack_int64 + + subroutine cslib_pack_float(ptr,id,value) bind(c) + use iso_c_binding + type(c_ptr), value :: ptr + integer(c_int), value :: id + real(c_float), value :: value + end subroutine cslib_pack_float + + subroutine cslib_pack_double(ptr,id,value) bind(c) + use iso_c_binding + type(c_ptr), value :: ptr + integer(c_int), value :: id + real(c_double), value :: value + end subroutine cslib_pack_double + + subroutine cslib_pack_string(ptr,id,value) bind(c) + use iso_c_binding + type(c_ptr), value :: ptr + integer(c_int), value :: id + character(c_char) :: value(*) + end subroutine cslib_pack_string + + subroutine cslib_pack(ptr,id,ftype,flen,data) bind(c) + use iso_c_binding + type(c_ptr), value :: ptr + integer(c_int), value :: id,ftype,flen + type(c_ptr), value :: data + end subroutine cslib_pack + + subroutine cslib_pack_parallel(ptr,id,ftype,nlocal,ids,nper,data) bind(c) + use iso_c_binding + type(c_ptr), value :: ptr + integer(c_int), value :: id,ftype,nlocal,nper + type(c_ptr), value :: ids,data + end subroutine cslib_pack_parallel + + function cslib_recv(ptr,nfield,fieldID,fieldtype,fieldlen) bind(c) + use iso_c_binding + integer(c_int) :: cslib_recv + type(c_ptr), value :: ptr + integer(c_int) :: nfield + type(c_ptr) :: fieldID,fieldtype,fieldlen + end function cslib_recv + + function cslib_unpack_int(ptr,id) bind(c) + use iso_c_binding + integer(c_int) :: cslib_unpack_int + type(c_ptr), value :: ptr + integer(c_int), value :: id + end function cslib_unpack_int + + function cslib_unpack_int64(ptr,id) bind(c) + use iso_c_binding + integer(c_int64_t) :: cslib_unpack_int64 + type(c_ptr), value :: ptr + integer(c_int), value :: id + end function cslib_unpack_int64 + + function cslib_unpack_float(ptr,id) bind(c) + use iso_c_binding + real(c_float) :: cslib_unpack_float + type(c_ptr), value :: ptr + integer(c_int), value :: id + end function cslib_unpack_float + + function cslib_unpack_double(ptr,id) bind(c) + use iso_c_binding + real(c_double) :: cslib_unpack_double + type(c_ptr), value :: ptr + integer(c_int), value :: id + end function cslib_unpack_double + + function cslib_unpack_string(ptr,id) bind(c) + use iso_c_binding + type(c_ptr) :: cslib_unpack_string + type(c_ptr), value :: ptr + integer(c_int), value :: id + end function cslib_unpack_string + + function cslib_unpack(ptr,id) bind(c) + use iso_c_binding + type(c_ptr) :: cslib_unpack + type(c_ptr), value :: ptr + integer(c_int), value :: id + end function cslib_unpack + + subroutine cslib_unpack_parallel(ptr,id,nlocal,ids,nper,data) bind(c) + use iso_c_binding + type(c_ptr), value :: ptr + integer(c_int), value :: id,nlocal,nper + type(c_ptr), value :: ids,data + end subroutine cslib_unpack_parallel + + function cslib_extract(ptr,flag) bind(c) + use iso_c_binding + integer(c_int) :: cslib_extract + type(c_ptr), value :: ptr + integer(c_int), value :: flag + end function cslib_extract +end interface + +end module cslib_wrap diff --git a/lib/message/cslib/src/cslib_wrap.h b/lib/message/cslib/src/cslib_wrap.h new file mode 100644 index 0000000000..bf7df029c3 --- /dev/null +++ b/lib/message/cslib/src/cslib_wrap.h @@ -0,0 +1,54 @@ +/* ---------------------------------------------------------------------- + CSlib - Client/server library for code coupling + http://cslib.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright 2018 National Technology & Engineering Solutions of + Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with + NTESS, the U.S. Government retains certain rights in this software. + This software is distributed under the modified Berkeley Software + Distribution (BSD) License. + + See the README file in the top-level CSlib directory. +------------------------------------------------------------------------- */ + +/* C style library interface to CSlib class + ifdefs allow this file to be included in a C program +*/ + +#ifdef __cplusplus +extern "C" { +#endif + +void cslib_open(int, const char *, const void *, const void *, void **); +void cslib_open_fortran(int, const char *, const char *, const void *, void **); +void cslib_open_fortran_mpi_one(int, const char *, const void *, + const void *, void **); +void cslib_close(void *); + +void cslib_send(void *, int, int); + +void cslib_pack_int(void *, int, int); +void cslib_pack_int64(void *, int, int64_t); +void cslib_pack_float(void *, int, float); +void cslib_pack_double(void *, int, double); +void cslib_pack_string(void *, int, char *); +void cslib_pack(void *, int, int, int, void *); +void cslib_pack_parallel(void *, int, int, int, int *, int, void *); + +int cslib_recv(void *, int *, int **, int **, int **); + +int cslib_unpack_int(void *, int); +int64_t cslib_unpack_int64(void *, int); +float cslib_unpack_float(void *, int); +double cslib_unpack_double(void *, int); +char *cslib_unpack_string(void *, int); +void *cslib_unpack(void *, int); +void cslib_unpack_data(void *, int, void *); +void cslib_unpack_parallel(void *, int, int, int *, int, void *); + +int cslib_extract(void *, int); + +#ifdef __cplusplus +} +#endif diff --git a/lib/message/cslib/src/msg.cpp b/lib/message/cslib/src/msg.cpp new file mode 100644 index 0000000000..c67e4a5c8c --- /dev/null +++ b/lib/message/cslib/src/msg.cpp @@ -0,0 +1,110 @@ +/* ---------------------------------------------------------------------- + CSlib - Client/server library for code coupling + http://cslib.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright 2018 National Technology & Engineering Solutions of + Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with + NTESS, the U.S. Government retains certain rights in this software. + This software is distributed under the modified Berkeley Software + Distribution (BSD) License. + + See the README file in the top-level CSlib directory. +------------------------------------------------------------------------- */ + +#include +#include +#include +#include + +#include "msg.h" + +using namespace CSLIB_NS; + +/* ---------------------------------------------------------------------- */ + +Msg::Msg(int csflag, const void *ptr, MPI_Comm cworld) +{ + world = cworld; + MPI_Comm_rank(world,&me); + MPI_Comm_size(world,&nprocs); + + init(csflag); +} + +/* ---------------------------------------------------------------------- */ + +Msg::Msg(int csflag, const void *ptr) +{ + world = 0; + me = 0; + nprocs = 1; + + init(csflag); +} + +/* ---------------------------------------------------------------------- */ + +void Msg::init(int csflag) +{ + client = server = 0; + if (csflag == 0) client = 1; + else if (csflag == 1) server = 1; + + nsend = nrecv = 0; +} + +/* ---------------------------------------------------------------------- */ + +void Msg::allocate(int nheader, int &maxheader, int *&header, + int nbuf, int &maxbuf, char *&buf) +{ + if (nheader > maxheader) { + sfree(header); + maxheader = nheader; + header = (int *) smalloc(maxheader*sizeof(int)); + } + + if (nbuf > maxbuf) { + sfree(buf); + maxbuf = nbuf; + buf = (char *) smalloc(maxbuf*sizeof(char)); + } +} + +/* ---------------------------------------------------------------------- */ + +void *Msg::smalloc(int nbytes) +{ + if (nbytes == 0) return NULL; + void *ptr = (void *) malloc(nbytes); + if (ptr == NULL) { + char str[128]; + sprintf(str,"Failed to allocate %d bytes",nbytes); + } + return ptr; +} + +/* ---------------------------------------------------------------------- */ + +void Msg::sfree(void *ptr) +{ + if (ptr == NULL) return; + free(ptr); +} + +/* ---------------------------------------------------------------------- */ + +void Msg::error_all(const char *str) +{ + if (me == 0) printf("CSlib ERROR: %s\n",str); + MPI_Abort(world,1); +} + +/* ---------------------------------------------------------------------- */ + +void Msg::error_one(const char *str) +{ + printf("CSlib ERROR: %s\n",str); + MPI_Abort(world,1); +} diff --git a/lib/message/cslib/src/msg.h b/lib/message/cslib/src/msg.h new file mode 100644 index 0000000000..f75942b027 --- /dev/null +++ b/lib/message/cslib/src/msg.h @@ -0,0 +1,52 @@ +/* ---------------------------------------------------------------------- + CSlib - Client/server library for code coupling + http://cslib.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright 2018 National Technology & Engineering Solutions of + Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with + NTESS, the U.S. Government retains certain rights in this software. + This software is distributed under the modified Berkeley Software + Distribution (BSD) License. + + See the README file in the top-level CSlib directory. +------------------------------------------------------------------------- */ + +#ifndef MSG_H +#define MSG_H + +#include + +namespace CSLIB_NS { + +class Msg { + public: + int nsend,nrecv; + MPI_Comm world; + + Msg(int, const void *, MPI_Comm); + Msg(int, const void *); + virtual ~Msg() {} + virtual void send(int, int *, int, char *) = 0; + virtual void recv(int &, int *&, int &, char *&) = 0; + + protected: + int me,nprocs; + int client,server; + + int nfield; + int *fieldID,*fieldtype,*fieldlen; + int lengths[2]; + + void init(int); + void allocate(int, int &, int *&, int, int &, char *&); + void *smalloc(int); + void sfree(void *); + void error_all(const char *); + void error_one(const char *); +}; + + +} + +#endif diff --git a/lib/message/cslib/src/msg_file.cpp b/lib/message/cslib/src/msg_file.cpp new file mode 100644 index 0000000000..d97e249fad --- /dev/null +++ b/lib/message/cslib/src/msg_file.cpp @@ -0,0 +1,143 @@ +/* ---------------------------------------------------------------------- + CSlib - Client/server library for code coupling + http://cslib.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright 2018 National Technology & Engineering Solutions of + Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with + NTESS, the U.S. Government retains certain rights in this software. + This software is distributed under the modified Berkeley Software + Distribution (BSD) License. + + See the README file in the top-level CSlib directory. +------------------------------------------------------------------------- */ + +#include +#include +#include +#include +#include +#include + +#include "msg_file.h" + +using namespace CSLIB_NS; + +#define MAXLINE 256 +#define SLEEP 0.1 // delay in CPU secs to check for message file + +/* ---------------------------------------------------------------------- */ + +MsgFile::MsgFile(int csflag, const void *ptr, MPI_Comm cworld) : + Msg(csflag, ptr, cworld) +{ + char *filename = (char *) ptr; + init(filename); +} + +/* ---------------------------------------------------------------------- */ + +MsgFile::MsgFile(int csflag, const void *ptr) : Msg(csflag, ptr) +{ + char *filename = (char *) ptr; + init(filename); +} + +/* ---------------------------------------------------------------------- */ + +MsgFile::~MsgFile() +{ + delete [] fileroot; +} + +/* ---------------------------------------------------------------------- */ + +void MsgFile::init(char *filename) +{ + int n = strlen(filename) + 1; + fileroot = new char[n]; + strcpy(fileroot,filename); +} + +/* ---------------------------------------------------------------------- */ + +void MsgFile::send(int nheader, int *header, int nbuf, char *buf) +{ + char filename[MAXLINE]; + + lengths[0] = nheader; + lengths[1] = nbuf; + + if (me == 0) { + if (client) sprintf(filename,"%s.%s",fileroot,"client"); + else if (server) sprintf(filename,"%s.%s",fileroot,"server"); + + fp = fopen(filename,"wb"); + if (!fp) error_one("send(): Could not open send message file"); + fwrite(lengths,sizeof(int),2,fp); + fwrite(header,sizeof(int),nheader,fp); + fwrite(buf,1,nbuf,fp); + fclose(fp); + } + + // create empty signal file + + if (me == 0) { + if (client) sprintf(filename,"%s.%s",fileroot,"client.signal"); + else if (server) sprintf(filename,"%s.%s",fileroot,"server.signal"); + fp = fopen(filename,"w"); + fclose(fp); + } +} + +/* ---------------------------------------------------------------------- */ + +void MsgFile::recv(int &maxheader, int *&header, int &maxbuf, char *&buf) +{ + char filename[MAXLINE]; + + // wait until signal file exists to open message file + + if (me == 0) { + if (client) sprintf(filename,"%s.%s",fileroot,"server.signal"); + else if (server) sprintf(filename,"%s.%s",fileroot,"client.signal"); + + int delay = (int) (1000000 * SLEEP); + while (1) { + fp = fopen(filename,"r"); + if (fp) break; + usleep(delay); + } + fclose(fp); + + if (client) sprintf(filename,"%s.%s",fileroot,"server"); + else if (server) sprintf(filename,"%s.%s",fileroot,"client"); + fp = fopen(filename,"rb"); + if (!fp) error_one("recv(): Could not open recv message file"); + } + + // read and broadcast data + + if (me == 0) fread(lengths,sizeof(int),2,fp); + if (nprocs > 1) MPI_Bcast(lengths,2,MPI_INT,0,world); + + int nheader = lengths[0]; + int nbuf = lengths[1]; + allocate(nheader,maxheader,header,nbuf,maxbuf,buf); + + if (me == 0) fread(header,sizeof(int),nheader,fp); + if (nprocs > 1) MPI_Bcast(header,nheader,MPI_INT,0,world); + + if (me == 0) fread(buf,1,nbuf,fp); + if (nprocs > 1) MPI_Bcast(buf,nbuf,MPI_CHAR,0,world); + + // delete both message and signal file + + if (me == 0) { + fclose(fp); + unlink(filename); + if (client) sprintf(filename,"%s.%s",fileroot,"server.signal"); + else if (server) sprintf(filename,"%s.%s",fileroot,"client.signal"); + unlink(filename); + } +} diff --git a/lib/message/cslib/src/msg_file.h b/lib/message/cslib/src/msg_file.h new file mode 100644 index 0000000000..d6bd802607 --- /dev/null +++ b/lib/message/cslib/src/msg_file.h @@ -0,0 +1,40 @@ +/* ---------------------------------------------------------------------- + CSlib - Client/server library for code coupling + http://cslib.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright 2018 National Technology & Engineering Solutions of + Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with + NTESS, the U.S. Government retains certain rights in this software. + This software is distributed under the modified Berkeley Software + Distribution (BSD) License. + + See the README file in the top-level CSlib directory. +------------------------------------------------------------------------- */ + +#ifndef MSG_FILE_H +#define MSG_FILE_H + +#include +#include "msg.h" + +namespace CSLIB_NS { + +class MsgFile : public Msg { + public: + MsgFile(int, const void *, MPI_Comm); + MsgFile(int, const void *); + ~MsgFile(); + void send(int, int *, int, char *); + void recv(int &, int *&, int &, char *&); + + private: + char *fileroot; + FILE *fp; + + void init(char *); +}; + +} + +#endif diff --git a/lib/message/cslib/src/msg_mpi_one.cpp b/lib/message/cslib/src/msg_mpi_one.cpp new file mode 100644 index 0000000000..db11735b27 --- /dev/null +++ b/lib/message/cslib/src/msg_mpi_one.cpp @@ -0,0 +1,82 @@ +/* ---------------------------------------------------------------------- + CSlib - Client/server library for code coupling + http://cslib.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright 2018 National Technology & Engineering Solutions of + Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with + NTESS, the U.S. Government retains certain rights in this software. + This software is distributed under the modified Berkeley Software + Distribution (BSD) License. + + See the README file in the top-level CSlib directory. +------------------------------------------------------------------------- */ + +#include +#include +#include +#include +#include +#include + +#include "msg_mpi_one.h" + +using namespace CSLIB_NS; + +/* ---------------------------------------------------------------------- */ + +MsgMPIOne::MsgMPIOne(int csflag, const void *ptr, MPI_Comm cworld) : + Msg(csflag, ptr, cworld) +{ + // NOTE: ideally would skip this call if mpi/two + init(ptr); +} + +/* ---------------------------------------------------------------------- */ + +void MsgMPIOne::init(const void *ptr) +{ + MPI_Comm *pbothcomm = (MPI_Comm *) ptr; + bothcomm = *pbothcomm; + + if (client) { + MPI_Comm_size(world,&nprocs); + otherroot = nprocs; + } else if (server) { + otherroot = 0; + } +} + +/* ---------------------------------------------------------------------- */ + +void MsgMPIOne::send(int nheader, int *header, int nbuf, char *buf) +{ + lengths[0] = nheader; + lengths[1] = nbuf; + + if (me == 0) { + MPI_Send(lengths,2,MPI_INT,otherroot,0,bothcomm); + MPI_Send(header,nheader,MPI_INT,otherroot,0,bothcomm); + MPI_Send(buf,nbuf,MPI_CHAR,otherroot,0,bothcomm); + } +} + +/* ---------------------------------------------------------------------- */ + +void MsgMPIOne::recv(int &maxheader, int *&header, int &maxbuf, char *&buf) +{ + MPI_Status status; + + if (me == 0) MPI_Recv(lengths,2,MPI_INT,otherroot,0,bothcomm,&status); + if (nprocs > 1) MPI_Bcast(lengths,2,MPI_INT,0,world); + + int nheader = lengths[0]; + int nbuf = lengths[1]; + allocate(nheader,maxheader,header,nbuf,maxbuf,buf); + + if (me == 0) MPI_Recv(header,nheader,MPI_INT,otherroot,0,bothcomm,&status); + if (nprocs > 1) MPI_Bcast(header,nheader,MPI_INT,0,world); + + if (me == 0) MPI_Recv(buf,nbuf,MPI_CHAR,otherroot,0,bothcomm,&status); + if (nprocs > 1) MPI_Bcast(buf,nbuf,MPI_CHAR,0,world); +} diff --git a/lib/message/cslib/src/msg_mpi_one.h b/lib/message/cslib/src/msg_mpi_one.h new file mode 100644 index 0000000000..4b4140a3f7 --- /dev/null +++ b/lib/message/cslib/src/msg_mpi_one.h @@ -0,0 +1,38 @@ +/* ---------------------------------------------------------------------- + CSlib - Client/server library for code coupling + http://cslib.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright 2018 National Technology & Engineering Solutions of + Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with + NTESS, the U.S. Government retains certain rights in this software. + This software is distributed under the modified Berkeley Software + Distribution (BSD) License. + + See the README file in the top-level CSlib directory. +------------------------------------------------------------------------- */ + +#ifndef MSG_MPI_ONE_H +#define MSG_MPI_ONE_H + +#include "msg.h" + +namespace CSLIB_NS { + +class MsgMPIOne : public Msg { + public: + MsgMPIOne(int, const void *, MPI_Comm); + virtual ~MsgMPIOne() {} + void send(int, int *, int, char *); + void recv(int &, int *&, int &, char *&); + + protected: + MPI_Comm bothcomm; + int otherroot; + + void init(const void *); +}; + +} + +#endif diff --git a/lib/message/cslib/src/msg_mpi_two.cpp b/lib/message/cslib/src/msg_mpi_two.cpp new file mode 100644 index 0000000000..e9a9e87eeb --- /dev/null +++ b/lib/message/cslib/src/msg_mpi_two.cpp @@ -0,0 +1,81 @@ +/* ---------------------------------------------------------------------- + CSlib - Client/server library for code coupling + http://cslib.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright 2018 National Technology & Engineering Solutions of + Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with + NTESS, the U.S. Government retains certain rights in this software. + This software is distributed under the modified Berkeley Software + Distribution (BSD) License. + + See the README file in the top-level CSlib directory. +------------------------------------------------------------------------- */ + +#include +#include +#include +#include +#include +#include + +#include "msg_mpi_two.h" + +using namespace CSLIB_NS; + +/* ---------------------------------------------------------------------- */ + +MsgMPITwo::MsgMPITwo(int csflag, const void *ptr, MPI_Comm cworld) : + MsgMPIOne(csflag, ptr, cworld) +{ + char *filename = (char *) ptr; + init(filename); +} + +/* ---------------------------------------------------------------------- */ + +MsgMPITwo::~MsgMPITwo() +{ + // free the inter comm that spans both client and server + + MPI_Comm_free(&bothcomm); + MPI_Close_port(port); +} + +/* ---------------------------------------------------------------------- */ + +void MsgMPITwo::init(char *filename) +{ + if (client) { + if (me == 0) { + FILE *fp = NULL; + while (!fp) { + fp = fopen(filename,"r"); + if (!fp) sleep(1); + } + fgets(port,MPI_MAX_PORT_NAME,fp); + //printf("Client port: %s\n",port); + fclose(fp); + } + + MPI_Bcast(port,MPI_MAX_PORT_NAME,MPI_CHAR,0,world); + MPI_Comm_connect(port,MPI_INFO_NULL,0,world,&bothcomm); + //if (me == 0) printf("CLIENT comm connect\n"); + if (me == 0) unlink(filename); + + } else if (server) { + MPI_Open_port(MPI_INFO_NULL,port); + + if (me == 0) { + //printf("Server name: %s\n",port); + FILE *fp = fopen(filename,"w"); + fprintf(fp,"%s",port); + fclose(fp); + } + + MPI_Comm_accept(port,MPI_INFO_NULL,0,world,&bothcomm); + //if (me == 0) printf("SERVER comm accept\n"); + } + + otherroot = 0; +} diff --git a/lib/message/cslib/src/msg_mpi_two.h b/lib/message/cslib/src/msg_mpi_two.h new file mode 100644 index 0000000000..7b31db5a63 --- /dev/null +++ b/lib/message/cslib/src/msg_mpi_two.h @@ -0,0 +1,35 @@ +/* ---------------------------------------------------------------------- + CSlib - Client/server library for code coupling + http://cslib.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright 2018 National Technology & Engineering Solutions of + Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with + NTESS, the U.S. Government retains certain rights in this software. + This software is distributed under the modified Berkeley Software + Distribution (BSD) License. + + See the README file in the top-level CSlib directory. +------------------------------------------------------------------------- */ + +#ifndef MSG_MPI_TWO_H +#define MSG_MPI_TWO_H + +#include "msg_mpi_one.h" + +namespace CSLIB_NS { + +class MsgMPITwo : public MsgMPIOne { + public: + MsgMPITwo(int, const void *, MPI_Comm); + ~MsgMPITwo(); + + private: + char port[MPI_MAX_PORT_NAME]; + + void init(char *); +}; + +} + +#endif diff --git a/lib/message/cslib/src/msg_zmq.cpp b/lib/message/cslib/src/msg_zmq.cpp new file mode 100644 index 0000000000..c2d408f3a5 --- /dev/null +++ b/lib/message/cslib/src/msg_zmq.cpp @@ -0,0 +1,140 @@ +/* ---------------------------------------------------------------------- + CSlib - Client/server library for code coupling + http://cslib.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright 2018 National Technology & Engineering Solutions of + Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with + NTESS, the U.S. Government retains certain rights in this software. + This software is distributed under the modified Berkeley Software + Distribution (BSD) License. + + See the README file in the top-level CSlib directory. +------------------------------------------------------------------------- */ + +#include +#include +#include +#include +#include +#include + +#include "msg_zmq.h" + +using namespace CSLIB_NS; + +/* ---------------------------------------------------------------------- */ + +MsgZMQ::MsgZMQ(int csflag, const void *ptr, MPI_Comm cworld) : + Msg(csflag, ptr, cworld) +{ + char *port = (char *) ptr; + init(port); +} + +MsgZMQ::MsgZMQ(int csflag, const void *ptr) : Msg(csflag, ptr) +{ + char *port = (char *) ptr; + init(port); +} + +/* ---------------------------------------------------------------------- */ + +MsgZMQ::~MsgZMQ() +{ + if (me == 0) { + zmq_close(socket); + zmq_ctx_destroy(context); + } +} + +/* ---------------------------------------------------------------------- */ + +void MsgZMQ::init(char *port) +{ +#ifdef ZMQ_NO + error_all("constructor(): Library not built with ZMQ support"); +#endif + + if (me == 0) { + int n = strlen(port) + 8; + char *socket_name = new char[n]; + strcpy(socket_name,"tcp://"); + strcat(socket_name,port); + + if (client) { + context = zmq_ctx_new(); + socket = zmq_socket(context,ZMQ_REQ); + zmq_connect(socket,socket_name); + } else if (server) { + context = zmq_ctx_new(); + socket = zmq_socket(context,ZMQ_REP); + int rc = zmq_bind(socket,socket_name); + if (rc) error_one("constructor(): Server could not make socket connection"); + } + + delete [] socket_name; + } +} + +/* ---------------------------------------------------------------------- + client/server sockets (REQ/REP) must follow this protocol: + client sends request (REQ) which server receives + server sends response (REP) which client receives + every exchange is of this form, server cannot initiate a send + thus each ZMQ send below has a following ZMQ recv, except last one + if client calls send(), it will next call recv() + if server calls send(), it will next call recv() from its wait loop + in either case, recv() issues a ZMQ recv to match last ZMQ send here +------------------------------------------------------------------------- */ + +void MsgZMQ::send(int nheader, int *header, int nbuf, char *buf) +{ + lengths[0] = nheader; + lengths[1] = nbuf; + + if (me == 0) { + zmq_send(socket,lengths,2*sizeof(int),0); + zmq_recv(socket,NULL,0,0); + } + + if (me == 0) { + zmq_send(socket,header,nheader*sizeof(int),0); + zmq_recv(socket,NULL,0,0); + } + + if (me == 0) zmq_send(socket,buf,nbuf,0); +} + +/* ---------------------------------------------------------------------- + client/server sockets (REQ/REP) must follow this protocol: + client sends request (REQ) which server receives + server sends response (REP) which client receives + every exchange is of this form, server cannot initiate a send + thus each ZMQ recv below has a following ZMQ send, except last one + if client calls recv(), it will next call send() to ping server again, + if server calls recv(), it will next call send() to respond to client + in either case, send() issues a ZMQ send to match last ZMQ recv here +------------------------------------------------------------------------- */ + +void MsgZMQ::recv(int &maxheader, int *&header, int &maxbuf, char *&buf) +{ + if (me == 0) { + zmq_recv(socket,lengths,2*sizeof(int),0); + zmq_send(socket,NULL,0,0); + } + if (nprocs > 1) MPI_Bcast(lengths,2,MPI_INT,0,world); + + int nheader = lengths[0]; + int nbuf = lengths[1]; + allocate(nheader,maxheader,header,nbuf,maxbuf,buf); + + if (me == 0) { + zmq_recv(socket,header,nheader*sizeof(int),0); + zmq_send(socket,NULL,0,0); + } + if (nprocs > 1) MPI_Bcast(header,nheader,MPI_INT,0,world); + + if (me == 0) zmq_recv(socket,buf,nbuf,0); + if (nprocs > 1) MPI_Bcast(buf,nbuf,MPI_CHAR,0,world); +} diff --git a/lib/message/cslib/src/msg_zmq.h b/lib/message/cslib/src/msg_zmq.h new file mode 100644 index 0000000000..c0621a26ff --- /dev/null +++ b/lib/message/cslib/src/msg_zmq.h @@ -0,0 +1,38 @@ +/* ---------------------------------------------------------------------- + CSlib - Client/server library for code coupling + http://cslib.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright 2018 National Technology & Engineering Solutions of + Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with + NTESS, the U.S. Government retains certain rights in this software. + This software is distributed under the modified Berkeley Software + Distribution (BSD) License. + + See the README file in the top-level CSlib directory. +------------------------------------------------------------------------- */ + +#ifndef MSG_ZMQ_H +#define MSG_ZMQ_H + +#include "msg.h" + +namespace CSLIB_NS { + +class MsgZMQ : public Msg { + public: + MsgZMQ(int, const void *, MPI_Comm); + MsgZMQ(int, const void *); + ~MsgZMQ(); + void send(int, int *, int, char *); + void recv(int &, int *&, int &, char *&); + + private: + void *context,*socket; + + void init(char *); +}; + +} + +#endif diff --git a/src/MESSAGE/Install.sh b/src/MESSAGE/Install.sh new file mode 100644 index 0000000000..853dbddcdd --- /dev/null +++ b/src/MESSAGE/Install.sh @@ -0,0 +1,67 @@ +# Install/unInstall package files in LAMMPS +# mode = 0/1/2 for uninstall/install/update + +mode=$1 + +# arg1 = file, arg2 = file it depends on + +# enforce using portable C locale +LC_ALL=C +export LC_ALL + +action () { + if (test $mode = 0) then + rm -f ../$1 + elif (! cmp -s $1 ../$1) then + if (test -z "$2" || test -e ../$2) then + cp $1 .. + if (test $mode = 2) then + echo " updating src/$1" + fi + fi + elif (test -n "$2") then + if (test ! -e ../$2) then + rm -f ../$1 + fi + fi +} + +# all package files with no dependencies + +for file in *.cpp *.h; do + test -f ${file} && action $file +done + +# edit 2 Makefile.package files to include/exclude package info + +if (test $1 = 1) then + + if (test -e ../Makefile.package) then + sed -i -e 's/[^ \t]*message[^ \t]* //' ../Makefile.package + sed -i -e 's|^PKG_INC =[ \t]*|&-I../../lib/message/cslib/src |' ../Makefile.package + sed -i -e 's|^PKG_PATH =[ \t]*|&-L../../lib/message/cslib/src |' ../Makefile.package + sed -i -e 's|^PKG_LIB =[ \t]*|&-lmessage |' ../Makefile.package + sed -i -e 's|^PKG_SYSINC =[ \t]*|&$(message_SYSINC) |' ../Makefile.package + sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(message_SYSLIB) |' ../Makefile.package + sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(message_SYSPATH) |' ../Makefile.package + fi + + if (test -e ../Makefile.package.settings) then + sed -i -e '/^include.*message.*$/d' ../Makefile.package.settings + # multiline form needed for BSD sed on Macs + sed -i -e '4 i \ +include ..\/..\/lib\/message\/Makefile.lammps +' ../Makefile.package.settings + fi + +elif (test $1 = 0) then + + if (test -e ../Makefile.package) then + sed -i -e 's/[^ \t]*message[^ \t]* //' ../Makefile.package + fi + + if (test -e ../Makefile.package.settings) then + sed -i -e '/^include.*message.*$/d' ../Makefile.package.settings + fi + +fi diff --git a/src/MESSAGE/fix_client_md.cpp b/src/MESSAGE/fix_client_md.cpp new file mode 100644 index 0000000000..aca5cd41f9 --- /dev/null +++ b/src/MESSAGE/fix_client_md.cpp @@ -0,0 +1,325 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include +#include +#include "fix_client_md.h" +#include "update.h" +#include "atom.h" +#include "comm.h" +#include "domain.h" +#include "force.h" +#include "memory.h" +#include "error.h" + +// CSlib interface + +#include "cslib.h" + +using namespace LAMMPS_NS; +using namespace CSLIB_NS; +using namespace FixConst; + +enum{OTHER,REAL,METAL}; +enum{SETUP=1,STEP}; +enum{DIM=1,PERIODICITY,ORIGIN,BOX,NATOMS,NTYPES,TYPES,COORDS,UNITS,CHARGE}; +enum{FORCES=1,ENERGY,PRESSURE,ERROR}; + +/* ---------------------------------------------------------------------- */ + +FixClientMD::FixClientMD(LAMMPS *lmp, int narg, char **arg) : + Fix(lmp, narg, arg) +{ + if (lmp->clientserver != 1) + error->all(FLERR,"Fix client/md requires LAMMPS be running as a client"); + if (!atom->map_style) error->all(FLERR,"Fix client/md requires atom map"); + + if (sizeof(tagint) != 4) + error->all(FLERR,"Fix client/md requires 4-byte atom IDs"); + + if (strcmp(update->unit_style,"real") == 0) units = REAL; + else if (strcmp(update->unit_style,"metal") == 0) units = METAL; + else units = OTHER; + + scalar_flag = 1; + global_freq = 1; + extscalar = 1; + virial_flag = 1; + thermo_virial = 1; + + inv_nprocs = 1.0 / comm->nprocs; + if (domain->dimension == 2) + box[0][2] = box[1][2] = box[2][0] = box[2][1] = box[2][2] = 0.0; + + maxatom = 0; + xpbc = NULL; + + // unit conversion factors for REAL + // otherwise not needed + // message received in METAL units, convert to local REAL units + + fconvert = econvert = pconvert = 1.0; + if (units == REAL) { + fconvert = econvert = 23.06035; // eV -> Kcal/mole + pconvert = 0.986923; // bars -> atmospheres + } +} + +/* ---------------------------------------------------------------------- */ + +FixClientMD::~FixClientMD() +{ + memory->destroy(xpbc); + + CSlib *cs = (CSlib *) lmp->cslib; + + // all-done message to server + + cs->send(-1,0); + + int nfield; + int *fieldID,*fieldtype,*fieldlen; + int msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen); + + // clean-up + + delete cs; + lmp->cslib = NULL; +} + +/* ---------------------------------------------------------------------- */ + +int FixClientMD::setmask() +{ + int mask = 0; + mask |= POST_FORCE; + mask |= MIN_POST_FORCE; + mask |= THERMO_ENERGY; + return mask; +} + +/* ---------------------------------------------------------------------- */ + +void FixClientMD::init() +{ + if (3*atom->natoms > INT_MAX) + error->all(FLERR,"Fix client/md max atoms is 1/3 of 2^31"); +} + +/* ---------------------------------------------------------------------- */ + +void FixClientMD::setup(int vflag) +{ + CSlib *cs = (CSlib *) lmp->cslib; + + // SETUP send at beginning of each run + // required fields: DIM, PERIODICTY, ORIGIN, BOX, NATOMS, NTYPES, TYPES, COORDS + // optional fields: others in enum above + + int nfields = 8; + if (units == OTHER) nfields++; + if (atom->q_flag) nfields++; + + cs->send(SETUP,nfields); + + cs->pack_int(DIM,domain->dimension); + cs->pack(PERIODICITY,1,3,domain->periodicity); + + pack_box(); + cs->pack(ORIGIN,4,3,domain->boxlo); + cs->pack(BOX,4,9,&box[0][0]); + + cs->pack_int(NATOMS,atom->natoms); + cs->pack_int(NTYPES,atom->ntypes); + + cs->pack_parallel(TYPES,1,atom->nlocal,atom->tag,1,atom->type); + pack_coords(); + cs->pack_parallel(COORDS,4,atom->nlocal,atom->tag,3,xpbc); + + if (units == OTHER) cs->pack_string(UNITS,update->unit_style); + + if (atom->q_flag) + cs->pack_parallel(CHARGE,4,atom->nlocal,atom->tag,1,atom->q); + + // receive initial forces, energy, virial + + receive_fev(vflag); + + if (server_error) { + char str[64]; + sprintf(str,"Fix client/md received server error %d\n",server_error); + error->all(FLERR,str); + } +} + +/* ---------------------------------------------------------------------- */ + +void FixClientMD::min_setup(int vflag) +{ + setup(vflag); +} + +/* ---------------------------------------------------------------------- */ + +void FixClientMD::post_force(int vflag) +{ + int i,j,m; + + // energy and virial setup + + if (vflag) v_setup(vflag); + else evflag = 0; + + // STEP send every step + // required fields: COORDS + // optional fields: ORIGIN, BOX + + // send coords + + CSlib *cs = (CSlib *) lmp->cslib; + + int nfields = 1; + if (domain->box_change) nfields += 2; + + cs->send(STEP,nfields); + + pack_coords(); + cs->pack_parallel(COORDS,4,atom->nlocal,atom->tag,3,xpbc); + + if (domain->box_change) { + pack_box(); + cs->pack(ORIGIN,4,3,domain->boxlo); + cs->pack(BOX,4,9,&box[0][0]); + } + + // receive forces, energy, virial + + receive_fev(vflag); + + if (server_error) { + char str[64]; + sprintf(str,"Fix client/md received server error %d\n",server_error); + error->all(FLERR,str); + } +} + +/* ---------------------------------------------------------------------- */ + +void FixClientMD::min_post_force(int vflag) +{ + post_force(vflag); +} + +/* ---------------------------------------------------------------------- + potential energy from server +------------------------------------------------------------------------- */ + +double FixClientMD::compute_scalar() +{ + return eng; +} + +/* ---------------------------------------------------------------------- + pack local coords into xpbc, enforcing PBC +------------------------------------------------------------------------- */ + +void FixClientMD::pack_coords() +{ + double **x = atom->x; + int nlocal = atom->nlocal; + + if (nlocal > maxatom) { + memory->destroy(xpbc); + maxatom = atom->nmax; + memory->create(xpbc,3*maxatom,"message:xpbc"); + } + + memcpy(xpbc,&x[0][0],3*nlocal*sizeof(double)); + + int j = 0; + for (int i = 0; i < nlocal; i++) { + domain->remap(&xpbc[j]); + j += 3; + } +} + +/* ---------------------------------------------------------------------- + pack box info into box = 3 edge vectors of simulation box +------------------------------------------------------------------------- */ + +void FixClientMD::pack_box() +{ + double *boxlo = domain->boxlo; + double *boxhi = domain->boxhi; + + box[0][0] = boxhi[0] - boxlo[0]; + box[0][1] = 0.0; + box[0][2] = 0.0; + box[1][0] = domain->xy; + box[1][1] = boxhi[1] - boxlo[1]; + box[1][2] = 0.0; + box[2][0] = domain->xz; + box[2][1] = domain->yz; + box[2][2] = boxhi[2] - boxlo[2]; +} + +/* ---------------------------------------------------------------------- + receive message from server + required fields: FORCES, ENERGY, PRESSURE + optional field: ERROR +------------------------------------------------------------------------- */ + +void FixClientMD::receive_fev(int vflag) +{ + CSlib *cs = (CSlib *) lmp->cslib; + + int nfield; + int *fieldID,*fieldtype,*fieldlen; + + int msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen); + + double *forces = (double *) cs->unpack(FORCES); + double **f = atom->f; + int nlocal = atom->nlocal; + bigint natoms = atom->natoms; + int m; + + int j = 0; + for (tagint id = 1; id <= natoms; id++) { + m = atom->map(id); + if (m < 0 || m >= nlocal) j += 3; + else { + f[m][0] += fconvert * forces[j++]; + f[m][1] += fconvert * forces[j++]; + f[m][2] += fconvert * forces[j++]; + } + } + + eng = econvert * cs->unpack_double(ENERGY); + + if (vflag) { + double *v = (double *) cs->unpack(PRESSURE); + + double nktv2p = force->nktv2p; + double volume = domain->xprd * domain->yprd * domain->zprd; + double factor = inv_nprocs * pconvert * volume / nktv2p; + + for (int i = 0; i < 6; i++) + virial[i] = factor * v[i]; + } + + // error return + + server_error = 0; + if (nfield == 4) server_error = cs->unpack_int(ERROR); +} diff --git a/src/MESSAGE/fix_client_md.h b/src/MESSAGE/fix_client_md.h new file mode 100644 index 0000000000..1c874c7278 --- /dev/null +++ b/src/MESSAGE/fix_client_md.h @@ -0,0 +1,65 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef FIX_CLASS + +FixStyle(client/md,FixClientMD) + +#else + +#ifndef LMP_FIX_CLIENT_MD_H +#define LMP_FIX_CLIENT_MD_H + +#include "fix.h" + +namespace LAMMPS_NS { + +class FixClientMD : public Fix { + public: + FixClientMD(class LAMMPS *, int, char **); + ~FixClientMD(); + int setmask(); + void init(); + void setup(int); + void min_setup(int); + void post_force(int); + void min_post_force(int); + double compute_scalar(); + + private: + int maxatom,units,server_error; + double eng; + double inv_nprocs; + double fconvert,econvert,pconvert; + double box[3][3]; + double *xpbc; + + void pack_coords(); + void pack_box(); + void receive_fev(int); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +*/ diff --git a/src/MESSAGE/message.cpp b/src/MESSAGE/message.cpp new file mode 100644 index 0000000000..329ce1fbd9 --- /dev/null +++ b/src/MESSAGE/message.cpp @@ -0,0 +1,90 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include +#include "message.h" +#include "error.h" + +// CSlib interface + +#include "cslib.h" + +using namespace LAMMPS_NS; +using namespace CSLIB_NS; + +// customize by adding a new server protocol enum + +enum{MD,MC}; + +/* ---------------------------------------------------------------------- */ + +void Message::command(int narg, char **arg) +{ + if (narg < 3) error->all(FLERR,"Illegal message command"); + + int clientserver; + if (strcmp(arg[0],"client") == 0) clientserver = 1; + else if (strcmp(arg[0],"server") == 0) clientserver = 2; + else error->all(FLERR,"Illegal message command"); + lmp->clientserver = clientserver; + + // customize by adding a new server protocol + + int protocol; + if (strcmp(arg[1],"md") == 0) protocol = MD; + else if (strcmp(arg[1],"mc") == 0) protocol = MC; + else error->all(FLERR,"Unknown message protocol"); + + // instantiate CSlib with chosen communication mode + + if (strcmp(arg[2],"file") == 0 || strcmp(arg[2],"zmq") == 0 || + strcmp(arg[2],"mpi/two") == 0) { + if (narg != 4) error->all(FLERR,"Illegal message command"); + lmp->cslib = new CSlib(clientserver-1,arg[2],arg[3],&world); + + } else if (strcmp(arg[2],"mpi/one") == 0) { + if (narg != 3) error->all(FLERR,"Illegal message command"); + if (!lmp->cscomm) + error->all(FLERR,"Message mpi/one mode, but -mpi cmdline arg not used"); + lmp->cslib = new CSlib(clientserver-1,arg[2],&lmp->cscomm,&world); + + } else error->all(FLERR,"Illegal message command"); + + // perform initial handshake between client and server + // other code being coupled to must perform similar operation + // client sends protocol with msgID = 0 + // server matches it and replies + + CSlib *cs = (CSlib *) lmp->cslib; + + if (clientserver == 1) { + cs->send(0,1); + cs->pack_string(1,arg[1]); + + int nfield; + int *fieldID,*fieldtype,*fieldlen; + int msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen); + if (msgID != 0) error->one(FLERR,"Bad initial client/server handshake"); + + } else { + int nfield; + int *fieldID,*fieldtype,*fieldlen; + int msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen); + if (msgID != 0) error->one(FLERR,"Bad initial client/server handshake"); + char *pstr = cs->unpack_string(1); + if (strcmp(pstr,arg[1]) != 0) + error->one(FLERR,"Mismatch in client/server protocol"); + + cs->send(0,0); + } +} diff --git a/src/MESSAGE/message.h b/src/MESSAGE/message.h new file mode 100644 index 0000000000..c384a5a7b7 --- /dev/null +++ b/src/MESSAGE/message.h @@ -0,0 +1,40 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef COMMAND_CLASS + +CommandStyle(message,Message) + +#else + +#ifndef LMP_MESSAGE_H +#define LMP_MESSAGE_H + +#include "pointers.h" + +namespace LAMMPS_NS { + +class Message : protected Pointers { + public: + Message(class LAMMPS *lmp) : Pointers(lmp) {}; + void command(int, char **); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/MESSAGE/server.cpp b/src/MESSAGE/server.cpp new file mode 100644 index 0000000000..f587fb76df --- /dev/null +++ b/src/MESSAGE/server.cpp @@ -0,0 +1,50 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include +#include "server.h" +#include "error.h" + +// customize by adding a new server protocol include and enum + +#include "server_md.h" +#include "server_mc.h" + +using namespace LAMMPS_NS; + +enum{MD,MC}; + +/* ---------------------------------------------------------------------- */ + +void Server::command(int narg, char **arg) +{ + if (narg != 1) error->all(FLERR,"Illegal server command"); + + if (lmp->clientserver != 2) + error->all(FLERR,"Message command not used to setup LAMMPS as a server"); + + // customize by adding a new server protocol + + int protocol; + if (strcmp(arg[0],"md") == 0) protocol = MD; + else if (strcmp(arg[0],"mc") == 0) protocol = MC; + else error->all(FLERR,"Unknown message protocol"); + + if (protocol == MD) { + ServerMD *server = new ServerMD(lmp); + server->loop(); + } else if (protocol == MC) { + ServerMC *server = new ServerMC(lmp); + server->loop(); + } +} diff --git a/src/MESSAGE/server.h b/src/MESSAGE/server.h new file mode 100644 index 0000000000..579f6ab6f1 --- /dev/null +++ b/src/MESSAGE/server.h @@ -0,0 +1,40 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef COMMAND_CLASS + +CommandStyle(server,Server) + +#else + +#ifndef LMP_SERVER_H +#define LMP_SERVER_H + +#include "pointers.h" + +namespace LAMMPS_NS { + +class Server : protected Pointers { + public: + Server(class LAMMPS *lmp) : Pointers(lmp) {}; + void command(int, char **); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/MESSAGE/server_mc.cpp b/src/MESSAGE/server_mc.cpp new file mode 100644 index 0000000000..8a7344e86b --- /dev/null +++ b/src/MESSAGE/server_mc.cpp @@ -0,0 +1,148 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "server_mc.h" +#include "atom.h" +#include "update.h" +#include "integrate.h" +#include "input.h" +#include "output.h" +#include "thermo.h" +#include "error.h" + +// CSlib interface + +#include "cslib.h" + +using namespace LAMMPS_NS; +using namespace CSLIB_NS; + +enum{NATOMS=1,EINIT,DISPLACE,ACCEPT,RUN}; + +/* ---------------------------------------------------------------------- */ + +ServerMC::ServerMC(LAMMPS *lmp) : Pointers(lmp) {} + +/* ---------------------------------------------------------------------- */ + +void ServerMC::loop() +{ + int i,j,m; + double xold[3],xnew[3]; + tagint atomid; + + CSlib *cs = (CSlib *) lmp->cslib; + + // require atom map + + if (!atom->map_style) error->all(FLERR,"Server mode requires atom map"); + + // initialize LAMMPS for dynamics + + input->one("run 0"); + + //update->whichflag = 1; + //lmp->init(); + + // loop on messages + // receive a message, process it, send return message if necessary + + int msgID,nfield; + int *fieldID,*fieldtype,*fieldlen; + + while (1) { + msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen); + if (msgID < 0) break; + + if (msgID == NATOMS) { + + cs->send(msgID,1); + cs->pack_int(1,atom->natoms); + + } else if (msgID == EINIT) { + + double dval; + output->thermo->evaluate_keyword((char *) "pe",&dval); + + cs->send(msgID,2); + cs->pack_double(1,dval); + double *coords = NULL; + if (atom->nlocal) coords = &atom->x[0][0]; + cs->pack_parallel(2,4,atom->nlocal,atom->tag,3,coords); + + } else if (msgID == DISPLACE) { + + atomid = cs->unpack_int(1); + double *xnew = (double *) cs->unpack(2); + double **x = atom->x; + + m = atom->map(atomid); + if (m >= 0 && m < atom->nlocal) { + xold[0] = x[m][0]; + xold[1] = x[m][1]; + xold[2] = x[m][2]; + x[m][0] = xnew[0]; + x[m][1] = xnew[1]; + x[m][2] = xnew[2]; + } + + input->one("run 0"); + double dval; + output->thermo->evaluate_keyword((char *) "pe",&dval); + + cs->send(msgID,1); + cs->pack_double(1,dval); + + } else if (msgID == ACCEPT) { + + int accept = cs->unpack_int(1); + double **x = atom->x; + + if (!accept) { + m = atom->map(atomid); + if (m >= 0 && m < atom->nlocal) { + x[m][0] = xold[0]; + x[m][1] = xold[1]; + x[m][2] = xold[2]; + } + } + + cs->send(msgID,0); + + } else if (msgID == RUN) { + + int nsteps = cs->unpack_int(1); + + //input->one("run 100"); + + update->nsteps = nsteps; + update->firststep = update->ntimestep; + update->laststep = update->ntimestep + nsteps; + + update->integrate->setup(1); + update->integrate->run(nsteps); + + cs->send(msgID,0); + + } else error->all(FLERR,"Server received unrecognized message"); + } + + // final reply to client + + cs->send(0,0); + + // clean up + + delete cs; + lmp->cslib = NULL; +} diff --git a/src/MESSAGE/server_mc.h b/src/MESSAGE/server_mc.h new file mode 100644 index 0000000000..d0fb489429 --- /dev/null +++ b/src/MESSAGE/server_mc.h @@ -0,0 +1,29 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifndef LMP_SERVER_MC_H +#define LMP_SERVER_MC_H + +#include "pointers.h" + +namespace LAMMPS_NS { + +class ServerMC : protected Pointers { + public: + ServerMC(class LAMMPS *); + void loop(); +}; + +} + +#endif diff --git a/src/MESSAGE/server_md.cpp b/src/MESSAGE/server_md.cpp new file mode 100644 index 0000000000..aa771b7d46 --- /dev/null +++ b/src/MESSAGE/server_md.cpp @@ -0,0 +1,389 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include +#include +#include "server_md.h" +#include "atom.h" +#include "atom_vec.h" +#include "update.h" +#include "integrate.h" +#include "kspace.h" +#include "force.h" +#include "pair.h" +#include "neighbor.h" +#include "comm.h" +#include "domain.h" +#include "memory.h" +#include "error.h" + +// CSlib interface + +#include "cslib.h" + +using namespace LAMMPS_NS; +using namespace CSLIB_NS; + +enum{OTHER,REAL,METAL}; +enum{SETUP=1,STEP}; +enum{DIM=1,PERIODICITY,ORIGIN,BOX,NATOMS,NTYPES,TYPES,COORDS,UNITS,CHARGE}; +enum{FORCES=1,ENERGY,PRESSURE,ERROR}; + +/* ---------------------------------------------------------------------- */ + +ServerMD::ServerMD(LAMMPS *lmp) : Pointers(lmp) +{ + if (domain->box_exist == 0) + error->all(FLERR,"Server command before simulation box is defined"); + + if (!atom->map_style) error->all(FLERR,"Server md requires atom map"); + if (atom->tag_enable == 0) error->all(FLERR,"Server md requires atom IDs"); + if (sizeof(tagint) != 4) error->all(FLERR,"Server md requires 4-byte atom IDs"); + + if (strcmp(update->unit_style,"real") == 0) units = REAL; + else if (strcmp(update->unit_style,"metal") == 0) units = METAL; + else units = OTHER; + + // unit conversion factors for REAL + // otherwise not needed + // local computation in REAL units, send message in METAL units + + fconvert = econvert = pconvert = 1.0; + if (units == REAL) { + fconvert = econvert = 1.0 / 23.06035; // Kcal/mole -> eV + pconvert = 1.0 / 0.986923; // atmospheres -> bars + } + + fcopy = NULL; +} + +/* ---------------------------------------------------------------------- */ + +ServerMD::~ServerMD() +{ + memory->destroy(fcopy); +} + +/* ---------------------------------------------------------------------- */ + +void ServerMD::loop() +{ + int i,j,m; + + // cs = instance of CSlib + + CSlib *cs = (CSlib *) lmp->cslib; + + // counters + + int forcecalls = 0; + int neighcalls = 0; + + // loop on messages + // receive a message, process it, send return message + + int msgID,nfield; + int *fieldID,*fieldtype,*fieldlen; + + while (1) { + msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen); + if (msgID < 0) break; + + // SETUP receive at beginning of each run + // required fields: DIM, PERIODICTY, ORIGIN, BOX, + // NATOMS, NTYPES, TYPES, COORDS + // optional fields: others in enum above + + if (msgID == SETUP) { + + int dim = 0; + int *periodicity = NULL; + int natoms = -1; + int ntypes = -1; + double *origin = NULL; + double *box = NULL; + int *types = NULL; + double *coords = NULL; + char *unit_style = NULL; + double *charge = NULL; + + for (int ifield = 0; ifield < nfield; ifield++) { + if (fieldID[ifield] == DIM) { + dim = cs->unpack_int(DIM); + if (dim != domain->dimension) + error->all(FLERR,"Server md dimension mis-match with client"); + } else if (fieldID[ifield] == PERIODICITY) { + periodicity = (int *) cs->unpack(PERIODICITY); + if (periodicity[0] != domain->periodicity[0] || + periodicity[1] != domain->periodicity[1] || + periodicity[2] != domain->periodicity[2]) + error->all(FLERR,"Server md periodicity mis-match with client"); + } else if (fieldID[ifield] == ORIGIN) { + origin = (double *) cs->unpack(ORIGIN); + } else if (fieldID[ifield] == BOX) { + box = (double *) cs->unpack(BOX); + } else if (fieldID[ifield] == NATOMS) { + natoms = cs->unpack_int(NATOMS); + if (3*natoms > INT_MAX) + error->all(FLERR,"Server md max atoms is 1/3 of 2^31"); + } else if (fieldID[ifield] == NTYPES) { + ntypes = cs->unpack_int(NTYPES); + if (ntypes != atom->ntypes) + error->all(FLERR,"Server md ntypes mis-match with client"); + } else if (fieldID[ifield] == TYPES) { + types = (int *) cs->unpack(TYPES); + } else if (fieldID[ifield] == COORDS) { + coords = (double *) cs->unpack(COORDS); + + } else if (fieldID[ifield] == UNITS) { + unit_style = (char *) cs->unpack(UNITS); + } else if (fieldID[ifield] == CHARGE) { + charge = (double *) cs->unpack(CHARGE); + } else error->all(FLERR,"Server md setup field unknown"); + } + + if (dim == 0 || !periodicity || !origin || !box || + natoms < 0 || ntypes < 0 || !types || !coords) + error->all(FLERR,"Required server md setup field not received"); + + if (unit_style && strcmp(unit_style,update->unit_style) != 0) + error->all(FLERR,"Server md does not match client units"); + + if (charge && atom->q_flag == 0) + error->all(FLERR,"Server md does not define atom attribute q"); + + // reset box, global and local + // reset proc decomposition + + if ((box[3] != 0.0 || box[6] != 0.0 || box[7] != 0.0) && + domain->triclinic == 0) + error->all(FLERR,"Server md is not initialized for a triclinic box"); + + box_change(origin,box); + + domain->set_initial_box(); + domain->set_global_box(); + comm->set_proc_grid(); + domain->set_local_box(); + + // clear all atoms + + atom->nlocal = 0; + atom->nghost = 0; + + // add atoms that are in my sub-box + + int nlocal = 0; + for (int i = 0; i < natoms; i++) { + if (!domain->ownatom(i+1,&coords[3*i],NULL,0)) continue; + atom->avec->create_atom(types[i],&coords[3*i]); + atom->tag[nlocal] = i+1; + if (charge) atom->q[nlocal] = charge[i]; + nlocal++; + } + + int ntotal; + MPI_Allreduce(&atom->nlocal,&ntotal,1,MPI_INT,MPI_SUM,world); + if (ntotal != natoms) + error->all(FLERR,"Server md atom count does not match client"); + + atom->map_init(); + atom->map_set(); + atom->natoms = natoms; + + // allocate fcopy if needed + + if (units == REAL) { + memory->destroy(fcopy); + memory->create(fcopy,atom->nlocal,3,"server/md:fcopy"); + } + + // perform system setup() for dynamics + // also OK for minimization, since client runs minimizer + // return forces, energy, virial to client + + update->whichflag = 1; + lmp->init(); + update->integrate->setup_minimal(1); + neighcalls++; + forcecalls++; + + send_fev(msgID); + + // STEP receive at each timestep of run or minimization + // required fields: COORDS + // optional fields: ORIGIN, BOX + + } else if (msgID == STEP) { + + double *coords = NULL; + double *origin = NULL; + double *box = NULL; + + for (int ifield = 0; ifield < nfield; ifield++) { + if (fieldID[ifield] == COORDS) { + coords = (double *) cs->unpack(COORDS); + } else if (fieldID[ifield] == ORIGIN) { + origin = (double *) cs->unpack(ORIGIN); + } else if (fieldID[ifield] == BOX) { + box = (double *) cs->unpack(BOX); + } else error->all(FLERR,"Server md step field unknown"); + } + + if (!coords) + error->all(FLERR,"Required server md step field not received"); + + // change box size/shape, only if origin and box received + // reset global/local box like FixDeform at end_of_step() + + if (origin && box) { + if ((box[3] != 0.0 || box[6] != 0.0 || box[7] != 0.0) && + domain->triclinic == 0) + error->all(FLERR,"Server md is not initialized for a triclinic box"); + box_change(origin,box); + domain->set_global_box(); + domain->set_local_box(); + } + + // assign received coords to owned atoms + // closest_image() insures xyz matches current server PBC + + double **x = atom->x; + int nlocal = atom->nlocal; + int nall = atom->natoms; + + j = 0; + for (tagint id = 1; id <= nall; id++) { + m = atom->map(id); + if (m < 0 || m >= nlocal) j += 3; + else { + domain->closest_image(x[m],&coords[j],x[m]); + j += 3; + } + } + + // if no need to reneighbor: + // ghost comm + // setup_minimal(0) which just computes forces + // else: + // setup_minimal(1) for pbc, reset_box, reneigh, forces + + int nflag = neighbor->decide(); + if (nflag == 0) { + comm->forward_comm(); + update->integrate->setup_minimal(0); + } else { + update->integrate->setup_minimal(1); + neighcalls++; + } + + forcecalls++; + + send_fev(msgID); + + } else error->all(FLERR,"Server MD received unrecognized message"); + } + + // final reply to client + + cs->send(0,0); + + // stats + + if (comm->me == 0) { + if (screen) { + fprintf(screen,"Server MD calls = %d\n",forcecalls); + fprintf(screen,"Server MD reneighborings = %d\n",neighcalls); + } + if (logfile) { + fprintf(logfile,"Server MD calls = %d\n",forcecalls); + fprintf(logfile,"Server MD reneighborings %d\n",neighcalls); + } + } + + // clean up + + delete cs; + lmp->cslib = NULL; +} + +/* ---------------------------------------------------------------------- + box change due to received message +------------------------------------------------------------------------- */ + +void ServerMD::box_change(double *origin, double *box) +{ + domain->boxlo[0] = origin[0]; + domain->boxlo[1] = origin[1]; + domain->boxlo[2] = origin[2]; + + domain->boxhi[0] = origin[0] + box[0]; + domain->boxhi[1] = origin[1] + box[4]; + domain->boxhi[2] = origin[2] + box[8]; + + domain->xy = box[3]; + domain->xz = box[6]; + domain->yz = box[7]; +} + +/* ---------------------------------------------------------------------- + return message with forces, energy, pressure tensor + pressure tensor should be just pair and KSpace contributions + required fields: FORCES, ENERGY, PRESSURE + optional field: ERROR (not ever sending) +------------------------------------------------------------------------- */ + +void ServerMD::send_fev(int msgID) +{ + CSlib *cs = (CSlib *) lmp->cslib; + + cs->send(msgID,3); + + double *forces = NULL; + if (atom->nlocal) { + if (units != REAL) forces = &atom->f[0][0]; + else { + double **f = atom->f; + int nlocal = atom->nlocal; + for (int i = 0; i < nlocal; i++) { + fcopy[i][0] = fconvert*f[i][0]; + fcopy[i][1] = fconvert*f[i][1]; + fcopy[i][2] = fconvert*f[i][2]; + } + forces = &fcopy[0][0]; + } + } + cs->pack_parallel(FORCES,4,atom->nlocal,atom->tag,3,forces); + + double eng = force->pair->eng_vdwl + force->pair->eng_coul; + double engall; + MPI_Allreduce(&eng,&engall,1,MPI_DOUBLE,MPI_SUM,world); + engall *= econvert; + cs->pack_double(ENERGY,engall); + + double v[6],vall[6]; + for (int i = 0; i < 6; i++) + v[i] = force->pair->virial[i]; + MPI_Allreduce(&v,&vall,6,MPI_DOUBLE,MPI_SUM,world); + + if (force->kspace) + for (int i = 0; i < 6; i++) + vall[i] += force->kspace->virial[i]; + + double nktv2p = force->nktv2p; + double volume = domain->xprd * domain->yprd * domain->zprd; + double factor = pconvert / volume * nktv2p; + for (int i = 0; i < 6; i++) vall[i] *= factor; + + cs->pack(PRESSURE,4,6,vall); +} diff --git a/src/MESSAGE/server_md.h b/src/MESSAGE/server_md.h new file mode 100644 index 0000000000..289d70bdd8 --- /dev/null +++ b/src/MESSAGE/server_md.h @@ -0,0 +1,38 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifndef LMP_SERVER_MD_H +#define LMP_SERVER_MD_H + +#include "pointers.h" + +namespace LAMMPS_NS { + +class ServerMD : protected Pointers { + public: + ServerMD(class LAMMPS *); + ~ServerMD(); + void loop(); + + private: + int units; + double fconvert,econvert,pconvert; + double **fcopy; + + void box_change(double *, double *); + void send_fev(int); +}; + +} + +#endif diff --git a/src/Makefile b/src/Makefile index 948d203cfe..b9cabfd67b 100644 --- a/src/Makefile +++ b/src/Makefile @@ -53,7 +53,7 @@ endif # PACKEXT = subset that require an external (downloaded) library PACKAGE = asphere body class2 colloid compress coreshell dipole gpu \ - granular kim kokkos kspace latte manybody mc meam misc \ + granular kim kokkos kspace latte manybody mc meam message misc \ molecule mpiio mscg opt peri poems \ python qeq reax replica rigid shock snap spin srd voronoi @@ -65,14 +65,14 @@ PACKUSER = user-atc user-awpmd user-bocs user-cgdna user-cgsdk user-colvars \ user-quip user-reaxc user-smd user-smtbq user-sph user-tally \ user-uef user-vtk -PACKLIB = compress gpu kim kokkos latte meam mpiio mscg poems \ +PACKLIB = compress gpu kim kokkos latte meam message mpiio mscg poems \ python reax voronoi \ user-atc user-awpmd user-colvars user-h5md user-lb user-molfile \ user-netcdf user-qmmm user-quip user-smd user-vtk PACKSYS = compress mpiio python user-lb -PACKINT = gpu kokkos meam poems reax user-atc user-awpmd user-colvars +PACKINT = gpu kokkos meam message poems reax user-atc user-awpmd user-colvars PACKEXT = kim mscg voronoi \ user-h5md user-molfile user-netcdf user-qmmm user-quip \ diff --git a/src/USER-MISC/pair_morse_smooth_linear.cpp b/src/USER-MISC/pair_morse_smooth_linear.cpp index 328c1bd27b..4181fd5479 100644 --- a/src/USER-MISC/pair_morse_smooth_linear.cpp +++ b/src/USER-MISC/pair_morse_smooth_linear.cpp @@ -30,7 +30,6 @@ using namespace LAMMPS_NS; PairMorseSmoothLinear::PairMorseSmoothLinear(LAMMPS *lmp) : Pair(lmp) { writedata = 1; - } /* ---------------------------------------------------------------------- */ @@ -117,7 +116,7 @@ void PairMorseSmoothLinear::compute(int eflag, int vflag) if (eflag) { evdwl = d0[itype][jtype] * (dexp*dexp - 2.0*dexp) - - offset[itype][jtype]; + offset[itype][jtype]; evdwl -= ( r - cut[itype][jtype] ) * der_at_cutoff[itype][jtype]; evdwl *= factor_lj; } @@ -203,6 +202,14 @@ void PairMorseSmoothLinear::coeff(int narg, char **arg) alpha[i][j] = alpha_one; r0[i][j] = r0_one; cut[i][j] = cut_one; + + morse1[i][j] = 2.0*d0[i][j]*alpha[i][j]; + + double alpha_dr = -alpha[i][j] * (cut[i][j] - r0[i][j]); + + offset[i][j] = d0[i][j] * (exp(2.0*alpha_dr) - 2.0*exp(alpha_dr)); + der_at_cutoff[i][j] = -2.0*alpha[i][j]*d0[i][j] * (exp(2.0*alpha_dr) - exp(alpha_dr)); + setflag[i][j] = 1; count++; } @@ -222,17 +229,13 @@ double PairMorseSmoothLinear::init_one(int i, int j) morse1[i][j] = 2.0*d0[i][j]*alpha[i][j]; - double alpha_dr = -alpha[i][j] * (cut[i][j] - r0[i][j]); - - offset[i][j] = d0[i][j] * (exp(2.0*alpha_dr) - 2.0*exp(alpha_dr)); - der_at_cutoff[i][j] = -2.0*alpha[i][j]*d0[i][j] * (exp(2.0*alpha_dr) - exp(alpha_dr)); - d0[j][i] = d0[i][j]; alpha[j][i] = alpha[i][j]; r0[j][i] = r0[i][j]; morse1[j][i] = morse1[i][j]; der_at_cutoff[j][i] = der_at_cutoff[i][j]; offset[j][i] = offset[i][j]; + cut[j][i] = cut[i][j]; return cut[i][j]; } diff --git a/src/atom.cpp b/src/atom.cpp index eb2f357890..95f5406d95 100644 --- a/src/atom.cpp +++ b/src/atom.cpp @@ -1533,7 +1533,8 @@ void Atom::set_mass(const char *file, int line, int /*narg*/, char **arg) } /* ---------------------------------------------------------------------- - set all masses as read in from restart file + set all masses + called from reading of restart file, also from ServerMD ------------------------------------------------------------------------- */ void Atom::set_mass(double *values) diff --git a/src/domain.cpp b/src/domain.cpp index 1eb848fe06..8238ab7eea 100644 --- a/src/domain.cpp +++ b/src/domain.cpp @@ -1176,12 +1176,12 @@ int Domain::closest_image(int i, int j) if J is not a valid index like -1, just return it ------------------------------------------------------------------------- */ -int Domain::closest_image(double *pos, int j) +int Domain::closest_image(const double * const pos, int j) { if (j < 0) return j; - int *sametag = atom->sametag; - double **x = atom->x; + const int * const sametag = atom->sametag; + const double * const * const x = atom->x; int closest = j; double delx = pos[0] - x[j][0]; @@ -1208,13 +1208,10 @@ int Domain::closest_image(double *pos, int j) /* ---------------------------------------------------------------------- find and return Xj image = periodic image of Xj that is closest to Xi for triclinic, add/subtract tilt factors in other dims as needed - not currently used (Jan 2017): - used to be called by pair TIP4P styles but no longer, - due to use of other closest_image() method + called by ServerMD class and LammpsInterface in lib/atc. ------------------------------------------------------------------------- */ -void Domain::closest_image(const double * const xi, const double * const xj, - double * const xjimage) +void Domain::closest_image(const double * const xi, const double * const xj, double * const xjimage) { double dx = xj[0] - xi[0]; double dy = xj[1] - xi[1]; diff --git a/src/domain.h b/src/domain.h index 5581f9a45f..9ebdd6ae94 100644 --- a/src/domain.h +++ b/src/domain.h @@ -115,9 +115,8 @@ class Domain : protected Pointers { void minimum_image(double *); void minimum_image_once(double *); int closest_image(int, int); - int closest_image(double *, int); - void closest_image(const double * const, const double * const, - double * const); + int closest_image(const double * const, int); + void closest_image(const double * const, const double * const, double * const); void remap(double *, imageint &); void remap(double *); void remap_near(double *, double *); diff --git a/src/fix_tmd.cpp b/src/fix_tmd.cpp index ea448bd178..dd11dfd0c7 100644 --- a/src/fix_tmd.cpp +++ b/src/fix_tmd.cpp @@ -412,7 +412,7 @@ void FixTMD::readfile(char *file) m++; } - MPI_Bcast(&eof,sizeof(char *)/sizeof(char),MPI_CHAR,0,world); + MPI_Bcast(&eof,sizeof(char *),MPI_CHAR,0,world); MPI_Bcast(&nlines,1,MPI_INT,0,world); MPI_Bcast(&m,1,MPI_INT,0,world); MPI_Bcast(buffer,m,MPI_CHAR,0,world); diff --git a/src/lammps.cpp b/src/lammps.cpp index b73b62537f..21335065f4 100644 --- a/src/lammps.cpp +++ b/src/lammps.cpp @@ -47,8 +47,8 @@ #include "accelerator_omp.h" #include "timer.h" #include "python.h" -#include "memory.h" #include "version.h" +#include "memory.h" #include "error.h" #include "lmpinstalledpkgs.h" @@ -73,12 +73,46 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) output = NULL; python = NULL; + clientserver = 0; + cslib = NULL; + cscomm = 0; + screen = NULL; logfile = NULL; infile = NULL; initclock = MPI_Wtime(); + // check if -mpi is first arg + // if so, then 2 apps were launched with one mpirun command + // this means passed communicator (e.g. MPI_COMM_WORLD) is bigger than LAMMPS + // e.g. for client/server coupling with another code + // in the future LAMMPS might leverage this in other ways + // universe communicator needs to shrink to be just LAMMPS + // syntax: -mpi color + // color = integer for this app, different than other app(s) + // do the following: + // perform an MPI_Comm_split() to create a new LAMMPS-only subcomm + // NOTE: this assumes other app(s) does same thing, else will hang! + // re-create universe with subcomm + // store full multi-app comm in cscomm + // cscomm is used by CSLIB package to exchange messages w/ other app + + int iarg = 1; + if (narg-iarg >= 2 && (strcmp(arg[iarg],"-mpi") == 0 || + strcmp(arg[iarg],"-m") == 0)) { + int me,nprocs; + MPI_Comm_rank(communicator,&me); + MPI_Comm_size(communicator,&nprocs); + int color = atoi(arg[iarg+1]); + MPI_Comm subcomm; + MPI_Comm_split(communicator,color,me,&subcomm); + cscomm = communicator; + communicator = subcomm; + delete universe; + universe = new Universe(this,communicator); + } + // parse input switches int inflag = 0; @@ -107,59 +141,30 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) int *pfirst = NULL; int *plast = NULL; - int iarg = 1; + iarg = 1; while (iarg < narg) { - if (strcmp(arg[iarg],"-partition") == 0 || - strcmp(arg[iarg],"-p") == 0) { - universe->existflag = 1; + + if (strcmp(arg[iarg],"-echo") == 0 || + strcmp(arg[iarg],"-e") == 0) { if (iarg+2 > narg) error->universe_all(FLERR,"Invalid command-line argument"); - iarg++; - while (iarg < narg && arg[iarg][0] != '-') { - universe->add_world(arg[iarg]); - iarg++; - } + iarg += 2; + + } else if (strcmp(arg[iarg],"-help") == 0 || + strcmp(arg[iarg],"-h") == 0) { + if (iarg+1 > narg) + error->universe_all(FLERR,"Invalid command-line argument"); + helpflag = 1; + citeflag = 0; + iarg += 1; + } else if (strcmp(arg[iarg],"-in") == 0 || strcmp(arg[iarg],"-i") == 0) { if (iarg+2 > narg) error->universe_all(FLERR,"Invalid command-line argument"); inflag = iarg + 1; iarg += 2; - } else if (strcmp(arg[iarg],"-screen") == 0 || - strcmp(arg[iarg],"-sc") == 0) { - if (iarg+2 > narg) - error->universe_all(FLERR,"Invalid command-line argument"); - screenflag = iarg + 1; - iarg += 2; - } else if (strcmp(arg[iarg],"-log") == 0 || - strcmp(arg[iarg],"-l") == 0) { - if (iarg+2 > narg) - error->universe_all(FLERR,"Invalid command-line argument"); - logflag = iarg + 1; - iarg += 2; - } else if (strcmp(arg[iarg],"-var") == 0 || - strcmp(arg[iarg],"-v") == 0) { - if (iarg+3 > narg) - error->universe_all(FLERR,"Invalid command-line argument"); - iarg += 3; - while (iarg < narg && arg[iarg][0] != '-') iarg++; - } else if (strcmp(arg[iarg],"-echo") == 0 || - strcmp(arg[iarg],"-e") == 0) { - if (iarg+2 > narg) - error->universe_all(FLERR,"Invalid command-line argument"); - iarg += 2; - } else if (strcmp(arg[iarg],"-pscreen") == 0 || - strcmp(arg[iarg],"-ps") == 0) { - if (iarg+2 > narg) - error->universe_all(FLERR,"Invalid command-line argument"); - partscreenflag = iarg + 1; - iarg += 2; - } else if (strcmp(arg[iarg],"-plog") == 0 || - strcmp(arg[iarg],"-pl") == 0) { - if (iarg+2 > narg) - error->universe_all(FLERR,"Invalid command-line argument"); - partlogflag = iarg + 1; - iarg += 2; + } else if (strcmp(arg[iarg],"-kokkos") == 0 || strcmp(arg[iarg],"-k") == 0) { if (iarg+2 > narg) @@ -172,6 +177,26 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) kkfirst = iarg; while (iarg < narg && arg[iarg][0] != '-') iarg++; kklast = iarg; + + } else if (strcmp(arg[iarg],"-log") == 0 || + strcmp(arg[iarg],"-l") == 0) { + if (iarg+2 > narg) + error->universe_all(FLERR,"Invalid command-line argument"); + logflag = iarg + 1; + iarg += 2; + + } else if (strcmp(arg[iarg],"-mpi") == 0 || + strcmp(arg[iarg],"-m") == 0) { + if (iarg+2 > narg) + error->universe_all(FLERR,"Invalid command-line argument"); + if (iarg != 1) error->universe_all(FLERR,"Invalid command-line argument"); + iarg += 2; + + } else if (strcmp(arg[iarg],"-nocite") == 0 || + strcmp(arg[iarg],"-nc") == 0) { + citeflag = 0; + iarg++; + } else if (strcmp(arg[iarg],"-package") == 0 || strcmp(arg[iarg],"-pk") == 0) { if (iarg+2 > narg) @@ -188,6 +213,69 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) else break; } plast[npack++] = iarg; + + } else if (strcmp(arg[iarg],"-partition") == 0 || + strcmp(arg[iarg],"-p") == 0) { + universe->existflag = 1; + if (iarg+2 > narg) + error->universe_all(FLERR,"Invalid command-line argument"); + iarg++; + while (iarg < narg && arg[iarg][0] != '-') { + universe->add_world(arg[iarg]); + iarg++; + } + + } else if (strcmp(arg[iarg],"-plog") == 0 || + strcmp(arg[iarg],"-pl") == 0) { + if (iarg+2 > narg) + error->universe_all(FLERR,"Invalid command-line argument"); + partlogflag = iarg + 1; + iarg += 2; + + } else if (strcmp(arg[iarg],"-pscreen") == 0 || + strcmp(arg[iarg],"-ps") == 0) { + if (iarg+2 > narg) + error->universe_all(FLERR,"Invalid command-line argument"); + partscreenflag = iarg + 1; + iarg += 2; + + } else if (strcmp(arg[iarg],"-reorder") == 0 || + strcmp(arg[iarg],"-ro") == 0) { + if (iarg+3 > narg) + error->universe_all(FLERR,"Invalid command-line argument"); + if (universe->existflag) + error->universe_all(FLERR,"Cannot use -reorder after -partition"); + universe->reorder(arg[iarg+1],arg[iarg+2]); + iarg += 3; + + } else if (strcmp(arg[iarg],"-restart") == 0 || + strcmp(arg[iarg],"-r") == 0) { + if (iarg+3 > narg) + error->universe_all(FLERR,"Invalid command-line argument"); + restartflag = 1; + rfile = arg[iarg+1]; + dfile = arg[iarg+2]; + // check for restart remap flag + if (strcmp(dfile,"remap") == 0) { + if (iarg+4 > narg) + error->universe_all(FLERR,"Invalid command-line argument"); + restartremapflag = 1; + dfile = arg[iarg+3]; + iarg++; + } + iarg += 3; + // delimit any extra args for the write_data command + wdfirst = iarg; + while (iarg < narg && arg[iarg][0] != '-') iarg++; + wdlast = iarg; + + } else if (strcmp(arg[iarg],"-screen") == 0 || + strcmp(arg[iarg],"-sc") == 0) { + if (iarg+2 > narg) + error->universe_all(FLERR,"Invalid command-line argument"); + screenflag = iarg + 1; + iarg += 2; + } else if (strcmp(arg[iarg],"-suffix") == 0 || strcmp(arg[iarg],"-sf") == 0) { if (iarg+2 > narg) @@ -213,50 +301,14 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) strcpy(suffix,arg[iarg+1]); iarg += 2; } - } else if (strcmp(arg[iarg],"-reorder") == 0 || - strcmp(arg[iarg],"-ro") == 0) { + + } else if (strcmp(arg[iarg],"-var") == 0 || + strcmp(arg[iarg],"-v") == 0) { if (iarg+3 > narg) error->universe_all(FLERR,"Invalid command-line argument"); - if (universe->existflag) - error->universe_all(FLERR,"Cannot use -reorder after -partition"); - universe->reorder(arg[iarg+1],arg[iarg+2]); iarg += 3; - } else if (strcmp(arg[iarg],"-restart") == 0 || - strcmp(arg[iarg],"-r") == 0) { - if (iarg+3 > narg) - error->universe_all(FLERR,"Invalid command-line argument"); - restartflag = 1; - rfile = arg[iarg+1]; - dfile = arg[iarg+2]; - // check for restart remap flag - if (strcmp(dfile,"remap") == 0) { - if (iarg+4 > narg) - error->universe_all(FLERR,"Invalid command-line argument"); - restartremapflag = 1; - dfile = arg[iarg+3]; - iarg++; - } - iarg += 3; - // delimit any extra args for the write_data command - wdfirst = iarg; while (iarg < narg && arg[iarg][0] != '-') iarg++; - wdlast = iarg; - } else if (strcmp(arg[iarg],"-nocite") == 0 || - strcmp(arg[iarg],"-nc") == 0) { - citeflag = 0; - iarg++; - } else if (strcmp(arg[iarg],"-help") == 0 || - strcmp(arg[iarg],"-h") == 0) { - if (iarg+1 > narg) - error->universe_all(FLERR,"Invalid command-line argument"); - helpflag = 1; - citeflag = 0; - iarg += 1; - } else { - char msg[2048]; - sprintf( msg, "Invalid command-line argument \"%s\"\n", arg[iarg] ); - error->universe_all(FLERR,msg); - } + } // if no partition command-line switch, universe is one world with all procs @@ -599,6 +651,14 @@ LAMMPS::~LAMMPS() delete [] suffix; delete [] suffix2; + // free the MPI comm created by -mpi command-line arg processed in constructor + // it was passed to universe as if original universe world + // may have been split later by partitions, universe will free the splits + // free a copy of uorig here, so check in universe destructor will still work + + MPI_Comm copy = universe->uorig; + if (cscomm) MPI_Comm_free(©); + delete input; delete universe; delete error; @@ -818,6 +878,7 @@ void LAMMPS::help() "-in filename : read input from file, not stdin (-i)\n" "-kokkos on/off ... : turn KOKKOS mode on or off (-k)\n" "-log none/filename : where to send log output (-l)\n" + "-mpicolor color : which exe in a multi-exe mpirun cmd (-m)\n" "-nocite : disable writing log.cite file (-nc)\n" "-package style ... : invoke package command (-pk)\n" "-partition size1 size2 ... : assign partition sizes (-p)\n" diff --git a/src/lammps.h b/src/lammps.h index b2c8673471..5ccef3026e 100644 --- a/src/lammps.h +++ b/src/lammps.h @@ -51,6 +51,10 @@ class LAMMPS { int num_package; // number of cmdline package commands int cite_enable; // 1 if generating log.cite, 0 if disabled + int clientserver; // 0 = neither, 1 = client, 2 = server + void *cslib; // client/server messaging via CSlib + MPI_Comm cscomm; // MPI comm for client+server in mpi/one mode + class KokkosLMP *kokkos; // KOKKOS accelerator class class AtomKokkos *atomKK; // KOKKOS version of Atom class class MemoryKokkos *memoryKK; // KOKKOS version of Memory class diff --git a/src/library.cpp b/src/library.cpp index 245ae7ba84..a46689da09 100644 --- a/src/library.cpp +++ b/src/library.cpp @@ -1515,7 +1515,8 @@ void lammps_create_atoms(void *ptr, int n, tagint *id, int *type, if (lmp->atom->natoms != natoms_prev + n) { char str[128]; sprintf(str,"Library warning in lammps_create_atoms, " - "invalid total atoms " BIGINT_FORMAT " %lld",lmp->atom->natoms,natoms_prev+n); + "invalid total atoms " BIGINT_FORMAT " " BIGINT_FORMAT, + lmp->atom->natoms,natoms_prev+n); if (lmp->comm->me == 0) lmp->error->warning(FLERR,str); } diff --git a/src/version.h b/src/version.h index 2192b25d91..fbeeabff8d 100644 --- a/src/version.h +++ b/src/version.h @@ -1 +1 @@ -#define LAMMPS_VERSION "22 Aug 2018" +#define LAMMPS_VERSION "31 Aug 2018" From c192236a7e50a4a83e0fdca78fffa9174f1ee790 Mon Sep 17 00:00:00 2001 From: Stefan Paquay Date: Wed, 5 Sep 2018 11:28:06 -0400 Subject: [PATCH 136/302] Commit before switching to old master. --- src/lammps.cpp | 1 + 1 file changed, 1 insertion(+) diff --git a/src/lammps.cpp b/src/lammps.cpp index 21335065f4..fcdfecf30a 100644 --- a/src/lammps.cpp +++ b/src/lammps.cpp @@ -309,6 +309,7 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) iarg += 3; while (iarg < narg && arg[iarg][0] != '-') iarg++; + } else error->universe_all(FLERR,"Invalid command-line argument"); } // if no partition command-line switch, universe is one world with all procs From 1c8feed69fa0d364c752ac768af263263c297db2 Mon Sep 17 00:00:00 2001 From: Stefan Paquay Date: Wed, 5 Sep 2018 11:38:04 -0400 Subject: [PATCH 137/302] Removed gpu makefile from wrong branch. --- lib/gpu/Makefile.linux | 52 ------------------------------------------ 1 file changed, 52 deletions(-) delete mode 100644 lib/gpu/Makefile.linux diff --git a/lib/gpu/Makefile.linux b/lib/gpu/Makefile.linux deleted file mode 100644 index b0218c8d39..0000000000 --- a/lib/gpu/Makefile.linux +++ /dev/null @@ -1,52 +0,0 @@ -# /* ---------------------------------------------------------------------- -# Generic Linux Makefile for CUDA -# - Change CUDA_ARCH for your GPU -# ------------------------------------------------------------------------- */ - -# which file will be copied to Makefile.lammps - -EXTRAMAKE = Makefile.lammps.standard - -ifeq ($(CUDA_HOME),) -CUDA_HOME = /opt/cuda -endif - -NVCC = nvcc - -# older CUDA -#CUDA_ARCH = -arch=sm_21 -# newer CUDA -#CUDA_ARCH = -arch=sm_13 -# older CUDA -#CUDA_ARCH = -arch=sm_10 -DCUDA_PRE_THREE -CUDA_ARCH = -arch=sm_61 - -# this setting should match LAMMPS Makefile -# one of LAMMPS_SMALLBIG (default), LAMMPS_BIGBIG and LAMMPS_SMALLSMALL - -LMP_INC = -DLAMMPS_SMALLBIG - -# precision for GPU calculations -# -D_SINGLE_SINGLE # Single precision for all calculations -# -D_DOUBLE_DOUBLE # Double precision for all calculations -# -D_SINGLE_DOUBLE # Accumulation of forces, etc. in double - -CUDA_PRECISION = -D_SINGLE_DOUBLE - -CUDA_INCLUDE = -I$(CUDA_HOME)/include -CUDA_LIB = -L$(CUDA_HOME)/lib64 -CUDA_OPTS = -DUNIX -O3 -Xptxas -v --use_fast_math $(LMP_INC) -Xcompiler -fPIC - -CUDR_CPP = mpicxx -DMPI_GERYON -DUCL_NO_EXIT -DMPICH_IGNORE_CXX_SEEK -DOMPI_SKIP_MPICXX=1 -fPIC -CUDR_OPTS = -O2 $(LMP_INC) # -xHost -no-prec-div -ansi-alias - -BIN_DIR = ./ -OBJ_DIR = ./ -LIB_DIR = ./ -AR = ar -BSH = /bin/sh - -CUDPP_OPT = -DUSE_CUDPP -Icudpp_mini - -include Nvidia.makefile - From 9b38a5b359f1622d68d9946119ee1053882c1a4b Mon Sep 17 00:00:00 2001 From: Stefan Paquay Date: Wed, 5 Sep 2018 11:39:41 -0400 Subject: [PATCH 138/302] Replaced gpu Makefile with the one from upstream so as not to delete it. --- lib/gpu/Makefile.linux | 52 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 lib/gpu/Makefile.linux diff --git a/lib/gpu/Makefile.linux b/lib/gpu/Makefile.linux new file mode 100644 index 0000000000..9580bfd4ae --- /dev/null +++ b/lib/gpu/Makefile.linux @@ -0,0 +1,52 @@ +# /* ---------------------------------------------------------------------- +# Generic Linux Makefile for CUDA +# - Change CUDA_ARCH for your GPU +# ------------------------------------------------------------------------- */ + +# which file will be copied to Makefile.lammps + +EXTRAMAKE = Makefile.lammps.standard + +ifeq ($(CUDA_HOME),) +CUDA_HOME = /usr/local/cuda +endif + +NVCC = nvcc + +# older CUDA +#CUDA_ARCH = -arch=sm_21 +# newer CUDA +#CUDA_ARCH = -arch=sm_13 +# older CUDA +#CUDA_ARCH = -arch=sm_10 -DCUDA_PRE_THREE +CUDA_ARCH = -arch=sm_35 + +# this setting should match LAMMPS Makefile +# one of LAMMPS_SMALLBIG (default), LAMMPS_BIGBIG and LAMMPS_SMALLSMALL + +LMP_INC = -DLAMMPS_SMALLBIG + +# precision for GPU calculations +# -D_SINGLE_SINGLE # Single precision for all calculations +# -D_DOUBLE_DOUBLE # Double precision for all calculations +# -D_SINGLE_DOUBLE # Accumulation of forces, etc. in double + +CUDA_PRECISION = -D_SINGLE_DOUBLE + +CUDA_INCLUDE = -I$(CUDA_HOME)/include +CUDA_LIB = -L$(CUDA_HOME)/lib64 +CUDA_OPTS = -DUNIX -O3 -Xptxas -v --use_fast_math $(LMP_INC) -Xcompiler -fPIC + +CUDR_CPP = mpicxx -DMPI_GERYON -DUCL_NO_EXIT -DMPICH_IGNORE_CXX_SEEK -DOMPI_SKIP_MPICXX=1 -fPIC +CUDR_OPTS = -O2 $(LMP_INC) # -xHost -no-prec-div -ansi-alias + +BIN_DIR = ./ +OBJ_DIR = ./ +LIB_DIR = ./ +AR = ar +BSH = /bin/sh + +CUDPP_OPT = -DUSE_CUDPP -Icudpp_mini + +include Nvidia.makefile + From 5003354fba49486aba084ca9af97cea5649e7414 Mon Sep 17 00:00:00 2001 From: Stefan Paquay Date: Wed, 5 Sep 2018 11:42:48 -0400 Subject: [PATCH 139/302] Replaced a tab with whitespace. --- src/USER-MISC/pair_morse_smooth_linear.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/USER-MISC/pair_morse_smooth_linear.cpp b/src/USER-MISC/pair_morse_smooth_linear.cpp index 4181fd5479..a88e7a1a27 100644 --- a/src/USER-MISC/pair_morse_smooth_linear.cpp +++ b/src/USER-MISC/pair_morse_smooth_linear.cpp @@ -116,7 +116,7 @@ void PairMorseSmoothLinear::compute(int eflag, int vflag) if (eflag) { evdwl = d0[itype][jtype] * (dexp*dexp - 2.0*dexp) - - offset[itype][jtype]; + offset[itype][jtype]; evdwl -= ( r - cut[itype][jtype] ) * der_at_cutoff[itype][jtype]; evdwl *= factor_lj; } From 510e09f4ef002cf633a1060497fef4e92c735904 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 5 Sep 2018 13:39:18 -0400 Subject: [PATCH 140/302] patch 5Sep18 --- doc/src/Manual.txt | 4 ++-- src/version.h | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/doc/src/Manual.txt b/doc/src/Manual.txt index e442aa1808..5af157d8ea 100644 --- a/doc/src/Manual.txt +++ b/doc/src/Manual.txt @@ -1,7 +1,7 @@ LAMMPS Users Manual - + @@ -21,7 +21,7 @@ :line LAMMPS Documentation :c,h1 -31 Aug 2018 version :c,h2 +5 Sep 2018 version :c,h2 "What is a LAMMPS version?"_Manual_version.html diff --git a/src/version.h b/src/version.h index fbeeabff8d..0b8c1e8736 100644 --- a/src/version.h +++ b/src/version.h @@ -1 +1 @@ -#define LAMMPS_VERSION "31 Aug 2018" +#define LAMMPS_VERSION "5 Sep 2018" From ad498811b1f254e946edc6812f64e827d44e63d1 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 5 Sep 2018 16:04:35 -0400 Subject: [PATCH 141/302] cmake: add missing fix_omp.h and fix_omp.cpp to compilation --- cmake/CMakeLists.txt | 3 ++- cmake/Modules/StyleHeaderUtils.cmake | 4 ++++ 2 files changed, 6 insertions(+), 1 deletion(-) diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index 3634138747..62a2fbdef4 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -777,6 +777,7 @@ if(PKG_USER-OMP) set(USER-OMP_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-OMP) set(USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/thr_data.cpp ${USER-OMP_SOURCES_DIR}/thr_omp.cpp + ${USER-OMP_SOURCES_DIR}/fix_omp.cpp ${USER-OMP_SOURCES_DIR}/fix_nh_omp.cpp ${USER-OMP_SOURCES_DIR}/fix_nh_sphere_omp.cpp ${USER-OMP_SOURCES_DIR}/domain_omp.cpp) @@ -785,7 +786,7 @@ if(PKG_USER-OMP) # detects styles which have USER-OMP version RegisterStylesExt(${USER-OMP_SOURCES_DIR} omp OMP_SOURCES) - + RegisterFixStyle("${USER-OMP_SOURCES_DIR}/fix_omp.h") get_property(USER-OMP_SOURCES GLOBAL PROPERTY OMP_SOURCES) diff --git a/cmake/Modules/StyleHeaderUtils.cmake b/cmake/Modules/StyleHeaderUtils.cmake index 2b00a81c8d..d621e4c9c0 100644 --- a/cmake/Modules/StyleHeaderUtils.cmake +++ b/cmake/Modules/StyleHeaderUtils.cmake @@ -85,6 +85,10 @@ function(RegisterNPairStyle path) AddStyleHeader(${path} NPAIR) endfunction(RegisterNPairStyle) +function(RegisterFixStyle path) + AddStyleHeader(${path} FIX) +endfunction(RegisterFixStyle) + function(RegisterStyles search_path) FindStyleHeaders(${search_path} ANGLE_CLASS angle_ ANGLE ) # angle ) # force FindStyleHeaders(${search_path} ATOM_CLASS atom_vec_ ATOM_VEC ) # atom ) # atom atom_vec_hybrid From ba1c5d3191da1effbcd8af6ab0df56b886578527 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 5 Sep 2018 21:39:09 -0400 Subject: [PATCH 142/302] Avoid buffer overflow during errors with long filenames --- src/error.cpp | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/error.cpp b/src/error.cpp index 3feaf1d1ac..913239ac49 100644 --- a/src/error.cpp +++ b/src/error.cpp @@ -75,7 +75,7 @@ void Error::universe_all(const char *file, int line, const char *str) update->whichflag = 0; char msg[100]; - sprintf(msg, "ERROR: %s (%s:%d)\n", str, file, line); + snprintf(msg, 100, "ERROR: %s (%s:%d)\n", str, truncpath(file), line); throw LAMMPSException(msg); #else MPI_Finalize(); @@ -100,7 +100,7 @@ void Error::universe_one(const char *file, int line, const char *str) update->whichflag = 0; char msg[100]; - sprintf(msg, "ERROR: %s (%s:%d)\n", str, file, line); + snprintf(msg, 100, "ERROR: %s (%s:%d)\n", str, truncpath(file), line); throw LAMMPSAbortException(msg, universe->uworld); #else MPI_Abort(universe->uworld,1); @@ -151,7 +151,7 @@ void Error::all(const char *file, int line, const char *str) update->whichflag = 0; char msg[100]; - sprintf(msg, "ERROR: %s (%s:%d)\n", str, file, line); + snprintf(msg, 100, "ERROR: %s (%s:%d)\n", str, truncpath(file), line); if (universe->nworlds > 1) { throw LAMMPSAbortException(msg, universe->uworld); @@ -201,7 +201,7 @@ void Error::one(const char *file, int line, const char *str) update->whichflag = 0; char msg[100]; - sprintf(msg, "ERROR on proc %d: %s (%s:%d)\n", me, str, file, line); + snprintf(msg, 100, "ERROR on proc %d: %s (%s:%d)\n", me, str, truncpath(file), line); throw LAMMPSAbortException(msg, world); #else MPI_Abort(world,1); From ca04e8f31c62224dc8b01d19d229d21bf0cbe89a Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 6 Sep 2018 02:57:53 -0400 Subject: [PATCH 143/302] use snprintf() in a bunch of cases to avoid overflowing fixed size buffers with unchecked strings --- src/fix_ave_chunk.cpp | 2 +- src/fix_ave_correlate.cpp | 2 +- src/fix_ave_histo.cpp | 2 +- src/fix_ave_time.cpp | 2 +- src/fix_enforce2d.cpp | 2 +- src/fix_print.cpp | 2 +- src/fix_property_atom.cpp | 8 ++++---- src/fix_tmd.cpp | 6 +++--- src/force.cpp | 4 ++-- src/input.cpp | 14 +++++++------- src/lammps.cpp | 16 ++++++++-------- src/memory.cpp | 3 ++- src/modify.cpp | 9 +++++---- src/molecule.cpp | 2 +- src/neighbor.cpp | 2 +- src/pair_coul_streitz.cpp | 2 +- 16 files changed, 40 insertions(+), 38 deletions(-) diff --git a/src/fix_ave_chunk.cpp b/src/fix_ave_chunk.cpp index 1aead70644..11ba4a41a5 100644 --- a/src/fix_ave_chunk.cpp +++ b/src/fix_ave_chunk.cpp @@ -225,7 +225,7 @@ FixAveChunk::FixAveChunk(LAMMPS *lmp, int narg, char **arg) : fp = fopen(arg[iarg+1],"w"); if (fp == NULL) { char str[128]; - sprintf(str,"Cannot open fix ave/chunk file %s",arg[iarg+1]); + snprintf(str,128,"Cannot open fix ave/chunk file %s",arg[iarg+1]); error->one(FLERR,str); } } diff --git a/src/fix_ave_correlate.cpp b/src/fix_ave_correlate.cpp index 198caf1514..5c95f20ec2 100644 --- a/src/fix_ave_correlate.cpp +++ b/src/fix_ave_correlate.cpp @@ -149,7 +149,7 @@ FixAveCorrelate::FixAveCorrelate(LAMMPS * lmp, int narg, char **arg): fp = fopen(arg[iarg+1],"w"); if (fp == NULL) { char str[128]; - sprintf(str,"Cannot open fix ave/correlate file %s",arg[iarg+1]); + snprintf(str,128,"Cannot open fix ave/correlate file %s",arg[iarg+1]); error->one(FLERR,str); } } diff --git a/src/fix_ave_histo.cpp b/src/fix_ave_histo.cpp index ce32167b74..a5bf8db557 100644 --- a/src/fix_ave_histo.cpp +++ b/src/fix_ave_histo.cpp @@ -937,7 +937,7 @@ void FixAveHisto::options(int iarg, int narg, char **arg) fp = fopen(arg[iarg+1],"w"); if (fp == NULL) { char str[128]; - sprintf(str,"Cannot open fix ave/histo file %s",arg[iarg+1]); + snprintf(str,128,"Cannot open fix ave/histo file %s",arg[iarg+1]); error->one(FLERR,str); } } diff --git a/src/fix_ave_time.cpp b/src/fix_ave_time.cpp index 53354ee066..50654b6561 100644 --- a/src/fix_ave_time.cpp +++ b/src/fix_ave_time.cpp @@ -1042,7 +1042,7 @@ void FixAveTime::options(int iarg, int narg, char **arg) fp = fopen(arg[iarg+1],"w"); if (fp == NULL) { char str[128]; - sprintf(str,"Cannot open fix ave/time file %s",arg[iarg+1]); + snprintf(str,128,"Cannot open fix ave/time file %s",arg[iarg+1]); error->one(FLERR,str); } } diff --git a/src/fix_enforce2d.cpp b/src/fix_enforce2d.cpp index ef7eb3a0ef..986ded5d16 100644 --- a/src/fix_enforce2d.cpp +++ b/src/fix_enforce2d.cpp @@ -78,7 +78,7 @@ void FixEnforce2D::init() flist[nfixlist++] = modify->fix[i]; else { char msg[256]; - sprintf(msg,"Fix enforce2d must be defined after fix %s",modify->fix[i]->style); + snprintf(msg,256,"Fix enforce2d must be defined after fix %s",modify->fix[i]->style); error->all(FLERR,msg); } } diff --git a/src/fix_print.cpp b/src/fix_print.cpp index 16218e0088..969fcf8140 100644 --- a/src/fix_print.cpp +++ b/src/fix_print.cpp @@ -60,7 +60,7 @@ FixPrint::FixPrint(LAMMPS *lmp, int narg, char **arg) : else fp = fopen(arg[iarg+1],"a"); if (fp == NULL) { char str[128]; - sprintf(str,"Cannot open fix print file %s",arg[iarg+1]); + snprintf(str,128,"Cannot open fix print file %s",arg[iarg+1]); error->one(FLERR,str); } } diff --git a/src/fix_property_atom.cpp b/src/fix_property_atom.cpp index 5b12b6def2..c89419f850 100644 --- a/src/fix_property_atom.cpp +++ b/src/fix_property_atom.cpp @@ -224,7 +224,7 @@ void FixPropertyAtom::read_data_section(char *keyword, int n, char *buf, if (nwords != nvalue+1) { char str[128]; - sprintf(str,"Incorrect %s format in data file",keyword); + snprintf(str,128,"Incorrect %s format in data file",keyword); error->all(FLERR,str); } @@ -242,7 +242,7 @@ void FixPropertyAtom::read_data_section(char *keyword, int n, char *buf, values[0] = strtok(buf," \t\n\r\f"); if (values[0] == NULL) { char str[128]; - sprintf(str,"Too few lines in %s section of data file",keyword); + snprintf(str,128,"Too few lines in %s section of data file",keyword); error->one(FLERR,str); } int format_ok = 1; @@ -252,14 +252,14 @@ void FixPropertyAtom::read_data_section(char *keyword, int n, char *buf, } if (!format_ok) { char str[128]; - sprintf(str,"Incorrect %s format in data file",keyword); + snprintf(str,128,"Incorrect %s format in data file",keyword); error->all(FLERR,str); } itag = ATOTAGINT(values[0]) + id_offset; if (itag <= 0 || itag > map_tag_max) { char str[128]; - sprintf(str,"Invalid atom ID in %s section of data file",keyword); + snprintf(str,128,"Invalid atom ID in %s section of data file",keyword); error->one(FLERR,str); } diff --git a/src/fix_tmd.cpp b/src/fix_tmd.cpp index dd11dfd0c7..4cbb244bc0 100644 --- a/src/fix_tmd.cpp +++ b/src/fix_tmd.cpp @@ -75,7 +75,7 @@ nfileevery(0), fp(NULL), xf(NULL), xold(NULL) fp = fopen(arg[6],"w"); if (fp == NULL) { char str[128]; - sprintf(str,"Cannot open fix tmd file %s",arg[6]); + snprintf(str,128,"Cannot open fix tmd file %s",arg[6]); error->one(FLERR,str); } fprintf(fp,"%s %s\n","# Step rho_target rho_old gamma_back", @@ -523,7 +523,7 @@ void FixTMD::open(char *file) else { #ifdef LAMMPS_GZIP char gunzip[128]; - sprintf(gunzip,"gzip -c -d %s",file); + snprintf(gunzip,128,"gzip -c -d %s",file); #ifdef _WIN32 fp = _popen(gunzip,"rb"); @@ -538,7 +538,7 @@ void FixTMD::open(char *file) if (fp == NULL) { char str[128]; - sprintf(str,"Cannot open file %s",file); + snprintf(str,128,"Cannot open file %s",file); error->one(FLERR,str); } } diff --git a/src/force.cpp b/src/force.cpp index 8ee301982d..91fccd7197 100644 --- a/src/force.cpp +++ b/src/force.cpp @@ -182,8 +182,8 @@ void Force::init() if (pair_restart) { if (!pair) { char msg[128]; - sprintf(msg,"Must re-specify non-restarted pair style (%s) " - "after read_restart", pair_restart); + snprintf(msg,128,"Must re-specify non-restarted pair style (%s) " + "after read_restart", pair_restart); error->all(FLERR,msg); } } diff --git a/src/input.cpp b/src/input.cpp index f41c8458ea..2834e36913 100644 --- a/src/input.cpp +++ b/src/input.cpp @@ -267,7 +267,7 @@ void Input::file(const char *filename) infile = fopen(filename,"r"); if (infile == NULL) { char str[128]; - sprintf(str,"Cannot open input script %s",filename); + snprintf(str,128,"Cannot open input script %s",filename); error->one(FLERR,str); } infiles[0] = infile; @@ -526,7 +526,7 @@ void Input::substitute(char *&str, char *&str2, int &max, int &max2, int flag) *fmtflag='\0'; } - sprintf(immediate,fmtstr,variable->compute_equal(var)); + snprintf(immediate,256,fmtstr,variable->compute_equal(var)); value = immediate; // single character variable name, e.g. $a @@ -541,7 +541,7 @@ void Input::substitute(char *&str, char *&str2, int &max, int &max2, int flag) if (value == NULL) { char str[128]; - sprintf(str,"Substitution for illegal variable %s",var); + snprintf(str,128,"Substitution for illegal variable %s",var); error->one(FLERR,str); } // check if storage in str2 needs to be expanded @@ -1047,7 +1047,7 @@ void Input::include() infile = fopen(arg[0],"r"); if (infile == NULL) { char str[128]; - sprintf(str,"Cannot open input script %s",arg[0]); + snprintf(str,128,"Cannot open input script %s",arg[0]); error->one(FLERR,str); } infiles[nfile++] = infile; @@ -1072,7 +1072,7 @@ void Input::jump() infile = fopen(arg[0],"r"); if (infile == NULL) { char str[128]; - sprintf(str,"Cannot open input script %s",arg[0]); + snprintf(str,128,"Cannot open input script %s",arg[0]); error->one(FLERR,str); } infiles[nfile-1] = infile; @@ -1117,7 +1117,7 @@ void Input::log() if (logfile == NULL) { char str[128]; - sprintf(str,"Cannot open logfile %s",arg[0]); + snprintf(str,128,"Cannot open logfile %s",arg[0]); error->one(FLERR,str); } } @@ -1196,7 +1196,7 @@ void Input::print() else fp = fopen(arg[iarg+1],"a"); if (fp == NULL) { char str[128]; - sprintf(str,"Cannot open print file %s",arg[iarg+1]); + snprintf(str,128,"Cannot open print file %s",arg[iarg+1]); error->one(FLERR,str); } } diff --git a/src/lammps.cpp b/src/lammps.cpp index fcdfecf30a..04d8daa478 100644 --- a/src/lammps.cpp +++ b/src/lammps.cpp @@ -385,7 +385,7 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) else infile = fopen(arg[inflag],"r"); if (infile == NULL) { char str[128]; - sprintf(str,"Cannot open input script %s",arg[inflag]); + snprintf(str,128,"Cannot open input script %s",arg[inflag]); error->one(FLERR,str); } } @@ -416,7 +416,7 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) screen = NULL; else { char str[128]; - sprintf(str,"%s.%d",arg[screenflag],universe->iworld); + snprintf(str,128,"%s.%d",arg[screenflag],universe->iworld); screen = fopen(str,"w"); if (screen == NULL) error->one(FLERR,"Cannot open screen file"); } @@ -424,7 +424,7 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) screen = NULL; else { char str[128]; - sprintf(str,"%s.%d",arg[partscreenflag],universe->iworld); + snprintf(str,128,"%s.%d",arg[partscreenflag],universe->iworld); screen = fopen(str,"w"); if (screen == NULL) error->one(FLERR,"Cannot open screen file"); } else screen = NULL; @@ -440,7 +440,7 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) logfile = NULL; else { char str[128]; - sprintf(str,"%s.%d",arg[logflag],universe->iworld); + snprintf(str,128,"%s.%d",arg[logflag],universe->iworld); logfile = fopen(str,"w"); if (logfile == NULL) error->one(FLERR,"Cannot open logfile"); } @@ -448,7 +448,7 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) logfile = NULL; else { char str[128]; - sprintf(str,"%s.%d",arg[partlogflag],universe->iworld); + snprintf(str,128,"%s.%d",arg[partlogflag],universe->iworld); logfile = fopen(str,"w"); if (logfile == NULL) error->one(FLERR,"Cannot open logfile"); } else logfile = NULL; @@ -457,7 +457,7 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) infile = fopen(arg[inflag],"r"); if (infile == NULL) { char str[128]; - sprintf(str,"Cannot open input script %s",arg[inflag]); + snprintf(str,128,"Cannot open input script %s",arg[inflag]); error->one(FLERR,str); } } else infile = NULL; @@ -579,10 +579,10 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) if (restartflag) { char cmd[128]; - sprintf(cmd,"read_restart %s\n",rfile); + snprintf(cmd,128,"read_restart %s\n",rfile); if (restartremapflag) strcat(cmd," remap\n"); input->one(cmd); - sprintf(cmd,"write_data %s",dfile); + snprintf(cmd,128,"write_data %s",dfile); for (iarg = wdfirst; iarg < wdlast; iarg++) sprintf(&cmd[strlen(cmd)]," %s",arg[iarg]); strcat(cmd," noinit\n"); diff --git a/src/memory.cpp b/src/memory.cpp index 429cf75c00..7a23a23079 100644 --- a/src/memory.cpp +++ b/src/memory.cpp @@ -121,6 +121,7 @@ void Memory::sfree(void *ptr) void Memory::fail(const char *name) { char str[128]; - sprintf(str,"Cannot create/grow a vector/array of pointers for %s",name); + snprintf(str,128, + "Cannot create/grow a vector/array of pointers for %s",name); error->one(FLERR,str); } diff --git a/src/modify.cpp b/src/modify.cpp index c5a680a3bd..8a0d1afa2c 100644 --- a/src/modify.cpp +++ b/src/modify.cpp @@ -239,7 +239,8 @@ void Modify::init() for (i = 0; i < nfix; i++) if (!fix[i]->dynamic_group_allow && group->dynamic[fix[i]->igroup]) { char str[128]; - sprintf(str,"Fix %s does not allow use of dynamic group",fix[i]->id); + snprintf(str,128, + "Fix %s does not allow use of dynamic group",fix[i]->id); error->all(FLERR,str); } @@ -247,7 +248,7 @@ void Modify::init() if (!compute[i]->dynamic_group_allow && group->dynamic[compute[i]->igroup]) { char str[128]; - sprintf(str,"Compute %s does not allow use of dynamic group",fix[i]->id); + snprintf(str,128,"Compute %s does not allow use of dynamic group",fix[i]->id); error->all(FLERR,str); } @@ -889,7 +890,7 @@ void Modify::add_fix(int narg, char **arg, int trysuffix) if (fix[ifix] == NULL) { char str[128]; - sprintf(str,"Unknown fix style %s",arg[2]); + snprintf(str,128,"Unknown fix style %s",arg[2]); error->all(FLERR,str); } @@ -1191,7 +1192,7 @@ void Modify::add_compute(int narg, char **arg, int trysuffix) if (compute[ncompute] == NULL) { char str[128]; - sprintf(str,"Unknown compute style %s",arg[2]); + snprintf(str,128,"Unknown compute style %s",arg[2]); error->all(FLERR,str); } diff --git a/src/molecule.cpp b/src/molecule.cpp index dfbe3e1e08..454459084a 100644 --- a/src/molecule.cpp +++ b/src/molecule.cpp @@ -1632,7 +1632,7 @@ void Molecule::open(char *file) fp = fopen(file,"r"); if (fp == NULL) { char str[128]; - sprintf(str,"Cannot open molecule file %s",file); + snprintf(str,128,"Cannot open molecule file %s",file); error->one(FLERR,str); } } diff --git a/src/neighbor.cpp b/src/neighbor.cpp index 759f84e29f..bc22fffc48 100644 --- a/src/neighbor.cpp +++ b/src/neighbor.cpp @@ -1408,7 +1408,7 @@ void Neighbor::init_topology() void Neighbor::print_pairwise_info() { int i,m; - char str[128]; + char str[256]; NeighRequest *rq; FILE *out; diff --git a/src/pair_coul_streitz.cpp b/src/pair_coul_streitz.cpp index 1d725f4ca8..920770ed7f 100644 --- a/src/pair_coul_streitz.cpp +++ b/src/pair_coul_streitz.cpp @@ -258,7 +258,7 @@ void PairCoulStreitz::read_file(char *file) fp = fopen(file,"r"); if (fp == NULL) { char str[128]; - sprintf(str,"Cannot open coul/streitz potential file %s",file); + snprintf(str,128,"Cannot open coul/streitz potential file %s",file); error->one(FLERR,str); } } From fbc1c1cfdd2194c78e0f77393bbc060e32a74a63 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 6 Sep 2018 09:57:10 -0400 Subject: [PATCH 144/302] replace fixed buffer sprintf() with straight fprintf() --- src/neighbor.cpp | 12 +++++------- 1 file changed, 5 insertions(+), 7 deletions(-) diff --git a/src/neighbor.cpp b/src/neighbor.cpp index bc22fffc48..84494bfbc5 100644 --- a/src/neighbor.cpp +++ b/src/neighbor.cpp @@ -1408,7 +1408,6 @@ void Neighbor::init_topology() void Neighbor::print_pairwise_info() { int i,m; - char str[256]; NeighRequest *rq; FILE *out; @@ -1457,18 +1456,17 @@ void Neighbor::print_pairwise_info() rq = requests[i]; if (rq->pair) { char *pname = force->pair_match_ptr((Pair *) rq->requestor); - sprintf(str," (%d) pair %s",i+1,pname); + fprintf(out," (%d) pair %s",i+1,pname); } else if (rq->fix) { - sprintf(str," (%d) fix %s",i+1,((Fix *) rq->requestor)->style); + fprintf(out," (%d) fix %s",i+1,((Fix *) rq->requestor)->style); } else if (rq->compute) { - sprintf(str," (%d) compute %s",i+1, + fprintf(out," (%d) compute %s",i+1, ((Compute *) rq->requestor)->style); } else if (rq->command) { - sprintf(str," (%d) command %s",i+1,rq->command_style); + fprintf(out," (%d) command %s",i+1,rq->command_style); } else if (rq->neigh) { - sprintf(str," (%d) neighbor class addition",i+1); + fprintf(out," (%d) neighbor class addition",i+1); } - fprintf(out,"%s",str); if (rq->occasional) fprintf(out,", occasional"); else fprintf(out,", perpetual"); From 4d52cb9245b74d7d4690637738efffb1045ce1e5 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 6 Sep 2018 09:57:43 -0400 Subject: [PATCH 145/302] more buffer overflow avoiding through using snprintf() --- src/pair_table.cpp | 2 +- src/read_data.cpp | 6 +++--- src/read_restart.cpp | 6 +++--- src/reader.cpp | 4 ++-- src/universe.cpp | 4 ++-- src/variable.cpp | 20 ++++++++++---------- src/write_coeff.cpp | 4 ++-- src/write_data.cpp | 2 +- src/write_restart.cpp | 4 ++-- 9 files changed, 26 insertions(+), 26 deletions(-) diff --git a/src/pair_table.cpp b/src/pair_table.cpp index 5c43761cab..0d692caccb 100644 --- a/src/pair_table.cpp +++ b/src/pair_table.cpp @@ -362,7 +362,7 @@ void PairTable::read_table(Table *tb, char *file, char *keyword) FILE *fp = force->open_potential(file); if (fp == NULL) { char str[128]; - sprintf(str,"Cannot open file %s",file); + snprintf(str,128,"Cannot open file %s",file); error->one(FLERR,str); } diff --git a/src/read_data.cpp b/src/read_data.cpp index 5faa8f9646..26c406c1d6 100644 --- a/src/read_data.cpp +++ b/src/read_data.cpp @@ -706,7 +706,7 @@ void ReadData::command(int narg, char **arg) } else { char str[128]; - sprintf(str,"Unknown identifier in data file: %s",keyword); + snprintf(str,128,"Unknown identifier in data file: %s",keyword); error->all(FLERR,str); } @@ -1919,7 +1919,7 @@ void ReadData::open(char *file) else { #ifdef LAMMPS_GZIP char gunzip[128]; - sprintf(gunzip,"gzip -c -d %s",file); + snprintf(gunzip,128,"gzip -c -d %s",file); #ifdef _WIN32 fp = _popen(gunzip,"rb"); @@ -1934,7 +1934,7 @@ void ReadData::open(char *file) if (fp == NULL) { char str[128]; - sprintf(str,"Cannot open file %s",file); + snprintf(str,128,"Cannot open file %s",file); error->one(FLERR,str); } } diff --git a/src/read_restart.cpp b/src/read_restart.cpp index 7d8e6ca395..9be035e1a1 100644 --- a/src/read_restart.cpp +++ b/src/read_restart.cpp @@ -138,7 +138,7 @@ void ReadRestart::command(int narg, char **arg) fp = fopen(hfile,"rb"); if (fp == NULL) { char str[128]; - sprintf(str,"Cannot open restart file %s",hfile); + snprintf(str,128,"Cannot open restart file %s",hfile); error->one(FLERR,str); } if (multiproc) delete [] hfile; @@ -297,7 +297,7 @@ void ReadRestart::command(int narg, char **arg) fp = fopen(procfile,"rb"); if (fp == NULL) { char str[128]; - sprintf(str,"Cannot open restart file %s",procfile); + snprintf(str,128,"Cannot open restart file %s",procfile); error->one(FLERR,str); } @@ -369,7 +369,7 @@ void ReadRestart::command(int narg, char **arg) fp = fopen(procfile,"rb"); if (fp == NULL) { char str[128]; - sprintf(str,"Cannot open restart file %s",procfile); + snprintf(str,128,"Cannot open restart file %s",procfile); error->one(FLERR,str); } delete [] procfile; diff --git a/src/reader.cpp b/src/reader.cpp index f6e8bd39eb..22a21812e6 100644 --- a/src/reader.cpp +++ b/src/reader.cpp @@ -41,7 +41,7 @@ void Reader::open_file(const char *file) else { #ifdef LAMMPS_GZIP char gunzip[1024]; - sprintf(gunzip,"gzip -c -d %s",file); + snprintf(gunzip,1024,"gzip -c -d %s",file); #ifdef _WIN32 fp = _popen(gunzip,"rb"); @@ -56,7 +56,7 @@ void Reader::open_file(const char *file) if (fp == NULL) { char str[128]; - sprintf(str,"Cannot open file %s",file); + snprintf(str,128,"Cannot open file %s",file); error->one(FLERR,str); } } diff --git a/src/universe.cpp b/src/universe.cpp index 45b4318ec9..410d12dcb3 100644 --- a/src/universe.cpp +++ b/src/universe.cpp @@ -204,7 +204,7 @@ void Universe::add_world(char *str) if (!valid) { char msg[128]; - sprintf(msg,"Invalid partition string '%s'",str); + snprintf(msg,128,"Invalid partition string '%s'",str); error->universe_all(FLERR,msg); } } else nper = nprocs; @@ -269,7 +269,7 @@ char *date2num(const char *version) year = atoi(version); } - char *ver = new char[10]; + char *ver = new char[64]; sprintf(ver,"%04d%02d%02d", year % 10000, month, day % 100); return ver; diff --git a/src/variable.cpp b/src/variable.cpp index 3c54eac1ef..1595456f33 100644 --- a/src/variable.cpp +++ b/src/variable.cpp @@ -528,7 +528,7 @@ void Variable::set(int narg, char **arg) for (int i = 0; i < n-1; i++) if (!isalnum(names[nvar][i]) && names[nvar][i] != '_') { char errmsg[128]; - sprintf(errmsg,"Variable name '%s' must have only alphanumeric " + snprintf(errmsg,128,"Variable name '%s' must have only alphanumeric " "characters or underscore",names[nvar]); error->all(FLERR,errmsg); } @@ -586,7 +586,7 @@ int Variable::next(int narg, char **arg) ivar = find(arg[iarg]); if (ivar < 0) { char errmsg[128]; - sprintf(errmsg,"Invalid variable '%s' in next command",arg[iarg]); + snprintf(errmsg,128,"Invalid variable '%s' in next command",arg[iarg]); error->all(FLERR,errmsg); } if (style[ivar] == ULOOP && style[find(arg[0])] == UNIVERSE) continue; @@ -886,7 +886,7 @@ char *Variable::retrieve(char *name) int ifunc = python->variable_match(data[ivar][0],name,0); if (ifunc < 0) { char errmsg[128]; - sprintf(errmsg,"Python variable '%s' does not match Python function",name); + snprintf(errmsg,128,"Python variable '%s' does not match Python function",name); error->all(FLERR,errmsg); } python->invoke_function(ifunc,data[ivar][1]); @@ -1597,7 +1597,7 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) int ifix = modify->find_fix(word+2); if (ifix < 0) { char msg[128]; - sprintf(msg,"Invalid fix ID '%s' in variable formula",word+2); + snprintf(msg,128,"Invalid fix ID '%s' in variable formula",word+2); print_var_error(FLERR,msg,ivar); } Fix *fix = modify->fix[ifix]; @@ -2032,8 +2032,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) argstack,nargstack,ivar)); else { char msg[128]; - sprintf(msg,"Invalid math/group/special function '%s()'" - "in variable formula", word); + snprintf(msg,128,"Invalid math/group/special function '%s()'" + "in variable formula", word); print_var_error(FLERR,msg,ivar); } delete [] contents; @@ -2092,7 +2092,7 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) int flag = output->thermo->evaluate_keyword(word,&value1); if (flag) { char msg[128]; - sprintf(msg,"Invalid thermo keyword '%s' in variable formula",word); + snprintf(msg,128,"Invalid thermo keyword '%s' in variable formula",word); print_var_error(FLERR,msg,ivar); } if (tree) { @@ -4013,7 +4013,7 @@ int Variable::special_function(char *word, char *contents, Tree **tree, int icompute = modify->find_compute(&args[0][2]); if (icompute < 0) { char msg[128]; - sprintf(msg,"Invalid compute ID '%s' in variable formula",word+2); + snprintf(msg,128,"Invalid compute ID '%s' in variable formula",word+2); print_var_error(FLERR,msg,ivar); } compute = modify->compute[icompute]; @@ -4656,7 +4656,7 @@ void Variable::print_var_error(const char *srcfile, int lineno, if ((ivar >= 0) && (ivar < nvar)) { char msg[128]; - sprintf(msg,"Variable %s: %s",names[ivar],errmsg); + snprintf(msg,128,"Variable %s: %s",names[ivar],errmsg); error->all(srcfile,lineno,msg); } else error->all(srcfile,lineno,errmsg); } @@ -4944,7 +4944,7 @@ VarReader::VarReader(LAMMPS *lmp, char *name, char *file, int flag) : fp = fopen(file,"r"); if (fp == NULL) { char str[128]; - sprintf(str,"Cannot open file variable file %s",file); + snprintf(str,128,"Cannot open file variable file %s",file); error->one(FLERR,str); } } diff --git a/src/write_coeff.cpp b/src/write_coeff.cpp index 5f82a480fd..99172c09f0 100644 --- a/src/write_coeff.cpp +++ b/src/write_coeff.cpp @@ -51,7 +51,7 @@ void WriteCoeff::command(int narg, char **arg) char str[256], coeff[256]; FILE *one = fopen(file,"wb+"); if (one == NULL) { - sprintf(str,"Cannot open coeff file %s",file); + snprintf(str,256,"Cannot open coeff file %s",file); error->one(FLERR,str); } @@ -86,7 +86,7 @@ void WriteCoeff::command(int narg, char **arg) FILE *two = fopen(file+4,"w"); if (two == NULL) { - sprintf(str,"Cannot open coeff file %s",file+4); + snprintf(str,256,"Cannot open coeff file %s",file+4); error->one(FLERR,str); } fprintf(two,"# LAMMPS coeff file via write_coeff, version %s\n", diff --git a/src/write_data.cpp b/src/write_data.cpp index 96bf081157..f18e30de52 100644 --- a/src/write_data.cpp +++ b/src/write_data.cpp @@ -183,7 +183,7 @@ void WriteData::write(char *file) fp = fopen(file,"w"); if (fp == NULL) { char str[128]; - sprintf(str,"Cannot open data file %s",file); + snprintf(str,128,"Cannot open data file %s",file); error->one(FLERR,str); } } diff --git a/src/write_restart.cpp b/src/write_restart.cpp index 1bfbb382a8..edb6dfa7e8 100644 --- a/src/write_restart.cpp +++ b/src/write_restart.cpp @@ -269,7 +269,7 @@ void WriteRestart::write(char *file) fp = fopen(hfile,"wb"); if (fp == NULL) { char str[128]; - sprintf(str,"Cannot open restart file %s",hfile); + snprintf(str,128,"Cannot open restart file %s",hfile); error->one(FLERR,str); } if (multiproc) delete [] hfile; @@ -334,7 +334,7 @@ void WriteRestart::write(char *file) fp = fopen(multiname,"wb"); if (fp == NULL) { char str[128]; - sprintf(str,"Cannot open restart file %s",multiname); + snprintf(str,128,"Cannot open restart file %s",multiname); error->one(FLERR,str); } write_int(PROCSPERFILE,nclusterprocs); From 9c27548a5c4dd6e7126c0fb76b3a366a9f0bef6a Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 6 Sep 2018 10:45:48 -0400 Subject: [PATCH 146/302] more replacing of sprintf() with snprintf() --- src/GPU/pair_eam_alloy_gpu.cpp | 2 +- src/GPU/pair_eam_fs_gpu.cpp | 2 +- src/GRANULAR/fix_wall_gran_region.cpp | 8 +- src/KOKKOS/pair_eam_alloy_kokkos.cpp | 2 +- src/KOKKOS/pair_eam_fs_kokkos.cpp | 2 +- src/KOKKOS/pair_exp6_rx_kokkos.cpp | 2 +- src/MANYBODY/fix_qeq_comb.cpp | 2 +- src/MANYBODY/pair_adp.cpp | 2 +- src/MANYBODY/pair_airebo.cpp | 4 +- src/MANYBODY/pair_bop.cpp | 4 +- src/MANYBODY/pair_comb.cpp | 2 +- src/MANYBODY/pair_comb3.cpp | 8 +- src/MANYBODY/pair_eam.cpp | 2 +- src/MANYBODY/pair_eam_alloy.cpp | 2 +- src/MANYBODY/pair_eam_cd.cpp | 2 +- src/MANYBODY/pair_eam_fs.cpp | 2 +- src/MANYBODY/pair_eim.cpp | 2 +- src/MANYBODY/pair_gw.cpp | 2 +- src/MANYBODY/pair_gw_zbl.cpp | 2 +- src/MANYBODY/pair_lcbop.cpp | 2 +- src/MANYBODY/pair_nb3b_harmonic.cpp | 2 +- src/MANYBODY/pair_polymorphic.cpp | 2 +- src/MANYBODY/pair_sw.cpp | 2 +- src/MANYBODY/pair_tersoff.cpp | 2 +- src/MANYBODY/pair_tersoff_mod.cpp | 2 +- src/MANYBODY/pair_tersoff_mod_c.cpp | 2 +- src/MANYBODY/pair_tersoff_zbl.cpp | 2 +- src/MANYBODY/pair_vashishta.cpp | 2 +- src/MEAM/pair_meam.cpp | 8 +- src/MISC/fix_ttm.cpp | 4 +- src/MOLECULE/angle_table.cpp | 2 +- src/MOLECULE/bond_table.cpp | 2 +- src/MOLECULE/fix_cmap.cpp | 4 +- src/POEMS/fix_poems.cpp | 4 +- src/QEQ/fix_qeq.cpp | 2 +- src/REAX/fix_reax_bonds.cpp | 11 +- src/REPLICA/neb.cpp | 4 +- src/REPLICA/tad.cpp | 5 +- src/RIGID/fix_rigid.cpp | 8 +- src/RIGID/fix_rigid_small.cpp | 8 +- src/SNAP/pair_snap.cpp | 4 +- src/USER-BOCS/fix_bocs.cpp | 39 +++---- src/USER-DIFFRACTION/fix_saed_vtk.cpp | 10 +- src/USER-DPD/fix_eos_table.cpp | 2 +- src/USER-DPD/fix_eos_table_rx.cpp | 4 +- src/USER-DPD/fix_rx.cpp | 4 +- src/USER-DPD/pair_exp6_rx.cpp | 4 +- src/USER-DPD/pair_multi_lucy.cpp | 2 +- src/USER-DPD/pair_multi_lucy_rx.cpp | 2 +- src/USER-INTEL/pair_eam_alloy_intel.cpp | 2 +- src/USER-INTEL/pair_eam_fs_intel.cpp | 2 +- src/USER-MEAMC/pair_meamc.cpp | 8 +- src/USER-MISC/fix_ave_correlate_long.cpp | 2 +- src/USER-MISC/fix_bond_react.cpp | 2 +- src/USER-MISC/fix_gle.cpp | 4 +- src/USER-MISC/fix_ttm_mod.cpp | 6 +- src/USER-MISC/pair_agni.cpp | 2 +- src/USER-MISC/pair_edip.cpp | 2 +- src/USER-MISC/pair_edip_multi.cpp | 2 +- src/USER-MISC/pair_extep.cpp | 2 +- src/USER-MISC/pair_ilp_graphene_hbn.cpp | 2 +- src/USER-MISC/pair_kolmogorov_crespi_full.cpp | 2 +- src/USER-MISC/pair_kolmogorov_crespi_z.cpp | 2 +- src/USER-MISC/pair_meam_spline.cpp | 2 +- src/USER-MISC/pair_meam_sw_spline.cpp | 100 +++++++++--------- src/USER-MISC/pair_tersoff_table.cpp | 2 +- src/USER-MOLFILE/reader_molfile.cpp | 4 +- 67 files changed, 168 insertions(+), 185 deletions(-) diff --git a/src/GPU/pair_eam_alloy_gpu.cpp b/src/GPU/pair_eam_alloy_gpu.cpp index 3a8e440bdc..11af562f15 100644 --- a/src/GPU/pair_eam_alloy_gpu.cpp +++ b/src/GPU/pair_eam_alloy_gpu.cpp @@ -364,7 +364,7 @@ void PairEAMAlloyGPU::read_file(char *filename) fptr = fopen(filename,"r"); if (fptr == NULL) { char str[128]; - sprintf(str,"Cannot open EAM potential file %s",filename); + snprintf(str,128,"Cannot open EAM potential file %s",filename); error->one(FLERR,str); } } diff --git a/src/GPU/pair_eam_fs_gpu.cpp b/src/GPU/pair_eam_fs_gpu.cpp index 51681d563b..ef8dd09e23 100644 --- a/src/GPU/pair_eam_fs_gpu.cpp +++ b/src/GPU/pair_eam_fs_gpu.cpp @@ -364,7 +364,7 @@ void PairEAMFSGPU::read_file(char *filename) fptr = force->open_potential(filename); if (fptr == NULL) { char str[128]; - sprintf(str,"Cannot open EAM potential file %s",filename); + snprintf(str,128,"Cannot open EAM potential file %s",filename); error->one(FLERR,str); } } diff --git a/src/GRANULAR/fix_wall_gran_region.cpp b/src/GRANULAR/fix_wall_gran_region.cpp index 4a6be5f3c9..8633587ad5 100644 --- a/src/GRANULAR/fix_wall_gran_region.cpp +++ b/src/GRANULAR/fix_wall_gran_region.cpp @@ -113,16 +113,16 @@ void FixWallGranRegion::init() strcmp(region_style,region->style) != 0 || nregion != region->nregion) { char str[256]; - sprintf(str,"Region properties for region %s changed between runs, " - "resetting its motion",idregion); + snprintf(str,256,"Region properties for region %s changed between runs, " + "resetting its motion",idregion); error->warning(FLERR,str); region->reset_vel(); } if (motion_resetflag){ char str[256]; - sprintf(str,"Region properties for region %s are inconsistent " - "with restart file, resetting its motion",idregion); + snprintf(str,256,"Region properties for region %s are inconsistent " + "with restart file, resetting its motion",idregion); error->warning(FLERR,str); region->reset_vel(); } diff --git a/src/KOKKOS/pair_eam_alloy_kokkos.cpp b/src/KOKKOS/pair_eam_alloy_kokkos.cpp index fc19da1c8a..49e1313c26 100644 --- a/src/KOKKOS/pair_eam_alloy_kokkos.cpp +++ b/src/KOKKOS/pair_eam_alloy_kokkos.cpp @@ -992,7 +992,7 @@ void PairEAMAlloyKokkos::read_file(char *filename) fptr = force->open_potential(filename); if (fptr == NULL) { char str[128]; - sprintf(str,"Cannot open EAM potential file %s",filename); + snprintf(str,128,"Cannot open EAM potential file %s",filename); error->one(FLERR,str); } } diff --git a/src/KOKKOS/pair_eam_fs_kokkos.cpp b/src/KOKKOS/pair_eam_fs_kokkos.cpp index 8f5571bf29..ee0a799826 100644 --- a/src/KOKKOS/pair_eam_fs_kokkos.cpp +++ b/src/KOKKOS/pair_eam_fs_kokkos.cpp @@ -992,7 +992,7 @@ void PairEAMFSKokkos::read_file(char *filename) fptr = force->open_potential(filename); if (fptr == NULL) { char str[128]; - sprintf(str,"Cannot open EAM potential file %s",filename); + snprintf(str,128,"Cannot open EAM potential file %s",filename); error->one(FLERR,str); } } diff --git a/src/KOKKOS/pair_exp6_rx_kokkos.cpp b/src/KOKKOS/pair_exp6_rx_kokkos.cpp index 810173d219..f38feea5f4 100644 --- a/src/KOKKOS/pair_exp6_rx_kokkos.cpp +++ b/src/KOKKOS/pair_exp6_rx_kokkos.cpp @@ -1725,7 +1725,7 @@ void PairExp6rxKokkos::read_file(char *file) fp = force->open_potential(file); if (fp == NULL) { char str[128]; - sprintf(str,"Cannot open exp6/rx potential file %s",file); + snprintf(str,128,"Cannot open exp6/rx potential file %s",file); error->one(FLERR,str); } } diff --git a/src/MANYBODY/fix_qeq_comb.cpp b/src/MANYBODY/fix_qeq_comb.cpp index e46da9bfe7..7146ee9d65 100644 --- a/src/MANYBODY/fix_qeq_comb.cpp +++ b/src/MANYBODY/fix_qeq_comb.cpp @@ -67,7 +67,7 @@ FixQEQComb::FixQEQComb(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg), fp = fopen(arg[iarg+1],"w"); if (fp == NULL) { char str[128]; - sprintf(str,"Cannot open fix qeq/comb file %s",arg[iarg+1]); + snprintf(str,128,"Cannot open fix qeq/comb file %s",arg[iarg+1]); error->one(FLERR,str); } } diff --git a/src/MANYBODY/pair_adp.cpp b/src/MANYBODY/pair_adp.cpp index 831f1d0efa..7b48522e84 100644 --- a/src/MANYBODY/pair_adp.cpp +++ b/src/MANYBODY/pair_adp.cpp @@ -551,7 +551,7 @@ void PairADP::read_file(char *filename) fp = force->open_potential(filename); if (fp == NULL) { char str[128]; - sprintf(str,"Cannot open ADP potential file %s",filename); + snprintf(str,128,"Cannot open ADP potential file %s",filename); error->one(FLERR,str); } } diff --git a/src/MANYBODY/pair_airebo.cpp b/src/MANYBODY/pair_airebo.cpp index ac3ed36a83..067eb1634f 100644 --- a/src/MANYBODY/pair_airebo.cpp +++ b/src/MANYBODY/pair_airebo.cpp @@ -3373,9 +3373,9 @@ void PairAIREBO::read_file(char *filename) if (fp == NULL) { char str[128]; if (morseflag) - sprintf(str,"Cannot open AIREBO-M potential file %s",filename); + snprintf(str,128,"Cannot open AIREBO-M potential file %s",filename); else - sprintf(str,"Cannot open AIREBO potential file %s",filename); + snprintf(str,128,"Cannot open AIREBO potential file %s",filename); error->one(FLERR,str); } diff --git a/src/MANYBODY/pair_bop.cpp b/src/MANYBODY/pair_bop.cpp index 87a23dff99..ca0f229068 100644 --- a/src/MANYBODY/pair_bop.cpp +++ b/src/MANYBODY/pair_bop.cpp @@ -4976,7 +4976,7 @@ void PairBOP::read_table(char *filename) FILE *fp = force->open_potential(filename); if (fp == NULL) { char str[128]; - sprintf(str,"Cannot open BOP potential file %s",filename); + snprintf(str,128,"Cannot open BOP potential file %s",filename); error->one(FLERR,str); } fgets(s,MAXLINE,fp); // skip first comment line @@ -5079,7 +5079,7 @@ void PairBOP::read_table(char *filename) FILE *fp = force->open_potential(filename); if (fp == NULL) { char str[128]; - sprintf(str,"Cannot open BOP potential file %s",filename); + snprintf(str,128,"Cannot open BOP potential file %s",filename); error->one(FLERR,str); } fgets(s,MAXLINE,fp); // skip first comment line diff --git a/src/MANYBODY/pair_comb.cpp b/src/MANYBODY/pair_comb.cpp index e7b0d27b6e..85ea4812bf 100644 --- a/src/MANYBODY/pair_comb.cpp +++ b/src/MANYBODY/pair_comb.cpp @@ -597,7 +597,7 @@ void PairComb::read_file(char *file) fp = force->open_potential(file); if (fp == NULL) { char str[128]; - sprintf(str,"Cannot open COMB potential file %s",file); + snprintf(str,128,"Cannot open COMB potential file %s",file); error->one(FLERR,str); } } diff --git a/src/MANYBODY/pair_comb3.cpp b/src/MANYBODY/pair_comb3.cpp index 72360be5f0..106b83eeba 100644 --- a/src/MANYBODY/pair_comb3.cpp +++ b/src/MANYBODY/pair_comb3.cpp @@ -320,11 +320,7 @@ void PairComb3::read_lib() if (comm->me == 0) { FILE *fp = force->open_potential("lib.comb3"); - if (fp == NULL) { - char str[128]; - sprintf(str,"Cannot open COMB3 lib.comb3 file"); - error->one(FLERR,str); - } + if (fp == NULL) error->one(FLERR,"Cannot open COMB3 lib.comb3 file"); // read and store at the same time fgets(s,MAXLIB,fp); @@ -607,7 +603,7 @@ void PairComb3::read_file(char *file) fp = force->open_potential(file); if (fp == NULL) { char str[128]; - sprintf(str,"Cannot open COMB3 potential file %s",file); + snprintf(str,128,"Cannot open COMB3 potential file %s",file); error->one(FLERR,str); } } diff --git a/src/MANYBODY/pair_eam.cpp b/src/MANYBODY/pair_eam.cpp index 87bcebb111..f4b4901075 100644 --- a/src/MANYBODY/pair_eam.cpp +++ b/src/MANYBODY/pair_eam.cpp @@ -460,7 +460,7 @@ void PairEAM::read_file(char *filename) fptr = force->open_potential(filename); if (fptr == NULL) { char str[128]; - sprintf(str,"Cannot open EAM potential file %s",filename); + snprintf(str,128,"Cannot open EAM potential file %s",filename); error->one(FLERR,str); } } diff --git a/src/MANYBODY/pair_eam_alloy.cpp b/src/MANYBODY/pair_eam_alloy.cpp index eed38f79e9..c004030240 100644 --- a/src/MANYBODY/pair_eam_alloy.cpp +++ b/src/MANYBODY/pair_eam_alloy.cpp @@ -127,7 +127,7 @@ void PairEAMAlloy::read_file(char *filename) fptr = force->open_potential(filename); if (fptr == NULL) { char str[128]; - sprintf(str,"Cannot open EAM potential file %s",filename); + snprintf(str,128,"Cannot open EAM potential file %s",filename); error->one(FLERR,str); } } diff --git a/src/MANYBODY/pair_eam_cd.cpp b/src/MANYBODY/pair_eam_cd.cpp index 5b8b241b45..8db1b6dd9a 100644 --- a/src/MANYBODY/pair_eam_cd.cpp +++ b/src/MANYBODY/pair_eam_cd.cpp @@ -504,7 +504,7 @@ void PairEAMCD::read_h_coeff(char *filename) fptr = force->open_potential(filename); if (fptr == NULL) { char str[128]; - sprintf(str,"Cannot open EAM potential file %s", filename); + snprintf(str,128,"Cannot open EAM potential file %s", filename); error->one(FLERR,str); } diff --git a/src/MANYBODY/pair_eam_fs.cpp b/src/MANYBODY/pair_eam_fs.cpp index 2b5d530d3a..bbda84fdf1 100644 --- a/src/MANYBODY/pair_eam_fs.cpp +++ b/src/MANYBODY/pair_eam_fs.cpp @@ -127,7 +127,7 @@ void PairEAMFS::read_file(char *filename) fptr = force->open_potential(filename); if (fptr == NULL) { char str[128]; - sprintf(str,"Cannot open EAM potential file %s",filename); + snprintf(str,128,"Cannot open EAM potential file %s",filename); error->one(FLERR,str); } } diff --git a/src/MANYBODY/pair_eim.cpp b/src/MANYBODY/pair_eim.cpp index 6703e159e6..b0fa1b1eef 100644 --- a/src/MANYBODY/pair_eim.cpp +++ b/src/MANYBODY/pair_eim.cpp @@ -461,7 +461,7 @@ void PairEIM::read_file(char *filename) fptr = force->open_potential(filename); if (fptr == NULL) { char str[128]; - sprintf(str,"Cannot open EIM potential file %s",filename); + snprintf(str,128,"Cannot open EIM potential file %s",filename); error->one(FLERR,str); } } diff --git a/src/MANYBODY/pair_gw.cpp b/src/MANYBODY/pair_gw.cpp index 0aff4970bb..f2d3b67eb0 100644 --- a/src/MANYBODY/pair_gw.cpp +++ b/src/MANYBODY/pair_gw.cpp @@ -381,7 +381,7 @@ void PairGW::read_file(char *file) fp = force->open_potential(file); if (fp == NULL) { char str[128]; - sprintf(str,"Cannot open GW potential file %s",file); + snprintf(str,128,"Cannot open GW potential file %s",file); error->one(FLERR,str); } } diff --git a/src/MANYBODY/pair_gw_zbl.cpp b/src/MANYBODY/pair_gw_zbl.cpp index 81d4866e84..f3dd1bc04b 100644 --- a/src/MANYBODY/pair_gw_zbl.cpp +++ b/src/MANYBODY/pair_gw_zbl.cpp @@ -77,7 +77,7 @@ void PairGWZBL::read_file(char *file) fp = force->open_potential(file); if (fp == NULL) { char str[128]; - sprintf(str,"Cannot open GW potential file %s",file); + snprintf(str,128,"Cannot open GW potential file %s",file); error->one(FLERR,str); } } diff --git a/src/MANYBODY/pair_lcbop.cpp b/src/MANYBODY/pair_lcbop.cpp index 57373c4f85..88477e48f3 100644 --- a/src/MANYBODY/pair_lcbop.cpp +++ b/src/MANYBODY/pair_lcbop.cpp @@ -978,7 +978,7 @@ void PairLCBOP::read_file(char *filename) FILE *fp = force->open_potential(filename); if (fp == NULL) { char str[128]; - sprintf(str,"Cannot open LCBOP potential file %s",filename); + snprintf(str,128,"Cannot open LCBOP potential file %s",filename); error->one(FLERR,str); } diff --git a/src/MANYBODY/pair_nb3b_harmonic.cpp b/src/MANYBODY/pair_nb3b_harmonic.cpp index 01718d14cd..ce449e4890 100644 --- a/src/MANYBODY/pair_nb3b_harmonic.cpp +++ b/src/MANYBODY/pair_nb3b_harmonic.cpp @@ -299,7 +299,7 @@ void PairNb3bHarmonic::read_file(char *file) fp = force->open_potential(file); if (fp == NULL) { char str[128]; - sprintf(str,"Cannot open nb3b/harmonic potential file %s",file); + snprintf(str,128,"Cannot open nb3b/harmonic potential file %s",file); error->one(FLERR,str); } } diff --git a/src/MANYBODY/pair_polymorphic.cpp b/src/MANYBODY/pair_polymorphic.cpp index ce9af66d30..41c5892d4e 100644 --- a/src/MANYBODY/pair_polymorphic.cpp +++ b/src/MANYBODY/pair_polymorphic.cpp @@ -573,7 +573,7 @@ void PairPolymorphic::read_file(char *file) fp = force->open_potential(file); if (fp == NULL) { char str[128]; - sprintf(str,"Cannot open polymorphic potential file %s",file); + snprintf(str,128,"Cannot open polymorphic potential file %s",file); error->one(FLERR,str); } // move past comments to first data line diff --git a/src/MANYBODY/pair_sw.cpp b/src/MANYBODY/pair_sw.cpp index da470d568a..91e11b3d26 100644 --- a/src/MANYBODY/pair_sw.cpp +++ b/src/MANYBODY/pair_sw.cpp @@ -363,7 +363,7 @@ void PairSW::read_file(char *file) fp = force->open_potential(file); if (fp == NULL) { char str[128]; - sprintf(str,"Cannot open Stillinger-Weber potential file %s",file); + snprintf(str,128,"Cannot open Stillinger-Weber potential file %s",file); error->one(FLERR,str); } } diff --git a/src/MANYBODY/pair_tersoff.cpp b/src/MANYBODY/pair_tersoff.cpp index 45068e5c2e..54101aef9e 100644 --- a/src/MANYBODY/pair_tersoff.cpp +++ b/src/MANYBODY/pair_tersoff.cpp @@ -404,7 +404,7 @@ void PairTersoff::read_file(char *file) fp = force->open_potential(file); if (fp == NULL) { char str[128]; - sprintf(str,"Cannot open Tersoff potential file %s",file); + snprintf(str,128,"Cannot open Tersoff potential file %s",file); error->one(FLERR,str); } } diff --git a/src/MANYBODY/pair_tersoff_mod.cpp b/src/MANYBODY/pair_tersoff_mod.cpp index 73297fb534..e8fdecfe01 100644 --- a/src/MANYBODY/pair_tersoff_mod.cpp +++ b/src/MANYBODY/pair_tersoff_mod.cpp @@ -60,7 +60,7 @@ void PairTersoffMOD::read_file(char *file) fp = force->open_potential(file); if (fp == NULL) { char str[128]; - sprintf(str,"Cannot open Tersoff potential file %s",file); + snprintf(str,128,"Cannot open Tersoff potential file %s",file); error->one(FLERR,str); } } diff --git a/src/MANYBODY/pair_tersoff_mod_c.cpp b/src/MANYBODY/pair_tersoff_mod_c.cpp index 0d0016664a..4a5904c106 100644 --- a/src/MANYBODY/pair_tersoff_mod_c.cpp +++ b/src/MANYBODY/pair_tersoff_mod_c.cpp @@ -55,7 +55,7 @@ void PairTersoffMODC::read_file(char *file) fp = force->open_potential(file); if (fp == NULL) { char str[128]; - sprintf(str,"Cannot open Tersoff potential file %s",file); + snprintf(str,128,"Cannot open Tersoff potential file %s",file); error->one(FLERR,str); } } diff --git a/src/MANYBODY/pair_tersoff_zbl.cpp b/src/MANYBODY/pair_tersoff_zbl.cpp index 1692c88a50..353e3d2264 100644 --- a/src/MANYBODY/pair_tersoff_zbl.cpp +++ b/src/MANYBODY/pair_tersoff_zbl.cpp @@ -77,7 +77,7 @@ void PairTersoffZBL::read_file(char *file) fp = force->open_potential(file); if (fp == NULL) { char str[128]; - sprintf(str,"Cannot open Tersoff potential file %s",file); + snprintf(str,128,"Cannot open Tersoff potential file %s",file); error->one(FLERR,str); } } diff --git a/src/MANYBODY/pair_vashishta.cpp b/src/MANYBODY/pair_vashishta.cpp index 54b184ea39..b4c3086ca8 100644 --- a/src/MANYBODY/pair_vashishta.cpp +++ b/src/MANYBODY/pair_vashishta.cpp @@ -369,7 +369,7 @@ void PairVashishta::read_file(char *file) fp = force->open_potential(file); if (fp == NULL) { char str[128]; - sprintf(str,"Cannot open Vashishta potential file %s",file); + snprintf(str,128,"Cannot open Vashishta potential file %s",file); error->one(FLERR,str); } } diff --git a/src/MEAM/pair_meam.cpp b/src/MEAM/pair_meam.cpp index 5aa13ab02e..b8f5291338 100644 --- a/src/MEAM/pair_meam.cpp +++ b/src/MEAM/pair_meam.cpp @@ -464,7 +464,7 @@ void PairMEAM::read_files(char *globalfile, char *userfile) fp = force->open_potential(globalfile); if (fp == NULL) { char str[128]; - sprintf(str,"Cannot open MEAM potential file %s",globalfile); + snprintf(str,128,"Cannot open MEAM potential file %s",globalfile); error->one(FLERR,str); } } @@ -645,7 +645,7 @@ void PairMEAM::read_files(char *globalfile, char *userfile) fp = force->open_potential(userfile); if (fp == NULL) { char str[128]; - sprintf(str,"Cannot open MEAM potential file %s",userfile); + snprintf(str,128,"Cannot open MEAM potential file %s",userfile); error->one(FLERR,str); } } @@ -694,8 +694,8 @@ void PairMEAM::read_files(char *globalfile, char *userfile) if (strcmp(params[0],keywords[which]) == 0) break; if (which == nkeywords) { char str[128]; - sprintf(str,"Keyword %s in MEAM parameter file not recognized", - params[0]); + snprintf(str,128,"Keyword %s in MEAM parameter file not recognized", + params[0]); error->all(FLERR,str); } nindex = nparams - 2; diff --git a/src/MISC/fix_ttm.cpp b/src/MISC/fix_ttm.cpp index c8f33c73b7..4e15581377 100644 --- a/src/MISC/fix_ttm.cpp +++ b/src/MISC/fix_ttm.cpp @@ -71,7 +71,7 @@ FixTTM::FixTTM(LAMMPS *lmp, int narg, char **arg) : fpr = fopen(arg[13],"r"); if (fpr == NULL) { char str[128]; - sprintf(str,"Cannot open file %s",arg[13]); + snprintf(str,128,"Cannot open file %s",arg[13]); error->one(FLERR,str); } @@ -84,7 +84,7 @@ FixTTM::FixTTM(LAMMPS *lmp, int narg, char **arg) : fp = fopen(arg[15],"w"); if (fp == NULL) { char str[128]; - sprintf(str,"Cannot open fix ttm file %s",arg[15]); + snprintf(str,128,"Cannot open fix ttm file %s",arg[15]); error->one(FLERR,str); } } diff --git a/src/MOLECULE/angle_table.cpp b/src/MOLECULE/angle_table.cpp index 235e9b4d5b..2867865497 100644 --- a/src/MOLECULE/angle_table.cpp +++ b/src/MOLECULE/angle_table.cpp @@ -369,7 +369,7 @@ void AngleTable::read_table(Table *tb, char *file, char *keyword) FILE *fp = force->open_potential(file); if (fp == NULL) { char str[128]; - sprintf(str,"Cannot open file %s",file); + snprintf(str,128,"Cannot open file %s",file); error->one(FLERR,str); } diff --git a/src/MOLECULE/bond_table.cpp b/src/MOLECULE/bond_table.cpp index a5c579042b..392904149d 100644 --- a/src/MOLECULE/bond_table.cpp +++ b/src/MOLECULE/bond_table.cpp @@ -298,7 +298,7 @@ void BondTable::read_table(Table *tb, char *file, char *keyword) FILE *fp = force->open_potential(file); if (fp == NULL) { char str[128]; - sprintf(str,"Cannot open file %s",file); + snprintf(str,128,"Cannot open file %s",file); error->one(FLERR,str); } diff --git a/src/MOLECULE/fix_cmap.cpp b/src/MOLECULE/fix_cmap.cpp index b527eef020..a889a8d0db 100644 --- a/src/MOLECULE/fix_cmap.cpp +++ b/src/MOLECULE/fix_cmap.cpp @@ -644,7 +644,7 @@ void FixCMAP::read_grid_map(char *cmapfile) fp = force->open_potential(cmapfile); if (fp == NULL) { char str[128]; - sprintf(str,"Cannot open fix cmap file %s",cmapfile); + snprintf(str,128,"Cannot open fix cmap file %s",cmapfile); error->one(FLERR,str); } } @@ -1076,7 +1076,7 @@ void FixCMAP::read_data_section(char *keyword, int n, char *buf, if (nwords != 7) { char str[128]; - sprintf(str,"Incorrect %s format in data file",keyword); + snprintf(str,128,"Incorrect %s format in data file",keyword); error->all(FLERR,str); } diff --git a/src/POEMS/fix_poems.cpp b/src/POEMS/fix_poems.cpp index 2c2fefb250..f345d52aab 100644 --- a/src/POEMS/fix_poems.cpp +++ b/src/POEMS/fix_poems.cpp @@ -369,7 +369,7 @@ void FixPOEMS::init() if (pflag && (modify->fmask[i] & POST_FORCE) && !modify->fix[i]->rigid_flag) { char str[128]; - sprintf(str,"Fix %s alters forces after fix poems",modify->fix[i]->id); + snprintf(str,128,"Fix %s alters forces after fix poems",modify->fix[i]->id); error->warning(FLERR,str); } } @@ -961,7 +961,7 @@ void FixPOEMS::readfile(char *file) fp = fopen(file,"r"); if (fp == NULL) { char str[128]; - sprintf(str,"Cannot open fix poems file %s",file); + snprintf(str,128,"Cannot open fix poems file %s",file); error->one(FLERR,str); } } diff --git a/src/QEQ/fix_qeq.cpp b/src/QEQ/fix_qeq.cpp index 0fe041209f..49e0a6d423 100644 --- a/src/QEQ/fix_qeq.cpp +++ b/src/QEQ/fix_qeq.cpp @@ -715,7 +715,7 @@ void FixQEq::read_file(char *file) fp = force->open_potential(file); if (fp == NULL) { char str[128]; - sprintf(str,"Cannot open fix qeq parameter file %s",file); + snprintf(str,128,"Cannot open fix qeq parameter file %s",file); error->one(FLERR,str); } } diff --git a/src/REAX/fix_reax_bonds.cpp b/src/REAX/fix_reax_bonds.cpp index 84e4a66e6c..5273cd1faa 100644 --- a/src/REAX/fix_reax_bonds.cpp +++ b/src/REAX/fix_reax_bonds.cpp @@ -53,7 +53,7 @@ FixReaxBonds::FixReaxBonds(LAMMPS *lmp, int narg, char **arg) : if (suffix && strcmp(suffix,".gz") == 0) { #ifdef LAMMPS_GZIP char gzip[128]; - sprintf(gzip,"gzip -6 > %s",arg[4]); + snprintf(gzip128,,"gzip -6 > %s",arg[4]); #ifdef _WIN32 fp = _popen(gzip,"wb"); #else @@ -66,7 +66,7 @@ FixReaxBonds::FixReaxBonds(LAMMPS *lmp, int narg, char **arg) : if (fp == NULL) { char str[128]; - sprintf(str,"Cannot open fix reax/bonds file %s",arg[4]); + snprintf(str,128,"Cannot open fix reax/bonds file %s",arg[4]); error->one(FLERR,str); } } @@ -222,11 +222,8 @@ void FixReaxBonds::OutputReaxBonds(bigint ntimestep, FILE *fp) numbonds = nint(buf[j+2]); fprintf(fp," %d %d %d",nint(buf[j]),nint(buf[j+1]),numbonds); j += 3; - if (numbonds > nsbmax_most) { - char str[128]; - sprintf(str,"Fix reax/bonds numbonds > nsbmax_most"); - error->one(FLERR,str); - } + if (numbonds > nsbmax_most) + error->one(FLERR,"Fix reax/bonds numbonds > nsbmax_most"); // print connection table diff --git a/src/REPLICA/neb.cpp b/src/REPLICA/neb.cpp index c9aedf7401..9a4de9ca0b 100644 --- a/src/REPLICA/neb.cpp +++ b/src/REPLICA/neb.cpp @@ -549,7 +549,7 @@ void NEB::open(char *file) else { #ifdef LAMMPS_GZIP char gunzip[128]; - sprintf(gunzip,"gzip -c -d %s",file); + snprintf(gunz128,ip,"gzip -c -d %s",file); #ifdef _WIN32 fp = _popen(gunzip,"rb"); @@ -564,7 +564,7 @@ void NEB::open(char *file) if (fp == NULL) { char str[128]; - sprintf(str,"Cannot open file %s",file); + snprintf(str,128,"Cannot open file %s",file); error->one(FLERR,str); } } diff --git a/src/REPLICA/tad.cpp b/src/REPLICA/tad.cpp index 46073952fc..da42ba6fae 100644 --- a/src/REPLICA/tad.cpp +++ b/src/REPLICA/tad.cpp @@ -712,10 +712,7 @@ void TAD::perform_neb(int ievent) args[0] = (char *) "neb"; args[1] = (char *) "all"; args[2] = (char *) "neb"; - char str[128]; - args[3] = str; - double kspring = 1.0; - sprintf(args[3],"%f",kspring); + args[3] = (char *) "1.0"; modify->add_fix(narg2,args); fix_neb = (Fix *) modify->fix[modify->nfix-1]; delete [] args; diff --git a/src/RIGID/fix_rigid.cpp b/src/RIGID/fix_rigid.cpp index c15a909ada..39c49ca1c4 100644 --- a/src/RIGID/fix_rigid.cpp +++ b/src/RIGID/fix_rigid.cpp @@ -730,7 +730,7 @@ void FixRigid::init() if (rflag && (modify->fmask[i] & POST_FORCE) && !modify->fix[i]->rigid_flag) { char str[128]; - sprintf(str,"Fix %s alters forces after fix rigid",modify->fix[i]->id); + snprintf(str,128,"Fix %s alters forces after fix rigid",modify->fix[i]->id); error->warning(FLERR,str); } } @@ -2271,7 +2271,7 @@ void FixRigid::readfile(int which, double *vec, fp = fopen(infile,"r"); if (fp == NULL) { char str[128]; - sprintf(str,"Cannot open fix rigid infile %s",infile); + snprintf(str,128,"Cannot open fix rigid infile %s",infile); error->one(FLERR,str); } @@ -2380,11 +2380,11 @@ void FixRigid::write_restart_file(char *file) if (me) return; char outfile[128]; - sprintf(outfile,"%s.rigid",file); + snprintf(outfile,128,"%s.rigid",file); FILE *fp = fopen(outfile,"w"); if (fp == NULL) { char str[192]; - sprintf(str,"Cannot open fix rigid restart file %s",outfile); + snprintf(str,192,"Cannot open fix rigid restart file %s",outfile); error->one(FLERR,str); } diff --git a/src/RIGID/fix_rigid_small.cpp b/src/RIGID/fix_rigid_small.cpp index d5d3d36083..44e1870e0a 100644 --- a/src/RIGID/fix_rigid_small.cpp +++ b/src/RIGID/fix_rigid_small.cpp @@ -569,7 +569,7 @@ void FixRigidSmall::init() if (rflag && (modify->fmask[i] & POST_FORCE) && !modify->fix[i]->rigid_flag) { char str[128]; - sprintf(str,"Fix %s alters forces after fix rigid",modify->fix[i]->id); + snprintf(str,128,"Fix %s alters forces after fix rigid",modify->fix[i]->id); error->warning(FLERR,str); } } @@ -2482,7 +2482,7 @@ void FixRigidSmall::readfile(int which, double **array, int *inbody) fp = fopen(infile,"r"); if (fp == NULL) { char str[128]; - sprintf(str,"Cannot open fix rigid/small infile %s",infile); + snprintf(str,128,"Cannot open fix rigid/small infile %s",infile); error->one(FLERR,str); } @@ -2597,11 +2597,11 @@ void FixRigidSmall::write_restart_file(char *file) if (me == 0) { char outfile[128]; - sprintf(outfile,"%s.rigid",file); + snprintf(outfile,128,"%s.rigid",file); fp = fopen(outfile,"w"); if (fp == NULL) { char str[128]; - sprintf(str,"Cannot open fix rigid restart file %s",outfile); + snprintf(str,128,"Cannot open fix rigid restart file %s",outfile); error->one(FLERR,str); } diff --git a/src/SNAP/pair_snap.cpp b/src/SNAP/pair_snap.cpp index eaefb0325d..9f4c6bf5e2 100644 --- a/src/SNAP/pair_snap.cpp +++ b/src/SNAP/pair_snap.cpp @@ -1591,7 +1591,7 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename) fpcoeff = force->open_potential(coefffilename); if (fpcoeff == NULL) { char str[128]; - sprintf(str,"Cannot open SNAP coefficient file %s",coefffilename); + snprintf(str,128,"Cannot open SNAP coefficient file %s",coefffilename); error->one(FLERR,str); } } @@ -1757,7 +1757,7 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename) fpparam = force->open_potential(paramfilename); if (fpparam == NULL) { char str[128]; - sprintf(str,"Cannot open SNAP parameter file %s",paramfilename); + snprintf(str,128,"Cannot open SNAP parameter file %s",paramfilename); error->one(FLERR,str); } } diff --git a/src/USER-BOCS/fix_bocs.cpp b/src/USER-BOCS/fix_bocs.cpp index 03fc94ae58..bf11b1d6ba 100644 --- a/src/USER-BOCS/fix_bocs.cpp +++ b/src/USER-BOCS/fix_bocs.cpp @@ -207,12 +207,11 @@ FixBocs::FixBocs(LAMMPS *lmp, int narg, char **arg) : p_basis_type = 2; spline_length = read_F_table( arg[iarg+1], p_basis_type ); iarg += 2; - } else - { - char * errmsg = (char *) calloc(150,sizeof(char)); - sprintf(errmsg,"CG basis type %s is not recognized\nSupported " - "basis types: analytic linear_spline cubic_spline",arg[iarg]); - error->all(FLERR,errmsg); + } else { + char errmsg[256]; + snprintf(errmsg,256,"CG basis type %s is not recognized\nSupported " + "basis types: analytic linear_spline cubic_spline",arg[iarg]); + error->all(FLERR,errmsg); } // END NJD MRD } else if (strcmp(arg[iarg],"tchain") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal fix bocs command"); @@ -243,9 +242,9 @@ FixBocs::FixBocs(LAMMPS *lmp, int narg, char **arg) : if (nc_pchain < 0) error->all(FLERR,"Illegal fix bocs command"); iarg += 2; } else { - char * errmsg = (char *) calloc(80,sizeof(char)); - sprintf(errmsg,"Illegal fix bocs command: unrecognized keyword %s" - ,arg[iarg]); + char errmsg[128]; + snprintf(errmsg,128,"Illegal fix bocs command: unrecognized keyword %s" + ,arg[iarg]); error->all(FLERR,errmsg); } } @@ -641,20 +640,16 @@ int FixBocs::read_F_table( char *filename, int p_basis_type ) { data[i] = (double *) calloc(n_entries,sizeof(double)); } - } - else - { - char * errmsg = (char *) calloc(50,sizeof(char)); - sprintf(errmsg,"Unable to open file: %s\n",filename); + } else { + char errmsg[128]; + snprintf(errmsg,128,"Unable to open file: %s\n",filename); error->all(FLERR,errmsg); } n_entries = 0; fpi = fopen(filename,"r"); - if (fpi) - { - while( fgets(line,199,fpi)) - { + if (fpi) { + while( fgets(line,199,fpi)) { ++n_entries; test_sscanf = sscanf(line," %f , %f ",&f1, &f2); if (test_sscanf == 2) @@ -668,11 +663,9 @@ int FixBocs::read_F_table( char *filename, int p_basis_type ) "line %d of file %s\n\tline: %s",n_entries,filename,line); } } - } - else - { - char * errmsg = (char *) calloc(50,sizeof(char)); - sprintf(errmsg,"Unable to open file: %s\n",filename); + } else { + char errmsg[128]; + snprintf(errmsg,128,"Unable to open file: %s\n",filename); error->all(FLERR,errmsg); } fclose(fpi); diff --git a/src/USER-DIFFRACTION/fix_saed_vtk.cpp b/src/USER-DIFFRACTION/fix_saed_vtk.cpp index ad9c76ac6b..882c13bc3e 100644 --- a/src/USER-DIFFRACTION/fix_saed_vtk.cpp +++ b/src/USER-DIFFRACTION/fix_saed_vtk.cpp @@ -424,12 +424,12 @@ void FixSAEDVTK::invoke_vector(bigint ntimestep) fclose(fp); char nName [128]; - sprintf(nName,"%s.%d.vtk",filename,nOutput); + snprintf(nName,128,"%s.%d.vtk",filename,nOutput); fp = fopen(nName,"w"); if (fp == NULL) { char str[128]; - sprintf(str,"Cannot open fix saed/vtk file %s",nName); + snprintf(str,128,"Cannot open fix saed/vtk file %s",nName); error->one(FLERR,str); } } @@ -550,13 +550,13 @@ void FixSAEDVTK::options(int narg, char **arg) filename = new char[n]; strcpy(filename,arg[iarg+1]); - char nName [128]; - sprintf(nName,"%s.%d.vtk",filename,nOutput); + char nName [128]; + snprintf(nName,128,"%s.%d.vtk",filename,nOutput); fp = fopen(nName,"w"); if (fp == NULL) { char str[128]; - sprintf(str,"Cannot open fix saed/vtk file %s",nName); + snprintf(str,128,"Cannot open fix saed/vtk file %s",nName); error->one(FLERR,str); } } diff --git a/src/USER-DPD/fix_eos_table.cpp b/src/USER-DPD/fix_eos_table.cpp index e57a3788bf..7d701f5fb8 100644 --- a/src/USER-DPD/fix_eos_table.cpp +++ b/src/USER-DPD/fix_eos_table.cpp @@ -200,7 +200,7 @@ void FixEOStable::read_table(Table *tb, Table *tb2, char *file, char *keyword) FILE *fp = force->open_potential(file); if (fp == NULL) { char str[128]; - sprintf(str,"Cannot open file %s",file); + snprintf(str,128,"Cannot open file %s",file); error->one(FLERR,str); } diff --git a/src/USER-DPD/fix_eos_table_rx.cpp b/src/USER-DPD/fix_eos_table_rx.cpp index 181c7dccfa..779cee0e8b 100644 --- a/src/USER-DPD/fix_eos_table_rx.cpp +++ b/src/USER-DPD/fix_eos_table_rx.cpp @@ -309,7 +309,7 @@ void FixEOStableRX::read_file(char *file) fp = fopen(file,"r"); if (fp == NULL) { char str[128]; - sprintf(str,"Cannot open eos table/rx potential file %s",file); + snprintf(str,128,"Cannot open eos table/rx potential file %s",file); error->one(FLERR,str); } } @@ -419,7 +419,7 @@ void FixEOStableRX::read_table(Table *tb, Table *tb2, char *file, char *keyword) FILE *fp = fopen(file,"r"); if (fp == NULL) { char str[128]; - sprintf(str,"Cannot open file %s",file); + snprintf(str,128,"Cannot open file %s",file); error->one(FLERR,str); } diff --git a/src/USER-DPD/fix_rx.cpp b/src/USER-DPD/fix_rx.cpp index 1a9c43704d..97668471c8 100644 --- a/src/USER-DPD/fix_rx.cpp +++ b/src/USER-DPD/fix_rx.cpp @@ -272,7 +272,7 @@ void FixRX::post_constructor() fp = force->open_potential(kineticsFile); if (fp == NULL) { char str[128]; - sprintf(str,"Cannot open rx file %s",kineticsFile); + snprintf(str,128,"Cannot open rx file %s",kineticsFile); error->one(FLERR,str); } } @@ -859,7 +859,7 @@ void FixRX::read_file(char *file) fp = force->open_potential(file); if (fp == NULL) { char str[128]; - sprintf(str,"Cannot open rx file %s",file); + snprintf(str,128,"Cannot open rx file %s",file); error->one(FLERR,str); } } diff --git a/src/USER-DPD/pair_exp6_rx.cpp b/src/USER-DPD/pair_exp6_rx.cpp index 057c8fa119..0251f019c5 100644 --- a/src/USER-DPD/pair_exp6_rx.cpp +++ b/src/USER-DPD/pair_exp6_rx.cpp @@ -730,7 +730,7 @@ void PairExp6rx::read_file(char *file) fp = force->open_potential(file); if (fp == NULL) { char str[128]; - sprintf(str,"Cannot open exp6/rx potential file %s",file); + snprintf(str,128,"Cannot open exp6/rx potential file %s",file); error->one(FLERR,str); } } @@ -841,7 +841,7 @@ void PairExp6rx::read_file2(char *file) fp = fopen(file,"r"); if (fp == NULL) { char str[128]; - sprintf(str,"Cannot open polynomial file %s",file); + snprintf(str,128,"Cannot open polynomial file %s",file); error->one(FLERR,str); } } diff --git a/src/USER-DPD/pair_multi_lucy.cpp b/src/USER-DPD/pair_multi_lucy.cpp index f911d8299e..19a4a02f0b 100644 --- a/src/USER-DPD/pair_multi_lucy.cpp +++ b/src/USER-DPD/pair_multi_lucy.cpp @@ -350,7 +350,7 @@ void PairMultiLucy::read_table(Table *tb, char *file, char *keyword) FILE *fp = fopen(file,"r"); if (fp == NULL) { char str[128]; - sprintf(str,"Cannot open file %s",file); + snprintf(str,128,"Cannot open file %s",file); error->one(FLERR,str); } diff --git a/src/USER-DPD/pair_multi_lucy_rx.cpp b/src/USER-DPD/pair_multi_lucy_rx.cpp index 13c838fe01..f3ad86eb2f 100644 --- a/src/USER-DPD/pair_multi_lucy_rx.cpp +++ b/src/USER-DPD/pair_multi_lucy_rx.cpp @@ -495,7 +495,7 @@ void PairMultiLucyRX::read_table(Table *tb, char *file, char *keyword) FILE *fp = force->open_potential(file); if (fp == NULL) { char str[128]; - sprintf(str,"Cannot open file %s",file); + snprintf(str,128,"Cannot open file %s",file); error->one(FLERR,str); } diff --git a/src/USER-INTEL/pair_eam_alloy_intel.cpp b/src/USER-INTEL/pair_eam_alloy_intel.cpp index 192b39b2e8..da8a180fff 100644 --- a/src/USER-INTEL/pair_eam_alloy_intel.cpp +++ b/src/USER-INTEL/pair_eam_alloy_intel.cpp @@ -126,7 +126,7 @@ void PairEAMAlloyIntel::read_file(char *filename) fptr = force->open_potential(filename); if (fptr == NULL) { char str[128]; - sprintf(str,"Cannot open EAM potential file %s",filename); + snprintf(str,128,"Cannot open EAM potential file %s",filename); error->one(FLERR,str); } } diff --git a/src/USER-INTEL/pair_eam_fs_intel.cpp b/src/USER-INTEL/pair_eam_fs_intel.cpp index 61bb6e0b4d..043f77db3e 100644 --- a/src/USER-INTEL/pair_eam_fs_intel.cpp +++ b/src/USER-INTEL/pair_eam_fs_intel.cpp @@ -126,7 +126,7 @@ void PairEAMFSIntel::read_file(char *filename) fptr = force->open_potential(filename); if (fptr == NULL) { char str[128]; - sprintf(str,"Cannot open EAM potential file %s",filename); + snprintf(str,128,"Cannot open EAM potential file %s",filename); error->one(FLERR,str); } } diff --git a/src/USER-MEAMC/pair_meamc.cpp b/src/USER-MEAMC/pair_meamc.cpp index eca1040c9c..ff2a1180b5 100644 --- a/src/USER-MEAMC/pair_meamc.cpp +++ b/src/USER-MEAMC/pair_meamc.cpp @@ -328,7 +328,7 @@ void PairMEAMC::read_files(char *globalfile, char *userfile) fp = force->open_potential(globalfile); if (fp == NULL) { char str[128]; - sprintf(str,"Cannot open MEAM potential file %s",globalfile); + snprintf(str,128,"Cannot open MEAM potential file %s",globalfile); error->one(FLERR,str); } } @@ -509,7 +509,7 @@ void PairMEAMC::read_files(char *globalfile, char *userfile) fp = force->open_potential(userfile); if (fp == NULL) { char str[128]; - sprintf(str,"Cannot open MEAM potential file %s",userfile); + snprintf(str,128,"Cannot open MEAM potential file %s",userfile); error->one(FLERR,str); } } @@ -558,8 +558,8 @@ void PairMEAMC::read_files(char *globalfile, char *userfile) if (strcmp(params[0],keywords[which]) == 0) break; if (which == nkeywords) { char str[128]; - sprintf(str,"Keyword %s in MEAM parameter file not recognized", - params[0]); + snprintf(str,128,"Keyword %s in MEAM parameter file not recognized", + params[0]); error->all(FLERR,str); } nindex = nparams - 2; diff --git a/src/USER-MISC/fix_ave_correlate_long.cpp b/src/USER-MISC/fix_ave_correlate_long.cpp index 0ce6121bf9..5c9f478a65 100644 --- a/src/USER-MISC/fix_ave_correlate_long.cpp +++ b/src/USER-MISC/fix_ave_correlate_long.cpp @@ -165,7 +165,7 @@ FixAveCorrelateLong::FixAveCorrelateLong(LAMMPS * lmp, int narg, char **arg): fp = fopen(arg[iarg+1],"w"); if (fp == NULL) { char str[128]; - sprintf(str,"Cannot open fix ave/correlate/long file %s",arg[iarg+1]); + snprintf(str,128,"Cannot open fix ave/correlate/long file %s",arg[iarg+1]); error->one(FLERR,str); } } diff --git a/src/USER-MISC/fix_bond_react.cpp b/src/USER-MISC/fix_bond_react.cpp index ceac93178d..ae4534f825 100644 --- a/src/USER-MISC/fix_bond_react.cpp +++ b/src/USER-MISC/fix_bond_react.cpp @@ -2529,7 +2529,7 @@ void FixBondReact::open(char *file) fp = fopen(file,"r"); if (fp == NULL) { char str[128]; - sprintf(str,"Cannot open superimpose file %s",file); + snprintf(str,128,"Cannot open superimpose file %s",file); error->one(FLERR,str); } } diff --git a/src/USER-MISC/fix_gle.cpp b/src/USER-MISC/fix_gle.cpp index 0b08fab4ca..01da7f87cf 100644 --- a/src/USER-MISC/fix_gle.cpp +++ b/src/USER-MISC/fix_gle.cpp @@ -232,7 +232,7 @@ FixGLE::FixGLE(LAMMPS *lmp, int narg, char **arg) : fgle = force->open_potential(fname); if (fgle == NULL) { char str[128]; - sprintf(str,"Cannot open A-matrix file %s",fname); + snprintf(str,128,"Cannot open A-matrix file %s",fname); error->one(FLERR,str); } if (screen) fprintf(screen,"Reading A-matrix from %s\n", fname); @@ -302,7 +302,7 @@ FixGLE::FixGLE(LAMMPS *lmp, int narg, char **arg) : fgle = force->open_potential(fname); if (fgle == NULL) { char str[128]; - sprintf(str,"Cannot open C-matrix file %s",fname); + snprintf(str,128,"Cannot open C-matrix file %s",fname); error->one(FLERR,str); } if (screen) diff --git a/src/USER-MISC/fix_ttm_mod.cpp b/src/USER-MISC/fix_ttm_mod.cpp index 65f8e90ec3..a423b510e5 100644 --- a/src/USER-MISC/fix_ttm_mod.cpp +++ b/src/USER-MISC/fix_ttm_mod.cpp @@ -86,7 +86,7 @@ FixTTMMod::FixTTMMod(LAMMPS *lmp, int narg, char **arg) : FILE *fpr_2 = force->open_potential(arg[4]); if (fpr_2 == NULL) { char str[128]; - sprintf(str,"Cannot open file %s",arg[4]); + snprintf(str,128,"Cannot open file %s",arg[4]); error->all(FLERR,str); } @@ -99,7 +99,7 @@ FixTTMMod::FixTTMMod(LAMMPS *lmp, int narg, char **arg) : FILE *fpr = force->open_potential(arg[8]); if (fpr == NULL) { char str[128]; - sprintf(str,"Cannot open file %s",arg[8]); + snprintf(str,128,"Cannot open file %s",arg[8]); error->all(FLERR,str); } @@ -111,7 +111,7 @@ FixTTMMod::FixTTMMod(LAMMPS *lmp, int narg, char **arg) : fp = fopen(arg[10],"w"); if (fp == NULL) { char str[128]; - sprintf(str,"Cannot open fix ttm/mod file %s",arg[10]); + snprintf(str,128,"Cannot open fix ttm/mod file %s",arg[10]); error->one(FLERR,str); } } diff --git a/src/USER-MISC/pair_agni.cpp b/src/USER-MISC/pair_agni.cpp index 998582f619..0277969d15 100644 --- a/src/USER-MISC/pair_agni.cpp +++ b/src/USER-MISC/pair_agni.cpp @@ -363,7 +363,7 @@ void PairAGNI::read_file(char *file) fp = force->open_potential(file); if (fp == NULL) { char str[128]; - sprintf(str,"Cannot open AGNI potential file %s",file); + snprintf(str,128,"Cannot open AGNI potential file %s",file); error->one(FLERR,str); } } diff --git a/src/USER-MISC/pair_edip.cpp b/src/USER-MISC/pair_edip.cpp index 4716e271d7..491268567f 100644 --- a/src/USER-MISC/pair_edip.cpp +++ b/src/USER-MISC/pair_edip.cpp @@ -877,7 +877,7 @@ void PairEDIP::read_file(char *file) fp = force->open_potential(file); if (fp == NULL) { char str[128]; - sprintf(str,"Cannot open EDIP potential file %s",file); + snprintf(str,128,"Cannot open EDIP potential file %s",file); error->one(FLERR,str); } } diff --git a/src/USER-MISC/pair_edip_multi.cpp b/src/USER-MISC/pair_edip_multi.cpp index fc76aadb0b..f56650d2f6 100644 --- a/src/USER-MISC/pair_edip_multi.cpp +++ b/src/USER-MISC/pair_edip_multi.cpp @@ -644,7 +644,7 @@ void PairEDIPMulti::read_file(char *file) fp = force->open_potential(file); if (fp == NULL) { char str[128]; - sprintf(str,"Cannot open EDIP potential file %s",file); + snprintf(str,128,"Cannot open EDIP potential file %s",file); error->one(FLERR,str); } } diff --git a/src/USER-MISC/pair_extep.cpp b/src/USER-MISC/pair_extep.cpp index 49c562471f..1e7d17f040 100644 --- a/src/USER-MISC/pair_extep.cpp +++ b/src/USER-MISC/pair_extep.cpp @@ -591,7 +591,7 @@ void PairExTeP::read_file(char *file) fp = force->open_potential(file); if (fp == NULL) { char str[128]; - sprintf(str,"Cannot open ExTeP potential file %s",file); + snprintf(str,128,"Cannot open ExTeP potential file %s",file); error->one(FLERR,str); } } diff --git a/src/USER-MISC/pair_ilp_graphene_hbn.cpp b/src/USER-MISC/pair_ilp_graphene_hbn.cpp index 7e11cdff4f..6b92595472 100644 --- a/src/USER-MISC/pair_ilp_graphene_hbn.cpp +++ b/src/USER-MISC/pair_ilp_graphene_hbn.cpp @@ -880,7 +880,7 @@ void PairILPGrapheneHBN::read_file(char *filename) fp = force->open_potential(filename); if (fp == NULL) { char str[128]; - sprintf(str,"Cannot open ILP potential file %s",filename); + snprintf(str,128,"Cannot open ILP potential file %s",filename); error->one(FLERR,str); } } diff --git a/src/USER-MISC/pair_kolmogorov_crespi_full.cpp b/src/USER-MISC/pair_kolmogorov_crespi_full.cpp index bc3bfaeba9..18870ef69a 100644 --- a/src/USER-MISC/pair_kolmogorov_crespi_full.cpp +++ b/src/USER-MISC/pair_kolmogorov_crespi_full.cpp @@ -885,7 +885,7 @@ void PairKolmogorovCrespiFull::read_file(char *filename) fp = force->open_potential(filename); if (fp == NULL) { char str[128]; - sprintf(str,"Cannot open KC potential file %s",filename); + snprintf(str,128,"Cannot open KC potential file %s",filename); error->one(FLERR,str); } } diff --git a/src/USER-MISC/pair_kolmogorov_crespi_z.cpp b/src/USER-MISC/pair_kolmogorov_crespi_z.cpp index fb7d5ae40e..b39b9fdb72 100644 --- a/src/USER-MISC/pair_kolmogorov_crespi_z.cpp +++ b/src/USER-MISC/pair_kolmogorov_crespi_z.cpp @@ -315,7 +315,7 @@ void PairKolmogorovCrespiZ::read_file(char *filename) fp = force->open_potential(filename); if (fp == NULL) { char str[128]; - sprintf(str,"Cannot open KC potential file %s",filename); + snprintf(str,128,"Cannot open KC potential file %s",filename); error->one(FLERR,str); } } diff --git a/src/USER-MISC/pair_meam_spline.cpp b/src/USER-MISC/pair_meam_spline.cpp index e6ea6c2ae4..0300e2c7a2 100644 --- a/src/USER-MISC/pair_meam_spline.cpp +++ b/src/USER-MISC/pair_meam_spline.cpp @@ -439,7 +439,7 @@ void PairMEAMSpline::read_file(const char* filename) FILE *fp = force->open_potential(filename); if(fp == NULL) { char str[1024]; - sprintf(str,"Cannot open spline MEAM potential file %s", filename); + snprintf(str,128,"Cannot open spline MEAM potential file %s", filename); error->one(FLERR,str); } diff --git a/src/USER-MISC/pair_meam_sw_spline.cpp b/src/USER-MISC/pair_meam_sw_spline.cpp index 891913ccfc..20dade5e5f 100644 --- a/src/USER-MISC/pair_meam_sw_spline.cpp +++ b/src/USER-MISC/pair_meam_sw_spline.cpp @@ -462,64 +462,64 @@ void PairMEAMSWSpline::coeff(int narg, char **arg) void PairMEAMSWSpline::read_file(const char* filename) { - if(comm->me == 0) { - FILE *fp = force->open_potential(filename); - if(fp == NULL) { - char str[1024]; - sprintf(str,"Cannot open spline MEAM potential file %s", filename); - error->one(FLERR,str); - } + if(comm->me == 0) { + FILE *fp = force->open_potential(filename); + if(fp == NULL) { + char str[1024]; + snprintf(str,128,"Cannot open spline MEAM potential file %s", filename); + error->one(FLERR,str); + } - // Skip first line of file. - char line[MAXLINE]; - fgets(line, MAXLINE, fp); + // Skip first line of file. + char line[MAXLINE]; + fgets(line, MAXLINE, fp); - // Parse spline functions. - phi.parse(fp, error); - F.parse(fp, error); - G.parse(fp, error); - rho.parse(fp, error); - U.parse(fp, error); - f.parse(fp, error); - g.parse(fp, error); + // Parse spline functions. + phi.parse(fp, error); + F.parse(fp, error); + G.parse(fp, error); + rho.parse(fp, error); + U.parse(fp, error); + f.parse(fp, error); + g.parse(fp, error); - fclose(fp); - } + fclose(fp); + } - // Transfer spline functions from master processor to all other processors. - phi.communicate(world, comm->me); - rho.communicate(world, comm->me); - f.communicate(world, comm->me); - U.communicate(world, comm->me); - g.communicate(world, comm->me); - F.communicate(world, comm->me); - G.communicate(world, comm->me); + // Transfer spline functions from master processor to all other processors. + phi.communicate(world, comm->me); + rho.communicate(world, comm->me); + f.communicate(world, comm->me); + U.communicate(world, comm->me); + g.communicate(world, comm->me); + F.communicate(world, comm->me); + G.communicate(world, comm->me); - // Calculate 'zero-point energy' of single atom in vacuum. - zero_atom_energy = U.eval(0.0); + // Calculate 'zero-point energy' of single atom in vacuum. + zero_atom_energy = U.eval(0.0); - // Determine maximum cutoff radius of all relevant spline functions. - cutoff = 0.0; - if(phi.cutoff() > cutoff) cutoff = phi.cutoff(); - if(rho.cutoff() > cutoff) cutoff = rho.cutoff(); - if(f.cutoff() > cutoff) cutoff = f.cutoff(); - if(F.cutoff() > cutoff) cutoff = F.cutoff(); + // Determine maximum cutoff radius of all relevant spline functions. + cutoff = 0.0; + if(phi.cutoff() > cutoff) cutoff = phi.cutoff(); + if(rho.cutoff() > cutoff) cutoff = rho.cutoff(); + if(f.cutoff() > cutoff) cutoff = f.cutoff(); + if(F.cutoff() > cutoff) cutoff = F.cutoff(); - // Set LAMMPS pair interaction flags. - for(int i = 1; i <= atom->ntypes; i++) { - for(int j = 1; j <= atom->ntypes; j++) { - setflag[i][j] = 1; - cutsq[i][j] = cutoff; - } - } + // Set LAMMPS pair interaction flags. + for(int i = 1; i <= atom->ntypes; i++) { + for(int j = 1; j <= atom->ntypes; j++) { + setflag[i][j] = 1; + cutsq[i][j] = cutoff; + } + } - // phi.writeGnuplot("phi.gp", "Phi(r)"); - // rho.writeGnuplot("rho.gp", "Rho(r)"); - // f.writeGnuplot("f.gp", "f(r)"); - // U.writeGnuplot("U.gp", "U(rho)"); - // g.writeGnuplot("g.gp", "g(x)"); - // F.writeGnuplot("F.gp", "F(r)"); - // G.writeGnuplot("G.gp", "G(x)"); + // phi.writeGnuplot("phi.gp", "Phi(r)"); + // rho.writeGnuplot("rho.gp", "Rho(r)"); + // f.writeGnuplot("f.gp", "f(r)"); + // U.writeGnuplot("U.gp", "U(rho)"); + // g.writeGnuplot("g.gp", "g(x)"); + // F.writeGnuplot("F.gp", "F(r)"); + // G.writeGnuplot("G.gp", "G(x)"); } /* ---------------------------------------------------------------------- diff --git a/src/USER-MISC/pair_tersoff_table.cpp b/src/USER-MISC/pair_tersoff_table.cpp index d7e28a1e40..d1044cc336 100644 --- a/src/USER-MISC/pair_tersoff_table.cpp +++ b/src/USER-MISC/pair_tersoff_table.cpp @@ -845,7 +845,7 @@ void PairTersoffTable::read_file(char *file) fp = force->open_potential(file); if (fp == NULL) { char str[128]; - sprintf(str,"Cannot open Tersoff potential file %s",file); + snprintf(str,128,"Cannot open Tersoff potential file %s",file); error->one(FLERR,str); } } diff --git a/src/USER-MOLFILE/reader_molfile.cpp b/src/USER-MOLFILE/reader_molfile.cpp index 6348009d8f..8e49f56d5c 100644 --- a/src/USER-MOLFILE/reader_molfile.cpp +++ b/src/USER-MOLFILE/reader_molfile.cpp @@ -113,12 +113,12 @@ void ReaderMolfile::open_file(const char *file) rv = mf->open(file,&natoms); if (rv != MFI::E_NONE) { - sprintf(str,"Cannot open file %s",file); + snprintf(str,1024,"Cannot open file %s",file); error->one(FLERR,str); } if (natoms < 1) { - sprintf(str,"No atoms in file %s",file); + snprintf(str,1024,"No atoms in file %s",file); error->one(FLERR,str); } From db510af5822fb39a9cdd76d72b73cd180682b48f Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 6 Sep 2018 11:32:44 -0400 Subject: [PATCH 147/302] more fixes for potential buffer overflows by using snprintf() instead of sprintf() --- src/USER-OMP/pair_eam_alloy_omp.cpp | 2 +- src/USER-OMP/pair_eam_fs_omp.cpp | 2 +- src/USER-OMP/pair_tersoff_zbl_omp.cpp | 2 +- src/USER-REAXC/fix_reaxc_bonds.cpp | 4 +- src/USER-REAXC/fix_reaxc_species.cpp | 6 +- src/USER-REAXC/pair_reaxc.cpp | 2 +- src/USER-SMD/fix_smd_integrate_tlsph.cpp | 2 +- src/USER-SMD/fix_smd_integrate_ulsph.cpp | 2 +- .../fix_smd_move_triangulated_surface.cpp | 2 +- src/USER-SMD/fix_smd_wall_surface.cpp | 415 +++++++++--------- 10 files changed, 213 insertions(+), 226 deletions(-) diff --git a/src/USER-OMP/pair_eam_alloy_omp.cpp b/src/USER-OMP/pair_eam_alloy_omp.cpp index bbb3b03b02..78b4735863 100644 --- a/src/USER-OMP/pair_eam_alloy_omp.cpp +++ b/src/USER-OMP/pair_eam_alloy_omp.cpp @@ -126,7 +126,7 @@ void PairEAMAlloyOMP::read_file(char *filename) fptr = force->open_potential(filename); if (fptr == NULL) { char str[128]; - sprintf(str,"Cannot open EAM potential file %s",filename); + snprintf(str,128,"Cannot open EAM potential file %s",filename); error->one(FLERR,str); } } diff --git a/src/USER-OMP/pair_eam_fs_omp.cpp b/src/USER-OMP/pair_eam_fs_omp.cpp index a678c887a0..17fecf9b4f 100644 --- a/src/USER-OMP/pair_eam_fs_omp.cpp +++ b/src/USER-OMP/pair_eam_fs_omp.cpp @@ -126,7 +126,7 @@ void PairEAMFSOMP::read_file(char *filename) fptr = force->open_potential(filename); if (fptr == NULL) { char str[128]; - sprintf(str,"Cannot open EAM potential file %s",filename); + snprintf(str,128,"Cannot open EAM potential file %s",filename); error->one(FLERR,str); } } diff --git a/src/USER-OMP/pair_tersoff_zbl_omp.cpp b/src/USER-OMP/pair_tersoff_zbl_omp.cpp index ce3e6fea75..096a42b1a8 100644 --- a/src/USER-OMP/pair_tersoff_zbl_omp.cpp +++ b/src/USER-OMP/pair_tersoff_zbl_omp.cpp @@ -97,7 +97,7 @@ void PairTersoffZBLOMP::read_file(char *file) fp = force->open_potential(file); if (fp == NULL) { char str[128]; - sprintf(str,"Cannot open Tersoff potential file %s",file); + snprintf(str,128,"Cannot open Tersoff potential file %s",file); error->one(FLERR,str); } } diff --git a/src/USER-REAXC/fix_reaxc_bonds.cpp b/src/USER-REAXC/fix_reaxc_bonds.cpp index fb40b2042e..9dc347826f 100644 --- a/src/USER-REAXC/fix_reaxc_bonds.cpp +++ b/src/USER-REAXC/fix_reaxc_bonds.cpp @@ -62,7 +62,7 @@ FixReaxCBonds::FixReaxCBonds(LAMMPS *lmp, int narg, char **arg) : if (suffix && strcmp(suffix,".gz") == 0) { #ifdef LAMMPS_GZIP char gzip[128]; - sprintf(gzip,"gzip -6 > %s",arg[4]); + snprintf(gzip,128,"gzip -6 > %s",arg[4]); #ifdef _WIN32 fp = _popen(gzip,"wb"); #else @@ -75,7 +75,7 @@ FixReaxCBonds::FixReaxCBonds(LAMMPS *lmp, int narg, char **arg) : if (fp == NULL) { char str[128]; - sprintf(str,"Cannot open fix reax/c/bonds file %s",arg[4]); + snprintf(str,128,"Cannot open fix reax/c/bonds file %s",arg[4]); error->one(FLERR,str); } } diff --git a/src/USER-REAXC/fix_reaxc_species.cpp b/src/USER-REAXC/fix_reaxc_species.cpp index 8ec7f4174f..46426d484a 100644 --- a/src/USER-REAXC/fix_reaxc_species.cpp +++ b/src/USER-REAXC/fix_reaxc_species.cpp @@ -98,9 +98,7 @@ FixReaxCSpecies::FixReaxCSpecies(LAMMPS *lmp, int narg, char **arg) : } if (me == 0 && rene_flag) { - char str[128]; - sprintf(str,"Resetting reneighboring criteria for fix reax/c/species"); - error->warning(FLERR,str); + error->warning(FLERR,"Resetting reneighboring criteria for fix reax/c/species"); } tmparg = NULL; @@ -127,7 +125,7 @@ FixReaxCSpecies::FixReaxCSpecies(LAMMPS *lmp, int narg, char **arg) : if (fp == NULL) { char str[128]; - sprintf(str,"Cannot open fix reax/c/species file %s",arg[6]); + snprintf(str,128,"Cannot open fix reax/c/species file %s",arg[6]); error->one(FLERR,str); } } diff --git a/src/USER-REAXC/pair_reaxc.cpp b/src/USER-REAXC/pair_reaxc.cpp index 378d20952c..85bd8471b4 100644 --- a/src/USER-REAXC/pair_reaxc.cpp +++ b/src/USER-REAXC/pair_reaxc.cpp @@ -301,7 +301,7 @@ void PairReaxC::coeff( int nargs, char **args ) Read_Force_Field(fp, &(system->reax_param), control); else { char str[128]; - sprintf(str,"Cannot open ReaxFF potential file %s",file); + snprintf(str,128,"Cannot open ReaxFF potential file %s",file); error->all(FLERR,str); } diff --git a/src/USER-SMD/fix_smd_integrate_tlsph.cpp b/src/USER-SMD/fix_smd_integrate_tlsph.cpp index 1eae45161f..f931ae94ff 100644 --- a/src/USER-SMD/fix_smd_integrate_tlsph.cpp +++ b/src/USER-SMD/fix_smd_integrate_tlsph.cpp @@ -86,7 +86,7 @@ FixSMDIntegrateTlsph::FixSMDIntegrateTlsph(LAMMPS *lmp, int narg, char **arg) : } } else { char msg[128]; - sprintf(msg, "Illegal keyword for smd/integrate_tlsph: %s\n", arg[iarg]); + snprintf(msg,128, "Illegal keyword for smd/integrate_tlsph: %s\n", arg[iarg]); error->all(FLERR, msg); } diff --git a/src/USER-SMD/fix_smd_integrate_ulsph.cpp b/src/USER-SMD/fix_smd_integrate_ulsph.cpp index 685d6af5a8..6c4705eb96 100644 --- a/src/USER-SMD/fix_smd_integrate_ulsph.cpp +++ b/src/USER-SMD/fix_smd_integrate_ulsph.cpp @@ -119,7 +119,7 @@ FixSMDIntegrateUlsph::FixSMDIntegrateUlsph(LAMMPS *lmp, int narg, char **arg) : } } else { char msg[128]; - sprintf(msg, "Illegal keyword for smd/integrate_ulsph: %s\n", arg[iarg]); + snprintf(msg,128, "Illegal keyword for smd/integrate_ulsph: %s\n", arg[iarg]); error->all(FLERR, msg); } diff --git a/src/USER-SMD/fix_smd_move_triangulated_surface.cpp b/src/USER-SMD/fix_smd_move_triangulated_surface.cpp index b0944f1186..fe8695b23e 100644 --- a/src/USER-SMD/fix_smd_move_triangulated_surface.cpp +++ b/src/USER-SMD/fix_smd_move_triangulated_surface.cpp @@ -200,7 +200,7 @@ FixSMDMoveTriSurf::FixSMDMoveTriSurf(LAMMPS *lmp, int narg, char **arg) : } else { char msg[128]; - sprintf(msg, "Illegal keyword for fix smd/move_tri_surf: %s\n", arg[iarg]); + snprintf(msg,128, "Illegal keyword for fix smd/move_tri_surf: %s\n", arg[iarg]); error->all(FLERR, msg); } diff --git a/src/USER-SMD/fix_smd_wall_surface.cpp b/src/USER-SMD/fix_smd_wall_surface.cpp index 4dd415f53e..a37ba67a80 100644 --- a/src/USER-SMD/fix_smd_wall_surface.cpp +++ b/src/USER-SMD/fix_smd_wall_surface.cpp @@ -223,62 +223,59 @@ int FixSMDWallSurface::count_words(const char *line) { void FixSMDWallSurface::read_triangles(int pass) { - double coord[3]; + double coord[3]; - int nlocal_previous = atom->nlocal; - int ilocal = nlocal_previous; - int m; - int me; + int nlocal_previous = atom->nlocal; + int ilocal = nlocal_previous; + int m; + int me; - bigint natoms_previous = atom->natoms; - Vector3d *vert; - vert = new Vector3d[3]; - Vector3d normal, center; + bigint natoms_previous = atom->natoms; + Vector3d *vert; + vert = new Vector3d[3]; + Vector3d normal, center; - FILE *fp = fopen(filename, "r"); - if (fp == NULL) { - char str[128]; - sprintf(str, "Cannot open file %s", filename); - error->one(FLERR, str); - } + FILE *fp = fopen(filename, "r"); + if (fp == NULL) { + char str[128]; + snprintf(str,128, "Cannot open file %s", filename); + error->one(FLERR, str); + } - MPI_Comm_rank(world, &me); - if (me == 0) { - if (screen) { - if (pass == 0) { - printf("\n>>========>>========>>========>>========>>========>>========>>========>>========\n"); - fprintf(screen, " scanning triangle pairs ...\n"); - } else { - fprintf(screen, " reading triangle pairs ...\n"); - } - } - if (logfile) { - if (pass == 0) { - fprintf(logfile, " scanning triangle pairs ...\n"); - } else { - fprintf(logfile, " reading triangle pairs ...\n"); - } - } - } + MPI_Comm_rank(world, &me); + if (me == 0) { + if (screen) { + if (pass == 0) { + printf("\n>>========>>========>>========>>========>>========>>========>>========>>========\n"); + fprintf(screen, " scanning triangle pairs ...\n"); + } else { + fprintf(screen, " reading triangle pairs ...\n"); + } + } + if (logfile) { + if (pass == 0) { + fprintf(logfile, " scanning triangle pairs ...\n"); + } else { + fprintf(logfile, " reading triangle pairs ...\n"); + } + } + } - char str[128]; - char line[256]; - char *retpointer; - char **values; - int nwords; + char line[256]; + char *retpointer; + char **values; + int nwords; - // read STL solid name - retpointer = fgets(line, sizeof(line), fp); - if (retpointer == NULL) { - sprintf(str, "error reading number of triangle pairs"); - error->one(FLERR, str); - } + // read STL solid name + retpointer = fgets(line, sizeof(line), fp); + if (retpointer == NULL) { + error->one(FLERR,"error reading number of triangle pairs"); + } - nwords = count_words(line); - if (nwords < 1) { - sprintf(str, "first line of file is incorrect"); - error->one(FLERR, str); - } + nwords = count_words(line); + if (nwords < 1) { + error->one(FLERR,"first line of file is incorrect"); + } // values = new char*[nwords]; // values[0] = strtok(line, " \t\n\r\f"); @@ -295,211 +292,203 @@ void FixSMDWallSurface::read_triangles(int pass) { // cout << "STL file contains solid body with name: " << values[1] << endl; // } - // iterate over STL facets util end of body is reached + // iterate over STL facets util end of body is reached - while (fgets(line, sizeof(line), fp)) { // read a line, should be the facet line + while (fgets(line, sizeof(line), fp)) { // read a line, should be the facet line - // evaluate facet line - nwords = count_words(line); - if (nwords != 5) { - //sprintf(str, "found end solid line"); - //error->message(FLERR, str); - break; - } else { - // should be facet line - } + // evaluate facet line + nwords = count_words(line); + if (nwords != 5) { + //sprintf(str, "found end solid line"); + //error->message(FLERR, str); + break; + } else { + // should be facet line + } - values = new char*[nwords]; - values[0] = strtok(line, " \t\n\r\f"); - if (values[0] == NULL) - error->all(FLERR, "Incorrect atom format in data file"); - for (m = 1; m < nwords; m++) { - values[m] = strtok(NULL, " \t\n\r\f"); - if (values[m] == NULL) - error->all(FLERR, "Incorrect atom format in data file"); - } + values = new char*[nwords]; + values[0] = strtok(line, " \t\n\r\f"); + if (values[0] == NULL) + error->all(FLERR, "Incorrect atom format in data file"); + for (m = 1; m < nwords; m++) { + values[m] = strtok(NULL, " \t\n\r\f"); + if (values[m] == NULL) + error->all(FLERR, "Incorrect atom format in data file"); + } - normal << force->numeric(FLERR, values[2]), force->numeric(FLERR, values[3]), force->numeric(FLERR, values[4]); - //cout << "normal is " << normal << endl; + normal << force->numeric(FLERR, values[2]), force->numeric(FLERR, values[3]), force->numeric(FLERR, values[4]); + //cout << "normal is " << normal << endl; - delete[] values; + delete[] values; - // read outer loop line - retpointer = fgets(line, sizeof(line), fp); - if (retpointer == NULL) { - sprintf(str, "error reading outer loop"); - error->one(FLERR, str); - } + // read outer loop line + retpointer = fgets(line, sizeof(line), fp); + if (retpointer == NULL) { + error->one(FLERR, "error reading outer loop"); + } - nwords = count_words(line); - if (nwords != 2) { - sprintf(str, "error reading outer loop"); - error->one(FLERR, str); - } + nwords = count_words(line); + if (nwords != 2) { + error->one(FLERR,"error reading outer loop"); + } - // read vertex lines + // read vertex lines - for (int k = 0; k < 3; k++) { - retpointer = fgets(line, sizeof(line), fp); - if (retpointer == NULL) { - sprintf(str, "error reading vertex line"); - error->one(FLERR, str); - } + for (int k = 0; k < 3; k++) { + retpointer = fgets(line, sizeof(line), fp); + if (retpointer == NULL) { + error->one(FLERR,"error reading vertex line"); + } - nwords = count_words(line); - if (nwords != 4) { - sprintf(str, "error reading vertex line"); - error->one(FLERR, str); - } + nwords = count_words(line); + if (nwords != 4) { + error->one(FLERR,"error reading vertex line"); + } - values = new char*[nwords]; - values[0] = strtok(line, " \t\n\r\f"); - if (values[0] == NULL) - error->all(FLERR, "Incorrect vertex line"); - for (m = 1; m < nwords; m++) { - values[m] = strtok(NULL, " \t\n\r\f"); - if (values[m] == NULL) - error->all(FLERR, "Incorrect vertex line"); - } + values = new char*[nwords]; + values[0] = strtok(line, " \t\n\r\f"); + if (values[0] == NULL) + error->all(FLERR,"Incorrect vertex line"); + for (m = 1; m < nwords; m++) { + values[m] = strtok(NULL, " \t\n\r\f"); + if (values[m] == NULL) + error->all(FLERR, "Incorrect vertex line"); + } - vert[k] << force->numeric(FLERR, values[1]), force->numeric(FLERR, values[2]), force->numeric(FLERR, values[3]); - //cout << "vertex is " << vert[k] << endl; - //printf("%s %s %s\n", values[1], values[2], values[3]); - delete[] values; - //exit(1); + vert[k] << force->numeric(FLERR, values[1]), force->numeric(FLERR, values[2]), force->numeric(FLERR, values[3]); + //cout << "vertex is " << vert[k] << endl; + //printf("%s %s %s\n", values[1], values[2], values[3]); + delete[] values; + //exit(1); - } + } - // read end loop line - retpointer = fgets(line, sizeof(line), fp); - if (retpointer == NULL) { - sprintf(str, "error reading endloop"); - error->one(FLERR, str); - } + // read end loop line + retpointer = fgets(line, sizeof(line), fp); + if (retpointer == NULL) { + error->one(FLERR, "error reading endloop"); + } - nwords = count_words(line); - if (nwords != 1) { - sprintf(str, "error reading endloop"); - error->one(FLERR, str); - } + nwords = count_words(line); + if (nwords != 1) { + error->one(FLERR,"error reading endloop"); + } - // read end facet line - retpointer = fgets(line, sizeof(line), fp); - if (retpointer == NULL) { - sprintf(str, "error reading endfacet"); - error->one(FLERR, str); - } + // read end facet line + retpointer = fgets(line, sizeof(line), fp); + if (retpointer == NULL) { + error->one(FLERR,"error reading endfacet"); + } - nwords = count_words(line); - if (nwords != 1) { - sprintf(str, "error reading endfacet"); - error->one(FLERR, str); - } + nwords = count_words(line); + if (nwords != 1) { + error->one(FLERR,"error reading endfacet"); + } - // now we have a normal and three vertices ... proceed with adding triangle + // now we have a normal and three vertices ... proceed with adding triangle - center = (vert[0] + vert[1] + vert[2]) / 3.0; + center = (vert[0] + vert[1] + vert[2]) / 3.0; - // cout << "center is " << center << endl; + // cout << "center is " << center << endl; - double r1 = (center - vert[0]).norm(); - double r2 = (center - vert[1]).norm(); - double r3 = (center - vert[2]).norm(); - double r = MAX(r1, r2); - r = MAX(r, r3); + double r1 = (center - vert[0]).norm(); + double r2 = (center - vert[1]).norm(); + double r3 = (center - vert[2]).norm(); + double r = MAX(r1, r2); + r = MAX(r, r3); - /* - * if atom/molecule is in my subbox, create it - * ... use x0 to hold triangle normal. - * ... use smd_data_9 to hold the three vertices - * ... use x to hold triangle center - * ... radius is the mmaximal distance from triangle center to all vertices - */ + /* + * if atom/molecule is in my subbox, create it + * ... use x0 to hold triangle normal. + * ... use smd_data_9 to hold the three vertices + * ... use x to hold triangle center + * ... radius is the mmaximal distance from triangle center to all vertices + */ - // printf("coord: %f %f %f\n", coord[0], coord[1], coord[2]); - // printf("sublo: %f %f %f\n", sublo[0], sublo[1], sublo[2]); - // printf("subhi: %f %f %f\n", subhi[0], subhi[1], subhi[2]); - //printf("ilocal = %d\n", ilocal); - if (center(0) >= sublo[0] && center(0) < subhi[0] && center(1) >= sublo[1] && center(1) < subhi[1] && center(2) >= sublo[2] - && center(2) < subhi[2]) { - //printf("******* KERATIN nlocal=%d ***\n", nlocal); - coord[0] = center(0); - coord[1] = center(1); - coord[2] = center(2); - atom->avec->create_atom(wall_particle_type, coord); + // printf("coord: %f %f %f\n", coord[0], coord[1], coord[2]); + // printf("sublo: %f %f %f\n", sublo[0], sublo[1], sublo[2]); + // printf("subhi: %f %f %f\n", subhi[0], subhi[1], subhi[2]); + //printf("ilocal = %d\n", ilocal); + if (center(0) >= sublo[0] && center(0) < subhi[0] && center(1) >= sublo[1] && center(1) < subhi[1] && center(2) >= sublo[2] + && center(2) < subhi[2]) { + //printf("******* KERATIN nlocal=%d ***\n", nlocal); + coord[0] = center(0); + coord[1] = center(1); + coord[2] = center(2); + atom->avec->create_atom(wall_particle_type, coord); - /* - * need to initialize pointers to atom vec arrays here, because they could have changed - * due to calling grow() in create_atoms() above; - */ + /* + * need to initialize pointers to atom vec arrays here, because they could have changed + * due to calling grow() in create_atoms() above; + */ - tagint *mol = atom->molecule; - int *type = atom->type; - double *radius = atom->radius; - double *contact_radius = atom->contact_radius; - double **smd_data_9 = atom->smd_data_9; - double **x0 = atom->x0; + tagint *mol = atom->molecule; + int *type = atom->type; + double *radius = atom->radius; + double *contact_radius = atom->contact_radius; + double **smd_data_9 = atom->smd_data_9; + double **x0 = atom->x0; - radius[ilocal] = r; //ilocal; - contact_radius[ilocal] = r; //ilocal; - mol[ilocal] = wall_molecule_id; - type[ilocal] = wall_particle_type; - x0[ilocal][0] = normal(0); - x0[ilocal][1] = normal(1); - x0[ilocal][2] = normal(2); - smd_data_9[ilocal][0] = vert[0](0); - smd_data_9[ilocal][1] = vert[0](1); - smd_data_9[ilocal][2] = vert[0](2); - smd_data_9[ilocal][3] = vert[1](0); - smd_data_9[ilocal][4] = vert[1](1); - smd_data_9[ilocal][5] = vert[1](2); - smd_data_9[ilocal][6] = vert[2](0); - smd_data_9[ilocal][7] = vert[2](1); - smd_data_9[ilocal][8] = vert[2](2); + radius[ilocal] = r; //ilocal; + contact_radius[ilocal] = r; //ilocal; + mol[ilocal] = wall_molecule_id; + type[ilocal] = wall_particle_type; + x0[ilocal][0] = normal(0); + x0[ilocal][1] = normal(1); + x0[ilocal][2] = normal(2); + smd_data_9[ilocal][0] = vert[0](0); + smd_data_9[ilocal][1] = vert[0](1); + smd_data_9[ilocal][2] = vert[0](2); + smd_data_9[ilocal][3] = vert[1](0); + smd_data_9[ilocal][4] = vert[1](1); + smd_data_9[ilocal][5] = vert[1](2); + smd_data_9[ilocal][6] = vert[2](0); + smd_data_9[ilocal][7] = vert[2](1); + smd_data_9[ilocal][8] = vert[2](2); - ilocal++; - } + ilocal++; + } - } + } // set new total # of atoms and error check - bigint nblocal = atom->nlocal; - MPI_Allreduce(&nblocal, &atom->natoms, 1, MPI_LMP_BIGINT, MPI_SUM, world); - if (atom->natoms < 0 || atom->natoms >= MAXBIGINT) - error->all(FLERR, "Too many total atoms"); + bigint nblocal = atom->nlocal; + MPI_Allreduce(&nblocal, &atom->natoms, 1, MPI_LMP_BIGINT, MPI_SUM, world); + if (atom->natoms < 0 || atom->natoms >= MAXBIGINT) + error->all(FLERR, "Too many total atoms"); // add IDs for newly created atoms // check that atom IDs are valid - if (atom->tag_enable) - atom->tag_extend(); - atom->tag_check(); + if (atom->tag_enable) + atom->tag_extend(); + atom->tag_check(); // create global mapping of atoms // zero nghost in case are adding new atoms to existing atoms - if (atom->map_style) { - atom->nghost = 0; - atom->map_init(); - atom->map_set(); - } + if (atom->map_style) { + atom->nghost = 0; + atom->map_init(); + atom->map_set(); + } // print status - if (comm->me == 0) { - if (screen) { - printf("... fix smd/wall_surface finished reading triangulated surface\n"); - fprintf(screen, "fix smd/wall_surface created " BIGINT_FORMAT " atoms\n", atom->natoms - natoms_previous); - printf(">>========>>========>>========>>========>>========>>========>>========>>========\n"); - } - if (logfile) { - fprintf(logfile, "... fix smd/wall_surface finished reading triangulated surface\n"); - fprintf(logfile, "fix smd/wall_surface created " BIGINT_FORMAT " atoms\n", atom->natoms - natoms_previous); - fprintf(logfile, ">>========>>========>>========>>========>>========>>========>>========>>========\n"); - } - } + if (comm->me == 0) { + if (screen) { + printf("... fix smd/wall_surface finished reading triangulated surface\n"); + fprintf(screen, "fix smd/wall_surface created " BIGINT_FORMAT " atoms\n", atom->natoms - natoms_previous); + printf(">>========>>========>>========>>========>>========>>========>>========>>========\n"); + } + if (logfile) { + fprintf(logfile, "... fix smd/wall_surface finished reading triangulated surface\n"); + fprintf(logfile, "fix smd/wall_surface created " BIGINT_FORMAT " atoms\n", atom->natoms - natoms_previous); + fprintf(logfile, ">>========>>========>>========>>========>>========>>========>>========>>========\n"); + } + } - delete[] vert; - fclose(fp); + delete[] vert; + fclose(fp); } From 84657f1531c0da11a7ee11b7d3e553b79d15cd1b Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 6 Sep 2018 12:00:04 -0400 Subject: [PATCH 148/302] final pass at sprintf() buffer overflow prevention. also fix typo in previous commit --- src/REPLICA/neb.cpp | 2 +- src/USER-SMD/pair_smd_tlsph.cpp | 4 ++-- src/USER-SMD/pair_smd_ulsph.cpp | 4 ++-- src/USER-SMTBQ/pair_smtbq.cpp | 2 +- src/USER-UEF/dump_cfg_uef.cpp | 4 +--- 5 files changed, 7 insertions(+), 9 deletions(-) diff --git a/src/REPLICA/neb.cpp b/src/REPLICA/neb.cpp index 9a4de9ca0b..3963379356 100644 --- a/src/REPLICA/neb.cpp +++ b/src/REPLICA/neb.cpp @@ -549,7 +549,7 @@ void NEB::open(char *file) else { #ifdef LAMMPS_GZIP char gunzip[128]; - snprintf(gunz128,ip,"gzip -c -d %s",file); + snprintf(gunzip,128,"gzip -c -d %s",file); #ifdef _WIN32 fp = _popen(gunzip,"rb"); diff --git a/src/USER-SMD/pair_smd_tlsph.cpp b/src/USER-SMD/pair_smd_tlsph.cpp index 09fe3b1180..ab6b7d2785 100644 --- a/src/USER-SMD/pair_smd_tlsph.cpp +++ b/src/USER-SMD/pair_smd_tlsph.cpp @@ -1684,8 +1684,8 @@ void PairTlsph::coeff(int narg, char **arg) { } // end energy release rate failure criterion else { - sprintf(str, "unknown *KEYWORD: %s", arg[ioffset]); - error->all(FLERR, str); + snprintf(str,128,"unknown *KEYWORD: %s", arg[ioffset]); + error->all(FLERR, str); } } diff --git a/src/USER-SMD/pair_smd_ulsph.cpp b/src/USER-SMD/pair_smd_ulsph.cpp index ff3720b2ff..50af6e2356 100644 --- a/src/USER-SMD/pair_smd_ulsph.cpp +++ b/src/USER-SMD/pair_smd_ulsph.cpp @@ -1331,8 +1331,8 @@ void PairULSPH::coeff(int narg, char **arg) { } // end *ARTIFICIAL_STRESS else { - sprintf(str, "unknown *KEYWORD: %s", arg[ioffset]); - error->all(FLERR, str); + snprintf(str,128, "unknown *KEYWORD: %s", arg[ioffset]); + error->all(FLERR, str); } } diff --git a/src/USER-SMTBQ/pair_smtbq.cpp b/src/USER-SMTBQ/pair_smtbq.cpp index a8cce49749..c2690dc864 100644 --- a/src/USER-SMTBQ/pair_smtbq.cpp +++ b/src/USER-SMTBQ/pair_smtbq.cpp @@ -399,7 +399,7 @@ void PairSMTBQ::read_file(char *file) fp = force->open_potential(file); if ( fp == NULL ) { char str[128]; - sprintf(str,"Cannot open SMTBQ potential file %s",file); + snprintf(str,128,"Cannot open SMTBQ potential file %s",file); error->one(FLERR,str); } diff --git a/src/USER-UEF/dump_cfg_uef.cpp b/src/USER-UEF/dump_cfg_uef.cpp index 44af823332..58b3ec5a1f 100644 --- a/src/USER-UEF/dump_cfg_uef.cpp +++ b/src/USER-UEF/dump_cfg_uef.cpp @@ -90,9 +90,7 @@ void DumpCFGUef::write_header(bigint n) if (atom->peri_flag) scale = atom->pdscale; else if (unwrapflag == 1) scale = UNWRAPEXPAND; - char str[64]; - sprintf(str,"Number of particles = %s\n",BIGINT_FORMAT); - fprintf(fp,str,n); + fprintf(fp,"Number of particles = " BIGINT_FORMAT "\n",n); fprintf(fp,"A = %g Angstrom (basic length-scale)\n",scale); // in box[][] columns are cell edges // in H0, rows are cell edges From b3079f3aec02e74ce14616b6fdf91454e2bd35f2 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 6 Sep 2018 12:05:32 -0400 Subject: [PATCH 149/302] rename files and classes for pair style eam/cd/omp to follow the rename of the non-threaded classes --- src/Purge.list | 3 +++ ...pair_cdeam_omp.cpp => pair_eam_cd_omp.cpp} | 14 ++++++------ .../{pair_cdeam_omp.h => pair_eam_cd_omp.h} | 22 +++++++++---------- 3 files changed, 21 insertions(+), 18 deletions(-) rename src/USER-OMP/{pair_cdeam_omp.cpp => pair_eam_cd_omp.cpp} (97%) rename src/USER-OMP/{pair_cdeam_omp.h => pair_eam_cd_omp.h} (71%) diff --git a/src/Purge.list b/src/Purge.list index cb98636b1c..c70392c935 100644 --- a/src/Purge.list +++ b/src/Purge.list @@ -24,6 +24,9 @@ style_nstencil.h style_ntopo.h # other auto-generated files lmpinstalledpkgs.h +# renamed on 6 September 2018 +pair_cdeam_omp.h +pair_cdeam_omp.cpp # renamed on 31 July 2018 pair_cdeam.h pair_cdeam.cpp diff --git a/src/USER-OMP/pair_cdeam_omp.cpp b/src/USER-OMP/pair_eam_cd_omp.cpp similarity index 97% rename from src/USER-OMP/pair_cdeam_omp.cpp rename to src/USER-OMP/pair_eam_cd_omp.cpp index c3a9454567..68c01c83d2 100644 --- a/src/USER-OMP/pair_cdeam_omp.cpp +++ b/src/USER-OMP/pair_eam_cd_omp.cpp @@ -15,7 +15,7 @@ #include #include -#include "pair_cdeam_omp.h" +#include "pair_eam_cd_omp.h" #include "atom.h" #include "comm.h" #include "error.h" @@ -44,8 +44,8 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -PairCDEAMOMP::PairCDEAMOMP(LAMMPS *lmp, int _cdeamVersion) : - PairEAM(lmp), PairCDEAM(lmp,_cdeamVersion), ThrOMP(lmp, THR_PAIR) +PairEAMCDOMP::PairEAMCDOMP(LAMMPS *lmp, int _cdeamVersion) : + PairEAM(lmp), PairEAMCD(lmp,_cdeamVersion), ThrOMP(lmp, THR_PAIR) { suffix_flag |= Suffix::OMP; respa_enable = 0; @@ -53,7 +53,7 @@ PairCDEAMOMP::PairCDEAMOMP(LAMMPS *lmp, int _cdeamVersion) : /* ---------------------------------------------------------------------- */ -void PairCDEAMOMP::compute(int eflag, int vflag) +void PairEAMCDOMP::compute(int eflag, int vflag) { if (eflag || vflag) { ev_setup(eflag,vflag); @@ -143,7 +143,7 @@ void PairCDEAMOMP::compute(int eflag, int vflag) } template -void PairCDEAMOMP::eval(int iifrom, int iito, ThrData * const thr) +void PairEAMCDOMP::eval(int iifrom, int iito, ThrData * const thr) { int i,j,ii,jj,jnum,itype,jtype; double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair; @@ -534,10 +534,10 @@ void PairCDEAMOMP::eval(int iifrom, int iito, ThrData * const thr) /* ---------------------------------------------------------------------- */ -double PairCDEAMOMP::memory_usage() +double PairEAMCDOMP::memory_usage() { double bytes = memory_usage_thr(); - bytes += PairCDEAM::memory_usage(); + bytes += PairEAMCD::memory_usage(); return bytes; } diff --git a/src/USER-OMP/pair_cdeam_omp.h b/src/USER-OMP/pair_eam_cd_omp.h similarity index 71% rename from src/USER-OMP/pair_cdeam_omp.h rename to src/USER-OMP/pair_eam_cd_omp.h index 2839ab0ed0..d46a5383f5 100644 --- a/src/USER-OMP/pair_cdeam_omp.h +++ b/src/USER-OMP/pair_eam_cd_omp.h @@ -17,23 +17,23 @@ #ifdef PAIR_CLASS -PairStyle(eam/cd/omp,PairCDEAM_OneSiteOMP) -PairStyle(eam/cd/old/omp,PairCDEAM_TwoSiteOMP) +PairStyle(eam/cd/omp,PairEAMCD_OneSiteOMP) +PairStyle(eam/cd/old/omp,PairEAMCD_TwoSiteOMP) #else -#ifndef LMP_PAIR_CDEAM_OMP_H -#define LMP_PAIR_CDEAM_OMP_H +#ifndef LMP_PAIR_EAM_CD_OMP_H +#define LMP_PAIR_EAM_CD_OMP_H -#include "pair_cdeam.h" +#include "pair_eam_cd.h" #include "thr_omp.h" namespace LAMMPS_NS { -class PairCDEAMOMP : public PairCDEAM, public ThrOMP { +class PairEAMCDOMP : public PairEAMCD, public ThrOMP { public: - PairCDEAMOMP(class LAMMPS *, int); + PairEAMCDOMP(class LAMMPS *, int); virtual void compute(int, int); virtual double memory_usage(); @@ -44,19 +44,19 @@ class PairCDEAMOMP : public PairCDEAM, public ThrOMP { }; /// The one-site concentration formulation of CD-EAM. - class PairCDEAM_OneSiteOMP : public PairCDEAMOMP + class PairEAMCD_OneSiteOMP : public PairEAMCDOMP { public: /// Constructor. - PairCDEAM_OneSiteOMP(class LAMMPS* lmp) : PairEAM(lmp), PairCDEAMOMP(lmp, 1) {} + PairEAMCD_OneSiteOMP(class LAMMPS* lmp) : PairEAM(lmp), PairEAMCDOMP(lmp, 1) {} }; /// The two-site concentration formulation of CD-EAM. - class PairCDEAM_TwoSiteOMP : public PairCDEAMOMP + class PairEAMCD_TwoSiteOMP : public PairEAMCDOMP { public: /// Constructor. - PairCDEAM_TwoSiteOMP(class LAMMPS* lmp) : PairEAM(lmp), PairCDEAMOMP(lmp, 2) {} + PairEAMCD_TwoSiteOMP(class LAMMPS* lmp) : PairEAM(lmp), PairEAMCDOMP(lmp, 2) {} }; } From b915716b6007ff25717640eda7246595352ba22c Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 6 Sep 2018 12:27:10 -0400 Subject: [PATCH 150/302] fix inconsistency resulting from error in auto-replace macro --- src/USER-MISC/pair_meam_sw_spline.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/USER-MISC/pair_meam_sw_spline.cpp b/src/USER-MISC/pair_meam_sw_spline.cpp index 20dade5e5f..e17c13865d 100644 --- a/src/USER-MISC/pair_meam_sw_spline.cpp +++ b/src/USER-MISC/pair_meam_sw_spline.cpp @@ -466,7 +466,7 @@ void PairMEAMSWSpline::read_file(const char* filename) FILE *fp = force->open_potential(filename); if(fp == NULL) { char str[1024]; - snprintf(str,128,"Cannot open spline MEAM potential file %s", filename); + snprintf(str,1024,"Cannot open spline MEAM potential file %s", filename); error->one(FLERR,str); } From efd582fb21d11dcb32c10a6cc4267b9578ece81d Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 6 Sep 2018 13:13:20 -0400 Subject: [PATCH 151/302] update list of code owners for automatic review requests. started assigning core files --- .github/CODEOWNERS | 67 ++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 67 insertions(+) diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS index b91e58a83f..4f561a4c19 100644 --- a/.github/CODEOWNERS +++ b/.github/CODEOWNERS @@ -17,6 +17,7 @@ src/GPU/* @ndtrung81 src/KOKKOS/* @stanmoore1 src/KIM/* @ellio167 src/LATTE/* @cnegre +src/MESSAGE/* @sjplimp src/SPIN/* @julient31 src/USER-CGDNA/* @ohenrich src/USER-CGSDK/* @akohlmey @@ -32,16 +33,82 @@ src/USER-PHONON/* @lingtikong src/USER-OMP/* @akohlmey src/USER-QMMM/* @akohlmey src/USER-REAXC/* @hasanmetin +src/USER-SCAFACOS/* @rhalver src/USER-TALLY/* @akohlmey src/USER-UEF/* @danicholson src/USER-VTK/* @rbberger + # individual files in packages src/GPU/pair_vashishta_gpu.* @andeplane src/KOKKOS/pair_vashishta_kokkos.* @andeplane src/MANYBODY/pair_vashishta_table.* @andeplane +src/MANYBODY/pair_atm.* @sergeylishchuk src/USER-MISC/fix_bond_react.* @jrgissing src/USER-MISC/*_grem.* @dstelter92 +src/USER-MISC/compute_stress_mop*.* @RomainVermorel + +# core LAMMPS classes +src/lammps.* @sjplimp +src/pointers.h @sjplimp +src/atom.* @sjplimp +src/atom_vec.* @sjplimp +src/angle.* @sjplimp +src/bond.* @sjplimp +src/comm*.* @sjplimp +src/compute.* @sjplimp +src/dihedral.* @sjplimp +src/domain.* @sjplimp +src/dump*.* @sjplimp +src/error.* @sjplimp +src/finish.* @sjplimp +src/fix.* @sjplimp +src/force.* @sjplimp +src/group.* @sjplimp +src/improper.* @sjplimp +src/kspace.* @sjplimp +src/lmptyp.h @sjplimp +src/library.* @sjplimp +src/main.cpp @sjplimp +src/memory.* @sjplimp +src/modify.* @sjplimp +src/molecule.* @sjplimp +src/my_page.h @sjplimp +src/my_pool_chunk.h @sjplimp +src/npair*.* @sjplimp +src/ntopo*.* @sjplimp +src/nstencil*.* @sjplimp +src/neighbor.* @sjplimp +src/nbin*.* @sjplimp +src/neigh_*.* @sjplimp +src/output.* @sjplimp +src/pair.* @sjplimp +src/rcb.* @sjplimp +src/random_*.* @sjplimp +src/region*.* @sjplimp +src/rcb.* @sjplimp +src/read*.* @sjplimp +src/rerun.* @sjplimp +src/run.* @sjplimp +src/respa.* @sjplimp +src/set.* @sjplimp +src/special.* @sjplimp +src/suffix.h @sjplimp +src/thermo.* @sjplimp +src/universe.* @sjplimp +src/update.* @sjplimp +src/variable.* @sjplimp +src/verlet.* @sjplimp +src/velocity.* @sjplimp +src/write_data.* @sjplimp +src/write_restart.* @sjplimp + +# overrides for specific files +src/dump_movie.* @akohlmey +src/exceptions.h @rbberger +src/fix_nh.* @athomps +src/info.* @akohlmey @rbberger +src/timer.* @akohlmey # tools tools/msi2lmp/* @akohlmey From d7b00f86f88cb2266de9eaaf3a8ef0729f9ce42a Mon Sep 17 00:00:00 2001 From: Christoph Junghans Date: Thu, 6 Sep 2018 14:18:28 -0600 Subject: [PATCH 152/302] cmake: fix Eigen3 detection For some reason FindEigen3.cmake defines all cap. variables, i.e. Eigen3_FOUND -> EIGEN3_FOUND --- cmake/CMakeLists.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index 2e238cdf2b..149f9da817 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -551,7 +551,7 @@ if(PKG_USER-SMD) list(APPEND LAMMPS_DEPS Eigen3_build) else() find_package(Eigen3) - if(NOT Eigen3_FOUND) + if(NOT EIGEN3_FOUND) message(FATAL_ERROR "Eigen3 not found, help CMake to find it by setting EIGEN3_INCLUDE_DIR, or set DOWNLOAD_EIGEN3=ON to download it") endif() endif() From 8f8aee65d20f9b11ab4e7f70e9412202ae9fdfc5 Mon Sep 17 00:00:00 2001 From: Christoph Junghans Date: Thu, 6 Sep 2018 14:37:08 -0600 Subject: [PATCH 153/302] cmake: fix globbing of emacs files Done by: sed -i '/GLOB/s@/\*\.@/[^.]*.@g' CMakeLists.txt --- cmake/CMakeLists.txt | 28 ++++++++++++++-------------- 1 file changed, 14 insertions(+), 14 deletions(-) diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index 2e238cdf2b..45e6870ce8 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -13,7 +13,7 @@ get_filename_component(LAMMPS_DOC_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../doc ABSOLUT # To avoid conflicts with the conventional Makefile build system, we build everything here -file(GLOB LIB_SOURCES ${LAMMPS_SOURCE_DIR}/*.cpp) +file(GLOB LIB_SOURCES ${LAMMPS_SOURCE_DIR}/[^.]*.cpp) file(GLOB LMP_SOURCES ${LAMMPS_SOURCE_DIR}/main.cpp) list(REMOVE_ITEM LIB_SOURCES ${LMP_SOURCES}) @@ -348,7 +348,7 @@ if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE) find_package(BLAS) if(NOT LAPACK_FOUND OR NOT BLAS_FOUND) enable_language(Fortran) - file(GLOB LAPACK_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/linalg/*.[fF]) + file(GLOB LAPACK_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/linalg/[^.]*.[fF]) add_library(linalg STATIC ${LAPACK_SOURCES}) set(LAPACK_LIBRARIES linalg) else() @@ -603,7 +603,7 @@ endif() if(PKG_MESSAGE) option(MESSAGE_ZMQ "Use ZeroMQ in MESSAGE package" OFF) - file(GLOB_RECURSE cslib_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/*.F + file(GLOB_RECURSE cslib_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.F ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/*.c ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/*.cpp) if(BUILD_SHARED_LIBS) @@ -720,8 +720,8 @@ RegisterStyles(${LAMMPS_SOURCE_DIR}) foreach(PKG ${DEFAULT_PACKAGES}) set(${PKG}_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/${PKG}) - file(GLOB ${PKG}_SOURCES ${${PKG}_SOURCES_DIR}/*.cpp) - file(GLOB ${PKG}_HEADERS ${${PKG}_SOURCES_DIR}/*.h) + file(GLOB ${PKG}_SOURCES ${${PKG}_SOURCES_DIR}/[^.]*.cpp) + file(GLOB ${PKG}_HEADERS ${${PKG}_SOURCES_DIR}/[^.]*.h) # check for package files in src directory due to old make system DetectBuildSystemConflict(${LAMMPS_SOURCE_DIR} ${${PKG}_SOURCES} ${${PKG}_HEADERS}) @@ -739,8 +739,8 @@ endforeach() foreach(PKG ${ACCEL_PACKAGES}) set(${PKG}_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/${PKG}) - file(GLOB ${PKG}_SOURCES ${${PKG}_SOURCES_DIR}/*.cpp) - file(GLOB ${PKG}_HEADERS ${${PKG}_SOURCES_DIR}/*.h) + file(GLOB ${PKG}_SOURCES ${${PKG}_SOURCES_DIR}/[^.]*.cpp) + file(GLOB ${PKG}_HEADERS ${${PKG}_SOURCES_DIR}/[^.]*.h) # check for package files in src directory due to old make system DetectBuildSystemConflict(${LAMMPS_SOURCE_DIR} ${${PKG}_SOURCES} ${${PKG}_HEADERS}) @@ -754,7 +754,7 @@ foreach(SIMPLE_LIB REAX MEAM POEMS USER-ATC USER-AWPMD USER-COLVARS USER-H5MD if(PKG_${SIMPLE_LIB}) string(REGEX REPLACE "^USER-" "" PKG_LIB "${SIMPLE_LIB}") string(TOLOWER "${PKG_LIB}" PKG_LIB) - file(GLOB_RECURSE ${PKG_LIB}_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/*.F + file(GLOB_RECURSE ${PKG_LIB}_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.F ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/*.c ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/*.cpp) add_library(${PKG_LIB} STATIC ${${PKG_LIB}_SOURCES}) list(APPEND LAMMPS_LINK_LIBS ${PKG_LIB}) @@ -1039,7 +1039,7 @@ if(PKG_GPU) set(GPU_PREC_SETTING "SINGLE_SINGLE") endif() - file(GLOB GPU_LIB_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/gpu/*.cpp) + file(GLOB GPU_LIB_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cpp) file(MAKE_DIRECTORY ${LAMMPS_LIB_BINARY_DIR}/gpu) if(GPU_API STREQUAL "CUDA") @@ -1052,15 +1052,15 @@ if(PKG_GPU) set(GPU_ARCH "sm_30" CACHE STRING "LAMMPS GPU CUDA SM architecture (e.g. sm_60)") - file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/*.cu ${CMAKE_CURRENT_SOURCE_DIR}/gpu/*.cu) + file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu ${CMAKE_CURRENT_SOURCE_DIR}/gpu/[^.]*.cu) list(REMOVE_ITEM GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_pppm.cu) cuda_include_directories(${LAMMPS_LIB_SOURCE_DIR}/gpu ${LAMMPS_LIB_BINARY_DIR}/gpu) if(CUDPP_OPT) cuda_include_directories(${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini) - file(GLOB GPU_LIB_CUDPP_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/*.cpp) - file(GLOB GPU_LIB_CUDPP_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/*.cu) + file(GLOB GPU_LIB_CUDPP_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/[^.]*.cpp) + file(GLOB GPU_LIB_CUDPP_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/[^.]*.cu) endif() cuda_compile_cubin(GPU_GEN_OBJS ${GPU_LIB_CU} OPTIONS @@ -1109,7 +1109,7 @@ if(PKG_GPU) include(OpenCLUtils) set(OCL_COMMON_HEADERS ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_preprocessor.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_aux_fun1.h) - file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/*.cu) + file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu) list(REMOVE_ITEM GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne.cu ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne_lj.cu) foreach(GPU_KERNEL ${GPU_LIB_CU}) @@ -1236,7 +1236,7 @@ if(BUILD_DOC) set(VIRTUALENV ${PYTHON_EXECUTABLE} -m virtualenv) - file(GLOB DOC_SOURCES ${LAMMPS_DOC_DIR}/src/*.txt) + file(GLOB DOC_SOURCES ${LAMMPS_DOC_DIR}/src/[^.]*.txt) file(GLOB PDF_EXTRA_SOURCES ${LAMMPS_DOC_DIR}/src/lammps_commands*.txt ${LAMMPS_DOC_DIR}/src/lammps_support.txt ${LAMMPS_DOC_DIR}/src/lammps_tutorials.txt) list(REMOVE_ITEM DOC_SOURCES ${PDF_EXTRA_SOURCES}) From 44fcdc40244a5f146f20c4ec01fab20720c60413 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 6 Sep 2018 21:20:47 -0400 Subject: [PATCH 154/302] update reference examples with versions that do not vary by MPI rank count --- examples/USER/misc/mop/data.mop | 2467 +++++++++++++++++ examples/USER/misc/mop/in.compute_stress_mop | 44 +- .../mop/log.5Sep18.compute_stress_mop.g++.1 | 111 + .../mop/log.5Sep18.compute_stress_mop.g++.4 | 111 + examples/USER/misc/mop/moppz.time.reference | 405 ++- examples/USER/misc/mop/mopz0.time.reference | 5 +- examples/USER/misc/mop/profile.z.reference | 227 -- 7 files changed, 2883 insertions(+), 487 deletions(-) create mode 100644 examples/USER/misc/mop/data.mop create mode 100644 examples/USER/misc/mop/log.5Sep18.compute_stress_mop.g++.1 create mode 100644 examples/USER/misc/mop/log.5Sep18.compute_stress_mop.g++.4 delete mode 100644 examples/USER/misc/mop/profile.z.reference diff --git a/examples/USER/misc/mop/data.mop b/examples/USER/misc/mop/data.mop new file mode 100644 index 0000000000..7f158d7626 --- /dev/null +++ b/examples/USER/misc/mop/data.mop @@ -0,0 +1,2467 @@ +LAMMPS data file via write_data, version 31 Aug 2018, timestep = 0 + +1224 atoms +2 atom types + +0.0000000000000000e+00 9.5244063118091962e+00 xlo xhi +0.0000000000000000e+00 9.5244063118091962e+00 ylo yhi +-2.0e+00 1.6e+01 zlo zhi + +Masses + +1 1 +2 1 + +Atoms # atomic + +793 2 0.0000000000000000e+00 0.0000000000000000e+00 -1.5874010519681994e+00 0 0 0 +794 2 7.9370052598409979e-01 7.9370052598409979e-01 -1.5874010519681994e+00 0 0 0 +797 2 1.5874010519681996e+00 0.0000000000000000e+00 -1.5874010519681994e+00 0 0 0 +798 2 2.3811015779522990e+00 7.9370052598409979e-01 -1.5874010519681994e+00 0 0 0 +801 2 3.1748021039363992e+00 0.0000000000000000e+00 -1.5874010519681994e+00 0 0 0 +802 2 3.9685026299204984e+00 7.9370052598409979e-01 -1.5874010519681994e+00 0 0 0 +805 2 4.7622031559045981e+00 0.0000000000000000e+00 -1.5874010519681994e+00 0 0 0 +806 2 5.5559036818886973e+00 7.9370052598409979e-01 -1.5874010519681994e+00 0 0 0 +809 2 6.3496042078727983e+00 0.0000000000000000e+00 -1.5874010519681994e+00 0 0 0 +810 2 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7.1433047338568993e+00 3.9685026299204984e+00 -1.5874010519681994e+00 0 0 0 +861 2 7.9370052598409968e+00 3.1748021039363992e+00 -1.5874010519681994e+00 0 0 0 +862 2 8.7307057858250960e+00 3.9685026299204984e+00 -1.5874010519681994e+00 0 0 0 +865 2 0.0000000000000000e+00 4.7622031559045981e+00 -1.5874010519681994e+00 0 0 0 +866 2 7.9370052598409979e-01 5.5559036818886973e+00 -1.5874010519681994e+00 0 0 0 +869 2 1.5874010519681996e+00 4.7622031559045981e+00 -1.5874010519681994e+00 0 0 0 +870 2 2.3811015779522990e+00 5.5559036818886973e+00 -1.5874010519681994e+00 0 0 0 +873 2 3.1748021039363992e+00 4.7622031559045981e+00 -1.5874010519681994e+00 0 0 0 +874 2 3.9685026299204984e+00 5.5559036818886973e+00 -1.5874010519681994e+00 0 0 0 +877 2 4.7622031559045981e+00 4.7622031559045981e+00 -1.5874010519681994e+00 0 0 0 +878 2 5.5559036818886973e+00 5.5559036818886973e+00 -1.5874010519681994e+00 0 0 0 +881 2 6.3496042078727983e+00 4.7622031559045981e+00 -1.5874010519681994e+00 0 0 0 +882 2 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0.0000000000000000e+00 0.0000000000000000e+00 -2.6803696685654556e-02 +1219 0.0000000000000000e+00 0.0000000000000000e+00 -2.6803696685654556e-02 +1221 0.0000000000000000e+00 0.0000000000000000e+00 -2.6803696685654556e-02 +1222 0.0000000000000000e+00 0.0000000000000000e+00 -2.6803696685654556e-02 +1223 0.0000000000000000e+00 0.0000000000000000e+00 -2.6803696685654556e-02 +1224 0.0000000000000000e+00 0.0000000000000000e+00 -2.6803696685654556e-02 diff --git a/examples/USER/misc/mop/in.compute_stress_mop b/examples/USER/misc/mop/in.compute_stress_mop index cfa97f5dfe..442596dcf1 100644 --- a/examples/USER/misc/mop/in.compute_stress_mop +++ b/examples/USER/misc/mop/in.compute_stress_mop @@ -1,30 +1,20 @@ variable T equal 0.8 variable p_solid equal 0.05 -lattice fcc 1.0 -region box block 0.0 6.0 0.0 6.0 -2.0 12.0 -create_box 2 box +read_data data.mop -mass * 1.0 pair_style lj/cut 2.5 pair_coeff * * 1.0 1.0 pair_coeff 1 2 0.5 1.0 pair_coeff 2 2 0.0 0.0 neigh_modify delay 0 -region solid_bottom block INF INF INF INF -1.1 0.1 -region liquid block INF INF INF INF 1.1 8.9 -region solid_up block INF INF INF INF 9.9 11.1 - -create_atoms 1 region liquid -delete_atoms porosity liquid 0.26 88765 -group liquid region liquid - -create_atoms 2 region solid_bottom -group solid_bottom region solid_bottom -create_atoms 2 region solid_up -group solid_up region solid_up -group solid union solid_bottom solid_up +group liquid type 1 +group solid type 2 +region bottom block INF INF INF INF INF 7.0 +group bottom region bottom +group solid_bottom intersect solid bottom +group solid_up subtract solid solid_bottom variable faSolid equal ${p_solid}*lx*ly/count(solid_up) fix piston_up solid_up aveforce NULL NULL -${faSolid} @@ -35,28 +25,16 @@ compute Tliq liquid temp fix nvtliq liquid nvt temp $T $T 0.5 fix_modify nvtliq temp Tliq -thermo 10000 +thermo 1000 thermo_modify flush yes temp Tliq -dump 1 all atom 10000 dump.lammpstrj - fix fxbal all balance 1000 1.05 shift z 10 1.05 -velocity liquid create $T 47298 dist gaussian rot yes -run 50000 -undump 1 -reset_timestep 0 - -compute bin_z liquid chunk/atom bin/1d z 0.0 0.1 units box - -compute liquidStress_ke liquid stress/atom NULL ke -compute liquidStress_vir liquid stress/atom NULL virial -fix profile_z liquid ave/chunk 10 1000 10000 bin_z density/number temp c_liquidStress_ke[1] c_liquidStress_ke[2] c_liquidStress_ke[3] c_liquidStress_ke[4] c_liquidStress_ke[5] c_liquidStress_ke[6] c_liquidStress_vir[1] c_liquidStress_vir[2] c_liquidStress_vir[3] c_liquidStress_vir[4] c_liquidStress_vir[5] c_liquidStress_vir[6] ave running overwrite file profile.z compute mopz0 all stress/mop z center kin conf -fix mopz0t all ave/time 10 1000 10000 c_mopz0[*] file mopz0.time +fix mopz0t all ave/time 1 1 1 c_mopz0[*] file mopz0.time compute moppz liquid stress/mop/profile z 0.0 0.1 kin conf -fix moppzt all ave/time 100 100 10000 c_moppz[*] ave running overwrite file moppz.time mode vector +fix moppzt all ave/time 1 1 1 c_moppz[*] ave running overwrite file moppz.time mode vector -run 40000 +run 0 diff --git a/examples/USER/misc/mop/log.5Sep18.compute_stress_mop.g++.1 b/examples/USER/misc/mop/log.5Sep18.compute_stress_mop.g++.1 new file mode 100644 index 0000000000..7b3f24cf38 --- /dev/null +++ b/examples/USER/misc/mop/log.5Sep18.compute_stress_mop.g++.1 @@ -0,0 +1,111 @@ +LAMMPS (5 Sep 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +variable T equal 0.8 +variable p_solid equal 0.05 + +read_data data.mop + orthogonal box = (0 0 -2) to (9.52441 9.52441 16) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 1224 atoms + reading velocities ... + 1224 velocities + +pair_style lj/cut 2.5 +pair_coeff * * 1.0 1.0 +pair_coeff 1 2 0.5 1.0 +pair_coeff 2 2 0.0 0.0 +neigh_modify delay 0 + +group liquid type 1 +792 atoms in group liquid +group solid type 2 +432 atoms in group solid +region bottom block INF INF INF INF INF 7.0 +group bottom region bottom +630 atoms in group bottom +group solid_bottom intersect solid bottom +216 atoms in group solid_bottom +group solid_up subtract solid solid_bottom +216 atoms in group solid_up + +variable faSolid equal ${p_solid}*lx*ly/count(solid_up) +variable faSolid equal 0.05*lx*ly/count(solid_up) +fix piston_up solid_up aveforce NULL NULL -${faSolid} +fix piston_up solid_up aveforce NULL NULL -0.0209986841649146 +fix freeze_up solid_up setforce 0.0 0.0 NULL +fix freeze_bottom solid_bottom setforce 0.0 0.0 0.0 +fix nvesol solid nve +compute Tliq liquid temp +fix nvtliq liquid nvt temp $T $T 0.5 +fix nvtliq liquid nvt temp 0.8 $T 0.5 +fix nvtliq liquid nvt temp 0.8 0.8 0.5 +fix_modify nvtliq temp Tliq +WARNING: Temperature for fix modify is not for group all (src/fix_nh.cpp:1404) + +thermo 1000 +thermo_modify flush yes temp Tliq +WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488) + +fix fxbal all balance 1000 1.05 shift z 10 1.05 + +compute mopz0 all stress/mop z center kin conf +fix mopz0t all ave/time 1 1 1 c_mopz0[*] file mopz0.time + +compute moppz liquid stress/mop/profile z 0.0 0.1 kin conf +fix moppzt all ave/time 1 1 1 c_moppz[*] ave running overwrite file moppz.time mode vector + +run 0 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 7 7 13 + 3 neighbor lists, perpetual/occasional/extra = 1 2 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard + (2) compute stress/mop, occasional, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (3) compute stress/mop/profile, occasional, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 3.596 | 3.596 | 3.596 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 0.82011245 -3.0642111 0 -2.2692246 0.16906107 1632.8577 +Loop time of 1.19209e-06 on 1 procs for 0 steps with 1224 atoms + +167.8% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 1.192e-06 | | |100.00 + +Nlocal: 1224 ave 1224 max 1224 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 2975 ave 2975 max 2975 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 40241 ave 40241 max 40241 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 40241 +Ave neighs/atom = 32.8766 +Neighbor list builds = 0 +Dangerous builds = 0 + +Total wall time: 0:00:00 diff --git a/examples/USER/misc/mop/log.5Sep18.compute_stress_mop.g++.4 b/examples/USER/misc/mop/log.5Sep18.compute_stress_mop.g++.4 new file mode 100644 index 0000000000..dd1dc0af0f --- /dev/null +++ b/examples/USER/misc/mop/log.5Sep18.compute_stress_mop.g++.4 @@ -0,0 +1,111 @@ +LAMMPS (5 Sep 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +variable T equal 0.8 +variable p_solid equal 0.05 + +read_data data.mop + orthogonal box = (0 0 -2) to (9.52441 9.52441 16) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 1224 atoms + reading velocities ... + 1224 velocities + +pair_style lj/cut 2.5 +pair_coeff * * 1.0 1.0 +pair_coeff 1 2 0.5 1.0 +pair_coeff 2 2 0.0 0.0 +neigh_modify delay 0 + +group liquid type 1 +792 atoms in group liquid +group solid type 2 +432 atoms in group solid +region bottom block INF INF INF INF INF 7.0 +group bottom region bottom +630 atoms in group bottom +group solid_bottom intersect solid bottom +216 atoms in group solid_bottom +group solid_up subtract solid solid_bottom +216 atoms in group solid_up + +variable faSolid equal ${p_solid}*lx*ly/count(solid_up) +variable faSolid equal 0.05*lx*ly/count(solid_up) +fix piston_up solid_up aveforce NULL NULL -${faSolid} +fix piston_up solid_up aveforce NULL NULL -0.0209986841649146 +fix freeze_up solid_up setforce 0.0 0.0 NULL +fix freeze_bottom solid_bottom setforce 0.0 0.0 0.0 +fix nvesol solid nve +compute Tliq liquid temp +fix nvtliq liquid nvt temp $T $T 0.5 +fix nvtliq liquid nvt temp 0.8 $T 0.5 +fix nvtliq liquid nvt temp 0.8 0.8 0.5 +fix_modify nvtliq temp Tliq +WARNING: Temperature for fix modify is not for group all (src/fix_nh.cpp:1404) + +thermo 1000 +thermo_modify flush yes temp Tliq +WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488) + +fix fxbal all balance 1000 1.05 shift z 10 1.05 + +compute mopz0 all stress/mop z center kin conf +fix mopz0t all ave/time 1 1 1 c_mopz0[*] file mopz0.time + +compute moppz liquid stress/mop/profile z 0.0 0.1 kin conf +fix moppzt all ave/time 1 1 1 c_moppz[*] ave running overwrite file moppz.time mode vector + +run 0 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 7 7 13 + 3 neighbor lists, perpetual/occasional/extra = 1 2 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard + (2) compute stress/mop, occasional, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (3) compute stress/mop/profile, occasional, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 3.509 | 3.51 | 3.511 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 0.82011245 -3.0642111 0 -2.2692246 0.16906107 1632.8577 +Loop time of 4.06504e-05 on 4 procs for 0 steps with 1224 atoms + +65.2% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 4.065e-05 | | |100.00 + +Nlocal: 306 ave 320 max 295 min +Histogram: 1 1 0 0 0 0 1 0 0 1 +Nghost: 1450.25 ave 1485 max 1422 min +Histogram: 2 0 0 0 0 0 0 1 0 1 +Neighs: 10060.2 ave 10866 max 9507 min +Histogram: 2 0 0 0 0 1 0 0 0 1 + +Total # of neighbors = 40241 +Ave neighs/atom = 32.8766 +Neighbor list builds = 0 +Dangerous builds = 0 + +Total wall time: 0:00:00 diff --git a/examples/USER/misc/mop/moppz.time.reference b/examples/USER/misc/mop/moppz.time.reference index f8d4b532ea..1550df422d 100644 --- a/examples/USER/misc/mop/moppz.time.reference +++ b/examples/USER/misc/mop/moppz.time.reference @@ -1,226 +1,185 @@ # Time-averaged data for fix moppzt # TimeStep Number-of-rows # Row c_moppz[1] c_moppz[2] c_moppz[3] c_moppz[4] c_moppz[5] c_moppz[6] c_moppz[7] -40000 222 -1 -3.1 0 0 0 0 0 0 -2 -3 0 0 0 0 0 0 -3 -2.9 0 0 0 0 0 0 -4 -2.8 0 0 0 0 0 0 -5 -2.7 0 0 0 0 0 0 -6 -2.6 0 0 0 0 0 0 -7 -2.5 0 0 0 0 0 0 -8 -2.4 0 0 0 0 0 0 -9 -2.3 0 0 0 0 0 0 -10 -2.2 0 0 0 0 0 0 -11 -2.1 0 0 0 0 0 0 -12 -2 0 0 0 0 0 0 -13 -1.9 0 0 0 0 0 0 -14 -1.8 0 0 0 0 0 0 -15 -1.7 0 0 0 0 0 0 -16 -1.6 0 0 0 0 0 0 -17 -1.5 0 0 0 3.64631e-06 1.00467e-05 -0.00413092 -18 -1.4 0 0 0 3.64631e-06 1.00467e-05 -0.00413092 -19 -1.3 0 0 0 3.64631e-06 1.00467e-05 -0.00413092 -20 -1.2 0 0 0 3.64631e-06 1.00467e-05 -0.00413092 -21 -1.1 0 0 0 3.64631e-06 1.00467e-05 -0.00413092 -22 -1 0 0 0 3.64631e-06 1.00467e-05 -0.00413092 -23 -0.9 0 0 0 3.64631e-06 1.00467e-05 -0.00413092 -24 -0.8 0 0 0 3.64631e-06 1.00467e-05 -0.00413092 -25 -0.7 0 0 0 2.27131e-05 -7.15899e-05 -0.291079 -26 -0.6 0 0 0 2.27131e-05 -7.15899e-05 -0.291079 -27 -0.5 0 0 0 2.27131e-05 -7.15899e-05 -0.291079 -28 -0.4 0 0 0 2.27131e-05 -7.15899e-05 -0.291079 -29 -0.3 0 0 0 2.27131e-05 -7.15899e-05 -0.291079 -30 -0.2 0 0 0 2.27131e-05 -7.15899e-05 -0.291079 -31 -0.1 0 0 0 2.27131e-05 -7.15899e-05 -0.291079 -32 0 0 0 0 2.27131e-05 -7.15899e-05 -0.291079 -33 0.1 0 0 0 -0.00643877 -0.00486842 0.0289193 -34 0.2 0 0 0 -0.00643877 -0.00486842 0.0289193 -35 0.3 0 0 0 -0.00643877 -0.00486842 0.0289193 -36 0.4 0 0 0 -0.00643877 -0.00486842 0.0289193 -37 0.5 0 0 0 -0.00643877 -0.00486842 0.0289193 -38 0.6 -0.00279194 0.0093508 0.013353 -0.00639358 -0.00380391 0.021025 -39 0.7 -0.00373537 0.0122501 0.0840939 -0.00503616 -0.0112127 -0.132562 -40 0.8 0.061158 -0.0280862 0.636594 0.00453591 -0.00214426 -0.557591 -41 0.9 -0.000266217 -0.0385723 0.969803 -0.0100643 0.00387732 -0.972644 -42 1 -0.0667633 -0.0208723 0.846848 0.0121337 -0.000646173 -0.936078 -43 1.1 -0.0479918 0.0444386 0.783228 0.0206387 -0.00229641 -0.640358 -44 1.2 0.0907347 -0.00458127 0.508479 0.0271462 -0.0136805 -0.427689 -45 1.3 0.0346947 -0.015182 0.397443 0.0162624 -0.0165167 -0.323227 -46 1.4 0.0576422 -0.00277706 0.359744 0.0291978 -0.0156949 -0.265795 -47 1.5 0.0596081 -0.00318334 0.238852 0.0157713 -0.0150214 -0.273303 -48 1.6 0.016955 0.0183139 0.459661 0.00421857 -0.0129777 -0.340127 -49 1.7 0.0697698 -0.0115622 0.431809 -0.0258679 0.00300245 -0.510533 -50 1.8 0.100399 -0.0797432 0.71209 -0.0501721 0.00810306 -0.680932 -51 1.9 0.0500614 -0.0191708 0.789407 -0.0486138 0.0173172 -0.750564 -52 2 -0.00914799 -0.0341791 0.626456 -0.0471521 0.000678372 -0.701829 -53 2.1 0.0369963 0.0256396 0.706456 -0.0509059 0.0173155 -0.620292 -54 2.2 -0.0579061 -0.0608427 0.484532 -0.0294166 0.000458726 -0.521648 -55 2.3 0.00709018 -0.0497913 0.439925 -0.0279961 -0.0102977 -0.43579 -56 2.4 -0.00695344 -0.000619047 0.441961 -0.0248115 -0.0244491 -0.417814 -57 2.5 -0.0375477 0.0725146 0.521221 -0.0140031 -0.0302539 -0.426543 -58 2.6 -0.00333415 0.0411399 0.550053 -0.0244236 -0.0246652 -0.444765 -59 2.7 0.0325652 -0.0422058 0.421026 -0.00606598 -0.038332 -0.507456 -60 2.8 -0.0246015 -0.0468897 0.635467 -0.035645 -0.0428363 -0.541653 -61 2.9 -0.00247499 0.00564888 0.643559 -0.0442198 -0.0211607 -0.539113 -62 3 -0.0320027 -0.0392749 0.603448 -0.0273872 -0.0458147 -0.544274 -63 3.1 -0.00250831 0.0294524 0.630966 -0.0228213 -0.00709569 -0.534171 -64 3.2 -0.0115271 0.0256808 0.597281 -0.00722677 0.00276478 -0.493192 -65 3.3 -0.00826942 -0.0763258 0.569383 -0.0294055 0.00152838 -0.470596 -66 3.4 -4.4607e-05 0.00409392 0.454468 0.00536302 0.00576224 -0.443972 -67 3.5 -0.00145279 -0.0180142 0.532694 0.0162497 0.0129368 -0.488614 -68 3.6 -0.0435087 -0.0436055 0.544955 0.0257295 0.0204122 -0.51687 -69 3.7 -0.0154394 0.0136176 0.609813 0.0132893 -0.00555839 -0.551156 -70 3.8 -0.011446 -0.00706375 0.661117 0.0380525 0.0191365 -0.531052 -71 3.9 -0.0804251 -0.0761665 0.563738 0.0489132 0.0190947 -0.509251 -72 4 0.0127481 0.0455454 0.566261 0.038016 0.0126592 -0.515555 -73 4.1 -0.00153026 -0.025983 0.584368 0.0243742 0.00388593 -0.487748 -74 4.2 0.0488435 0.00522856 0.535885 0.0161854 -0.000859699 -0.487082 -75 4.3 -0.118588 0.134127 0.503423 -0.00404382 -0.00428885 -0.494589 -76 4.4 0.0134608 -0.0373908 0.598776 -0.0285097 -0.00468738 -0.48047 -77 4.5 0.0765487 0.055302 0.608029 -0.0450575 -0.0157753 -0.509701 -78 4.6 -0.05585 -0.0462818 0.618931 -0.0170038 -0.0358189 -0.55692 -79 4.7 0.0164839 -0.0352014 0.611466 -0.0237058 -0.0240414 -0.617077 -80 4.8 0.0436038 -0.00458656 0.612365 0.00997088 -0.0562156 -0.613109 -81 4.9 0.0352871 -0.0611231 0.776314 0.0338943 -0.0604021 -0.613378 -82 5 -0.0568251 -0.0247083 0.510044 0.00279028 -0.028082 -0.595866 -83 5.1 -1.10188e-05 -0.0120973 0.53437 0.00398708 -0.02584 -0.573631 -84 5.2 0.00992898 0.0313027 0.59329 0.00561749 0.00711019 -0.522198 -85 5.3 0.00120683 -0.0356538 0.548184 -0.0200955 0.0381984 -0.52012 -86 5.4 0.0762501 -0.00822531 0.541107 -0.0241871 0.0330327 -0.540077 -87 5.5 0.0461718 0.0519605 0.629188 -0.0222764 0.0226954 -0.551385 -88 5.6 -0.0590515 0.0287662 0.549344 -0.0420534 0.031427 -0.540878 -89 5.7 -0.021125 -0.0231434 0.508528 -0.0342499 0.0495904 -0.52078 -90 5.8 0.00366259 0.0218644 0.572742 -0.0417272 0.0150681 -0.502333 -91 5.9 -0.0198693 -0.0259311 0.564659 -0.0309091 0.0326989 -0.512076 -92 6 0.00390271 -0.00109073 0.543964 -0.00911548 -0.00232516 -0.51614 -93 6.1 0.0628801 -0.0660743 0.587361 0.00381158 0.0024442 -0.515185 -94 6.2 0.00152013 0.0147332 0.572594 0.0229772 0.0059129 -0.507687 -95 6.3 0.026454 0.0873166 0.571276 0.0178474 0.00279111 -0.513827 -96 6.4 0.0951526 -0.0589118 0.598299 0.00448651 0.0259024 -0.53599 -97 6.5 0.0619766 0.0863723 0.669836 -0.00873277 -0.00553461 -0.523788 -98 6.6 -0.0634325 0.0307315 0.69454 -0.0196477 0.0147324 -0.502773 -99 6.7 0.012962 0.00747902 0.51076 -0.0151695 0.0156039 -0.52839 -100 6.8 -0.039811 -0.00360989 0.6489 0.0120414 0.00259849 -0.491579 -101 6.9 -0.0327932 0.0484302 0.616791 -0.0091501 0.0040499 -0.499037 -102 7 0.0490981 0.105001 0.502159 0.0042417 0.00326159 -0.506754 -103 7.1 -0.0581682 0.0395551 0.590876 -0.00115276 0.025084 -0.510536 -104 7.2 -0.0278943 -0.0337449 0.607452 -0.0238974 0.0310696 -0.495835 -105 7.3 -0.0493484 -0.0370496 0.660977 0.0111283 0.0129981 -0.491408 -106 7.4 -0.0206342 -0.0567824 0.5974 0.0172099 -0.00710845 -0.51165 -107 7.5 -0.00940992 0.0303369 0.49934 0.0124837 -0.03568 -0.524051 -108 7.6 -0.0366305 0.0394555 0.459697 -0.00731655 -0.0233235 -0.52555 -109 7.7 -0.0110182 0.0639483 0.563437 -0.00857366 -0.00211197 -0.542335 -110 7.8 0.010323 0.0810661 0.550813 0.00585594 0.0131706 -0.540418 -111 7.9 -0.048191 0.0123444 0.551013 -0.0166757 0.00475367 -0.538792 -112 8 -0.0214946 0.0509729 0.576751 0.0195793 0.0328914 -0.532263 -113 8.1 0.0456292 0.0094789 0.558949 0.00867662 0.0158926 -0.524578 -114 8.2 -0.0512688 -0.091908 0.641645 0.00301901 0.00974779 -0.534635 -115 8.3 -0.00783193 -0.0632416 0.552394 0.00796143 0.0380808 -0.524053 -116 8.4 0.01777 -0.0376654 0.511021 0.0161297 0.0278027 -0.542342 -117 8.5 -0.0327248 -0.0899092 0.578655 0.0137482 0.0472277 -0.524035 -118 8.6 -0.0636407 -0.0252334 0.590898 -0.00601759 0.049413 -0.533022 -119 8.7 -0.0572488 0.0633104 0.744174 0.00670858 0.0337276 -0.548476 -120 8.8 -0.100349 0.0190862 0.738246 0.0194621 0.0386781 -0.547124 -121 8.9 0.0284238 -0.0710504 0.616557 -0.00223469 0.0256231 -0.545488 -122 9 0.0455527 0.0379271 0.549399 0.0219986 7.02084e-05 -0.554089 -123 9.1 -0.00572797 -0.0537564 0.619963 0.0151132 0.00535174 -0.541016 -124 9.2 0.0209666 0.0411495 0.526906 0.00505244 -0.0117546 -0.543559 -125 9.3 0.0350478 0.0441003 0.520438 -0.0102555 -0.0105673 -0.536683 -126 9.4 0.0546092 -0.0171837 0.598682 0.00942578 -0.0283571 -0.520765 -127 9.5 0.0180568 0.00850647 0.720246 0.0282267 -0.0412171 -0.533637 -128 9.6 0.0106648 0.0437645 0.575689 0.0151481 -0.0346536 -0.558032 -129 9.7 -0.155141 -0.00267266 0.637799 0.00208151 -0.0132553 -0.567237 -130 9.8 -0.00666603 -0.103109 0.55371 -0.00920682 0.0140328 -0.515539 -131 9.9 0.0146007 0.0526576 0.484032 -0.0113123 -0.0112639 -0.503197 -132 10 0.0146807 0.0352591 0.573481 0.015403 -0.0258601 -0.471611 -133 10.1 0.00213124 -0.036368 0.623151 0.00161826 -0.0216583 -0.471559 -134 10.2 -1.19073e-05 -0.0619808 0.588624 -0.0259091 0.00687593 -0.462229 -135 10.3 0.0570578 0.0539259 0.656283 -0.0441705 0.000600941 -0.490565 -136 10.4 -0.00888513 0.0460147 0.630823 -0.0474928 0.00205316 -0.502978 -137 10.5 0.0573266 0.0238284 0.547514 -0.0310441 0.00283003 -0.511855 -138 10.6 0.121504 0.0275327 0.615782 -0.030126 -0.0249915 -0.502326 -139 10.7 -0.0156129 -0.0437632 0.630716 0.00504067 -0.0180025 -0.545656 -140 10.8 -0.0218563 -0.0432434 0.605473 0.0104081 -0.041452 -0.579481 -141 10.9 -0.020486 0.0829505 0.610883 0.0122548 -0.0306657 -0.542298 -142 11 0.0195236 0.0729355 0.664827 0.0428504 -0.0338841 -0.517077 -143 11.1 0.0139034 0.0474138 0.664459 0.0249658 -0.0397278 -0.50611 -144 11.2 0.0179999 0.0121222 0.559603 0.0412521 -0.0516893 -0.454643 -145 11.3 0.0268913 -0.0259516 0.494548 0.0514919 -0.0324735 -0.432382 -146 11.4 0.0700355 0.00851857 0.474027 0.0146607 -0.0194147 -0.460328 -147 11.5 0.0274298 -0.0148551 0.667014 0.0264921 -0.0415723 -0.515389 -148 11.6 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0.81454 0.440323 -0.461359 +145 12.4 0 0 0 -0.110025 0.200698 -0.996706 +146 12.5 0 0 0 -0.149791 0.165599 -1.02233 +147 12.6 0 0 0 -0.170933 0.0644682 -0.866174 +148 12.7 0 0 0 -0.122869 -0.0196287 -0.801348 +149 12.8 0 0 0 -0.0693832 -0.0673091 -0.382802 +150 12.9 0 0 0 -0.0693832 -0.0673091 -0.382802 +151 13 0 0 0 -0.0693832 -0.0673091 -0.382802 +152 13.1 0 0 0 -0.0693832 -0.0673091 -0.382802 +153 13.2 0 0 0 -0.0693832 -0.0673091 -0.382802 +154 13.3 0 0 0 -0.0693832 -0.0673091 -0.382802 +155 13.4 0 0 0 -0.0693832 -0.0673091 -0.382802 +156 13.5 0 0 0 -0.000502433 0.000137492 -0.227425 +157 13.6 0 0 0 -0.000502433 0.000137492 -0.227425 +158 13.7 0 0 0 -0.000502433 0.000137492 -0.227425 +159 13.8 0 0 0 -0.000502433 0.000137492 -0.227425 +160 13.9 0 0 0 -0.000502433 0.000137492 -0.227425 +161 14 0 0 0 -0.000502433 0.000137492 -0.227425 +162 14.1 0 0 0 -0.000502433 0.000137492 -0.227425 +163 14.2 0 0 0 -0.000502433 0.000137492 -0.227425 +164 14.3 0 0 0 5.79042e-05 4.68687e-05 -0.00286094 +165 14.4 0 0 0 5.79042e-05 4.68687e-05 -0.00286094 +166 14.5 0 0 0 5.79042e-05 4.68687e-05 -0.00286094 +167 14.6 0 0 0 5.79042e-05 4.68687e-05 -0.00286094 +168 14.7 0 0 0 5.79042e-05 4.68687e-05 -0.00286094 +169 14.8 0 0 0 5.79042e-05 4.68687e-05 -0.00286094 +170 14.9 0 0 0 5.79042e-05 4.68687e-05 -0.00286094 +171 15 0 0 0 5.79042e-05 4.68687e-05 -0.00286094 +172 15.1 0 0 0 0 0 0 +173 15.2 0 0 0 0 0 0 +174 15.3 0 0 0 0 0 0 +175 15.4 0 0 0 0 0 0 +176 15.5 0 0 0 0 0 0 +177 15.6 0 0 0 0 0 0 +178 15.7 0 0 0 0 0 0 +179 15.8 0 0 0 0 0 0 +180 15.9 0 0 0 0 0 0 +181 16 0 0 0 0 0 0 diff --git a/examples/USER/misc/mop/mopz0.time.reference b/examples/USER/misc/mop/mopz0.time.reference index 6341d22906..d6dbb2ff09 100644 --- a/examples/USER/misc/mop/mopz0.time.reference +++ b/examples/USER/misc/mop/mopz0.time.reference @@ -1,6 +1,3 @@ # Time-averaged data for fix mopz0t # TimeStep c_mopz0[1] c_mopz0[2] c_mopz0[3] c_mopz0[4] c_mopz0[5] c_mopz0[6] -10000 -0.0267908 -0.0366912 0.634417 0.00702203 0.00200985 -0.552264 -20000 0.0202912 -0.0217482 0.597513 -0.00157669 -0.00587006 -0.537147 -30000 -0.00244239 -0.02829 0.616384 0.00640645 0.00932437 -0.561132 -40000 0.00541112 -0.0764546 0.613812 -0.00450554 -0.0038376 -0.537305 +0 1.62633 1.08234 0.844097 1.18575 -0.408792 -0.752394 diff --git a/examples/USER/misc/mop/profile.z.reference b/examples/USER/misc/mop/profile.z.reference deleted file mode 100644 index 1e0d1bf26b..0000000000 --- a/examples/USER/misc/mop/profile.z.reference +++ /dev/null @@ -1,227 +0,0 @@ -# Chunk-averaged data for fix profile_z and group temp -# Timestep Number-of-chunks Total-count -# Chunk Coord1 Ncount density/number temp c_liquidStress_ke[1] c_liquidStress_ke[2] c_liquidStress_ke[3] c_liquidStress_ke[4] c_liquidStress_ke[5] c_liquidStress_ke[6] c_liquidStress_vir[1] c_liquidStress_vir[2] c_liquidStress_vir[3] c_liquidStress_vir[4] c_liquidStress_vir[5] c_liquidStress_vir[6] -40000 223 3292 - 1 -3.15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 - 2 -3.05 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 - 3 -2.95 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 - 4 -2.85 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 - 5 -2.75 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 - 6 -2.65 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 - 7 -2.55 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 - 8 -2.45 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 - 9 -2.35 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 - 10 -2.25 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 - 11 -2.15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 - 12 -2.05 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 - 13 -1.95 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 - 14 -1.85 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 - 15 -1.75 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 - 16 -1.65 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 - 17 -1.55 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 - 18 -1.45 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 - 19 -1.35 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 - 20 -1.25 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 - 21 -1.15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 - 22 -1.05 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 - 23 -0.95 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 - 24 -0.85 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 - 25 -0.75 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 - 26 -0.65 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 - 27 -0.55 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 - 28 -0.45 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 - 29 -0.35 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 - 30 -0.25 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 - 31 -0.15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 - 32 -0.05 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 - 33 0.05 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 - 34 0.15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 - 35 0.25 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 - 36 0.35 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 - 37 0.45 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 - 38 0.55 0.0155 0.00170866 0.77827 -0.823106 -0.662616 -0.84909 0.0895728 -0.0915996 -0.0170938 -9.39041 -10.0498 -10.5424 -0.265868 -0.0729269 -0.626454 - 39 0.65 0.65625 0.0723425 0.805015 -0.786824 -0.81346 -0.814762 0.0155975 0.0168616 -0.0213122 -2.89739 -2.89092 -5.81642 -0.0313195 0.230066 -0.0388364 - 40 0.75 4.18625 0.461476 0.79884 -0.814511 -0.792997 -0.789012 -0.00942159 0.00597072 -0.00127992 -0.0143748 -0.0512459 -2.64067 0.0488393 0.0797603 0.0243815 - 41 0.85 9.79625 1.0799 0.79714 -0.80439 -0.79918 -0.78785 -0.00331374 0.00487411 -0.00151215 1.12418 1.08693 -0.84425 -0.00560715 -0.00540606 0.0136964 - 42 0.95 11.8853 1.31018 0.796174 -0.794167 -0.80514 -0.789215 0.00723814 -0.00234092 0.00056184 1.42901 1.47052 0.953436 0.0152978 -0.00835816 -0.0143227 - 43 1.05 9.50925 1.04826 0.790145 -0.778307 -0.798065 -0.794064 -0.00458567 0.00288496 0.00383306 1.34248 1.35909 2.2058 -0.00480159 -0.00651465 0.0107925 - 44 1.15 6.62475 0.730287 0.792109 -0.78276 -0.792956 -0.80061 -0.000304313 0.00429876 -0.000168134 1.26277 1.22489 2.4073 -0.00702209 0.0123268 0.0158178 - 45 1.25 4.843 0.533874 0.782372 -0.788056 -0.769346 -0.789713 -0.00686069 0.00712471 0.00418369 1.11904 1.10737 2.14058 -0.0215052 -0.0228293 0.0027643 - 46 1.35 3.83075 0.422287 0.79523 -0.795215 -0.781756 -0.808717 0.00249536 0.00991401 0.00380274 0.82578 0.918645 1.46731 0.0226069 0.0224161 0.0177933 - 47 1.45 3.677 0.405338 0.795643 -0.800148 -0.796298 -0.790481 -0.00645737 0.00817994 0.00550917 0.759125 0.737731 0.94736 0.0047934 -0.0525048 0.0098318 - 48 1.55 4.02825 0.444059 0.7931 -0.809145 -0.767991 -0.802164 0.00796467 -0.00254477 -0.00515821 0.711573 0.700294 0.278708 -0.00223064 0.0425578 -0.0182506 - 49 1.65 5.21025 0.574358 0.786639 -0.782146 -0.790073 -0.787698 -0.00628926 0.0029031 -0.00469372 0.731644 0.711902 -0.4288 0.0255459 0.0230297 -0.0116029 - 50 1.75 7.042 0.776283 0.790913 -0.78969 -0.794201 -0.788849 0.00258833 -0.00622832 -0.00564932 0.890595 0.855746 -0.411099 -0.0301627 0.0064535 0.0103202 - 51 1.85 8.46525 0.933177 0.792581 -0.802268 -0.785881 -0.789593 -0.0101489 -0.00231339 -0.00725399 0.995328 0.96239 0.0331328 -0.0719804 -0.00124182 0.00072388 - 52 1.95 8.65475 0.954067 0.787864 -0.781802 -0.789244 -0.792545 0.00513504 0.00406419 -0.00879172 1.00435 0.961078 0.632404 -0.0517082 -0.0159131 0.00526744 - 53 2.05 7.8595 0.866401 0.786055 -0.770225 -0.794059 -0.79388 -0.00752288 0.00623117 -0.00420196 1.00125 0.93989 1.08666 -0.0435495 0.0161905 0.0286065 - 54 2.15 6.82475 0.752334 0.77991 -0.776702 -0.775219 -0.78781 0.00471997 0.00826834 0.00277604 0.85253 0.86241 1.24674 0.0246189 0.00530171 0.0353102 - 55 2.25 5.89225 0.649539 0.781394 -0.766258 -0.795723 -0.782202 -0.00469749 7.49004e-05 -0.00738222 0.761321 0.690047 1.13698 0.0102827 0.00209006 -0.0164468 - 56 2.35 5.42025 0.597508 0.785789 -0.774668 -0.790234 -0.792466 -0.00930276 0.00394548 -0.0106206 0.655063 0.695732 0.918347 -0.0225504 -0.0119507 0.0511995 - 57 2.45 5.34525 0.58924 0.797039 -0.787684 -0.791749 -0.811683 0.00599798 0.00191556 -0.00434674 0.694615 0.671933 0.640961 -0.00323138 0.0273467 -0.0105561 - 58 2.55 5.87275 0.64739 0.794482 -0.795196 -0.793495 -0.794755 -0.0158646 -0.00938029 -0.00871214 0.665991 0.601126 0.314868 -0.0128127 0.0289784 -0.0535967 - 59 2.65 6.54775 0.721799 0.793027 -0.795599 -0.807693 -0.775789 -0.00379113 -0.00798908 0.00414433 0.687052 0.625958 0.250015 0.0223168 -0.0142519 0.0240892 - 60 2.75 7.17375 0.790807 0.789337 -0.803269 -0.779503 -0.78524 0.00170161 -0.00681561 0.00356121 0.775713 0.774137 0.355147 -0.0206119 0.0273384 0.0344849 - 61 2.85 7.55625 0.832972 0.79018 -0.795909 -0.795401 -0.77923 -0.00518976 -0.00312522 0.00106728 0.775982 0.753619 0.582624 -0.05471 0.00361953 -0.0185739 - 62 2.95 7.527 0.829748 0.7962 -0.797786 -0.802568 -0.788245 -0.00144501 0.00681308 0.00249422 0.768233 0.757786 0.735976 -0.0169325 0.0354933 -0.0135924 - 63 3.05 7.1165 0.784496 0.791519 -0.78266 -0.793301 -0.798598 -0.00508069 -0.00392219 -0.0044803 0.72029 0.727861 0.817503 0.0196124 -0.0195464 -0.000180423 - 64 3.15 6.748 0.743874 0.787019 -0.788624 -0.784329 -0.788105 -0.00409978 0.00754204 -0.00376577 0.82418 0.828474 1.02821 0.023471 0.00271621 0.019013 - 65 3.25 6.3735 0.70259 0.783471 -0.776587 -0.779256 -0.79457 0.00612107 0.0112575 -0.000948099 0.737637 0.71468 0.973695 0.037504 -0.0135665 0.0206408 - 66 3.35 6.1145 0.674039 0.788572 -0.784829 -0.790459 -0.790427 0.00916602 0.00152291 0.00176958 0.738898 0.720059 0.737 -0.0166567 -0.0248098 -0.0100902 - 67 3.45 6.084 0.670677 0.790939 -0.776032 -0.798423 -0.798362 0.00657912 0.00516364 0.00806608 0.707573 0.728111 0.646469 -0.00434771 0.0298935 0.0274583 - 68 3.55 6.2495 0.688921 0.80175 -0.78949 -0.810302 -0.805458 0.0075139 0.00779127 0.00389764 0.75039 0.720311 0.511161 0.0236026 0.00162861 -0.00166792 - 69 3.65 6.6325 0.731141 0.803451 -0.803591 -0.806982 -0.79978 -0.00461138 -0.00459482 0.00473225 0.779721 0.744737 0.552971 -0.0150463 -0.00642588 -0.0295497 - 70 3.75 6.971 0.768456 0.808547 -0.806043 -0.813343 -0.806255 -0.00925156 0.00268258 0.00090066 0.744282 0.762925 0.567676 -0.0318066 0.0408179 -0.00835009 - 71 3.85 7.1 0.782677 0.799797 -0.798806 -0.808842 -0.791743 0.0083713 0.0015049 0.00199971 0.773977 0.691287 0.697931 -0.0198143 -0.0249366 -0.00393322 - 72 3.95 7.17575 0.791027 0.802594 -0.812903 -0.812093 -0.782785 0.00703788 -0.00324207 0.00761052 0.733269 0.752146 0.791832 -0.0395465 0.00580315 0.0286545 - 73 4.05 6.99075 0.770634 0.795518 -0.80226 -0.79798 -0.786315 0.0122005 -0.00478061 0.000893514 0.799847 0.728761 0.789021 -0.0372739 -0.00232149 -0.0123966 - 74 4.15 6.63325 0.731224 0.788958 -0.784387 -0.79358 -0.788908 0.00967517 0.000167712 0.00326278 0.789434 0.71762 0.850289 -0.00332636 0.0214256 -0.0217507 - 75 4.25 6.51625 0.718327 0.794347 -0.791742 -0.804454 -0.786846 -0.00243681 -0.00168731 0.000255925 0.768127 0.780211 0.814895 -0.00667813 0.000850794 0.0139248 - 76 4.35 6.33 0.697795 0.797045 -0.775316 -0.815977 -0.799844 0.0116175 -0.000273637 0.00449768 0.717286 0.734205 0.78421 0.0254211 -0.010795 0.00276479 - 77 4.45 6.3695 0.702149 0.796504 -0.786627 -0.801566 -0.801318 0.000926263 -0.00328496 0.0042481 0.686859 0.690608 0.656291 -0.00255999 0.0291884 0.0134828 - 78 4.55 6.524 0.719181 0.791851 -0.780964 -0.796493 -0.798096 0.00819391 -0.0084824 0.00247244 0.714591 0.703478 0.605479 -0.00576472 0.0567365 -0.00235557 - 79 4.65 6.828 0.752693 0.78994 -0.762817 -0.80441 -0.802592 -0.00498795 -0.00309736 0.00541576 0.584756 0.726155 0.629168 0.0132298 -0.0150115 0.00455343 - 80 4.75 6.918 0.762614 0.799579 -0.784014 -0.801499 -0.813224 -0.00217864 -0.00902066 -0.00311969 0.718298 0.790586 0.685399 0.0081029 0.00122457 0.00972159 - 81 4.85 6.85725 0.755917 0.793016 -0.782179 -0.794223 -0.802647 0.00894915 0.00273159 -0.0049975 0.811278 0.77816 0.749069 -0.00808841 -0.0153742 0.025963 - 82 4.95 6.88525 0.759004 0.792271 -0.799321 -0.786408 -0.791085 0.00776404 0.00486042 -0.00662182 0.817743 0.736976 0.759098 -0.00403309 0.00808132 0.00835263 - 83 5.05 6.793 0.748834 0.801986 -0.800948 -0.807757 -0.797254 0.0106879 -0.000146493 0.00155296 0.709013 0.772363 0.793633 -0.0139702 0.00712344 -0.0200135 - 84 5.15 6.6525 0.733346 0.810787 -0.813136 -0.819216 -0.800009 -0.00359744 0.00380139 -0.00208336 0.719394 0.745495 0.766329 -0.00792452 0.0170179 -0.0358864 - 85 5.25 6.5775 0.725079 0.802145 -0.807938 -0.806407 -0.79209 0.00194264 0.00680636 0.00255785 0.762581 0.749394 0.802442 0.0226611 0.0117815 0.00120192 - 86 5.35 6.46875 0.71309 0.793883 -0.786346 -0.788403 -0.8069 -0.00758512 0.000998786 -0.00390616 0.710114 0.70501 0.664796 0.00317618 -0.0176755 0.022752 - 87 5.45 6.53875 0.720807 0.801231 -0.800747 -0.796176 -0.80677 0.00511125 -0.00251377 -0.00243123 0.669788 0.706546 0.615508 0.0451377 0.0299293 0.0528018 - 88 5.55 6.62975 0.730838 0.791321 -0.776569 -0.802757 -0.794637 -0.00506451 -0.00362665 -0.00368862 0.762371 0.739366 0.739619 0.00957177 0.0313395 -0.0196574 - 89 5.65 6.6465 0.732685 0.798658 -0.794121 -0.791451 -0.810401 -0.00216349 0.00985297 -0.00138523 0.70729 0.723195 0.776541 -0.00306725 -0.0408094 0.0086485 - 90 5.75 6.7405 0.743047 0.795471 -0.801584 -0.794404 -0.790426 0.00782568 0.00160367 0.00182854 0.690869 0.674459 0.726716 0.061492 0.053632 0.0244218 - 91 5.85 6.73 0.74189 0.796108 -0.790869 -0.801021 -0.796432 0.00113528 -0.00463009 -0.00303962 0.735497 0.620093 0.674994 0.0119071 0.00355182 -0.0039355 - 92 5.95 6.768 0.746078 0.804154 -0.80949 -0.800843 -0.802128 -0.00230974 -0.000631483 -0.000660115 0.68955 0.662997 0.752679 0.00842575 -0.0359974 -0.00432479 - 93 6.05 6.84625 0.754704 0.795076 -0.797854 -0.802926 -0.784448 -0.001677 -0.00234194 -0.00338465 0.728808 0.71192 0.777096 -0.0219522 -0.00970982 -0.00236182 - 94 6.15 6.644 0.732409 0.80624 -0.814272 -0.802433 -0.802016 -0.00360482 -0.00214059 0.00449124 0.724172 0.693115 0.797569 0.0172132 0.0560035 0.00166631 - 95 6.25 6.61375 0.729075 0.814345 -0.826054 -0.825197 -0.791784 0.00363171 0.00327744 0.000350599 0.687352 0.67675 0.681632 0.029371 -0.00122278 0.00361507 - 96 6.35 6.58325 0.725712 0.81549 -0.803825 -0.839613 -0.803033 0.000544035 -0.00137045 0.000992479 0.768956 0.672422 0.731122 -0.000378553 0.0216666 0.00894304 - 97 6.45 6.49525 0.716012 0.807476 -0.802426 -0.803908 -0.816095 -0.005319 -0.00501193 0.00697519 0.715972 0.652573 0.738936 0.0254408 -0.004102 -0.0473245 - 98 6.55 6.63 0.730866 0.803084 -0.797573 -0.802396 -0.809284 0.00450783 0.00547812 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0.81595 0.597829 -0.0170772 -0.0118633 -0.00667559 - 143 11.05 6.3715 0.70237 0.812611 -0.804489 -0.818657 -0.814685 -0.0111996 0.00212941 -0.0105114 0.79318 0.694842 0.430366 0.0162314 0.0306282 -0.0432507 - 144 11.15 5.99025 0.660342 0.810481 -0.804842 -0.802955 -0.823644 0.0136279 -0.00477508 -0.00804219 0.735454 0.788358 0.431007 -0.0429171 0.000235044 0.0207342 - 145 11.25 5.84825 0.644689 0.800577 -0.781391 -0.800625 -0.819715 0.0131729 0.00482168 0.00221727 0.739467 0.715937 0.679698 -0.0104751 -0.0177938 0.00468151 - 146 11.35 6.0255 0.664228 0.799503 -0.790112 -0.813938 -0.79446 0.00610092 -0.00356609 0.00528215 0.663651 0.637587 0.775373 -0.0220442 0.0110108 -0.0254637 - 147 11.45 6.4185 0.707551 0.800508 -0.790724 -0.818412 -0.792388 -0.00176802 -0.0100995 -0.000335942 0.737901 0.721074 1.00438 0.0121646 0.00623362 0.0474194 - 148 11.55 6.9715 0.768512 0.805139 -0.797432 -0.807462 -0.810523 -0.00796199 -0.00562452 0.0109241 0.863915 0.846335 1.03536 0.00595087 0.0354208 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0 0 0 0 0 0 0 0 0 0 0 0 0 - 213 18.05 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 - 214 18.15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 - 215 18.25 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 - 216 18.35 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 - 217 18.45 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 - 218 18.55 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 - 219 18.65 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 - 220 18.75 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 - 221 18.85 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 - 222 18.95 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 - 223 19.05 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 From dd64c063cf804205bfb5ea90ed1be325243814d9 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 6 Sep 2018 22:28:20 -0400 Subject: [PATCH 155/302] various fixes for the manual to address breakage from merging MESSAGE and USER-SCAFACOS packages --- doc/src/Build_package.txt | 4 ++-- doc/src/Howto_client_server.txt | 2 +- doc/src/Packages_details.txt | 4 ++-- doc/src/Run_options.txt | 2 +- doc/src/commands_list.txt | 2 ++ doc/src/fix_client_md.txt | 2 +- doc/src/fixes.txt | 1 + doc/src/kspace_modify.txt | 2 +- doc/src/kspace_style.txt | 4 ++-- doc/src/lammps.book | 1 + 10 files changed, 14 insertions(+), 10 deletions(-) diff --git a/doc/src/Build_package.txt b/doc/src/Build_package.txt index 285220e6c6..f1aa4bb671 100644 --- a/doc/src/Build_package.txt +++ b/doc/src/Build_package.txt @@ -42,7 +42,7 @@ packages: "KOKKOS"_Build_extras.html#kokkos, "LATTE"_Build_extras.html#latte, "MEAM"_Build_extras.html#meam, -"MESSAGE"_#Build_extras.html#message, +"MESSAGE"_Build_extras.html#message, "MSCG"_Build_extras.html#mscg, "OPT"_Build_extras.html#opt, "POEMS"_Build_extras.html#poems, @@ -59,7 +59,7 @@ packages: "USER-OMP"_Build_extras.html#user-omp, "USER-QMMM"_Build_extras.html#user-qmmm, "USER-QUIP"_Build_extras.html#user-quip, -"USER-SCAFACOS"_#Build_extras.html#user-scafacos, +"USER-SCAFACOS"_Build_extras.html#user-scafacos, "USER-SMD"_Build_extras.html#user-smd, "USER-VTK"_Build_extras.html#user-vtk :tb(c=6,ea=c,a=l) diff --git a/doc/src/Howto_client_server.txt b/doc/src/Howto_client_server.txt index 714c23f066..061c4efb68 100644 --- a/doc/src/Howto_client_server.txt +++ b/doc/src/Howto_client_server.txt @@ -7,7 +7,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :line -Using LAMMPS in client/server mode +Using LAMMPS in client/server mode :h3 Client/server coupling of two codes is where one code is the "client" and sends request messages to a "server" code. The server responds to diff --git a/doc/src/Packages_details.txt b/doc/src/Packages_details.txt index 443d78922c..b0b72f1f13 100644 --- a/doc/src/Packages_details.txt +++ b/doc/src/Packages_details.txt @@ -92,7 +92,7 @@ as contained in the file name. "USER-QTB"_#PKG-USER-QTB, "USER-QUIP"_#PKG-USER-QUIP, "USER-REAXC"_#PKG-USER-REAXC, -"USER-SCAFACOS"_#USER-SCAFACOS, +"USER-SCAFACOS"_#PKG-USER-SCAFACOS, "USER-SMD"_#PKG-USER-SMD, "USER-SMTBQ"_#PKG-USER-SMTBQ, "USER-SPH"_#PKG-USER-SPH, @@ -1860,7 +1860,7 @@ examples/reax :ul :line -USER-SCAFACOS package :link(USER-SCAFACOS),h4 +USER-SCAFACOS package :link(PKG-USER-SCAFACOS),h4 [Contents:] diff --git a/doc/src/Run_options.txt b/doc/src/Run_options.txt index 27f436ed55..1fc00bc2e3 100644 --- a/doc/src/Run_options.txt +++ b/doc/src/Run_options.txt @@ -176,7 +176,7 @@ Option -plog will override the name of the partition log files file.N. :line -[-mpicolor] color :link(mpi) +[-mpicolor] color :link(mpicolor) If used, this must be the first command-line argument after the LAMMPS executable name. It is only used when LAMMPS is launched by an mpirun diff --git a/doc/src/commands_list.txt b/doc/src/commands_list.txt index 8fae57a718..db3ef36ddf 100644 --- a/doc/src/commands_list.txt +++ b/doc/src/commands_list.txt @@ -89,6 +89,8 @@ Commands :h1 run run_style server + server_mc + server_md set shell special_bonds diff --git a/doc/src/fix_client_md.txt b/doc/src/fix_client_md.txt index 5b62d5617d..77f6b82c5e 100644 --- a/doc/src/fix_client_md.txt +++ b/doc/src/fix_client_md.txt @@ -50,7 +50,7 @@ md"_server_md.html doc page. Note that when using LAMMPS as an MD client, your LAMMPS input script should not normally contain force field commands, like a -"pair_style"_doc/pair_style.html, "bond_style"_doc/bond_style.html, or +"pair_style"_pair_style.html, "bond_style"_bond_style.html, or "kspace_style"_kspace_style.html commmand. However it is possible for a server code to only compute a portion of the full force-field, while LAMMPS computes the remaining part. Your LAMMPS script can also diff --git a/doc/src/fixes.txt b/doc/src/fixes.txt index 7a45ed8086..f2f257b134 100644 --- a/doc/src/fixes.txt +++ b/doc/src/fixes.txt @@ -26,6 +26,7 @@ Fixes :h1 fix_bond_swap fix_bond_react fix_box_relax + fix_client_md fix_cmap fix_colvars fix_controller diff --git a/doc/src/kspace_modify.txt b/doc/src/kspace_modify.txt index 7e40323664..41973601d7 100644 --- a/doc/src/kspace_modify.txt +++ b/doc/src/kspace_modify.txt @@ -133,7 +133,7 @@ the code will stop with an error message. When this option is set to For a typical application, using the automatic parameter generation will provide simulations that are either inaccurate or slow. Using this option is thus not recommended. For guidelines on how to obtain good -parameters, see the "How-To"_Section_howto.html#howto_24 discussion. +parameters, see the "How-To"_Howto_dispersion.html discussion. :line diff --git a/doc/src/kspace_style.txt b/doc/src/kspace_style.txt index ddf4e15703..6d8a289470 100644 --- a/doc/src/kspace_style.txt +++ b/doc/src/kspace_style.txt @@ -383,8 +383,8 @@ dimensions. The only exception is if the slab option is set with must be periodic and the z dimension must be non-periodic. The scafacos KSpace style will only be enabled if LAMMPS is built with -the USER-SCAFACOS package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +the USER-SCAFACOS package. See the "Build package"_Build_package.html +doc page for more info. The use of ScaFaCos in LAMMPS does not yet support molecular charged systems where the short-range Coulombic interactions between atoms in diff --git a/doc/src/lammps.book b/doc/src/lammps.book index 72a07945e7..828863ae67 100644 --- a/doc/src/lammps.book +++ b/doc/src/lammps.book @@ -67,6 +67,7 @@ Howto_multiple.html Howto_replica.html Howto_library.html Howto_couple.html +Howto_client_server.html Howto_output.html Howto_chunk.html Howto_2d.html From 861a7acdf0b9de61dade59ef873e1f338673a9d2 Mon Sep 17 00:00:00 2001 From: Christoph Junghans Date: Fri, 7 Sep 2018 06:40:06 -0600 Subject: [PATCH 156/302] cmake: fix globbing in some more places --- cmake/CMakeLists.txt | 9 ++++++--- cmake/Modules/StyleHeaderUtils.cmake | 6 +++--- 2 files changed, 9 insertions(+), 6 deletions(-) diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index 45e6870ce8..21170a384d 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -604,7 +604,8 @@ endif() if(PKG_MESSAGE) option(MESSAGE_ZMQ "Use ZeroMQ in MESSAGE package" OFF) file(GLOB_RECURSE cslib_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.F - ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/*.c ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/*.cpp) + ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.c + ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.cpp) if(BUILD_SHARED_LIBS) add_library(cslib SHARED ${cslib_SOURCES}) @@ -754,8 +755,10 @@ foreach(SIMPLE_LIB REAX MEAM POEMS USER-ATC USER-AWPMD USER-COLVARS USER-H5MD if(PKG_${SIMPLE_LIB}) string(REGEX REPLACE "^USER-" "" PKG_LIB "${SIMPLE_LIB}") string(TOLOWER "${PKG_LIB}" PKG_LIB) - file(GLOB_RECURSE ${PKG_LIB}_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.F - ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/*.c ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/*.cpp) + file(GLOB_RECURSE ${PKG_LIB}_SOURCES + ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.F + ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.c + ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.cpp) add_library(${PKG_LIB} STATIC ${${PKG_LIB}_SOURCES}) list(APPEND LAMMPS_LINK_LIBS ${PKG_LIB}) if(PKG_LIB STREQUAL awpmd) diff --git a/cmake/Modules/StyleHeaderUtils.cmake b/cmake/Modules/StyleHeaderUtils.cmake index d621e4c9c0..a89d098dd0 100644 --- a/cmake/Modules/StyleHeaderUtils.cmake +++ b/cmake/Modules/StyleHeaderUtils.cmake @@ -94,14 +94,14 @@ function(RegisterStyles search_path) FindStyleHeaders(${search_path} ATOM_CLASS atom_vec_ ATOM_VEC ) # atom ) # atom atom_vec_hybrid FindStyleHeaders(${search_path} BODY_CLASS body_ BODY ) # body ) # atom_vec_body FindStyleHeaders(${search_path} BOND_CLASS bond_ BOND ) # bond ) # force - FindStyleHeaders(${search_path} COMMAND_CLASS "" COMMAND ) # command ) # input + FindStyleHeaders(${search_path} COMMAND_CLASS "[^.]" COMMAND ) # command ) # input FindStyleHeaders(${search_path} COMPUTE_CLASS compute_ COMPUTE ) # compute ) # modify FindStyleHeaders(${search_path} DIHEDRAL_CLASS dihedral_ DIHEDRAL ) # dihedral ) # force FindStyleHeaders(${search_path} DUMP_CLASS dump_ DUMP ) # dump ) # output write_dump FindStyleHeaders(${search_path} FIX_CLASS fix_ FIX ) # fix ) # modify FindStyleHeaders(${search_path} IMPROPER_CLASS improper_ IMPROPER ) # improper ) # force - FindStyleHeaders(${search_path} INTEGRATE_CLASS "" INTEGRATE ) # integrate ) # update - FindStyleHeaders(${search_path} KSPACE_CLASS "" KSPACE ) # kspace ) # force + FindStyleHeaders(${search_path} INTEGRATE_CLASS "[^.]" INTEGRATE ) # integrate ) # update + FindStyleHeaders(${search_path} KSPACE_CLASS "[^.]" KSPACE ) # kspace ) # force FindStyleHeaders(${search_path} MINIMIZE_CLASS min_ MINIMIZE ) # minimize ) # update FindStyleHeaders(${search_path} NBIN_CLASS nbin_ NBIN ) # nbin ) # neighbor FindStyleHeaders(${search_path} NPAIR_CLASS npair_ NPAIR ) # npair ) # neighbor From 25907c856e1463cf4986de98e61b3cafd422b3d5 Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Fri, 7 Sep 2018 09:56:03 -0600 Subject: [PATCH 157/302] small doc page changes, format and content on doc page tarballs --- doc/src/Build_basics.txt | 4 ++++ doc/src/Howto_client_server.txt | 2 +- doc/src/Install_tarball.txt | 6 +++++- doc/src/Packages_details.txt | 1 + 4 files changed, 11 insertions(+), 2 deletions(-) diff --git a/doc/src/Build_basics.txt b/doc/src/Build_basics.txt index 6924e73417..4b3a347bf1 100644 --- a/doc/src/Build_basics.txt +++ b/doc/src/Build_basics.txt @@ -292,6 +292,10 @@ This will create a lammps/doc/html dir with the HTML doc pages so that you can browse them locally on your system. Type "make" from the lammps/doc dir to see other options. +NOTE: You can also download a tarball of the documention for the +current LAMMPS version (HTML and PDF files), from the website +"download page"_http://lammps.sandia.gov/download.html. + :line Install LAMMPS after a build :h4,link(install) diff --git a/doc/src/Howto_client_server.txt b/doc/src/Howto_client_server.txt index 714c23f066..061c4efb68 100644 --- a/doc/src/Howto_client_server.txt +++ b/doc/src/Howto_client_server.txt @@ -7,7 +7,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :line -Using LAMMPS in client/server mode +Using LAMMPS in client/server mode :h3 Client/server coupling of two codes is where one code is the "client" and sends request messages to a "server" code. The server responds to diff --git a/doc/src/Install_tarball.txt b/doc/src/Install_tarball.txt index b672c5ff25..7ba5d15ac4 100644 --- a/doc/src/Install_tarball.txt +++ b/doc/src/Install_tarball.txt @@ -7,7 +7,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :line -Download source as a tarball :h3 +Download source and documentation as a tarball :h3 You can download a current LAMMPS tarball from the "download page"_download of the "LAMMPS website"_lws. @@ -22,6 +22,10 @@ few times per year, and undergo more testing before release. Patch releases occur a couple times per month. The new contents in all releases are listed on the "bug and feature page"_bug of the website. +Both tarballs include LAMMPS documentation (HTML and PDF files) +corresponding to that version. The download page also has an option +to download the current-version LAMMPS documentation by itself. + Older versions of LAMMPS can also be downloaded from "this page"_older. diff --git a/doc/src/Packages_details.txt b/doc/src/Packages_details.txt index 443d78922c..1fb0549c8d 100644 --- a/doc/src/Packages_details.txt +++ b/doc/src/Packages_details.txt @@ -46,6 +46,7 @@ as contained in the file name. "MANYBODY"_#PKG-MANYBODY, "MC"_#PKG-MC, "MEAM"_#PKG-MEAM, +"MESSAGE"_#PKG-MESSAGE, "MISC"_#PKG-MISC, "MOLECULE"_#PKG-MOLECULE, "MPIIO"_#PKG-MPIIO, From 0384ef89670de96f83b0f7821c4e22484d491ed9 Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Fri, 7 Sep 2018 14:00:39 -0600 Subject: [PATCH 158/302] more tweaks to client/server doc pages --- doc/src/Howto_client_server.txt | 4 ++-- doc/src/server_mc.txt | 6 +++--- doc/src/server_md.txt | 16 +++++++++------- 3 files changed, 14 insertions(+), 12 deletions(-) diff --git a/doc/src/Howto_client_server.txt b/doc/src/Howto_client_server.txt index 061c4efb68..aa6b8eab76 100644 --- a/doc/src/Howto_client_server.txt +++ b/doc/src/Howto_client_server.txt @@ -61,7 +61,7 @@ client or server. "message"_message.html "fix client md"_fix_client_md.html = LAMMPS is a client for running MD "server md"_server_md.html = LAMMPS is a server for computing MD forces -"server mc"_server_mc.html = LAMMPS is a server for computing a Monte Carlo energy +"server mc"_server_mc.html = LAMMPS is a server for computing a Monte Carlo energy :ul The server doc files give details of the message protocols for data that is exchanged bewteen the client and server. @@ -119,7 +119,7 @@ For message exchange in {mpi/one} mode: Launch both codes in a single mpirun command: -mpirun -np 2 lmp_mpi -mpicolor 0 -in in.message.client -log log.client : -np 4 lmp_mpi -mpicolor 1 -in in.message.server -log log.server +mpirun -np 2 lmp_mpi -mpicolor 0 -in in.message.client -log log.client : -np 4 lmp_mpi -mpicolor 1 -in in.message.server -log log.server :pre The two -np values determine how many procs the client and the server run on. diff --git a/doc/src/server_mc.txt b/doc/src/server_mc.txt index 53ccfc8ecd..58ca415be3 100644 --- a/doc/src/server_mc.txt +++ b/doc/src/server_mc.txt @@ -63,7 +63,7 @@ See the src/MESSAGE/server_mc.cpp file for details on how LAMMPS uses these messages. See the examples/COUPLE/lammmps_mc/mc.cpp file for an example of how an MC driver code can use these messages. -Let NATOMS=1, EINIT=2, DISPLACE=3, ACCEPT=4, RUN=5. +Define NATOMS=1, EINIT=2, DISPLACE=3, ACCEPT=4, RUN=5. [Client sends one of these kinds of message]: @@ -93,9 +93,9 @@ cs->pack(2,3*natoms,x) # 2nd field = 3N coords of Natoms :pre cs->send(DISPLACE,1) # msgID = 3 with 1 field cs->pack_double(1,poteng) # 1st field = new potential energy of system :pre -cs->send(ACCEPT,0) # msgID = 4 with no fields +cs->send(ACCEPT,0) # msgID = 4 with no fields :pre -cs->send(RUN,0) # msgID = 5 with no fields +cs->send(RUN,0) # msgID = 5 with no fields :pre :line diff --git a/doc/src/server_md.txt b/doc/src/server_md.txt index 0db7bbe16b..753542dc75 100644 --- a/doc/src/server_md.txt +++ b/doc/src/server_md.txt @@ -51,9 +51,9 @@ can complete the timestep. This command could also be used with a client code that performs energy minimization, using the server to compute forces and energy each iteration of its minimizer. -When using the "fix client/md" command, LAMMPS (as the client code) -does the timestepping and receives needed energy, forces, and pressure -values from the server code. +When using the "fix client/md"_fix_client_md.html command, LAMMPS (as +the client code) does the timestepping and receives needed energy, +forces, and pressure values from the server code. The format and content of the exchanged messages are explained here in a conceptual sense. Python-style pseudo code for the library calls to @@ -69,9 +69,11 @@ a quantum code (VASP) can use use these messages. The following pseudo-code uses these values, defined as enums. -enum{SETUP=1,STEP}; -enum{DIM=1,PERIODICITY,ORIGIN,BOX,NATOMS,NTYPES,TYPES,COORDS,UNITS,CHARGE}; -enum{FORCES=1,ENERGY,PRESSURE,ERROR}; :pre +Define: + +SETUP=1, STEP=2 +DIM=1, PERIODICITY=2, ORIGIN=3, BOX=4, NATOMS=5, NTYPES=6, TYPES=7, COORDS=8, UNITS-9, CHARGE=10 +FORCES=1, ENERGY=2, PRESSURE=3, ERROR=4 :pre [Client sends 2 kinds of messages]: @@ -98,7 +100,7 @@ cs->send(STEP,nfields) # msgID with nfields :pre cs->pack(COORDS,3*natoms,x) # vector of 3N atom coords cs->pack(ORIGIN,3,origin) # lower-left corner of simulation box -cs->pack(BOX,9,box) # 3 edge vectors of simulation box +cs->pack(BOX,9,box) # 3 edge vectors of simulation box :pre [Server replies to either kind of message]: From b488f1072e17e6f574cb45a479572783bc147fca Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Fri, 7 Sep 2018 14:22:38 -0600 Subject: [PATCH 159/302] recent package links --- doc/src/Packages_details.txt | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/src/Packages_details.txt b/doc/src/Packages_details.txt index 1fb0549c8d..494f393a16 100644 --- a/doc/src/Packages_details.txt +++ b/doc/src/Packages_details.txt @@ -93,7 +93,7 @@ as contained in the file name. "USER-QTB"_#PKG-USER-QTB, "USER-QUIP"_#PKG-USER-QUIP, "USER-REAXC"_#PKG-USER-REAXC, -"USER-SCAFACOS"_#USER-SCAFACOS, +"USER-SCAFACOS"_#PKG-USER-SCAFACOS, "USER-SMD"_#PKG-USER-SMD, "USER-SMTBQ"_#PKG-USER-SMTBQ, "USER-SPH"_#PKG-USER-SPH, @@ -1861,7 +1861,7 @@ examples/reax :ul :line -USER-SCAFACOS package :link(USER-SCAFACOS),h4 +USER-SCAFACOS package :link(PKG-USER-SCAFACOS),h4 [Contents:] From 3b073de3572a41f476243c3aa56ce28a9532fd6e Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 9 Sep 2018 01:21:37 -0400 Subject: [PATCH 160/302] make it less likely to have people get confused by Eigen3_DIR --- cmake/CMakeLists.txt | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index 149f9da817..80eb035fee 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -538,6 +538,13 @@ if(PKG_USER-NETCDF) endif() if(PKG_USER-SMD) + # hack alert! + # something defines the Eigen3_DIR variable, but it has no effect + # yet shows up in the TUI/GUI display as "not found". + # and due to not being marked as advanced, it can mislead people + # as the EIGEN3_INCLUDE_DIR variable which does have an effect + # is marked as advanced. Tested on Fedora28 with Eigen3-3.3.5 rpm. + mark_as_advanced(Eigen3_DIR) option(DOWNLOAD_EIGEN3 "Download Eigen3 (instead of using the system's one)" OFF) if(DOWNLOAD_EIGEN3) include(ExternalProject) From 46b87518b8b62fac583e8718b9a9b3b5baf7417f Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Mon, 10 Sep 2018 00:35:55 -0400 Subject: [PATCH 161/302] cmake: use NO_MODULE for Eigen3 --- cmake/CMakeLists.txt | 10 ++-------- 1 file changed, 2 insertions(+), 8 deletions(-) diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index 80eb035fee..7bfd7905f2 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -538,13 +538,6 @@ if(PKG_USER-NETCDF) endif() if(PKG_USER-SMD) - # hack alert! - # something defines the Eigen3_DIR variable, but it has no effect - # yet shows up in the TUI/GUI display as "not found". - # and due to not being marked as advanced, it can mislead people - # as the EIGEN3_INCLUDE_DIR variable which does have an effect - # is marked as advanced. Tested on Fedora28 with Eigen3-3.3.5 rpm. - mark_as_advanced(Eigen3_DIR) option(DOWNLOAD_EIGEN3 "Download Eigen3 (instead of using the system's one)" OFF) if(DOWNLOAD_EIGEN3) include(ExternalProject) @@ -557,7 +550,8 @@ if(PKG_USER-SMD) set(EIGEN3_INCLUDE_DIR ${SOURCE_DIR}) list(APPEND LAMMPS_DEPS Eigen3_build) else() - find_package(Eigen3) + find_package(Eigen3 NO_MODULE) + mark_as_advanced(Eigen3_DIR) if(NOT EIGEN3_FOUND) message(FATAL_ERROR "Eigen3 not found, help CMake to find it by setting EIGEN3_INCLUDE_DIR, or set DOWNLOAD_EIGEN3=ON to download it") endif() From 02b653c0cea83448cdeda39d231f423836d35fdf Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 10 Sep 2018 22:22:42 -0400 Subject: [PATCH 162/302] correct end of itemized list to be compatible with txt2rst conversion --- doc/src/Howto_chunk.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/src/Howto_chunk.txt b/doc/src/Howto_chunk.txt index 611b71dac7..82a4450d17 100644 --- a/doc/src/Howto_chunk.txt +++ b/doc/src/Howto_chunk.txt @@ -125,7 +125,7 @@ molecule diffusion rates. :l As input to special functions of "equal-style variables"_variable.html, like sum() and max() and ave(). E.g. to find the largest cluster or fastest diffusing molecule or average -radius-of-gyration of a set of molecules (chunks). :l :ule +radius-of-gyration of a set of molecules (chunks). :l,ule Other chunk commands: :h4 From 3d2c7317092a9952b88ac4e6c6e16193c333093a Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 10 Sep 2018 22:32:56 -0400 Subject: [PATCH 163/302] avoid class initialization order warnings --- src/compute_chunk_spread_atom.cpp | 2 +- src/compute_chunk_spread_atom.h | 3 +-- src/compute_reduce_chunk.cpp | 4 ++-- 3 files changed, 4 insertions(+), 5 deletions(-) diff --git a/src/compute_chunk_spread_atom.cpp b/src/compute_chunk_spread_atom.cpp index 93a4d30a2e..c5fd27b0c1 100644 --- a/src/compute_chunk_spread_atom.cpp +++ b/src/compute_chunk_spread_atom.cpp @@ -37,7 +37,7 @@ enum{COMPUTE,FIX}; ComputeChunkSpreadAtom:: ComputeChunkSpreadAtom(LAMMPS *lmp, int narg, char **arg) : Compute(lmp, narg, arg), - which(NULL), argindex(NULL), ids(NULL), value2index(NULL), idchunk(NULL) + idchunk(NULL), ids(NULL), which(NULL), argindex(NULL), value2index(NULL) { if (narg < 5) error->all(FLERR,"Illegal compute chunk/spread/atom command"); diff --git a/src/compute_chunk_spread_atom.h b/src/compute_chunk_spread_atom.h index 9a4df080ca..80ee186450 100644 --- a/src/compute_chunk_spread_atom.h +++ b/src/compute_chunk_spread_atom.h @@ -35,9 +35,8 @@ class ComputeChunkSpreadAtom : public Compute { protected: int mode,nvalues; char *idchunk; - - int *which,*argindex,*value2index; char **ids; + int *which,*argindex,*value2index; int nmax; class ComputeChunkAtom *cchunk; diff --git a/src/compute_reduce_chunk.cpp b/src/compute_reduce_chunk.cpp index 40e9dad8dd..beebc5f411 100644 --- a/src/compute_reduce_chunk.cpp +++ b/src/compute_reduce_chunk.cpp @@ -38,8 +38,8 @@ enum{COMPUTE,FIX,VARIABLE}; ComputeReduceChunk::ComputeReduceChunk(LAMMPS *lmp, int narg, char **arg) : Compute(lmp, narg, arg), - vlocal(NULL), vglobal(NULL), alocal(NULL), aglobal(NULL), varatom(NULL), - which(NULL), argindex(NULL), value2index(NULL), idchunk(NULL), ids(NULL) + which(NULL), argindex(NULL), value2index(NULL), idchunk(NULL), ids(NULL), + vlocal(NULL), vglobal(NULL), alocal(NULL), aglobal(NULL), varatom(NULL) { if (narg < 6) error->all(FLERR,"Illegal compute reduce/chunk command"); From 0305cca1df30b355f60799bed967e7456e2a3bac Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 10 Sep 2018 22:47:45 -0400 Subject: [PATCH 164/302] make certain that *_freq flags are initialized. use -1 instead of 0 to avoid division by zero --- src/fix.cpp | 1 + 1 file changed, 1 insertion(+) diff --git a/src/fix.cpp b/src/fix.cpp index 051ac12bbe..634bc2393d 100644 --- a/src/fix.cpp +++ b/src/fix.cpp @@ -81,6 +81,7 @@ Fix::Fix(LAMMPS *lmp, int /*narg*/, char **arg) : scalar_flag = vector_flag = array_flag = 0; peratom_flag = local_flag = 0; + global_freq = local_freq = peratom_freq = -1; size_vector_variable = size_array_rows_variable = 0; comm_forward = comm_reverse = comm_border = 0; From 983e8bb110a6faeab4675137ccccb51e3f986739 Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Tue, 11 Sep 2018 11:36:37 -0600 Subject: [PATCH 165/302] doc page clarifications --- doc/src/fix_shake.txt | 6 ++++-- doc/src/minimize.txt | 13 +++++++++---- 2 files changed, 13 insertions(+), 6 deletions(-) diff --git a/doc/src/fix_shake.txt b/doc/src/fix_shake.txt index 77bb5794f6..5c11f96b98 100644 --- a/doc/src/fix_shake.txt +++ b/doc/src/fix_shake.txt @@ -214,8 +214,10 @@ which can lead to poor energy conservation. You can test for this in your system by running a constant NVE simulation with a particular set of SHAKE parameters and monitoring the energy versus time. -SHAKE or RATTLE should not be used to constrain an angle at 180 degrees -(e.g. linear CO2 molecule). This causes numeric difficulties. +SHAKE or RATTLE should not be used to constrain an angle at 180 +degrees (e.g. linear CO2 molecule). This causes numeric difficulties. +You can use "fix rigid or fix rigid/small"_fix_rigid.html instead to +make a linear molecule rigid. [Related commands:] none diff --git a/doc/src/minimize.txt b/doc/src/minimize.txt index 910fc7f821..73858fc249 100644 --- a/doc/src/minimize.txt +++ b/doc/src/minimize.txt @@ -216,10 +216,10 @@ The "fix box/relax"_fix_box_relax.html command can be used to apply an external pressure to the simulation box and allow it to shrink/expand during the minimization. -Only a few other fixes (typically those that apply force constraints) -are invoked during minimization. See the doc pages for individual -"fix"_fix.html commands to see which ones are relevant. Current -examples of fixes that can be used include: +Only a few other fixes (typically those that add forces) are invoked +during minimization. See the doc pages for individual "fix"_fix.html +commands to see which ones are relevant. Current examples of fixes +that can be used include: "fix addforce"_fix_addforce.html "fix addtorque"_fix_addtorque.html @@ -242,6 +242,11 @@ you MUST enable the "fix_modify"_fix_modify.html {energy} option for that fix. The doc pages for individual "fix"_fix.html commands specify if this should be done. +NOTE: The minimizers in LAMMPS do not allow for bonds (or angles, etc) +to be held fixed while atom coordinates are being relaxed, e.g. via +"fix shake"_fix_shake.html or "fix rigid"_fix_rigid.html. See more +info in the Restrictions section below. + :line [Restrictions:] From 7f328d3f79bba1b3ce517084d556fccefc3e5bc4 Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Tue, 11 Sep 2018 11:49:46 -0600 Subject: [PATCH 166/302] cite a good book on SLLOD thermostatting for molecular systems --- doc/src/Howto_nemd.txt | 11 +++++++++++ doc/src/Howto_thermostat.txt | 11 +++++++++++ doc/src/Howto_viscosity.txt | 11 +++++++++++ doc/src/fix_nvt_sllod.txt | 9 +++++++++ 4 files changed, 42 insertions(+) diff --git a/doc/src/Howto_nemd.txt b/doc/src/Howto_nemd.txt index f787801c36..0a76859dcf 100644 --- a/doc/src/Howto_nemd.txt +++ b/doc/src/Howto_nemd.txt @@ -24,6 +24,11 @@ by subtracting out the streaming velocity of the shearing atoms. The velocity profile or other properties of the fluid can be monitored via the "fix ave/chunk"_fix_ave_chunk.html command. +NOTE: A recent (2017) book by "(Daivis and Todd)"_#Daivis2 discusses +use of the SLLOD method and non-equilibrium MD (NEMD) thermosttating +generally, for both simple and complex fluids, e.g. molecular systems. +The latter can be tricky to do correctly. + As discussed in the previous section on non-orthogonal simulation boxes, the amount of tilt or skew that can be applied is limited by LAMMPS for computational efficiency to be 1/2 of the parallel box @@ -46,3 +51,9 @@ An alternative method for calculating viscosities is provided via the NEMD simulations can also be used to measure transport properties of a fluid through a pore or channel. Simulations of steady-state flow can be performed using the "fix flow/gauss"_fix_flow_gauss.html command. + +:line + +:link(Daivis2) +[(Daivis and Todd)] Daivis and Todd, Nonequilibrium Molecular Dyanmics (book), +Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017). diff --git a/doc/src/Howto_thermostat.txt b/doc/src/Howto_thermostat.txt index 0e2feb1869..6a0095e741 100644 --- a/doc/src/Howto_thermostat.txt +++ b/doc/src/Howto_thermostat.txt @@ -43,6 +43,11 @@ nvt/asphere"_fix_nvt_asphere.html thermostat not only translation velocities but also rotational velocities for spherical and aspherical particles. +NOTE: A recent (2017) book by "(Daivis and Todd)"_#Daivis2 discusses +use of the SLLOD method and non-equilibrium MD (NEMD) thermosttating +generally, for both simple and complex fluids, e.g. molecular systems. +The latter can be tricky to do correctly. + DPD thermostatting alters pairwise interactions in a manner analogous to the per-particle thermostatting of "fix langevin"_fix_langevin.html. @@ -87,3 +92,9 @@ specify them explicitly via the "thermo_style custom"_thermo_style.html command. Or you can use the "thermo_modify"_thermo_modify.html command to re-define what temperature compute is used for default thermodynamic output. + +:line + +:link(Daivis2) +[(Daivis and Todd)] Daivis and Todd, Nonequilibrium Molecular Dyanmics (book), +Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017). diff --git a/doc/src/Howto_viscosity.txt b/doc/src/Howto_viscosity.txt index 8bcab6dd24..adfabf8279 100644 --- a/doc/src/Howto_viscosity.txt +++ b/doc/src/Howto_viscosity.txt @@ -37,6 +37,11 @@ used to shear the fluid in between them, again with some kind of thermostat that modifies only the thermal (non-shearing) components of velocity to prevent the fluid from heating up. +NOTE: A recent (2017) book by "(Daivis and Todd)"_#Daivis2 discusses +use of the SLLOD method and non-equilibrium MD (NEMD) thermosttating +generally, for both simple and complex fluids, e.g. molecular systems. +The latter can be tricky to do correctly. + In both cases, the velocity profile setup in the fluid by this procedure can be monitored by the "fix ave/chunk"_fix_ave_chunk.html command, which determines grad(Vstream) in the equation above. @@ -131,3 +136,9 @@ mean-square-displacement formulation for self-diffusivity. The time-integrated momentum fluxes play the role of Cartesian coordinates, whose mean-square displacement increases linearly with time at sufficiently long times. + +:line + +:link(Daivis2) +[(Daivis and Todd)] Daivis and Todd, Nonequilibrium Molecular Dyanmics (book), +Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017). diff --git a/doc/src/fix_nvt_sllod.txt b/doc/src/fix_nvt_sllod.txt index 97a864a231..67c4d76417 100644 --- a/doc/src/fix_nvt_sllod.txt +++ b/doc/src/fix_nvt_sllod.txt @@ -63,6 +63,11 @@ implemented in LAMMPS, they are coupled to a Nose/Hoover chain thermostat in a velocity Verlet formulation, closely following the implementation used for the "fix nvt"_fix_nh.html command. +NOTE: A recent (2017) book by "(Daivis and Todd)"_#Daivis2 discusses +use of the SLLOD method and non-equilibrium MD (NEMD) thermosttating +generally, for both simple and complex fluids, e.g. molecular systems. +The latter can be tricky to do correctly. + Additional parameters affecting the thermostat are specified by keywords and values documented with the "fix nvt"_fix_nh.html command. See, for example, discussion of the {temp} and {drag} @@ -177,3 +182,7 @@ Same as "fix nvt"_fix_nh.html, except tchain = 1. :link(Daivis) [(Daivis and Todd)] Daivis and Todd, J Chem Phys, 124, 194103 (2006). + +:link(Daivis2) +[(Daivis and Todd)] Daivis and Todd, Nonequilibrium Molecular Dyanmics (book), +Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017). From c3ece2f0861b48d39b4f3da2350f2f969f11d40d Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Tue, 11 Sep 2018 12:44:35 -0600 Subject: [PATCH 167/302] typo in fix relax/box doc page --- doc/src/fix_box_relax.txt | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/src/fix_box_relax.txt b/doc/src/fix_box_relax.txt index 29ebeaeef3..d41607e2ed 100644 --- a/doc/src/fix_box_relax.txt +++ b/doc/src/fix_box_relax.txt @@ -221,8 +221,8 @@ This equation only applies when the box dimensions are equal to those of the reference dimensions. If this is not the case, then the converged stress tensor will not equal that specified by the user. We can resolve this problem by periodically resetting the reference -dimensions. The keyword {nreset_ref} controls how often this is done. -If this keyword is not used, or is given a value of zero, then the +dimensions. The keyword {nreset} controls how often this is done. If +this keyword is not used, or is given a value of zero, then the reference dimensions are set to those of the initial simulation domain and are never changed. A value of {nstep} means that every {nstep} minimization steps, the reference dimensions are set to those of the From b7c75b6c4efa38e5a4ec549bd7b6d7d1f9a06cd5 Mon Sep 17 00:00:00 2001 From: pmla Date: Tue, 11 Sep 2018 16:41:44 -0400 Subject: [PATCH 168/302] Added compute for Polyhedral Template Matching --- doc/src/Eqs/ptm_rmsd.jpg | Bin 0 -> 6833 bytes doc/src/Eqs/ptm_rmsd.tex | 21 + doc/src/compute_ptm_atom.txt | 117 ++ src/USER-PTM/LICENSE | 7 + src/USER-PTM/alloy_types.cpp | 101 ++ src/USER-PTM/alloy_types.h | 9 + src/USER-PTM/canonical_coloured.cpp | 167 ++ src/USER-PTM/canonical_coloured.h | 9 + src/USER-PTM/cell.cpp | 1368 ++++++++++++++ src/USER-PTM/cell.h | 324 ++++ src/USER-PTM/compute_ptm_atom.cpp | 307 ++++ src/USER-PTM/compute_ptm_atom.h | 48 + src/USER-PTM/config.h | 129 ++ src/USER-PTM/convex_hull_incremental.cpp | 363 ++++ src/USER-PTM/convex_hull_incremental.h | 27 + src/USER-PTM/deformation_gradient.cpp | 37 + src/USER-PTM/deformation_gradient.h | 142 ++ src/USER-PTM/fundamental_mappings.h | 180 ++ src/USER-PTM/graph_data.cpp | 2059 ++++++++++++++++++++++ src/USER-PTM/graph_data.h | 37 + src/USER-PTM/graph_tools.cpp | 52 + src/USER-PTM/graph_tools.h | 11 + src/USER-PTM/index_ptm.cpp | 218 +++ src/USER-PTM/initialize_data.cpp | 71 + src/USER-PTM/initialize_data.h | 61 + src/USER-PTM/neighbour_ordering.cpp | 203 +++ src/USER-PTM/neighbour_ordering.h | 13 + src/USER-PTM/normalize_vertices.cpp | 55 + src/USER-PTM/normalize_vertices.h | 8 + src/USER-PTM/polar.cpp | 337 ++++ src/USER-PTM/polar.h | 12 + src/USER-PTM/ptm_constants.h | 174 ++ src/USER-PTM/ptm_functions.h | 27 + src/USER-PTM/quat.cpp | 396 +++++ src/USER-PTM/quat.h | 32 + src/USER-PTM/structure_matcher.cpp | 294 +++ src/USER-PTM/structure_matcher.h | 21 + 37 files changed, 7437 insertions(+) create mode 100644 doc/src/Eqs/ptm_rmsd.jpg create mode 100644 doc/src/Eqs/ptm_rmsd.tex create mode 100644 doc/src/compute_ptm_atom.txt create mode 100644 src/USER-PTM/LICENSE create mode 100644 src/USER-PTM/alloy_types.cpp create mode 100644 src/USER-PTM/alloy_types.h create mode 100644 src/USER-PTM/canonical_coloured.cpp create mode 100644 src/USER-PTM/canonical_coloured.h create mode 100644 src/USER-PTM/cell.cpp create mode 100644 src/USER-PTM/cell.h create mode 100644 src/USER-PTM/compute_ptm_atom.cpp create mode 100644 src/USER-PTM/compute_ptm_atom.h create mode 100644 src/USER-PTM/config.h create mode 100644 src/USER-PTM/convex_hull_incremental.cpp create mode 100644 src/USER-PTM/convex_hull_incremental.h create mode 100644 src/USER-PTM/deformation_gradient.cpp create mode 100644 src/USER-PTM/deformation_gradient.h create mode 100644 src/USER-PTM/fundamental_mappings.h create mode 100644 src/USER-PTM/graph_data.cpp create mode 100644 src/USER-PTM/graph_data.h create mode 100644 src/USER-PTM/graph_tools.cpp create mode 100644 src/USER-PTM/graph_tools.h create mode 100644 src/USER-PTM/index_ptm.cpp create mode 100644 src/USER-PTM/initialize_data.cpp create mode 100644 src/USER-PTM/initialize_data.h create mode 100644 src/USER-PTM/neighbour_ordering.cpp create mode 100644 src/USER-PTM/neighbour_ordering.h create mode 100644 src/USER-PTM/normalize_vertices.cpp create mode 100644 src/USER-PTM/normalize_vertices.h create mode 100644 src/USER-PTM/polar.cpp create mode 100644 src/USER-PTM/polar.h create mode 100644 src/USER-PTM/ptm_constants.h create mode 100644 src/USER-PTM/ptm_functions.h create mode 100644 src/USER-PTM/quat.cpp create mode 100644 src/USER-PTM/quat.h create mode 100644 src/USER-PTM/structure_matcher.cpp create mode 100644 src/USER-PTM/structure_matcher.h diff --git a/doc/src/Eqs/ptm_rmsd.jpg b/doc/src/Eqs/ptm_rmsd.jpg new file mode 100644 index 0000000000000000000000000000000000000000..2d20da706ef61194305123d5673042d2318aec23 GIT binary patch literal 6833 zcmcI|cT`l(vhSV&hKw^XGo&Hs%#fqxoQ51lvSbMolnjF8oIwdHS)za5O1Hr<^1%vQz76H6}_@FC20KhR8O$Go^ zozyL9G!5Uqfd12gv#APx(IQAR2mmlIigufmL=}i*G6k^0$*uvnG~@wq2+blMh)F8X^aq>*+dx*%ZwmVfS-%f18vZ|bCcXd*IE9mlsI)t~Jo7i*A z8tdJW1Eb&m@HXjK97_CPySLRzEInds77*TSHoI*|kr)RX{c{7*uJmOUT`b3D%*|5; 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zgp937%H!A=H}@;HiY!~fHL|xi_ke@}Bc3S%u__4tATXi4t4}#a{&hl32<+qc+ZAKd zTA;p7cdkuN)pG;bFkP0`AThX&!qO2}Ii{X{)mVest7-C5k`wJw5Kz-0X(E#a8&#+y z0Pr)BrLDXzdRCOhE&j+c#()=vITq{^E!7o`xEq>I!P?mP;h@U;NI=2OhqIK7<~+6^ ztQ59axOp~B5nl?dq%Z!^?ITgbHrU<<7*7W*0$g+R<-B z%oIu9GtgXfa`|SdYsDtWJ?(kUT9*&G&`%L2Lq=$s&zeO;=W?E-tP%1v+AwKl%6!wWo}lLg7hcEDo9V1?090CY zKj}b>Je +#include "ptm_constants.h" +#include "initialize_data.h" + + +#define NUM_ALLOY_TYPES 3 +static uint32_t typedata[NUM_ALLOY_TYPES][3] = { + {PTM_MATCH_FCC, PTM_ALLOY_L10, 0x000001fe}, + {PTM_MATCH_FCC, PTM_ALLOY_L12_CU, 0x0000001e}, + {PTM_MATCH_FCC, PTM_ALLOY_L12_AU, 0x00001ffe}, +}; + +static bool test_pure(int num_nbrs, int32_t* numbers) +{ + for (int i=1;inum_nbrs+1;i++) + binary[i] = numbers[mapping[i]] == numbers[0] ? 0 : 1; + + for (int i=1;inum_nbrs+1;i++) + if (binary[i] != binary[0]) + return false; + + return true; +} + +static int32_t canonical_alloy_representation(const refdata_t* ref, int8_t* mapping, int32_t* numbers) +{ + int8_t binary[PTM_MAX_POINTS]; + for (int i=0;inum_nbrs+1;i++) + binary[i] = numbers[mapping[i]] == numbers[0] ? 0 : 1; + + int8_t temp[PTM_MAX_POINTS]; + uint32_t best = 0xFFFFFFFF; + for (int j=0;jnum_mappings;j++) + { + for (int i=0;inum_nbrs+1;i++) + temp[ref->mapping[j][i]] = binary[i]; + + uint32_t code = 0; + for (int i=0;inum_nbrs+1;i++) + code |= (temp[i] << i); + + best = std::min(best, code); + } + + return best; +} + +int32_t find_alloy_type(const refdata_t* ref, int8_t* mapping, int32_t* numbers) +{ + if (test_pure(ref->num_nbrs, numbers)) + return PTM_ALLOY_PURE; + + if (!test_binary(ref->num_nbrs, numbers)) + return PTM_ALLOY_NONE; + + uint32_t code = canonical_alloy_representation(ref, mapping, numbers); + for (int i=0;itype == typedata[i][0] && code == typedata[i][2]) + return typedata[i][1]; + + if (ref->type == PTM_MATCH_BCC) + if (test_shell_structure(ref, mapping, numbers, 8)) + return PTM_ALLOY_B2; + + if (ref->type == PTM_MATCH_DCUB || ref->type == PTM_MATCH_DHEX) + if (test_shell_structure(ref, mapping, numbers, 4)) + return PTM_ALLOY_SIC; + + return PTM_ALLOY_NONE; +} + diff --git a/src/USER-PTM/alloy_types.h b/src/USER-PTM/alloy_types.h new file mode 100644 index 0000000000..1f2980593a --- /dev/null +++ b/src/USER-PTM/alloy_types.h @@ -0,0 +1,9 @@ +#ifndef ALLOY_TYPES_H +#define ALLOY_TYPES_H + +#include "initialize_data.h" + +int32_t find_alloy_type(const refdata_t* ref, int8_t* mapping, int32_t* numbers); + +#endif + diff --git a/src/USER-PTM/canonical_coloured.cpp b/src/USER-PTM/canonical_coloured.cpp new file mode 100644 index 0000000000..af446e1a95 --- /dev/null +++ b/src/USER-PTM/canonical_coloured.cpp @@ -0,0 +1,167 @@ +#include +#include +#include +#include "graph_tools.h" +#include "ptm_constants.h" + + +static bool weinberg_coloured(int num_nodes, int num_edges, int8_t common[PTM_MAX_NBRS][PTM_MAX_NBRS], int8_t* colours, int8_t* best_code, int8_t* canonical_labelling, int a, int b) +{ + bool m[PTM_MAX_NBRS][PTM_MAX_NBRS]; + memset(m, 0, sizeof(bool) * PTM_MAX_NBRS * PTM_MAX_NBRS); + + int8_t index[PTM_MAX_NBRS]; + memset(index, -1, sizeof(int8_t) * PTM_MAX_NBRS); + + + int n = 0; + index[a] = colours[a] * num_nodes + n++; + if (index[a] > best_code[0]) + return false; + + bool winning = false; + if (index[a] < best_code[0]) + { + best_code[0] = index[a]; + winning = true; + } + + int c = -1; + for (int it=1;it<2*num_edges;it++) + { + bool newvertex = index[b] == -1; + + if (newvertex) + index[b] = colours[b] * num_nodes + n++; + + if (!winning && index[b] > best_code[it]) + return false; + + if (winning || index[b] < best_code[it]) + { + winning = true; + best_code[it] = index[b]; + } + + if (newvertex) + { + //When a new vertex is reached, take the right-most edge + //relative to the edge on which the vertex is reached. + + c = common[a][b]; + } + else if (m[b][a] == false) + { + //When an old vertex is reached on a new path, go back + //in the opposite direction. + + c = a; + } + else + { + //When an old vertex is reached on an old path, leave the + //vertex on the right-most edge that has not previously + //been traversed in that direction. + + c = common[a][b]; + while (m[b][c] == true) + c = common[c][b]; + } + + m[a][b] = true; + a = b; + b = c; + } + + if (winning) + { + memcpy(canonical_labelling, index, sizeof(int8_t) * num_nodes); + return true; + } + + return false; +} + +int canonical_form_coloured(int num_facets, int8_t facets[][3], int num_nodes, int8_t* degree, int8_t* colours, int8_t* canonical_labelling, int8_t* best_code, uint64_t* p_hash) +{ + int8_t common[PTM_MAX_NBRS][PTM_MAX_NBRS] = {{0}}; + int num_edges = 3 * num_facets / 2; + if (!build_facet_map(num_facets, facets, common)) + return -1; + + memset(best_code, SCHAR_MAX, sizeof(int8_t) * 2 * PTM_MAX_EDGES); + + bool equal = true; + for (int i = 1;i=0;i--) + canonical_labelling[i+1] = (canonical_labelling[i] % num_nodes) + 1; + canonical_labelling[0] = 0; + + uint64_t hash = 0; + for (int i = 0;i<2 * num_edges;i++) + { + uint64_t e = best_code[i]; + e += i % 8; + e &= 0xF; + e <<= (4 * i) % 64; + hash ^= e; + } + + *p_hash = hash; + return PTM_NO_ERROR; +} + diff --git a/src/USER-PTM/canonical_coloured.h b/src/USER-PTM/canonical_coloured.h new file mode 100644 index 0000000000..4a7b5f5a4a --- /dev/null +++ b/src/USER-PTM/canonical_coloured.h @@ -0,0 +1,9 @@ +#ifndef CANONICAL_COLOURED_H +#define CANONICAL_COLOURED_H + +#include + +int canonical_form_coloured(int num_facets, int8_t facets[][3], int num_nodes, int8_t* degree, int8_t* colours, int8_t* canonical_labelling, int8_t* best_code, uint64_t* p_hash); + +#endif + diff --git a/src/USER-PTM/cell.cpp b/src/USER-PTM/cell.cpp new file mode 100644 index 0000000000..f88e310b74 --- /dev/null +++ b/src/USER-PTM/cell.cpp @@ -0,0 +1,1368 @@ +// Voro++, a 3D cell-based Voronoi library +// +// Author : Chris H. Rycroft (LBL / UC Berkeley) +// Email : chr@alum.mit.edu +// Date : August 30th 2011 +// +// Modified by PM Larsen for use in Polyhedral Template Matching + +/** \file cell.cc + * \brief Function implementations for the voronoicell and related classes. */ + +#include +#include +#include +#include "config.h" +#include "cell.h" + +namespace voro { + +inline void voro_fatal_error(const char *p,int status) { + fprintf(stderr,"voro++: %s\n",p); + exit(status); + //return -1;//status; +} + +/** Constructs a Voronoi cell and sets up the initial memory. */ +voronoicell_base::voronoicell_base() : + current_vertices(init_vertices), current_vertex_order(init_vertex_order), + current_delete_size(init_delete_size), current_delete2_size(init_delete2_size), + ed(new int*[current_vertices]), nu(new int[current_vertices]), + pts(new double[3*current_vertices]), mem(new int[current_vertex_order]), + mec(new int[current_vertex_order]), mep(new int*[current_vertex_order]), + ds(new int[current_delete_size]), stacke(ds+current_delete_size), + ds2(new int[current_delete2_size]), stacke2(ds2+current_delete_size), + current_marginal(init_marginal), marg(new int[current_marginal]) { + int i; + for(i=0;i<3;i++) { + mem[i]=init_n_vertices;mec[i]=0; + mep[i]=new int[init_n_vertices*((i<<1)+1)]; + } + mem[3]=init_3_vertices;mec[3]=0; + mep[3]=new int[init_3_vertices*7]; + for(i=4;i=0;i--) if(mem[i]>0) delete [] mep[i]; + delete [] marg; + delete [] ds2;delete [] ds; + delete [] mep;delete [] mec; + delete [] mem;delete [] pts; + delete [] nu;delete [] ed; +} + +/** Ensures that enough memory is allocated prior to carrying out a copy. + * \param[in] vc a reference to the specialized version of the calling class. + * \param[in] vb a pointered to the class to be copied. */ +template +void voronoicell_base::check_memory_for_copy(vc_class &vc,voronoicell_base* vb) { + while(current_vertex_ordercurrent_vertex_order) add_memory_vorder(vc); + for(int i=0;imec[i]) add_memory(vc,i,ds2); + while(current_verticesp) add_memory_vertices(vc); +} + +/** Increases the memory storage for a particular vertex order, by increasing + * the size of the of the corresponding mep array. If the arrays already exist, + * their size is doubled; if they don't exist, then new ones of size + * init_n_vertices are allocated. The routine also ensures that the pointers in + * the ed array are updated, by making use of the back pointers. For the cases + * where the back pointer has been temporarily overwritten in the marginal + * vertex code, the auxiliary delete stack is scanned to find out how to update + * the ed value. If the template has been instantiated with the neighbor + * tracking turned on, then the routine also reallocates the corresponding mne + * array. + * \param[in] i the order of the vertex memory to be increased. */ +template +void voronoicell_base::add_memory(vc_class &vc,int i,int *stackp2) { + int s=(i<<1)+1; + if(mem[i]==0) { + vc.n_allocate(i,init_n_vertices); + mep[i]=new int[init_n_vertices*s]; + mem[i]=init_n_vertices; +#if VOROPP_VERBOSE >=2 + fprintf(stderr,"Order %d vertex memory created\n",i); +#endif + } else { + int j=0,k,*l; + mem[i]<<=1; + if(mem[i]>max_n_vertices) voro_fatal_error("Point memory allocation exceeded absolute maximum",VOROPP_MEMORY_ERROR); +#if VOROPP_VERBOSE >=2 + fprintf(stderr,"Order %d vertex memory scaled up to %d\n",i,mem[i]); +#endif + l=new int[s*mem[i]]; + int m=0; + vc.n_allocate_aux1(i); + while(j=0) { + ed[k]=l+j; + vc.n_set_to_aux1_offset(k,m); + } else { + int *dsp; + for(dsp=ds2;dsp=3 + fputs("Relocated dangling pointer",stderr); +#endif + } + for(k=0;k +void voronoicell_base::add_memory_vertices(vc_class &vc) { + +printf("nope: %d\n", current_vertices); +exit(3); + + int i=(current_vertices<<1),j,**pp,*pnu; + if(i>max_vertices) voro_fatal_error("Vertex memory allocation exceeded absolute maximum",VOROPP_MEMORY_ERROR); +#if VOROPP_VERBOSE >=2 + fprintf(stderr,"Vertex memory scaled up to %d\n",i); +#endif + double *ppts; + pp=new int*[i]; + for(j=0;j +void voronoicell_base::add_memory_vorder(vc_class &vc) { + int i=(current_vertex_order<<1),j,*p1,**p2; + if(i>max_vertex_order) voro_fatal_error("Vertex order memory allocation exceeded absolute maximum",VOROPP_MEMORY_ERROR); +#if VOROPP_VERBOSE >=2 + fprintf(stderr,"Vertex order memory scaled up to %d\n",i); +#endif + p1=new int[i]; + for(j=0;jmax_delete_size) voro_fatal_error("Delete stack 1 memory allocation exceeded absolute maximum",VOROPP_MEMORY_ERROR); +#if VOROPP_VERBOSE >=2 + fprintf(stderr,"Delete stack 1 memory scaled up to %d\n",current_delete_size); +#endif + int *dsn=new int[current_delete_size],*dsnp=dsn,*dsp=ds; + while(dspmax_delete2_size) voro_fatal_error("Delete stack 2 memory allocation exceeded absolute maximum",VOROPP_MEMORY_ERROR); +#if VOROPP_VERBOSE >=2 + fprintf(stderr,"Delete stack 2 memory scaled up to %d\n",current_delete2_size); +#endif + int *dsn=new int[current_delete2_size],*dsnp=dsn,*dsp=ds2; + while(dsp +inline bool voronoicell_base::search_for_outside_edge(vc_class &vc,int &up) { + int i,lp,lw,*j(ds2),*stackp2(ds2); + double l; + *(stackp2++)=up; + while(j +inline void voronoicell_base::add_to_stack(vc_class &vc,int lp,int *&stackp2) { + for(int *k(ds2);k +bool voronoicell_base::nplane(vc_class &vc,double x,double y,double z,double rsq,int p_id) { + int count=0,i,j,k,lp=up,cp,qp,rp,*stackp(ds),*stackp2(ds2),*dsp; + int us=0,ls=0,qs,iqs,cs,uw,qw,lw; + int *edp,*edd; + double u,l,r,q;bool complicated_setup=false,new_double_edge=false,double_edge=false; + + // Initialize the safe testing routine + n_marg=0;px=x;py=y;pz=z;prsq=rsq; + + // Test approximately sqrt(n)/4 points for their proximity to the plane + // and keep the one which is closest + uw=m_test(up,u); + + // Starting from an initial guess, we now move from vertex to vertex, + // to try and find an edge which intersects the cutting plane, + // or a vertex which is on the plane + try { + if(uw==1) { + + // The test point is inside the cutting plane. + us=0; + do { + lp=ed[up][us]; + lw=m_test(lp,l); + if(l=p) throw true; + u=l;up=lp; + for(us=0;us=p) throw true; + u=q;up=qp; + for(us=0;us=1 + fputs("Bailed out of convex calculation\n",stderr); +#endif + qw=1;lw=0; + for(qp=0;qp=current_vertex_order) add_memory_vorder(vc); + if(mec[nu[p]]==mem[nu[p]]) add_memory(vc,nu[p],stackp2); + vc.n_set_pointer(p,nu[p]); + ed[p]=mep[nu[p]]+((nu[p]<<1)+1)*mec[nu[p]]++; + ed[p][nu[p]<<1]=p; + + // Copy the edges of the original vertex into the new + // one. Delete the edges of the original vertex, and + // update the relational table. + us=cycle_down(i,up); + while(i=current_vertex_order) add_memory_vorder(vc); + if(mec[nu[p]]==mem[nu[p]]) add_memory(vc,nu[p],stackp2); + + // Copy the edges of the original vertex into the new + // one. Delete the edges of the original vertex, and + // update the relational table. + vc.n_set_pointer(p,nu[p]); + ed[p]=mep[nu[p]]+((nu[p]<<1)+1)*mec[nu[p]]++; + ed[p][nu[p]<<1]=p; + us=i++; + while(i0) k+=nu[j]; + } else { + if(j>0) { + + // This vertex was visited before, so + // count those vertices to the ones we + // already have. + k+=nu[j]; + + // The only time when we might make a + // duplicate edge is if the point we're + // going to move to next is also a + // marginal point, so test for that + // first. + if(lw==0) { + + // Now see whether this marginal point + // has been visited before. + i=-ed[lp][nu[lp]<<1]; + if(i>0) { + + // Now see if the last edge of that other + // marginal point actually ends up here. + if(ed[i][nu[i]-1]==j) { + new_double_edge=true; + k-=1; + } else new_double_edge=false; + } else { + + // That marginal point hasn't been visited + // before, so we probably don't have to worry + // about duplicate edges, except in the + // case when that's the way into the end + // of the facet, because that way always creates + // an edge. + if(j==rp&&lp==up&&ed[qp][nu[qp]+qs]==us) { + new_double_edge=true; + k-=1; + } else new_double_edge=false; + } + } else new_double_edge=false; + } else { + + // The vertex hasn't been visited + // before, but let's see if it's + // marginal + if(lw==0) { + + // If it is, we need to check + // for the case that it's a + // small branch, and that we're + // heading right back to where + // we came from + i=-ed[lp][nu[lp]<<1]; + if(i==cp) { + new_double_edge=true; + k-=1; + } else new_double_edge=false; + } else new_double_edge=false; + } + } + + // k now holds the number of edges of the new vertex + // we are forming. Add memory for it if it doesn't exist + // already. + while(k>=current_vertex_order) add_memory_vorder(vc); + if(mec[k]==mem[k]) add_memory(vc,k,stackp2); + + // Now create a new vertex with order k, or augment + // the existing one + if(j>0) { + + // If we're augmenting a vertex but we don't + // actually need any more edges, just skip this + // routine to avoid memory confusion + if(nu[j]!=k) { + // Allocate memory and copy the edges + // of the previous instance into it + vc.n_set_aux1(k); + edp=mep[k]+((k<<1)+1)*mec[k]++; + i=0; + while(ids) { + --p; + while(ed[p][nu[p]]==-1) { + j=nu[p]; + edp=ed[p];edd=(mep[j]+((j<<1)+1)*--mec[j]); + while(edp0) voro_fatal_error("Zero order vertex formed",VOROPP_INTERNAL_ERROR); + + // Collapse any order 2 vertices and exit + return collapse_order2(vc); +} + +/** During the creation of a new facet in the plane routine, it is possible + * that some order two vertices may arise. This routine removes them. + * Suppose an order two vertex joins c and d. If there's a edge between + * c and d already, then the order two vertex is just removed; otherwise, + * the order two vertex is removed and c and d are joined together directly. + * It is possible this process will create order two or order one vertices, + * and the routine is continually run until all of them are removed. + * \return False if the vertex removal was unsuccessful, indicative of the cell + * reducing to zero volume and disappearing; true if the vertex removal + * was successful. */ +template +inline bool voronoicell_base::collapse_order2(vc_class &vc) { + if(!collapse_order1(vc)) return false; + int a,b,i,j,k,l; + while(mec[2]>0) { + + // Pick a order 2 vertex and read in its edges + i=--mec[2]; + j=mep[2][5*i];k=mep[2][5*i+1]; + if(j==k) { +#if VOROPP_VERBOSE >=1 + fputs("Order two vertex joins itself",stderr); +#endif + return false; + } + + // Scan the edges of j to see if joins k + for(l=0;l +inline bool voronoicell_base::collapse_order1(vc_class &vc) { + int i,j,k; + while(mec[1]>0) { + up=0; +#if VOROPP_VERBOSE >=1 + fputs("Order one collapse\n",stderr); +#endif + i=--mec[1]; + j=mep[1][3*i];k=mep[1][3*i+1]; + i=mep[1][3*i+2]; + if(!delete_connection(vc,j,k,false)) return false; + --p; + if(up==i) up=0; + if(p!=i) { + if(up==p) up=i; + pts[3*i]=pts[3*p]; + pts[3*i+1]=pts[3*p+1]; + pts[3*i+2]=pts[3*p+2]; + for(k=0;k +inline bool voronoicell_base::delete_connection(vc_class &vc,int j,int k,bool hand) { + int q=hand?k:cycle_up(k,j); + int i=nu[j]-1,l,*edp,*edd,m; +#if VOROPP_VERBOSE >=1 + if(i<1) { + fputs("Zero order vertex formed\n",stderr); + return false; + } +#endif + if(mec[i]==mem[i]) add_memory(vc,i,ds2); + vc.n_set_aux1(i); + for(l=0;l &v) { + double area; + v.clear(); + int i,j,k,l,m,n; + double ux,uy,uz,vx,vy,vz,wx,wy,wz; + for(i=1;i=0) { + area=0; + ed[i][j]=-1-k; + l=cycle_up(ed[i][nu[i]+j],k); + m=ed[k][l];ed[k][l]=-1-m; + while(m!=i) { + n=cycle_up(ed[k][nu[k]+l],m); + ux=pts[3*k]-pts[3*i]; + uy=pts[3*k+1]-pts[3*i+1]; + uz=pts[3*k+2]-pts[3*i+2]; + vx=pts[3*m]-pts[3*i]; + vy=pts[3*m+1]-pts[3*i+1]; + vz=pts[3*m+2]-pts[3*i+2]; + wx=uy*vz-uz*vy; + wy=uz*vx-ux*vz; + wz=ux*vy-uy*vx; + area+=sqrt(wx*wx+wy*wy+wz*wz); + k=m;l=n; + m=ed[k][l];ed[k][l]=-1-m; + } + v.push_back(0.125*area); + } + } + reset_edges(); +} + +/** Several routines in the class that gather cell-based statistics internally + * track their progress by flipping edges to negative so that they know what + * parts of the cell have already been tested. This function resets them back + * to positive. When it is called, it assumes that every edge in the routine + * should have already been flipped to negative, and it bails out with an + * internal error if it encounters a positive edge. */ +inline void voronoicell_base::reset_edges() { + int i,j; + for(i=0;i=0) voro_fatal_error("Edge reset routine found a previously untested edge",VOROPP_INTERNAL_ERROR); + ed[i][j]=-1-ed[i][j]; + } +} + +/** Checks to see if a given vertex is inside, outside or within the test + * plane. If the point is far away from the test plane, the routine immediately + * returns whether it is inside or outside. If the routine is close the the + * plane and within the specified tolerance, then the special check_marginal() + * routine is called. + * \param[in] n the vertex to test. + * \param[out] ans the result of the scalar product used in evaluating the + * location of the point. + * \return -1 if the point is inside the plane, 1 if the point is outside the + * plane, or 0 if the point is within the plane. */ +inline int voronoicell_base::m_test(int n,double &ans) { + double *pp=pts+n+(n<<1); + ans=*(pp++)*px; + ans+=*(pp++)*py; + ans+=*pp*pz-prsq; + if(ans<-tolerance2) { + return -1; + } else if(ans>tolerance2) { + return 1; + } + return check_marginal(n,ans); +} + +/** Checks to see if a given vertex is inside, outside or within the test + * plane, for the case when the point has been detected to be very close to the + * plane. The routine ensures that the returned results are always consistent + * with previous tests, by keeping a table of any marginal results. The routine + * first sees if the vertex is in the table, and if it finds a previously + * computed result it uses that. Otherwise, it computes a result for this + * vertex and adds it the table. + * \param[in] n the vertex to test. + * \param[in] ans the result of the scalar product used in evaluating + * the location of the point. + * \return -1 if the point is inside the plane, 1 if the point is outside the + * plane, or 0 if the point is within the plane. */ +int voronoicell_base::check_marginal(int n,double &ans) { + int i; + for(i=0;imax_marginal) + voro_fatal_error("Marginal case buffer allocation exceeded absolute maximum",VOROPP_MEMORY_ERROR); +#if VOROPP_VERBOSE >=2 + fprintf(stderr,"Marginal cases buffer scaled up to %d\n",i); +#endif + int *pmarg=new int[current_marginal]; + for(int j=0;jtolerance?1:(ans<-tolerance?-1:0); + return marg[n_marg-1]; +} + +/** This initializes the class to be a rectangular box. It calls the base class + * initialization routine to set up the edge and vertex information, and then + * sets up the neighbor information, with initial faces being assigned ID + * numbers from -1 to -6. + * \param[in] (xmin,xmax) the minimum and maximum x coordinates. + * \param[in] (ymin,ymax) the minimum and maximum y coordinates. + * \param[in] (zmin,zmax) the minimum and maximum z coordinates. */ +void voronoicell_neighbor::init(double xmin,double xmax,double ymin,double ymax,double zmin,double zmax) { + init_base(xmin,xmax,ymin,ymax,zmin,zmax); + int *q=mne[3]; + *q=-5;q[1]=-3;q[2]=-1; + q[3]=-5;q[4]=-2;q[5]=-3; + q[6]=-5;q[7]=-1;q[8]=-4; + q[9]=-5;q[10]=-4;q[11]=-2; + q[12]=-6;q[13]=-1;q[14]=-3; + q[15]=-6;q[16]=-3;q[17]=-2; + q[18]=-6;q[19]=-4;q[20]=-1; + q[21]=-6;q[22]=-2;q[23]=-4; + *ne=q;ne[1]=q+3;ne[2]=q+6;ne[3]=q+9; + ne[4]=q+12;ne[5]=q+15;ne[6]=q+18;ne[7]=q+21; +} + +/** This routine checks to make sure the neighbor information of each face is + * consistent. */ +void voronoicell_neighbor::check_facets() { + int i,j,k,l,m,q; + for(i=1;i=0) { + ed[i][j]=-1-k; + q=ne[i][j]; + l=cycle_up(ed[i][nu[i]+j],k); + do { + m=ed[k][l]; + ed[k][l]=-1-m; + if(ne[k][l]!=q) fprintf(stderr,"Facet error at (%d,%d)=%d, started from (%d,%d)=%d\n",k,l,ne[k][l],i,j,q); + l=cycle_up(ed[k][nu[k]+l],m); + k=m; + } while (k!=i); + } + } + reset_edges(); +} + +/** The class constructor allocates memory for storing neighbor information. */ +voronoicell_neighbor::voronoicell_neighbor() { + int i; + mne=new int*[current_vertex_order]; + ne=new int*[current_vertices]; + for(i=0;i<3;i++) mne[i]=new int[init_n_vertices*i]; + mne[3]=new int[init_3_vertices*3]; + for(i=4;i=0;i--) if(mem[i]>0) delete [] mne[i]; + delete [] mne; + delete [] ne; +} + +/** Computes a vector list of neighbors. */ +void voronoicell_neighbor::neighbors(std::vector &v) { + v.clear(); + int i,j,k,l,m; + for(i=1;i=0) { + v.push_back(ne[i][j]); + ed[i][j]=-1-k; + l=cycle_up(ed[i][nu[i]+j],k); + do { + m=ed[k][l]; + ed[k][l]=-1-m; + l=cycle_up(ed[k][nu[k]+l],m); + k=m; + } while (k!=i); + } + } + reset_edges(); +} + +// Explicit instantiation +template bool voronoicell_base::nplane(voronoicell_neighbor&,double,double,double,double,int); +template void voronoicell_base::check_memory_for_copy(voronoicell_neighbor&,voronoicell_base*); + +} + diff --git a/src/USER-PTM/cell.h b/src/USER-PTM/cell.h new file mode 100644 index 0000000000..51a0cbb9ef --- /dev/null +++ b/src/USER-PTM/cell.h @@ -0,0 +1,324 @@ +// Voro++, a 3D cell-based Voronoi library +// +// Author : Chris H. Rycroft (LBL / UC Berkeley) +// Email : chr@alum.mit.edu +// Date : August 30th 2011 +// +// Modified by PM Larsen for use in Polyhedral Template Matching + +/** \file cell.hh + * \brief Header file for the voronoicell and related classes. */ + +#ifndef VOROPP_CELL_HH +#define VOROPP_CELL_HH + +#include +#include + +#include "config.h" + +namespace voro { + +/** \brief A class representing a single Voronoi cell. + * + * This class represents a single Voronoi cell, as a collection of vertices + * that are connected by edges. The class contains routines for initializing + * the Voronoi cell to be simple shapes such as a box, tetrahedron, or octahedron. + * It the contains routines for recomputing the cell based on cutting it + * by a plane, which forms the key routine for the Voronoi cell computation. + * It contains numerous routine for computing statistics about the Voronoi cell, + * and it can output the cell in several formats. + * + * This class is not intended for direct use, but forms the base of the + * voronoicell and voronoicell_neighbor classes, which extend it based on + * whether neighboring particle ID information needs to be tracked. */ +class voronoicell_base { + public: + /** This holds the current size of the arrays ed and nu, which + * hold the vertex information. If more vertices are created + * than can fit in this array, then it is dynamically extended + * using the add_memory_vertices routine. */ + int current_vertices; + /** This holds the current maximum allowed order of a vertex, + * which sets the size of the mem, mep, and mec arrays. If a + * vertex is created with more vertices than this, the arrays + * are dynamically extended using the add_memory_vorder routine. + */ + int current_vertex_order; + /** This sets the size of the main delete stack. */ + int current_delete_size; + /** This sets the size of the auxiliary delete stack. */ + int current_delete2_size; + /** This sets the total number of vertices in the current cell. + */ + int p; + /** This is the index of particular point in the cell, which is + * used to start the tracing routines for plane intersection + * and cutting. These routines will work starting from any + * point, but it's often most efficient to start from the last + * point considered, since in many cases, the cell construction + * algorithm may consider many planes with similar vectors + * concurrently. */ + int up; + /** This is a two dimensional array that holds information + * about the edge connections of the vertices that make up the + * cell. The two dimensional array is not allocated in the + * usual method. To account for the fact the different vertices + * have different orders, and thus require different amounts of + * storage, the elements of ed[i] point to one-dimensional + * arrays in the mep[] array of different sizes. + * + * More specifically, if vertex i has order m, then ed[i] + * points to a one-dimensional array in mep[m] that has 2*m+1 + * entries. The first m elements hold the neighboring edges, so + * that the jth edge of vertex i is held in ed[i][j]. The next + * m elements hold a table of relations which is redundant but + * helps speed up the computation. It satisfies the relation + * ed[ed[i][j]][ed[i][m+j]]=i. The final entry holds a back + * pointer, so that ed[i+2*m]=i. The back pointers are used + * when rearranging the memory. */ + int **ed; + /** This array holds the order of the vertices in the Voronoi + * cell. This array is dynamically allocated, with its current + * size held by current_vertices. */ + int *nu; + /** This in an array with size 3*current_vertices for holding + * the positions of the vertices. */ + double *pts; + voronoicell_base(); + virtual ~voronoicell_base(); + void init_base(double xmin,double xmax,double ymin,double ymax,double zmin,double zmax); + void init_octahedron_base(double l); + void init_tetrahedron_base(double x0,double y0,double z0,double x1,double y1,double z1,double x2,double y2,double z2,double x3,double y3,double z3); + void translate(double x,double y,double z); + double volume(); + double max_radius_squared(); + double total_edge_distance(); + double surface_area(); + void centroid(double &cx,double &cy,double &cz); + int number_of_faces(); + int number_of_edges(); + void vertex_orders(std::vector &v); + void vertices(std::vector &v); + void vertices(double x,double y,double z,std::vector &v); + void face_areas(std::vector &v); + void face_orders(std::vector &v); + void face_freq_table(std::vector &v); + void face_vertices(std::vector &v); + void face_perimeters(std::vector &v); + void normals(std::vector &v); + template + bool nplane(vc_class &vc,double x,double y,double z,double rsq,int p_id); + bool plane_intersects(double x,double y,double z,double rsq); + bool plane_intersects_guess(double x,double y,double z,double rsq); + void construct_relations(); + void check_relations(); + void check_duplicates(); + /** Returns a list of IDs of neighboring particles + * corresponding to each face. + * \param[out] v a reference to a vector in which to return the + * results. If no neighbor information is + * available, a blank vector is returned. */ + virtual void neighbors(std::vector &v) {v.clear();} + /** This a virtual function that is overridden by a routine to + * print the neighboring particle IDs for a given vertex. By + * default, when no neighbor information is available, the + * routine does nothing. + * \param[in] i the vertex to consider. */ + /** This is a simple inline function for picking out the index + * of the next edge counterclockwise at the current vertex. + * \param[in] a the index of an edge of the current vertex. + * \param[in] p the number of the vertex. + * \return 0 if a=nu[p]-1, or a+1 otherwise. */ + inline int cycle_up(int a,int p) {return a==nu[p]-1?0:a+1;} + /** This is a simple inline function for picking out the index + * of the next edge clockwise from the current vertex. + * \param[in] a the index of an edge of the current vertex. + * \param[in] p the number of the vertex. + * \return nu[p]-1 if a=0, or a-1 otherwise. */ + inline int cycle_down(int a,int p) {return a==0?nu[p]-1:a-1;} + protected: + /** This a one dimensional array that holds the current sizes + * of the memory allocations for them mep array.*/ + int *mem; + /** This is a one dimensional array that holds the current + * number of vertices of order p that are stored in the mep[p] + * array. */ + int *mec; + /** This is a two dimensional array for holding the information + * about the edges of the Voronoi cell. mep[p] is a + * one-dimensional array for holding the edge information about + * all vertices of order p, with each vertex holding 2*p+1 + * integers of information. The total number of vertices held + * on mep[p] is stored in mem[p]. If the space runs out, the + * code allocates more using the add_memory() routine. */ + int **mep; + inline void reset_edges(); + template + void check_memory_for_copy(vc_class &vc,voronoicell_base* vb); + void copy(voronoicell_base* vb); + private: + /** This is the delete stack, used to store the vertices which + * are going to be deleted during the plane cutting procedure. + */ + int *ds,*stacke; + /** This is the auxiliary delete stack, which has size set by + * current_delete2_size. */ + int *ds2,*stacke2; + /** This stores the current memory allocation for the marginal + * cases. */ + int current_marginal; + /** This stores the total number of marginal points which are + * currently in the buffer. */ + int n_marg; + /** This array contains a list of the marginal points, and also + * the outcomes of the marginal tests. */ + int *marg; + /** The x coordinate of the normal vector to the test plane. */ + double px; + /** The y coordinate of the normal vector to the test plane. */ + double py; + /** The z coordinate of the normal vector to the test plane. */ + double pz; + /** The magnitude of the normal vector to the test plane. */ + double prsq; + template + void add_memory(vc_class &vc,int i,int *stackp2); + template + void add_memory_vertices(vc_class &vc); + template + void add_memory_vorder(vc_class &vc); + void add_memory_ds(int *&stackp); + void add_memory_ds2(int *&stackp2); + template + inline bool collapse_order1(vc_class &vc); + template + inline bool collapse_order2(vc_class &vc); + template + inline bool delete_connection(vc_class &vc,int j,int k,bool hand); + template + inline bool search_for_outside_edge(vc_class &vc,int &up); + template + inline void add_to_stack(vc_class &vc,int lp,int *&stackp2); + inline bool plane_intersects_track(double x,double y,double z,double rs,double g); + inline void normals_search(std::vector &v,int i,int j,int k); + inline bool search_edge(int l,int &m,int &k); + inline int m_test(int n,double &ans); + int check_marginal(int n,double &ans); + friend class voronoicell; + friend class voronoicell_neighbor; +}; + +/** \brief Extension of the voronoicell_base class to represent a Voronoi cell + * with neighbor information. + * + * This class is an extension of the voronoicell_base class, in cases when the + * IDs of neighboring particles associated with each face of the Voronoi cell. + * It contains additional data structures mne and ne for storing this + * information. */ +class voronoicell_neighbor : public voronoicell_base { + public: + using voronoicell_base::nplane; + /** This two dimensional array holds the neighbor information + * associated with each vertex. mne[p] is a one dimensional + * array which holds all of the neighbor information for + * vertices of order p. */ + int **mne; + /** This is a two dimensional array that holds the neighbor + * information associated with each vertex. ne[i] points to a + * one-dimensional array in mne[nu[i]]. ne[i][j] holds the + * neighbor information associated with the jth edge of vertex + * i. It is set to the ID number of the plane that made the + * face that is clockwise from the jth edge. */ + int **ne; + voronoicell_neighbor(); + ~voronoicell_neighbor(); + void operator=(voronoicell_neighbor &c); + /** Cuts the Voronoi cell by a particle whose center is at a + * separation of (x,y,z) from the cell center. The value of rsq + * should be initially set to \f$x^2+y^2+z^2\f$. + * \param[in] (x,y,z) the normal vector to the plane. + * \param[in] rsq the distance along this vector of the plane. + * \param[in] p_id the plane ID (for neighbor tracking only). + * \return False if the plane cut deleted the cell entirely, + * true otherwise. */ + inline bool nplane(double x,double y,double z,double rsq,int p_id) { + return nplane(*this,x,y,z,rsq,p_id); + } + /** This routine calculates the modulus squared of the vector + * before passing it to the main nplane() routine with full + * arguments. + * \param[in] (x,y,z) the vector to cut the cell by. + * \param[in] p_id the plane ID (for neighbor tracking only). + * \return False if the plane cut deleted the cell entirely, + * true otherwise. */ + inline bool nplane(double x,double y,double z,int p_id) { + double rsq=x*x+y*y+z*z; + return nplane(*this,x,y,z,rsq,p_id); + } + /** This version of the plane routine just makes up the plane + * ID to be zero. It will only be referenced if neighbor + * tracking is enabled. + * \param[in] (x,y,z) the vector to cut the cell by. + * \param[in] rsq the modulus squared of the vector. + * \return False if the plane cut deleted the cell entirely, + * true otherwise. */ + inline bool plane(double x,double y,double z,double rsq) { + return nplane(*this,x,y,z,rsq,0); + } + /** Cuts a Voronoi cell using the influence of a particle at + * (x,y,z), first calculating the modulus squared of this + * vector before passing it to the main nplane() routine. Zero + * is supplied as the plane ID, which will be ignored unless + * neighbor tracking is enabled. + * \param[in] (x,y,z) the vector to cut the cell by. + * \return False if the plane cut deleted the cell entirely, + * true otherwise. */ + inline bool plane(double x,double y,double z) { + double rsq=x*x+y*y+z*z; + return nplane(*this,x,y,z,rsq,0); + } + void init(double xmin,double xmax,double ymin,double ymax,double zmin,double zmax); + void check_facets(); + virtual void neighbors(std::vector &v); + + private: + int *paux1; + int *paux2; + inline void n_allocate(int i,int m) {mne[i]=new int[m*i];} + inline void n_add_memory_vertices(int i) { + int **pp=new int*[i]; + for(int j=0;j +#include +#include +#include + +#include "atom.h" +#include "comm.h" +#include "compute_ptm_atom.h" +#include "error.h" +#include "force.h" +#include "memory.h" +#include "modify.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" +#include "pair.h" +#include "update.h" + +#include "ptm_functions.h" + +#define MAX_NEIGHBORS 30 +#define NUM_COLUMNS 7 +#define UNKNOWN 0 +#define OTHER 8 + +using namespace LAMMPS_NS; + +static const char cite_user_ptm_package[] = + "USER-PTM package:\n\n" + "@Article{larsen2016ptm,\n" + " author={Larsen, Peter Mahler and Schmidt, S{\o}ren and Schi{\o}tz, " + "Jakob},\n" + " title={Robust structural identification via polyhedral template " + "matching},\n" + " journal={Modelling~Simul.~Mater.~Sci.~Eng.},\n" + " year={2016},\n" + " number={5},\n" + " volume={24},\n" + " pages={055007},\n" + " DOI = {10.1088/0965-0393/24/5/055007}" + "}\n\n"; + +/* ---------------------------------------------------------------------- */ + +ComputePTMAtom::ComputePTMAtom(LAMMPS *lmp, int narg, char **arg) + : Compute(lmp, narg, arg), list(NULL), output(NULL) { + if (narg != 5) + error->all(FLERR, "Illegal compute ptm/atom command"); + + char *structures = arg[3]; + char *ptr = structures; + + const char *strings[] = {"fcc", "hcp", "bcc", "ico", "sc", + "dcub", "dhex", "all", "default"}; + int32_t flags[] = { + PTM_CHECK_FCC, + PTM_CHECK_HCP, + PTM_CHECK_BCC, + PTM_CHECK_ICO, + PTM_CHECK_SC, + PTM_CHECK_DCUB, + PTM_CHECK_DHEX, + PTM_CHECK_ALL, + PTM_CHECK_FCC | PTM_CHECK_HCP | PTM_CHECK_BCC | PTM_CHECK_ICO}; + + input_flags = 0; + while (*ptr != '\0') { + + bool found = false; + for (int i = 0; i < 9; i++) { + int len = strlen(strings[i]); + if (strncmp(ptr, strings[i], len) == 0) { + input_flags |= flags[i]; + ptr += len; + found = true; + break; + } + } + + if (!found) + error->all(FLERR, + "Illegal compute ptm/atom command (invalid structure type)"); + + if (*ptr == '\0') + break; + + if (*ptr != '-') + error->all(FLERR, + "Illegal compute ptm/atom command (invalid structure type)"); + + ptr++; + } + + double threshold = force->numeric(FLERR, arg[4]); + if (threshold < 0.0) + error->all(FLERR, + "Illegal compute ptm/atom command (threshold is negative)"); + rmsd_threshold = threshold; + if (rmsd_threshold == 0) + rmsd_threshold = INFINITY; + + peratom_flag = 1; + size_peratom_cols = NUM_COLUMNS; + create_attribute = 1; + nmax = 0; +} + +/* ---------------------------------------------------------------------- */ + +ComputePTMAtom::~ComputePTMAtom() { memory->destroy(output); } + +/* ---------------------------------------------------------------------- */ + +void ComputePTMAtom::init() { + if (force->pair == NULL) + error->all(FLERR, "Compute ptm/atom requires a pair style be defined"); + + int count = 0; + for (int i = 0; i < modify->ncompute; i++) + if (strcmp(modify->compute[i]->style, "ptm/atom") == 0) + count++; + if (count > 1 && comm->me == 0) + error->warning(FLERR, "More than one compute ptm/atom defined"); + + // need an occasional full neighbor list + + int irequest = neighbor->request(this, instance_me); + neighbor->requests[irequest]->pair = 0; + neighbor->requests[irequest]->compute = 1; + neighbor->requests[irequest]->half = 0; + neighbor->requests[irequest]->full = 1; + neighbor->requests[irequest]->occasional = 1; +} + +/* ---------------------------------------------------------------------- */ + +void ComputePTMAtom::init_list(int id, NeighList *ptr) { list = ptr; } + +/* ---------------------------------------------------------------------- */ + +typedef struct { + int index; + double d; +} ptmnbr_t; + +static bool sorthelper_compare(ptmnbr_t const &a, ptmnbr_t const &b) { + return a.d < b.d; +} + +static int get_neighbors(double *pos, int jnum, int *jlist, double **x, + double (*nbr)[3]) { + + ptmnbr_t *nbr_order = new ptmnbr_t[jnum]; + + for (int jj = 0; jj < jnum; jj++) { + int j = jlist[jj]; + j &= NEIGHMASK; + + double dx = pos[0] - x[j][0]; + double dy = pos[1] - x[j][1]; + double dz = pos[2] - x[j][2]; + double rsq = dx * dx + dy * dy + dz * dz; + + nbr_order[jj].index = j; + nbr_order[jj].d = rsq; + } + + std::sort(nbr_order, nbr_order + jnum, &sorthelper_compare); + int num_nbrs = std::min(MAX_NEIGHBORS, jnum); + + nbr[0][0] = nbr[0][1] = nbr[0][2] = 0; + for (int jj = 0; jj < num_nbrs; jj++) { + + int j = nbr_order[jj].index; + nbr[jj + 1][0] = x[j][0] - pos[0]; + nbr[jj + 1][1] = x[j][1] - pos[1]; + nbr[jj + 1][2] = x[j][2] - pos[2]; + } + + delete[] nbr_order; + return num_nbrs; +} + +void ComputePTMAtom::compute_peratom() { + // PTM global initialization. If already initialized this function does + // nothing. + ptm_initialize_global(); + + // initialize PTM local storage + ptm_local_handle_t local_handle = ptm_initialize_local(); + + invoked_peratom = update->ntimestep; + + // grow arrays if necessary + if (atom->nmax > nmax) { + memory->destroy(output); + nmax = atom->nmax; + + memory->create(output, nmax, NUM_COLUMNS, "ptm:ptm_output"); + array_atom = output; + } + + // invoke full neighbor list (will copy or build if necessary) + neighbor->build_one(list); + + int inum = list->inum; + int *ilist = list->ilist; + int *numneigh = list->numneigh; + int **firstneigh = list->firstneigh; + + double **x = atom->x; + int *mask = atom->mask; + int nlocal = atom->nlocal; + + for (int ii = 0; ii < inum; ii++) { + + int i = ilist[ii]; + output[i][0] = UNKNOWN; + if (!(mask[i] & groupbit)) + continue; + + double *pos = x[i]; + + int *jlist = firstneigh[i]; + int jnum = numneigh[i]; + if (jnum <= 0) + continue; + + // get neighbours ordered by increasing distance + double nbr[MAX_NEIGHBORS + 1][3]; + int num_nbrs = get_neighbors(pos, jnum, jlist, x, nbr); + + // check that we have enough neighbours for the desired structure types + int32_t flags = 0; + if (num_nbrs >= PTM_NUM_NBRS_SC && (input_flags & PTM_CHECK_SC)) + flags |= PTM_CHECK_SC; + if (num_nbrs >= PTM_NUM_NBRS_FCC && (input_flags & PTM_CHECK_FCC)) + flags |= PTM_CHECK_FCC; + if (num_nbrs >= PTM_NUM_NBRS_HCP && (input_flags & PTM_CHECK_HCP)) + flags |= PTM_CHECK_HCP; + if (num_nbrs >= PTM_NUM_NBRS_ICO && (input_flags & PTM_CHECK_ICO)) + flags |= PTM_CHECK_ICO; + if (num_nbrs >= PTM_NUM_NBRS_BCC && (input_flags & PTM_CHECK_BCC)) + flags |= PTM_CHECK_BCC; + if (num_nbrs >= PTM_NUM_NBRS_DCUB && (input_flags & PTM_CHECK_DCUB)) + flags |= PTM_CHECK_DCUB; + if (num_nbrs >= PTM_NUM_NBRS_DHEX && (input_flags & PTM_CHECK_DHEX)) + flags |= PTM_CHECK_DHEX; + + // now run PTM + int8_t mapping[MAX_NEIGHBORS + 1]; + int32_t type, alloy_type; + double scale, rmsd, interatomic_distance, lattice_constant; + double q[4], F[9], F_res[3], U[9], P[9]; + ptm_index(local_handle, flags, num_nbrs + 1, nbr, NULL, true, &type, + &alloy_type, &scale, &rmsd, q, F, F_res, U, P, mapping, + &interatomic_distance, &lattice_constant); + + if (rmsd > rmsd_threshold) { + type = PTM_MATCH_NONE; + } + + // printf("%d type=%d rmsd=%f\n", i, type, rmsd); + + if (type == PTM_MATCH_NONE) + type = OTHER; + + output[i][0] = type; + output[i][1] = rmsd; + output[i][2] = interatomic_distance; + output[i][3] = q[0]; + output[i][4] = q[1]; + output[i][5] = q[2]; + output[i][6] = q[3]; + } + + // printf("finished ptm analysis\n"); + ptm_uninitialize_local(local_handle); +} + +/* ---------------------------------------------------------------------- + memory usage of local atom-based array +------------------------------------------------------------------------- */ + +double ComputePTMAtom::memory_usage() { + double bytes = nmax * NUM_COLUMNS * sizeof(double); + bytes += nmax * sizeof(double); + return bytes; +} diff --git a/src/USER-PTM/compute_ptm_atom.h b/src/USER-PTM/compute_ptm_atom.h new file mode 100644 index 0000000000..5c10e0c443 --- /dev/null +++ b/src/USER-PTM/compute_ptm_atom.h @@ -0,0 +1,48 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef COMPUTE_CLASS + +ComputeStyle(ptm/atom,ComputePTMAtom) + +#else + +#ifndef LMP_COMPUTE_PTM_ATOM_H +#define LMP_COMPUTE_PTM_ATOM_H + +#include "compute.h" + +namespace LAMMPS_NS { + +class ComputePTMAtom : public Compute { + public: + ComputePTMAtom(class LAMMPS *, int, char **); + ~ComputePTMAtom(); + void init(); + void init_list(int, class NeighList *); + void compute_peratom(); + double memory_usage(); + + private: + int nmax; + int32_t input_flags; + double rmsd_threshold; + class NeighList *list; + double **output; +}; + +} + +#endif +#endif + diff --git a/src/USER-PTM/config.h b/src/USER-PTM/config.h new file mode 100644 index 0000000000..eba69b3373 --- /dev/null +++ b/src/USER-PTM/config.h @@ -0,0 +1,129 @@ +// Voro++, a 3D cell-based Voronoi library +// +// Author : Chris H. Rycroft (LBL / UC Berkeley) +// Email : chr@alum.mit.edu +// Date : August 30th 2011 +// +// Modified by PM Larsen for use in Polyhedral Template Matching + +/** \file config.hh + * \brief Master configuration file for setting various compile-time options. */ + +#ifndef VOROPP_CONFIG_HH +#define VOROPP_CONFIG_HH + +namespace voro { + +// These constants set the initial memory allocation for the Voronoi cell +/** The initial memory allocation for the number of vertices. */ +const int init_vertices=256; +/** The initial memory allocation for the maximum vertex order. */ +const int init_vertex_order=64; +/** The initial memory allocation for the number of regular vertices of order + * 3. */ +const int init_3_vertices=256; +/** The initial memory allocation for the number of vertices of higher order. + */ +const int init_n_vertices=8; +/** The initial buffer size for marginal cases used by the suretest class. */ +const int init_marginal=64; +/** The initial size for the delete stack. */ +const int init_delete_size=256; +/** The initial size for the auxiliary delete stack. */ +const int init_delete2_size=256; +/** The initial size for the wall pointer array. */ +const int init_wall_size=32; +/** The default initial size for the ordering class. */ +const int init_ordering_size=4096; +/** The initial size of the pre_container chunk index. */ +const int init_chunk_size=256; + +// If the initial memory is too small, the program dynamically allocates more. +// However, if the limits below are reached, then the program bails out. +/** The maximum memory allocation for the number of vertices. */ +const int max_vertices=16777216; +/** The maximum memory allocation for the maximum vertex order. */ +const int max_vertex_order=2048; +/** The maximum memory allocation for the any particular order of vertex. */ +const int max_n_vertices=16777216; +/** The maximum buffer size for marginal cases used by the suretest class. */ +const int max_marginal=16777216; +/** The maximum size for the delete stack. */ +const int max_delete_size=16777216; +/** The maximum size for the auxiliary delete stack. */ +const int max_delete2_size=16777216; +/** The maximum amount of particle memory allocated for a single region. */ +const int max_particle_memory=16777216; +/** The maximum size for the wall pointer array. */ +const int max_wall_size=2048; +/** The maximum size for the ordering class. */ +const int max_ordering_size=67108864; +/** The maximum size for the pre_container chunk index. */ +const int max_chunk_size=65536; + +/** The chunk size in the pre_container classes. */ +const int pre_container_chunk_size=1024; + +#ifndef VOROPP_VERBOSE +/** Voro++ can print a number of different status and debugging messages to + * notify the user of special behavior, and this macro sets the amount which + * are displayed. At level 0, no messages are printed. At level 1, messages + * about unusual cases during cell construction are printed, such as when the + * plane routine bails out due to floating point problems. At level 2, general + * messages about memory expansion are printed. At level 3, technical details + * about memory management are printed. */ +#define VOROPP_VERBOSE 0 +#endif + +/** If a point is within this distance of a cutting plane, then the code + * assumes that point exactly lies on the plane. */ +const double tolerance=1e-11; + +/** If a point is within this distance of a cutting plane, then the code stores + * whether this point is inside, outside, or exactly on the cutting plane in + * the marginal cases buffer, to prevent the test giving a different result on + * a subsequent evaluation due to floating point rounding errors. */ +const double tolerance2=2e-11; + +/** The square of the tolerance, used when deciding whether some squared + * quantities are large enough to be used. */ +const double tolerance_sq=tolerance*tolerance; + +/** A large number that is used in the computation. */ +const double large_number=1e30; + +/** A radius to use as a placeholder when no other information is available. */ +const double default_radius=0.5; + +/** The maximum number of shells of periodic images to test over. */ +const int max_unit_voro_shells=10; + +/** A guess for the optimal number of particles per block, used to set up the + * container grid. */ +const double optimal_particles=5.6; + +/** If this is set to 1, then the code reports any instances of particles being + * put outside of the container geometry. */ +#define VOROPP_REPORT_OUT_OF_BOUNDS 0 + +/** Voro++ returns this status code if there is a file-related error, such as + * not being able to open file. */ +#define VOROPP_FILE_ERROR 1 + +/** Voro++ returns this status code if there is a memory allocation error, if + * one of the safe memory limits is exceeded. */ +#define VOROPP_MEMORY_ERROR 2 + +/** Voro++ returns this status code if there is any type of internal error, if + * it detects that representation of the Voronoi cell is inconsistent. This + * status code will generally indicate a bug, and the developer should be + * contacted. */ +#define VOROPP_INTERNAL_ERROR 3 + +/** Voro++ returns this status code if it could not interpret the command line + * arguments passed to the command line utility. */ +#define VOROPP_CMD_LINE_ERROR 4 + +} + +#endif diff --git a/src/USER-PTM/convex_hull_incremental.cpp b/src/USER-PTM/convex_hull_incremental.cpp new file mode 100644 index 0000000000..bfe173cc02 --- /dev/null +++ b/src/USER-PTM/convex_hull_incremental.cpp @@ -0,0 +1,363 @@ +#include +#include +#include +#include +#include +#include "convex_hull_incremental.h" +#include "ptm_constants.h" + + +#define VISIBLE 1 +#define INVISIBLE 2 +#define BOTH 3 +#define TOLERANCE 1E-8 + +static double norm_squared(double* p) +{ + double x = p[0]; + double y = p[1]; + double z = p[2]; + + return x*x + y*y + z*z; +} + +static double dot_product(const double* a, const double* b) +{ + return a[0]*b[0] + a[1]*b[1] + a[2]*b[2]; +} + +static void cross_product(double* a, double* b, double* c) +{ + c[0] = a[1] * b[2] - a[2] * b[1]; + c[1] = a[2] * b[0] - a[0] * b[2]; + c[2] = a[0] * b[1] - a[1] * b[0]; +} + +static void calculate_plane_normal(const double (*points)[3], int a, int b, int c, double* plane_normal) +{ + double u[3] = { points[b][0] - points[a][0], + points[b][1] - points[a][1], + points[b][2] - points[a][2] }; + + double v[3] = { points[c][0] - points[a][0], + points[c][1] - points[a][1], + points[c][2] - points[a][2] }; + + cross_product(u, v, plane_normal); + double norm = sqrt(norm_squared(plane_normal)); + plane_normal[0] /= norm; + plane_normal[1] /= norm; + plane_normal[2] /= norm; +} + +static double point_plane_distance(const double* w, const double* plane_point, const double* plane_cross) +{ + return plane_cross[0] * (plane_point[0] - w[0]) + + plane_cross[1] * (plane_point[1] - w[1]) + + plane_cross[2] * (plane_point[2] - w[2]); +} + +static bool calc_max_extent(int num_points, const double (*points)[3], int* min_index, int* max_index) +{ + for (int j=0;j<3;j++) + { + double dmin = DBL_MAX, dmax = -DBL_MAX; + int imin = 0, imax = 0; + + for (int i = 0;i dmax) + { + dmax = d; + imax = i; + } + } + + if (imin == imax) + return false; //degenerate point set + + min_index[j] = imin; + max_index[j] = imax; + } + + return true; +} + +static bool find_third_point(int num_points, const double (*points)[3], int a, int b, int* p_c) +{ + const double* x1 = points[a]; + const double* x2 = points[b]; + + double x2x1[3] = {x2[0] - x1[0], x2[1] - x1[1], x2[2] - x1[2]}; + double ns_x2x1 = norm_squared(x2x1); + + int bi = -1; + double max_dist = 0.0; + for (int i = 0;i max_dist) + { + max_dist = dist; + bi = i; + } + } + + *p_c = bi; + return max_dist > TOLERANCE; +} + +static bool find_fourth_point(int num_points, const double (*points)[3], int a, int b, int c, int* p_d) +{ + double plane_normal[3]; + calculate_plane_normal(points, a, b, c, plane_normal); + + + int bi = -1; + double max_dist = 0.0; + for (int i = 0;i max_dist) + { + max_dist = dist; + bi = i; + } + } + + *p_d = bi; + return max_dist > TOLERANCE; +} + +static int initial_simplex(int num_points, const double (*points)[3], int* initial_vertices) +{ + int min_index[3] = {0}; + int max_index[3] = {0}; + if (!calc_max_extent(num_points, points, min_index, max_index)) + return -1; + + int bi = -1; + double max_dist = 0.0; + for (int i = 0;i<3;i++) + { + int a = min_index[i], b = max_index[i]; + double delta[3] = { points[a][0] - points[b][0], + points[a][1] - points[b][1], + points[a][2] - points[b][2] }; + double dist = norm_squared(delta); + if (dist > max_dist) + { + bi = i; + max_dist = dist; + } + } + + //first two points are (a, b) + int a = min_index[bi], b = max_index[bi], c = -1, d = -1; + + if (!find_third_point(num_points, points, a, b, &c)) + return -2; + + if (!find_fourth_point(num_points, points, a, b, c, &d)) + return -3; + + initial_vertices[0] = a; + initial_vertices[1] = b; + initial_vertices[2] = c; + initial_vertices[3] = d; + return 0; +} + +static bool visible(const double* w, const double* plane_point, const double* plane_normal) +{ + return point_plane_distance(w, plane_point, plane_normal) > 0; +} + +void add_facet(const double (*points)[3], int a, int b, int c, int8_t* facet, double* plane_normal, double* barycentre) +{ + calculate_plane_normal(points, a, b, c, plane_normal); + if (visible(barycentre, points[a], plane_normal)) + { + plane_normal[0] = -plane_normal[0]; + plane_normal[1] = -plane_normal[1]; + plane_normal[2] = -plane_normal[2]; + + facet[0] = b; + facet[1] = a; + facet[2] = c; + } + else + { + facet[0] = a; + facet[1] = b; + facet[2] = c; + } +} + +static int initialize_convex_hull(int num_points, const double (*points)[3], int8_t facets[][3], double plane_normal[][3], bool* processed, int* initial_vertices, double* barycentre) +{ + memset(processed, 0, PTM_MAX_POINTS * sizeof(bool)); + memset(barycentre, 0, 3 * sizeof(double)); + int ret = initial_simplex(num_points, points, initial_vertices); + if (ret != 0) + return ret; + + for (int i = 0;i<4;i++) + { + int a = initial_vertices[i]; + processed[a] = true; + + barycentre[0] += points[a][0]; + barycentre[1] += points[a][1]; + barycentre[2] += points[a][2]; + } + barycentre[0] /= 4; + barycentre[1] /= 4; + barycentre[2] /= 4; + + add_facet(points, initial_vertices[0], initial_vertices[1], initial_vertices[2], facets[0], plane_normal[0], barycentre); + add_facet(points, initial_vertices[0], initial_vertices[1], initial_vertices[3], facets[1], plane_normal[1], barycentre); + add_facet(points, initial_vertices[0], initial_vertices[2], initial_vertices[3], facets[2], plane_normal[2], barycentre); + add_facet(points, initial_vertices[1], initial_vertices[2], initial_vertices[3], facets[3], plane_normal[3], barycentre); + return 0; +} + +int get_convex_hull(int num_points, const double (*points)[3], convexhull_t* ch, int8_t simplex[][3]) +{ + assert( num_points == PTM_NUM_POINTS_FCC + || num_points == PTM_NUM_POINTS_HCP + || num_points == PTM_NUM_POINTS_BCC + || num_points == PTM_NUM_POINTS_ICO + || num_points == PTM_NUM_POINTS_SC + || num_points == PTM_NUM_POINTS_DCUB + || num_points == PTM_NUM_POINTS_DHEX); + + int ret = 0; + int num_prev = ch->num_prev; + ch->num_prev = num_points; + if (!ch->ok || 0) + { + ret = initialize_convex_hull(num_points, points, ch->facets, ch->plane_normal, ch->processed, ch->initial_vertices, ch->barycentre); + if (ret != 0) + return ret; + + ch->num_facets = 4; + num_prev = 0; + } + + for (int i = num_prev;iprocessed[i]) + continue; + ch->processed[i] = true; + + int num_to_add = 0; + int8_t to_add[PTM_MAX_FACETS][3]; + int8_t edge_visible[PTM_MAX_POINTS][PTM_MAX_POINTS]; + memset(edge_visible, 0, sizeof(int8_t) * PTM_MAX_POINTS * PTM_MAX_POINTS); + for (int j = 0;jnum_facets;j++) + { + int a = ch->facets[j][0]; + int b = ch->facets[j][1]; + int c = ch->facets[j][2]; + + int u = 0, v = 0, w = 0; + + double distance = point_plane_distance(points[i], points[a], ch->plane_normal[j]); + bool vis = distance > TOLERANCE; + if (vis) + { + u = edge_visible[a][b] |= VISIBLE; + edge_visible[b][a] |= VISIBLE; + + v = edge_visible[b][c] |= VISIBLE; + edge_visible[c][b] |= VISIBLE; + + w = edge_visible[c][a] |= VISIBLE; + edge_visible[a][c] |= VISIBLE; + + memcpy(ch->facets[j], ch->facets[ch->num_facets-1], 3 * sizeof(int8_t)); + memcpy(ch->plane_normal[j], ch->plane_normal[ch->num_facets-1], 3 * sizeof(double)); + ch->num_facets--; + j--; + } + else + { + u = edge_visible[a][b] |= INVISIBLE; + edge_visible[b][a] |= INVISIBLE; + + v = edge_visible[b][c] |= INVISIBLE; + edge_visible[c][b] |= INVISIBLE; + + w = edge_visible[c][a] |= INVISIBLE; + edge_visible[a][c] |= INVISIBLE; + } + + if (u == BOTH) + { + to_add[num_to_add][0] = i; + to_add[num_to_add][1] = a; + to_add[num_to_add][2] = b; + num_to_add++; + } + + if (v == BOTH) + { + to_add[num_to_add][0] = i; + to_add[num_to_add][1] = b; + to_add[num_to_add][2] = c; + num_to_add++; + } + + if (w == BOTH) + { + to_add[num_to_add][0] = i; + to_add[num_to_add][1] = c; + to_add[num_to_add][2] = a; + num_to_add++; + } + } + + for (int j = 0;jnum_facets >= PTM_MAX_FACETS) + return -4; + + add_facet(points, to_add[j][0], to_add[j][1], to_add[j][2], ch->facets[ch->num_facets], ch->plane_normal[ch->num_facets], ch->barycentre); ch->num_facets++; + } + } + + for (int i=0;inum_facets;i++) + { + int a = ch->facets[i][0]; + int b = ch->facets[i][1]; + int c = ch->facets[i][2]; + if (a == 0 || b == 0 || c == 0) + return 1; //central atom contained in convex hull + + simplex[i][0] = a - 1; + simplex[i][1] = b - 1; + simplex[i][2] = c - 1; + } + + return ret; +} + diff --git a/src/USER-PTM/convex_hull_incremental.h b/src/USER-PTM/convex_hull_incremental.h new file mode 100644 index 0000000000..d384a0457e --- /dev/null +++ b/src/USER-PTM/convex_hull_incremental.h @@ -0,0 +1,27 @@ +#ifndef CONVEX_HULL_INCREMENTAL_H +#define CONVEX_HULL_INCREMENTAL_H + + +#include +#include +#include "ptm_constants.h" + + +typedef struct +{ + int8_t facets[PTM_MAX_FACETS][3]; + double plane_normal[PTM_MAX_FACETS][3]; + bool processed[PTM_MAX_POINTS]; + int initial_vertices[4]; + double barycentre[3]; + int num_facets; + int num_prev; + bool ok; + +} convexhull_t; + +void add_facet(const double (*points)[3], int a, int b, int c, int8_t* facet, double* plane_normal, double* barycentre); +int get_convex_hull(int num_points, const double (*points)[3], convexhull_t* ch, int8_t simplex[][3]); + +#endif + diff --git a/src/USER-PTM/deformation_gradient.cpp b/src/USER-PTM/deformation_gradient.cpp new file mode 100644 index 0000000000..9a86dff6a3 --- /dev/null +++ b/src/USER-PTM/deformation_gradient.cpp @@ -0,0 +1,37 @@ +#include "deformation_gradient.h" + + +void calculate_deformation_gradient(int num_points, const double (*ideal_points)[3], int8_t* mapping, double (*normalized)[3], const double (*penrose)[3], double* F, double* res) +{ + for (int i = 0;i<3;i++) + { + for (int j = 0;j<3;j++) + { + double acc = 0.0; + for (int k = 0;k +#include "ptm_constants.h" + +void calculate_deformation_gradient(int num_points, const double (*ideal_points)[3], int8_t* mapping, double (*normalized)[3], const double (*penrose)[3], double* F, double* res); + +//sc +#define k_sc 0.5 +const double penrose_sc[PTM_NUM_POINTS_SC][3] = { + {0, 0, 0}, + {0, 0, -k_sc}, + {0, 0, k_sc}, + {0, -k_sc, 0}, + {0, k_sc, 0}, + {-k_sc, 0, 0}, + {k_sc, 0, 0}, + }; + +//fcc +#define k_fcc 0.17677669529663678216 +const double penrose_fcc[PTM_NUM_POINTS_FCC][3] = { + {0, 0, 0}, + {0, k_fcc, k_fcc}, + {0, -k_fcc, -k_fcc}, + {0, k_fcc, -k_fcc}, + {0, -k_fcc, k_fcc}, + {k_fcc, 0, k_fcc}, + {-k_fcc, 0, -k_fcc}, + {k_fcc, 0, -k_fcc}, + {-k_fcc, 0, k_fcc}, + {k_fcc, k_fcc, -0}, + {-k_fcc, -k_fcc, 0}, + {k_fcc, -k_fcc, 0}, + {-k_fcc, k_fcc, -0}, + }; + +//hcp +#define k_hcp 0.17677669529663678216 +const double penrose_hcp[PTM_NUM_POINTS_HCP][3] = { + {0, 0, 0}, + {k_hcp, 0, k_hcp}, + {-k_hcp/3, -4*k_hcp/3, -k_hcp/3}, + {k_hcp, k_hcp, 0}, + {-k_hcp/3, -k_hcp/3, -4*k_hcp/3}, + {0, k_hcp, k_hcp}, + {-4*k_hcp/3, -k_hcp/3, -k_hcp/3}, + {-k_hcp, k_hcp, -0}, + {0, k_hcp, -k_hcp}, + {k_hcp, 0, -k_hcp}, + {k_hcp, -k_hcp, 0}, + {-k_hcp, 0, k_hcp}, + {0, -k_hcp, k_hcp}, + }; + +//ico +#define k_ico 0.13143277802974323576 +#define phi 1.61803398874989490253 +//((1.0 + sqrt(5)) / 2) +const double penrose_ico[PTM_NUM_POINTS_ICO][3] = { + {0, 0, 0}, + {0, k_ico, phi*k_ico}, + {0, -k_ico, -phi*k_ico}, + {0, k_ico, -phi*k_ico}, + {0, -k_ico, phi*k_ico}, + {-k_ico, -phi*k_ico, -0}, + {k_ico, phi*k_ico, 0}, + {k_ico, -phi*k_ico, 0}, + {-k_ico, phi*k_ico, -0}, + {-phi*k_ico, 0, -k_ico}, + {phi*k_ico, 0, k_ico}, + {phi*k_ico, 0, -k_ico}, + {-phi*k_ico, 0, k_ico}, + }; + +//bcc +#define k_bcc 0.11543038598460284017 +const double penrose_bcc[PTM_NUM_POINTS_BCC][3] = { + {0, 0, 0}, + {-k_bcc, -k_bcc, -k_bcc}, + {k_bcc, k_bcc, k_bcc}, + {k_bcc, -k_bcc, -k_bcc}, + {-k_bcc, k_bcc, k_bcc}, + {-k_bcc, k_bcc, -k_bcc}, + {k_bcc, -k_bcc, k_bcc}, + {-k_bcc, -k_bcc, k_bcc}, + {k_bcc, k_bcc, -k_bcc}, + {0, 0, -2*k_bcc}, + {0, 0, 2*k_bcc}, + {0, -2*k_bcc, 0}, + {0, 2*k_bcc, 0}, + {-2*k_bcc, 0, 0}, + {2*k_bcc, 0, -0}, + }; + +//dcub +#define kdcub 0.07095369570691034689 +const double penrose_dcub[PTM_NUM_POINTS_DCUB][3] = { + { 0, 0, 0 }, + { -kdcub, kdcub, kdcub }, + { -kdcub, -kdcub, -kdcub }, + { kdcub, -kdcub, kdcub }, + { kdcub, kdcub, -kdcub }, + { -2 * kdcub, 0, 2 * kdcub }, + { -2 * kdcub, 2 * kdcub, 0 }, + { 0, 2 * kdcub, 2 * kdcub }, + { -2 * kdcub, -2 * kdcub, 0 }, + { -2 * kdcub, 0, -2 * kdcub }, + { 0, -2 * kdcub, -2 * kdcub }, + { 0, -2 * kdcub, 2 * kdcub }, + { 2 * kdcub, -2 * kdcub, 0 }, + { 2 * kdcub, 0, 2 * kdcub }, + { 0, 2 * kdcub, -2 * kdcub }, + { 2 * kdcub, 0, -2 * kdcub }, + { 2 * kdcub, 2 * kdcub, 0 }, + }; + + +#define kdhex 0.04730246380471011397 +const double penrose_dhex[PTM_NUM_POINTS_DHEX][3] = { + { 0, 0, 0 }, + { -kdcub, -kdcub, -kdcub }, + { kdcub, -kdcub, kdcub }, + { -kdcub, kdcub, kdcub }, + { kdcub, kdcub, -kdcub }, + { -kdhex, -4 * kdhex, -kdhex }, + { -4 * kdhex, -kdhex, -kdhex }, + { -kdhex, -kdhex, -4 * kdhex }, + { 2 * kdcub, 0, 2 * kdcub }, + { 2 * kdcub, -2 * kdcub, 0 }, + { 0, -2 * kdcub, 2 * kdcub }, + { 0, 2 * kdcub, 2 * kdcub }, + { -2 * kdcub, 2 * kdcub, 0 }, + { -2 * kdcub, 0, 2 * kdcub }, + { 2 * kdcub, 2 * kdcub, 0 }, + { 0, 2 * kdcub, -2 * kdcub }, + { 2 * kdcub, 0, -2 * kdcub }, + }; +#endif + + diff --git a/src/USER-PTM/fundamental_mappings.h b/src/USER-PTM/fundamental_mappings.h new file mode 100644 index 0000000000..9030d3a2b2 --- /dev/null +++ b/src/USER-PTM/fundamental_mappings.h @@ -0,0 +1,180 @@ +#ifndef FUNDAMENTAL_MAPPINGS_H +#define FUNDAMENTAL_MAPPINGS_H + +#include + +#define NUM_CUBIC_MAPPINGS 24 +#define NUM_ICO_MAPPINGS 60 +#define NUM_HEX_MAPPINGS 6 +#define NUM_DCUB_MAPPINGS 12 +#define NUM_DHEX_MAPPINGS 3 + +const int8_t mapping_sc[NUM_CUBIC_MAPPINGS][PTM_MAX_POINTS] = { + {0, 1, 2, 3, 4, 5, 6}, + {0, 2, 1, 4, 3, 5, 6}, + {0, 2, 1, 3, 4, 6, 5}, + {0, 1, 2, 4, 3, 6, 5}, + {0, 3, 4, 5, 6, 1, 2}, + {0, 5, 6, 2, 1, 4, 3}, + {0, 6, 5, 1, 2, 4, 3}, + {0, 4, 3, 5, 6, 2, 1}, + {0, 5, 6, 1, 2, 3, 4}, + {0, 4, 3, 6, 5, 1, 2}, + {0, 3, 4, 6, 5, 2, 1}, + {0, 6, 5, 2, 1, 3, 4}, + {0, 3, 4, 2, 1, 5, 6}, + {0, 6, 5, 3, 4, 1, 2}, + {0, 1, 2, 5, 6, 4, 3}, + {0, 4, 3, 1, 2, 5, 6}, + {0, 5, 6, 3, 4, 2, 1}, + {0, 1, 2, 6, 5, 3, 4}, + {0, 2, 1, 5, 6, 3, 4}, + {0, 5, 6, 4, 3, 1, 2}, + {0, 3, 4, 1, 2, 6, 5}, + {0, 2, 1, 6, 5, 4, 3}, + {0, 6, 5, 4, 3, 2, 1}, + {0, 4, 3, 2, 1, 6, 5} }; + +const int8_t mapping_fcc[NUM_CUBIC_MAPPINGS][PTM_MAX_POINTS] = { + {0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12}, + {0, 2, 1, 4, 3, 7, 8, 5, 6, 11, 12, 9, 10}, + {0, 3, 4, 1, 2, 6, 5, 8, 7, 12, 11, 10, 9}, + {0, 4, 3, 2, 1, 8, 7, 6, 5, 10, 9, 12, 11}, + {0, 9, 10, 11, 12, 1, 2, 4, 3, 5, 6, 8, 7}, + {0, 7, 8, 6, 5, 11, 12, 10, 9, 2, 1, 4, 3}, + {0, 8, 7, 5, 6, 10, 9, 11, 12, 4, 3, 2, 1}, + {0, 11, 12, 9, 10, 2, 1, 3, 4, 7, 8, 6, 5}, + {0, 5, 6, 8, 7, 9, 10, 12, 11, 1, 2, 3, 4}, + {0, 10, 9, 12, 11, 4, 3, 1, 2, 8, 7, 5, 6}, + {0, 12, 11, 10, 9, 3, 4, 2, 1, 6, 5, 7, 8}, + {0, 6, 5, 7, 8, 12, 11, 9, 10, 3, 4, 1, 2}, + {0, 3, 4, 2, 1, 9, 10, 11, 12, 7, 8, 5, 6}, + {0, 12, 11, 9, 10, 8, 7, 5, 6, 1, 2, 4, 3}, + {0, 5, 6, 7, 8, 4, 3, 2, 1, 11, 12, 10, 9}, + {0, 4, 3, 1, 2, 11, 12, 9, 10, 5, 6, 7, 8}, + {0, 9, 10, 12, 11, 7, 8, 6, 5, 3, 4, 2, 1}, + {0, 8, 7, 6, 5, 1, 2, 3, 4, 12, 11, 9, 10}, + {0, 7, 8, 5, 6, 3, 4, 1, 2, 9, 10, 12, 11}, + {0, 11, 12, 10, 9, 5, 6, 8, 7, 4, 3, 1, 2}, + {0, 1, 2, 4, 3, 12, 11, 10, 9, 8, 7, 6, 5}, + {0, 6, 5, 8, 7, 2, 1, 4, 3, 10, 9, 11, 12}, + {0, 10, 9, 11, 12, 6, 5, 7, 8, 2, 1, 3, 4}, + {0, 2, 1, 3, 4, 10, 9, 12, 11, 6, 5, 8, 7} }; + +const int8_t mapping_bcc[NUM_CUBIC_MAPPINGS][PTM_MAX_POINTS] = { + {0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14}, + {0, 4, 3, 2, 1, 7, 8, 5, 6, 10, 9, 12, 11, 13, 14}, + {0, 6, 5, 7, 8, 2, 1, 3, 4, 10, 9, 11, 12, 14, 13}, + {0, 8, 7, 5, 6, 3, 4, 2, 1, 9, 10, 12, 11, 14, 13}, + {0, 1, 2, 7, 8, 3, 4, 5, 6, 11, 12, 13, 14, 9, 10}, + {0, 4, 3, 7, 8, 5, 6, 2, 1, 13, 14, 10, 9, 12, 11}, + {0, 8, 7, 3, 4, 2, 1, 5, 6, 14, 13, 9, 10, 12, 11}, + {0, 4, 3, 5, 6, 2, 1, 7, 8, 12, 11, 13, 14, 10, 9}, + {0, 1, 2, 5, 6, 7, 8, 3, 4, 13, 14, 9, 10, 11, 12}, + {0, 8, 7, 2, 1, 5, 6, 3, 4, 12, 11, 14, 13, 9, 10}, + {0, 6, 5, 3, 4, 7, 8, 2, 1, 11, 12, 14, 13, 10, 9}, + {0, 6, 5, 2, 1, 3, 4, 7, 8, 14, 13, 10, 9, 11, 12}, + {0, 7, 8, 6, 5, 1, 2, 4, 3, 11, 12, 10, 9, 13, 14}, + {0, 3, 4, 6, 5, 8, 7, 1, 2, 14, 13, 11, 12, 9, 10}, + {0, 5, 6, 1, 2, 8, 7, 4, 3, 9, 10, 13, 14, 12, 11}, + {0, 5, 6, 8, 7, 4, 3, 1, 2, 12, 11, 9, 10, 13, 14}, + {0, 7, 8, 1, 2, 4, 3, 6, 5, 13, 14, 11, 12, 10, 9}, + {0, 3, 4, 8, 7, 1, 2, 6, 5, 9, 10, 14, 13, 11, 12}, + {0, 7, 8, 4, 3, 6, 5, 1, 2, 10, 9, 13, 14, 11, 12}, + {0, 5, 6, 4, 3, 1, 2, 8, 7, 13, 14, 12, 11, 9, 10}, + {0, 3, 4, 1, 2, 6, 5, 8, 7, 11, 12, 9, 10, 14, 13}, + {0, 2, 1, 6, 5, 4, 3, 8, 7, 10, 9, 14, 13, 12, 11}, + {0, 2, 1, 8, 7, 6, 5, 4, 3, 14, 13, 12, 11, 10, 9}, + {0, 2, 1, 4, 3, 8, 7, 6, 5, 12, 11, 10, 9, 14, 13} }; + +const int8_t mapping_ico[NUM_ICO_MAPPINGS][PTM_MAX_POINTS] = { + {0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12}, + {0, 10, 9, 8, 7, 5, 6, 2, 1, 12, 11, 3, 4}, + {0, 1, 2, 9, 10, 7, 8, 11, 12, 5, 6, 3, 4}, + {0, 4, 3, 8, 7, 2, 1, 11, 12, 9, 10, 6, 5}, + {0, 6, 5, 9, 10, 4, 3, 7, 8, 12, 11, 2, 1}, + {0, 12, 11, 3, 4, 7, 8, 10, 9, 2, 1, 6, 5}, + {0, 4, 3, 6, 5, 9, 10, 2, 1, 8, 7, 11, 12}, + {0, 8, 7, 2, 1, 4, 3, 10, 9, 5, 6, 11, 12}, + {0, 10, 9, 3, 4, 12, 11, 5, 6, 8, 7, 2, 1}, + {0, 12, 11, 6, 5, 2, 1, 7, 8, 3, 4, 10, 9}, + {0, 1, 2, 11, 12, 9, 10, 5, 6, 3, 4, 7, 8}, + {0, 8, 7, 11, 12, 5, 6, 4, 3, 2, 1, 10, 9}, + {0, 6, 5, 2, 1, 12, 11, 4, 3, 9, 10, 7, 8}, + {0, 3, 4, 5, 6, 1, 2, 10, 9, 12, 11, 7, 8}, + {0, 3, 4, 7, 8, 12, 11, 1, 2, 5, 6, 10, 9}, + {0, 6, 5, 7, 8, 9, 10, 12, 11, 2, 1, 4, 3}, + {0, 9, 10, 11, 12, 4, 3, 1, 2, 7, 8, 6, 5}, + {0, 11, 12, 9, 10, 1, 2, 4, 3, 8, 7, 5, 6}, + {0, 8, 7, 5, 6, 10, 9, 11, 12, 4, 3, 2, 1}, + {0, 10, 9, 2, 1, 8, 7, 12, 11, 3, 4, 5, 6}, + {0, 12, 11, 2, 1, 10, 9, 6, 5, 7, 8, 3, 4}, + {0, 9, 10, 6, 5, 7, 8, 4, 3, 11, 12, 1, 2}, + {0, 8, 7, 10, 9, 2, 1, 5, 6, 11, 12, 4, 3}, + {0, 6, 5, 12, 11, 7, 8, 2, 1, 4, 3, 9, 10}, + {0, 11, 12, 8, 7, 4, 3, 5, 6, 1, 2, 9, 10}, + {0, 4, 3, 11, 12, 8, 7, 9, 10, 6, 5, 2, 1}, + {0, 4, 3, 9, 10, 11, 12, 6, 5, 2, 1, 8, 7}, + {0, 12, 11, 10, 9, 3, 4, 2, 1, 6, 5, 7, 8}, + {0, 5, 6, 8, 7, 11, 12, 10, 9, 3, 4, 1, 2}, + {0, 7, 8, 6, 5, 12, 11, 9, 10, 1, 2, 3, 4}, + {0, 10, 9, 12, 11, 2, 1, 3, 4, 5, 6, 8, 7}, + {0, 7, 8, 1, 2, 9, 10, 3, 4, 12, 11, 6, 5}, + {0, 5, 6, 1, 2, 3, 4, 11, 12, 8, 7, 10, 9}, + {0, 7, 8, 12, 11, 3, 4, 6, 5, 9, 10, 1, 2}, + {0, 1, 2, 5, 6, 11, 12, 3, 4, 7, 8, 9, 10}, + {0, 11, 12, 1, 2, 5, 6, 9, 10, 4, 3, 8, 7}, + {0, 5, 6, 3, 4, 10, 9, 1, 2, 11, 12, 8, 7}, + {0, 5, 6, 10, 9, 8, 7, 3, 4, 1, 2, 11, 12}, + {0, 3, 4, 12, 11, 10, 9, 7, 8, 1, 2, 5, 6}, + {0, 9, 10, 7, 8, 1, 2, 6, 5, 4, 3, 11, 12}, + {0, 9, 10, 1, 2, 11, 12, 7, 8, 6, 5, 4, 3}, + {0, 7, 8, 3, 4, 1, 2, 12, 11, 6, 5, 9, 10}, + {0, 11, 12, 5, 6, 8, 7, 1, 2, 9, 10, 4, 3}, + {0, 1, 2, 7, 8, 3, 4, 9, 10, 11, 12, 5, 6}, + {0, 3, 4, 10, 9, 5, 6, 12, 11, 7, 8, 1, 2}, + {0, 2, 1, 4, 3, 8, 7, 6, 5, 12, 11, 10, 9}, + {0, 2, 1, 12, 11, 6, 5, 10, 9, 8, 7, 4, 3}, + {0, 9, 10, 4, 3, 6, 5, 11, 12, 1, 2, 7, 8}, + {0, 11, 12, 4, 3, 9, 10, 8, 7, 5, 6, 1, 2}, + {0, 2, 1, 10, 9, 12, 11, 8, 7, 4, 3, 6, 5}, + {0, 5, 6, 11, 12, 1, 2, 8, 7, 10, 9, 3, 4}, + {0, 10, 9, 5, 6, 3, 4, 8, 7, 2, 1, 12, 11}, + {0, 12, 11, 7, 8, 6, 5, 3, 4, 10, 9, 2, 1}, + {0, 7, 8, 9, 10, 6, 5, 1, 2, 3, 4, 12, 11}, + {0, 2, 1, 8, 7, 10, 9, 4, 3, 6, 5, 12, 11}, + {0, 8, 7, 4, 3, 11, 12, 2, 1, 10, 9, 5, 6}, + {0, 6, 5, 4, 3, 2, 1, 9, 10, 7, 8, 12, 11}, + {0, 2, 1, 6, 5, 4, 3, 12, 11, 10, 9, 8, 7}, + {0, 3, 4, 1, 2, 7, 8, 5, 6, 10, 9, 12, 11}, + {0, 4, 3, 2, 1, 6, 5, 8, 7, 11, 12, 9, 10} }; + +const int8_t mapping_hcp[NUM_HEX_MAPPINGS][PTM_MAX_POINTS] = { + {0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12}, + {0, 5, 6, 1, 2, 3, 4, 9, 10, 12, 11, 8, 7}, + {0, 3, 4, 5, 6, 1, 2, 12, 11, 7, 8, 10, 9}, + {0, 4, 3, 2, 1, 6, 5, 11, 12, 10, 9, 7, 8}, + {0, 2, 1, 6, 5, 4, 3, 8, 7, 11, 12, 9, 10}, + {0, 6, 5, 4, 3, 2, 1, 10, 9, 8, 7, 12, 11} }; + +const int8_t mapping_dcub[NUM_DCUB_MAPPINGS][PTM_MAX_POINTS] = { + {0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16}, + {0, 2, 1, 4, 3, 9, 8, 10, 6, 5, 7, 14, 16, 15, 11, 13, 12}, + {0, 4, 3, 2, 1, 15, 16, 14, 12, 13, 11, 10, 8, 9, 7, 5, 6}, + {0, 3, 4, 1, 2, 13, 12, 11, 16, 15, 14, 7, 6, 5, 10, 9, 8}, + {0, 4, 2, 1, 3, 14, 15, 16, 9, 10, 8, 6, 5, 7, 12, 11, 13}, + {0, 4, 1, 3, 2, 16, 14, 15, 7, 6, 5, 13, 11, 12, 9, 8, 10}, + {0, 1, 4, 2, 3, 6, 7, 5, 14, 16, 15, 9, 10, 8, 13, 12, 11}, + {0, 3, 1, 2, 4, 11, 13, 12, 5, 7, 6, 8, 9, 10, 16, 14, 15}, + {0, 3, 2, 4, 1, 12, 11, 13, 10, 8, 9, 15, 14, 16, 5, 6, 7}, + {0, 2, 4, 3, 1, 10, 9, 8, 15, 14, 16, 12, 13, 11, 6, 7, 5}, + {0, 1, 3, 4, 2, 7, 5, 6, 13, 11, 12, 16, 15, 14, 8, 10, 9}, + {0, 2, 3, 1, 4, 8, 10, 9, 11, 12, 13, 5, 7, 6, 15, 16, 14} }; + +const int8_t mapping_dhex[NUM_DHEX_MAPPINGS][PTM_MAX_POINTS] = { + {0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16}, + {0, 1, 3, 4, 2, 6, 7, 5, 11, 13, 12, 14, 16, 15, 8, 9, 10}, + {0, 1, 4, 2, 3, 7, 5, 6, 14, 15, 16, 8, 10, 9, 11, 13, 12} }; + +#endif + diff --git a/src/USER-PTM/graph_data.cpp b/src/USER-PTM/graph_data.cpp new file mode 100644 index 0000000000..aea2e59eac --- /dev/null +++ b/src/USER-PTM/graph_data.cpp @@ -0,0 +1,2059 @@ +#include "graph_data.h" + + +int8_t automorphisms[65][17] = { + { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16}, + { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, -1, -1, -1, -1}, + { 0, 4, 3, 10, 9, 5, 6, 12, 11, 8, 7, 1, 2, -1, -1, -1, -1}, + { 0, 5, 6, 11, 12, 8, 7, 2, 1, 4, 3, 10, 9, -1, -1, -1, -1}, + { 0, 8, 7, 1, 2, 4, 3, 9, 10, 5, 6, 11, 12, -1, -1, -1, -1}, + { 0, 8, 7, 10, 9, 1, 2, 6, 5, 12, 11, 3, 4, -1, -1, -1, -1}, + { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, -1, -1, -1, -1}, + { 0, 12, 3, 2, 7, 10, 8, 4, 6, 11, 5, 9, 1, -1, -1, -1, -1}, + { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, -1, -1, -1, -1}, + { 0, 4, 11, 8, 1, 9, 12, 10, 3, 5, 7, 2, 6, -1, -1, -1, -1}, + { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, -1, -1, -1, -1}, + { 0, 2, 1, 6, 5, 4, 3, 9, 8, 7, 11, 10, 12, -1, -1, -1, -1}, + { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, -1, -1, -1, -1}, + { 0, 1, 7, 10, 11, 9, 6, 4, 2, 12, 5, 8, 3, -1, -1, -1, -1}, + { 0, 1, 11, 9, 2, 3, 6, 8, 4, 10, 12, 7, 5, -1, -1, -1, -1}, + { 0, 3, 6, 1, 11, 9, 2, 10, 12, 5, 7, 4, 8, -1, -1, -1, -1}, + { 0, 3, 11, 9, 12, 8, 2, 4, 10, 1, 5, 6, 7, -1, -1, -1, -1}, + { 0, 8, 2, 3, 11, 9, 12, 1, 5, 7, 6, 10, 4, -1, -1, -1, -1}, + { 0, 9, 2, 3, 6, 1, 11, 5, 7, 8, 4, 12, 10, -1, -1, -1, -1}, + { 0, 9, 6, 1, 7, 10, 11, 12, 5, 3, 8, 2, 4, -1, -1, -1, -1}, + { 0, 9, 12, 8, 2, 3, 11, 7, 6, 4, 10, 5, 1, -1, -1, -1, -1}, + { 0, 10, 11, 9, 6, 1, 7, 3, 8, 4, 2, 5, 12, -1, -1, -1, -1}, + { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, -1, -1, -1, -1}, + { 0, 3, 2, 8, 6, 5, 12, 11, 7, 4, 9, 1, 10, -1, -1, -1, -1}, + { 0, 3, 11, 10, 6, 9, 7, 4, 2, 12, 1, 8, 5, -1, -1, -1, -1}, + { 0, 3, 12, 9, 6, 8, 11, 7, 4, 2, 10, 5, 1, -1, -1, -1, -1}, + { 0, 5, 12, 3, 2, 8, 6, 4, 9, 10, 1, 7, 11, -1, -1, -1, -1}, + { 0, 8, 6, 5, 12, 3, 2, 10, 1, 11, 7, 9, 4, -1, -1, -1, -1}, + { 0, 8, 11, 3, 12, 9, 6, 2, 10, 1, 5, 4, 7, -1, -1, -1, -1}, + { 0, 9, 6, 8, 11, 3, 12, 1, 5, 7, 4, 10, 2, -1, -1, -1, -1}, + { 0, 9, 7, 3, 11, 10, 6, 12, 1, 5, 8, 2, 4, -1, -1, -1, -1}, + { 0, 10, 6, 9, 7, 3, 11, 5, 8, 4, 2, 1, 12, -1, -1, -1, -1}, + { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, -1, -1}, + { 0, 3, 4, 6, 5, 2, 1, 9, 10, 14, 13, 11, 12, 8, 7, -1, -1}, + { 0, 4, 3, 1, 2, 5, 6, 10, 9, 13, 14, 7, 8, 12, 11, -1, -1}, + { 0, 6, 5, 1, 2, 4, 3, 14, 13, 7, 8, 11, 12, 10, 9, -1, -1}, + { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, -1, -1}, + { 0, 12, 11, 10, 9, 13, 14, 8, 7, 4, 3, 2, 1, 5, 6, -1, -1}, + { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, -1, -1}, + { 0, 9, 10, 13, 14, 11, 12, 8, 7, 1, 2, 5, 6, 3, 4, -1, -1}, + { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, -1, -1}, + { 0, 6, 5, 4, 3, 2, 1, 11, 12, 10, 9, 7, 8, 14, 13, -1, -1}, + { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, -1, -1}, + { 0, 12, 11, 10, 9, 13, 14, 8, 7, 4, 3, 2, 1, 5, 6, -1, -1}, + { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, -1, -1}, + { 0, 9, 10, 13, 14, 11, 12, 8, 7, 1, 2, 5, 6, 3, 4, -1, -1}, + { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, -1, -1}, + { 0, 3, 10, 14, 5, 9, 7, 13, 2, 8, 4, 11, 12, 1, 6, -1, -1}, + { 0, 13, 8, 1, 10, 4, 14, 6, 9, 5, 2, 11, 12, 7, 3, -1, -1}, + { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, -1, -1}, + { 0, 11, 12, 14, 13, 9, 10, 7, 8, 3, 4, 6, 5, 1, 2, -1, -1}, + { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, -1, -1}, + { 0, 13, 14, 11, 12, 5, 6, 10, 9, 1, 2, 7, 8, 4, 3, -1, -1}, + { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16}, + { 0, 4, 3, 2, 1, 15, 14, 16, 13, 12, 11, 10, 9, 8, 6, 5, 7}, + { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16}, + { 0, 4, 1, 3, 2, 15, 14, 16, 5, 7, 6, 13, 11, 12, 10, 8, 9}, + { 0, 4, 2, 1, 3, 16, 15, 14, 10, 8, 9, 5, 6, 7, 13, 12, 11}, + { 0, 4, 3, 2, 1, 14, 16, 15, 13, 12, 11, 10, 9, 8, 5, 7, 6}, + { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16}, + { 0, 3, 4, 1, 2, 12, 13, 11, 16, 14, 15, 7, 5, 6, 9, 10, 8}, + { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16}, + { 0, 4, 1, 3, 2, 16, 15, 14, 6, 5, 7, 13, 11, 12, 10, 8, 9}, + { 0, 4, 2, 1, 3, 14, 16, 15, 10, 8, 9, 6, 7, 5, 13, 12, 11}, + { 0, 4, 3, 2, 1, 15, 14, 16, 13, 12, 11, 10, 9, 8, 6, 5, 7}, +}; + +graph_t graphs_sc[NUM_SC_GRAPHS] = { + +{0, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{1,3,4},{1,3,5},{0,3,4},{0,3,5},{1,2,5},{1,2,4},{0,2,4},{0,2,5}}}, + +}; + +graph_t graphs_ico[NUM_ICO_GRAPHS] = { + +{0, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{0,5,9},{1,2,8},{0,5,7},{2,7,8},{2,5,7},{1,4,8},{1,2,10},{5,9,10},{2,5,10},{4,8,11},{7,8,11},{0,7,11},{0,3,9},{0,3,11},{3,4,11},{3,6,9},{3,4,6},{6,9,10},{1,4,6},{1,6,10}}}, + +}; + +graph_t graphs_fcc[NUM_FCC_GRAPHS] = { + +{0, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{0,4,8},{3,7,9},{2,5,11},{0,7,11},{1,5,9},{2,6,8},{3,4,10},{1,6,10},{3,4,7},{0,4,7},{0,2,11},{0,2,8},{5,7,11},{5,7,9},{1,2,6},{1,2,5},{1,3,10},{1,3,9},{4,6,10},{4,6,8}}}, + +{1, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{0,4,8},{3,7,9},{2,5,11},{0,7,11},{1,5,9},{2,6,8},{3,4,10},{1,6,10},{3,4,7},{0,4,7},{0,2,11},{0,2,8},{5,7,11},{5,7,9},{1,2,6},{1,2,5},{1,3,10},{1,3,9},{6,8,10},{4,8,10}}}, + +{2, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{0,4,8},{3,7,9},{2,5,11},{0,7,11},{1,5,9},{2,6,8},{3,4,10},{1,6,10},{3,4,7},{0,4,7},{0,2,11},{0,2,8},{5,7,11},{5,7,9},{1,2,6},{1,2,5},{3,9,10},{1,9,10},{6,8,10},{4,8,10}}}, + +{3, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{0,4,8},{3,7,9},{2,5,11},{0,7,11},{1,5,9},{2,6,8},{3,4,10},{1,6,10},{3,4,7},{0,4,7},{0,2,11},{0,2,8},{5,7,11},{5,7,9},{2,5,6},{1,5,6},{1,3,10},{1,3,9},{4,6,10},{4,6,8}}}, + +{4, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{0,4,8},{3,7,9},{2,5,11},{0,7,11},{1,5,9},{2,6,8},{3,4,10},{1,6,10},{3,4,7},{0,4,7},{0,2,11},{0,2,8},{5,7,11},{5,7,9},{2,5,6},{1,5,6},{1,3,10},{1,3,9},{6,8,10},{4,8,10}}}, + +{5, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{0,4,8},{3,7,9},{2,5,11},{0,7,11},{1,5,9},{2,6,8},{3,4,10},{1,6,10},{3,4,7},{0,4,7},{0,2,11},{0,2,8},{5,7,11},{5,7,9},{2,5,6},{1,5,6},{3,9,10},{1,9,10},{4,6,10},{4,6,8}}}, + +{6, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{0,4,8},{3,7,9},{2,5,11},{0,7,11},{1,5,9},{2,6,8},{3,4,10},{1,6,10},{3,4,7},{0,4,7},{0,2,11},{0,2,8},{7,9,11},{5,9,11},{1,2,6},{1,2,5},{3,9,10},{1,9,10},{4,6,10},{4,6,8}}}, + +{7, +0, +1, +5, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{0,4,8},{3,7,9},{2,5,11},{0,7,11},{1,5,9},{2,6,8},{3,4,10},{1,6,10},{3,4,7},{0,4,7},{0,2,11},{0,2,8},{7,9,11},{5,9,11},{2,5,6},{1,5,6},{1,3,10},{1,3,9},{6,8,10},{4,8,10}}}, + +}; + +graph_t graphs_hcp[NUM_HCP_GRAPHS] = { + +{0, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{3,8,9},{1,3,9},{2,8,9},{0,2,9},{0,10,11},{0,4,10},{2,6,7},{2,4,6}}}, + +{1, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{3,8,9},{1,3,9},{2,8,9},{0,2,9},{0,10,11},{0,4,10},{4,6,7},{2,4,7}}}, + +{2, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{3,8,9},{1,3,9},{2,8,9},{0,2,9},{4,10,11},{0,4,11},{2,6,7},{2,4,6}}}, + +{3, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{3,8,9},{1,3,9},{2,8,9},{0,2,9},{4,10,11},{0,4,11},{4,6,7},{2,4,7}}}, + +{4, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{3,8,9},{1,3,9},{0,8,9},{0,2,8},{0,10,11},{0,4,10},{2,6,7},{2,4,6}}}, + +{5, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{3,8,9},{1,3,9},{0,8,9},{0,2,8},{0,10,11},{0,4,10},{4,6,7},{2,4,7}}}, + +{6, +0, +6, +2, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{3,8,9},{1,3,9},{0,8,9},{0,2,8},{4,10,11},{0,4,11},{2,6,7},{2,4,6}}}, + +{7, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{3,8,9},{1,3,9},{0,8,9},{0,2,8},{4,10,11},{0,4,11},{4,6,7},{2,4,7}}}, + +{8, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{1,8,9},{1,3,8},{2,8,9},{0,2,9},{0,10,11},{0,4,10},{2,6,7},{2,4,6}}}, + +{9, +0, +8, +2, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{1,8,9},{1,3,8},{2,8,9},{0,2,9},{0,10,11},{0,4,10},{4,6,7},{2,4,7}}}, + +{10, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{1,8,9},{1,3,8},{2,8,9},{0,2,9},{4,10,11},{0,4,11},{4,6,7},{2,4,7}}}, + +{11, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{1,8,9},{1,3,8},{0,8,9},{0,2,8},{0,10,11},{0,4,10},{4,6,7},{2,4,7}}}, + +{12, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{1,8,9},{1,3,8},{0,8,9},{0,2,8},{4,10,11},{0,4,11},{2,6,7},{2,4,6}}}, + +{13, +0, +10, +2, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{5,6,7},{3,5,7},{3,8,9},{1,3,9},{2,8,9},{0,2,9},{0,10,11},{0,4,10},{4,6,7},{2,4,7}}}, + +{14, +0, +12, +10, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{5,6,7},{3,5,7},{3,8,9},{1,3,9},{0,8,9},{0,2,8},{4,10,11},{0,4,11},{2,6,7},{2,4,6}}}, + +{15, +0, +22, +10, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{5,10,11},{1,5,11},{3,6,7},{3,5,6},{1,8,9},{1,3,8},{2,8,9},{0,2,9},{0,10,11},{0,4,10},{4,6,7},{2,4,7}}}, + +}; + +graph_t graphs_bcc[NUM_BCC_GRAPHS] = { + +{0, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{6,9,10},{5,9,10},{4,8,12},{0,8,12},{6,10,12},{0,10,12},{7,8,13},{2,8,13},{5,10,13},{2,10,13},{2,8,10},{0,8,10}}}, + +{1, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{6,9,10},{5,9,10},{4,8,12},{0,8,12},{6,10,12},{0,10,12},{7,8,13},{2,8,13},{5,10,13},{2,10,13},{0,2,10},{0,2,8}}}, + +{2, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{6,9,10},{5,9,10},{4,8,12},{0,8,12},{6,10,12},{0,10,12},{7,8,13},{2,8,13},{2,5,13},{2,5,10},{0,2,10},{0,2,8}}}, + +{3, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{6,9,10},{5,9,10},{4,8,12},{0,8,12},{6,10,12},{0,10,12},{2,7,13},{2,7,8},{2,5,13},{2,5,10},{0,2,10},{0,2,8}}}, + +{4, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{6,9,10},{5,9,10},{4,8,12},{0,8,12},{0,6,12},{0,6,10},{7,8,13},{2,8,13},{2,5,13},{2,5,10},{2,8,10},{0,8,10}}}, + +{5, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{6,9,10},{5,9,10},{4,8,12},{0,8,12},{0,6,12},{0,6,10},{7,8,13},{2,8,13},{2,5,13},{2,5,10},{0,2,10},{0,2,8}}}, + +{6, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{6,9,10},{5,9,10},{4,8,12},{0,8,12},{0,6,12},{0,6,10},{2,7,13},{2,7,8},{5,10,13},{2,10,13},{2,8,10},{0,8,10}}}, + +{7, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{6,9,10},{5,9,10},{4,8,12},{0,8,12},{0,6,12},{0,6,10},{2,7,13},{2,7,8},{5,10,13},{2,10,13},{0,2,10},{0,2,8}}}, + +{8, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{6,9,10},{5,9,10},{4,8,12},{0,8,12},{0,6,12},{0,6,10},{2,7,13},{2,7,8},{2,5,13},{2,5,10},{2,8,10},{0,8,10}}}, + +{9, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{6,9,10},{5,9,10},{4,8,12},{0,8,12},{0,6,12},{0,6,10},{2,7,13},{2,7,8},{2,5,13},{2,5,10},{0,2,10},{0,2,8}}}, + +{10, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, 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+{{1,3,11},{1,3,9},{3,4,12},{3,4,11},{1,7,13},{1,7,11},{4,7,11},{4,7,8},{1,5,13},{1,5,9},{3,6,12},{3,6,9},{5,6,10},{5,6,9},{0,4,12},{0,4,8},{0,6,12},{0,6,10},{2,7,13},{2,7,8},{2,5,13},{2,5,10},{0,2,10},{0,2,8}}}, + +}; + +graph_t graphs_dcub[NUM_DCUB_GRAPHS] = { + +{0, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{4,7,10},{0,5,6},{0,4,5},{0,4,6},{2,11,12},{2,10,12},{2,10,11},{1,7,8},{1,8,9},{1,7,9},{6,12,15},{5,8,13},{3,13,15},{3,13,14},{9,11,14},{3,14,15},{5,7,8},{4,5,7},{6,10,12},{4,6,10},{7,10,11},{7,9,11},{5,13,15},{5,6,15},{9,13,14},{8,9,13},{11,14,15},{11,12,15}}}, + +{1, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{4,7,10},{0,5,6},{0,4,5},{0,4,6},{2,11,12},{2,10,12},{2,10,11},{1,7,8},{1,8,9},{1,7,9},{6,12,15},{5,8,13},{3,13,15},{3,13,14},{9,11,14},{3,14,15},{5,7,8},{4,5,7},{6,10,12},{4,6,10},{7,10,11},{7,9,11},{5,13,15},{5,6,15},{9,13,14},{8,9,13},{12,14,15},{11,12,14}}}, + +{2, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{4,7,10},{0,5,6},{0,4,5},{0,4,6},{2,11,12},{2,10,12},{2,10,11},{1,7,8},{1,8,9},{1,7,9},{6,12,15},{5,8,13},{3,13,15},{3,13,14},{9,11,14},{3,14,15},{5,7,8},{4,5,7},{6,10,12},{4,6,10},{7,10,11},{7,9,11},{5,13,15},{5,6,15},{8,13,14},{8,9,14},{11,14,15},{11,12,15}}}, + +{3, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{4,7,10},{0,5,6},{0,4,5},{0,4,6},{2,11,12},{2,10,12},{2,10,11},{1,7,8},{1,8,9},{1,7,9},{6,12,15},{5,8,13},{3,13,15},{3,13,14},{9,11,14},{3,14,15},{5,7,8},{4,5,7},{6,10,12},{4,6,10},{7,10,11},{7,9,11},{5,13,15},{5,6,15},{8,13,14},{8,9,14},{12,14,15},{11,12,14}}}, + +{4, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{4,7,10},{0,5,6},{0,4,5},{0,4,6},{2,11,12},{2,10,12},{2,10,11},{1,7,8},{1,8,9},{1,7,9},{6,12,15},{5,8,13},{3,13,15},{3,13,14},{9,11,14},{3,14,15},{5,7,8},{4,5,7},{6,10,12},{4,6,10},{7,10,11},{7,9,11},{6,13,15},{5,6,13},{9,13,14},{8,9,13},{11,14,15},{11,12,15}}}, + +{5, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{4,7,10},{0,5,6},{0,4,5},{0,4,6},{2,11,12},{2,10,12},{2,10,11},{1,7,8},{1,8,9},{1,7,9},{6,12,15},{5,8,13},{3,13,15},{3,13,14},{9,11,14},{3,14,15},{5,7,8},{4,5,7},{6,10,12},{4,6,10},{7,10,11},{7,9,11},{6,13,15},{5,6,13},{8,13,14},{8,9,14},{11,14,15},{11,12,15}}}, + +{6, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{4,7,10},{0,5,6},{0,4,5},{0,4,6},{2,11,12},{2,10,12},{2,10,11},{1,7,8},{1,8,9},{1,7,9},{6,12,15},{5,8,13},{3,13,15},{3,13,14},{9,11,14},{3,14,15},{5,7,8},{4,5,7},{6,10,12},{4,6,10},{7,10,11},{7,9,11},{6,13,15},{5,6,13},{8,13,14},{8,9,14},{12,14,15},{11,12,14}}}, + +{7, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{4,7,10},{0,5,6},{0,4,5},{0,4,6},{2,11,12},{2,10,12},{2,10,11},{1,7,8},{1,8,9},{1,7,9},{6,12,15},{5,8,13},{3,13,15},{3,13,14},{9,11,14},{3,14,15},{5,7,8},{4,5,7},{6,10,12},{4,6,10},{9,10,11},{7,9,10},{5,13,15},{5,6,15},{8,13,14},{8,9,14},{12,14,15},{11,12,14}}}, + +{8, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{4,7,10},{0,5,6},{0,4,5},{0,4,6},{2,11,12},{2,10,12},{2,10,11},{1,7,8},{1,8,9},{1,7,9},{6,12,15},{5,8,13},{3,13,15},{3,13,14},{9,11,14},{3,14,15},{5,7,8},{4,5,7},{6,10,12},{4,6,10},{9,10,11},{7,9,10},{6,13,15},{5,6,13},{9,13,14},{8,9,13},{11,14,15},{11,12,15}}}, + +{9, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{4,7,10},{0,5,6},{0,4,5},{0,4,6},{2,11,12},{2,10,12},{2,10,11},{1,7,8},{1,8,9},{1,7,9},{6,12,15},{5,8,13},{3,13,15},{3,13,14},{9,11,14},{3,14,15},{5,7,8},{4,5,7},{6,10,12},{4,6,10},{9,10,11},{7,9,10},{6,13,15},{5,6,13},{8,13,14},{8,9,14},{11,14,15},{11,12,15}}}, + +{10, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{4,7,10},{0,5,6},{0,4,5},{0,4,6},{2,11,12},{2,10,12},{2,10,11},{1,7,8},{1,8,9},{1,7,9},{6,12,15},{5,8,13},{3,13,15},{3,13,14},{9,11,14},{3,14,15},{5,7,8},{4,5,7},{4,10,12},{4,6,12},{9,10,11},{7,9,10},{6,13,15},{5,6,13},{8,13,14},{8,9,14},{11,14,15},{11,12,15}}}, + +{11, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{4,7,10},{0,5,6},{0,4,5},{0,4,6},{2,11,12},{2,10,12},{2,10,11},{1,7,8},{1,8,9},{1,7,9},{6,12,15},{5,8,13},{3,13,15},{3,13,14},{9,11,14},{3,14,15},{4,7,8},{4,5,8},{6,10,12},{4,6,10},{7,10,11},{7,9,11},{5,13,15},{5,6,15},{9,13,14},{8,9,13},{12,14,15},{11,12,14}}}, + +}; + +graph_t graphs_dhex[NUM_DHEX_GRAPHS] = { + +{0, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{5,9,12},{4,5,9},{11,13,14},{10,11,13},{6,11,14},{5,6,11},{4,8,15},{4,6,15},{7,13,15},{7,8,15}}}, + +{1, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{5,9,12},{4,5,9},{11,13,14},{10,11,13},{6,11,14},{5,6,11},{4,8,15},{4,6,15},{8,13,15},{7,8,13}}}, + +{2, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{5,9,12},{4,5,9},{11,13,14},{10,11,13},{6,11,14},{5,6,11},{6,8,15},{4,6,8},{7,13,15},{7,8,15}}}, + +{3, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{5,9,12},{4,5,9},{11,13,14},{10,11,13},{6,11,14},{5,6,11},{6,8,15},{4,6,8},{8,13,15},{7,8,13}}}, + +{4, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{5,9,12},{4,5,9},{11,13,14},{10,11,13},{5,11,14},{5,6,14},{4,8,15},{4,6,15},{8,13,15},{7,8,13}}}, + +{5, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{5,9,12},{4,5,9},{11,13,14},{10,11,13},{5,11,14},{5,6,14},{6,8,15},{4,6,8},{7,13,15},{7,8,15}}}, + +{6, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{5,9,12},{4,5,9},{11,13,14},{10,11,13},{5,11,14},{5,6,14},{6,8,15},{4,6,8},{8,13,15},{7,8,13}}}, + +{7, +0, +53, +2, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{5,9,12},{4,5,9},{10,13,14},{10,11,14},{6,11,14},{5,6,11},{4,8,15},{4,6,15},{8,13,15},{7,8,13}}}, + +{8, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{5,9,12},{4,5,9},{10,13,14},{10,11,14},{6,11,14},{5,6,11},{6,8,15},{4,6,8},{7,13,15},{7,8,15}}}, + +{9, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{5,9,12},{4,5,9},{10,13,14},{10,11,14},{6,11,14},{5,6,11},{6,8,15},{4,6,8},{8,13,15},{7,8,13}}}, + +{10, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{5,9,12},{4,5,9},{10,13,14},{10,11,14},{5,11,14},{5,6,14},{4,8,15},{4,6,15},{8,13,15},{7,8,13}}}, + +{11, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{5,9,12},{4,5,9},{10,13,14},{10,11,14},{5,11,14},{5,6,14},{6,8,15},{4,6,8},{7,13,15},{7,8,15}}}, + +{12, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{5,9,12},{4,5,9},{10,13,14},{10,11,14},{5,11,14},{5,6,14},{6,8,15},{4,6,8},{8,13,15},{7,8,13}}}, + +{13, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{4,9,12},{4,5,12},{11,13,14},{10,11,13},{5,11,14},{5,6,14},{4,8,15},{4,6,15},{8,13,15},{7,8,13}}}, + +{14, +0, +55, +4, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{4,9,12},{4,5,12},{11,13,14},{10,11,13},{5,11,14},{5,6,14},{6,8,15},{4,6,8},{7,13,15},{7,8,15}}}, + +{15, +0, +59, +2, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{4,9,12},{4,5,12},{11,13,14},{10,11,13},{5,11,14},{5,6,14},{6,8,15},{4,6,8},{8,13,15},{7,8,13}}}, + +{16, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{4,9,12},{4,5,12},{10,13,14},{10,11,14},{6,11,14},{5,6,11},{4,8,15},{4,6,15},{8,13,15},{7,8,13}}}, + +{17, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{4,9,12},{4,5,12},{10,13,14},{10,11,14},{6,11,14},{5,6,11},{6,8,15},{4,6,8},{8,13,15},{7,8,13}}}, + +{18, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{4,9,12},{4,5,12},{10,13,14},{10,11,14},{5,11,14},{5,6,14},{4,8,15},{4,6,15},{8,13,15},{7,8,13}}}, + +{19, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{4,9,12},{4,5,12},{10,13,14},{10,11,14},{5,11,14},{5,6,14},{6,8,15},{4,6,8},{8,13,15},{7,8,13}}}, + +{20, +0, +61, +4, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{7,10,12},{7,9,12},{5,9,12},{4,5,9},{10,13,14},{10,11,14},{6,11,14},{5,6,11},{4,8,15},{4,6,15},{8,13,15},{7,8,13}}}, + +{21, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{7,10,12},{7,9,12},{5,9,12},{4,5,9},{10,13,14},{10,11,14},{6,11,14},{5,6,11},{6,8,15},{4,6,8},{8,13,15},{7,8,13}}}, + +{22, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{7,10,12},{7,9,12},{5,9,12},{4,5,9},{10,13,14},{10,11,14},{5,11,14},{5,6,14},{6,8,15},{4,6,8},{8,13,15},{7,8,13}}}, + +{23, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{7,10,12},{7,9,12},{4,9,12},{4,5,12},{10,13,14},{10,11,14},{5,11,14},{5,6,14},{6,8,15},{4,6,8},{8,13,15},{7,8,13}}}, + +}; + diff --git a/src/USER-PTM/graph_data.h b/src/USER-PTM/graph_data.h new file mode 100644 index 0000000000..3a8a5c7ae7 --- /dev/null +++ b/src/USER-PTM/graph_data.h @@ -0,0 +1,37 @@ +#ifndef GRAPH_DATA_H +#define GRAPH_DATA_H + +#include +#include "ptm_constants.h" + + +typedef struct +{ + int id; + uint64_t hash; + int automorphism_index; + int num_automorphisms; + int8_t canonical_labelling[PTM_MAX_POINTS]; + int8_t facets[PTM_MAX_FACETS][3]; +} graph_t; + +#define NUM_SC_GRAPHS 1 +#define NUM_ICO_GRAPHS 1 +#define NUM_FCC_GRAPHS 8 +#define NUM_HCP_GRAPHS 16 +#define NUM_BCC_GRAPHS 218 +#define NUM_DCUB_GRAPHS 12 +#define NUM_DHEX_GRAPHS 24 + +extern int8_t automorphisms[][PTM_MAX_POINTS]; + +extern graph_t graphs_sc[NUM_SC_GRAPHS]; +extern graph_t graphs_fcc[NUM_FCC_GRAPHS]; +extern graph_t graphs_hcp[NUM_HCP_GRAPHS]; +extern graph_t graphs_ico[NUM_ICO_GRAPHS]; +extern graph_t graphs_bcc[NUM_BCC_GRAPHS]; +extern graph_t graphs_dcub[NUM_DCUB_GRAPHS]; +extern graph_t graphs_dhex[NUM_DHEX_GRAPHS]; + +#endif + diff --git a/src/USER-PTM/graph_tools.cpp b/src/USER-PTM/graph_tools.cpp new file mode 100644 index 0000000000..864e921b51 --- /dev/null +++ b/src/USER-PTM/graph_tools.cpp @@ -0,0 +1,52 @@ +#include +#include +#include "graph_tools.h" +#include "ptm_constants.h" + + +bool build_facet_map(int num_facets, int8_t facets[][3], int8_t common[PTM_MAX_NBRS][PTM_MAX_NBRS]) +{ + memset(common, -1, sizeof(int8_t) * PTM_MAX_NBRS * PTM_MAX_NBRS); + + for (int i = 0;i +#include "ptm_constants.h" + +bool build_facet_map(int num_facets, int8_t facets[][3], int8_t common[PTM_MAX_NBRS][PTM_MAX_NBRS]); +int graph_degree(int num_facets, int8_t facets[][3], int num_nodes, int8_t* degree); + +#endif + diff --git a/src/USER-PTM/index_ptm.cpp b/src/USER-PTM/index_ptm.cpp new file mode 100644 index 0000000000..2683323ac5 --- /dev/null +++ b/src/USER-PTM/index_ptm.cpp @@ -0,0 +1,218 @@ +#include +#include +#include +#include +#include +#include +#include +#include "convex_hull_incremental.h" +#include "graph_data.h" +#include "deformation_gradient.h" +#include "alloy_types.h" +#include "neighbour_ordering.h" +#include "normalize_vertices.h" +#include "quat.h" +#include "polar.h" +#include "initialize_data.h" +#include "structure_matcher.h" +#include "ptm_functions.h" +#include "ptm_constants.h" + + +//todo: verify that c == norm(template[1]) +static double calculate_interatomic_distance(int type, double scale) +{ + assert(type >= 1 && type <= 7); + double c[8] = {0, 1, 1, (7. - 3.5 * sqrt(3)), 1, 1, sqrt(3) * 4. / (6 * sqrt(2) + sqrt(3)), sqrt(3) * 4. / (6 * sqrt(2) + sqrt(3))}; + return c[type] / scale; +} + +static double calculate_lattice_constant(int type, double interatomic_distance) +{ + assert(type >= 1 && type <= 7); + double c[8] = {0, 2 / sqrt(2), 2 / sqrt(2), 2. / sqrt(3), 2 / sqrt(2), 1, 4 / sqrt(3), 4 / sqrt(3)}; + return c[type] * interatomic_distance; +} + +static int rotate_into_fundamental_zone(int type, double* q) +{ + if (type == PTM_MATCH_SC) return rotate_quaternion_into_cubic_fundamental_zone(q); + if (type == PTM_MATCH_FCC) return rotate_quaternion_into_cubic_fundamental_zone(q); + if (type == PTM_MATCH_BCC) return rotate_quaternion_into_cubic_fundamental_zone(q); + if (type == PTM_MATCH_ICO) return rotate_quaternion_into_icosahedral_fundamental_zone(q); + if (type == PTM_MATCH_HCP) return rotate_quaternion_into_hcp_fundamental_zone(q); + if (type == PTM_MATCH_DCUB) return rotate_quaternion_into_diamond_cubic_fundamental_zone(q); + if (type == PTM_MATCH_DHEX) return rotate_quaternion_into_diamond_hexagonal_fundamental_zone(q); + return -1; +} + +static void order_points(ptm_local_handle_t local_handle, int num_points, double (*unpermuted_points)[3], int32_t* unpermuted_numbers, bool topological_ordering, + int8_t* ordering, double (*points)[3], int32_t* numbers) +{ + if (topological_ordering) + { + double normalized_points[PTM_MAX_INPUT_POINTS][3]; + normalize_vertices(num_points, unpermuted_points, normalized_points); + int ret = calculate_neighbour_ordering((void*)local_handle, num_points, (const double (*)[3])normalized_points, ordering); + if (ret != 0) + topological_ordering = false; + } + + if (!topological_ordering) + for (int i=0;iref_struct; + if (ref == NULL) + return; + + *p_type = ref->type; + if (p_alloy_type != NULL && unpermuted_numbers != NULL) + *p_alloy_type = find_alloy_type(ref, res->mapping, numbers); + + int bi = rotate_into_fundamental_zone(ref->type, res->q); + int8_t temp[PTM_MAX_POINTS]; + for (int i=0;inum_nbrs+1;i++) + temp[ref->mapping[bi][i]] = res->mapping[i]; + + memcpy(res->mapping, temp, (ref->num_nbrs+1) * sizeof(int8_t)); + + if (F != NULL && F_res != NULL) + { + double scaled_points[PTM_MAX_INPUT_POINTS][3]; + + subtract_barycentre(ref->num_nbrs + 1, points, scaled_points); + for (int i = 0;inum_nbrs + 1;i++) + { + scaled_points[i][0] *= res->scale; + scaled_points[i][1] *= res->scale; + scaled_points[i][2] *= res->scale; + } + calculate_deformation_gradient(ref->num_nbrs + 1, ref->points, res->mapping, scaled_points, ref->penrose, F, F_res); + + if (P != NULL && U != NULL) + polar_decomposition_3x3(F, false, U, P); + } + + if (mapping != NULL) + for (int i=0;inum_nbrs + 1;i++) + mapping[i] = ordering[res->mapping[i]]; + + double interatomic_distance = calculate_interatomic_distance(ref->type, res->scale); + double lattice_constant = calculate_lattice_constant(ref->type, interatomic_distance); + + if (p_interatomic_distance != NULL) + *p_interatomic_distance = interatomic_distance; + + if (p_lattice_constant != NULL) + *p_lattice_constant = lattice_constant; + + *p_rmsd = res->rmsd; + *p_scale = res->scale; + memcpy(q, res->q, 4 * sizeof(double)); +} + + +extern bool ptm_initialized; + +int ptm_index( ptm_local_handle_t local_handle, int32_t flags, + int num_points, double (*unpermuted_points)[3], int32_t* unpermuted_numbers, bool topological_ordering, + int32_t* p_type, int32_t* p_alloy_type, double* p_scale, double* p_rmsd, double* q, double* F, double* F_res, + double* U, double* P, int8_t* mapping, double* p_interatomic_distance, double* p_lattice_constant) +{ + assert(ptm_initialized); + assert(num_points <= PTM_MAX_INPUT_POINTS); + + if (flags & PTM_CHECK_SC) + assert(num_points >= PTM_NUM_POINTS_SC); + + if (flags & PTM_CHECK_BCC) + assert(num_points >= PTM_NUM_POINTS_BCC); + + if (flags & (PTM_CHECK_FCC | PTM_CHECK_HCP | PTM_CHECK_ICO)) + assert(num_points >= PTM_NUM_POINTS_FCC); + + if (flags & (PTM_CHECK_DCUB | PTM_CHECK_DHEX)) + assert(num_points >= PTM_NUM_POINTS_DCUB); + + int ret = 0; + result_t res; + res.ref_struct = NULL; + res.rmsd = INFINITY; + + int8_t ordering[PTM_MAX_INPUT_POINTS]; + double points[PTM_MAX_POINTS][3]; + int32_t numbers[PTM_MAX_POINTS]; + + int8_t dordering[PTM_MAX_INPUT_POINTS]; + double dpoints[PTM_MAX_POINTS][3]; + int32_t dnumbers[PTM_MAX_POINTS]; + + convexhull_t ch; + double ch_points[PTM_MAX_INPUT_POINTS][3]; + + if (flags & (PTM_CHECK_SC | PTM_CHECK_FCC | PTM_CHECK_HCP | PTM_CHECK_ICO | PTM_CHECK_BCC)) + { + int num_lpoints = std::min(std::min(PTM_MAX_POINTS, 20), num_points); + order_points(local_handle, num_lpoints, unpermuted_points, unpermuted_numbers, topological_ordering, ordering, points, numbers); + normalize_vertices(num_lpoints, points, ch_points); + ch.ok = false; + + if (flags & PTM_CHECK_SC) + ret = match_general(&structure_sc, ch_points, points, &ch, &res); + + if (flags & (PTM_CHECK_FCC | PTM_CHECK_HCP | PTM_CHECK_ICO)) + ret = match_fcc_hcp_ico(ch_points, points, flags, &ch, &res); + + if (flags & PTM_CHECK_BCC) + ret = match_general(&structure_bcc, ch_points, points, &ch, &res); + } + + if (flags & (PTM_CHECK_DCUB | PTM_CHECK_DHEX)) + { + ret = calculate_diamond_neighbour_ordering(num_points, unpermuted_points, unpermuted_numbers, dordering, dpoints, dnumbers); + if (ret == 0) + { + normalize_vertices(PTM_NUM_NBRS_DCUB + 1, dpoints, ch_points); + ch.ok = false; + + ret = match_dcub_dhex(ch_points, dpoints, flags, &ch, &res); + } + } + + if (res.ref_struct != NULL && (res.ref_struct->type == PTM_MATCH_DCUB || res.ref_struct->type == PTM_MATCH_DHEX)) + { + output_data( &res, num_points, unpermuted_numbers, dpoints, dnumbers, dordering, + p_type, p_alloy_type, p_scale, p_rmsd, q, F, F_res, + U, P, mapping, p_interatomic_distance, p_lattice_constant); + } + else + { + output_data( &res, num_points, unpermuted_numbers, points, numbers, ordering, + p_type, p_alloy_type, p_scale, p_rmsd, q, F, F_res, + U, P, mapping, p_interatomic_distance, p_lattice_constant); + } + + return PTM_NO_ERROR; +} + diff --git a/src/USER-PTM/initialize_data.cpp b/src/USER-PTM/initialize_data.cpp new file mode 100644 index 0000000000..6c177bfb70 --- /dev/null +++ b/src/USER-PTM/initialize_data.cpp @@ -0,0 +1,71 @@ +#include +#include +#include +#include +#include +#include +#include +#include "initialize_data.h" + + +static void make_facets_clockwise(int num_facets, int8_t (*facets)[3], const double (*points)[3]) +{ + double plane_normal[3]; + double origin[3] = {0, 0, 0}; + + for (int i = 0;inum_graphs;i++) + { + int8_t code[2 * PTM_MAX_EDGES]; + int8_t degree[PTM_MAX_NBRS]; + int _max_degree = graph_degree(s->num_facets, s->graphs[i].facets, s->num_nbrs, degree); + assert(_max_degree <= s->max_degree); + + make_facets_clockwise(s->num_facets, s->graphs[i].facets, &s->points[1]); + int ret = canonical_form_coloured(s->num_facets, s->graphs[i].facets, s->num_nbrs, degree, colours, s->graphs[i].canonical_labelling, (int8_t*)&code[0], &s->graphs[i].hash); + if (ret != 0) + return ret; + } + + return PTM_NO_ERROR; +} + +bool ptm_initialized = false; +int ptm_initialize_global() +{ + if (ptm_initialized) + return PTM_NO_ERROR; + + int8_t colours[PTM_MAX_POINTS] = {0}; + int8_t dcolours[PTM_MAX_POINTS] = {1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}; + + int ret = initialize_graphs(&structure_sc, colours); + ret |= initialize_graphs(&structure_fcc, colours); + ret |= initialize_graphs(&structure_hcp, colours); + ret |= initialize_graphs(&structure_ico, colours); + ret |= initialize_graphs(&structure_bcc, colours); + ret |= initialize_graphs(&structure_dcub, dcolours); + ret |= initialize_graphs(&structure_dhex, dcolours); + + if (ret == PTM_NO_ERROR) + ptm_initialized = true; + + return ret; +} + +ptm_local_handle_t ptm_initialize_local() +{ + assert(ptm_initialized); + return (ptm_local_handle_t)voronoi_initialize_local(); +} + +void ptm_uninitialize_local(ptm_local_handle_t ptr) +{ + voronoi_uninitialize_local(ptr); +} + diff --git a/src/USER-PTM/initialize_data.h b/src/USER-PTM/initialize_data.h new file mode 100644 index 0000000000..644dfea8c4 --- /dev/null +++ b/src/USER-PTM/initialize_data.h @@ -0,0 +1,61 @@ +#ifndef INITIALIZE_DATA_H +#define INITIALIZE_DATA_H + + +#include "graph_data.h" +#include "graph_tools.h" +#include "deformation_gradient.h" +#include "fundamental_mappings.h" +#include "neighbour_ordering.h" +#include "canonical_coloured.h" +#include "convex_hull_incremental.h" + + +typedef struct +{ + int type; + int num_nbrs; + int num_facets; + int max_degree; + int num_graphs; + int num_mappings; + graph_t* graphs; + const double (*points)[3]; + const double (*penrose)[3]; + const int8_t (*mapping)[PTM_MAX_POINTS]; +} refdata_t; + + +//refdata_t structure_sc = { .type = PTM_MATCH_SC, .num_nbrs = 6, .num_facets = 8, .max_degree = 4, .num_graphs = NUM_SC_GRAPHS, .graphs = graphs_sc, .points = ptm_template_sc, .penrose = penrose_sc , .mapping = mapping_sc }; +const refdata_t structure_sc = { PTM_MATCH_SC, 6, 8, 4, NUM_SC_GRAPHS, NUM_CUBIC_MAPPINGS, graphs_sc, ptm_template_sc, penrose_sc, mapping_sc }; +const refdata_t structure_fcc = { PTM_MATCH_FCC, 12, 20, 6, NUM_FCC_GRAPHS, NUM_CUBIC_MAPPINGS, graphs_fcc, ptm_template_fcc, penrose_fcc, mapping_fcc }; +const refdata_t structure_hcp = { PTM_MATCH_HCP, 12, 20, 6, NUM_HCP_GRAPHS, NUM_HEX_MAPPINGS, graphs_hcp, ptm_template_hcp, penrose_hcp, mapping_hcp }; +const refdata_t structure_ico = { PTM_MATCH_ICO, 12, 20, 6, NUM_ICO_GRAPHS, NUM_ICO_MAPPINGS, graphs_ico, ptm_template_ico, penrose_ico, mapping_ico }; +const refdata_t structure_bcc = { PTM_MATCH_BCC, 14, 24, 8, NUM_BCC_GRAPHS, NUM_CUBIC_MAPPINGS, graphs_bcc, ptm_template_bcc, penrose_bcc, mapping_bcc }; +const refdata_t structure_dcub = { PTM_MATCH_DCUB, 16, 28, 8, NUM_DCUB_GRAPHS, NUM_DCUB_MAPPINGS, graphs_dcub, ptm_template_dcub, penrose_dcub, mapping_dcub }; +const refdata_t structure_dhex = { PTM_MATCH_DHEX, 16, 28, 8, NUM_DHEX_GRAPHS, NUM_DHEX_MAPPINGS, graphs_dhex, ptm_template_dhex, penrose_dhex, mapping_dhex }; + + +#ifdef __cplusplus +extern "C" { +#endif + +typedef struct ptm_local_handle* ptm_local_handle_t; +ptm_local_handle_t ptm_initialize_local(); +void ptm_uninitialize_local(ptm_local_handle_t ptr); + +int ptm_initialize_global(); + +//------------------------------------ +// global initialization switch +//------------------------------------ +extern bool ptm_initialized; + + +#ifdef __cplusplus +} +#endif + + +#endif + diff --git a/src/USER-PTM/neighbour_ordering.cpp b/src/USER-PTM/neighbour_ordering.cpp new file mode 100644 index 0000000000..8e8b016cfc --- /dev/null +++ b/src/USER-PTM/neighbour_ordering.cpp @@ -0,0 +1,203 @@ +#include +#include +#include +#include +#include +#include "ptm_constants.h" +#include "cell.h" +using namespace voro; + + + +typedef struct +{ + double area; + double dist; + int index; +} sorthelper_t; + +static bool sorthelper_compare(sorthelper_t const& a, sorthelper_t const& b) +{ + if (a.area > b.area) + return true; + + if (a.area < b.area) + return false; + + if (a.dist < b.dist) + return true; + + return false; +} + +//todo: change voronoi code to return errors rather than exiting +static int calculate_voronoi_face_areas(int num_points, const double (*_points)[3], double* normsq, double max_norm, voronoicell_neighbor* v, std::vector& nbr_indices, std::vector& face_areas) +{ + const double k = 1000 * max_norm; //todo: reduce this constant + v->init(-k,k,-k,k,-k,k); + + for (int i=1;inplane(x,y,z,normsq[i],i); + } + + v->neighbors(nbr_indices); + v->face_areas(face_areas); + return 0; +} + +int calculate_neighbour_ordering(void* _voronoi_handle, int num_points, const double (*_points)[3], int8_t* ordering) +{ + assert(num_points <= PTM_MAX_INPUT_POINTS); + + voronoicell_neighbor* voronoi_handle = (voronoicell_neighbor*)_voronoi_handle; + + double max_norm = 0; + double points[PTM_MAX_INPUT_POINTS][3]; + double normsq[PTM_MAX_INPUT_POINTS]; + for (int i = 0;i nbr_indices(num_points + 6); + std::vector face_areas(num_points + 6); + int ret = calculate_voronoi_face_areas(num_points, points, normsq, max_norm, voronoi_handle, nbr_indices, face_areas); + if (ret != 0) + return ret; + + double areas[PTM_MAX_INPUT_POINTS]; + memset(areas, 0, num_points * sizeof(double)); + areas[0] = INFINITY; + for (size_t i=0;i 0) + areas[index] = face_areas[i]; + } + + sorthelper_t data[PTM_MAX_INPUT_POINTS]; + for (int i=0;i= 3) + continue; + + ordering[1 + 4 + 3 * p + counts[p]] = q; + counts[p]++; + index++; + num_found++; + if (num_found >= 12) + break; + } + + if (num_found != 12) + return -1; + + for (int i=0;i + + +void subtract_barycentre(int num, double (*points)[3], double (*normalized)[3]) +{ + //calculate barycentre + double sum[3] = {0, 0, 0}; + for (int i=0;i nor the names of its contributors may be used to + * endorse or promote products derived from this software without specific prior written + * permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS + * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT + * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A + * PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT + * HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT + * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, + * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY + * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE + * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + * Source: started anew. + * + * Change History: + * 2009/04/13 Started source + * 2010/03/28 Modified FastCalcRMSDAndRotation() to handle tiny qsqr + * If trying all rows of the adjoint still gives too small + * qsqr, then just return identity matrix. (DLT) + * 2010/06/30 Fixed prob in assigning A[9] = 0 in InnerProduct() + * invalid mem access + * 2011/02/21 Made CenterCoords use weights + * 2011/05/02 Finally changed CenterCoords declaration in qcprot.h + * Also changed some functions to static + * 2011/07/08 put in fabs() to fix taking sqrt of small neg numbers, fp error + * 2012/07/26 minor changes to comments and main.c, more info (v.1.4) + * + * 2016/05/29 QCP method adapted for polar decomposition of a 3x3 matrix, + * for use in Polyhedral Template Matching. + * + ******************************************************************************/ + +#include +#include +#include +#include "quat.h" + + +static void matmul_3x3(double* A, double* x, double* b) +{ + b[0] = A[0] * x[0] + A[1] * x[3] + A[2] * x[6]; + b[3] = A[3] * x[0] + A[4] * x[3] + A[5] * x[6]; + b[6] = A[6] * x[0] + A[7] * x[3] + A[8] * x[6]; + + b[1] = A[0] * x[1] + A[1] * x[4] + A[2] * x[7]; + b[4] = A[3] * x[1] + A[4] * x[4] + A[5] * x[7]; + b[7] = A[6] * x[1] + A[7] * x[4] + A[8] * x[7]; + + b[2] = A[0] * x[2] + A[1] * x[5] + A[2] * x[8]; + b[5] = A[3] * x[2] + A[4] * x[5] + A[5] * x[8]; + b[8] = A[6] * x[2] + A[7] * x[5] + A[8] * x[8]; +} + +static double matrix_determinant_3x3(double* A) +{ + return A[0] * (A[4]*A[8] - A[5]*A[7]) + - A[1] * (A[3]*A[8] - A[5]*A[6]) + + A[2] * (A[3]*A[7] - A[4]*A[6]); +} + +static void flip_matrix(double* A) +{ + for (int i=0;i<9;i++) + A[i] = -A[i]; +} + +static bool optimal_quaternion(double* A, bool polar, double E0, double* p_nrmsdsq, double* qopt) +{ + const double evecprec = 1e-6; + const double evalprec = 1e-11; + + double Sxx = A[0], Sxy = A[1], Sxz = A[2], + Syx = A[3], Syy = A[4], Syz = A[5], + Szx = A[6], Szy = A[7], Szz = A[8]; + + double Sxx2 = Sxx * Sxx, Syy2 = Syy * Syy, Szz2 = Szz * Szz, + Sxy2 = Sxy * Sxy, Syz2 = Syz * Syz, Sxz2 = Sxz * Sxz, + Syx2 = Syx * Syx, Szy2 = Szy * Szy, Szx2 = Szx * Szx; + + double fnorm_squared = Sxx2 + Syy2 + Szz2 + Sxy2 + Syz2 + Sxz2 + Syx2 + Szy2 + Szx2; + + double SyzSzymSyySzz2 = 2.0 * (Syz * Szy - Syy * Szz); + double Sxx2Syy2Szz2Syz2Szy2 = Syy2 + Szz2 - Sxx2 + Syz2 + Szy2; + double SxzpSzx = Sxz + Szx; + double SyzpSzy = Syz + Szy; + double SxypSyx = Sxy + Syx; + double SyzmSzy = Syz - Szy; + double SxzmSzx = Sxz - Szx; + double SxymSyx = Sxy - Syx; + double SxxpSyy = Sxx + Syy; + double SxxmSyy = Sxx - Syy; + double Sxy2Sxz2Syx2Szx2 = Sxy2 + Sxz2 - Syx2 - Szx2; + + double C[3]; + C[0] = Sxy2Sxz2Syx2Szx2 * Sxy2Sxz2Syx2Szx2 + + (Sxx2Syy2Szz2Syz2Szy2 + SyzSzymSyySzz2) * (Sxx2Syy2Szz2Syz2Szy2 - SyzSzymSyySzz2) + + (-(SxzpSzx)*(SyzmSzy)+(SxymSyx)*(SxxmSyy-Szz)) * (-(SxzmSzx)*(SyzpSzy)+(SxymSyx)*(SxxmSyy+Szz)) + + (-(SxzpSzx)*(SyzpSzy)-(SxypSyx)*(SxxpSyy-Szz)) * (-(SxzmSzx)*(SyzmSzy)-(SxypSyx)*(SxxpSyy+Szz)) + + (+(SxypSyx)*(SyzpSzy)+(SxzpSzx)*(SxxmSyy+Szz)) * (-(SxymSyx)*(SyzmSzy)+(SxzpSzx)*(SxxpSyy+Szz)) + + (+(SxypSyx)*(SyzmSzy)+(SxzmSzx)*(SxxmSyy-Szz)) * (-(SxymSyx)*(SyzpSzy)+(SxzmSzx)*(SxxpSyy-Szz)); + + C[1] = 8.0 * (Sxx*Syz*Szy + Syy*Szx*Sxz + Szz*Sxy*Syx - Sxx*Syy*Szz - Syz*Szx*Sxy - Szy*Syx*Sxz); + C[2] = -2.0 * fnorm_squared; + + //Newton-Raphson + double mxEigenV = polar ? sqrt(3 * fnorm_squared) : E0; + if (mxEigenV > evalprec) + { + for (int i=0;i<50;i++) + { + double oldg = mxEigenV; + double x2 = mxEigenV*mxEigenV; + double b = (x2 + C[2])*mxEigenV; + double a = b + C[1]; + double delta = ((a * mxEigenV + C[0]) / (2 * x2 * mxEigenV + b + a)); + mxEigenV -= delta; + if (fabs(mxEigenV - oldg) < fabs(evalprec * mxEigenV)) + break; + } + } + else + { + mxEigenV = 0.0; + } + + (*p_nrmsdsq) = std::max(0.0, 2.0 * (E0 - mxEigenV)); + + double a11 = SxxpSyy + Szz - mxEigenV; + double a12 = SyzmSzy; + double a13 = -SxzmSzx; + double a14 = SxymSyx; + + double a21 = SyzmSzy; + double a22 = SxxmSyy - Szz -mxEigenV; + double a23 = SxypSyx; + double a24 = SxzpSzx; + + double a31 = a13; + double a32 = a23; + double a33 = Syy - Sxx - Szz - mxEigenV; + double a34 = SyzpSzy; + + double a41 = a14; + double a42 = a24; + double a43 = a34; + double a44 = Szz - SxxpSyy - mxEigenV; + + double a3344_4334 = a33 * a44 - a43 * a34; + double a3244_4234 = a32 * a44 - a42 * a34; + double a3243_4233 = a32 * a43 - a42 * a33; + double a3143_4133 = a31 * a43 - a41 * a33; + double a3144_4134 = a31 * a44 - a41 * a34; + double a3142_4132 = a31 * a42 - a41 * a32; + double a1324_1423 = a13 * a24 - a14 * a23; + double a1224_1422 = a12 * a24 - a14 * a22; + double a1223_1322 = a12 * a23 - a13 * a22; + double a1124_1421 = a11 * a24 - a14 * a21; + double a1123_1321 = a11 * a23 - a13 * a21; + double a1122_1221 = a11 * a22 - a12 * a21; + + double q[4][4]; + q[0][0] = a12 * a3344_4334 - a13 * a3244_4234 + a14 * a3243_4233; + q[0][1] = -a11 * a3344_4334 + a13 * a3144_4134 - a14 * a3143_4133; + q[0][2] = a11 * a3244_4234 - a12 * a3144_4134 + a14 * a3142_4132; + q[0][3] = -a11 * a3243_4233 + a12 * a3143_4133 - a13 * a3142_4132; + + q[1][0] = a22 * a3344_4334 - a23 * a3244_4234 + a24 * a3243_4233; + q[1][1] = -a21 * a3344_4334 + a23 * a3144_4134 - a24 * a3143_4133; + q[1][2] = a21 * a3244_4234 - a22 * a3144_4134 + a24 * a3142_4132; + q[1][3] = -a21 * a3243_4233 + a22 * a3143_4133 - a23 * a3142_4132; + + q[2][0] = a32 * a1324_1423 - a33 * a1224_1422 + a34 * a1223_1322; + q[2][1] = -a31 * a1324_1423 + a33 * a1124_1421 - a34 * a1123_1321; + q[2][2] = a31 * a1224_1422 - a32 * a1124_1421 + a34 * a1122_1221; + q[2][3] = -a31 * a1223_1322 + a32 * a1123_1321 - a33 * a1122_1221; + + q[3][0] = a42 * a1324_1423 - a43 * a1224_1422 + a44 * a1223_1322; + q[3][1] = -a41 * a1324_1423 + a43 * a1124_1421 - a44 * a1123_1321; + q[3][2] = a41 * a1224_1422 - a42 * a1124_1421 + a44 * a1122_1221; + q[3][3] = -a41 * a1223_1322 + a42 * a1123_1321 - a43 * a1122_1221; + + double qsqr[4]; + for (int i=0;i<4;i++) + qsqr[i] = q[i][0]*q[i][0] + q[i][1]*q[i][1] + q[i][2]*q[i][2] + q[i][3]*q[i][3]; + + int bi = 0; + double max = 0; + for (int i=0;i<4;i++) + { + if (qsqr[i] > max) + { + bi = i; + max = qsqr[i]; + } + } + + bool too_small = false; + if (qsqr[bi] < evecprec) + { + //if qsqr is still too small, return the identity rotation. + q[bi][0] = 1; + q[bi][1] = 0; + q[bi][2] = 0; + q[bi][3] = 0; + too_small = true; + } + else + { + double normq = sqrt(qsqr[bi]); + q[bi][0] /= normq; + q[bi][1] /= normq; + q[bi][2] /= normq; + q[bi][3] /= normq; + } + + memcpy(qopt, q[bi], 4 * sizeof(double)); + return !too_small; +} + +int polar_decomposition_3x3(double* _A, bool right_sided, double* U, double* P) +{ + double A[9]; + memcpy(A, _A, 9 * sizeof(double)); + + double det = matrix_determinant_3x3(A); + if (det < 0) + flip_matrix(A); + + double q[4]; + double nrmsdsq = 0; + optimal_quaternion(A, true, -1, &nrmsdsq, q); + q[0] = -q[0]; + quaternion_to_rotation_matrix(q, U); + + if (det < 0) + flip_matrix(U); + + double UT[9] = {U[0], U[3], U[6], U[1], U[4], U[7], U[2], U[5], U[8]}; + + if (right_sided) + matmul_3x3(UT, _A, P); + else + matmul_3x3(_A, UT, P); + + return 0; +} + +void InnerProduct(double *A, int num, const double (*coords1)[3], double (*coords2)[3], int8_t* permutation) +{ + A[0] = A[1] = A[2] = A[3] = A[4] = A[5] = A[6] = A[7] = A[8] = 0.0; + + for (int i = 0; i < num; ++i) + { + double x1 = coords1[i][0]; + double y1 = coords1[i][1]; + double z1 = coords1[i][2]; + + double x2 = coords2[permutation[i]][0]; + double y2 = coords2[permutation[i]][1]; + double z2 = coords2[permutation[i]][2]; + + A[0] += x1 * x2; + A[1] += x1 * y2; + A[2] += x1 * z2; + + A[3] += y1 * x2; + A[4] += y1 * y2; + A[5] += y1 * z2; + + A[6] += z1 * x2; + A[7] += z1 * y2; + A[8] += z1 * z2; + } +} + +int FastCalcRMSDAndRotation(double *A, double E0, double *p_nrmsdsq, double *q, double* U) +{ + optimal_quaternion(A, false, E0, p_nrmsdsq, q); + quaternion_to_rotation_matrix(q, U); + return 0; +} + diff --git a/src/USER-PTM/polar.h b/src/USER-PTM/polar.h new file mode 100644 index 0000000000..3ec025b806 --- /dev/null +++ b/src/USER-PTM/polar.h @@ -0,0 +1,12 @@ +#ifndef POLAR_H +#define POLAR_H + +#include +#include + +int polar_decomposition_3x3(double* _A, bool right_sided, double* U, double* P); +void InnerProduct(double *A, int num, const double (*coords1)[3], double (*coords2)[3], int8_t* permutation); +int FastCalcRMSDAndRotation(double *A, double E0, double *p_nrmsdsq, double *q, double* U); + +#endif + diff --git a/src/USER-PTM/ptm_constants.h b/src/USER-PTM/ptm_constants.h new file mode 100644 index 0000000000..f868f51e84 --- /dev/null +++ b/src/USER-PTM/ptm_constants.h @@ -0,0 +1,174 @@ +#ifndef PTM_CONSTANTS_H +#define PTM_CONSTANTS_H + +//------------------------------------ +// definitions +//------------------------------------ +#define PTM_NO_ERROR 0 + + +#define PTM_CHECK_FCC (1 << 0) +#define PTM_CHECK_HCP (1 << 1) +#define PTM_CHECK_BCC (1 << 2) +#define PTM_CHECK_ICO (1 << 3) +#define PTM_CHECK_SC (1 << 4) +#define PTM_CHECK_DCUB (1 << 5) +#define PTM_CHECK_DHEX (1 << 6) +#define PTM_CHECK_NONDIAMOND (PTM_CHECK_SC | PTM_CHECK_FCC | PTM_CHECK_HCP | PTM_CHECK_ICO | PTM_CHECK_BCC) +#define PTM_CHECK_ALL (PTM_CHECK_SC | PTM_CHECK_FCC | PTM_CHECK_HCP | PTM_CHECK_ICO | PTM_CHECK_BCC | PTM_CHECK_DCUB | PTM_CHECK_DHEX) + +#define PTM_MATCH_NONE 0 +#define PTM_MATCH_FCC 1 +#define PTM_MATCH_HCP 2 +#define PTM_MATCH_BCC 3 +#define PTM_MATCH_ICO 4 +#define PTM_MATCH_SC 5 +#define PTM_MATCH_DCUB 6 +#define PTM_MATCH_DHEX 7 + +#define PTM_ALLOY_NONE 0 +#define PTM_ALLOY_PURE 1 +#define PTM_ALLOY_L10 2 +#define PTM_ALLOY_L12_CU 3 +#define PTM_ALLOY_L12_AU 4 +#define PTM_ALLOY_B2 5 +#define PTM_ALLOY_SIC 6 + + +#define PTM_MAX_INPUT_POINTS 35 +#define PTM_MAX_NBRS 16 +#define PTM_MAX_POINTS (PTM_MAX_NBRS + 1) +#define PTM_MAX_FACETS 28 //2 * PTM_MAX_NBRS - 4 +#define PTM_MAX_EDGES 42 //3 * PTM_MAX_NBRS - 6 + + +//------------------------------------ +// number of neighbours +//------------------------------------ +#define PTM_NUM_NBRS_FCC 12 +#define PTM_NUM_NBRS_HCP 12 +#define PTM_NUM_NBRS_BCC 14 +#define PTM_NUM_NBRS_ICO 12 +#define PTM_NUM_NBRS_SC 6 +#define PTM_NUM_NBRS_DCUB 16 +#define PTM_NUM_NBRS_DHEX 16 + +#define PTM_NUM_POINTS_FCC (PTM_NUM_NBRS_FCC + 1) +#define PTM_NUM_POINTS_HCP (PTM_NUM_NBRS_HCP + 1) +#define PTM_NUM_POINTS_BCC (PTM_NUM_NBRS_BCC + 1) +#define PTM_NUM_POINTS_ICO (PTM_NUM_NBRS_ICO + 1) +#define PTM_NUM_POINTS_SC (PTM_NUM_NBRS_SC + 1) +#define PTM_NUM_POINTS_DCUB (PTM_NUM_NBRS_DCUB + 1) +#define PTM_NUM_POINTS_DHEX (PTM_NUM_NBRS_DHEX + 1) + +const int ptm_num_nbrs[8] = {0, PTM_NUM_NBRS_FCC, PTM_NUM_NBRS_HCP, PTM_NUM_NBRS_BCC, PTM_NUM_NBRS_ICO, PTM_NUM_NBRS_SC, PTM_NUM_NBRS_DCUB, PTM_NUM_NBRS_DHEX}; + +//------------------------------------ +// template structures +//------------------------------------ + +//these point sets have barycentre {0, 0, 0} and are scaled such that the mean neighbour distance is 1 + +const double ptm_template_fcc[PTM_NUM_POINTS_FCC][3] = { { 0. , 0. , 0. }, + { 0. , 0.707106781187, 0.707106781187 }, + { 0. , -0.707106781187, -0.707106781187 }, + { 0. , 0.707106781187, -0.707106781187 }, + { 0. , -0.707106781187, 0.707106781187 }, + { 0.707106781187, 0. , 0.707106781187 }, + { -0.707106781187, 0. , -0.707106781187 }, + { 0.707106781187, 0. , -0.707106781187 }, + { -0.707106781187, 0. , 0.707106781187 }, + { 0.707106781187, 0.707106781187, 0. }, + { -0.707106781187, -0.707106781187, 0. }, + { 0.707106781187, -0.707106781187, 0. }, + { -0.707106781187, 0.707106781187, 0. } }; + +const double ptm_template_hcp[PTM_NUM_POINTS_HCP][3] = { { 0. , 0. , 0. }, + { 0.707106781186, 0. , 0.707106781186 }, + { -0.235702260395, -0.942809041583, -0.235702260395 }, + { 0.707106781186, 0.707106781186, 0. }, + { -0.235702260395, -0.235702260395, -0.942809041583 }, + { 0. , 0.707106781186, 0.707106781186 }, + { -0.942809041583, -0.235702260395, -0.235702260395 }, + { -0.707106781186, 0.707106781186, 0. }, + { 0. , 0.707106781186, -0.707106781186 }, + { 0.707106781186, 0. , -0.707106781186 }, + { 0.707106781186, -0.707106781186, 0. }, + { -0.707106781186, 0. , 0.707106781186 }, + { 0. , -0.707106781186, 0.707106781186 } }; + +const double ptm_template_bcc[PTM_NUM_POINTS_BCC][3] = { { 0. , 0. , 0. }, + { -0.541451884327, -0.541451884327, -0.541451884327 }, + { 0.541451884327, 0.541451884327, 0.541451884327 }, + { 0.541451884327, -0.541451884327, -0.541451884327 }, + { -0.541451884327, 0.541451884327, 0.541451884327 }, + { -0.541451884327, 0.541451884327, -0.541451884327 }, + { 0.541451884327, -0.541451884327, 0.541451884327 }, + { -0.541451884327, -0.541451884327, 0.541451884327 }, + { 0.541451884327, 0.541451884327, -0.541451884327 }, + { 0. , 0. , -1.082903768655 }, + { 0. , 0. , 1.082903768655 }, + { 0. , -1.082903768655, 0. }, + { 0. , 1.082903768655, 0. }, + { -1.082903768655, 0. , 0. }, + { 1.082903768655, 0. , 0. } }; + +const double ptm_template_ico[PTM_NUM_POINTS_ICO][3] = { { 0. , 0. , 0. }, + { 0. , 0.525731112119, 0.850650808352 }, + { 0. , -0.525731112119, -0.850650808352 }, + { 0. , 0.525731112119, -0.850650808352 }, + { 0. , -0.525731112119, 0.850650808352 }, + { -0.525731112119, -0.850650808352, 0. }, + { 0.525731112119, 0.850650808352, 0. }, + { 0.525731112119, -0.850650808352, 0. }, + { -0.525731112119, 0.850650808352, 0. }, + { -0.850650808352, 0. , -0.525731112119 }, + { 0.850650808352, 0. , 0.525731112119 }, + { 0.850650808352, 0. , -0.525731112119 }, + { -0.850650808352, 0. , 0.525731112119 } }; + +const double ptm_template_sc[PTM_NUM_POINTS_SC][3] = { { 0. , 0. , 0. }, + { 0. , 0. , -1. }, + { 0. , 0. , 1. }, + { 0. , -1. , 0. }, + { 0. , 1. , 0. }, + { -1. , 0. , 0. }, + { 1. , 0. , 0. } }; + +const double ptm_template_dcub[PTM_NUM_POINTS_DCUB][3] = { { 0. , 0. , 0. }, + { -0.391491627053, 0.391491627053, 0.391491627053 }, + { -0.391491627053, -0.391491627053, -0.391491627053 }, + { 0.391491627053, -0.391491627053, 0.391491627053 }, + { 0.391491627053, 0.391491627053, -0.391491627053 }, + { -0.782983254107, 0. , 0.782983254107 }, + { -0.782983254107, 0.782983254107, 0. }, + { 0. , 0.782983254107, 0.782983254107 }, + { -0.782983254107, -0.782983254107, 0. }, + { -0.782983254107, 0. , -0.782983254107 }, + { 0. , -0.782983254107, -0.782983254107 }, + { 0. , -0.782983254107, 0.782983254107 }, + { 0.782983254107, -0.782983254107, 0. }, + { 0.782983254107, 0. , 0.782983254107 }, + { 0. , 0.782983254107, -0.782983254107 }, + { 0.782983254107, 0. , -0.782983254107 }, + { 0.782983254107, 0.782983254107, 0. } }; + +const double ptm_template_dhex[PTM_NUM_POINTS_DHEX][3] = { { 0. , 0. , 0. }, + { -0.391491627053, -0.391491627053, -0.391491627053 }, + { 0.391491627053, -0.391491627053, 0.391491627053 }, + { -0.391491627053, 0.391491627053, 0.391491627053 }, + { 0.391491627053, 0.391491627053, -0.391491627053 }, + { -0.260994418036, -1.043977672142, -0.260994418036 }, + { -1.043977672142, -0.260994418036, -0.260994418036 }, + { -0.260994418036, -0.260994418036, -1.043977672142 }, + { 0.782983254107, 0. , 0.782983254107 }, + { 0.782983254107, -0.782983254107, 0. }, + { 0. , -0.782983254107, 0.782983254107 }, + { 0. , 0.782983254107, 0.782983254107 }, + { -0.782983254107, 0.782983254107, 0. }, + { -0.782983254107, 0. , 0.782983254107 }, + { 0.782983254107, 0.782983254107, 0. }, + { 0. , 0.782983254107, -0.782983254107 }, + { 0.782983254107, 0. , -0.782983254107 } }; +#endif + diff --git a/src/USER-PTM/ptm_functions.h b/src/USER-PTM/ptm_functions.h new file mode 100644 index 0000000000..69141a37c4 --- /dev/null +++ b/src/USER-PTM/ptm_functions.h @@ -0,0 +1,27 @@ +#ifndef PTM_FUNCTIONS_H +#define PTM_FUNCTIONS_H + +#include +#include +#include "initialize_data.h" +#include "ptm_constants.h" + + +//------------------------------------ +// function declarations +//------------------------------------ +#ifdef __cplusplus +extern "C" { +#endif + + +int ptm_index( ptm_local_handle_t local_handle, int32_t flags, int num_points, double (*atomic_positions)[3], int32_t* atomic_numbers, bool topological_ordering, //inputs + int32_t* p_type, int32_t* p_alloy_type, double* p_scale, double* p_rmsd, double* q, double* F, double* F_res, double* U, double* P, int8_t* mapping, double* p_interatomic_distance, double* p_lattice_constant); //outputs + + +#ifdef __cplusplus +} +#endif + +#endif + diff --git a/src/USER-PTM/quat.cpp b/src/USER-PTM/quat.cpp new file mode 100644 index 0000000000..f55aff3d2b --- /dev/null +++ b/src/USER-PTM/quat.cpp @@ -0,0 +1,396 @@ +#include +#include +#include + + +#define SIGN(x) (x >= 0 ? 1 : -1) +#define MIN(X, Y) (((X) < (Y)) ? (X) : (Y)) +#define MAX(X, Y) (((X) > (Y)) ? (X) : (Y)) + + +#define SQRT_2 1.4142135623730951454746218587388284504414 +#define HALF_SQRT_2 0.7071067811865474617150084668537601828575 + +#define PHI 1.6180339887498949025257388711906969547272 +#define HALF_PHI 0.8090169943749474512628694355953484773636 + +#define INV_PHI 0.6180339887498947915034364086750429123640 +#define HALF_INV_PHI 0.3090169943749473957517182043375214561820 + +#define SQRT_5_ 2.23606797749978969640917366873127623544061835961152572427089 +#define SQRT_2_3 0.8164965809277260344600790631375275552273 +#define SQRT_1_6 0.4082482904638630172300395315687637776136 + + +double generator_cubic[24][4] = { {1, 0, 0, 0 }, + {0, 1, 0, 0 }, + {0, 0, 1, 0 }, + {0, 0, 0, 1 }, + {0.5, 0.5, 0.5, 0.5 }, + {0.5, 0.5, -0.5, 0.5 }, + {0.5, -0.5, 0.5, 0.5 }, + {0.5, -0.5, -0.5, 0.5 }, + {-0.5, 0.5, 0.5, 0.5 }, + {-0.5, 0.5, -0.5, 0.5 }, + {-0.5, -0.5, 0.5, 0.5 }, + {-0.5, -0.5, -0.5, 0.5 }, + {HALF_SQRT_2, HALF_SQRT_2, 0, 0 }, + {HALF_SQRT_2, 0, HALF_SQRT_2, 0 }, + {HALF_SQRT_2, 0, 0, HALF_SQRT_2 }, + {-HALF_SQRT_2, HALF_SQRT_2, 0, 0 }, + {-HALF_SQRT_2, 0, HALF_SQRT_2, 0 }, + {-HALF_SQRT_2, 0, 0, HALF_SQRT_2 }, + {0, HALF_SQRT_2, HALF_SQRT_2, 0 }, + {0, HALF_SQRT_2, 0, HALF_SQRT_2 }, + {0, 0, HALF_SQRT_2, HALF_SQRT_2 }, + {0, -HALF_SQRT_2, HALF_SQRT_2, 0 }, + {0, -HALF_SQRT_2, 0, HALF_SQRT_2 }, + {0, 0, -HALF_SQRT_2, HALF_SQRT_2 } }; + +double generator_diamond_cubic[12][4] = { {1, 0, 0, 0 }, + {0, 1, 0, 0 }, + {0, 0, 1, 0 }, + {0, 0, 0, 1 }, + {0.5, 0.5, 0.5, 0.5 }, + {0.5, 0.5, -0.5, 0.5 }, + {0.5, -0.5, 0.5, 0.5 }, + {0.5, -0.5, -0.5, 0.5 }, + {-0.5, 0.5, 0.5, 0.5 }, + {-0.5, 0.5, -0.5, 0.5 }, + {-0.5, -0.5, 0.5, 0.5 }, + {-0.5, -0.5, -0.5, 0.5 } }; + +double generator_hcp[6][4] = { {1, 0, 0, 0}, + {0.5, 0.5, 0.5, 0.5}, + {0.5, -0.5, -0.5, -0.5}, + {0, SQRT_2_3, -SQRT_1_6, -SQRT_1_6}, + {0, SQRT_1_6, -SQRT_2_3, SQRT_1_6}, + {0, SQRT_1_6, SQRT_1_6, -SQRT_2_3} }; + +double generator_diamond_hexagonal[3][4] = { {1, 0, 0, 0}, + {0.5, 0.5, 0.5, 0.5}, + {0.5, -0.5, -0.5, -0.5} }; + +double generator_icosahedral[60][4] = { {1, 0, 0, 0}, + {HALF_PHI, -HALF_INV_PHI, -0.5, 0}, + {HALF_PHI, 0, -HALF_INV_PHI, -0.5}, + {HALF_PHI, -0.5, 0, -HALF_INV_PHI}, + {HALF_PHI, HALF_INV_PHI, -0.5, 0}, + {HALF_PHI, 0, HALF_INV_PHI, -0.5}, + {HALF_PHI, -0.5, 0, HALF_INV_PHI}, + {HALF_PHI, 0.5, 0, -HALF_INV_PHI}, + {HALF_PHI, 0, -HALF_INV_PHI, 0.5}, + {HALF_PHI, -HALF_INV_PHI, 0.5, 0}, + {HALF_PHI, 0, HALF_INV_PHI, 0.5}, + {HALF_PHI, HALF_INV_PHI, 0.5, 0}, + {HALF_PHI, 0.5, 0, HALF_INV_PHI}, + {0.5, HALF_PHI, -HALF_INV_PHI, 0}, + {0.5, HALF_PHI, HALF_INV_PHI, 0}, + {0.5, 0.5, 0.5, 0.5}, + {0.5, 0.5, 0.5, -0.5}, + {0.5, 0.5, -0.5, 0.5}, + {0.5, 0.5, -0.5, -0.5}, + {0.5, HALF_INV_PHI, 0, HALF_PHI}, + {0.5, HALF_INV_PHI, 0, -HALF_PHI}, + {0.5, 0, HALF_PHI, -HALF_INV_PHI}, + {0.5, 0, HALF_PHI, HALF_INV_PHI}, + {0.5, 0, -HALF_PHI, -HALF_INV_PHI}, + {0.5, 0, -HALF_PHI, HALF_INV_PHI}, + {0.5, -HALF_INV_PHI, 0, HALF_PHI}, + {0.5, -HALF_INV_PHI, 0, -HALF_PHI}, + {0.5, -0.5, 0.5, 0.5}, + {0.5, -0.5, 0.5, -0.5}, + {0.5, -0.5, -0.5, 0.5}, + {0.5, -0.5, -0.5, -0.5}, + {0.5, -HALF_PHI, -HALF_INV_PHI, 0}, + {0.5, -HALF_PHI, HALF_INV_PHI, 0}, + {HALF_INV_PHI, -HALF_PHI, 0, -0.5}, + {HALF_INV_PHI, 0, -0.5, -HALF_PHI}, + {HALF_INV_PHI, -0.5, -HALF_PHI, 0}, + {HALF_INV_PHI, 0, 0.5, -HALF_PHI}, + {HALF_INV_PHI, -HALF_PHI, 0, 0.5}, + {HALF_INV_PHI, 0.5, -HALF_PHI, 0}, + {HALF_INV_PHI, HALF_PHI, 0, -0.5}, + {HALF_INV_PHI, -0.5, HALF_PHI, 0}, + {HALF_INV_PHI, 0, -0.5, HALF_PHI}, + {HALF_INV_PHI, HALF_PHI, 0, 0.5}, + {HALF_INV_PHI, 0, 0.5, HALF_PHI}, + {HALF_INV_PHI, 0.5, HALF_PHI, 0}, + {0, 1, 0, 0}, + {0, HALF_PHI, -0.5, HALF_INV_PHI}, + {0, HALF_PHI, -0.5, -HALF_INV_PHI}, + {0, HALF_PHI, 0.5, HALF_INV_PHI}, + {0, HALF_PHI, 0.5, -HALF_INV_PHI}, + {0, 0.5, HALF_INV_PHI, -HALF_PHI}, + {0, 0.5, HALF_INV_PHI, HALF_PHI}, + {0, 0.5, -HALF_INV_PHI, -HALF_PHI}, + {0, 0.5, -HALF_INV_PHI, HALF_PHI}, + {0, HALF_INV_PHI, -HALF_PHI, 0.5}, + {0, HALF_INV_PHI, -HALF_PHI, -0.5}, + {0, HALF_INV_PHI, HALF_PHI, 0.5}, + {0, HALF_INV_PHI, HALF_PHI, -0.5}, + {0, 0, 1, 0}, + {0, 0, 0, 1} }; + +static void quat_rot(double* r, double* a, double* b) +{ + b[0] = (r[0] * a[0] - r[1] * a[1] - r[2] * a[2] - r[3] * a[3]); + b[1] = (r[0] * a[1] + r[1] * a[0] + r[2] * a[3] - r[3] * a[2]); + b[2] = (r[0] * a[2] - r[1] * a[3] + r[2] * a[0] + r[3] * a[1]); + b[3] = (r[0] * a[3] + r[1] * a[2] - r[2] * a[1] + r[3] * a[0]); +} + +static int rotate_quaternion_into_fundamental_zone(int num_generators, double (*generator)[4], double* q) +{ + double max = 0.0; + int i = 0, bi = -1; + for (i=0;i max) + { + max = t; + bi = i; + } + } + + double f[4]; + quat_rot(q, generator[bi], f); + memcpy(q, &f, 4 * sizeof(double)); + if (q[0] < 0) + { + q[0] = -q[0]; + q[1] = -q[1]; + q[2] = -q[2]; + q[3] = -q[3]; + } + + return bi; +} + +int rotate_quaternion_into_cubic_fundamental_zone(double* q) +{ + return rotate_quaternion_into_fundamental_zone(24, generator_cubic, q); +} + +int rotate_quaternion_into_diamond_cubic_fundamental_zone(double* q) +{ + return rotate_quaternion_into_fundamental_zone(12, generator_diamond_cubic, q); +} + +int rotate_quaternion_into_icosahedral_fundamental_zone(double* q) +{ + return rotate_quaternion_into_fundamental_zone(60, generator_icosahedral, q); +} + +int rotate_quaternion_into_hcp_fundamental_zone(double* q) +{ + return rotate_quaternion_into_fundamental_zone(6, generator_hcp, q); +} + +int rotate_quaternion_into_diamond_hexagonal_fundamental_zone(double* q) +{ + return rotate_quaternion_into_fundamental_zone(3, generator_diamond_hexagonal, q); +} + +double quat_dot(double* a, double* b) +{ + return a[0] * b[0] + + a[1] * b[1] + + a[2] * b[2] + + a[3] * b[3]; +} + +double quat_size(double* q) +{ + return sqrt(quat_dot(q, q)); +} + +void normalize_quaternion(double* q) +{ + double size = quat_size(q); + + q[0] /= size; + q[1] /= size; + q[2] /= size; + q[3] /= size; +} + +void rotation_matrix_to_quaternion(double* u, double* q) +{ + double r11 = u[0]; + double r12 = u[1]; + double r13 = u[2]; + double r21 = u[3]; + double r22 = u[4]; + double r23 = u[5]; + double r31 = u[6]; + double r32 = u[7]; + double r33 = u[8]; + + q[0] = (1.0 + r11 + r22 + r33) / 4.0; + q[1] = (1.0 + r11 - r22 - r33) / 4.0; + q[2] = (1.0 - r11 + r22 - r33) / 4.0; + q[3] = (1.0 - r11 - r22 + r33) / 4.0; + + q[0] = sqrt(MAX(0, q[0])); + q[1] = sqrt(MAX(0, q[1])); + q[2] = sqrt(MAX(0, q[2])); + q[3] = sqrt(MAX(0, q[3])); + + double m0 = MAX(q[0], q[1]); + double m1 = MAX(q[2], q[3]); + double max = MAX(m0, m1); + + int i = 0; + for (i=0;i<4;i++) + if (q[i] == max) + break; + + if (i == 0) + { + q[1] *= SIGN(r32 - r23); + q[2] *= SIGN(r13 - r31); + q[3] *= SIGN(r21 - r12); + } + else if (i == 1) + { + q[0] *= SIGN(r32 - r23); + q[2] *= SIGN(r21 + r12); + q[3] *= SIGN(r13 + r31); + } + else if (i == 2) + { + q[0] *= SIGN(r13 - r31); + q[1] *= SIGN(r21 + r12); + q[3] *= SIGN(r32 + r23); + } + else if (i == 3) + { + q[0] *= SIGN(r21 - r12); + q[1] *= SIGN(r31 + r13); + q[2] *= SIGN(r32 + r23); + } + + normalize_quaternion(q); +} + +void quaternion_to_rotation_matrix(double* q, double* u) +{ + double a = q[0]; + double b = q[1]; + double c = q[2]; + double d = q[3]; + + u[0] = a*a + b*b - c*c - d*d; + u[1] = 2*b*c - 2*a*d; + u[2] = 2*b*d + 2*a*c; + + u[3] = 2*b*c + 2*a*d; + u[4] = a*a - b*b + c*c - d*d; + u[5] = 2*c*d - 2*a*b; + + u[6] = 2*b*d - 2*a*c; + u[7] = 2*c*d + 2*a*b; + u[8] = a*a - b*b - c*c + d*d; +} + +double quat_quick_misorientation(double* q1, double* q2) +{ + double t = quat_dot(q1, q2); + t = MIN(1, MAX(-1, t)); + return 2 * t * t - 1; +} + +double quat_misorientation(double* q1, double* q2) +{ + return acos(quat_quick_misorientation(q1, q2)); +} + + +double quat_quick_disorientation_cubic(double* q0, double* q1) +{ + double qrot[4]; + double qinv[4] = {q0[0], -q0[1], -q0[2], -q0[3]}; + quat_rot(qinv, q1, qrot); + + rotate_quaternion_into_cubic_fundamental_zone(qrot); + double t = qrot[0]; + t = MIN(1, MAX(-1, t)); + return 2 * t * t - 1; +} + +double quat_disorientation_cubic(double* q0, double* q1) +{ + return acos(quat_quick_disorientation_cubic(q0, q1)); +} + +double quat_quick_disorientation_diamond_cubic(double* q0, double* q1) +{ + double qrot[4]; + double qinv[4] = {q0[0], -q0[1], -q0[2], -q0[3]}; + quat_rot(qinv, q1, qrot); + + rotate_quaternion_into_diamond_cubic_fundamental_zone(qrot); + double t = qrot[0]; + t = MIN(1, MAX(-1, t)); + return 2 * t * t - 1; +} + +double quat_disorientation_diamond_cubic(double* q0, double* q1) +{ + return acos(quat_quick_disorientation_diamond_cubic(q0, q1)); +} + +double quat_quick_disorientation_hcp(double* q0, double* q1) +{ + double qrot[4]; + double qinv[4] = {q0[0], -q0[1], -q0[2], -q0[3]}; + quat_rot(qinv, q1, qrot); + + rotate_quaternion_into_hcp_fundamental_zone(qrot); + double t = qrot[0]; + t = MIN(1, MAX(-1, t)); + return 2 * t * t - 1; +} + +double quat_disorientation_hcp(double* q0, double* q1) +{ + return acos(quat_quick_disorientation_hcp(q0, q1)); +} + +double quat_quick_disorientation_diamond_hexagonal(double* q0, double* q1) +{ + double qrot[4]; + double qinv[4] = {q0[0], -q0[1], -q0[2], -q0[3]}; + quat_rot(qinv, q1, qrot); + + rotate_quaternion_into_diamond_hexagonal_fundamental_zone(qrot); + double t = qrot[0]; + t = MIN(1, MAX(-1, t)); + return 2 * t * t - 1; +} + +double quat_disorientation_diamond_hexagonal(double* q0, double* q1) +{ + return acos(quat_quick_disorientation_diamond_hexagonal(q0, q1)); +} + +double quat_quick_disorientation_icosahedral(double* q0, double* q1) +{ + double qrot[4]; + double qinv[4] = {q0[0], -q0[1], -q0[2], -q0[3]}; + quat_rot(qinv, q1, qrot); + + rotate_quaternion_into_icosahedral_fundamental_zone(qrot); + double t = qrot[0]; + t = MIN(1, MAX(-1, t)); + return 2 * t * t - 1; +} + +double quat_disorientation_icosahedral(double* q0, double* q1) +{ + return acos(quat_quick_disorientation_icosahedral(q0, q1)); +} + diff --git a/src/USER-PTM/quat.h b/src/USER-PTM/quat.h new file mode 100644 index 0000000000..725086322c --- /dev/null +++ b/src/USER-PTM/quat.h @@ -0,0 +1,32 @@ +#ifndef QUAT_H +#define QUAT_H + +int rotate_quaternion_into_cubic_fundamental_zone(double* q); +int rotate_quaternion_into_diamond_cubic_fundamental_zone(double* q); +int rotate_quaternion_into_icosahedral_fundamental_zone(double* q); +int rotate_quaternion_into_hcp_fundamental_zone(double* q); +int rotate_quaternion_into_diamond_hexagonal_fundamental_zone(double* q); + +void normalize_quaternion(double* q); +void quaternion_to_rotation_matrix(double* q, double* U); +void rotation_matrix_to_quaternion(double* u, double* q); +double quat_dot(double* a, double* b); +double quat_quick_misorientation(double* q1, double* q2); +double quat_misorientation(double* q1, double* q2); + +double quat_quick_disorientation_cubic(double* q0, double* q1); +double quat_disorientation_cubic(double* q0, double* q1); +double quat_quick_disorientation_diamond_cubic(double* q0, double* q1); +double quat_disorientation_diamond_cubic(double* q0, double* q1); +double quat_quick_disorientation_hcp(double* q0, double* q1); +double quat_disorientation_hcp(double* q0, double* q1); +double quat_quick_disorientation_diamond_hexagonal(double* q0, double* q1); +double quat_disorientation_diamond_hexagonal(double* q0, double* q1); +double quat_quick_disorientation_icosahedral(double* q0, double* q1); +double quat_disorientation_icosahedral(double* q0, double* q1); + +#endif + + + + diff --git a/src/USER-PTM/structure_matcher.cpp b/src/USER-PTM/structure_matcher.cpp new file mode 100644 index 0000000000..dad8e3599a --- /dev/null +++ b/src/USER-PTM/structure_matcher.cpp @@ -0,0 +1,294 @@ +#include +#include +#include +#include +#include +#include +#include +#include "convex_hull_incremental.h" +#include "canonical_coloured.h" +#include "graph_data.h" +#include "graph_tools.h" +#include "normalize_vertices.h" +#include "polar.h" +#include "structure_matcher.h" +#include "ptm_constants.h" + + +static double calc_rmsd(int num_points, const double (*ideal_points)[3], double (*normalized)[3], int8_t* mapping, + double G1, double G2, double E0, double* q, double* p_scale) +{ + double A0[9]; + InnerProduct(A0, num_points, ideal_points, normalized, mapping); + + double nrmsdsq, rot[9]; + FastCalcRMSDAndRotation(A0, E0, &nrmsdsq, q, rot); + + double k0 = 0; + for (int i=0;inum_nbrs + 1; + const double (*ideal_points)[3] = s->points; + int8_t inverse_labelling[PTM_MAX_POINTS]; + int8_t mapping[PTM_MAX_POINTS]; + + for (int i=0; inum_graphs;i++) + { + if (hash != s->graphs[i].hash) + continue; + + graph_t* gref = &s->graphs[i]; + for (int j = 0;jnum_automorphisms;j++) + { + for (int k=0;kautomorphism_index + j][k]] = inverse_labelling[ gref->canonical_labelling[k] ]; + + double q[4], scale = 0; + double rmsd = calc_rmsd(num_points, ideal_points, normalized, mapping, G1, G2, E0, q, &scale); + if (rmsd < res->rmsd) + { + res->rmsd = rmsd; + res->scale = scale; + res->ref_struct = s; + memcpy(res->q, q, 4 * sizeof(double)); + memcpy(res->mapping, mapping, sizeof(int8_t) * num_points); + } + } + } +} + +int match_general(const refdata_t* s, double (*ch_points)[3], double (*points)[3], convexhull_t* ch, result_t* res) +{ + int8_t degree[PTM_MAX_NBRS]; + int8_t facets[PTM_MAX_FACETS][3]; + + int ret = get_convex_hull(s->num_nbrs + 1, (const double (*)[3])ch_points, ch, facets); + ch->ok = ret >= 0; + if (ret != 0) + return PTM_NO_ERROR; + + if (ch->num_facets != s->num_facets) + return PTM_NO_ERROR; //incorrect number of facets in convex hull + + int max_degree = graph_degree(s->num_facets, facets, s->num_nbrs, degree); + if (max_degree > s->max_degree) + return PTM_NO_ERROR; + + if (s->type == PTM_MATCH_SC) + for (int i = 0;inum_nbrs;i++) + if (degree[i] != 4) + return PTM_NO_ERROR; + + double normalized[PTM_MAX_POINTS][3]; + subtract_barycentre(s->num_nbrs + 1, points, normalized); + + int8_t code[2 * PTM_MAX_EDGES]; + int8_t colours[PTM_MAX_POINTS] = {0}; + int8_t canonical_labelling[PTM_MAX_POINTS]; + uint64_t hash = 0; + ret = canonical_form_coloured(s->num_facets, facets, s->num_nbrs, degree, colours, canonical_labelling, &code[0], &hash); + if (ret != PTM_NO_ERROR) + return ret; + + check_graphs(s, hash, canonical_labelling, normalized, res); + return PTM_NO_ERROR; +} + +int match_fcc_hcp_ico(double (*ch_points)[3], double (*points)[3], int32_t flags, convexhull_t* ch, result_t* res) +{ + int num_nbrs = structure_fcc.num_nbrs; + int num_facets = structure_fcc.num_facets; + int max_degree = structure_fcc.max_degree; + + int8_t degree[PTM_MAX_NBRS]; + int8_t facets[PTM_MAX_FACETS][3]; + + int ret = get_convex_hull(num_nbrs + 1, (const double (*)[3])ch_points, ch, facets); + ch->ok = ret >= 0; + if (ret != 0) + return PTM_NO_ERROR; + + if (ch->num_facets != num_facets) + return PTM_NO_ERROR; //incorrect number of facets in convex hull + + int _max_degree = graph_degree(num_facets, facets, num_nbrs, degree); + if (_max_degree > max_degree) + return PTM_NO_ERROR; + + double normalized[PTM_MAX_POINTS][3]; + subtract_barycentre(num_nbrs + 1, points, normalized); + + int8_t code[2 * PTM_MAX_EDGES]; + int8_t colours[PTM_MAX_POINTS] = {0}; + int8_t canonical_labelling[PTM_MAX_POINTS]; + uint64_t hash = 0; + ret = canonical_form_coloured(num_facets, facets, num_nbrs, degree, colours, canonical_labelling, &code[0], &hash); + if (ret != PTM_NO_ERROR) + return ret; + + if (flags & PTM_CHECK_FCC) check_graphs(&structure_fcc, hash, canonical_labelling, normalized, res); + if (flags & PTM_CHECK_HCP) check_graphs(&structure_hcp, hash, canonical_labelling, normalized, res); + if (flags & PTM_CHECK_ICO) check_graphs(&structure_ico, hash, canonical_labelling, normalized, res); + return PTM_NO_ERROR; +} + +int match_dcub_dhex(double (*ch_points)[3], double (*points)[3], int32_t flags, convexhull_t* ch, result_t* res) +{ + int num_nbrs = structure_dcub.num_nbrs; + int num_facets = structure_fcc.num_facets; + int max_degree = structure_dcub.max_degree; + + + int8_t facets[PTM_MAX_FACETS][3]; + int ret = get_convex_hull(num_nbrs + 1, (const double (*)[3])ch_points, ch, facets); + ch->ok = ret >= 0; + if (ret != 0) + return PTM_NO_ERROR; + + //check for facets with multiple inner atoms + bool inverted[4] = {false, false, false, false}; + for (int i=0;inum_facets;i++) + { + int n = 0; + for (int j=0;j<3;j++) + { + if (facets[i][j] <= 3) + { + inverted[facets[i][j]] = true; + n++; + } + } + if (n > 1) + return PTM_NO_ERROR; + } + + int num_inverted = 0; + for (int i=0;i<4;i++) + num_inverted += inverted[i] ? 1 : 0; + + if (ch->num_facets != num_facets + 2 * num_inverted) + return PTM_NO_ERROR; //incorrect number of facets in convex hull + + int8_t degree[PTM_MAX_NBRS]; + int _max_degree = graph_degree(num_facets, facets, num_nbrs, degree); + if (_max_degree > max_degree) + return PTM_NO_ERROR; + + int num_found = 0; + int8_t toadd[4][3]; + for (int i=0;inum_facets;i++) + { + int a = facets[i][0]; + int b = facets[i][1]; + int c = facets[i][2]; + if (a <= 3 || b <= 3 || c <= 3) + continue; + + int i0 = (a - 4) / 3; + int i1 = (b - 4) / 3; + int i2 = (c - 4) / 3; + + if (i0 == i1 && i0 == i2) + { + if (num_found + num_inverted >= 4) + return PTM_NO_ERROR; + + toadd[num_found][0] = a; + toadd[num_found][1] = b; + toadd[num_found][2] = c; + num_found++; + + memcpy(&facets[i], &facets[ch->num_facets - 1], 3 * sizeof(int8_t)); + ch->num_facets--; + i--; + } + } + + if (num_found + num_inverted != 4) + return PTM_NO_ERROR; + + for (int i=0;inum_facets][0] = i0; + facets[ch->num_facets][1] = b; + facets[ch->num_facets][2] = c; + ch->num_facets++; + + facets[ch->num_facets][0] = a; + facets[ch->num_facets][1] = i0; + facets[ch->num_facets][2] = c; + ch->num_facets++; + + facets[ch->num_facets][0] = a; + facets[ch->num_facets][1] = b; + facets[ch->num_facets][2] = i0; + ch->num_facets++; + } + + _max_degree = graph_degree(ch->num_facets, facets, num_nbrs, degree); + if (_max_degree > max_degree) + return PTM_NO_ERROR; + + double normalized[PTM_MAX_POINTS][3]; + subtract_barycentre(num_nbrs + 1, points, normalized); + + int8_t code[2 * PTM_MAX_EDGES]; + int8_t colours[PTM_MAX_POINTS] = {1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}; + int8_t canonical_labelling[PTM_MAX_POINTS]; + uint64_t hash = 0; + ret = canonical_form_coloured(ch->num_facets, facets, num_nbrs, degree, colours, canonical_labelling, &code[0], &hash); + if (ret != PTM_NO_ERROR) + return ret; + + if (flags & PTM_CHECK_DCUB) check_graphs(&structure_dcub, hash, canonical_labelling, normalized, res); + if (flags & PTM_CHECK_DHEX) check_graphs(&structure_dhex, hash, canonical_labelling, normalized, res); + + return PTM_NO_ERROR; +} + diff --git a/src/USER-PTM/structure_matcher.h b/src/USER-PTM/structure_matcher.h new file mode 100644 index 0000000000..25e80a94e1 --- /dev/null +++ b/src/USER-PTM/structure_matcher.h @@ -0,0 +1,21 @@ +#ifndef STRUCTURE_MATCHER_H +#define STRUCTURE_MATCHER_H + +#include "initialize_data.h" +#include "ptm_constants.h" + +typedef struct +{ + double rmsd; + double scale; + double q[4]; //rotation in quaternion form (rigid body transformation) + int8_t mapping[PTM_MAX_POINTS]; + const refdata_t* ref_struct; +} result_t; + +int match_general(const refdata_t* s, double (*ch_points)[3], double (*points)[3], convexhull_t* ch, result_t* res); +int match_fcc_hcp_ico(double (*ch_points)[3], double (*points)[3], int32_t flags, convexhull_t* ch, result_t* res); +int match_dcub_dhex(double (*ch_points)[3], double (*points)[3], int32_t flags, convexhull_t* ch, result_t* res); + +#endif + From 83b6d6ae960ce0e7f8edb32d95edb3540ae5f764 Mon Sep 17 00:00:00 2001 From: oywg11 Date: Wed, 12 Sep 2018 17:47:16 +0300 Subject: [PATCH 169/302] small modifications of potential #839 --- doc/src/pair_coul_shield.txt | 8 ++++- doc/src/pair_ilp_graphene_hbn.txt | 20 ++++++----- doc/src/pair_kolmogorov_crespi_full.txt | 34 +++++++++++-------- potentials/BNCH.ILP | 2 +- potentials/CH.KC | 4 +-- potentials/CH_taper.KC | 10 ++++++ src/USER-MISC/pair_ilp_graphene_hbn.cpp | 27 +++++++-------- src/USER-MISC/pair_kolmogorov_crespi_full.cpp | 27 +++++++-------- 8 files changed, 76 insertions(+), 56 deletions(-) create mode 100644 potentials/CH_taper.KC diff --git a/doc/src/pair_coul_shield.txt b/doc/src/pair_coul_shield.txt index 19f69688d5..517cb47740 100644 --- a/doc/src/pair_coul_shield.txt +++ b/doc/src/pair_coul_shield.txt @@ -38,7 +38,7 @@ charge and molecule ID information is included. Where Tap(r_ij) is the taper function which provides a continuous cutoff (up to third derivative) for inter-atomic separations larger than r_c -"(Maaravi)"_#Maaravi1. Here {lambda} is the shielding parameter that +"(Leven1)"_#Leven2, "(Leven2)"_#Leven3 and "(Maaravi)"_#Maaravi1. Here {lambda} is the shielding parameter that eliminates the short-range singularity of the classical mono-polar electrostatic interaction expression "(Maaravi)"_#Maaravi1. @@ -82,5 +82,11 @@ LAMMPS"_Section_start.html#start_2_3 section for more info. :line +:link(Leven2) +[(Leven)] I. Leven, I. Azuri, L. Kronik and O. Hod, J. Chem. Phys. 140, 104106 (2014). + +:link(Leven3) +[(Leven)] I. Leven et al, J. Chem.Theory Comput. 12, 2896-905 (2016). + :link(Maaravi1) [(Maaravi)] T. Maaravi et al, J. Phys. Chem. C 121, 22826-22835 (2017). diff --git a/doc/src/pair_ilp_graphene_hbn.txt b/doc/src/pair_ilp_graphene_hbn.txt index 127b8e9103..dd175b3b4f 100644 --- a/doc/src/pair_ilp_graphene_hbn.txt +++ b/doc/src/pair_ilp_graphene_hbn.txt @@ -31,7 +31,7 @@ pair_coeff 2 2 coul/shield 0.69 :pre [Description:] The {ilp/graphene/hbn} style computes the registry-dependent interlayer -potential (ILP) potential as described in "(Leven)"_#Leven and +potential (ILP) potential as described in "(Leven1)"_#Leven1, "(Leven2)"_#Leven and "(Maaravi)"_#Maaravi2. The normals are calculated in the way as described in "(Kolmogorov)"_#Kolmogorov2. @@ -40,7 +40,7 @@ in "(Kolmogorov)"_#Kolmogorov2. Where Tap(r_ij) is the taper function which provides a continuous cutoff (up to third derivative) for interatomic separations larger than r_c "(Maaravi)"_#Maaravi2. The definitons of each parameter in the above -equation can be found in "(Leven)"_#Leven and "(Maaravi)"_#Maaravi2. +equation can be found in "(Leven)"_#Leven1 and "(Maaravi)"_#Maaravi2. It is important to include all the pairs to build the neighbor list for calculating the normals. @@ -62,9 +62,10 @@ are fitted with taper function by setting the cutoff equal to 16.0 Angstrom. Using different cutoff or taper function should be careful. NOTE: Two new sets of parameters of ILP for two-dimensional hexagonal Materials are presented in "(Ouyang)"_#Ouyang. -These parameters provide a good description in both short- and long-range interaction regime. -While the old ILP parameters published in "(Leven)"_#Leven and "(Maaravi)"_#Maaravi2 are only suitable for long-range interaction regime. -This feature is essential for simulations in high pressure regime (i.e., interlayer distance smaller than the equilibrium distance). +These parameters provide a good description in both short- and long-range interaction regimes. +While the old ILP parameters published in "(Leven)"_#Leven and "(Maaravi)"_#Maaravi2 are +only suitable for long-range interaction regime. This feature is essential for simulations +in high pressure regime (i.e., the interlayer distance is smaller than the equilibrium distance). The benchmark tests and comparison of these parameters can be found in "(Ouyang)"_#Ouyang. This potential must be used in combination with hybrid/overlay. @@ -110,14 +111,17 @@ units, if your simulation does not use {metal} units. :line +:link(Leven1) +[(Leven)] I. Leven, I. Azuri, L. Kronik and O. Hod, J. Chem. Phys. 140, 104106 (2014). + :link(Leven) -[(Leven)] I. Leven et al, J. Chem.Theory Comput. 12, 2896-905 (2016) +[(Leven)] I. Leven et al, J. Chem.Theory Comput. 12, 2896-905 (2016). :link(Maaravi2) [(Maaravi)] T. Maaravi et al, J. Phys. Chem. C 121, 22826-22835 (2017). :link(Kolmogorov2) -[(Kolmogorov)] A. N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005) +[(Kolmogorov)] A. N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005). :link(Ouyang) -[(Ouyang)] W. Ouyang, D. Mandelli, M. Urbakh, O. Hod, arXiv:1806.09555 (2018). +[(Ouyang)] W. Ouyang, D. Mandelli, M. Urbakh and O. Hod, Nano Lett. 18, 6009-6016 (2018). diff --git a/doc/src/pair_kolmogorov_crespi_full.txt b/doc/src/pair_kolmogorov_crespi_full.txt index 10bb8a5224..09f0aaaed0 100644 --- a/doc/src/pair_kolmogorov_crespi_full.txt +++ b/doc/src/pair_kolmogorov_crespi_full.txt @@ -19,11 +19,11 @@ tap_flag = 0/1 to turn off/on the taper function pair_style hybrid/overlay kolmogorov/crespi/full 20.0 0 pair_coeff * * none -pair_coeff * * kolmogorov/crespi/full CC.KC C C :pre +pair_coeff * * kolmogorov/crespi/full CH.KC C C :pre -pair_style hybrid/overlay rebo kolmogorov/crespi/full 16.0 -pair_coeff * * rebo CH.airebo C C -pair_coeff * * kolmogorov/crespi/full CC.KC C C :pre +pair_style hybrid/overlay rebo kolmogorov/crespi/full 16.0 1 +pair_coeff * * rebo CH.airebo C H +pair_coeff * * kolmogorov/crespi/full CH_taper.KC C H :pre [Description:] @@ -38,24 +38,30 @@ forces and to include all the pairs to build the neighbor list for calculating the normals. Energies are shifted so that they go continuously to zero at the cutoff assuming that the exponential part of {Vij} (first term) decays sufficiently fast. This shift is achieved by -the last term in the equation for {Vij} above. +the last term in the equation for {Vij} above. This is essential only +when the tapper function is turned off. The formula of taper function +can be found in pair style "ilp/graphene/hbn"_pair_ilp_graphene_hbn.html. NOTE: This potential is intended for interactions between two different graphene layers. Therefore, to avoid interaction within the same layers, each layer should have a separate molecule id and is recommended to use "full" atom style in the data file. -The parameter file (e.g. CC.KC), is intended for use with {metal} +The parameter file (e.g. CH.KC), is intended for use with {metal} "units"_units.html, with energies in meV. Two additional parameters, {S}, and {rcut} are included in the parameter file. {S} is designed to facilitate scaling of energies. {rcut} is designed to build the neighbor list for calculating the normals for each atom pair. -NOTE: A new set of parameters of KC potential for hydrocarbons (CH.KC) is presented in "(Ouyang)"_#Ouyang. -The parameters in CH.KC provides a good description in both short- and long-range interaction regime. -While the original parameters (CC.KC) published in "(Kolmogorov)"_#Kolmogorov1 are only suitable for long-range interaction regime. -This feature is essential for simulations in high pressure regime (i.e., interlayer distance smaller than the equilibrium distance). -The benchmark tests and comparison of these parameters can be found in "(Ouyang)"_#Ouyang. +NOTE: Two new sets of parameters of KC potential for hydrocarbons, CH.KC (without the taper function) +and CH_taper.KC (with the taper function) are presented in "(Ouyang)"_#Ouyang1. +The energy for the KC potential with the taper function goes continuously to zero at the cutoff. +The parameters in both CH.KC and CH_taper.KC provide a good description in +both short- and long-range interaction regimes. While the original parameters (CC.KC) +published in "(Kolmogorov)"_#Kolmogorov1 are only suitable for long-range interaction regime. +This feature is essential for simulations in high pressure regime +(i.e., the interlayer distance is smaller than the equilibrium distance). +The benchmark tests and comparison of these parameters can be found in "(Ouyang)"_#Ouyang1. This potential must be used in combination with hybrid/overlay. Other interactions can be set to zero using pair_style {none}. @@ -81,7 +87,7 @@ LAMMPS"_Section_start.html#start_3 section for more info. This pair potential requires the newton setting to be {on} for pair interactions. -The CC.KC potential file provided with LAMMPS (see the potentials +The CH.KC potential file provided with LAMMPS (see the potentials folder) are parameterized for metal units. You can use this potential with any LAMMPS units, but you would need to create your own custom CC.KC potential file with all coefficients converted to the appropriate @@ -102,5 +108,5 @@ units. :link(Kolmogorov1) [(Kolmogorov)] A. N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005) -:link(Ouyang) -[(Ouyang)] W. Ouyang, D. Mandelli, M. Urbakh, O. Hod, arXiv:1806.09555 (2018). +:link(Ouyang1) +[(Ouyang)] W. Ouyang, D. Mandelli, M. Urbakh and O. Hod, Nano Lett. 18, 6009-6016 (2018). diff --git a/potentials/BNCH.ILP b/potentials/BNCH.ILP index 3f38b5e35a..6ca56ca186 100644 --- a/potentials/BNCH.ILP +++ b/potentials/BNCH.ILP @@ -1,6 +1,6 @@ # Interlayer Potential (ILP) for graphene/graphene, graphene/hBN and hBN/hBN junctions # -# Cite as Wengen Ouyang,Davide Mandelli, Michael Urbakh, Oded Hod, arXiv:1806.09555 (2018). +# Cite as W. Ouyang, D. Mandelli, M. Urbakh and O. Hod, Nano Letters 18, 6009-6016 (2018). # # ----------------- Repulsion Potential ------------------++++++++++++++ Vdw Potential ++++++++++++++++************ # beta(A) alpha delta(A) epsilon(meV) C(meV) d sR reff(A) C6(meV*A^6) S rcut diff --git a/potentials/CH.KC b/potentials/CH.KC index 2005472395..1b4f7503ea 100644 --- a/potentials/CH.KC +++ b/potentials/CH.KC @@ -1,6 +1,6 @@ -# Refined parameters for Kolmogorov-Crespi Potential +# Refined parameters for Kolmogorov-Crespi Potential without taper function # -# Cite as Wengen Ouyang,Davide Mandelli, Michael Urbakh, Oded Hod, arXiv:1806.09555 (2018). +# Cite as W. Ouyang, D. Mandelli, M. Urbakh and O. Hod, Nano Letters 18, 6009-6016 (2018). # # z0 C0 C2 C4 C delta lambda A S rcut C C 3.328819 21.847167 12.060173 4.711099 6.678908e-4 0.7718101 3.143921 12.660270 1.0 2.0 diff --git a/potentials/CH_taper.KC b/potentials/CH_taper.KC new file mode 100644 index 0000000000..0f08b2e6dd --- /dev/null +++ b/potentials/CH_taper.KC @@ -0,0 +1,10 @@ +# Refined parameters for Kolmogorov-Crespi Potential with taper function +# +# Cite as W. Ouyang, D. Mandelli, M. Urbakh and O. Hod, Nano Letters 18, 6009-6016 (2018). +# +# z0 C0 C2 C4 C delta lambda A S rcut +C C 3.416084 20.021583 10.9055107 4.2756354 1.0010836E-2 0.8447122 2.9360584 14.3132588 1.0 2.0 +C H 2.849054 72.557245 1.0164169E-2 65.923312 8.7962504E-5 0.3349237 3.0402632 14.7533201 1.0 1.5 +H H 2.187478 3.915802E-5 5.0896431E-5 3.6657827 1.5373722446 0.9633581 0.4249989 1.570737E-4 1.0 1.2 +H C 2.849054 72.557245 1.0164169E-2 65.923312 8.7962504E-5 0.3349237 3.0402632 14.7533201 1.0 2.2 + diff --git a/src/USER-MISC/pair_ilp_graphene_hbn.cpp b/src/USER-MISC/pair_ilp_graphene_hbn.cpp index 30ee2e7a5a..7c637e4faf 100644 --- a/src/USER-MISC/pair_ilp_graphene_hbn.cpp +++ b/src/USER-MISC/pair_ilp_graphene_hbn.cpp @@ -249,11 +249,9 @@ void PairILPGrapheneHBN::compute(int eflag, int vflag) f[i][0] += fkcx - fprod1[0]*Tap; f[i][1] += fkcy - fprod1[1]*Tap; f[i][2] += fkcz - fprod1[2]*Tap; - if (newton_pair || j < nlocal) { - f[j][0] -= fkcx + fprod2[0]*Tap; - f[j][1] -= fkcy + fprod2[1]*Tap; - f[j][2] -= fkcz + fprod2[2]*Tap; - } + f[j][0] -= fkcx + fprod2[0]*Tap; + f[j][1] -= fkcy + fprod2[1]*Tap; + f[j][2] -= fkcz + fprod2[2]*Tap; // calculate the forces acted on the neighbors of atom i from atom j ILP_neighs_i = ILP_firstneigh[i]; @@ -274,15 +272,13 @@ void PairILPGrapheneHBN::compute(int eflag, int vflag) for (ll = 0; ll < ILP_numneigh[j]; ll++) { l = ILP_neighs_j[ll]; if (l == j) continue; - if (newton_pair || l < nlocal) { - // derivatives of the product of rji and nj respect to rl, l=0,1,2, where atom l is the neighbors of atom j - dprodnorm2[0] = dnormal[0][0][ll][j]*delx + dnormal[1][0][ll][j]*dely + dnormal[2][0][ll][j]*delz; - dprodnorm2[1] = dnormal[0][1][ll][j]*delx + dnormal[1][1][ll][j]*dely + dnormal[2][1][ll][j]*delz; - dprodnorm2[2] = dnormal[0][2][ll][j]*delx + dnormal[1][2][ll][j]*dely + dnormal[2][2][ll][j]*delz; - f[l][0] += (-prodnorm2*dprodnorm2[0]*fpair2)*Tap; - f[l][1] += (-prodnorm2*dprodnorm2[1]*fpair2)*Tap; - f[l][2] += (-prodnorm2*dprodnorm2[2]*fpair2)*Tap; - } + // derivatives of the product of rji and nj respect to rl, l=0,1,2, where atom l is the neighbors of atom j + dprodnorm2[0] = dnormal[0][0][ll][j]*delx + dnormal[1][0][ll][j]*dely + dnormal[2][0][ll][j]*delz; + dprodnorm2[1] = dnormal[0][1][ll][j]*delx + dnormal[1][1][ll][j]*dely + dnormal[2][1][ll][j]*delz; + dprodnorm2[2] = dnormal[0][2][ll][j]*delx + dnormal[1][2][ll][j]*dely + dnormal[2][2][ll][j]*delz; + f[l][0] += (-prodnorm2*dprodnorm2[0]*fpair2)*Tap; + f[l][1] += (-prodnorm2*dprodnorm2[1]*fpair2)*Tap; + f[l][2] += (-prodnorm2*dprodnorm2[2]*fpair2)*Tap; } if (eflag) { @@ -729,7 +725,8 @@ void PairILPGrapheneHBN::ILP_neigh() ILP_firstneigh[i] = neighptr; ILP_numneigh[i] = n; - if (n > 3) error->all(FLERR,"There are too many neighbors for some atoms, please reduce the cutoff for normals"); + if (n == 0) error->all(FLERR,"Could not build neighbor list to calculate normals, please check your configuration"); + if (n > 3) error->all(FLERR,"There are too many neighbors for some atoms, please check your configuration"); ipage->vgot(n); if (ipage->status()) error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); diff --git a/src/USER-MISC/pair_kolmogorov_crespi_full.cpp b/src/USER-MISC/pair_kolmogorov_crespi_full.cpp index be0e81d48d..93a2376c33 100644 --- a/src/USER-MISC/pair_kolmogorov_crespi_full.cpp +++ b/src/USER-MISC/pair_kolmogorov_crespi_full.cpp @@ -249,11 +249,9 @@ void PairKolmogorovCrespiFull::compute(int eflag, int vflag) f[i][0] += fkcx - fprod1[0]*Tap; f[i][1] += fkcy - fprod1[1]*Tap; f[i][2] += fkcz - fprod1[2]*Tap; - if (newton_pair || j < nlocal) { - f[j][0] -= fkcx + fprod2[0]*Tap; - f[j][1] -= fkcy + fprod2[1]*Tap; - f[j][2] -= fkcz + fprod2[2]*Tap; - } + f[j][0] -= fkcx + fprod2[0]*Tap; + f[j][1] -= fkcy + fprod2[1]*Tap; + f[j][2] -= fkcz + fprod2[2]*Tap; // calculate the forces acted on the neighbors of atom i from atom j KC_neighs_i = KC_firstneigh[i]; @@ -274,15 +272,13 @@ void PairKolmogorovCrespiFull::compute(int eflag, int vflag) for (ll = 0; ll < KC_numneigh[j]; ll++) { l = KC_neighs_j[ll]; if (l == j) continue; - if (newton_pair || l < nlocal) { - // derivatives of the product of rji and nj respect to rl, l=0,1,2, where atom l is the neighbors of atom j - dprodnorm2[0] = dnormal[0][0][ll][j]*delx + dnormal[1][0][ll][j]*dely + dnormal[2][0][ll][j]*delz; - dprodnorm2[1] = dnormal[0][1][ll][j]*delx + dnormal[1][1][ll][j]*dely + dnormal[2][1][ll][j]*delz; - dprodnorm2[2] = dnormal[0][2][ll][j]*delx + dnormal[1][2][ll][j]*dely + dnormal[2][2][ll][j]*delz; - f[l][0] += (-prodnorm2*dprodnorm2[0]*fpair2)*Tap; - f[l][1] += (-prodnorm2*dprodnorm2[1]*fpair2)*Tap; - f[l][2] += (-prodnorm2*dprodnorm2[2]*fpair2)*Tap; - } + // derivatives of the product of rji and nj respect to rl, l=0,1,2, where atom l is the neighbors of atom j + dprodnorm2[0] = dnormal[0][0][ll][j]*delx + dnormal[1][0][ll][j]*dely + dnormal[2][0][ll][j]*delz; + dprodnorm2[1] = dnormal[0][1][ll][j]*delx + dnormal[1][1][ll][j]*dely + dnormal[2][1][ll][j]*delz; + dprodnorm2[2] = dnormal[0][2][ll][j]*delx + dnormal[1][2][ll][j]*dely + dnormal[2][2][ll][j]*delz; + f[l][0] += (-prodnorm2*dprodnorm2[0]*fpair2)*Tap; + f[l][1] += (-prodnorm2*dprodnorm2[1]*fpair2)*Tap; + f[l][2] += (-prodnorm2*dprodnorm2[2]*fpair2)*Tap; } if (eflag) { @@ -734,7 +730,8 @@ void PairKolmogorovCrespiFull::KC_neigh() KC_firstneigh[i] = neighptr; KC_numneigh[i] = n; - if (n > 3) error->all(FLERR,"There are too many neighbors for some atoms, please reduce the cutoff for normals"); + if (n == 0) error->all(FLERR,"Could not build neighbor list to calculate normals, please check your configuration"); + if (n > 3) error->all(FLERR,"There are too many neighbors for some atoms, please check your configuration"); ipage->vgot(n); if (ipage->status()) error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); From 01beaf38a1162c0d81ad9591b490782b73997179 Mon Sep 17 00:00:00 2001 From: oywg11 Date: Wed, 12 Sep 2018 21:51:57 +0300 Subject: [PATCH 170/302] small modifications for potential #839 --- doc/src/pair_coul_shield.txt | 10 +++++----- doc/src/pair_ilp_graphene_hbn.txt | 10 +++++----- 2 files changed, 10 insertions(+), 10 deletions(-) diff --git a/doc/src/pair_coul_shield.txt b/doc/src/pair_coul_shield.txt index 517cb47740..c6eb7bf7a1 100644 --- a/doc/src/pair_coul_shield.txt +++ b/doc/src/pair_coul_shield.txt @@ -38,7 +38,7 @@ charge and molecule ID information is included. Where Tap(r_ij) is the taper function which provides a continuous cutoff (up to third derivative) for inter-atomic separations larger than r_c -"(Leven1)"_#Leven2, "(Leven2)"_#Leven3 and "(Maaravi)"_#Maaravi1. Here {lambda} is the shielding parameter that +"(Leven1)"_#Leven3, "(Leven2)"_#Leven4 and "(Maaravi)"_#Maaravi1. Here {lambda} is the shielding parameter that eliminates the short-range singularity of the classical mono-polar electrostatic interaction expression "(Maaravi)"_#Maaravi1. @@ -82,11 +82,11 @@ LAMMPS"_Section_start.html#start_2_3 section for more info. :line -:link(Leven2) -[(Leven)] I. Leven, I. Azuri, L. Kronik and O. Hod, J. Chem. Phys. 140, 104106 (2014). - :link(Leven3) -[(Leven)] I. Leven et al, J. Chem.Theory Comput. 12, 2896-905 (2016). +[(Leven1)] I. Leven, I. Azuri, L. Kronik and O. Hod, J. Chem. Phys. 140, 104106 (2014). + +:link(Leven4) +[(Leven2)] I. Leven et al, J. Chem.Theory Comput. 12, 2896-905 (2016). :link(Maaravi1) [(Maaravi)] T. Maaravi et al, J. Phys. Chem. C 121, 22826-22835 (2017). diff --git a/doc/src/pair_ilp_graphene_hbn.txt b/doc/src/pair_ilp_graphene_hbn.txt index dd175b3b4f..d5d8a29fbe 100644 --- a/doc/src/pair_ilp_graphene_hbn.txt +++ b/doc/src/pair_ilp_graphene_hbn.txt @@ -31,7 +31,7 @@ pair_coeff 2 2 coul/shield 0.69 :pre [Description:] The {ilp/graphene/hbn} style computes the registry-dependent interlayer -potential (ILP) potential as described in "(Leven1)"_#Leven1, "(Leven2)"_#Leven and +potential (ILP) potential as described in "(Leven1)"_#Leven1, "(Leven2)"_#Leven2 and "(Maaravi)"_#Maaravi2. The normals are calculated in the way as described in "(Kolmogorov)"_#Kolmogorov2. @@ -40,7 +40,7 @@ in "(Kolmogorov)"_#Kolmogorov2. Where Tap(r_ij) is the taper function which provides a continuous cutoff (up to third derivative) for interatomic separations larger than r_c "(Maaravi)"_#Maaravi2. The definitons of each parameter in the above -equation can be found in "(Leven)"_#Leven1 and "(Maaravi)"_#Maaravi2. +equation can be found in "(Leven1)"_#Leven1 and "(Maaravi)"_#Maaravi2. It is important to include all the pairs to build the neighbor list for calculating the normals. @@ -112,10 +112,10 @@ units, if your simulation does not use {metal} units. :line :link(Leven1) -[(Leven)] I. Leven, I. Azuri, L. Kronik and O. Hod, J. Chem. Phys. 140, 104106 (2014). +[(Leven1)] I. Leven, I. Azuri, L. Kronik and O. Hod, J. Chem. Phys. 140, 104106 (2014). -:link(Leven) -[(Leven)] I. Leven et al, J. Chem.Theory Comput. 12, 2896-905 (2016). +:link(Leven2) +[(Leven2)] I. Leven et al, J. Chem.Theory Comput. 12, 2896-905 (2016). :link(Maaravi2) [(Maaravi)] T. Maaravi et al, J. Phys. Chem. C 121, 22826-22835 (2017). From e14db00d522bbc7802a648c1844c44ded1417fa1 Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Fri, 14 Sep 2018 17:31:33 -0600 Subject: [PATCH 171/302] doc link adjustments --- doc/src/Howto_nemd.txt | 10 +++++----- doc/src/Howto_thermostat.txt | 10 +++++----- doc/src/Howto_viscosity.txt | 10 +++++----- doc/src/fix_nvt_sllod.txt | 10 +++++----- 4 files changed, 20 insertions(+), 20 deletions(-) diff --git a/doc/src/Howto_nemd.txt b/doc/src/Howto_nemd.txt index 0a76859dcf..3387611d4e 100644 --- a/doc/src/Howto_nemd.txt +++ b/doc/src/Howto_nemd.txt @@ -24,10 +24,10 @@ by subtracting out the streaming velocity of the shearing atoms. The velocity profile or other properties of the fluid can be monitored via the "fix ave/chunk"_fix_ave_chunk.html command. -NOTE: A recent (2017) book by "(Daivis and Todd)"_#Daivis2 discusses -use of the SLLOD method and non-equilibrium MD (NEMD) thermosttating -generally, for both simple and complex fluids, e.g. molecular systems. -The latter can be tricky to do correctly. +NOTE: A recent (2017) book by "(Daivis and Todd)"_#Daivis-nemd +discusses use of the SLLOD method and non-equilibrium MD (NEMD) +thermosttating generally, for both simple and complex fluids, +e.g. molecular systems. The latter can be tricky to do correctly. As discussed in the previous section on non-orthogonal simulation boxes, the amount of tilt or skew that can be applied is limited by @@ -54,6 +54,6 @@ using the "fix flow/gauss"_fix_flow_gauss.html command. :line -:link(Daivis2) +:link(Daivis-nemd) [(Daivis and Todd)] Daivis and Todd, Nonequilibrium Molecular Dyanmics (book), Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017). diff --git a/doc/src/Howto_thermostat.txt b/doc/src/Howto_thermostat.txt index 6a0095e741..ccc9674641 100644 --- a/doc/src/Howto_thermostat.txt +++ b/doc/src/Howto_thermostat.txt @@ -43,10 +43,10 @@ nvt/asphere"_fix_nvt_asphere.html thermostat not only translation velocities but also rotational velocities for spherical and aspherical particles. -NOTE: A recent (2017) book by "(Daivis and Todd)"_#Daivis2 discusses -use of the SLLOD method and non-equilibrium MD (NEMD) thermosttating -generally, for both simple and complex fluids, e.g. molecular systems. -The latter can be tricky to do correctly. +NOTE: A recent (2017) book by "(Daivis and Todd)"_#Daivis-thermostat +discusses use of the SLLOD method and non-equilibrium MD (NEMD) +thermosttating generally, for both simple and complex fluids, +e.g. molecular systems. The latter can be tricky to do correctly. DPD thermostatting alters pairwise interactions in a manner analogous to the per-particle thermostatting of "fix @@ -95,6 +95,6 @@ temperature compute is used for default thermodynamic output. :line -:link(Daivis2) +:link(Daivis-thermostat) [(Daivis and Todd)] Daivis and Todd, Nonequilibrium Molecular Dyanmics (book), Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017). diff --git a/doc/src/Howto_viscosity.txt b/doc/src/Howto_viscosity.txt index adfabf8279..0b3892c1ad 100644 --- a/doc/src/Howto_viscosity.txt +++ b/doc/src/Howto_viscosity.txt @@ -37,10 +37,10 @@ used to shear the fluid in between them, again with some kind of thermostat that modifies only the thermal (non-shearing) components of velocity to prevent the fluid from heating up. -NOTE: A recent (2017) book by "(Daivis and Todd)"_#Daivis2 discusses -use of the SLLOD method and non-equilibrium MD (NEMD) thermosttating -generally, for both simple and complex fluids, e.g. molecular systems. -The latter can be tricky to do correctly. +NOTE: A recent (2017) book by "(Daivis and Todd)"_#Daivis-viscosity +discusses use of the SLLOD method and non-equilibrium MD (NEMD) +thermosttating generally, for both simple and complex fluids, +e.g. molecular systems. The latter can be tricky to do correctly. In both cases, the velocity profile setup in the fluid by this procedure can be monitored by the "fix ave/chunk"_fix_ave_chunk.html @@ -139,6 +139,6 @@ with time at sufficiently long times. :line -:link(Daivis2) +:link(Daivis-viscosity) [(Daivis and Todd)] Daivis and Todd, Nonequilibrium Molecular Dyanmics (book), Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017). diff --git a/doc/src/fix_nvt_sllod.txt b/doc/src/fix_nvt_sllod.txt index 67c4d76417..fbc3143af3 100644 --- a/doc/src/fix_nvt_sllod.txt +++ b/doc/src/fix_nvt_sllod.txt @@ -63,10 +63,10 @@ implemented in LAMMPS, they are coupled to a Nose/Hoover chain thermostat in a velocity Verlet formulation, closely following the implementation used for the "fix nvt"_fix_nh.html command. -NOTE: A recent (2017) book by "(Daivis and Todd)"_#Daivis2 discusses -use of the SLLOD method and non-equilibrium MD (NEMD) thermosttating -generally, for both simple and complex fluids, e.g. molecular systems. -The latter can be tricky to do correctly. +NOTE: A recent (2017) book by "(Daivis and Todd)"_#Daivis-sllod +discusses use of the SLLOD method and non-equilibrium MD (NEMD) +thermosttating generally, for both simple and complex fluids, +e.g. molecular systems. The latter can be tricky to do correctly. Additional parameters affecting the thermostat are specified by keywords and values documented with the "fix nvt"_fix_nh.html @@ -183,6 +183,6 @@ Same as "fix nvt"_fix_nh.html, except tchain = 1. :link(Daivis) [(Daivis and Todd)] Daivis and Todd, J Chem Phys, 124, 194103 (2006). -:link(Daivis2) +:link(Daivis-sllod) [(Daivis and Todd)] Daivis and Todd, Nonequilibrium Molecular Dyanmics (book), Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017). From 8fa80081df3513dfd20fb6ab92471b6a451bc55a Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 17 Sep 2018 05:08:22 -0400 Subject: [PATCH 172/302] fix typo --- doc/src/Howto_nemd.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/src/Howto_nemd.txt b/doc/src/Howto_nemd.txt index 3387611d4e..10139d907c 100644 --- a/doc/src/Howto_nemd.txt +++ b/doc/src/Howto_nemd.txt @@ -26,7 +26,7 @@ the "fix ave/chunk"_fix_ave_chunk.html command. NOTE: A recent (2017) book by "(Daivis and Todd)"_#Daivis-nemd discusses use of the SLLOD method and non-equilibrium MD (NEMD) -thermosttating generally, for both simple and complex fluids, +thermostatting generally, for both simple and complex fluids, e.g. molecular systems. The latter can be tricky to do correctly. As discussed in the previous section on non-orthogonal simulation From 39ee7876c48dcdf1367b05f7f184f2f88048618a Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 17 Sep 2018 05:09:23 -0400 Subject: [PATCH 173/302] fix typo --- doc/src/Howto_thermostat.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/src/Howto_thermostat.txt b/doc/src/Howto_thermostat.txt index ccc9674641..9f7e2f3000 100644 --- a/doc/src/Howto_thermostat.txt +++ b/doc/src/Howto_thermostat.txt @@ -45,7 +45,7 @@ particles. NOTE: A recent (2017) book by "(Daivis and Todd)"_#Daivis-thermostat discusses use of the SLLOD method and non-equilibrium MD (NEMD) -thermosttating generally, for both simple and complex fluids, +thermostatting generally, for both simple and complex fluids, e.g. molecular systems. The latter can be tricky to do correctly. DPD thermostatting alters pairwise interactions in a manner analogous From 494b1492720bf34c7dee6b9ade18c570c38dcf48 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 17 Sep 2018 05:10:56 -0400 Subject: [PATCH 174/302] fix typo --- doc/src/Howto_viscosity.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/src/Howto_viscosity.txt b/doc/src/Howto_viscosity.txt index 0b3892c1ad..b4e441557d 100644 --- a/doc/src/Howto_viscosity.txt +++ b/doc/src/Howto_viscosity.txt @@ -39,7 +39,7 @@ velocity to prevent the fluid from heating up. NOTE: A recent (2017) book by "(Daivis and Todd)"_#Daivis-viscosity discusses use of the SLLOD method and non-equilibrium MD (NEMD) -thermosttating generally, for both simple and complex fluids, +thermostatting generally, for both simple and complex fluids, e.g. molecular systems. The latter can be tricky to do correctly. In both cases, the velocity profile setup in the fluid by this From 5f6b5c5400019d1b4e09f0138eb0aac4b789d5fe Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 17 Sep 2018 05:11:59 -0400 Subject: [PATCH 175/302] fix typo --- doc/src/fix_nvt_sllod.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/src/fix_nvt_sllod.txt b/doc/src/fix_nvt_sllod.txt index fbc3143af3..7a350e48b5 100644 --- a/doc/src/fix_nvt_sllod.txt +++ b/doc/src/fix_nvt_sllod.txt @@ -65,7 +65,7 @@ implementation used for the "fix nvt"_fix_nh.html command. NOTE: A recent (2017) book by "(Daivis and Todd)"_#Daivis-sllod discusses use of the SLLOD method and non-equilibrium MD (NEMD) -thermosttating generally, for both simple and complex fluids, +thermostatting generally, for both simple and complex fluids, e.g. molecular systems. The latter can be tricky to do correctly. Additional parameters affecting the thermostat are specified by From d753c51c450064c5a4ac8a7157fac6ddadb4a0dc Mon Sep 17 00:00:00 2001 From: Aidan Thompson Date: Mon, 17 Sep 2018 19:44:32 -0600 Subject: [PATCH 176/302] The sna*/atom computes were not destroying SNA objects. Fixed. --- src/SNAP/compute_sna_atom.cpp | 5 ++++- src/SNAP/compute_sna_atom.h | 1 + src/SNAP/compute_snad_atom.cpp | 2 ++ src/SNAP/compute_snad_atom.h | 1 + src/SNAP/compute_snav_atom.cpp | 3 +++ src/SNAP/compute_snav_atom.h | 1 + 6 files changed, 12 insertions(+), 1 deletion(-) diff --git a/src/SNAP/compute_sna_atom.cpp b/src/SNAP/compute_sna_atom.cpp index a2c1f55788..5ca63a7e85 100644 --- a/src/SNAP/compute_sna_atom.cpp +++ b/src/SNAP/compute_sna_atom.cpp @@ -115,7 +115,8 @@ ComputeSNAAtom::ComputeSNAAtom(LAMMPS *lmp, int narg, char **arg) : } else error->all(FLERR,"Illegal compute sna/atom command"); } - snaptr = new SNA*[comm->nthreads]; + nthreads = comm->nthreads; + snaptr = new SNA*[nthreads]; #if defined(_OPENMP) #pragma omp parallel default(none) shared(lmp,rfac0,twojmax,rmin0,switchflag,bzeroflag) #endif @@ -146,6 +147,8 @@ ComputeSNAAtom::~ComputeSNAAtom() memory->destroy(radelem); memory->destroy(wjelem); memory->destroy(cutsq); + for (int tid = 0; tiddestroy(radelem); memory->destroy(wjelem); memory->destroy(cutsq); + for (int tid = 0; tiddestroy(radelem); memory->destroy(wjelem); memory->destroy(cutsq); + + for (int tid = 0; tid Date: Tue, 18 Sep 2018 17:24:10 -0400 Subject: [PATCH 177/302] patch 18Sep18 --- doc/src/Manual.txt | 4 ++-- src/version.h | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/doc/src/Manual.txt b/doc/src/Manual.txt index 5af157d8ea..ecee17269a 100644 --- a/doc/src/Manual.txt +++ b/doc/src/Manual.txt @@ -1,7 +1,7 @@ LAMMPS Users Manual - + @@ -21,7 +21,7 @@ :line LAMMPS Documentation :c,h1 -5 Sep 2018 version :c,h2 +18 Sep 2018 version :c,h2 "What is a LAMMPS version?"_Manual_version.html diff --git a/src/version.h b/src/version.h index 0b8c1e8736..469d74fed7 100644 --- a/src/version.h +++ b/src/version.h @@ -1 +1 @@ -#define LAMMPS_VERSION "5 Sep 2018" +#define LAMMPS_VERSION "18 Sep 2018" From 4bfac61b1a72aa254d0a4831881661457806a97a Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 18 Sep 2018 17:41:02 -0400 Subject: [PATCH 178/302] fix typo in gzip support for fix reax/bonds --- src/REAX/fix_reax_bonds.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/REAX/fix_reax_bonds.cpp b/src/REAX/fix_reax_bonds.cpp index 5273cd1faa..c6c1d309ee 100644 --- a/src/REAX/fix_reax_bonds.cpp +++ b/src/REAX/fix_reax_bonds.cpp @@ -53,7 +53,7 @@ FixReaxBonds::FixReaxBonds(LAMMPS *lmp, int narg, char **arg) : if (suffix && strcmp(suffix,".gz") == 0) { #ifdef LAMMPS_GZIP char gzip[128]; - snprintf(gzip128,,"gzip -6 > %s",arg[4]); + snprintf(gzip,128,"gzip -6 > %s",arg[4]); #ifdef _WIN32 fp = _popen(gzip,"wb"); #else From cda89283aa3c3d5221305515ab5a914feec626ff Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 18 Sep 2018 22:13:17 -0400 Subject: [PATCH 179/302] warn more loudly about REAX and MEAM going away soon --- src/MEAM/pair_meam.cpp | 4 ++-- src/REAX/pair_reax.cpp | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/src/MEAM/pair_meam.cpp b/src/MEAM/pair_meam.cpp index b8f5291338..38e8e97810 100644 --- a/src/MEAM/pair_meam.cpp +++ b/src/MEAM/pair_meam.cpp @@ -48,8 +48,8 @@ static const char *keywords[] = { PairMEAM::PairMEAM(LAMMPS *lmp) : Pair(lmp) { if (comm->me == 0) - error->warning(FLERR,"The pair_style meam command is unsupported. " - "Please use pair_style meam/c instead"); + error->warning(FLERR,"THE pair_style meam COMMAND IS OBSOLETE AND " + "WILL BE REMOVED VERY SOON. PLEASE USE meam/c"); single_enable = 0; restartinfo = 0; diff --git a/src/REAX/pair_reax.cpp b/src/REAX/pair_reax.cpp index 24083a288a..a430380711 100644 --- a/src/REAX/pair_reax.cpp +++ b/src/REAX/pair_reax.cpp @@ -46,8 +46,8 @@ using namespace LAMMPS_NS; PairREAX::PairREAX(LAMMPS *lmp) : Pair(lmp) { if (comm->me == 0) - error->warning(FLERR,"The pair_style reax command is unsupported. " - "Please switch to pair_style reax/c instead"); + error->warning(FLERR,"THE pair_style reax COMMAND IS OBSOLETE AND " + "WILL BE REMOVED VERY SOON. PLEASE USE reax/c"); single_enable = 0; restartinfo = 0; From c705e8d0e6a3b1a739f2ddf6cd1ee40a3241d40a Mon Sep 17 00:00:00 2001 From: pmla Date: Wed, 19 Sep 2018 20:46:48 -0400 Subject: [PATCH 180/302] renamed files for LAMMPS build system compatibility --- src/PTM/compute_ptm_atom.cpp | 307 ++++ src/PTM/compute_ptm_atom.h | 48 + src/PTM/ptm_alloy_types.cpp | 101 ++ src/PTM/ptm_alloy_types.h | 9 + src/PTM/ptm_canonical_coloured.cpp | 167 ++ src/PTM/ptm_canonical_coloured.h | 9 + src/PTM/ptm_constants.h | 174 ++ src/PTM/ptm_convex_hull_incremental.cpp | 363 ++++ src/PTM/ptm_convex_hull_incremental.h | 27 + src/PTM/ptm_deformation_gradient.cpp | 37 + src/PTM/ptm_deformation_gradient.h | 142 ++ src/PTM/ptm_functions.h | 27 + src/PTM/ptm_fundamental_mappings.h | 180 ++ src/PTM/ptm_graph_data.cpp | 2059 +++++++++++++++++++++++ src/PTM/ptm_graph_data.h | 37 + src/PTM/ptm_graph_tools.cpp | 52 + src/PTM/ptm_graph_tools.h | 11 + src/PTM/ptm_index.cpp | 218 +++ src/PTM/ptm_initialize_data.cpp | 71 + src/PTM/ptm_initialize_data.h | 61 + src/PTM/ptm_neighbour_ordering.cpp | 203 +++ src/PTM/ptm_neighbour_ordering.h | 13 + src/PTM/ptm_normalize_vertices.cpp | 55 + src/PTM/ptm_normalize_vertices.h | 8 + src/PTM/ptm_polar.cpp | 337 ++++ src/PTM/ptm_polar.h | 12 + src/PTM/ptm_quat.cpp | 396 +++++ src/PTM/ptm_quat.h | 32 + src/PTM/ptm_structure_matcher.cpp | 294 ++++ src/PTM/ptm_structure_matcher.h | 21 + src/PTM/ptm_voronoi_cell.cpp | 1368 +++++++++++++++ src/PTM/ptm_voronoi_cell.h | 324 ++++ src/PTM/ptm_voronoi_config.h | 129 ++ 33 files changed, 7292 insertions(+) create mode 100644 src/PTM/compute_ptm_atom.cpp create mode 100644 src/PTM/compute_ptm_atom.h create mode 100644 src/PTM/ptm_alloy_types.cpp create mode 100644 src/PTM/ptm_alloy_types.h create mode 100644 src/PTM/ptm_canonical_coloured.cpp create mode 100644 src/PTM/ptm_canonical_coloured.h create mode 100644 src/PTM/ptm_constants.h create mode 100644 src/PTM/ptm_convex_hull_incremental.cpp create mode 100644 src/PTM/ptm_convex_hull_incremental.h create mode 100644 src/PTM/ptm_deformation_gradient.cpp create mode 100644 src/PTM/ptm_deformation_gradient.h create mode 100644 src/PTM/ptm_functions.h create mode 100644 src/PTM/ptm_fundamental_mappings.h create mode 100644 src/PTM/ptm_graph_data.cpp create mode 100644 src/PTM/ptm_graph_data.h create mode 100644 src/PTM/ptm_graph_tools.cpp create mode 100644 src/PTM/ptm_graph_tools.h create mode 100644 src/PTM/ptm_index.cpp create mode 100644 src/PTM/ptm_initialize_data.cpp create mode 100644 src/PTM/ptm_initialize_data.h create mode 100644 src/PTM/ptm_neighbour_ordering.cpp create mode 100644 src/PTM/ptm_neighbour_ordering.h create mode 100644 src/PTM/ptm_normalize_vertices.cpp create mode 100644 src/PTM/ptm_normalize_vertices.h create mode 100644 src/PTM/ptm_polar.cpp create mode 100644 src/PTM/ptm_polar.h create mode 100644 src/PTM/ptm_quat.cpp create mode 100644 src/PTM/ptm_quat.h create mode 100644 src/PTM/ptm_structure_matcher.cpp create mode 100644 src/PTM/ptm_structure_matcher.h create mode 100644 src/PTM/ptm_voronoi_cell.cpp create mode 100644 src/PTM/ptm_voronoi_cell.h create mode 100644 src/PTM/ptm_voronoi_config.h diff --git a/src/PTM/compute_ptm_atom.cpp b/src/PTM/compute_ptm_atom.cpp new file mode 100644 index 0000000000..b6b4a9786c --- /dev/null +++ b/src/PTM/compute_ptm_atom.cpp @@ -0,0 +1,307 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed +under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: PM Larsen (MIT) +------------------------------------------------------------------------- */ + +#include +#include +#include +#include + +#include "atom.h" +#include "comm.h" +#include "compute_ptm_atom.h" +#include "error.h" +#include "force.h" +#include "memory.h" +#include "modify.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" +#include "pair.h" +#include "update.h" + +#include "ptm_functions.h" + +#define MAX_NEIGHBORS 30 +#define NUM_COLUMNS 7 +#define UNKNOWN 0 +#define OTHER 8 + +using namespace LAMMPS_NS; + +static const char cite_user_ptm_package[] = + "USER-PTM package:\n\n" + "@Article{larsen2016ptm,\n" + " author={Larsen, Peter Mahler and Schmidt, S{\o}ren and Schi{\o}tz, " + "Jakob},\n" + " title={Robust structural identification via polyhedral template " + "matching},\n" + " journal={Modelling~Simul.~Mater.~Sci.~Eng.},\n" + " year={2016},\n" + " number={5},\n" + " volume={24},\n" + " pages={055007},\n" + " DOI = {10.1088/0965-0393/24/5/055007}" + "}\n\n"; + +/* ---------------------------------------------------------------------- */ + +ComputePTMAtom::ComputePTMAtom(LAMMPS *lmp, int narg, char **arg) + : Compute(lmp, narg, arg), list(NULL), output(NULL) { + if (narg != 5) + error->all(FLERR, "Illegal compute ptm/atom command"); + + char *structures = arg[3]; + char *ptr = structures; + + const char *strings[] = {"fcc", "hcp", "bcc", "ico", "sc", + "dcub", "dhex", "all", "default"}; + int32_t flags[] = { + PTM_CHECK_FCC, + PTM_CHECK_HCP, + PTM_CHECK_BCC, + PTM_CHECK_ICO, + PTM_CHECK_SC, + PTM_CHECK_DCUB, + PTM_CHECK_DHEX, + PTM_CHECK_ALL, + PTM_CHECK_FCC | PTM_CHECK_HCP | PTM_CHECK_BCC | PTM_CHECK_ICO}; + + input_flags = 0; + while (*ptr != '\0') { + + bool found = false; + for (int i = 0; i < 9; i++) { + int len = strlen(strings[i]); + if (strncmp(ptr, strings[i], len) == 0) { + input_flags |= flags[i]; + ptr += len; + found = true; + break; + } + } + + if (!found) + error->all(FLERR, + "Illegal compute ptm/atom command (invalid structure type)"); + + if (*ptr == '\0') + break; + + if (*ptr != '-') + error->all(FLERR, + "Illegal compute ptm/atom command (invalid structure type)"); + + ptr++; + } + + double threshold = force->numeric(FLERR, arg[4]); + if (threshold < 0.0) + error->all(FLERR, + "Illegal compute ptm/atom command (threshold is negative)"); + rmsd_threshold = threshold; + if (rmsd_threshold == 0) + rmsd_threshold = INFINITY; + + peratom_flag = 1; + size_peratom_cols = NUM_COLUMNS; + create_attribute = 1; + nmax = 0; +} + +/* ---------------------------------------------------------------------- */ + +ComputePTMAtom::~ComputePTMAtom() { memory->destroy(output); } + +/* ---------------------------------------------------------------------- */ + +void ComputePTMAtom::init() { + if (force->pair == NULL) + error->all(FLERR, "Compute ptm/atom requires a pair style be defined"); + + int count = 0; + for (int i = 0; i < modify->ncompute; i++) + if (strcmp(modify->compute[i]->style, "ptm/atom") == 0) + count++; + if (count > 1 && comm->me == 0) + error->warning(FLERR, "More than one compute ptm/atom defined"); + + // need an occasional full neighbor list + + int irequest = neighbor->request(this, instance_me); + neighbor->requests[irequest]->pair = 0; + neighbor->requests[irequest]->compute = 1; + neighbor->requests[irequest]->half = 0; + neighbor->requests[irequest]->full = 1; + neighbor->requests[irequest]->occasional = 1; +} + +/* ---------------------------------------------------------------------- */ + +void ComputePTMAtom::init_list(int id, NeighList *ptr) { list = ptr; } + +/* ---------------------------------------------------------------------- */ + +typedef struct { + int index; + double d; +} ptmnbr_t; + +static bool sorthelper_compare(ptmnbr_t const &a, ptmnbr_t const &b) { + return a.d < b.d; +} + +static int get_neighbors(double *pos, int jnum, int *jlist, double **x, + double (*nbr)[3]) { + + ptmnbr_t *nbr_order = new ptmnbr_t[jnum]; + + for (int jj = 0; jj < jnum; jj++) { + int j = jlist[jj]; + j &= NEIGHMASK; + + double dx = pos[0] - x[j][0]; + double dy = pos[1] - x[j][1]; + double dz = pos[2] - x[j][2]; + double rsq = dx * dx + dy * dy + dz * dz; + + nbr_order[jj].index = j; + nbr_order[jj].d = rsq; + } + + std::sort(nbr_order, nbr_order + jnum, &sorthelper_compare); + int num_nbrs = std::min(MAX_NEIGHBORS, jnum); + + nbr[0][0] = nbr[0][1] = nbr[0][2] = 0; + for (int jj = 0; jj < num_nbrs; jj++) { + + int j = nbr_order[jj].index; + nbr[jj + 1][0] = x[j][0] - pos[0]; + nbr[jj + 1][1] = x[j][1] - pos[1]; + nbr[jj + 1][2] = x[j][2] - pos[2]; + } + + delete[] nbr_order; + return num_nbrs; +} + +void ComputePTMAtom::compute_peratom() { + // PTM global initialization. If already initialized this function does + // nothing. + ptm_initialize_global(); + + // initialize PTM local storage + ptm_local_handle_t local_handle = ptm_initialize_local(); + + invoked_peratom = update->ntimestep; + + // grow arrays if necessary + if (atom->nmax > nmax) { + memory->destroy(output); + nmax = atom->nmax; + + memory->create(output, nmax, NUM_COLUMNS, "ptm:ptm_output"); + array_atom = output; + } + + // invoke full neighbor list (will copy or build if necessary) + neighbor->build_one(list); + + int inum = list->inum; + int *ilist = list->ilist; + int *numneigh = list->numneigh; + int **firstneigh = list->firstneigh; + + double **x = atom->x; + int *mask = atom->mask; + int nlocal = atom->nlocal; + + for (int ii = 0; ii < inum; ii++) { + + int i = ilist[ii]; + output[i][0] = UNKNOWN; + if (!(mask[i] & groupbit)) + continue; + + double *pos = x[i]; + + int *jlist = firstneigh[i]; + int jnum = numneigh[i]; + if (jnum <= 0) + continue; + + // get neighbours ordered by increasing distance + double nbr[MAX_NEIGHBORS + 1][3]; + int num_nbrs = get_neighbors(pos, jnum, jlist, x, nbr); + + // check that we have enough neighbours for the desired structure types + int32_t flags = 0; + if (num_nbrs >= PTM_NUM_NBRS_SC && (input_flags & PTM_CHECK_SC)) + flags |= PTM_CHECK_SC; + if (num_nbrs >= PTM_NUM_NBRS_FCC && (input_flags & PTM_CHECK_FCC)) + flags |= PTM_CHECK_FCC; + if (num_nbrs >= PTM_NUM_NBRS_HCP && (input_flags & PTM_CHECK_HCP)) + flags |= PTM_CHECK_HCP; + if (num_nbrs >= PTM_NUM_NBRS_ICO && (input_flags & PTM_CHECK_ICO)) + flags |= PTM_CHECK_ICO; + if (num_nbrs >= PTM_NUM_NBRS_BCC && (input_flags & PTM_CHECK_BCC)) + flags |= PTM_CHECK_BCC; + if (num_nbrs >= PTM_NUM_NBRS_DCUB && (input_flags & PTM_CHECK_DCUB)) + flags |= PTM_CHECK_DCUB; + if (num_nbrs >= PTM_NUM_NBRS_DHEX && (input_flags & PTM_CHECK_DHEX)) + flags |= PTM_CHECK_DHEX; + + // now run PTM + int8_t mapping[MAX_NEIGHBORS + 1]; + int32_t type, alloy_type; + double scale, rmsd, interatomic_distance, lattice_constant; + double q[4], F[9], F_res[3], U[9], P[9]; + ptm_index(local_handle, flags, num_nbrs + 1, nbr, NULL, true, &type, + &alloy_type, &scale, &rmsd, q, F, F_res, U, P, mapping, + &interatomic_distance, &lattice_constant); + + if (rmsd > rmsd_threshold) { + type = PTM_MATCH_NONE; + } + + // printf("%d type=%d rmsd=%f\n", i, type, rmsd); + + if (type == PTM_MATCH_NONE) + type = OTHER; + + output[i][0] = type; + output[i][1] = rmsd; + output[i][2] = interatomic_distance; + output[i][3] = q[0]; + output[i][4] = q[1]; + output[i][5] = q[2]; + output[i][6] = q[3]; + } + + // printf("finished ptm analysis\n"); + ptm_uninitialize_local(local_handle); +} + +/* ---------------------------------------------------------------------- + memory usage of local atom-based array +------------------------------------------------------------------------- */ + +double ComputePTMAtom::memory_usage() { + double bytes = nmax * NUM_COLUMNS * sizeof(double); + bytes += nmax * sizeof(double); + return bytes; +} diff --git a/src/PTM/compute_ptm_atom.h b/src/PTM/compute_ptm_atom.h new file mode 100644 index 0000000000..5c10e0c443 --- /dev/null +++ b/src/PTM/compute_ptm_atom.h @@ -0,0 +1,48 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef COMPUTE_CLASS + +ComputeStyle(ptm/atom,ComputePTMAtom) + +#else + +#ifndef LMP_COMPUTE_PTM_ATOM_H +#define LMP_COMPUTE_PTM_ATOM_H + +#include "compute.h" + +namespace LAMMPS_NS { + +class ComputePTMAtom : public Compute { + public: + ComputePTMAtom(class LAMMPS *, int, char **); + ~ComputePTMAtom(); + void init(); + void init_list(int, class NeighList *); + void compute_peratom(); + double memory_usage(); + + private: + int nmax; + int32_t input_flags; + double rmsd_threshold; + class NeighList *list; + double **output; +}; + +} + +#endif +#endif + diff --git a/src/PTM/ptm_alloy_types.cpp b/src/PTM/ptm_alloy_types.cpp new file mode 100644 index 0000000000..e14d06db99 --- /dev/null +++ b/src/PTM/ptm_alloy_types.cpp @@ -0,0 +1,101 @@ +#include +#include "ptm_constants.h" +#include "ptm_initialize_data.h" + + +#define NUM_ALLOY_TYPES 3 +static uint32_t typedata[NUM_ALLOY_TYPES][3] = { + {PTM_MATCH_FCC, PTM_ALLOY_L10, 0x000001fe}, + {PTM_MATCH_FCC, PTM_ALLOY_L12_CU, 0x0000001e}, + {PTM_MATCH_FCC, PTM_ALLOY_L12_AU, 0x00001ffe}, +}; + +static bool test_pure(int num_nbrs, int32_t* numbers) +{ + for (int i=1;inum_nbrs+1;i++) + binary[i] = numbers[mapping[i]] == numbers[0] ? 0 : 1; + + for (int i=1;inum_nbrs+1;i++) + if (binary[i] != binary[0]) + return false; + + return true; +} + +static int32_t canonical_alloy_representation(const refdata_t* ref, int8_t* mapping, int32_t* numbers) +{ + int8_t binary[PTM_MAX_POINTS]; + for (int i=0;inum_nbrs+1;i++) + binary[i] = numbers[mapping[i]] == numbers[0] ? 0 : 1; + + int8_t temp[PTM_MAX_POINTS]; + uint32_t best = 0xFFFFFFFF; + for (int j=0;jnum_mappings;j++) + { + for (int i=0;inum_nbrs+1;i++) + temp[ref->mapping[j][i]] = binary[i]; + + uint32_t code = 0; + for (int i=0;inum_nbrs+1;i++) + code |= (temp[i] << i); + + best = std::min(best, code); + } + + return best; +} + +int32_t find_alloy_type(const refdata_t* ref, int8_t* mapping, int32_t* numbers) +{ + if (test_pure(ref->num_nbrs, numbers)) + return PTM_ALLOY_PURE; + + if (!test_binary(ref->num_nbrs, numbers)) + return PTM_ALLOY_NONE; + + uint32_t code = canonical_alloy_representation(ref, mapping, numbers); + for (int i=0;itype == typedata[i][0] && code == typedata[i][2]) + return typedata[i][1]; + + if (ref->type == PTM_MATCH_BCC) + if (test_shell_structure(ref, mapping, numbers, 8)) + return PTM_ALLOY_B2; + + if (ref->type == PTM_MATCH_DCUB || ref->type == PTM_MATCH_DHEX) + if (test_shell_structure(ref, mapping, numbers, 4)) + return PTM_ALLOY_SIC; + + return PTM_ALLOY_NONE; +} + diff --git a/src/PTM/ptm_alloy_types.h b/src/PTM/ptm_alloy_types.h new file mode 100644 index 0000000000..6ea6ed1b8a --- /dev/null +++ b/src/PTM/ptm_alloy_types.h @@ -0,0 +1,9 @@ +#ifndef PTM_ALLOY_TYPES_H +#define PTM_ALLOY_TYPES_H + +#include "ptm_initialize_data.h" + +int32_t find_alloy_type(const refdata_t* ref, int8_t* mapping, int32_t* numbers); + +#endif + diff --git a/src/PTM/ptm_canonical_coloured.cpp b/src/PTM/ptm_canonical_coloured.cpp new file mode 100644 index 0000000000..551f52d7e4 --- /dev/null +++ b/src/PTM/ptm_canonical_coloured.cpp @@ -0,0 +1,167 @@ +#include +#include +#include +#include "ptm_graph_tools.h" +#include "ptm_constants.h" + + +static bool weinberg_coloured(int num_nodes, int num_edges, int8_t common[PTM_MAX_NBRS][PTM_MAX_NBRS], int8_t* colours, int8_t* best_code, int8_t* canonical_labelling, int a, int b) +{ + bool m[PTM_MAX_NBRS][PTM_MAX_NBRS]; + memset(m, 0, sizeof(bool) * PTM_MAX_NBRS * PTM_MAX_NBRS); + + int8_t index[PTM_MAX_NBRS]; + memset(index, -1, sizeof(int8_t) * PTM_MAX_NBRS); + + + int n = 0; + index[a] = colours[a] * num_nodes + n++; + if (index[a] > best_code[0]) + return false; + + bool winning = false; + if (index[a] < best_code[0]) + { + best_code[0] = index[a]; + winning = true; + } + + int c = -1; + for (int it=1;it<2*num_edges;it++) + { + bool newvertex = index[b] == -1; + + if (newvertex) + index[b] = colours[b] * num_nodes + n++; + + if (!winning && index[b] > best_code[it]) + return false; + + if (winning || index[b] < best_code[it]) + { + winning = true; + best_code[it] = index[b]; + } + + if (newvertex) + { + //When a new vertex is reached, take the right-most edge + //relative to the edge on which the vertex is reached. + + c = common[a][b]; + } + else if (m[b][a] == false) + { + //When an old vertex is reached on a new path, go back + //in the opposite direction. + + c = a; + } + else + { + //When an old vertex is reached on an old path, leave the + //vertex on the right-most edge that has not previously + //been traversed in that direction. + + c = common[a][b]; + while (m[b][c] == true) + c = common[c][b]; + } + + m[a][b] = true; + a = b; + b = c; + } + + if (winning) + { + memcpy(canonical_labelling, index, sizeof(int8_t) * num_nodes); + return true; + } + + return false; +} + +int canonical_form_coloured(int num_facets, int8_t facets[][3], int num_nodes, int8_t* degree, int8_t* colours, int8_t* canonical_labelling, int8_t* best_code, uint64_t* p_hash) +{ + int8_t common[PTM_MAX_NBRS][PTM_MAX_NBRS] = {{0}}; + int num_edges = 3 * num_facets / 2; + if (!build_facet_map(num_facets, facets, common)) + return -1; + + memset(best_code, SCHAR_MAX, sizeof(int8_t) * 2 * PTM_MAX_EDGES); + + bool equal = true; + for (int i = 1;i=0;i--) + canonical_labelling[i+1] = (canonical_labelling[i] % num_nodes) + 1; + canonical_labelling[0] = 0; + + uint64_t hash = 0; + for (int i = 0;i<2 * num_edges;i++) + { + uint64_t e = best_code[i]; + e += i % 8; + e &= 0xF; + e <<= (4 * i) % 64; + hash ^= e; + } + + *p_hash = hash; + return PTM_NO_ERROR; +} + diff --git a/src/PTM/ptm_canonical_coloured.h b/src/PTM/ptm_canonical_coloured.h new file mode 100644 index 0000000000..e71bb08bfc --- /dev/null +++ b/src/PTM/ptm_canonical_coloured.h @@ -0,0 +1,9 @@ +#ifndef PTM_CANONICAL_COLOURED_H +#define PTM_CANONICAL_COLOURED_H + +#include + +int canonical_form_coloured(int num_facets, int8_t facets[][3], int num_nodes, int8_t* degree, int8_t* colours, int8_t* canonical_labelling, int8_t* best_code, uint64_t* p_hash); + +#endif + diff --git a/src/PTM/ptm_constants.h b/src/PTM/ptm_constants.h new file mode 100644 index 0000000000..f868f51e84 --- /dev/null +++ b/src/PTM/ptm_constants.h @@ -0,0 +1,174 @@ +#ifndef PTM_CONSTANTS_H +#define PTM_CONSTANTS_H + +//------------------------------------ +// definitions +//------------------------------------ +#define PTM_NO_ERROR 0 + + +#define PTM_CHECK_FCC (1 << 0) +#define PTM_CHECK_HCP (1 << 1) +#define PTM_CHECK_BCC (1 << 2) +#define PTM_CHECK_ICO (1 << 3) +#define PTM_CHECK_SC (1 << 4) +#define PTM_CHECK_DCUB (1 << 5) +#define PTM_CHECK_DHEX (1 << 6) +#define PTM_CHECK_NONDIAMOND (PTM_CHECK_SC | PTM_CHECK_FCC | PTM_CHECK_HCP | PTM_CHECK_ICO | PTM_CHECK_BCC) +#define PTM_CHECK_ALL (PTM_CHECK_SC | PTM_CHECK_FCC | PTM_CHECK_HCP | PTM_CHECK_ICO | PTM_CHECK_BCC | PTM_CHECK_DCUB | PTM_CHECK_DHEX) + +#define PTM_MATCH_NONE 0 +#define PTM_MATCH_FCC 1 +#define PTM_MATCH_HCP 2 +#define PTM_MATCH_BCC 3 +#define PTM_MATCH_ICO 4 +#define PTM_MATCH_SC 5 +#define PTM_MATCH_DCUB 6 +#define PTM_MATCH_DHEX 7 + +#define PTM_ALLOY_NONE 0 +#define PTM_ALLOY_PURE 1 +#define PTM_ALLOY_L10 2 +#define PTM_ALLOY_L12_CU 3 +#define PTM_ALLOY_L12_AU 4 +#define PTM_ALLOY_B2 5 +#define PTM_ALLOY_SIC 6 + + +#define PTM_MAX_INPUT_POINTS 35 +#define PTM_MAX_NBRS 16 +#define PTM_MAX_POINTS (PTM_MAX_NBRS + 1) +#define PTM_MAX_FACETS 28 //2 * PTM_MAX_NBRS - 4 +#define PTM_MAX_EDGES 42 //3 * PTM_MAX_NBRS - 6 + + +//------------------------------------ +// number of neighbours +//------------------------------------ +#define PTM_NUM_NBRS_FCC 12 +#define PTM_NUM_NBRS_HCP 12 +#define PTM_NUM_NBRS_BCC 14 +#define PTM_NUM_NBRS_ICO 12 +#define PTM_NUM_NBRS_SC 6 +#define PTM_NUM_NBRS_DCUB 16 +#define PTM_NUM_NBRS_DHEX 16 + +#define PTM_NUM_POINTS_FCC (PTM_NUM_NBRS_FCC + 1) +#define PTM_NUM_POINTS_HCP (PTM_NUM_NBRS_HCP + 1) +#define PTM_NUM_POINTS_BCC (PTM_NUM_NBRS_BCC + 1) +#define PTM_NUM_POINTS_ICO (PTM_NUM_NBRS_ICO + 1) +#define PTM_NUM_POINTS_SC (PTM_NUM_NBRS_SC + 1) +#define PTM_NUM_POINTS_DCUB (PTM_NUM_NBRS_DCUB + 1) +#define PTM_NUM_POINTS_DHEX (PTM_NUM_NBRS_DHEX + 1) + +const int ptm_num_nbrs[8] = {0, PTM_NUM_NBRS_FCC, PTM_NUM_NBRS_HCP, PTM_NUM_NBRS_BCC, PTM_NUM_NBRS_ICO, PTM_NUM_NBRS_SC, PTM_NUM_NBRS_DCUB, PTM_NUM_NBRS_DHEX}; + +//------------------------------------ +// template structures +//------------------------------------ + +//these point sets have barycentre {0, 0, 0} and are scaled such that the mean neighbour distance is 1 + +const double ptm_template_fcc[PTM_NUM_POINTS_FCC][3] = { { 0. , 0. , 0. }, + { 0. , 0.707106781187, 0.707106781187 }, + { 0. , -0.707106781187, -0.707106781187 }, + { 0. , 0.707106781187, -0.707106781187 }, + { 0. , -0.707106781187, 0.707106781187 }, + { 0.707106781187, 0. , 0.707106781187 }, + { -0.707106781187, 0. , -0.707106781187 }, + { 0.707106781187, 0. , -0.707106781187 }, + { -0.707106781187, 0. , 0.707106781187 }, + { 0.707106781187, 0.707106781187, 0. }, + { -0.707106781187, -0.707106781187, 0. }, + { 0.707106781187, -0.707106781187, 0. }, + { -0.707106781187, 0.707106781187, 0. } }; + +const double ptm_template_hcp[PTM_NUM_POINTS_HCP][3] = { { 0. , 0. , 0. }, + { 0.707106781186, 0. , 0.707106781186 }, + { -0.235702260395, -0.942809041583, -0.235702260395 }, + { 0.707106781186, 0.707106781186, 0. }, + { -0.235702260395, -0.235702260395, -0.942809041583 }, + { 0. , 0.707106781186, 0.707106781186 }, + { -0.942809041583, -0.235702260395, -0.235702260395 }, + { -0.707106781186, 0.707106781186, 0. }, + { 0. , 0.707106781186, -0.707106781186 }, + { 0.707106781186, 0. , -0.707106781186 }, + { 0.707106781186, -0.707106781186, 0. }, + { -0.707106781186, 0. , 0.707106781186 }, + { 0. , -0.707106781186, 0.707106781186 } }; + +const double ptm_template_bcc[PTM_NUM_POINTS_BCC][3] = { { 0. , 0. , 0. }, + { -0.541451884327, -0.541451884327, -0.541451884327 }, + { 0.541451884327, 0.541451884327, 0.541451884327 }, + { 0.541451884327, -0.541451884327, -0.541451884327 }, + { -0.541451884327, 0.541451884327, 0.541451884327 }, + { -0.541451884327, 0.541451884327, -0.541451884327 }, + { 0.541451884327, -0.541451884327, 0.541451884327 }, + { -0.541451884327, -0.541451884327, 0.541451884327 }, + { 0.541451884327, 0.541451884327, -0.541451884327 }, + { 0. , 0. , -1.082903768655 }, + { 0. , 0. , 1.082903768655 }, + { 0. , -1.082903768655, 0. }, + { 0. , 1.082903768655, 0. }, + { -1.082903768655, 0. , 0. }, + { 1.082903768655, 0. , 0. } }; + +const double ptm_template_ico[PTM_NUM_POINTS_ICO][3] = { { 0. , 0. , 0. }, + { 0. , 0.525731112119, 0.850650808352 }, + { 0. , -0.525731112119, -0.850650808352 }, + { 0. , 0.525731112119, -0.850650808352 }, + { 0. , -0.525731112119, 0.850650808352 }, + { -0.525731112119, -0.850650808352, 0. }, + { 0.525731112119, 0.850650808352, 0. }, + { 0.525731112119, -0.850650808352, 0. }, + { -0.525731112119, 0.850650808352, 0. }, + { -0.850650808352, 0. , -0.525731112119 }, + { 0.850650808352, 0. , 0.525731112119 }, + { 0.850650808352, 0. , -0.525731112119 }, + { -0.850650808352, 0. , 0.525731112119 } }; + +const double ptm_template_sc[PTM_NUM_POINTS_SC][3] = { { 0. , 0. , 0. }, + { 0. , 0. , -1. }, + { 0. , 0. , 1. }, + { 0. , -1. , 0. }, + { 0. , 1. , 0. }, + { -1. , 0. , 0. }, + { 1. , 0. , 0. } }; + +const double ptm_template_dcub[PTM_NUM_POINTS_DCUB][3] = { { 0. , 0. , 0. }, + { -0.391491627053, 0.391491627053, 0.391491627053 }, + { -0.391491627053, -0.391491627053, -0.391491627053 }, + { 0.391491627053, -0.391491627053, 0.391491627053 }, + { 0.391491627053, 0.391491627053, -0.391491627053 }, + { -0.782983254107, 0. , 0.782983254107 }, + { -0.782983254107, 0.782983254107, 0. }, + { 0. , 0.782983254107, 0.782983254107 }, + { -0.782983254107, -0.782983254107, 0. }, + { -0.782983254107, 0. , -0.782983254107 }, + { 0. , -0.782983254107, -0.782983254107 }, + { 0. , -0.782983254107, 0.782983254107 }, + { 0.782983254107, -0.782983254107, 0. }, + { 0.782983254107, 0. , 0.782983254107 }, + { 0. , 0.782983254107, -0.782983254107 }, + { 0.782983254107, 0. , -0.782983254107 }, + { 0.782983254107, 0.782983254107, 0. } }; + +const double ptm_template_dhex[PTM_NUM_POINTS_DHEX][3] = { { 0. , 0. , 0. }, + { -0.391491627053, -0.391491627053, -0.391491627053 }, + { 0.391491627053, -0.391491627053, 0.391491627053 }, + { -0.391491627053, 0.391491627053, 0.391491627053 }, + { 0.391491627053, 0.391491627053, -0.391491627053 }, + { -0.260994418036, -1.043977672142, -0.260994418036 }, + { -1.043977672142, -0.260994418036, -0.260994418036 }, + { -0.260994418036, -0.260994418036, -1.043977672142 }, + { 0.782983254107, 0. , 0.782983254107 }, + { 0.782983254107, -0.782983254107, 0. }, + { 0. , -0.782983254107, 0.782983254107 }, + { 0. , 0.782983254107, 0.782983254107 }, + { -0.782983254107, 0.782983254107, 0. }, + { -0.782983254107, 0. , 0.782983254107 }, + { 0.782983254107, 0.782983254107, 0. }, + { 0. , 0.782983254107, -0.782983254107 }, + { 0.782983254107, 0. , -0.782983254107 } }; +#endif + diff --git a/src/PTM/ptm_convex_hull_incremental.cpp b/src/PTM/ptm_convex_hull_incremental.cpp new file mode 100644 index 0000000000..c996b17b58 --- /dev/null +++ b/src/PTM/ptm_convex_hull_incremental.cpp @@ -0,0 +1,363 @@ +#include +#include +#include +#include +#include +#include "ptm_convex_hull_incremental.h" +#include "ptm_constants.h" + + +#define VISIBLE 1 +#define INVISIBLE 2 +#define BOTH 3 +#define TOLERANCE 1E-8 + +static double norm_squared(double* p) +{ + double x = p[0]; + double y = p[1]; + double z = p[2]; + + return x*x + y*y + z*z; +} + +static double dot_product(const double* a, const double* b) +{ + return a[0]*b[0] + a[1]*b[1] + a[2]*b[2]; +} + +static void cross_product(double* a, double* b, double* c) +{ + c[0] = a[1] * b[2] - a[2] * b[1]; + c[1] = a[2] * b[0] - a[0] * b[2]; + c[2] = a[0] * b[1] - a[1] * b[0]; +} + +static void calculate_plane_normal(const double (*points)[3], int a, int b, int c, double* plane_normal) +{ + double u[3] = { points[b][0] - points[a][0], + points[b][1] - points[a][1], + points[b][2] - points[a][2] }; + + double v[3] = { points[c][0] - points[a][0], + points[c][1] - points[a][1], + points[c][2] - points[a][2] }; + + cross_product(u, v, plane_normal); + double norm = sqrt(norm_squared(plane_normal)); + plane_normal[0] /= norm; + plane_normal[1] /= norm; + plane_normal[2] /= norm; +} + +static double point_plane_distance(const double* w, const double* plane_point, const double* plane_cross) +{ + return plane_cross[0] * (plane_point[0] - w[0]) + + plane_cross[1] * (plane_point[1] - w[1]) + + plane_cross[2] * (plane_point[2] - w[2]); +} + +static bool calc_max_extent(int num_points, const double (*points)[3], int* min_index, int* max_index) +{ + for (int j=0;j<3;j++) + { + double dmin = DBL_MAX, dmax = -DBL_MAX; + int imin = 0, imax = 0; + + for (int i = 0;i dmax) + { + dmax = d; + imax = i; + } + } + + if (imin == imax) + return false; //degenerate point set + + min_index[j] = imin; + max_index[j] = imax; + } + + return true; +} + +static bool find_third_point(int num_points, const double (*points)[3], int a, int b, int* p_c) +{ + const double* x1 = points[a]; + const double* x2 = points[b]; + + double x2x1[3] = {x2[0] - x1[0], x2[1] - x1[1], x2[2] - x1[2]}; + double ns_x2x1 = norm_squared(x2x1); + + int bi = -1; + double max_dist = 0.0; + for (int i = 0;i max_dist) + { + max_dist = dist; + bi = i; + } + } + + *p_c = bi; + return max_dist > TOLERANCE; +} + +static bool find_fourth_point(int num_points, const double (*points)[3], int a, int b, int c, int* p_d) +{ + double plane_normal[3]; + calculate_plane_normal(points, a, b, c, plane_normal); + + + int bi = -1; + double max_dist = 0.0; + for (int i = 0;i max_dist) + { + max_dist = dist; + bi = i; + } + } + + *p_d = bi; + return max_dist > TOLERANCE; +} + +static int initial_simplex(int num_points, const double (*points)[3], int* initial_vertices) +{ + int min_index[3] = {0}; + int max_index[3] = {0}; + if (!calc_max_extent(num_points, points, min_index, max_index)) + return -1; + + int bi = -1; + double max_dist = 0.0; + for (int i = 0;i<3;i++) + { + int a = min_index[i], b = max_index[i]; + double delta[3] = { points[a][0] - points[b][0], + points[a][1] - points[b][1], + points[a][2] - points[b][2] }; + double dist = norm_squared(delta); + if (dist > max_dist) + { + bi = i; + max_dist = dist; + } + } + + //first two points are (a, b) + int a = min_index[bi], b = max_index[bi], c = -1, d = -1; + + if (!find_third_point(num_points, points, a, b, &c)) + return -2; + + if (!find_fourth_point(num_points, points, a, b, c, &d)) + return -3; + + initial_vertices[0] = a; + initial_vertices[1] = b; + initial_vertices[2] = c; + initial_vertices[3] = d; + return 0; +} + +static bool visible(const double* w, const double* plane_point, const double* plane_normal) +{ + return point_plane_distance(w, plane_point, plane_normal) > 0; +} + +void add_facet(const double (*points)[3], int a, int b, int c, int8_t* facet, double* plane_normal, double* barycentre) +{ + calculate_plane_normal(points, a, b, c, plane_normal); + if (visible(barycentre, points[a], plane_normal)) + { + plane_normal[0] = -plane_normal[0]; + plane_normal[1] = -plane_normal[1]; + plane_normal[2] = -plane_normal[2]; + + facet[0] = b; + facet[1] = a; + facet[2] = c; + } + else + { + facet[0] = a; + facet[1] = b; + facet[2] = c; + } +} + +static int initialize_convex_hull(int num_points, const double (*points)[3], int8_t facets[][3], double plane_normal[][3], bool* processed, int* initial_vertices, double* barycentre) +{ + memset(processed, 0, PTM_MAX_POINTS * sizeof(bool)); + memset(barycentre, 0, 3 * sizeof(double)); + int ret = initial_simplex(num_points, points, initial_vertices); + if (ret != 0) + return ret; + + for (int i = 0;i<4;i++) + { + int a = initial_vertices[i]; + processed[a] = true; + + barycentre[0] += points[a][0]; + barycentre[1] += points[a][1]; + barycentre[2] += points[a][2]; + } + barycentre[0] /= 4; + barycentre[1] /= 4; + barycentre[2] /= 4; + + add_facet(points, initial_vertices[0], initial_vertices[1], initial_vertices[2], facets[0], plane_normal[0], barycentre); + add_facet(points, initial_vertices[0], initial_vertices[1], initial_vertices[3], facets[1], plane_normal[1], barycentre); + add_facet(points, initial_vertices[0], initial_vertices[2], initial_vertices[3], facets[2], plane_normal[2], barycentre); + add_facet(points, initial_vertices[1], initial_vertices[2], initial_vertices[3], facets[3], plane_normal[3], barycentre); + return 0; +} + +int get_convex_hull(int num_points, const double (*points)[3], convexhull_t* ch, int8_t simplex[][3]) +{ + assert( num_points == PTM_NUM_POINTS_FCC + || num_points == PTM_NUM_POINTS_HCP + || num_points == PTM_NUM_POINTS_BCC + || num_points == PTM_NUM_POINTS_ICO + || num_points == PTM_NUM_POINTS_SC + || num_points == PTM_NUM_POINTS_DCUB + || num_points == PTM_NUM_POINTS_DHEX); + + int ret = 0; + int num_prev = ch->num_prev; + ch->num_prev = num_points; + if (!ch->ok || 0) + { + ret = initialize_convex_hull(num_points, points, ch->facets, ch->plane_normal, ch->processed, ch->initial_vertices, ch->barycentre); + if (ret != 0) + return ret; + + ch->num_facets = 4; + num_prev = 0; + } + + for (int i = num_prev;iprocessed[i]) + continue; + ch->processed[i] = true; + + int num_to_add = 0; + int8_t to_add[PTM_MAX_FACETS][3]; + int8_t edge_visible[PTM_MAX_POINTS][PTM_MAX_POINTS]; + memset(edge_visible, 0, sizeof(int8_t) * PTM_MAX_POINTS * PTM_MAX_POINTS); + for (int j = 0;jnum_facets;j++) + { + int a = ch->facets[j][0]; + int b = ch->facets[j][1]; + int c = ch->facets[j][2]; + + int u = 0, v = 0, w = 0; + + double distance = point_plane_distance(points[i], points[a], ch->plane_normal[j]); + bool vis = distance > TOLERANCE; + if (vis) + { + u = edge_visible[a][b] |= VISIBLE; + edge_visible[b][a] |= VISIBLE; + + v = edge_visible[b][c] |= VISIBLE; + edge_visible[c][b] |= VISIBLE; + + w = edge_visible[c][a] |= VISIBLE; + edge_visible[a][c] |= VISIBLE; + + memcpy(ch->facets[j], ch->facets[ch->num_facets-1], 3 * sizeof(int8_t)); + memcpy(ch->plane_normal[j], ch->plane_normal[ch->num_facets-1], 3 * sizeof(double)); + ch->num_facets--; + j--; + } + else + { + u = edge_visible[a][b] |= INVISIBLE; + edge_visible[b][a] |= INVISIBLE; + + v = edge_visible[b][c] |= INVISIBLE; + edge_visible[c][b] |= INVISIBLE; + + w = edge_visible[c][a] |= INVISIBLE; + edge_visible[a][c] |= INVISIBLE; + } + + if (u == BOTH) + { + to_add[num_to_add][0] = i; + to_add[num_to_add][1] = a; + to_add[num_to_add][2] = b; + num_to_add++; + } + + if (v == BOTH) + { + to_add[num_to_add][0] = i; + to_add[num_to_add][1] = b; + to_add[num_to_add][2] = c; + num_to_add++; + } + + if (w == BOTH) + { + to_add[num_to_add][0] = i; + to_add[num_to_add][1] = c; + to_add[num_to_add][2] = a; + num_to_add++; + } + } + + for (int j = 0;jnum_facets >= PTM_MAX_FACETS) + return -4; + + add_facet(points, to_add[j][0], to_add[j][1], to_add[j][2], ch->facets[ch->num_facets], ch->plane_normal[ch->num_facets], ch->barycentre); ch->num_facets++; + } + } + + for (int i=0;inum_facets;i++) + { + int a = ch->facets[i][0]; + int b = ch->facets[i][1]; + int c = ch->facets[i][2]; + if (a == 0 || b == 0 || c == 0) + return 1; //central atom contained in convex hull + + simplex[i][0] = a - 1; + simplex[i][1] = b - 1; + simplex[i][2] = c - 1; + } + + return ret; +} + diff --git a/src/PTM/ptm_convex_hull_incremental.h b/src/PTM/ptm_convex_hull_incremental.h new file mode 100644 index 0000000000..563a0c436a --- /dev/null +++ b/src/PTM/ptm_convex_hull_incremental.h @@ -0,0 +1,27 @@ +#ifndef PTM_CONVEX_HULL_INCREMENTAL_H +#define PTM_CONVEX_HULL_INCREMENTAL_H + + +#include +#include +#include "ptm_constants.h" + + +typedef struct +{ + int8_t facets[PTM_MAX_FACETS][3]; + double plane_normal[PTM_MAX_FACETS][3]; + bool processed[PTM_MAX_POINTS]; + int initial_vertices[4]; + double barycentre[3]; + int num_facets; + int num_prev; + bool ok; + +} convexhull_t; + +void add_facet(const double (*points)[3], int a, int b, int c, int8_t* facet, double* plane_normal, double* barycentre); +int get_convex_hull(int num_points, const double (*points)[3], convexhull_t* ch, int8_t simplex[][3]); + +#endif + diff --git a/src/PTM/ptm_deformation_gradient.cpp b/src/PTM/ptm_deformation_gradient.cpp new file mode 100644 index 0000000000..d566d5ca11 --- /dev/null +++ b/src/PTM/ptm_deformation_gradient.cpp @@ -0,0 +1,37 @@ +#include "ptm_deformation_gradient.h" + + +void calculate_deformation_gradient(int num_points, const double (*ideal_points)[3], int8_t* mapping, double (*normalized)[3], const double (*penrose)[3], double* F, double* res) +{ + for (int i = 0;i<3;i++) + { + for (int j = 0;j<3;j++) + { + double acc = 0.0; + for (int k = 0;k +#include "ptm_constants.h" + +void calculate_deformation_gradient(int num_points, const double (*ideal_points)[3], int8_t* mapping, double (*normalized)[3], const double (*penrose)[3], double* F, double* res); + +//sc +#define k_sc 0.5 +const double penrose_sc[PTM_NUM_POINTS_SC][3] = { + {0, 0, 0}, + {0, 0, -k_sc}, + {0, 0, k_sc}, + {0, -k_sc, 0}, + {0, k_sc, 0}, + {-k_sc, 0, 0}, + {k_sc, 0, 0}, + }; + +//fcc +#define k_fcc 0.17677669529663678216 +const double penrose_fcc[PTM_NUM_POINTS_FCC][3] = { + {0, 0, 0}, + {0, k_fcc, k_fcc}, + {0, -k_fcc, -k_fcc}, + {0, k_fcc, -k_fcc}, + {0, -k_fcc, k_fcc}, + {k_fcc, 0, k_fcc}, + {-k_fcc, 0, -k_fcc}, + {k_fcc, 0, -k_fcc}, + {-k_fcc, 0, k_fcc}, + {k_fcc, k_fcc, -0}, + {-k_fcc, -k_fcc, 0}, + {k_fcc, -k_fcc, 0}, + {-k_fcc, k_fcc, -0}, + }; + +//hcp +#define k_hcp 0.17677669529663678216 +const double penrose_hcp[PTM_NUM_POINTS_HCP][3] = { + {0, 0, 0}, + {k_hcp, 0, k_hcp}, + {-k_hcp/3, -4*k_hcp/3, -k_hcp/3}, + {k_hcp, k_hcp, 0}, + {-k_hcp/3, -k_hcp/3, -4*k_hcp/3}, + {0, k_hcp, k_hcp}, + {-4*k_hcp/3, -k_hcp/3, -k_hcp/3}, + {-k_hcp, k_hcp, -0}, + {0, k_hcp, -k_hcp}, + {k_hcp, 0, -k_hcp}, + {k_hcp, -k_hcp, 0}, + {-k_hcp, 0, k_hcp}, + {0, -k_hcp, k_hcp}, + }; + +//ico +#define k_ico 0.13143277802974323576 +#define phi 1.61803398874989490253 +//((1.0 + sqrt(5)) / 2) +const double penrose_ico[PTM_NUM_POINTS_ICO][3] = { + {0, 0, 0}, + {0, k_ico, phi*k_ico}, + {0, -k_ico, -phi*k_ico}, + {0, k_ico, -phi*k_ico}, + {0, -k_ico, phi*k_ico}, + {-k_ico, -phi*k_ico, -0}, + {k_ico, phi*k_ico, 0}, + {k_ico, -phi*k_ico, 0}, + {-k_ico, phi*k_ico, -0}, + {-phi*k_ico, 0, -k_ico}, + {phi*k_ico, 0, k_ico}, + {phi*k_ico, 0, -k_ico}, + {-phi*k_ico, 0, k_ico}, + }; + +//bcc +#define k_bcc 0.11543038598460284017 +const double penrose_bcc[PTM_NUM_POINTS_BCC][3] = { + {0, 0, 0}, + {-k_bcc, -k_bcc, -k_bcc}, + {k_bcc, k_bcc, k_bcc}, + {k_bcc, -k_bcc, -k_bcc}, + {-k_bcc, k_bcc, k_bcc}, + {-k_bcc, k_bcc, -k_bcc}, + {k_bcc, -k_bcc, k_bcc}, + {-k_bcc, -k_bcc, k_bcc}, + {k_bcc, k_bcc, -k_bcc}, + {0, 0, -2*k_bcc}, + {0, 0, 2*k_bcc}, + {0, -2*k_bcc, 0}, + {0, 2*k_bcc, 0}, + {-2*k_bcc, 0, 0}, + {2*k_bcc, 0, -0}, + }; + +//dcub +#define kdcub 0.07095369570691034689 +const double penrose_dcub[PTM_NUM_POINTS_DCUB][3] = { + { 0, 0, 0 }, + { -kdcub, kdcub, kdcub }, + { -kdcub, -kdcub, -kdcub }, + { kdcub, -kdcub, kdcub }, + { kdcub, kdcub, -kdcub }, + { -2 * kdcub, 0, 2 * kdcub }, + { -2 * kdcub, 2 * kdcub, 0 }, + { 0, 2 * kdcub, 2 * kdcub }, + { -2 * kdcub, -2 * kdcub, 0 }, + { -2 * kdcub, 0, -2 * kdcub }, + { 0, -2 * kdcub, -2 * kdcub }, + { 0, -2 * kdcub, 2 * kdcub }, + { 2 * kdcub, -2 * kdcub, 0 }, + { 2 * kdcub, 0, 2 * kdcub }, + { 0, 2 * kdcub, -2 * kdcub }, + { 2 * kdcub, 0, -2 * kdcub }, + { 2 * kdcub, 2 * kdcub, 0 }, + }; + + +#define kdhex 0.04730246380471011397 +const double penrose_dhex[PTM_NUM_POINTS_DHEX][3] = { + { 0, 0, 0 }, + { -kdcub, -kdcub, -kdcub }, + { kdcub, -kdcub, kdcub }, + { -kdcub, kdcub, kdcub }, + { kdcub, kdcub, -kdcub }, + { -kdhex, -4 * kdhex, -kdhex }, + { -4 * kdhex, -kdhex, -kdhex }, + { -kdhex, -kdhex, -4 * kdhex }, + { 2 * kdcub, 0, 2 * kdcub }, + { 2 * kdcub, -2 * kdcub, 0 }, + { 0, -2 * kdcub, 2 * kdcub }, + { 0, 2 * kdcub, 2 * kdcub }, + { -2 * kdcub, 2 * kdcub, 0 }, + { -2 * kdcub, 0, 2 * kdcub }, + { 2 * kdcub, 2 * kdcub, 0 }, + { 0, 2 * kdcub, -2 * kdcub }, + { 2 * kdcub, 0, -2 * kdcub }, + }; +#endif + + diff --git a/src/PTM/ptm_functions.h b/src/PTM/ptm_functions.h new file mode 100644 index 0000000000..cd67d4940d --- /dev/null +++ b/src/PTM/ptm_functions.h @@ -0,0 +1,27 @@ +#ifndef PTM_FUNCTIONS_H +#define PTM_FUNCTIONS_H + +#include +#include +#include "ptm_initialize_data.h" +#include "ptm_constants.h" + + +//------------------------------------ +// function declarations +//------------------------------------ +#ifdef __cplusplus +extern "C" { +#endif + + +int ptm_index( ptm_local_handle_t local_handle, int32_t flags, int num_points, double (*atomic_positions)[3], int32_t* atomic_numbers, bool topological_ordering, //inputs + int32_t* p_type, int32_t* p_alloy_type, double* p_scale, double* p_rmsd, double* q, double* F, double* F_res, double* U, double* P, int8_t* mapping, double* p_interatomic_distance, double* p_lattice_constant); //outputs + + +#ifdef __cplusplus +} +#endif + +#endif + diff --git a/src/PTM/ptm_fundamental_mappings.h b/src/PTM/ptm_fundamental_mappings.h new file mode 100644 index 0000000000..3dd7c39cbb --- /dev/null +++ b/src/PTM/ptm_fundamental_mappings.h @@ -0,0 +1,180 @@ +#ifndef PTM_FUNDAMENTAL_MAPPINGS_H +#define PTM_FUNDAMENTAL_MAPPINGS_H + +#include + +#define NUM_CUBIC_MAPPINGS 24 +#define NUM_ICO_MAPPINGS 60 +#define NUM_HEX_MAPPINGS 6 +#define NUM_DCUB_MAPPINGS 12 +#define NUM_DHEX_MAPPINGS 3 + +const int8_t mapping_sc[NUM_CUBIC_MAPPINGS][PTM_MAX_POINTS] = { + {0, 1, 2, 3, 4, 5, 6}, + {0, 2, 1, 4, 3, 5, 6}, + {0, 2, 1, 3, 4, 6, 5}, + {0, 1, 2, 4, 3, 6, 5}, + {0, 3, 4, 5, 6, 1, 2}, + {0, 5, 6, 2, 1, 4, 3}, + {0, 6, 5, 1, 2, 4, 3}, + {0, 4, 3, 5, 6, 2, 1}, + {0, 5, 6, 1, 2, 3, 4}, + {0, 4, 3, 6, 5, 1, 2}, + {0, 3, 4, 6, 5, 2, 1}, + {0, 6, 5, 2, 1, 3, 4}, + {0, 3, 4, 2, 1, 5, 6}, + {0, 6, 5, 3, 4, 1, 2}, + {0, 1, 2, 5, 6, 4, 3}, + {0, 4, 3, 1, 2, 5, 6}, + {0, 5, 6, 3, 4, 2, 1}, + {0, 1, 2, 6, 5, 3, 4}, + {0, 2, 1, 5, 6, 3, 4}, + {0, 5, 6, 4, 3, 1, 2}, + {0, 3, 4, 1, 2, 6, 5}, + {0, 2, 1, 6, 5, 4, 3}, + {0, 6, 5, 4, 3, 2, 1}, + {0, 4, 3, 2, 1, 6, 5} }; + +const int8_t mapping_fcc[NUM_CUBIC_MAPPINGS][PTM_MAX_POINTS] = { + {0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12}, + {0, 2, 1, 4, 3, 7, 8, 5, 6, 11, 12, 9, 10}, + {0, 3, 4, 1, 2, 6, 5, 8, 7, 12, 11, 10, 9}, + {0, 4, 3, 2, 1, 8, 7, 6, 5, 10, 9, 12, 11}, + {0, 9, 10, 11, 12, 1, 2, 4, 3, 5, 6, 8, 7}, + {0, 7, 8, 6, 5, 11, 12, 10, 9, 2, 1, 4, 3}, + {0, 8, 7, 5, 6, 10, 9, 11, 12, 4, 3, 2, 1}, + {0, 11, 12, 9, 10, 2, 1, 3, 4, 7, 8, 6, 5}, + {0, 5, 6, 8, 7, 9, 10, 12, 11, 1, 2, 3, 4}, + {0, 10, 9, 12, 11, 4, 3, 1, 2, 8, 7, 5, 6}, + {0, 12, 11, 10, 9, 3, 4, 2, 1, 6, 5, 7, 8}, + {0, 6, 5, 7, 8, 12, 11, 9, 10, 3, 4, 1, 2}, + {0, 3, 4, 2, 1, 9, 10, 11, 12, 7, 8, 5, 6}, + {0, 12, 11, 9, 10, 8, 7, 5, 6, 1, 2, 4, 3}, + {0, 5, 6, 7, 8, 4, 3, 2, 1, 11, 12, 10, 9}, + {0, 4, 3, 1, 2, 11, 12, 9, 10, 5, 6, 7, 8}, + {0, 9, 10, 12, 11, 7, 8, 6, 5, 3, 4, 2, 1}, + {0, 8, 7, 6, 5, 1, 2, 3, 4, 12, 11, 9, 10}, + {0, 7, 8, 5, 6, 3, 4, 1, 2, 9, 10, 12, 11}, + {0, 11, 12, 10, 9, 5, 6, 8, 7, 4, 3, 1, 2}, + {0, 1, 2, 4, 3, 12, 11, 10, 9, 8, 7, 6, 5}, + {0, 6, 5, 8, 7, 2, 1, 4, 3, 10, 9, 11, 12}, + {0, 10, 9, 11, 12, 6, 5, 7, 8, 2, 1, 3, 4}, + {0, 2, 1, 3, 4, 10, 9, 12, 11, 6, 5, 8, 7} }; + +const int8_t mapping_bcc[NUM_CUBIC_MAPPINGS][PTM_MAX_POINTS] = { + {0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14}, + {0, 4, 3, 2, 1, 7, 8, 5, 6, 10, 9, 12, 11, 13, 14}, + {0, 6, 5, 7, 8, 2, 1, 3, 4, 10, 9, 11, 12, 14, 13}, + {0, 8, 7, 5, 6, 3, 4, 2, 1, 9, 10, 12, 11, 14, 13}, + {0, 1, 2, 7, 8, 3, 4, 5, 6, 11, 12, 13, 14, 9, 10}, + {0, 4, 3, 7, 8, 5, 6, 2, 1, 13, 14, 10, 9, 12, 11}, + {0, 8, 7, 3, 4, 2, 1, 5, 6, 14, 13, 9, 10, 12, 11}, + {0, 4, 3, 5, 6, 2, 1, 7, 8, 12, 11, 13, 14, 10, 9}, + {0, 1, 2, 5, 6, 7, 8, 3, 4, 13, 14, 9, 10, 11, 12}, + {0, 8, 7, 2, 1, 5, 6, 3, 4, 12, 11, 14, 13, 9, 10}, + {0, 6, 5, 3, 4, 7, 8, 2, 1, 11, 12, 14, 13, 10, 9}, + {0, 6, 5, 2, 1, 3, 4, 7, 8, 14, 13, 10, 9, 11, 12}, + {0, 7, 8, 6, 5, 1, 2, 4, 3, 11, 12, 10, 9, 13, 14}, + {0, 3, 4, 6, 5, 8, 7, 1, 2, 14, 13, 11, 12, 9, 10}, + {0, 5, 6, 1, 2, 8, 7, 4, 3, 9, 10, 13, 14, 12, 11}, + {0, 5, 6, 8, 7, 4, 3, 1, 2, 12, 11, 9, 10, 13, 14}, + {0, 7, 8, 1, 2, 4, 3, 6, 5, 13, 14, 11, 12, 10, 9}, + {0, 3, 4, 8, 7, 1, 2, 6, 5, 9, 10, 14, 13, 11, 12}, + {0, 7, 8, 4, 3, 6, 5, 1, 2, 10, 9, 13, 14, 11, 12}, + {0, 5, 6, 4, 3, 1, 2, 8, 7, 13, 14, 12, 11, 9, 10}, + {0, 3, 4, 1, 2, 6, 5, 8, 7, 11, 12, 9, 10, 14, 13}, + {0, 2, 1, 6, 5, 4, 3, 8, 7, 10, 9, 14, 13, 12, 11}, + {0, 2, 1, 8, 7, 6, 5, 4, 3, 14, 13, 12, 11, 10, 9}, + {0, 2, 1, 4, 3, 8, 7, 6, 5, 12, 11, 10, 9, 14, 13} }; + +const int8_t mapping_ico[NUM_ICO_MAPPINGS][PTM_MAX_POINTS] = { + {0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12}, + {0, 10, 9, 8, 7, 5, 6, 2, 1, 12, 11, 3, 4}, + {0, 1, 2, 9, 10, 7, 8, 11, 12, 5, 6, 3, 4}, + {0, 4, 3, 8, 7, 2, 1, 11, 12, 9, 10, 6, 5}, + {0, 6, 5, 9, 10, 4, 3, 7, 8, 12, 11, 2, 1}, + {0, 12, 11, 3, 4, 7, 8, 10, 9, 2, 1, 6, 5}, + {0, 4, 3, 6, 5, 9, 10, 2, 1, 8, 7, 11, 12}, + {0, 8, 7, 2, 1, 4, 3, 10, 9, 5, 6, 11, 12}, + {0, 10, 9, 3, 4, 12, 11, 5, 6, 8, 7, 2, 1}, + {0, 12, 11, 6, 5, 2, 1, 7, 8, 3, 4, 10, 9}, + {0, 1, 2, 11, 12, 9, 10, 5, 6, 3, 4, 7, 8}, + {0, 8, 7, 11, 12, 5, 6, 4, 3, 2, 1, 10, 9}, + {0, 6, 5, 2, 1, 12, 11, 4, 3, 9, 10, 7, 8}, + {0, 3, 4, 5, 6, 1, 2, 10, 9, 12, 11, 7, 8}, + {0, 3, 4, 7, 8, 12, 11, 1, 2, 5, 6, 10, 9}, + {0, 6, 5, 7, 8, 9, 10, 12, 11, 2, 1, 4, 3}, + {0, 9, 10, 11, 12, 4, 3, 1, 2, 7, 8, 6, 5}, + {0, 11, 12, 9, 10, 1, 2, 4, 3, 8, 7, 5, 6}, + {0, 8, 7, 5, 6, 10, 9, 11, 12, 4, 3, 2, 1}, + {0, 10, 9, 2, 1, 8, 7, 12, 11, 3, 4, 5, 6}, + {0, 12, 11, 2, 1, 10, 9, 6, 5, 7, 8, 3, 4}, + {0, 9, 10, 6, 5, 7, 8, 4, 3, 11, 12, 1, 2}, + {0, 8, 7, 10, 9, 2, 1, 5, 6, 11, 12, 4, 3}, + {0, 6, 5, 12, 11, 7, 8, 2, 1, 4, 3, 9, 10}, + {0, 11, 12, 8, 7, 4, 3, 5, 6, 1, 2, 9, 10}, + {0, 4, 3, 11, 12, 8, 7, 9, 10, 6, 5, 2, 1}, + {0, 4, 3, 9, 10, 11, 12, 6, 5, 2, 1, 8, 7}, + {0, 12, 11, 10, 9, 3, 4, 2, 1, 6, 5, 7, 8}, + {0, 5, 6, 8, 7, 11, 12, 10, 9, 3, 4, 1, 2}, + {0, 7, 8, 6, 5, 12, 11, 9, 10, 1, 2, 3, 4}, + {0, 10, 9, 12, 11, 2, 1, 3, 4, 5, 6, 8, 7}, + {0, 7, 8, 1, 2, 9, 10, 3, 4, 12, 11, 6, 5}, + {0, 5, 6, 1, 2, 3, 4, 11, 12, 8, 7, 10, 9}, + {0, 7, 8, 12, 11, 3, 4, 6, 5, 9, 10, 1, 2}, + {0, 1, 2, 5, 6, 11, 12, 3, 4, 7, 8, 9, 10}, + {0, 11, 12, 1, 2, 5, 6, 9, 10, 4, 3, 8, 7}, + {0, 5, 6, 3, 4, 10, 9, 1, 2, 11, 12, 8, 7}, + {0, 5, 6, 10, 9, 8, 7, 3, 4, 1, 2, 11, 12}, + {0, 3, 4, 12, 11, 10, 9, 7, 8, 1, 2, 5, 6}, + {0, 9, 10, 7, 8, 1, 2, 6, 5, 4, 3, 11, 12}, + {0, 9, 10, 1, 2, 11, 12, 7, 8, 6, 5, 4, 3}, + {0, 7, 8, 3, 4, 1, 2, 12, 11, 6, 5, 9, 10}, + {0, 11, 12, 5, 6, 8, 7, 1, 2, 9, 10, 4, 3}, + {0, 1, 2, 7, 8, 3, 4, 9, 10, 11, 12, 5, 6}, + {0, 3, 4, 10, 9, 5, 6, 12, 11, 7, 8, 1, 2}, + {0, 2, 1, 4, 3, 8, 7, 6, 5, 12, 11, 10, 9}, + {0, 2, 1, 12, 11, 6, 5, 10, 9, 8, 7, 4, 3}, + {0, 9, 10, 4, 3, 6, 5, 11, 12, 1, 2, 7, 8}, + {0, 11, 12, 4, 3, 9, 10, 8, 7, 5, 6, 1, 2}, + {0, 2, 1, 10, 9, 12, 11, 8, 7, 4, 3, 6, 5}, + {0, 5, 6, 11, 12, 1, 2, 8, 7, 10, 9, 3, 4}, + {0, 10, 9, 5, 6, 3, 4, 8, 7, 2, 1, 12, 11}, + {0, 12, 11, 7, 8, 6, 5, 3, 4, 10, 9, 2, 1}, + {0, 7, 8, 9, 10, 6, 5, 1, 2, 3, 4, 12, 11}, + {0, 2, 1, 8, 7, 10, 9, 4, 3, 6, 5, 12, 11}, + {0, 8, 7, 4, 3, 11, 12, 2, 1, 10, 9, 5, 6}, + {0, 6, 5, 4, 3, 2, 1, 9, 10, 7, 8, 12, 11}, + {0, 2, 1, 6, 5, 4, 3, 12, 11, 10, 9, 8, 7}, + {0, 3, 4, 1, 2, 7, 8, 5, 6, 10, 9, 12, 11}, + {0, 4, 3, 2, 1, 6, 5, 8, 7, 11, 12, 9, 10} }; + +const int8_t mapping_hcp[NUM_HEX_MAPPINGS][PTM_MAX_POINTS] = { + {0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12}, + {0, 5, 6, 1, 2, 3, 4, 9, 10, 12, 11, 8, 7}, + {0, 3, 4, 5, 6, 1, 2, 12, 11, 7, 8, 10, 9}, + {0, 4, 3, 2, 1, 6, 5, 11, 12, 10, 9, 7, 8}, + {0, 2, 1, 6, 5, 4, 3, 8, 7, 11, 12, 9, 10}, + {0, 6, 5, 4, 3, 2, 1, 10, 9, 8, 7, 12, 11} }; + +const int8_t mapping_dcub[NUM_DCUB_MAPPINGS][PTM_MAX_POINTS] = { + {0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16}, + {0, 2, 1, 4, 3, 9, 8, 10, 6, 5, 7, 14, 16, 15, 11, 13, 12}, + {0, 4, 3, 2, 1, 15, 16, 14, 12, 13, 11, 10, 8, 9, 7, 5, 6}, + {0, 3, 4, 1, 2, 13, 12, 11, 16, 15, 14, 7, 6, 5, 10, 9, 8}, + {0, 4, 2, 1, 3, 14, 15, 16, 9, 10, 8, 6, 5, 7, 12, 11, 13}, + {0, 4, 1, 3, 2, 16, 14, 15, 7, 6, 5, 13, 11, 12, 9, 8, 10}, + {0, 1, 4, 2, 3, 6, 7, 5, 14, 16, 15, 9, 10, 8, 13, 12, 11}, + {0, 3, 1, 2, 4, 11, 13, 12, 5, 7, 6, 8, 9, 10, 16, 14, 15}, + {0, 3, 2, 4, 1, 12, 11, 13, 10, 8, 9, 15, 14, 16, 5, 6, 7}, + {0, 2, 4, 3, 1, 10, 9, 8, 15, 14, 16, 12, 13, 11, 6, 7, 5}, + {0, 1, 3, 4, 2, 7, 5, 6, 13, 11, 12, 16, 15, 14, 8, 10, 9}, + {0, 2, 3, 1, 4, 8, 10, 9, 11, 12, 13, 5, 7, 6, 15, 16, 14} }; + +const int8_t mapping_dhex[NUM_DHEX_MAPPINGS][PTM_MAX_POINTS] = { + {0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16}, + {0, 1, 3, 4, 2, 6, 7, 5, 11, 13, 12, 14, 16, 15, 8, 9, 10}, + {0, 1, 4, 2, 3, 7, 5, 6, 14, 15, 16, 8, 10, 9, 11, 13, 12} }; + +#endif + diff --git a/src/PTM/ptm_graph_data.cpp b/src/PTM/ptm_graph_data.cpp new file mode 100644 index 0000000000..a591dbf993 --- /dev/null +++ b/src/PTM/ptm_graph_data.cpp @@ -0,0 +1,2059 @@ +#include "ptm_graph_data.h" + + +int8_t automorphisms[65][17] = { + { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16}, + { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, -1, -1, -1, -1}, + { 0, 4, 3, 10, 9, 5, 6, 12, 11, 8, 7, 1, 2, -1, -1, -1, -1}, + { 0, 5, 6, 11, 12, 8, 7, 2, 1, 4, 3, 10, 9, -1, -1, -1, -1}, + { 0, 8, 7, 1, 2, 4, 3, 9, 10, 5, 6, 11, 12, -1, -1, -1, -1}, + { 0, 8, 7, 10, 9, 1, 2, 6, 5, 12, 11, 3, 4, -1, -1, -1, -1}, + { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, -1, -1, -1, -1}, + { 0, 12, 3, 2, 7, 10, 8, 4, 6, 11, 5, 9, 1, -1, -1, -1, -1}, + { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, -1, -1, -1, -1}, + { 0, 4, 11, 8, 1, 9, 12, 10, 3, 5, 7, 2, 6, -1, -1, -1, -1}, + { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, -1, -1, -1, -1}, + { 0, 2, 1, 6, 5, 4, 3, 9, 8, 7, 11, 10, 12, -1, -1, -1, -1}, + { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, -1, -1, -1, -1}, + { 0, 1, 7, 10, 11, 9, 6, 4, 2, 12, 5, 8, 3, -1, -1, -1, -1}, + { 0, 1, 11, 9, 2, 3, 6, 8, 4, 10, 12, 7, 5, -1, -1, -1, -1}, + { 0, 3, 6, 1, 11, 9, 2, 10, 12, 5, 7, 4, 8, -1, -1, -1, -1}, + { 0, 3, 11, 9, 12, 8, 2, 4, 10, 1, 5, 6, 7, -1, -1, -1, -1}, + { 0, 8, 2, 3, 11, 9, 12, 1, 5, 7, 6, 10, 4, -1, -1, -1, -1}, + { 0, 9, 2, 3, 6, 1, 11, 5, 7, 8, 4, 12, 10, -1, -1, -1, -1}, + { 0, 9, 6, 1, 7, 10, 11, 12, 5, 3, 8, 2, 4, -1, -1, -1, -1}, + { 0, 9, 12, 8, 2, 3, 11, 7, 6, 4, 10, 5, 1, -1, -1, -1, -1}, + { 0, 10, 11, 9, 6, 1, 7, 3, 8, 4, 2, 5, 12, -1, -1, -1, -1}, + { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, -1, -1, -1, -1}, + { 0, 3, 2, 8, 6, 5, 12, 11, 7, 4, 9, 1, 10, -1, -1, -1, -1}, + { 0, 3, 11, 10, 6, 9, 7, 4, 2, 12, 1, 8, 5, -1, -1, -1, -1}, + { 0, 3, 12, 9, 6, 8, 11, 7, 4, 2, 10, 5, 1, -1, -1, -1, -1}, + { 0, 5, 12, 3, 2, 8, 6, 4, 9, 10, 1, 7, 11, -1, -1, -1, -1}, + { 0, 8, 6, 5, 12, 3, 2, 10, 1, 11, 7, 9, 4, -1, -1, -1, -1}, + { 0, 8, 11, 3, 12, 9, 6, 2, 10, 1, 5, 4, 7, -1, -1, -1, -1}, + { 0, 9, 6, 8, 11, 3, 12, 1, 5, 7, 4, 10, 2, -1, -1, -1, -1}, + { 0, 9, 7, 3, 11, 10, 6, 12, 1, 5, 8, 2, 4, -1, -1, -1, -1}, + { 0, 10, 6, 9, 7, 3, 11, 5, 8, 4, 2, 1, 12, -1, -1, -1, -1}, + { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, -1, -1}, + { 0, 3, 4, 6, 5, 2, 1, 9, 10, 14, 13, 11, 12, 8, 7, -1, -1}, + { 0, 4, 3, 1, 2, 5, 6, 10, 9, 13, 14, 7, 8, 12, 11, -1, -1}, + { 0, 6, 5, 1, 2, 4, 3, 14, 13, 7, 8, 11, 12, 10, 9, -1, -1}, + { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, -1, -1}, + { 0, 12, 11, 10, 9, 13, 14, 8, 7, 4, 3, 2, 1, 5, 6, -1, -1}, + { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, -1, -1}, + { 0, 9, 10, 13, 14, 11, 12, 8, 7, 1, 2, 5, 6, 3, 4, -1, -1}, + { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, -1, -1}, + { 0, 6, 5, 4, 3, 2, 1, 11, 12, 10, 9, 7, 8, 14, 13, -1, -1}, + { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, -1, -1}, + { 0, 12, 11, 10, 9, 13, 14, 8, 7, 4, 3, 2, 1, 5, 6, -1, -1}, + { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, -1, -1}, + { 0, 9, 10, 13, 14, 11, 12, 8, 7, 1, 2, 5, 6, 3, 4, -1, -1}, + { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, -1, -1}, + { 0, 3, 10, 14, 5, 9, 7, 13, 2, 8, 4, 11, 12, 1, 6, -1, -1}, + { 0, 13, 8, 1, 10, 4, 14, 6, 9, 5, 2, 11, 12, 7, 3, -1, -1}, + { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, -1, -1}, + { 0, 11, 12, 14, 13, 9, 10, 7, 8, 3, 4, 6, 5, 1, 2, -1, -1}, + { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, -1, -1}, + { 0, 13, 14, 11, 12, 5, 6, 10, 9, 1, 2, 7, 8, 4, 3, -1, -1}, + { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16}, + { 0, 4, 3, 2, 1, 15, 14, 16, 13, 12, 11, 10, 9, 8, 6, 5, 7}, + { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16}, + { 0, 4, 1, 3, 2, 15, 14, 16, 5, 7, 6, 13, 11, 12, 10, 8, 9}, + { 0, 4, 2, 1, 3, 16, 15, 14, 10, 8, 9, 5, 6, 7, 13, 12, 11}, + { 0, 4, 3, 2, 1, 14, 16, 15, 13, 12, 11, 10, 9, 8, 5, 7, 6}, + { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16}, + { 0, 3, 4, 1, 2, 12, 13, 11, 16, 14, 15, 7, 5, 6, 9, 10, 8}, + { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16}, + { 0, 4, 1, 3, 2, 16, 15, 14, 6, 5, 7, 13, 11, 12, 10, 8, 9}, + { 0, 4, 2, 1, 3, 14, 16, 15, 10, 8, 9, 6, 7, 5, 13, 12, 11}, + { 0, 4, 3, 2, 1, 15, 14, 16, 13, 12, 11, 10, 9, 8, 6, 5, 7}, +}; + +graph_t graphs_sc[NUM_SC_GRAPHS] = { + +{0, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{1,3,4},{1,3,5},{0,3,4},{0,3,5},{1,2,5},{1,2,4},{0,2,4},{0,2,5}}}, + +}; + +graph_t graphs_ico[NUM_ICO_GRAPHS] = { + +{0, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{0,5,9},{1,2,8},{0,5,7},{2,7,8},{2,5,7},{1,4,8},{1,2,10},{5,9,10},{2,5,10},{4,8,11},{7,8,11},{0,7,11},{0,3,9},{0,3,11},{3,4,11},{3,6,9},{3,4,6},{6,9,10},{1,4,6},{1,6,10}}}, + +}; + +graph_t graphs_fcc[NUM_FCC_GRAPHS] = { + +{0, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{0,4,8},{3,7,9},{2,5,11},{0,7,11},{1,5,9},{2,6,8},{3,4,10},{1,6,10},{3,4,7},{0,4,7},{0,2,11},{0,2,8},{5,7,11},{5,7,9},{1,2,6},{1,2,5},{1,3,10},{1,3,9},{4,6,10},{4,6,8}}}, + +{1, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{0,4,8},{3,7,9},{2,5,11},{0,7,11},{1,5,9},{2,6,8},{3,4,10},{1,6,10},{3,4,7},{0,4,7},{0,2,11},{0,2,8},{5,7,11},{5,7,9},{1,2,6},{1,2,5},{1,3,10},{1,3,9},{6,8,10},{4,8,10}}}, + +{2, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{0,4,8},{3,7,9},{2,5,11},{0,7,11},{1,5,9},{2,6,8},{3,4,10},{1,6,10},{3,4,7},{0,4,7},{0,2,11},{0,2,8},{5,7,11},{5,7,9},{1,2,6},{1,2,5},{3,9,10},{1,9,10},{6,8,10},{4,8,10}}}, + +{3, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{0,4,8},{3,7,9},{2,5,11},{0,7,11},{1,5,9},{2,6,8},{3,4,10},{1,6,10},{3,4,7},{0,4,7},{0,2,11},{0,2,8},{5,7,11},{5,7,9},{2,5,6},{1,5,6},{1,3,10},{1,3,9},{4,6,10},{4,6,8}}}, + +{4, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{0,4,8},{3,7,9},{2,5,11},{0,7,11},{1,5,9},{2,6,8},{3,4,10},{1,6,10},{3,4,7},{0,4,7},{0,2,11},{0,2,8},{5,7,11},{5,7,9},{2,5,6},{1,5,6},{1,3,10},{1,3,9},{6,8,10},{4,8,10}}}, + +{5, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{0,4,8},{3,7,9},{2,5,11},{0,7,11},{1,5,9},{2,6,8},{3,4,10},{1,6,10},{3,4,7},{0,4,7},{0,2,11},{0,2,8},{5,7,11},{5,7,9},{2,5,6},{1,5,6},{3,9,10},{1,9,10},{4,6,10},{4,6,8}}}, + +{6, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{0,4,8},{3,7,9},{2,5,11},{0,7,11},{1,5,9},{2,6,8},{3,4,10},{1,6,10},{3,4,7},{0,4,7},{0,2,11},{0,2,8},{7,9,11},{5,9,11},{1,2,6},{1,2,5},{3,9,10},{1,9,10},{4,6,10},{4,6,8}}}, + +{7, +0, +1, +5, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{0,4,8},{3,7,9},{2,5,11},{0,7,11},{1,5,9},{2,6,8},{3,4,10},{1,6,10},{3,4,7},{0,4,7},{0,2,11},{0,2,8},{7,9,11},{5,9,11},{2,5,6},{1,5,6},{1,3,10},{1,3,9},{6,8,10},{4,8,10}}}, + +}; + +graph_t graphs_hcp[NUM_HCP_GRAPHS] = { + +{0, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{3,8,9},{1,3,9},{2,8,9},{0,2,9},{0,10,11},{0,4,10},{2,6,7},{2,4,6}}}, + +{1, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{3,8,9},{1,3,9},{2,8,9},{0,2,9},{0,10,11},{0,4,10},{4,6,7},{2,4,7}}}, + +{2, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{3,8,9},{1,3,9},{2,8,9},{0,2,9},{4,10,11},{0,4,11},{2,6,7},{2,4,6}}}, + +{3, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{3,8,9},{1,3,9},{2,8,9},{0,2,9},{4,10,11},{0,4,11},{4,6,7},{2,4,7}}}, + +{4, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{3,8,9},{1,3,9},{0,8,9},{0,2,8},{0,10,11},{0,4,10},{2,6,7},{2,4,6}}}, + +{5, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{3,8,9},{1,3,9},{0,8,9},{0,2,8},{0,10,11},{0,4,10},{4,6,7},{2,4,7}}}, + +{6, +0, +6, +2, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{3,8,9},{1,3,9},{0,8,9},{0,2,8},{4,10,11},{0,4,11},{2,6,7},{2,4,6}}}, + +{7, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{3,8,9},{1,3,9},{0,8,9},{0,2,8},{4,10,11},{0,4,11},{4,6,7},{2,4,7}}}, + +{8, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{1,8,9},{1,3,8},{2,8,9},{0,2,9},{0,10,11},{0,4,10},{2,6,7},{2,4,6}}}, + +{9, +0, +8, +2, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{1,8,9},{1,3,8},{2,8,9},{0,2,9},{0,10,11},{0,4,10},{4,6,7},{2,4,7}}}, + +{10, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{1,8,9},{1,3,8},{2,8,9},{0,2,9},{4,10,11},{0,4,11},{4,6,7},{2,4,7}}}, + +{11, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{1,8,9},{1,3,8},{0,8,9},{0,2,8},{0,10,11},{0,4,10},{4,6,7},{2,4,7}}}, + +{12, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{1,8,9},{1,3,8},{0,8,9},{0,2,8},{4,10,11},{0,4,11},{2,6,7},{2,4,6}}}, + +{13, +0, +10, +2, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{5,6,7},{3,5,7},{3,8,9},{1,3,9},{2,8,9},{0,2,9},{0,10,11},{0,4,10},{4,6,7},{2,4,7}}}, + +{14, +0, +12, +10, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{5,6,7},{3,5,7},{3,8,9},{1,3,9},{0,8,9},{0,2,8},{4,10,11},{0,4,11},{2,6,7},{2,4,6}}}, + +{15, +0, +22, +10, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{5,10,11},{1,5,11},{3,6,7},{3,5,6},{1,8,9},{1,3,8},{2,8,9},{0,2,9},{0,10,11},{0,4,10},{4,6,7},{2,4,7}}}, + +}; + +graph_t graphs_bcc[NUM_BCC_GRAPHS] = { + +{0, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{6,9,10},{5,9,10},{4,8,12},{0,8,12},{6,10,12},{0,10,12},{7,8,13},{2,8,13},{5,10,13},{2,10,13},{2,8,10},{0,8,10}}}, + +{1, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{6,9,10},{5,9,10},{4,8,12},{0,8,12},{6,10,12},{0,10,12},{7,8,13},{2,8,13},{5,10,13},{2,10,13},{0,2,10},{0,2,8}}}, + +{2, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{6,9,10},{5,9,10},{4,8,12},{0,8,12},{6,10,12},{0,10,12},{7,8,13},{2,8,13},{2,5,13},{2,5,10},{0,2,10},{0,2,8}}}, + +{3, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{6,9,10},{5,9,10},{4,8,12},{0,8,12},{6,10,12},{0,10,12},{2,7,13},{2,7,8},{2,5,13},{2,5,10},{0,2,10},{0,2,8}}}, + +{4, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{6,9,10},{5,9,10},{4,8,12},{0,8,12},{0,6,12},{0,6,10},{7,8,13},{2,8,13},{2,5,13},{2,5,10},{2,8,10},{0,8,10}}}, + +{5, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{6,9,10},{5,9,10},{4,8,12},{0,8,12},{0,6,12},{0,6,10},{7,8,13},{2,8,13},{2,5,13},{2,5,10},{0,2,10},{0,2,8}}}, + +{6, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{6,9,10},{5,9,10},{4,8,12},{0,8,12},{0,6,12},{0,6,10},{2,7,13},{2,7,8},{5,10,13},{2,10,13},{2,8,10},{0,8,10}}}, + +{7, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{6,9,10},{5,9,10},{4,8,12},{0,8,12},{0,6,12},{0,6,10},{2,7,13},{2,7,8},{5,10,13},{2,10,13},{0,2,10},{0,2,8}}}, + +{8, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{6,9,10},{5,9,10},{4,8,12},{0,8,12},{0,6,12},{0,6,10},{2,7,13},{2,7,8},{2,5,13},{2,5,10},{2,8,10},{0,8,10}}}, + +{9, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{6,9,10},{5,9,10},{4,8,12},{0,8,12},{0,6,12},{0,6,10},{2,7,13},{2,7,8},{2,5,13},{2,5,10},{0,2,10},{0,2,8}}}, + +{10, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{6,9,10},{5,9,10},{0,4,12},{0,4,8},{6,10,12},{0,10,12},{7,8,13},{2,8,13},{2,5,13},{2,5,10},{2,8,10},{0,8,10}}}, + +{11, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{6,9,10},{5,9,10},{0,4,12},{0,4,8},{6,10,12},{0,10,12},{7,8,13},{2,8,13},{2,5,13},{2,5,10},{0,2,10},{0,2,8}}}, + +{12, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{6,9,10},{5,9,10},{0,4,12},{0,4,8},{6,10,12},{0,10,12},{2,7,13},{2,7,8},{2,5,13},{2,5,10},{2,8,10},{0,8,10}}}, + +{13, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{6,9,10},{5,9,10},{0,4,12},{0,4,8},{6,10,12},{0,10,12},{2,7,13},{2,7,8},{2,5,13},{2,5,10},{0,2,10},{0,2,8}}}, + +{14, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{6,9,10},{5,9,10},{0,4,12},{0,4,8},{0,6,12},{0,6,10},{2,7,13},{2,7,8},{2,5,13},{2,5,10},{2,8,10},{0,8,10}}}, + +{15, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{6,9,10},{5,9,10},{0,4,12},{0,4,8},{0,6,12},{0,6,10},{2,7,13},{2,7,8},{2,5,13},{2,5,10},{0,2,10},{0,2,8}}}, + +{16, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{5,6,10},{5,6,9},{4,8,12},{0,8,12},{0,6,12},{0,6,10},{7,8,13},{2,8,13},{2,5,13},{2,5,10},{0,2,10},{0,2,8}}}, + +{17, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{5,6,10},{5,6,9},{4,8,12},{0,8,12},{0,6,12},{0,6,10},{2,7,13},{2,7,8},{5,10,13},{2,10,13},{2,8,10},{0,8,10}}}, + +{18, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{5,6,10},{5,6,9},{4,8,12},{0,8,12},{0,6,12},{0,6,10},{2,7,13},{2,7,8},{5,10,13},{2,10,13},{0,2,10},{0,2,8}}}, + +{19, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{5,6,10},{5,6,9},{4,8,12},{0,8,12},{0,6,12},{0,6,10},{2,7,13},{2,7,8},{2,5,13},{2,5,10},{2,8,10},{0,8,10}}}, + +{20, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, 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0, 0, 0, 0}, +{{4,7,10},{0,5,6},{0,4,5},{0,4,6},{2,11,12},{2,10,12},{2,10,11},{1,7,8},{1,8,9},{1,7,9},{6,12,15},{5,8,13},{3,13,15},{3,13,14},{9,11,14},{3,14,15},{5,7,8},{4,5,7},{6,10,12},{4,6,10},{7,10,11},{7,9,11},{5,13,15},{5,6,15},{8,13,14},{8,9,14},{12,14,15},{11,12,14}}}, + +{4, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{4,7,10},{0,5,6},{0,4,5},{0,4,6},{2,11,12},{2,10,12},{2,10,11},{1,7,8},{1,8,9},{1,7,9},{6,12,15},{5,8,13},{3,13,15},{3,13,14},{9,11,14},{3,14,15},{5,7,8},{4,5,7},{6,10,12},{4,6,10},{7,10,11},{7,9,11},{6,13,15},{5,6,13},{9,13,14},{8,9,13},{11,14,15},{11,12,15}}}, + +{5, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{4,7,10},{0,5,6},{0,4,5},{0,4,6},{2,11,12},{2,10,12},{2,10,11},{1,7,8},{1,8,9},{1,7,9},{6,12,15},{5,8,13},{3,13,15},{3,13,14},{9,11,14},{3,14,15},{5,7,8},{4,5,7},{6,10,12},{4,6,10},{7,10,11},{7,9,11},{6,13,15},{5,6,13},{8,13,14},{8,9,14},{11,14,15},{11,12,15}}}, + +{6, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{4,7,10},{0,5,6},{0,4,5},{0,4,6},{2,11,12},{2,10,12},{2,10,11},{1,7,8},{1,8,9},{1,7,9},{6,12,15},{5,8,13},{3,13,15},{3,13,14},{9,11,14},{3,14,15},{5,7,8},{4,5,7},{6,10,12},{4,6,10},{7,10,11},{7,9,11},{6,13,15},{5,6,13},{8,13,14},{8,9,14},{12,14,15},{11,12,14}}}, + +{7, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{4,7,10},{0,5,6},{0,4,5},{0,4,6},{2,11,12},{2,10,12},{2,10,11},{1,7,8},{1,8,9},{1,7,9},{6,12,15},{5,8,13},{3,13,15},{3,13,14},{9,11,14},{3,14,15},{5,7,8},{4,5,7},{6,10,12},{4,6,10},{9,10,11},{7,9,10},{5,13,15},{5,6,15},{8,13,14},{8,9,14},{12,14,15},{11,12,14}}}, + +{8, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{4,7,10},{0,5,6},{0,4,5},{0,4,6},{2,11,12},{2,10,12},{2,10,11},{1,7,8},{1,8,9},{1,7,9},{6,12,15},{5,8,13},{3,13,15},{3,13,14},{9,11,14},{3,14,15},{5,7,8},{4,5,7},{6,10,12},{4,6,10},{9,10,11},{7,9,10},{6,13,15},{5,6,13},{9,13,14},{8,9,13},{11,14,15},{11,12,15}}}, + +{9, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{4,7,10},{0,5,6},{0,4,5},{0,4,6},{2,11,12},{2,10,12},{2,10,11},{1,7,8},{1,8,9},{1,7,9},{6,12,15},{5,8,13},{3,13,15},{3,13,14},{9,11,14},{3,14,15},{5,7,8},{4,5,7},{6,10,12},{4,6,10},{9,10,11},{7,9,10},{6,13,15},{5,6,13},{8,13,14},{8,9,14},{11,14,15},{11,12,15}}}, + +{10, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{4,7,10},{0,5,6},{0,4,5},{0,4,6},{2,11,12},{2,10,12},{2,10,11},{1,7,8},{1,8,9},{1,7,9},{6,12,15},{5,8,13},{3,13,15},{3,13,14},{9,11,14},{3,14,15},{5,7,8},{4,5,7},{4,10,12},{4,6,12},{9,10,11},{7,9,10},{6,13,15},{5,6,13},{8,13,14},{8,9,14},{11,14,15},{11,12,15}}}, + +{11, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{4,7,10},{0,5,6},{0,4,5},{0,4,6},{2,11,12},{2,10,12},{2,10,11},{1,7,8},{1,8,9},{1,7,9},{6,12,15},{5,8,13},{3,13,15},{3,13,14},{9,11,14},{3,14,15},{4,7,8},{4,5,8},{6,10,12},{4,6,10},{7,10,11},{7,9,11},{5,13,15},{5,6,15},{9,13,14},{8,9,13},{12,14,15},{11,12,14}}}, + +}; + +graph_t graphs_dhex[NUM_DHEX_GRAPHS] = { + +{0, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{5,9,12},{4,5,9},{11,13,14},{10,11,13},{6,11,14},{5,6,11},{4,8,15},{4,6,15},{7,13,15},{7,8,15}}}, + +{1, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{5,9,12},{4,5,9},{11,13,14},{10,11,13},{6,11,14},{5,6,11},{4,8,15},{4,6,15},{8,13,15},{7,8,13}}}, + +{2, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{5,9,12},{4,5,9},{11,13,14},{10,11,13},{6,11,14},{5,6,11},{6,8,15},{4,6,8},{7,13,15},{7,8,15}}}, + +{3, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{5,9,12},{4,5,9},{11,13,14},{10,11,13},{6,11,14},{5,6,11},{6,8,15},{4,6,8},{8,13,15},{7,8,13}}}, + +{4, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{5,9,12},{4,5,9},{11,13,14},{10,11,13},{5,11,14},{5,6,14},{4,8,15},{4,6,15},{8,13,15},{7,8,13}}}, + +{5, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{5,9,12},{4,5,9},{11,13,14},{10,11,13},{5,11,14},{5,6,14},{6,8,15},{4,6,8},{7,13,15},{7,8,15}}}, + +{6, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{5,9,12},{4,5,9},{11,13,14},{10,11,13},{5,11,14},{5,6,14},{6,8,15},{4,6,8},{8,13,15},{7,8,13}}}, + +{7, +0, +53, +2, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{5,9,12},{4,5,9},{10,13,14},{10,11,14},{6,11,14},{5,6,11},{4,8,15},{4,6,15},{8,13,15},{7,8,13}}}, + +{8, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{5,9,12},{4,5,9},{10,13,14},{10,11,14},{6,11,14},{5,6,11},{6,8,15},{4,6,8},{7,13,15},{7,8,15}}}, + +{9, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{5,9,12},{4,5,9},{10,13,14},{10,11,14},{6,11,14},{5,6,11},{6,8,15},{4,6,8},{8,13,15},{7,8,13}}}, + +{10, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{5,9,12},{4,5,9},{10,13,14},{10,11,14},{5,11,14},{5,6,14},{4,8,15},{4,6,15},{8,13,15},{7,8,13}}}, + +{11, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{5,9,12},{4,5,9},{10,13,14},{10,11,14},{5,11,14},{5,6,14},{6,8,15},{4,6,8},{7,13,15},{7,8,15}}}, + +{12, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{5,9,12},{4,5,9},{10,13,14},{10,11,14},{5,11,14},{5,6,14},{6,8,15},{4,6,8},{8,13,15},{7,8,13}}}, + +{13, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{4,9,12},{4,5,12},{11,13,14},{10,11,13},{5,11,14},{5,6,14},{4,8,15},{4,6,15},{8,13,15},{7,8,13}}}, + +{14, +0, +55, +4, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{4,9,12},{4,5,12},{11,13,14},{10,11,13},{5,11,14},{5,6,14},{6,8,15},{4,6,8},{7,13,15},{7,8,15}}}, + +{15, +0, +59, +2, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{4,9,12},{4,5,12},{11,13,14},{10,11,13},{5,11,14},{5,6,14},{6,8,15},{4,6,8},{8,13,15},{7,8,13}}}, + +{16, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{4,9,12},{4,5,12},{10,13,14},{10,11,14},{6,11,14},{5,6,11},{4,8,15},{4,6,15},{8,13,15},{7,8,13}}}, + +{17, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{4,9,12},{4,5,12},{10,13,14},{10,11,14},{6,11,14},{5,6,11},{6,8,15},{4,6,8},{8,13,15},{7,8,13}}}, + +{18, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{4,9,12},{4,5,12},{10,13,14},{10,11,14},{5,11,14},{5,6,14},{4,8,15},{4,6,15},{8,13,15},{7,8,13}}}, + +{19, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{4,9,12},{4,5,12},{10,13,14},{10,11,14},{5,11,14},{5,6,14},{6,8,15},{4,6,8},{8,13,15},{7,8,13}}}, + +{20, +0, +61, +4, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{7,10,12},{7,9,12},{5,9,12},{4,5,9},{10,13,14},{10,11,14},{6,11,14},{5,6,11},{4,8,15},{4,6,15},{8,13,15},{7,8,13}}}, + +{21, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{7,10,12},{7,9,12},{5,9,12},{4,5,9},{10,13,14},{10,11,14},{6,11,14},{5,6,11},{6,8,15},{4,6,8},{8,13,15},{7,8,13}}}, + +{22, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{7,10,12},{7,9,12},{5,9,12},{4,5,9},{10,13,14},{10,11,14},{5,11,14},{5,6,14},{6,8,15},{4,6,8},{8,13,15},{7,8,13}}}, + +{23, +0, +0, +1, +{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, +{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{7,10,12},{7,9,12},{4,9,12},{4,5,12},{10,13,14},{10,11,14},{5,11,14},{5,6,14},{6,8,15},{4,6,8},{8,13,15},{7,8,13}}}, + +}; + diff --git a/src/PTM/ptm_graph_data.h b/src/PTM/ptm_graph_data.h new file mode 100644 index 0000000000..11f46a471f --- /dev/null +++ b/src/PTM/ptm_graph_data.h @@ -0,0 +1,37 @@ +#ifndef PTM_GRAPH_DATA_H +#define PTM_GRAPH_DATA_H + +#include +#include "ptm_constants.h" + + +typedef struct +{ + int id; + uint64_t hash; + int automorphism_index; + int num_automorphisms; + int8_t canonical_labelling[PTM_MAX_POINTS]; + int8_t facets[PTM_MAX_FACETS][3]; +} graph_t; + +#define NUM_SC_GRAPHS 1 +#define NUM_ICO_GRAPHS 1 +#define NUM_FCC_GRAPHS 8 +#define NUM_HCP_GRAPHS 16 +#define NUM_BCC_GRAPHS 218 +#define NUM_DCUB_GRAPHS 12 +#define NUM_DHEX_GRAPHS 24 + +extern int8_t automorphisms[][PTM_MAX_POINTS]; + +extern graph_t graphs_sc[NUM_SC_GRAPHS]; +extern graph_t graphs_fcc[NUM_FCC_GRAPHS]; +extern graph_t graphs_hcp[NUM_HCP_GRAPHS]; +extern graph_t graphs_ico[NUM_ICO_GRAPHS]; +extern graph_t graphs_bcc[NUM_BCC_GRAPHS]; +extern graph_t graphs_dcub[NUM_DCUB_GRAPHS]; +extern graph_t graphs_dhex[NUM_DHEX_GRAPHS]; + +#endif + diff --git a/src/PTM/ptm_graph_tools.cpp b/src/PTM/ptm_graph_tools.cpp new file mode 100644 index 0000000000..89d07fc87a --- /dev/null +++ b/src/PTM/ptm_graph_tools.cpp @@ -0,0 +1,52 @@ +#include +#include +#include "ptm_graph_tools.h" +#include "ptm_constants.h" + + +bool build_facet_map(int num_facets, int8_t facets[][3], int8_t common[PTM_MAX_NBRS][PTM_MAX_NBRS]) +{ + memset(common, -1, sizeof(int8_t) * PTM_MAX_NBRS * PTM_MAX_NBRS); + + for (int i = 0;i +#include "ptm_constants.h" + +bool build_facet_map(int num_facets, int8_t facets[][3], int8_t common[PTM_MAX_NBRS][PTM_MAX_NBRS]); +int graph_degree(int num_facets, int8_t facets[][3], int num_nodes, int8_t* degree); + +#endif + diff --git a/src/PTM/ptm_index.cpp b/src/PTM/ptm_index.cpp new file mode 100644 index 0000000000..7b6618848e --- /dev/null +++ b/src/PTM/ptm_index.cpp @@ -0,0 +1,218 @@ +#include +#include +#include +#include +#include +#include +#include +#include "ptm_convex_hull_incremental.h" +#include "ptm_graph_data.h" +#include "ptm_deformation_gradient.h" +#include "ptm_alloy_types.h" +#include "ptm_neighbour_ordering.h" +#include "ptm_normalize_vertices.h" +#include "ptm_quat.h" +#include "ptm_polar.h" +#include "ptm_initialize_data.h" +#include "ptm_structure_matcher.h" +#include "ptm_functions.h" +#include "ptm_constants.h" + + +//todo: verify that c == norm(template[1]) +static double calculate_interatomic_distance(int type, double scale) +{ + assert(type >= 1 && type <= 7); + double c[8] = {0, 1, 1, (7. - 3.5 * sqrt(3)), 1, 1, sqrt(3) * 4. / (6 * sqrt(2) + sqrt(3)), sqrt(3) * 4. / (6 * sqrt(2) + sqrt(3))}; + return c[type] / scale; +} + +static double calculate_lattice_constant(int type, double interatomic_distance) +{ + assert(type >= 1 && type <= 7); + double c[8] = {0, 2 / sqrt(2), 2 / sqrt(2), 2. / sqrt(3), 2 / sqrt(2), 1, 4 / sqrt(3), 4 / sqrt(3)}; + return c[type] * interatomic_distance; +} + +static int rotate_into_fundamental_zone(int type, double* q) +{ + if (type == PTM_MATCH_SC) return rotate_quaternion_into_cubic_fundamental_zone(q); + if (type == PTM_MATCH_FCC) return rotate_quaternion_into_cubic_fundamental_zone(q); + if (type == PTM_MATCH_BCC) return rotate_quaternion_into_cubic_fundamental_zone(q); + if (type == PTM_MATCH_ICO) return rotate_quaternion_into_icosahedral_fundamental_zone(q); + if (type == PTM_MATCH_HCP) return rotate_quaternion_into_hcp_fundamental_zone(q); + if (type == PTM_MATCH_DCUB) return rotate_quaternion_into_diamond_cubic_fundamental_zone(q); + if (type == PTM_MATCH_DHEX) return rotate_quaternion_into_diamond_hexagonal_fundamental_zone(q); + return -1; +} + +static void order_points(ptm_local_handle_t local_handle, int num_points, double (*unpermuted_points)[3], int32_t* unpermuted_numbers, bool topological_ordering, + int8_t* ordering, double (*points)[3], int32_t* numbers) +{ + if (topological_ordering) + { + double normalized_points[PTM_MAX_INPUT_POINTS][3]; + normalize_vertices(num_points, unpermuted_points, normalized_points); + int ret = calculate_neighbour_ordering((void*)local_handle, num_points, (const double (*)[3])normalized_points, ordering); + if (ret != 0) + topological_ordering = false; + } + + if (!topological_ordering) + for (int i=0;iref_struct; + if (ref == NULL) + return; + + *p_type = ref->type; + if (p_alloy_type != NULL && unpermuted_numbers != NULL) + *p_alloy_type = find_alloy_type(ref, res->mapping, numbers); + + int bi = rotate_into_fundamental_zone(ref->type, res->q); + int8_t temp[PTM_MAX_POINTS]; + for (int i=0;inum_nbrs+1;i++) + temp[ref->mapping[bi][i]] = res->mapping[i]; + + memcpy(res->mapping, temp, (ref->num_nbrs+1) * sizeof(int8_t)); + + if (F != NULL && F_res != NULL) + { + double scaled_points[PTM_MAX_INPUT_POINTS][3]; + + subtract_barycentre(ref->num_nbrs + 1, points, scaled_points); + for (int i = 0;inum_nbrs + 1;i++) + { + scaled_points[i][0] *= res->scale; + scaled_points[i][1] *= res->scale; + scaled_points[i][2] *= res->scale; + } + calculate_deformation_gradient(ref->num_nbrs + 1, ref->points, res->mapping, scaled_points, ref->penrose, F, F_res); + + if (P != NULL && U != NULL) + polar_decomposition_3x3(F, false, U, P); + } + + if (mapping != NULL) + for (int i=0;inum_nbrs + 1;i++) + mapping[i] = ordering[res->mapping[i]]; + + double interatomic_distance = calculate_interatomic_distance(ref->type, res->scale); + double lattice_constant = calculate_lattice_constant(ref->type, interatomic_distance); + + if (p_interatomic_distance != NULL) + *p_interatomic_distance = interatomic_distance; + + if (p_lattice_constant != NULL) + *p_lattice_constant = lattice_constant; + + *p_rmsd = res->rmsd; + *p_scale = res->scale; + memcpy(q, res->q, 4 * sizeof(double)); +} + + +extern bool ptm_initialized; + +int ptm_index( ptm_local_handle_t local_handle, int32_t flags, + int num_points, double (*unpermuted_points)[3], int32_t* unpermuted_numbers, bool topological_ordering, + int32_t* p_type, int32_t* p_alloy_type, double* p_scale, double* p_rmsd, double* q, double* F, double* F_res, + double* U, double* P, int8_t* mapping, double* p_interatomic_distance, double* p_lattice_constant) +{ + assert(ptm_initialized); + assert(num_points <= PTM_MAX_INPUT_POINTS); + + if (flags & PTM_CHECK_SC) + assert(num_points >= PTM_NUM_POINTS_SC); + + if (flags & PTM_CHECK_BCC) + assert(num_points >= PTM_NUM_POINTS_BCC); + + if (flags & (PTM_CHECK_FCC | PTM_CHECK_HCP | PTM_CHECK_ICO)) + assert(num_points >= PTM_NUM_POINTS_FCC); + + if (flags & (PTM_CHECK_DCUB | PTM_CHECK_DHEX)) + assert(num_points >= PTM_NUM_POINTS_DCUB); + + int ret = 0; + result_t res; + res.ref_struct = NULL; + res.rmsd = INFINITY; + + int8_t ordering[PTM_MAX_INPUT_POINTS]; + double points[PTM_MAX_POINTS][3]; + int32_t numbers[PTM_MAX_POINTS]; + + int8_t dordering[PTM_MAX_INPUT_POINTS]; + double dpoints[PTM_MAX_POINTS][3]; + int32_t dnumbers[PTM_MAX_POINTS]; + + convexhull_t ch; + double ch_points[PTM_MAX_INPUT_POINTS][3]; + + if (flags & (PTM_CHECK_SC | PTM_CHECK_FCC | PTM_CHECK_HCP | PTM_CHECK_ICO | PTM_CHECK_BCC)) + { + int num_lpoints = std::min(std::min(PTM_MAX_POINTS, 20), num_points); + order_points(local_handle, num_lpoints, unpermuted_points, unpermuted_numbers, topological_ordering, ordering, points, numbers); + normalize_vertices(num_lpoints, points, ch_points); + ch.ok = false; + + if (flags & PTM_CHECK_SC) + ret = match_general(&structure_sc, ch_points, points, &ch, &res); + + if (flags & (PTM_CHECK_FCC | PTM_CHECK_HCP | PTM_CHECK_ICO)) + ret = match_fcc_hcp_ico(ch_points, points, flags, &ch, &res); + + if (flags & PTM_CHECK_BCC) + ret = match_general(&structure_bcc, ch_points, points, &ch, &res); + } + + if (flags & (PTM_CHECK_DCUB | PTM_CHECK_DHEX)) + { + ret = calculate_diamond_neighbour_ordering(num_points, unpermuted_points, unpermuted_numbers, dordering, dpoints, dnumbers); + if (ret == 0) + { + normalize_vertices(PTM_NUM_NBRS_DCUB + 1, dpoints, ch_points); + ch.ok = false; + + ret = match_dcub_dhex(ch_points, dpoints, flags, &ch, &res); + } + } + + if (res.ref_struct != NULL && (res.ref_struct->type == PTM_MATCH_DCUB || res.ref_struct->type == PTM_MATCH_DHEX)) + { + output_data( &res, num_points, unpermuted_numbers, dpoints, dnumbers, dordering, + p_type, p_alloy_type, p_scale, p_rmsd, q, F, F_res, + U, P, mapping, p_interatomic_distance, p_lattice_constant); + } + else + { + output_data( &res, num_points, unpermuted_numbers, points, numbers, ordering, + p_type, p_alloy_type, p_scale, p_rmsd, q, F, F_res, + U, P, mapping, p_interatomic_distance, p_lattice_constant); + } + + return PTM_NO_ERROR; +} + diff --git a/src/PTM/ptm_initialize_data.cpp b/src/PTM/ptm_initialize_data.cpp new file mode 100644 index 0000000000..6157ff862f --- /dev/null +++ b/src/PTM/ptm_initialize_data.cpp @@ -0,0 +1,71 @@ +#include +#include +#include +#include +#include +#include +#include +#include "ptm_initialize_data.h" + + +static void make_facets_clockwise(int num_facets, int8_t (*facets)[3], const double (*points)[3]) +{ + double plane_normal[3]; + double origin[3] = {0, 0, 0}; + + for (int i = 0;inum_graphs;i++) + { + int8_t code[2 * PTM_MAX_EDGES]; + int8_t degree[PTM_MAX_NBRS]; + int _max_degree = graph_degree(s->num_facets, s->graphs[i].facets, s->num_nbrs, degree); + assert(_max_degree <= s->max_degree); + + make_facets_clockwise(s->num_facets, s->graphs[i].facets, &s->points[1]); + int ret = canonical_form_coloured(s->num_facets, s->graphs[i].facets, s->num_nbrs, degree, colours, s->graphs[i].canonical_labelling, (int8_t*)&code[0], &s->graphs[i].hash); + if (ret != 0) + return ret; + } + + return PTM_NO_ERROR; +} + +bool ptm_initialized = false; +int ptm_initialize_global() +{ + if (ptm_initialized) + return PTM_NO_ERROR; + + int8_t colours[PTM_MAX_POINTS] = {0}; + int8_t dcolours[PTM_MAX_POINTS] = {1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}; + + int ret = initialize_graphs(&structure_sc, colours); + ret |= initialize_graphs(&structure_fcc, colours); + ret |= initialize_graphs(&structure_hcp, colours); + ret |= initialize_graphs(&structure_ico, colours); + ret |= initialize_graphs(&structure_bcc, colours); + ret |= initialize_graphs(&structure_dcub, dcolours); + ret |= initialize_graphs(&structure_dhex, dcolours); + + if (ret == PTM_NO_ERROR) + ptm_initialized = true; + + return ret; +} + +ptm_local_handle_t ptm_initialize_local() +{ + assert(ptm_initialized); + return (ptm_local_handle_t)voronoi_initialize_local(); +} + +void ptm_uninitialize_local(ptm_local_handle_t ptr) +{ + voronoi_uninitialize_local(ptr); +} + diff --git a/src/PTM/ptm_initialize_data.h b/src/PTM/ptm_initialize_data.h new file mode 100644 index 0000000000..f381dd864b --- /dev/null +++ b/src/PTM/ptm_initialize_data.h @@ -0,0 +1,61 @@ +#ifndef PTM_INITIALIZE_DATA_H +#define PTM_INITIALIZE_DATA_H + + +#include "ptm_graph_data.h" +#include "ptm_graph_tools.h" +#include "ptm_deformation_gradient.h" +#include "ptm_fundamental_mappings.h" +#include "ptm_neighbour_ordering.h" +#include "ptm_canonical_coloured.h" +#include "ptm_convex_hull_incremental.h" + + +typedef struct +{ + int type; + int num_nbrs; + int num_facets; + int max_degree; + int num_graphs; + int num_mappings; + graph_t* graphs; + const double (*points)[3]; + const double (*penrose)[3]; + const int8_t (*mapping)[PTM_MAX_POINTS]; +} refdata_t; + + +//refdata_t structure_sc = { .type = PTM_MATCH_SC, .num_nbrs = 6, .num_facets = 8, .max_degree = 4, .num_graphs = NUM_SC_GRAPHS, .graphs = graphs_sc, .points = ptm_template_sc, .penrose = penrose_sc , .mapping = mapping_sc }; +const refdata_t structure_sc = { PTM_MATCH_SC, 6, 8, 4, NUM_SC_GRAPHS, NUM_CUBIC_MAPPINGS, graphs_sc, ptm_template_sc, penrose_sc, mapping_sc }; +const refdata_t structure_fcc = { PTM_MATCH_FCC, 12, 20, 6, NUM_FCC_GRAPHS, NUM_CUBIC_MAPPINGS, graphs_fcc, ptm_template_fcc, penrose_fcc, mapping_fcc }; +const refdata_t structure_hcp = { PTM_MATCH_HCP, 12, 20, 6, NUM_HCP_GRAPHS, NUM_HEX_MAPPINGS, graphs_hcp, ptm_template_hcp, penrose_hcp, mapping_hcp }; +const refdata_t structure_ico = { PTM_MATCH_ICO, 12, 20, 6, NUM_ICO_GRAPHS, NUM_ICO_MAPPINGS, graphs_ico, ptm_template_ico, penrose_ico, mapping_ico }; +const refdata_t structure_bcc = { PTM_MATCH_BCC, 14, 24, 8, NUM_BCC_GRAPHS, NUM_CUBIC_MAPPINGS, graphs_bcc, ptm_template_bcc, penrose_bcc, mapping_bcc }; +const refdata_t structure_dcub = { PTM_MATCH_DCUB, 16, 28, 8, NUM_DCUB_GRAPHS, NUM_DCUB_MAPPINGS, graphs_dcub, ptm_template_dcub, penrose_dcub, mapping_dcub }; +const refdata_t structure_dhex = { PTM_MATCH_DHEX, 16, 28, 8, NUM_DHEX_GRAPHS, NUM_DHEX_MAPPINGS, graphs_dhex, ptm_template_dhex, penrose_dhex, mapping_dhex }; + + +#ifdef __cplusplus +extern "C" { +#endif + +typedef struct ptm_local_handle* ptm_local_handle_t; +ptm_local_handle_t ptm_initialize_local(); +void ptm_uninitialize_local(ptm_local_handle_t ptr); + +int ptm_initialize_global(); + +//------------------------------------ +// global initialization switch +//------------------------------------ +extern bool ptm_initialized; + + +#ifdef __cplusplus +} +#endif + + +#endif + diff --git a/src/PTM/ptm_neighbour_ordering.cpp b/src/PTM/ptm_neighbour_ordering.cpp new file mode 100644 index 0000000000..6b5ac9601a --- /dev/null +++ b/src/PTM/ptm_neighbour_ordering.cpp @@ -0,0 +1,203 @@ +#include +#include +#include +#include +#include +#include "ptm_constants.h" +#include "ptm_voronoi_cell.h" +using namespace voro; + + + +typedef struct +{ + double area; + double dist; + int index; +} sorthelper_t; + +static bool sorthelper_compare(sorthelper_t const& a, sorthelper_t const& b) +{ + if (a.area > b.area) + return true; + + if (a.area < b.area) + return false; + + if (a.dist < b.dist) + return true; + + return false; +} + +//todo: change voronoi code to return errors rather than exiting +static int calculate_voronoi_face_areas(int num_points, const double (*_points)[3], double* normsq, double max_norm, voronoicell_neighbor* v, std::vector& nbr_indices, std::vector& face_areas) +{ + const double k = 1000 * max_norm; //todo: reduce this constant + v->init(-k,k,-k,k,-k,k); + + for (int i=1;inplane(x,y,z,normsq[i],i); + } + + v->neighbors(nbr_indices); + v->face_areas(face_areas); + return 0; +} + +int calculate_neighbour_ordering(void* _voronoi_handle, int num_points, const double (*_points)[3], int8_t* ordering) +{ + assert(num_points <= PTM_MAX_INPUT_POINTS); + + voronoicell_neighbor* voronoi_handle = (voronoicell_neighbor*)_voronoi_handle; + + double max_norm = 0; + double points[PTM_MAX_INPUT_POINTS][3]; + double normsq[PTM_MAX_INPUT_POINTS]; + for (int i = 0;i nbr_indices(num_points + 6); + std::vector face_areas(num_points + 6); + int ret = calculate_voronoi_face_areas(num_points, points, normsq, max_norm, voronoi_handle, nbr_indices, face_areas); + if (ret != 0) + return ret; + + double areas[PTM_MAX_INPUT_POINTS]; + memset(areas, 0, num_points * sizeof(double)); + areas[0] = INFINITY; + for (size_t i=0;i 0) + areas[index] = face_areas[i]; + } + + sorthelper_t data[PTM_MAX_INPUT_POINTS]; + for (int i=0;i= 3) + continue; + + ordering[1 + 4 + 3 * p + counts[p]] = q; + counts[p]++; + index++; + num_found++; + if (num_found >= 12) + break; + } + + if (num_found != 12) + return -1; + + for (int i=0;i + + +void subtract_barycentre(int num, double (*points)[3], double (*normalized)[3]) +{ + //calculate barycentre + double sum[3] = {0, 0, 0}; + for (int i=0;i nor the names of its contributors may be used to + * endorse or promote products derived from this software without specific prior written + * permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS + * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT + * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A + * PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT + * HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT + * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, + * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY + * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE + * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + * Source: started anew. + * + * Change History: + * 2009/04/13 Started source + * 2010/03/28 Modified FastCalcRMSDAndRotation() to handle tiny qsqr + * If trying all rows of the adjoint still gives too small + * qsqr, then just return identity matrix. (DLT) + * 2010/06/30 Fixed prob in assigning A[9] = 0 in InnerProduct() + * invalid mem access + * 2011/02/21 Made CenterCoords use weights + * 2011/05/02 Finally changed CenterCoords declaration in qcprot.h + * Also changed some functions to static + * 2011/07/08 put in fabs() to fix taking sqrt of small neg numbers, fp error + * 2012/07/26 minor changes to comments and main.c, more info (v.1.4) + * + * 2016/05/29 QCP method adapted for polar decomposition of a 3x3 matrix, + * for use in Polyhedral Template Matching. + * + ******************************************************************************/ + +#include +#include +#include +#include "ptm_quat.h" + + +static void matmul_3x3(double* A, double* x, double* b) +{ + b[0] = A[0] * x[0] + A[1] * x[3] + A[2] * x[6]; + b[3] = A[3] * x[0] + A[4] * x[3] + A[5] * x[6]; + b[6] = A[6] * x[0] + A[7] * x[3] + A[8] * x[6]; + + b[1] = A[0] * x[1] + A[1] * x[4] + A[2] * x[7]; + b[4] = A[3] * x[1] + A[4] * x[4] + A[5] * x[7]; + b[7] = A[6] * x[1] + A[7] * x[4] + A[8] * x[7]; + + b[2] = A[0] * x[2] + A[1] * x[5] + A[2] * x[8]; + b[5] = A[3] * x[2] + A[4] * x[5] + A[5] * x[8]; + b[8] = A[6] * x[2] + A[7] * x[5] + A[8] * x[8]; +} + +static double matrix_determinant_3x3(double* A) +{ + return A[0] * (A[4]*A[8] - A[5]*A[7]) + - A[1] * (A[3]*A[8] - A[5]*A[6]) + + A[2] * (A[3]*A[7] - A[4]*A[6]); +} + +static void flip_matrix(double* A) +{ + for (int i=0;i<9;i++) + A[i] = -A[i]; +} + +static bool optimal_quaternion(double* A, bool polar, double E0, double* p_nrmsdsq, double* qopt) +{ + const double evecprec = 1e-6; + const double evalprec = 1e-11; + + double Sxx = A[0], Sxy = A[1], Sxz = A[2], + Syx = A[3], Syy = A[4], Syz = A[5], + Szx = A[6], Szy = A[7], Szz = A[8]; + + double Sxx2 = Sxx * Sxx, Syy2 = Syy * Syy, Szz2 = Szz * Szz, + Sxy2 = Sxy * Sxy, Syz2 = Syz * Syz, Sxz2 = Sxz * Sxz, + Syx2 = Syx * Syx, Szy2 = Szy * Szy, Szx2 = Szx * Szx; + + double fnorm_squared = Sxx2 + Syy2 + Szz2 + Sxy2 + Syz2 + Sxz2 + Syx2 + Szy2 + Szx2; + + double SyzSzymSyySzz2 = 2.0 * (Syz * Szy - Syy * Szz); + double Sxx2Syy2Szz2Syz2Szy2 = Syy2 + Szz2 - Sxx2 + Syz2 + Szy2; + double SxzpSzx = Sxz + Szx; + double SyzpSzy = Syz + Szy; + double SxypSyx = Sxy + Syx; + double SyzmSzy = Syz - Szy; + double SxzmSzx = Sxz - Szx; + double SxymSyx = Sxy - Syx; + double SxxpSyy = Sxx + Syy; + double SxxmSyy = Sxx - Syy; + double Sxy2Sxz2Syx2Szx2 = Sxy2 + Sxz2 - Syx2 - Szx2; + + double C[3]; + C[0] = Sxy2Sxz2Syx2Szx2 * Sxy2Sxz2Syx2Szx2 + + (Sxx2Syy2Szz2Syz2Szy2 + SyzSzymSyySzz2) * (Sxx2Syy2Szz2Syz2Szy2 - SyzSzymSyySzz2) + + (-(SxzpSzx)*(SyzmSzy)+(SxymSyx)*(SxxmSyy-Szz)) * (-(SxzmSzx)*(SyzpSzy)+(SxymSyx)*(SxxmSyy+Szz)) + + (-(SxzpSzx)*(SyzpSzy)-(SxypSyx)*(SxxpSyy-Szz)) * (-(SxzmSzx)*(SyzmSzy)-(SxypSyx)*(SxxpSyy+Szz)) + + (+(SxypSyx)*(SyzpSzy)+(SxzpSzx)*(SxxmSyy+Szz)) * (-(SxymSyx)*(SyzmSzy)+(SxzpSzx)*(SxxpSyy+Szz)) + + (+(SxypSyx)*(SyzmSzy)+(SxzmSzx)*(SxxmSyy-Szz)) * (-(SxymSyx)*(SyzpSzy)+(SxzmSzx)*(SxxpSyy-Szz)); + + C[1] = 8.0 * (Sxx*Syz*Szy + Syy*Szx*Sxz + Szz*Sxy*Syx - Sxx*Syy*Szz - Syz*Szx*Sxy - Szy*Syx*Sxz); + C[2] = -2.0 * fnorm_squared; + + //Newton-Raphson + double mxEigenV = polar ? sqrt(3 * fnorm_squared) : E0; + if (mxEigenV > evalprec) + { + for (int i=0;i<50;i++) + { + double oldg = mxEigenV; + double x2 = mxEigenV*mxEigenV; + double b = (x2 + C[2])*mxEigenV; + double a = b + C[1]; + double delta = ((a * mxEigenV + C[0]) / (2 * x2 * mxEigenV + b + a)); + mxEigenV -= delta; + if (fabs(mxEigenV - oldg) < fabs(evalprec * mxEigenV)) + break; + } + } + else + { + mxEigenV = 0.0; + } + + (*p_nrmsdsq) = std::max(0.0, 2.0 * (E0 - mxEigenV)); + + double a11 = SxxpSyy + Szz - mxEigenV; + double a12 = SyzmSzy; + double a13 = -SxzmSzx; + double a14 = SxymSyx; + + double a21 = SyzmSzy; + double a22 = SxxmSyy - Szz -mxEigenV; + double a23 = SxypSyx; + double a24 = SxzpSzx; + + double a31 = a13; + double a32 = a23; + double a33 = Syy - Sxx - Szz - mxEigenV; + double a34 = SyzpSzy; + + double a41 = a14; + double a42 = a24; + double a43 = a34; + double a44 = Szz - SxxpSyy - mxEigenV; + + double a3344_4334 = a33 * a44 - a43 * a34; + double a3244_4234 = a32 * a44 - a42 * a34; + double a3243_4233 = a32 * a43 - a42 * a33; + double a3143_4133 = a31 * a43 - a41 * a33; + double a3144_4134 = a31 * a44 - a41 * a34; + double a3142_4132 = a31 * a42 - a41 * a32; + double a1324_1423 = a13 * a24 - a14 * a23; + double a1224_1422 = a12 * a24 - a14 * a22; + double a1223_1322 = a12 * a23 - a13 * a22; + double a1124_1421 = a11 * a24 - a14 * a21; + double a1123_1321 = a11 * a23 - a13 * a21; + double a1122_1221 = a11 * a22 - a12 * a21; + + double q[4][4]; + q[0][0] = a12 * a3344_4334 - a13 * a3244_4234 + a14 * a3243_4233; + q[0][1] = -a11 * a3344_4334 + a13 * a3144_4134 - a14 * a3143_4133; + q[0][2] = a11 * a3244_4234 - a12 * a3144_4134 + a14 * a3142_4132; + q[0][3] = -a11 * a3243_4233 + a12 * a3143_4133 - a13 * a3142_4132; + + q[1][0] = a22 * a3344_4334 - a23 * a3244_4234 + a24 * a3243_4233; + q[1][1] = -a21 * a3344_4334 + a23 * a3144_4134 - a24 * a3143_4133; + q[1][2] = a21 * a3244_4234 - a22 * a3144_4134 + a24 * a3142_4132; + q[1][3] = -a21 * a3243_4233 + a22 * a3143_4133 - a23 * a3142_4132; + + q[2][0] = a32 * a1324_1423 - a33 * a1224_1422 + a34 * a1223_1322; + q[2][1] = -a31 * a1324_1423 + a33 * a1124_1421 - a34 * a1123_1321; + q[2][2] = a31 * a1224_1422 - a32 * a1124_1421 + a34 * a1122_1221; + q[2][3] = -a31 * a1223_1322 + a32 * a1123_1321 - a33 * a1122_1221; + + q[3][0] = a42 * a1324_1423 - a43 * a1224_1422 + a44 * a1223_1322; + q[3][1] = -a41 * a1324_1423 + a43 * a1124_1421 - a44 * a1123_1321; + q[3][2] = a41 * a1224_1422 - a42 * a1124_1421 + a44 * a1122_1221; + q[3][3] = -a41 * a1223_1322 + a42 * a1123_1321 - a43 * a1122_1221; + + double qsqr[4]; + for (int i=0;i<4;i++) + qsqr[i] = q[i][0]*q[i][0] + q[i][1]*q[i][1] + q[i][2]*q[i][2] + q[i][3]*q[i][3]; + + int bi = 0; + double max = 0; + for (int i=0;i<4;i++) + { + if (qsqr[i] > max) + { + bi = i; + max = qsqr[i]; + } + } + + bool too_small = false; + if (qsqr[bi] < evecprec) + { + //if qsqr is still too small, return the identity rotation. + q[bi][0] = 1; + q[bi][1] = 0; + q[bi][2] = 0; + q[bi][3] = 0; + too_small = true; + } + else + { + double normq = sqrt(qsqr[bi]); + q[bi][0] /= normq; + q[bi][1] /= normq; + q[bi][2] /= normq; + q[bi][3] /= normq; + } + + memcpy(qopt, q[bi], 4 * sizeof(double)); + return !too_small; +} + +int polar_decomposition_3x3(double* _A, bool right_sided, double* U, double* P) +{ + double A[9]; + memcpy(A, _A, 9 * sizeof(double)); + + double det = matrix_determinant_3x3(A); + if (det < 0) + flip_matrix(A); + + double q[4]; + double nrmsdsq = 0; + optimal_quaternion(A, true, -1, &nrmsdsq, q); + q[0] = -q[0]; + quaternion_to_rotation_matrix(q, U); + + if (det < 0) + flip_matrix(U); + + double UT[9] = {U[0], U[3], U[6], U[1], U[4], U[7], U[2], U[5], U[8]}; + + if (right_sided) + matmul_3x3(UT, _A, P); + else + matmul_3x3(_A, UT, P); + + return 0; +} + +void InnerProduct(double *A, int num, const double (*coords1)[3], double (*coords2)[3], int8_t* permutation) +{ + A[0] = A[1] = A[2] = A[3] = A[4] = A[5] = A[6] = A[7] = A[8] = 0.0; + + for (int i = 0; i < num; ++i) + { + double x1 = coords1[i][0]; + double y1 = coords1[i][1]; + double z1 = coords1[i][2]; + + double x2 = coords2[permutation[i]][0]; + double y2 = coords2[permutation[i]][1]; + double z2 = coords2[permutation[i]][2]; + + A[0] += x1 * x2; + A[1] += x1 * y2; + A[2] += x1 * z2; + + A[3] += y1 * x2; + A[4] += y1 * y2; + A[5] += y1 * z2; + + A[6] += z1 * x2; + A[7] += z1 * y2; + A[8] += z1 * z2; + } +} + +int FastCalcRMSDAndRotation(double *A, double E0, double *p_nrmsdsq, double *q, double* U) +{ + optimal_quaternion(A, false, E0, p_nrmsdsq, q); + quaternion_to_rotation_matrix(q, U); + return 0; +} + diff --git a/src/PTM/ptm_polar.h b/src/PTM/ptm_polar.h new file mode 100644 index 0000000000..d5aa3d9540 --- /dev/null +++ b/src/PTM/ptm_polar.h @@ -0,0 +1,12 @@ +#ifndef PTM_POLAR_H +#define PTM_POLAR_H + +#include +#include + +int polar_decomposition_3x3(double* _A, bool right_sided, double* U, double* P); +void InnerProduct(double *A, int num, const double (*coords1)[3], double (*coords2)[3], int8_t* permutation); +int FastCalcRMSDAndRotation(double *A, double E0, double *p_nrmsdsq, double *q, double* U); + +#endif + diff --git a/src/PTM/ptm_quat.cpp b/src/PTM/ptm_quat.cpp new file mode 100644 index 0000000000..f55aff3d2b --- /dev/null +++ b/src/PTM/ptm_quat.cpp @@ -0,0 +1,396 @@ +#include +#include +#include + + +#define SIGN(x) (x >= 0 ? 1 : -1) +#define MIN(X, Y) (((X) < (Y)) ? (X) : (Y)) +#define MAX(X, Y) (((X) > (Y)) ? (X) : (Y)) + + +#define SQRT_2 1.4142135623730951454746218587388284504414 +#define HALF_SQRT_2 0.7071067811865474617150084668537601828575 + +#define PHI 1.6180339887498949025257388711906969547272 +#define HALF_PHI 0.8090169943749474512628694355953484773636 + +#define INV_PHI 0.6180339887498947915034364086750429123640 +#define HALF_INV_PHI 0.3090169943749473957517182043375214561820 + +#define SQRT_5_ 2.23606797749978969640917366873127623544061835961152572427089 +#define SQRT_2_3 0.8164965809277260344600790631375275552273 +#define SQRT_1_6 0.4082482904638630172300395315687637776136 + + +double generator_cubic[24][4] = { {1, 0, 0, 0 }, + {0, 1, 0, 0 }, + {0, 0, 1, 0 }, + {0, 0, 0, 1 }, + {0.5, 0.5, 0.5, 0.5 }, + {0.5, 0.5, -0.5, 0.5 }, + {0.5, -0.5, 0.5, 0.5 }, + {0.5, -0.5, -0.5, 0.5 }, + {-0.5, 0.5, 0.5, 0.5 }, + {-0.5, 0.5, -0.5, 0.5 }, + {-0.5, -0.5, 0.5, 0.5 }, + {-0.5, -0.5, -0.5, 0.5 }, + {HALF_SQRT_2, HALF_SQRT_2, 0, 0 }, + {HALF_SQRT_2, 0, HALF_SQRT_2, 0 }, + {HALF_SQRT_2, 0, 0, HALF_SQRT_2 }, + {-HALF_SQRT_2, HALF_SQRT_2, 0, 0 }, + {-HALF_SQRT_2, 0, HALF_SQRT_2, 0 }, + {-HALF_SQRT_2, 0, 0, HALF_SQRT_2 }, + {0, HALF_SQRT_2, HALF_SQRT_2, 0 }, + {0, HALF_SQRT_2, 0, HALF_SQRT_2 }, + {0, 0, HALF_SQRT_2, HALF_SQRT_2 }, + {0, -HALF_SQRT_2, HALF_SQRT_2, 0 }, + {0, -HALF_SQRT_2, 0, HALF_SQRT_2 }, + {0, 0, -HALF_SQRT_2, HALF_SQRT_2 } }; + +double generator_diamond_cubic[12][4] = { {1, 0, 0, 0 }, + {0, 1, 0, 0 }, + {0, 0, 1, 0 }, + {0, 0, 0, 1 }, + {0.5, 0.5, 0.5, 0.5 }, + {0.5, 0.5, -0.5, 0.5 }, + {0.5, -0.5, 0.5, 0.5 }, + {0.5, -0.5, -0.5, 0.5 }, + {-0.5, 0.5, 0.5, 0.5 }, + {-0.5, 0.5, -0.5, 0.5 }, + {-0.5, -0.5, 0.5, 0.5 }, + {-0.5, -0.5, -0.5, 0.5 } }; + +double generator_hcp[6][4] = { {1, 0, 0, 0}, + {0.5, 0.5, 0.5, 0.5}, + {0.5, -0.5, -0.5, -0.5}, + {0, SQRT_2_3, -SQRT_1_6, -SQRT_1_6}, + {0, SQRT_1_6, -SQRT_2_3, SQRT_1_6}, + {0, SQRT_1_6, SQRT_1_6, -SQRT_2_3} }; + +double generator_diamond_hexagonal[3][4] = { {1, 0, 0, 0}, + {0.5, 0.5, 0.5, 0.5}, + {0.5, -0.5, -0.5, -0.5} }; + +double generator_icosahedral[60][4] = { {1, 0, 0, 0}, + {HALF_PHI, -HALF_INV_PHI, -0.5, 0}, + {HALF_PHI, 0, -HALF_INV_PHI, -0.5}, + {HALF_PHI, -0.5, 0, -HALF_INV_PHI}, + {HALF_PHI, HALF_INV_PHI, -0.5, 0}, + {HALF_PHI, 0, HALF_INV_PHI, -0.5}, + {HALF_PHI, -0.5, 0, HALF_INV_PHI}, + {HALF_PHI, 0.5, 0, -HALF_INV_PHI}, + {HALF_PHI, 0, -HALF_INV_PHI, 0.5}, + {HALF_PHI, -HALF_INV_PHI, 0.5, 0}, + {HALF_PHI, 0, HALF_INV_PHI, 0.5}, + {HALF_PHI, HALF_INV_PHI, 0.5, 0}, + {HALF_PHI, 0.5, 0, HALF_INV_PHI}, + {0.5, HALF_PHI, -HALF_INV_PHI, 0}, + {0.5, HALF_PHI, HALF_INV_PHI, 0}, + {0.5, 0.5, 0.5, 0.5}, + {0.5, 0.5, 0.5, -0.5}, + {0.5, 0.5, -0.5, 0.5}, + {0.5, 0.5, -0.5, -0.5}, + {0.5, HALF_INV_PHI, 0, HALF_PHI}, + {0.5, HALF_INV_PHI, 0, -HALF_PHI}, + {0.5, 0, HALF_PHI, -HALF_INV_PHI}, + {0.5, 0, HALF_PHI, HALF_INV_PHI}, + {0.5, 0, -HALF_PHI, -HALF_INV_PHI}, + {0.5, 0, -HALF_PHI, HALF_INV_PHI}, + {0.5, -HALF_INV_PHI, 0, HALF_PHI}, + {0.5, -HALF_INV_PHI, 0, -HALF_PHI}, + {0.5, -0.5, 0.5, 0.5}, + {0.5, -0.5, 0.5, -0.5}, + {0.5, -0.5, -0.5, 0.5}, + {0.5, -0.5, -0.5, -0.5}, + {0.5, -HALF_PHI, -HALF_INV_PHI, 0}, + {0.5, -HALF_PHI, HALF_INV_PHI, 0}, + {HALF_INV_PHI, -HALF_PHI, 0, -0.5}, + {HALF_INV_PHI, 0, -0.5, -HALF_PHI}, + {HALF_INV_PHI, -0.5, -HALF_PHI, 0}, + {HALF_INV_PHI, 0, 0.5, -HALF_PHI}, + {HALF_INV_PHI, -HALF_PHI, 0, 0.5}, + {HALF_INV_PHI, 0.5, -HALF_PHI, 0}, + {HALF_INV_PHI, HALF_PHI, 0, -0.5}, + {HALF_INV_PHI, -0.5, HALF_PHI, 0}, + {HALF_INV_PHI, 0, -0.5, HALF_PHI}, + {HALF_INV_PHI, HALF_PHI, 0, 0.5}, + {HALF_INV_PHI, 0, 0.5, HALF_PHI}, + {HALF_INV_PHI, 0.5, HALF_PHI, 0}, + {0, 1, 0, 0}, + {0, HALF_PHI, -0.5, HALF_INV_PHI}, + {0, HALF_PHI, -0.5, -HALF_INV_PHI}, + {0, HALF_PHI, 0.5, HALF_INV_PHI}, + {0, HALF_PHI, 0.5, -HALF_INV_PHI}, + {0, 0.5, HALF_INV_PHI, -HALF_PHI}, + {0, 0.5, HALF_INV_PHI, HALF_PHI}, + {0, 0.5, -HALF_INV_PHI, -HALF_PHI}, + {0, 0.5, -HALF_INV_PHI, HALF_PHI}, + {0, HALF_INV_PHI, -HALF_PHI, 0.5}, + {0, HALF_INV_PHI, -HALF_PHI, -0.5}, + {0, HALF_INV_PHI, HALF_PHI, 0.5}, + {0, HALF_INV_PHI, HALF_PHI, -0.5}, + {0, 0, 1, 0}, + {0, 0, 0, 1} }; + +static void quat_rot(double* r, double* a, double* b) +{ + b[0] = (r[0] * a[0] - r[1] * a[1] - r[2] * a[2] - r[3] * a[3]); + b[1] = (r[0] * a[1] + r[1] * a[0] + r[2] * a[3] - r[3] * a[2]); + b[2] = (r[0] * a[2] - r[1] * a[3] + r[2] * a[0] + r[3] * a[1]); + b[3] = (r[0] * a[3] + r[1] * a[2] - r[2] * a[1] + r[3] * a[0]); +} + +static int rotate_quaternion_into_fundamental_zone(int num_generators, double (*generator)[4], double* q) +{ + double max = 0.0; + int i = 0, bi = -1; + for (i=0;i max) + { + max = t; + bi = i; + } + } + + double f[4]; + quat_rot(q, generator[bi], f); + memcpy(q, &f, 4 * sizeof(double)); + if (q[0] < 0) + { + q[0] = -q[0]; + q[1] = -q[1]; + q[2] = -q[2]; + q[3] = -q[3]; + } + + return bi; +} + +int rotate_quaternion_into_cubic_fundamental_zone(double* q) +{ + return rotate_quaternion_into_fundamental_zone(24, generator_cubic, q); +} + +int rotate_quaternion_into_diamond_cubic_fundamental_zone(double* q) +{ + return rotate_quaternion_into_fundamental_zone(12, generator_diamond_cubic, q); +} + +int rotate_quaternion_into_icosahedral_fundamental_zone(double* q) +{ + return rotate_quaternion_into_fundamental_zone(60, generator_icosahedral, q); +} + +int rotate_quaternion_into_hcp_fundamental_zone(double* q) +{ + return rotate_quaternion_into_fundamental_zone(6, generator_hcp, q); +} + +int rotate_quaternion_into_diamond_hexagonal_fundamental_zone(double* q) +{ + return rotate_quaternion_into_fundamental_zone(3, generator_diamond_hexagonal, q); +} + +double quat_dot(double* a, double* b) +{ + return a[0] * b[0] + + a[1] * b[1] + + a[2] * b[2] + + a[3] * b[3]; +} + +double quat_size(double* q) +{ + return sqrt(quat_dot(q, q)); +} + +void normalize_quaternion(double* q) +{ + double size = quat_size(q); + + q[0] /= size; + q[1] /= size; + q[2] /= size; + q[3] /= size; +} + +void rotation_matrix_to_quaternion(double* u, double* q) +{ + double r11 = u[0]; + double r12 = u[1]; + double r13 = u[2]; + double r21 = u[3]; + double r22 = u[4]; + double r23 = u[5]; + double r31 = u[6]; + double r32 = u[7]; + double r33 = u[8]; + + q[0] = (1.0 + r11 + r22 + r33) / 4.0; + q[1] = (1.0 + r11 - r22 - r33) / 4.0; + q[2] = (1.0 - r11 + r22 - r33) / 4.0; + q[3] = (1.0 - r11 - r22 + r33) / 4.0; + + q[0] = sqrt(MAX(0, q[0])); + q[1] = sqrt(MAX(0, q[1])); + q[2] = sqrt(MAX(0, q[2])); + q[3] = sqrt(MAX(0, q[3])); + + double m0 = MAX(q[0], q[1]); + double m1 = MAX(q[2], q[3]); + double max = MAX(m0, m1); + + int i = 0; + for (i=0;i<4;i++) + if (q[i] == max) + break; + + if (i == 0) + { + q[1] *= SIGN(r32 - r23); + q[2] *= SIGN(r13 - r31); + q[3] *= SIGN(r21 - r12); + } + else if (i == 1) + { + q[0] *= SIGN(r32 - r23); + q[2] *= SIGN(r21 + r12); + q[3] *= SIGN(r13 + r31); + } + else if (i == 2) + { + q[0] *= SIGN(r13 - r31); + q[1] *= SIGN(r21 + r12); + q[3] *= SIGN(r32 + r23); + } + else if (i == 3) + { + q[0] *= SIGN(r21 - r12); + q[1] *= SIGN(r31 + r13); + q[2] *= SIGN(r32 + r23); + } + + normalize_quaternion(q); +} + +void quaternion_to_rotation_matrix(double* q, double* u) +{ + double a = q[0]; + double b = q[1]; + double c = q[2]; + double d = q[3]; + + u[0] = a*a + b*b - c*c - d*d; + u[1] = 2*b*c - 2*a*d; + u[2] = 2*b*d + 2*a*c; + + u[3] = 2*b*c + 2*a*d; + u[4] = a*a - b*b + c*c - d*d; + u[5] = 2*c*d - 2*a*b; + + u[6] = 2*b*d - 2*a*c; + u[7] = 2*c*d + 2*a*b; + u[8] = a*a - b*b - c*c + d*d; +} + +double quat_quick_misorientation(double* q1, double* q2) +{ + double t = quat_dot(q1, q2); + t = MIN(1, MAX(-1, t)); + return 2 * t * t - 1; +} + +double quat_misorientation(double* q1, double* q2) +{ + return acos(quat_quick_misorientation(q1, q2)); +} + + +double quat_quick_disorientation_cubic(double* q0, double* q1) +{ + double qrot[4]; + double qinv[4] = {q0[0], -q0[1], -q0[2], -q0[3]}; + quat_rot(qinv, q1, qrot); + + rotate_quaternion_into_cubic_fundamental_zone(qrot); + double t = qrot[0]; + t = MIN(1, MAX(-1, t)); + return 2 * t * t - 1; +} + +double quat_disorientation_cubic(double* q0, double* q1) +{ + return acos(quat_quick_disorientation_cubic(q0, q1)); +} + +double quat_quick_disorientation_diamond_cubic(double* q0, double* q1) +{ + double qrot[4]; + double qinv[4] = {q0[0], -q0[1], -q0[2], -q0[3]}; + quat_rot(qinv, q1, qrot); + + rotate_quaternion_into_diamond_cubic_fundamental_zone(qrot); + double t = qrot[0]; + t = MIN(1, MAX(-1, t)); + return 2 * t * t - 1; +} + +double quat_disorientation_diamond_cubic(double* q0, double* q1) +{ + return acos(quat_quick_disorientation_diamond_cubic(q0, q1)); +} + +double quat_quick_disorientation_hcp(double* q0, double* q1) +{ + double qrot[4]; + double qinv[4] = {q0[0], -q0[1], -q0[2], -q0[3]}; + quat_rot(qinv, q1, qrot); + + rotate_quaternion_into_hcp_fundamental_zone(qrot); + double t = qrot[0]; + t = MIN(1, MAX(-1, t)); + return 2 * t * t - 1; +} + +double quat_disorientation_hcp(double* q0, double* q1) +{ + return acos(quat_quick_disorientation_hcp(q0, q1)); +} + +double quat_quick_disorientation_diamond_hexagonal(double* q0, double* q1) +{ + double qrot[4]; + double qinv[4] = {q0[0], -q0[1], -q0[2], -q0[3]}; + quat_rot(qinv, q1, qrot); + + rotate_quaternion_into_diamond_hexagonal_fundamental_zone(qrot); + double t = qrot[0]; + t = MIN(1, MAX(-1, t)); + return 2 * t * t - 1; +} + +double quat_disorientation_diamond_hexagonal(double* q0, double* q1) +{ + return acos(quat_quick_disorientation_diamond_hexagonal(q0, q1)); +} + +double quat_quick_disorientation_icosahedral(double* q0, double* q1) +{ + double qrot[4]; + double qinv[4] = {q0[0], -q0[1], -q0[2], -q0[3]}; + quat_rot(qinv, q1, qrot); + + rotate_quaternion_into_icosahedral_fundamental_zone(qrot); + double t = qrot[0]; + t = MIN(1, MAX(-1, t)); + return 2 * t * t - 1; +} + +double quat_disorientation_icosahedral(double* q0, double* q1) +{ + return acos(quat_quick_disorientation_icosahedral(q0, q1)); +} + diff --git a/src/PTM/ptm_quat.h b/src/PTM/ptm_quat.h new file mode 100644 index 0000000000..381c3ce876 --- /dev/null +++ b/src/PTM/ptm_quat.h @@ -0,0 +1,32 @@ +#ifndef PTM_QUAT_H +#define PTM_QUAT_H + +int rotate_quaternion_into_cubic_fundamental_zone(double* q); +int rotate_quaternion_into_diamond_cubic_fundamental_zone(double* q); +int rotate_quaternion_into_icosahedral_fundamental_zone(double* q); +int rotate_quaternion_into_hcp_fundamental_zone(double* q); +int rotate_quaternion_into_diamond_hexagonal_fundamental_zone(double* q); + +void normalize_quaternion(double* q); +void quaternion_to_rotation_matrix(double* q, double* U); +void rotation_matrix_to_quaternion(double* u, double* q); +double quat_dot(double* a, double* b); +double quat_quick_misorientation(double* q1, double* q2); +double quat_misorientation(double* q1, double* q2); + +double quat_quick_disorientation_cubic(double* q0, double* q1); +double quat_disorientation_cubic(double* q0, double* q1); +double quat_quick_disorientation_diamond_cubic(double* q0, double* q1); +double quat_disorientation_diamond_cubic(double* q0, double* q1); +double quat_quick_disorientation_hcp(double* q0, double* q1); +double quat_disorientation_hcp(double* q0, double* q1); +double quat_quick_disorientation_diamond_hexagonal(double* q0, double* q1); +double quat_disorientation_diamond_hexagonal(double* q0, double* q1); +double quat_quick_disorientation_icosahedral(double* q0, double* q1); +double quat_disorientation_icosahedral(double* q0, double* q1); + +#endif + + + + diff --git a/src/PTM/ptm_structure_matcher.cpp b/src/PTM/ptm_structure_matcher.cpp new file mode 100644 index 0000000000..7eb0a44143 --- /dev/null +++ b/src/PTM/ptm_structure_matcher.cpp @@ -0,0 +1,294 @@ +#include +#include +#include +#include +#include +#include +#include +#include "ptm_convex_hull_incremental.h" +#include "ptm_canonical_coloured.h" +#include "ptm_graph_data.h" +#include "ptm_graph_tools.h" +#include "ptm_normalize_vertices.h" +#include "ptm_polar.h" +#include "ptm_structure_matcher.h" +#include "ptm_constants.h" + + +static double calc_rmsd(int num_points, const double (*ideal_points)[3], double (*normalized)[3], int8_t* mapping, + double G1, double G2, double E0, double* q, double* p_scale) +{ + double A0[9]; + InnerProduct(A0, num_points, ideal_points, normalized, mapping); + + double nrmsdsq, rot[9]; + FastCalcRMSDAndRotation(A0, E0, &nrmsdsq, q, rot); + + double k0 = 0; + for (int i=0;inum_nbrs + 1; + const double (*ideal_points)[3] = s->points; + int8_t inverse_labelling[PTM_MAX_POINTS]; + int8_t mapping[PTM_MAX_POINTS]; + + for (int i=0; inum_graphs;i++) + { + if (hash != s->graphs[i].hash) + continue; + + graph_t* gref = &s->graphs[i]; + for (int j = 0;jnum_automorphisms;j++) + { + for (int k=0;kautomorphism_index + j][k]] = inverse_labelling[ gref->canonical_labelling[k] ]; + + double q[4], scale = 0; + double rmsd = calc_rmsd(num_points, ideal_points, normalized, mapping, G1, G2, E0, q, &scale); + if (rmsd < res->rmsd) + { + res->rmsd = rmsd; + res->scale = scale; + res->ref_struct = s; + memcpy(res->q, q, 4 * sizeof(double)); + memcpy(res->mapping, mapping, sizeof(int8_t) * num_points); + } + } + } +} + +int match_general(const refdata_t* s, double (*ch_points)[3], double (*points)[3], convexhull_t* ch, result_t* res) +{ + int8_t degree[PTM_MAX_NBRS]; + int8_t facets[PTM_MAX_FACETS][3]; + + int ret = get_convex_hull(s->num_nbrs + 1, (const double (*)[3])ch_points, ch, facets); + ch->ok = ret >= 0; + if (ret != 0) + return PTM_NO_ERROR; + + if (ch->num_facets != s->num_facets) + return PTM_NO_ERROR; //incorrect number of facets in convex hull + + int max_degree = graph_degree(s->num_facets, facets, s->num_nbrs, degree); + if (max_degree > s->max_degree) + return PTM_NO_ERROR; + + if (s->type == PTM_MATCH_SC) + for (int i = 0;inum_nbrs;i++) + if (degree[i] != 4) + return PTM_NO_ERROR; + + double normalized[PTM_MAX_POINTS][3]; + subtract_barycentre(s->num_nbrs + 1, points, normalized); + + int8_t code[2 * PTM_MAX_EDGES]; + int8_t colours[PTM_MAX_POINTS] = {0}; + int8_t canonical_labelling[PTM_MAX_POINTS]; + uint64_t hash = 0; + ret = canonical_form_coloured(s->num_facets, facets, s->num_nbrs, degree, colours, canonical_labelling, &code[0], &hash); + if (ret != PTM_NO_ERROR) + return ret; + + check_graphs(s, hash, canonical_labelling, normalized, res); + return PTM_NO_ERROR; +} + +int match_fcc_hcp_ico(double (*ch_points)[3], double (*points)[3], int32_t flags, convexhull_t* ch, result_t* res) +{ + int num_nbrs = structure_fcc.num_nbrs; + int num_facets = structure_fcc.num_facets; + int max_degree = structure_fcc.max_degree; + + int8_t degree[PTM_MAX_NBRS]; + int8_t facets[PTM_MAX_FACETS][3]; + + int ret = get_convex_hull(num_nbrs + 1, (const double (*)[3])ch_points, ch, facets); + ch->ok = ret >= 0; + if (ret != 0) + return PTM_NO_ERROR; + + if (ch->num_facets != num_facets) + return PTM_NO_ERROR; //incorrect number of facets in convex hull + + int _max_degree = graph_degree(num_facets, facets, num_nbrs, degree); + if (_max_degree > max_degree) + return PTM_NO_ERROR; + + double normalized[PTM_MAX_POINTS][3]; + subtract_barycentre(num_nbrs + 1, points, normalized); + + int8_t code[2 * PTM_MAX_EDGES]; + int8_t colours[PTM_MAX_POINTS] = {0}; + int8_t canonical_labelling[PTM_MAX_POINTS]; + uint64_t hash = 0; + ret = canonical_form_coloured(num_facets, facets, num_nbrs, degree, colours, canonical_labelling, &code[0], &hash); + if (ret != PTM_NO_ERROR) + return ret; + + if (flags & PTM_CHECK_FCC) check_graphs(&structure_fcc, hash, canonical_labelling, normalized, res); + if (flags & PTM_CHECK_HCP) check_graphs(&structure_hcp, hash, canonical_labelling, normalized, res); + if (flags & PTM_CHECK_ICO) check_graphs(&structure_ico, hash, canonical_labelling, normalized, res); + return PTM_NO_ERROR; +} + +int match_dcub_dhex(double (*ch_points)[3], double (*points)[3], int32_t flags, convexhull_t* ch, result_t* res) +{ + int num_nbrs = structure_dcub.num_nbrs; + int num_facets = structure_fcc.num_facets; + int max_degree = structure_dcub.max_degree; + + + int8_t facets[PTM_MAX_FACETS][3]; + int ret = get_convex_hull(num_nbrs + 1, (const double (*)[3])ch_points, ch, facets); + ch->ok = ret >= 0; + if (ret != 0) + return PTM_NO_ERROR; + + //check for facets with multiple inner atoms + bool inverted[4] = {false, false, false, false}; + for (int i=0;inum_facets;i++) + { + int n = 0; + for (int j=0;j<3;j++) + { + if (facets[i][j] <= 3) + { + inverted[facets[i][j]] = true; + n++; + } + } + if (n > 1) + return PTM_NO_ERROR; + } + + int num_inverted = 0; + for (int i=0;i<4;i++) + num_inverted += inverted[i] ? 1 : 0; + + if (ch->num_facets != num_facets + 2 * num_inverted) + return PTM_NO_ERROR; //incorrect number of facets in convex hull + + int8_t degree[PTM_MAX_NBRS]; + int _max_degree = graph_degree(num_facets, facets, num_nbrs, degree); + if (_max_degree > max_degree) + return PTM_NO_ERROR; + + int num_found = 0; + int8_t toadd[4][3]; + for (int i=0;inum_facets;i++) + { + int a = facets[i][0]; + int b = facets[i][1]; + int c = facets[i][2]; + if (a <= 3 || b <= 3 || c <= 3) + continue; + + int i0 = (a - 4) / 3; + int i1 = (b - 4) / 3; + int i2 = (c - 4) / 3; + + if (i0 == i1 && i0 == i2) + { + if (num_found + num_inverted >= 4) + return PTM_NO_ERROR; + + toadd[num_found][0] = a; + toadd[num_found][1] = b; + toadd[num_found][2] = c; + num_found++; + + memcpy(&facets[i], &facets[ch->num_facets - 1], 3 * sizeof(int8_t)); + ch->num_facets--; + i--; + } + } + + if (num_found + num_inverted != 4) + return PTM_NO_ERROR; + + for (int i=0;inum_facets][0] = i0; + facets[ch->num_facets][1] = b; + facets[ch->num_facets][2] = c; + ch->num_facets++; + + facets[ch->num_facets][0] = a; + facets[ch->num_facets][1] = i0; + facets[ch->num_facets][2] = c; + ch->num_facets++; + + facets[ch->num_facets][0] = a; + facets[ch->num_facets][1] = b; + facets[ch->num_facets][2] = i0; + ch->num_facets++; + } + + _max_degree = graph_degree(ch->num_facets, facets, num_nbrs, degree); + if (_max_degree > max_degree) + return PTM_NO_ERROR; + + double normalized[PTM_MAX_POINTS][3]; + subtract_barycentre(num_nbrs + 1, points, normalized); + + int8_t code[2 * PTM_MAX_EDGES]; + int8_t colours[PTM_MAX_POINTS] = {1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}; + int8_t canonical_labelling[PTM_MAX_POINTS]; + uint64_t hash = 0; + ret = canonical_form_coloured(ch->num_facets, facets, num_nbrs, degree, colours, canonical_labelling, &code[0], &hash); + if (ret != PTM_NO_ERROR) + return ret; + + if (flags & PTM_CHECK_DCUB) check_graphs(&structure_dcub, hash, canonical_labelling, normalized, res); + if (flags & PTM_CHECK_DHEX) check_graphs(&structure_dhex, hash, canonical_labelling, normalized, res); + + return PTM_NO_ERROR; +} + diff --git a/src/PTM/ptm_structure_matcher.h b/src/PTM/ptm_structure_matcher.h new file mode 100644 index 0000000000..4b6f969597 --- /dev/null +++ b/src/PTM/ptm_structure_matcher.h @@ -0,0 +1,21 @@ +#ifndef PTM_STRUCTURE_MATCHER_H +#define PTM_STRUCTURE_MATCHER_H + +#include "ptm_initialize_data.h" +#include "ptm_constants.h" + +typedef struct +{ + double rmsd; + double scale; + double q[4]; //rotation in quaternion form (rigid body transformation) + int8_t mapping[PTM_MAX_POINTS]; + const refdata_t* ref_struct; +} result_t; + +int match_general(const refdata_t* s, double (*ch_points)[3], double (*points)[3], convexhull_t* ch, result_t* res); +int match_fcc_hcp_ico(double (*ch_points)[3], double (*points)[3], int32_t flags, convexhull_t* ch, result_t* res); +int match_dcub_dhex(double (*ch_points)[3], double (*points)[3], int32_t flags, convexhull_t* ch, result_t* res); + +#endif + diff --git a/src/PTM/ptm_voronoi_cell.cpp b/src/PTM/ptm_voronoi_cell.cpp new file mode 100644 index 0000000000..6503ea16c6 --- /dev/null +++ b/src/PTM/ptm_voronoi_cell.cpp @@ -0,0 +1,1368 @@ +// Voro++, a 3D cell-based Voronoi library +// +// Author : Chris H. Rycroft (LBL / UC Berkeley) +// Email : chr@alum.mit.edu +// Date : August 30th 2011 +// +// Modified by PM Larsen for use in Polyhedral Template Matching + +/** \file cell.cc + * \brief Function implementations for the voronoicell and related classes. */ + +#include +#include +#include +#include "ptm_voronoi_config.h" +#include "ptm_voronoi_cell.h" + +namespace voro { + +inline void voro_fatal_error(const char *p,int status) { + fprintf(stderr,"voro++: %s\n",p); + exit(status); + //return -1;//status; +} + +/** Constructs a Voronoi cell and sets up the initial memory. */ +voronoicell_base::voronoicell_base() : + current_vertices(init_vertices), current_vertex_order(init_vertex_order), + current_delete_size(init_delete_size), current_delete2_size(init_delete2_size), + ed(new int*[current_vertices]), nu(new int[current_vertices]), + pts(new double[3*current_vertices]), mem(new int[current_vertex_order]), + mec(new int[current_vertex_order]), mep(new int*[current_vertex_order]), + ds(new int[current_delete_size]), stacke(ds+current_delete_size), + ds2(new int[current_delete2_size]), stacke2(ds2+current_delete_size), + current_marginal(init_marginal), marg(new int[current_marginal]) { + int i; + for(i=0;i<3;i++) { + mem[i]=init_n_vertices;mec[i]=0; + mep[i]=new int[init_n_vertices*((i<<1)+1)]; + } + mem[3]=init_3_vertices;mec[3]=0; + mep[3]=new int[init_3_vertices*7]; + for(i=4;i=0;i--) if(mem[i]>0) delete [] mep[i]; + delete [] marg; + delete [] ds2;delete [] ds; + delete [] mep;delete [] mec; + delete [] mem;delete [] pts; + delete [] nu;delete [] ed; +} + +/** Ensures that enough memory is allocated prior to carrying out a copy. + * \param[in] vc a reference to the specialized version of the calling class. + * \param[in] vb a pointered to the class to be copied. */ +template +void voronoicell_base::check_memory_for_copy(vc_class &vc,voronoicell_base* vb) { + while(current_vertex_ordercurrent_vertex_order) add_memory_vorder(vc); + for(int i=0;imec[i]) add_memory(vc,i,ds2); + while(current_verticesp) add_memory_vertices(vc); +} + +/** Increases the memory storage for a particular vertex order, by increasing + * the size of the of the corresponding mep array. If the arrays already exist, + * their size is doubled; if they don't exist, then new ones of size + * init_n_vertices are allocated. The routine also ensures that the pointers in + * the ed array are updated, by making use of the back pointers. For the cases + * where the back pointer has been temporarily overwritten in the marginal + * vertex code, the auxiliary delete stack is scanned to find out how to update + * the ed value. If the template has been instantiated with the neighbor + * tracking turned on, then the routine also reallocates the corresponding mne + * array. + * \param[in] i the order of the vertex memory to be increased. */ +template +void voronoicell_base::add_memory(vc_class &vc,int i,int *stackp2) { + int s=(i<<1)+1; + if(mem[i]==0) { + vc.n_allocate(i,init_n_vertices); + mep[i]=new int[init_n_vertices*s]; + mem[i]=init_n_vertices; +#if VOROPP_VERBOSE >=2 + fprintf(stderr,"Order %d vertex memory created\n",i); +#endif + } else { + int j=0,k,*l; + mem[i]<<=1; + if(mem[i]>max_n_vertices) voro_fatal_error("Point memory allocation exceeded absolute maximum",VOROPP_MEMORY_ERROR); +#if VOROPP_VERBOSE >=2 + fprintf(stderr,"Order %d vertex memory scaled up to %d\n",i,mem[i]); +#endif + l=new int[s*mem[i]]; + int m=0; + vc.n_allocate_aux1(i); + while(j=0) { + ed[k]=l+j; + vc.n_set_to_aux1_offset(k,m); + } else { + int *dsp; + for(dsp=ds2;dsp=3 + fputs("Relocated dangling pointer",stderr); +#endif + } + for(k=0;k +void voronoicell_base::add_memory_vertices(vc_class &vc) { + +printf("nope: %d\n", current_vertices); +exit(3); + + int i=(current_vertices<<1),j,**pp,*pnu; + if(i>max_vertices) voro_fatal_error("Vertex memory allocation exceeded absolute maximum",VOROPP_MEMORY_ERROR); +#if VOROPP_VERBOSE >=2 + fprintf(stderr,"Vertex memory scaled up to %d\n",i); +#endif + double *ppts; + pp=new int*[i]; + for(j=0;j +void voronoicell_base::add_memory_vorder(vc_class &vc) { + int i=(current_vertex_order<<1),j,*p1,**p2; + if(i>max_vertex_order) voro_fatal_error("Vertex order memory allocation exceeded absolute maximum",VOROPP_MEMORY_ERROR); +#if VOROPP_VERBOSE >=2 + fprintf(stderr,"Vertex order memory scaled up to %d\n",i); +#endif + p1=new int[i]; + for(j=0;jmax_delete_size) voro_fatal_error("Delete stack 1 memory allocation exceeded absolute maximum",VOROPP_MEMORY_ERROR); +#if VOROPP_VERBOSE >=2 + fprintf(stderr,"Delete stack 1 memory scaled up to %d\n",current_delete_size); +#endif + int *dsn=new int[current_delete_size],*dsnp=dsn,*dsp=ds; + while(dspmax_delete2_size) voro_fatal_error("Delete stack 2 memory allocation exceeded absolute maximum",VOROPP_MEMORY_ERROR); +#if VOROPP_VERBOSE >=2 + fprintf(stderr,"Delete stack 2 memory scaled up to %d\n",current_delete2_size); +#endif + int *dsn=new int[current_delete2_size],*dsnp=dsn,*dsp=ds2; + while(dsp +inline bool voronoicell_base::search_for_outside_edge(vc_class &vc,int &up) { + int i,lp,lw,*j(ds2),*stackp2(ds2); + double l; + *(stackp2++)=up; + while(j +inline void voronoicell_base::add_to_stack(vc_class &vc,int lp,int *&stackp2) { + for(int *k(ds2);k +bool voronoicell_base::nplane(vc_class &vc,double x,double y,double z,double rsq,int p_id) { + int count=0,i,j,k,lp=up,cp,qp,rp,*stackp(ds),*stackp2(ds2),*dsp; + int us=0,ls=0,qs,iqs,cs,uw,qw,lw; + int *edp,*edd; + double u,l,r,q;bool complicated_setup=false,new_double_edge=false,double_edge=false; + + // Initialize the safe testing routine + n_marg=0;px=x;py=y;pz=z;prsq=rsq; + + // Test approximately sqrt(n)/4 points for their proximity to the plane + // and keep the one which is closest + uw=m_test(up,u); + + // Starting from an initial guess, we now move from vertex to vertex, + // to try and find an edge which intersects the cutting plane, + // or a vertex which is on the plane + try { + if(uw==1) { + + // The test point is inside the cutting plane. + us=0; + do { + lp=ed[up][us]; + lw=m_test(lp,l); + if(l=p) throw true; + u=l;up=lp; + for(us=0;us=p) throw true; + u=q;up=qp; + for(us=0;us=1 + fputs("Bailed out of convex calculation\n",stderr); +#endif + qw=1;lw=0; + for(qp=0;qp=current_vertex_order) add_memory_vorder(vc); + if(mec[nu[p]]==mem[nu[p]]) add_memory(vc,nu[p],stackp2); + vc.n_set_pointer(p,nu[p]); + ed[p]=mep[nu[p]]+((nu[p]<<1)+1)*mec[nu[p]]++; + ed[p][nu[p]<<1]=p; + + // Copy the edges of the original vertex into the new + // one. Delete the edges of the original vertex, and + // update the relational table. + us=cycle_down(i,up); + while(i=current_vertex_order) add_memory_vorder(vc); + if(mec[nu[p]]==mem[nu[p]]) add_memory(vc,nu[p],stackp2); + + // Copy the edges of the original vertex into the new + // one. Delete the edges of the original vertex, and + // update the relational table. + vc.n_set_pointer(p,nu[p]); + ed[p]=mep[nu[p]]+((nu[p]<<1)+1)*mec[nu[p]]++; + ed[p][nu[p]<<1]=p; + us=i++; + while(i0) k+=nu[j]; + } else { + if(j>0) { + + // This vertex was visited before, so + // count those vertices to the ones we + // already have. + k+=nu[j]; + + // The only time when we might make a + // duplicate edge is if the point we're + // going to move to next is also a + // marginal point, so test for that + // first. + if(lw==0) { + + // Now see whether this marginal point + // has been visited before. + i=-ed[lp][nu[lp]<<1]; + if(i>0) { + + // Now see if the last edge of that other + // marginal point actually ends up here. + if(ed[i][nu[i]-1]==j) { + new_double_edge=true; + k-=1; + } else new_double_edge=false; + } else { + + // That marginal point hasn't been visited + // before, so we probably don't have to worry + // about duplicate edges, except in the + // case when that's the way into the end + // of the facet, because that way always creates + // an edge. + if(j==rp&&lp==up&&ed[qp][nu[qp]+qs]==us) { + new_double_edge=true; + k-=1; + } else new_double_edge=false; + } + } else new_double_edge=false; + } else { + + // The vertex hasn't been visited + // before, but let's see if it's + // marginal + if(lw==0) { + + // If it is, we need to check + // for the case that it's a + // small branch, and that we're + // heading right back to where + // we came from + i=-ed[lp][nu[lp]<<1]; + if(i==cp) { + new_double_edge=true; + k-=1; + } else new_double_edge=false; + } else new_double_edge=false; + } + } + + // k now holds the number of edges of the new vertex + // we are forming. Add memory for it if it doesn't exist + // already. + while(k>=current_vertex_order) add_memory_vorder(vc); + if(mec[k]==mem[k]) add_memory(vc,k,stackp2); + + // Now create a new vertex with order k, or augment + // the existing one + if(j>0) { + + // If we're augmenting a vertex but we don't + // actually need any more edges, just skip this + // routine to avoid memory confusion + if(nu[j]!=k) { + // Allocate memory and copy the edges + // of the previous instance into it + vc.n_set_aux1(k); + edp=mep[k]+((k<<1)+1)*mec[k]++; + i=0; + while(ids) { + --p; + while(ed[p][nu[p]]==-1) { + j=nu[p]; + edp=ed[p];edd=(mep[j]+((j<<1)+1)*--mec[j]); + while(edp0) voro_fatal_error("Zero order vertex formed",VOROPP_INTERNAL_ERROR); + + // Collapse any order 2 vertices and exit + return collapse_order2(vc); +} + +/** During the creation of a new facet in the plane routine, it is possible + * that some order two vertices may arise. This routine removes them. + * Suppose an order two vertex joins c and d. If there's a edge between + * c and d already, then the order two vertex is just removed; otherwise, + * the order two vertex is removed and c and d are joined together directly. + * It is possible this process will create order two or order one vertices, + * and the routine is continually run until all of them are removed. + * \return False if the vertex removal was unsuccessful, indicative of the cell + * reducing to zero volume and disappearing; true if the vertex removal + * was successful. */ +template +inline bool voronoicell_base::collapse_order2(vc_class &vc) { + if(!collapse_order1(vc)) return false; + int a,b,i,j,k,l; + while(mec[2]>0) { + + // Pick a order 2 vertex and read in its edges + i=--mec[2]; + j=mep[2][5*i];k=mep[2][5*i+1]; + if(j==k) { +#if VOROPP_VERBOSE >=1 + fputs("Order two vertex joins itself",stderr); +#endif + return false; + } + + // Scan the edges of j to see if joins k + for(l=0;l +inline bool voronoicell_base::collapse_order1(vc_class &vc) { + int i,j,k; + while(mec[1]>0) { + up=0; +#if VOROPP_VERBOSE >=1 + fputs("Order one collapse\n",stderr); +#endif + i=--mec[1]; + j=mep[1][3*i];k=mep[1][3*i+1]; + i=mep[1][3*i+2]; + if(!delete_connection(vc,j,k,false)) return false; + --p; + if(up==i) up=0; + if(p!=i) { + if(up==p) up=i; + pts[3*i]=pts[3*p]; + pts[3*i+1]=pts[3*p+1]; + pts[3*i+2]=pts[3*p+2]; + for(k=0;k +inline bool voronoicell_base::delete_connection(vc_class &vc,int j,int k,bool hand) { + int q=hand?k:cycle_up(k,j); + int i=nu[j]-1,l,*edp,*edd,m; +#if VOROPP_VERBOSE >=1 + if(i<1) { + fputs("Zero order vertex formed\n",stderr); + return false; + } +#endif + if(mec[i]==mem[i]) add_memory(vc,i,ds2); + vc.n_set_aux1(i); + for(l=0;l &v) { + double area; + v.clear(); + int i,j,k,l,m,n; + double ux,uy,uz,vx,vy,vz,wx,wy,wz; + for(i=1;i=0) { + area=0; + ed[i][j]=-1-k; + l=cycle_up(ed[i][nu[i]+j],k); + m=ed[k][l];ed[k][l]=-1-m; + while(m!=i) { + n=cycle_up(ed[k][nu[k]+l],m); + ux=pts[3*k]-pts[3*i]; + uy=pts[3*k+1]-pts[3*i+1]; + uz=pts[3*k+2]-pts[3*i+2]; + vx=pts[3*m]-pts[3*i]; + vy=pts[3*m+1]-pts[3*i+1]; + vz=pts[3*m+2]-pts[3*i+2]; + wx=uy*vz-uz*vy; + wy=uz*vx-ux*vz; + wz=ux*vy-uy*vx; + area+=sqrt(wx*wx+wy*wy+wz*wz); + k=m;l=n; + m=ed[k][l];ed[k][l]=-1-m; + } + v.push_back(0.125*area); + } + } + reset_edges(); +} + +/** Several routines in the class that gather cell-based statistics internally + * track their progress by flipping edges to negative so that they know what + * parts of the cell have already been tested. This function resets them back + * to positive. When it is called, it assumes that every edge in the routine + * should have already been flipped to negative, and it bails out with an + * internal error if it encounters a positive edge. */ +inline void voronoicell_base::reset_edges() { + int i,j; + for(i=0;i=0) voro_fatal_error("Edge reset routine found a previously untested edge",VOROPP_INTERNAL_ERROR); + ed[i][j]=-1-ed[i][j]; + } +} + +/** Checks to see if a given vertex is inside, outside or within the test + * plane. If the point is far away from the test plane, the routine immediately + * returns whether it is inside or outside. If the routine is close the the + * plane and within the specified tolerance, then the special check_marginal() + * routine is called. + * \param[in] n the vertex to test. + * \param[out] ans the result of the scalar product used in evaluating the + * location of the point. + * \return -1 if the point is inside the plane, 1 if the point is outside the + * plane, or 0 if the point is within the plane. */ +inline int voronoicell_base::m_test(int n,double &ans) { + double *pp=pts+n+(n<<1); + ans=*(pp++)*px; + ans+=*(pp++)*py; + ans+=*pp*pz-prsq; + if(ans<-tolerance2) { + return -1; + } else if(ans>tolerance2) { + return 1; + } + return check_marginal(n,ans); +} + +/** Checks to see if a given vertex is inside, outside or within the test + * plane, for the case when the point has been detected to be very close to the + * plane. The routine ensures that the returned results are always consistent + * with previous tests, by keeping a table of any marginal results. The routine + * first sees if the vertex is in the table, and if it finds a previously + * computed result it uses that. Otherwise, it computes a result for this + * vertex and adds it the table. + * \param[in] n the vertex to test. + * \param[in] ans the result of the scalar product used in evaluating + * the location of the point. + * \return -1 if the point is inside the plane, 1 if the point is outside the + * plane, or 0 if the point is within the plane. */ +int voronoicell_base::check_marginal(int n,double &ans) { + int i; + for(i=0;imax_marginal) + voro_fatal_error("Marginal case buffer allocation exceeded absolute maximum",VOROPP_MEMORY_ERROR); +#if VOROPP_VERBOSE >=2 + fprintf(stderr,"Marginal cases buffer scaled up to %d\n",i); +#endif + int *pmarg=new int[current_marginal]; + for(int j=0;jtolerance?1:(ans<-tolerance?-1:0); + return marg[n_marg-1]; +} + +/** This initializes the class to be a rectangular box. It calls the base class + * initialization routine to set up the edge and vertex information, and then + * sets up the neighbor information, with initial faces being assigned ID + * numbers from -1 to -6. + * \param[in] (xmin,xmax) the minimum and maximum x coordinates. + * \param[in] (ymin,ymax) the minimum and maximum y coordinates. + * \param[in] (zmin,zmax) the minimum and maximum z coordinates. */ +void voronoicell_neighbor::init(double xmin,double xmax,double ymin,double ymax,double zmin,double zmax) { + init_base(xmin,xmax,ymin,ymax,zmin,zmax); + int *q=mne[3]; + *q=-5;q[1]=-3;q[2]=-1; + q[3]=-5;q[4]=-2;q[5]=-3; + q[6]=-5;q[7]=-1;q[8]=-4; + q[9]=-5;q[10]=-4;q[11]=-2; + q[12]=-6;q[13]=-1;q[14]=-3; + q[15]=-6;q[16]=-3;q[17]=-2; + q[18]=-6;q[19]=-4;q[20]=-1; + q[21]=-6;q[22]=-2;q[23]=-4; + *ne=q;ne[1]=q+3;ne[2]=q+6;ne[3]=q+9; + ne[4]=q+12;ne[5]=q+15;ne[6]=q+18;ne[7]=q+21; +} + +/** This routine checks to make sure the neighbor information of each face is + * consistent. */ +void voronoicell_neighbor::check_facets() { + int i,j,k,l,m,q; + for(i=1;i=0) { + ed[i][j]=-1-k; + q=ne[i][j]; + l=cycle_up(ed[i][nu[i]+j],k); + do { + m=ed[k][l]; + ed[k][l]=-1-m; + if(ne[k][l]!=q) fprintf(stderr,"Facet error at (%d,%d)=%d, started from (%d,%d)=%d\n",k,l,ne[k][l],i,j,q); + l=cycle_up(ed[k][nu[k]+l],m); + k=m; + } while (k!=i); + } + } + reset_edges(); +} + +/** The class constructor allocates memory for storing neighbor information. */ +voronoicell_neighbor::voronoicell_neighbor() { + int i; + mne=new int*[current_vertex_order]; + ne=new int*[current_vertices]; + for(i=0;i<3;i++) mne[i]=new int[init_n_vertices*i]; + mne[3]=new int[init_3_vertices*3]; + for(i=4;i=0;i--) if(mem[i]>0) delete [] mne[i]; + delete [] mne; + delete [] ne; +} + +/** Computes a vector list of neighbors. */ +void voronoicell_neighbor::neighbors(std::vector &v) { + v.clear(); + int i,j,k,l,m; + for(i=1;i=0) { + v.push_back(ne[i][j]); + ed[i][j]=-1-k; + l=cycle_up(ed[i][nu[i]+j],k); + do { + m=ed[k][l]; + ed[k][l]=-1-m; + l=cycle_up(ed[k][nu[k]+l],m); + k=m; + } while (k!=i); + } + } + reset_edges(); +} + +// Explicit instantiation +template bool voronoicell_base::nplane(voronoicell_neighbor&,double,double,double,double,int); +template void voronoicell_base::check_memory_for_copy(voronoicell_neighbor&,voronoicell_base*); + +} + diff --git a/src/PTM/ptm_voronoi_cell.h b/src/PTM/ptm_voronoi_cell.h new file mode 100644 index 0000000000..80a0501b3c --- /dev/null +++ b/src/PTM/ptm_voronoi_cell.h @@ -0,0 +1,324 @@ +// Voro++, a 3D cell-based Voronoi library +// +// Author : Chris H. Rycroft (LBL / UC Berkeley) +// Email : chr@alum.mit.edu +// Date : August 30th 2011 +// +// Modified by PM Larsen for use in Polyhedral Template Matching + +/** \file cell.hh + * \brief Header file for the voronoicell and related classes. */ + +#ifndef PTM_VOROPP_CELL_HH +#define PTM_VOROPP_CELL_HH + +#include +#include + +#include "ptm_voronoi_config.h" + +namespace voro { + +/** \brief A class representing a single Voronoi cell. + * + * This class represents a single Voronoi cell, as a collection of vertices + * that are connected by edges. The class contains routines for initializing + * the Voronoi cell to be simple shapes such as a box, tetrahedron, or octahedron. + * It the contains routines for recomputing the cell based on cutting it + * by a plane, which forms the key routine for the Voronoi cell computation. + * It contains numerous routine for computing statistics about the Voronoi cell, + * and it can output the cell in several formats. + * + * This class is not intended for direct use, but forms the base of the + * voronoicell and voronoicell_neighbor classes, which extend it based on + * whether neighboring particle ID information needs to be tracked. */ +class voronoicell_base { + public: + /** This holds the current size of the arrays ed and nu, which + * hold the vertex information. If more vertices are created + * than can fit in this array, then it is dynamically extended + * using the add_memory_vertices routine. */ + int current_vertices; + /** This holds the current maximum allowed order of a vertex, + * which sets the size of the mem, mep, and mec arrays. If a + * vertex is created with more vertices than this, the arrays + * are dynamically extended using the add_memory_vorder routine. + */ + int current_vertex_order; + /** This sets the size of the main delete stack. */ + int current_delete_size; + /** This sets the size of the auxiliary delete stack. */ + int current_delete2_size; + /** This sets the total number of vertices in the current cell. + */ + int p; + /** This is the index of particular point in the cell, which is + * used to start the tracing routines for plane intersection + * and cutting. These routines will work starting from any + * point, but it's often most efficient to start from the last + * point considered, since in many cases, the cell construction + * algorithm may consider many planes with similar vectors + * concurrently. */ + int up; + /** This is a two dimensional array that holds information + * about the edge connections of the vertices that make up the + * cell. The two dimensional array is not allocated in the + * usual method. To account for the fact the different vertices + * have different orders, and thus require different amounts of + * storage, the elements of ed[i] point to one-dimensional + * arrays in the mep[] array of different sizes. + * + * More specifically, if vertex i has order m, then ed[i] + * points to a one-dimensional array in mep[m] that has 2*m+1 + * entries. The first m elements hold the neighboring edges, so + * that the jth edge of vertex i is held in ed[i][j]. The next + * m elements hold a table of relations which is redundant but + * helps speed up the computation. It satisfies the relation + * ed[ed[i][j]][ed[i][m+j]]=i. The final entry holds a back + * pointer, so that ed[i+2*m]=i. The back pointers are used + * when rearranging the memory. */ + int **ed; + /** This array holds the order of the vertices in the Voronoi + * cell. This array is dynamically allocated, with its current + * size held by current_vertices. */ + int *nu; + /** This in an array with size 3*current_vertices for holding + * the positions of the vertices. */ + double *pts; + voronoicell_base(); + virtual ~voronoicell_base(); + void init_base(double xmin,double xmax,double ymin,double ymax,double zmin,double zmax); + void init_octahedron_base(double l); + void init_tetrahedron_base(double x0,double y0,double z0,double x1,double y1,double z1,double x2,double y2,double z2,double x3,double y3,double z3); + void translate(double x,double y,double z); + double volume(); + double max_radius_squared(); + double total_edge_distance(); + double surface_area(); + void centroid(double &cx,double &cy,double &cz); + int number_of_faces(); + int number_of_edges(); + void vertex_orders(std::vector &v); + void vertices(std::vector &v); + void vertices(double x,double y,double z,std::vector &v); + void face_areas(std::vector &v); + void face_orders(std::vector &v); + void face_freq_table(std::vector &v); + void face_vertices(std::vector &v); + void face_perimeters(std::vector &v); + void normals(std::vector &v); + template + bool nplane(vc_class &vc,double x,double y,double z,double rsq,int p_id); + bool plane_intersects(double x,double y,double z,double rsq); + bool plane_intersects_guess(double x,double y,double z,double rsq); + void construct_relations(); + void check_relations(); + void check_duplicates(); + /** Returns a list of IDs of neighboring particles + * corresponding to each face. + * \param[out] v a reference to a vector in which to return the + * results. If no neighbor information is + * available, a blank vector is returned. */ + virtual void neighbors(std::vector &v) {v.clear();} + /** This a virtual function that is overridden by a routine to + * print the neighboring particle IDs for a given vertex. By + * default, when no neighbor information is available, the + * routine does nothing. + * \param[in] i the vertex to consider. */ + /** This is a simple inline function for picking out the index + * of the next edge counterclockwise at the current vertex. + * \param[in] a the index of an edge of the current vertex. + * \param[in] p the number of the vertex. + * \return 0 if a=nu[p]-1, or a+1 otherwise. */ + inline int cycle_up(int a,int p) {return a==nu[p]-1?0:a+1;} + /** This is a simple inline function for picking out the index + * of the next edge clockwise from the current vertex. + * \param[in] a the index of an edge of the current vertex. + * \param[in] p the number of the vertex. + * \return nu[p]-1 if a=0, or a-1 otherwise. */ + inline int cycle_down(int a,int p) {return a==0?nu[p]-1:a-1;} + protected: + /** This a one dimensional array that holds the current sizes + * of the memory allocations for them mep array.*/ + int *mem; + /** This is a one dimensional array that holds the current + * number of vertices of order p that are stored in the mep[p] + * array. */ + int *mec; + /** This is a two dimensional array for holding the information + * about the edges of the Voronoi cell. mep[p] is a + * one-dimensional array for holding the edge information about + * all vertices of order p, with each vertex holding 2*p+1 + * integers of information. The total number of vertices held + * on mep[p] is stored in mem[p]. If the space runs out, the + * code allocates more using the add_memory() routine. */ + int **mep; + inline void reset_edges(); + template + void check_memory_for_copy(vc_class &vc,voronoicell_base* vb); + void copy(voronoicell_base* vb); + private: + /** This is the delete stack, used to store the vertices which + * are going to be deleted during the plane cutting procedure. + */ + int *ds,*stacke; + /** This is the auxiliary delete stack, which has size set by + * current_delete2_size. */ + int *ds2,*stacke2; + /** This stores the current memory allocation for the marginal + * cases. */ + int current_marginal; + /** This stores the total number of marginal points which are + * currently in the buffer. */ + int n_marg; + /** This array contains a list of the marginal points, and also + * the outcomes of the marginal tests. */ + int *marg; + /** The x coordinate of the normal vector to the test plane. */ + double px; + /** The y coordinate of the normal vector to the test plane. */ + double py; + /** The z coordinate of the normal vector to the test plane. */ + double pz; + /** The magnitude of the normal vector to the test plane. */ + double prsq; + template + void add_memory(vc_class &vc,int i,int *stackp2); + template + void add_memory_vertices(vc_class &vc); + template + void add_memory_vorder(vc_class &vc); + void add_memory_ds(int *&stackp); + void add_memory_ds2(int *&stackp2); + template + inline bool collapse_order1(vc_class &vc); + template + inline bool collapse_order2(vc_class &vc); + template + inline bool delete_connection(vc_class &vc,int j,int k,bool hand); + template + inline bool search_for_outside_edge(vc_class &vc,int &up); + template + inline void add_to_stack(vc_class &vc,int lp,int *&stackp2); + inline bool plane_intersects_track(double x,double y,double z,double rs,double g); + inline void normals_search(std::vector &v,int i,int j,int k); + inline bool search_edge(int l,int &m,int &k); + inline int m_test(int n,double &ans); + int check_marginal(int n,double &ans); + friend class voronoicell; + friend class voronoicell_neighbor; +}; + +/** \brief Extension of the voronoicell_base class to represent a Voronoi cell + * with neighbor information. + * + * This class is an extension of the voronoicell_base class, in cases when the + * IDs of neighboring particles associated with each face of the Voronoi cell. + * It contains additional data structures mne and ne for storing this + * information. */ +class voronoicell_neighbor : public voronoicell_base { + public: + using voronoicell_base::nplane; + /** This two dimensional array holds the neighbor information + * associated with each vertex. mne[p] is a one dimensional + * array which holds all of the neighbor information for + * vertices of order p. */ + int **mne; + /** This is a two dimensional array that holds the neighbor + * information associated with each vertex. ne[i] points to a + * one-dimensional array in mne[nu[i]]. ne[i][j] holds the + * neighbor information associated with the jth edge of vertex + * i. It is set to the ID number of the plane that made the + * face that is clockwise from the jth edge. */ + int **ne; + voronoicell_neighbor(); + ~voronoicell_neighbor(); + void operator=(voronoicell_neighbor &c); + /** Cuts the Voronoi cell by a particle whose center is at a + * separation of (x,y,z) from the cell center. The value of rsq + * should be initially set to \f$x^2+y^2+z^2\f$. + * \param[in] (x,y,z) the normal vector to the plane. + * \param[in] rsq the distance along this vector of the plane. + * \param[in] p_id the plane ID (for neighbor tracking only). + * \return False if the plane cut deleted the cell entirely, + * true otherwise. */ + inline bool nplane(double x,double y,double z,double rsq,int p_id) { + return nplane(*this,x,y,z,rsq,p_id); + } + /** This routine calculates the modulus squared of the vector + * before passing it to the main nplane() routine with full + * arguments. + * \param[in] (x,y,z) the vector to cut the cell by. + * \param[in] p_id the plane ID (for neighbor tracking only). + * \return False if the plane cut deleted the cell entirely, + * true otherwise. */ + inline bool nplane(double x,double y,double z,int p_id) { + double rsq=x*x+y*y+z*z; + return nplane(*this,x,y,z,rsq,p_id); + } + /** This version of the plane routine just makes up the plane + * ID to be zero. It will only be referenced if neighbor + * tracking is enabled. + * \param[in] (x,y,z) the vector to cut the cell by. + * \param[in] rsq the modulus squared of the vector. + * \return False if the plane cut deleted the cell entirely, + * true otherwise. */ + inline bool plane(double x,double y,double z,double rsq) { + return nplane(*this,x,y,z,rsq,0); + } + /** Cuts a Voronoi cell using the influence of a particle at + * (x,y,z), first calculating the modulus squared of this + * vector before passing it to the main nplane() routine. Zero + * is supplied as the plane ID, which will be ignored unless + * neighbor tracking is enabled. + * \param[in] (x,y,z) the vector to cut the cell by. + * \return False if the plane cut deleted the cell entirely, + * true otherwise. */ + inline bool plane(double x,double y,double z) { + double rsq=x*x+y*y+z*z; + return nplane(*this,x,y,z,rsq,0); + } + void init(double xmin,double xmax,double ymin,double ymax,double zmin,double zmax); + void check_facets(); + virtual void neighbors(std::vector &v); + + private: + int *paux1; + int *paux2; + inline void n_allocate(int i,int m) {mne[i]=new int[m*i];} + inline void n_add_memory_vertices(int i) { + int **pp=new int*[i]; + for(int j=0;j Date: Thu, 20 Sep 2018 00:04:07 -0400 Subject: [PATCH 181/302] Fixed folder structure --- src/PTM/compute_ptm_atom.cpp | 307 --- src/PTM/compute_ptm_atom.h | 48 - src/PTM/ptm_constants.h | 174 -- src/PTM/ptm_functions.h | 27 - src/USER-PTM/alloy_types.cpp | 101 - src/USER-PTM/alloy_types.h | 9 - src/USER-PTM/canonical_coloured.cpp | 167 -- src/USER-PTM/canonical_coloured.h | 9 - src/USER-PTM/cell.cpp | 1368 ----------- src/USER-PTM/cell.h | 324 --- src/USER-PTM/config.h | 129 -- src/USER-PTM/convex_hull_incremental.cpp | 363 --- src/USER-PTM/convex_hull_incremental.h | 27 - src/USER-PTM/deformation_gradient.cpp | 37 - src/USER-PTM/deformation_gradient.h | 142 -- src/USER-PTM/fundamental_mappings.h | 180 -- src/USER-PTM/graph_data.cpp | 2059 ----------------- src/USER-PTM/graph_data.h | 37 - src/USER-PTM/graph_tools.cpp | 52 - src/USER-PTM/graph_tools.h | 11 - src/USER-PTM/index_ptm.cpp | 218 -- src/USER-PTM/initialize_data.cpp | 71 - src/USER-PTM/initialize_data.h | 61 - src/USER-PTM/neighbour_ordering.cpp | 203 -- src/USER-PTM/neighbour_ordering.h | 13 - src/USER-PTM/normalize_vertices.cpp | 55 - src/USER-PTM/normalize_vertices.h | 8 - src/USER-PTM/polar.cpp | 337 --- src/USER-PTM/polar.h | 12 - src/{PTM => USER-PTM}/ptm_alloy_types.cpp | 0 src/{PTM => USER-PTM}/ptm_alloy_types.h | 0 .../ptm_canonical_coloured.cpp | 0 .../ptm_canonical_coloured.h | 0 .../ptm_convex_hull_incremental.cpp | 0 .../ptm_convex_hull_incremental.h | 0 .../ptm_deformation_gradient.cpp | 0 .../ptm_deformation_gradient.h | 0 src/USER-PTM/ptm_functions.h | 2 +- .../ptm_fundamental_mappings.h | 0 src/{PTM => USER-PTM}/ptm_graph_data.cpp | 0 src/{PTM => USER-PTM}/ptm_graph_data.h | 0 src/{PTM => USER-PTM}/ptm_graph_tools.cpp | 0 src/{PTM => USER-PTM}/ptm_graph_tools.h | 0 src/{PTM => USER-PTM}/ptm_index.cpp | 0 src/{PTM => USER-PTM}/ptm_initialize_data.cpp | 0 src/{PTM => USER-PTM}/ptm_initialize_data.h | 0 .../ptm_neighbour_ordering.cpp | 0 .../ptm_neighbour_ordering.h | 0 .../ptm_normalize_vertices.cpp | 0 .../ptm_normalize_vertices.h | 0 src/{PTM => USER-PTM}/ptm_polar.cpp | 0 src/{PTM => USER-PTM}/ptm_polar.h | 0 src/{PTM => USER-PTM}/ptm_quat.cpp | 0 src/{PTM => USER-PTM}/ptm_quat.h | 0 .../ptm_structure_matcher.cpp | 0 src/{PTM => USER-PTM}/ptm_structure_matcher.h | 0 src/{PTM => USER-PTM}/ptm_voronoi_cell.cpp | 0 src/{PTM => USER-PTM}/ptm_voronoi_cell.h | 0 src/{PTM => USER-PTM}/ptm_voronoi_config.h | 0 src/USER-PTM/quat.cpp | 396 ---- src/USER-PTM/quat.h | 32 - src/USER-PTM/structure_matcher.cpp | 294 --- src/USER-PTM/structure_matcher.h | 21 - 63 files changed, 1 insertion(+), 7293 deletions(-) delete mode 100644 src/PTM/compute_ptm_atom.cpp delete mode 100644 src/PTM/compute_ptm_atom.h delete mode 100644 src/PTM/ptm_constants.h delete mode 100644 src/PTM/ptm_functions.h delete mode 100644 src/USER-PTM/alloy_types.cpp delete mode 100644 src/USER-PTM/alloy_types.h delete mode 100644 src/USER-PTM/canonical_coloured.cpp delete mode 100644 src/USER-PTM/canonical_coloured.h delete mode 100644 src/USER-PTM/cell.cpp delete mode 100644 src/USER-PTM/cell.h delete mode 100644 src/USER-PTM/config.h delete mode 100644 src/USER-PTM/convex_hull_incremental.cpp delete mode 100644 src/USER-PTM/convex_hull_incremental.h delete mode 100644 src/USER-PTM/deformation_gradient.cpp delete mode 100644 src/USER-PTM/deformation_gradient.h delete mode 100644 src/USER-PTM/fundamental_mappings.h delete mode 100644 src/USER-PTM/graph_data.cpp delete mode 100644 src/USER-PTM/graph_data.h delete mode 100644 src/USER-PTM/graph_tools.cpp delete mode 100644 src/USER-PTM/graph_tools.h delete mode 100644 src/USER-PTM/index_ptm.cpp delete mode 100644 src/USER-PTM/initialize_data.cpp delete mode 100644 src/USER-PTM/initialize_data.h delete mode 100644 src/USER-PTM/neighbour_ordering.cpp delete mode 100644 src/USER-PTM/neighbour_ordering.h delete mode 100644 src/USER-PTM/normalize_vertices.cpp delete mode 100644 src/USER-PTM/normalize_vertices.h delete mode 100644 src/USER-PTM/polar.cpp delete mode 100644 src/USER-PTM/polar.h rename src/{PTM => USER-PTM}/ptm_alloy_types.cpp (100%) rename src/{PTM => USER-PTM}/ptm_alloy_types.h (100%) rename src/{PTM => USER-PTM}/ptm_canonical_coloured.cpp (100%) rename src/{PTM => USER-PTM}/ptm_canonical_coloured.h (100%) rename src/{PTM => USER-PTM}/ptm_convex_hull_incremental.cpp (100%) rename src/{PTM => USER-PTM}/ptm_convex_hull_incremental.h (100%) rename src/{PTM => USER-PTM}/ptm_deformation_gradient.cpp (100%) rename src/{PTM => USER-PTM}/ptm_deformation_gradient.h (100%) rename src/{PTM => USER-PTM}/ptm_fundamental_mappings.h (100%) rename src/{PTM => USER-PTM}/ptm_graph_data.cpp (100%) rename src/{PTM => USER-PTM}/ptm_graph_data.h (100%) rename src/{PTM => USER-PTM}/ptm_graph_tools.cpp (100%) rename src/{PTM => USER-PTM}/ptm_graph_tools.h (100%) rename src/{PTM => USER-PTM}/ptm_index.cpp (100%) rename src/{PTM => USER-PTM}/ptm_initialize_data.cpp (100%) rename src/{PTM => USER-PTM}/ptm_initialize_data.h (100%) rename src/{PTM => USER-PTM}/ptm_neighbour_ordering.cpp (100%) rename src/{PTM => USER-PTM}/ptm_neighbour_ordering.h (100%) rename src/{PTM => USER-PTM}/ptm_normalize_vertices.cpp (100%) rename src/{PTM => USER-PTM}/ptm_normalize_vertices.h (100%) rename src/{PTM => USER-PTM}/ptm_polar.cpp (100%) rename src/{PTM => USER-PTM}/ptm_polar.h (100%) rename src/{PTM => USER-PTM}/ptm_quat.cpp (100%) rename src/{PTM => USER-PTM}/ptm_quat.h (100%) rename src/{PTM => USER-PTM}/ptm_structure_matcher.cpp (100%) rename src/{PTM => USER-PTM}/ptm_structure_matcher.h (100%) rename src/{PTM => USER-PTM}/ptm_voronoi_cell.cpp (100%) rename src/{PTM => USER-PTM}/ptm_voronoi_cell.h (100%) rename src/{PTM => USER-PTM}/ptm_voronoi_config.h (100%) delete mode 100644 src/USER-PTM/quat.cpp delete mode 100644 src/USER-PTM/quat.h delete mode 100644 src/USER-PTM/structure_matcher.cpp delete mode 100644 src/USER-PTM/structure_matcher.h diff --git a/src/PTM/compute_ptm_atom.cpp b/src/PTM/compute_ptm_atom.cpp deleted file mode 100644 index b6b4a9786c..0000000000 --- a/src/PTM/compute_ptm_atom.cpp +++ /dev/null @@ -1,307 +0,0 @@ -/* ---------------------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed -under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -/* ---------------------------------------------------------------------- - Contributing author: PM Larsen (MIT) -------------------------------------------------------------------------- */ - -#include -#include -#include -#include - -#include "atom.h" -#include "comm.h" -#include "compute_ptm_atom.h" -#include "error.h" -#include "force.h" -#include "memory.h" -#include "modify.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "neighbor.h" -#include "pair.h" -#include "update.h" - -#include "ptm_functions.h" - -#define MAX_NEIGHBORS 30 -#define NUM_COLUMNS 7 -#define UNKNOWN 0 -#define OTHER 8 - -using namespace LAMMPS_NS; - -static const char cite_user_ptm_package[] = - "USER-PTM package:\n\n" - "@Article{larsen2016ptm,\n" - " author={Larsen, Peter Mahler and Schmidt, S{\o}ren and Schi{\o}tz, " - "Jakob},\n" - " title={Robust structural identification via polyhedral template " - "matching},\n" - " journal={Modelling~Simul.~Mater.~Sci.~Eng.},\n" - " year={2016},\n" - " number={5},\n" - " volume={24},\n" - " pages={055007},\n" - " DOI = {10.1088/0965-0393/24/5/055007}" - "}\n\n"; - -/* ---------------------------------------------------------------------- */ - -ComputePTMAtom::ComputePTMAtom(LAMMPS *lmp, int narg, char **arg) - : Compute(lmp, narg, arg), list(NULL), output(NULL) { - if (narg != 5) - error->all(FLERR, "Illegal compute ptm/atom command"); - - char *structures = arg[3]; - char *ptr = structures; - - const char *strings[] = {"fcc", "hcp", "bcc", "ico", "sc", - "dcub", "dhex", "all", "default"}; - int32_t flags[] = { - PTM_CHECK_FCC, - PTM_CHECK_HCP, - PTM_CHECK_BCC, - PTM_CHECK_ICO, - PTM_CHECK_SC, - PTM_CHECK_DCUB, - PTM_CHECK_DHEX, - PTM_CHECK_ALL, - PTM_CHECK_FCC | PTM_CHECK_HCP | PTM_CHECK_BCC | PTM_CHECK_ICO}; - - input_flags = 0; - while (*ptr != '\0') { - - bool found = false; - for (int i = 0; i < 9; i++) { - int len = strlen(strings[i]); - if (strncmp(ptr, strings[i], len) == 0) { - input_flags |= flags[i]; - ptr += len; - found = true; - break; - } - } - - if (!found) - error->all(FLERR, - "Illegal compute ptm/atom command (invalid structure type)"); - - if (*ptr == '\0') - break; - - if (*ptr != '-') - error->all(FLERR, - "Illegal compute ptm/atom command (invalid structure type)"); - - ptr++; - } - - double threshold = force->numeric(FLERR, arg[4]); - if (threshold < 0.0) - error->all(FLERR, - "Illegal compute ptm/atom command (threshold is negative)"); - rmsd_threshold = threshold; - if (rmsd_threshold == 0) - rmsd_threshold = INFINITY; - - peratom_flag = 1; - size_peratom_cols = NUM_COLUMNS; - create_attribute = 1; - nmax = 0; -} - -/* ---------------------------------------------------------------------- */ - -ComputePTMAtom::~ComputePTMAtom() { memory->destroy(output); } - -/* ---------------------------------------------------------------------- */ - -void ComputePTMAtom::init() { - if (force->pair == NULL) - error->all(FLERR, "Compute ptm/atom requires a pair style be defined"); - - int count = 0; - for (int i = 0; i < modify->ncompute; i++) - if (strcmp(modify->compute[i]->style, "ptm/atom") == 0) - count++; - if (count > 1 && comm->me == 0) - error->warning(FLERR, "More than one compute ptm/atom defined"); - - // need an occasional full neighbor list - - int irequest = neighbor->request(this, instance_me); - neighbor->requests[irequest]->pair = 0; - neighbor->requests[irequest]->compute = 1; - neighbor->requests[irequest]->half = 0; - neighbor->requests[irequest]->full = 1; - neighbor->requests[irequest]->occasional = 1; -} - -/* ---------------------------------------------------------------------- */ - -void ComputePTMAtom::init_list(int id, NeighList *ptr) { list = ptr; } - -/* ---------------------------------------------------------------------- */ - -typedef struct { - int index; - double d; -} ptmnbr_t; - -static bool sorthelper_compare(ptmnbr_t const &a, ptmnbr_t const &b) { - return a.d < b.d; -} - -static int get_neighbors(double *pos, int jnum, int *jlist, double **x, - double (*nbr)[3]) { - - ptmnbr_t *nbr_order = new ptmnbr_t[jnum]; - - for (int jj = 0; jj < jnum; jj++) { - int j = jlist[jj]; - j &= NEIGHMASK; - - double dx = pos[0] - x[j][0]; - double dy = pos[1] - x[j][1]; - double dz = pos[2] - x[j][2]; - double rsq = dx * dx + dy * dy + dz * dz; - - nbr_order[jj].index = j; - nbr_order[jj].d = rsq; - } - - std::sort(nbr_order, nbr_order + jnum, &sorthelper_compare); - int num_nbrs = std::min(MAX_NEIGHBORS, jnum); - - nbr[0][0] = nbr[0][1] = nbr[0][2] = 0; - for (int jj = 0; jj < num_nbrs; jj++) { - - int j = nbr_order[jj].index; - nbr[jj + 1][0] = x[j][0] - pos[0]; - nbr[jj + 1][1] = x[j][1] - pos[1]; - nbr[jj + 1][2] = x[j][2] - pos[2]; - } - - delete[] nbr_order; - return num_nbrs; -} - -void ComputePTMAtom::compute_peratom() { - // PTM global initialization. If already initialized this function does - // nothing. - ptm_initialize_global(); - - // initialize PTM local storage - ptm_local_handle_t local_handle = ptm_initialize_local(); - - invoked_peratom = update->ntimestep; - - // grow arrays if necessary - if (atom->nmax > nmax) { - memory->destroy(output); - nmax = atom->nmax; - - memory->create(output, nmax, NUM_COLUMNS, "ptm:ptm_output"); - array_atom = output; - } - - // invoke full neighbor list (will copy or build if necessary) - neighbor->build_one(list); - - int inum = list->inum; - int *ilist = list->ilist; - int *numneigh = list->numneigh; - int **firstneigh = list->firstneigh; - - double **x = atom->x; - int *mask = atom->mask; - int nlocal = atom->nlocal; - - for (int ii = 0; ii < inum; ii++) { - - int i = ilist[ii]; - output[i][0] = UNKNOWN; - if (!(mask[i] & groupbit)) - continue; - - double *pos = x[i]; - - int *jlist = firstneigh[i]; - int jnum = numneigh[i]; - if (jnum <= 0) - continue; - - // get neighbours ordered by increasing distance - double nbr[MAX_NEIGHBORS + 1][3]; - int num_nbrs = get_neighbors(pos, jnum, jlist, x, nbr); - - // check that we have enough neighbours for the desired structure types - int32_t flags = 0; - if (num_nbrs >= PTM_NUM_NBRS_SC && (input_flags & PTM_CHECK_SC)) - flags |= PTM_CHECK_SC; - if (num_nbrs >= PTM_NUM_NBRS_FCC && (input_flags & PTM_CHECK_FCC)) - flags |= PTM_CHECK_FCC; - if (num_nbrs >= PTM_NUM_NBRS_HCP && (input_flags & PTM_CHECK_HCP)) - flags |= PTM_CHECK_HCP; - if (num_nbrs >= PTM_NUM_NBRS_ICO && (input_flags & PTM_CHECK_ICO)) - flags |= PTM_CHECK_ICO; - if (num_nbrs >= PTM_NUM_NBRS_BCC && (input_flags & PTM_CHECK_BCC)) - flags |= PTM_CHECK_BCC; - if (num_nbrs >= PTM_NUM_NBRS_DCUB && (input_flags & PTM_CHECK_DCUB)) - flags |= PTM_CHECK_DCUB; - if (num_nbrs >= PTM_NUM_NBRS_DHEX && (input_flags & PTM_CHECK_DHEX)) - flags |= PTM_CHECK_DHEX; - - // now run PTM - int8_t mapping[MAX_NEIGHBORS + 1]; - int32_t type, alloy_type; - double scale, rmsd, interatomic_distance, lattice_constant; - double q[4], F[9], F_res[3], U[9], P[9]; - ptm_index(local_handle, flags, num_nbrs + 1, nbr, NULL, true, &type, - &alloy_type, &scale, &rmsd, q, F, F_res, U, P, mapping, - &interatomic_distance, &lattice_constant); - - if (rmsd > rmsd_threshold) { - type = PTM_MATCH_NONE; - } - - // printf("%d type=%d rmsd=%f\n", i, type, rmsd); - - if (type == PTM_MATCH_NONE) - type = OTHER; - - output[i][0] = type; - output[i][1] = rmsd; - output[i][2] = interatomic_distance; - output[i][3] = q[0]; - output[i][4] = q[1]; - output[i][5] = q[2]; - output[i][6] = q[3]; - } - - // printf("finished ptm analysis\n"); - ptm_uninitialize_local(local_handle); -} - -/* ---------------------------------------------------------------------- - memory usage of local atom-based array -------------------------------------------------------------------------- */ - -double ComputePTMAtom::memory_usage() { - double bytes = nmax * NUM_COLUMNS * sizeof(double); - bytes += nmax * sizeof(double); - return bytes; -} diff --git a/src/PTM/compute_ptm_atom.h b/src/PTM/compute_ptm_atom.h deleted file mode 100644 index 5c10e0c443..0000000000 --- a/src/PTM/compute_ptm_atom.h +++ /dev/null @@ -1,48 +0,0 @@ -/* -*- c++ -*- ---------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -#ifdef COMPUTE_CLASS - -ComputeStyle(ptm/atom,ComputePTMAtom) - -#else - -#ifndef LMP_COMPUTE_PTM_ATOM_H -#define LMP_COMPUTE_PTM_ATOM_H - -#include "compute.h" - -namespace LAMMPS_NS { - -class ComputePTMAtom : public Compute { - public: - ComputePTMAtom(class LAMMPS *, int, char **); - ~ComputePTMAtom(); - void init(); - void init_list(int, class NeighList *); - void compute_peratom(); - double memory_usage(); - - private: - int nmax; - int32_t input_flags; - double rmsd_threshold; - class NeighList *list; - double **output; -}; - -} - -#endif -#endif - diff --git a/src/PTM/ptm_constants.h b/src/PTM/ptm_constants.h deleted file mode 100644 index f868f51e84..0000000000 --- a/src/PTM/ptm_constants.h +++ /dev/null @@ -1,174 +0,0 @@ -#ifndef PTM_CONSTANTS_H -#define PTM_CONSTANTS_H - -//------------------------------------ -// definitions -//------------------------------------ -#define PTM_NO_ERROR 0 - - -#define PTM_CHECK_FCC (1 << 0) -#define PTM_CHECK_HCP (1 << 1) -#define PTM_CHECK_BCC (1 << 2) -#define PTM_CHECK_ICO (1 << 3) -#define PTM_CHECK_SC (1 << 4) -#define PTM_CHECK_DCUB (1 << 5) -#define PTM_CHECK_DHEX (1 << 6) -#define PTM_CHECK_NONDIAMOND (PTM_CHECK_SC | PTM_CHECK_FCC | PTM_CHECK_HCP | PTM_CHECK_ICO | PTM_CHECK_BCC) -#define PTM_CHECK_ALL (PTM_CHECK_SC | PTM_CHECK_FCC | PTM_CHECK_HCP | PTM_CHECK_ICO | PTM_CHECK_BCC | PTM_CHECK_DCUB | PTM_CHECK_DHEX) - -#define PTM_MATCH_NONE 0 -#define PTM_MATCH_FCC 1 -#define PTM_MATCH_HCP 2 -#define PTM_MATCH_BCC 3 -#define PTM_MATCH_ICO 4 -#define PTM_MATCH_SC 5 -#define PTM_MATCH_DCUB 6 -#define PTM_MATCH_DHEX 7 - -#define PTM_ALLOY_NONE 0 -#define PTM_ALLOY_PURE 1 -#define PTM_ALLOY_L10 2 -#define PTM_ALLOY_L12_CU 3 -#define PTM_ALLOY_L12_AU 4 -#define PTM_ALLOY_B2 5 -#define PTM_ALLOY_SIC 6 - - -#define PTM_MAX_INPUT_POINTS 35 -#define PTM_MAX_NBRS 16 -#define PTM_MAX_POINTS (PTM_MAX_NBRS + 1) -#define PTM_MAX_FACETS 28 //2 * PTM_MAX_NBRS - 4 -#define PTM_MAX_EDGES 42 //3 * PTM_MAX_NBRS - 6 - - -//------------------------------------ -// number of neighbours -//------------------------------------ -#define PTM_NUM_NBRS_FCC 12 -#define PTM_NUM_NBRS_HCP 12 -#define PTM_NUM_NBRS_BCC 14 -#define PTM_NUM_NBRS_ICO 12 -#define PTM_NUM_NBRS_SC 6 -#define PTM_NUM_NBRS_DCUB 16 -#define PTM_NUM_NBRS_DHEX 16 - -#define PTM_NUM_POINTS_FCC (PTM_NUM_NBRS_FCC + 1) -#define PTM_NUM_POINTS_HCP (PTM_NUM_NBRS_HCP + 1) -#define PTM_NUM_POINTS_BCC (PTM_NUM_NBRS_BCC + 1) -#define PTM_NUM_POINTS_ICO (PTM_NUM_NBRS_ICO + 1) -#define PTM_NUM_POINTS_SC (PTM_NUM_NBRS_SC + 1) -#define PTM_NUM_POINTS_DCUB (PTM_NUM_NBRS_DCUB + 1) -#define PTM_NUM_POINTS_DHEX (PTM_NUM_NBRS_DHEX + 1) - -const int ptm_num_nbrs[8] = {0, PTM_NUM_NBRS_FCC, PTM_NUM_NBRS_HCP, PTM_NUM_NBRS_BCC, PTM_NUM_NBRS_ICO, PTM_NUM_NBRS_SC, PTM_NUM_NBRS_DCUB, PTM_NUM_NBRS_DHEX}; - -//------------------------------------ -// template structures -//------------------------------------ - -//these point sets have barycentre {0, 0, 0} and are scaled such that the mean neighbour distance is 1 - -const double ptm_template_fcc[PTM_NUM_POINTS_FCC][3] = { { 0. , 0. , 0. }, - { 0. , 0.707106781187, 0.707106781187 }, - { 0. , -0.707106781187, -0.707106781187 }, - { 0. , 0.707106781187, -0.707106781187 }, - { 0. , -0.707106781187, 0.707106781187 }, - { 0.707106781187, 0. , 0.707106781187 }, - { -0.707106781187, 0. , -0.707106781187 }, - { 0.707106781187, 0. , -0.707106781187 }, - { -0.707106781187, 0. , 0.707106781187 }, - { 0.707106781187, 0.707106781187, 0. }, - { -0.707106781187, -0.707106781187, 0. }, - { 0.707106781187, -0.707106781187, 0. }, - { -0.707106781187, 0.707106781187, 0. } }; - -const double ptm_template_hcp[PTM_NUM_POINTS_HCP][3] = { { 0. , 0. , 0. }, - { 0.707106781186, 0. , 0.707106781186 }, - { -0.235702260395, -0.942809041583, -0.235702260395 }, - { 0.707106781186, 0.707106781186, 0. }, - { -0.235702260395, -0.235702260395, -0.942809041583 }, - { 0. , 0.707106781186, 0.707106781186 }, - { -0.942809041583, -0.235702260395, -0.235702260395 }, - { -0.707106781186, 0.707106781186, 0. }, - { 0. , 0.707106781186, -0.707106781186 }, - { 0.707106781186, 0. , -0.707106781186 }, - { 0.707106781186, -0.707106781186, 0. }, - { -0.707106781186, 0. , 0.707106781186 }, - { 0. , -0.707106781186, 0.707106781186 } }; - -const double ptm_template_bcc[PTM_NUM_POINTS_BCC][3] = { { 0. , 0. , 0. }, - { -0.541451884327, -0.541451884327, -0.541451884327 }, - { 0.541451884327, 0.541451884327, 0.541451884327 }, - { 0.541451884327, -0.541451884327, -0.541451884327 }, - { -0.541451884327, 0.541451884327, 0.541451884327 }, - { -0.541451884327, 0.541451884327, -0.541451884327 }, - { 0.541451884327, -0.541451884327, 0.541451884327 }, - { -0.541451884327, -0.541451884327, 0.541451884327 }, - { 0.541451884327, 0.541451884327, -0.541451884327 }, - { 0. , 0. , -1.082903768655 }, - { 0. , 0. , 1.082903768655 }, - { 0. , -1.082903768655, 0. }, - { 0. , 1.082903768655, 0. }, - { -1.082903768655, 0. , 0. }, - { 1.082903768655, 0. , 0. } }; - -const double ptm_template_ico[PTM_NUM_POINTS_ICO][3] = { { 0. , 0. , 0. }, - { 0. , 0.525731112119, 0.850650808352 }, - { 0. , -0.525731112119, -0.850650808352 }, - { 0. , 0.525731112119, -0.850650808352 }, - { 0. , -0.525731112119, 0.850650808352 }, - { -0.525731112119, -0.850650808352, 0. }, - { 0.525731112119, 0.850650808352, 0. }, - { 0.525731112119, -0.850650808352, 0. }, - { -0.525731112119, 0.850650808352, 0. }, - { -0.850650808352, 0. , -0.525731112119 }, - { 0.850650808352, 0. , 0.525731112119 }, - { 0.850650808352, 0. , -0.525731112119 }, - { -0.850650808352, 0. , 0.525731112119 } }; - -const double ptm_template_sc[PTM_NUM_POINTS_SC][3] = { { 0. , 0. , 0. }, - { 0. , 0. , -1. }, - { 0. , 0. , 1. }, - { 0. , -1. , 0. }, - { 0. , 1. , 0. }, - { -1. , 0. , 0. }, - { 1. , 0. , 0. } }; - -const double ptm_template_dcub[PTM_NUM_POINTS_DCUB][3] = { { 0. , 0. , 0. }, - { -0.391491627053, 0.391491627053, 0.391491627053 }, - { -0.391491627053, -0.391491627053, -0.391491627053 }, - { 0.391491627053, -0.391491627053, 0.391491627053 }, - { 0.391491627053, 0.391491627053, -0.391491627053 }, - { -0.782983254107, 0. , 0.782983254107 }, - { -0.782983254107, 0.782983254107, 0. }, - { 0. , 0.782983254107, 0.782983254107 }, - { -0.782983254107, -0.782983254107, 0. }, - { -0.782983254107, 0. , -0.782983254107 }, - { 0. , -0.782983254107, -0.782983254107 }, - { 0. , -0.782983254107, 0.782983254107 }, - { 0.782983254107, -0.782983254107, 0. }, - { 0.782983254107, 0. , 0.782983254107 }, - { 0. , 0.782983254107, -0.782983254107 }, - { 0.782983254107, 0. , -0.782983254107 }, - { 0.782983254107, 0.782983254107, 0. } }; - -const double ptm_template_dhex[PTM_NUM_POINTS_DHEX][3] = { { 0. , 0. , 0. }, - { -0.391491627053, -0.391491627053, -0.391491627053 }, - { 0.391491627053, -0.391491627053, 0.391491627053 }, - { -0.391491627053, 0.391491627053, 0.391491627053 }, - { 0.391491627053, 0.391491627053, -0.391491627053 }, - { -0.260994418036, -1.043977672142, -0.260994418036 }, - { -1.043977672142, -0.260994418036, -0.260994418036 }, - { -0.260994418036, -0.260994418036, -1.043977672142 }, - { 0.782983254107, 0. , 0.782983254107 }, - { 0.782983254107, -0.782983254107, 0. }, - { 0. , -0.782983254107, 0.782983254107 }, - { 0. , 0.782983254107, 0.782983254107 }, - { -0.782983254107, 0.782983254107, 0. }, - { -0.782983254107, 0. , 0.782983254107 }, - { 0.782983254107, 0.782983254107, 0. }, - { 0. , 0.782983254107, -0.782983254107 }, - { 0.782983254107, 0. , -0.782983254107 } }; -#endif - diff --git a/src/PTM/ptm_functions.h b/src/PTM/ptm_functions.h deleted file mode 100644 index cd67d4940d..0000000000 --- a/src/PTM/ptm_functions.h +++ /dev/null @@ -1,27 +0,0 @@ -#ifndef PTM_FUNCTIONS_H -#define PTM_FUNCTIONS_H - -#include -#include -#include "ptm_initialize_data.h" -#include "ptm_constants.h" - - -//------------------------------------ -// function declarations -//------------------------------------ -#ifdef __cplusplus -extern "C" { -#endif - - -int ptm_index( ptm_local_handle_t local_handle, int32_t flags, int num_points, double (*atomic_positions)[3], int32_t* atomic_numbers, bool topological_ordering, //inputs - int32_t* p_type, int32_t* p_alloy_type, double* p_scale, double* p_rmsd, double* q, double* F, double* F_res, double* U, double* P, int8_t* mapping, double* p_interatomic_distance, double* p_lattice_constant); //outputs - - -#ifdef __cplusplus -} -#endif - -#endif - diff --git a/src/USER-PTM/alloy_types.cpp b/src/USER-PTM/alloy_types.cpp deleted file mode 100644 index bde51c19b1..0000000000 --- a/src/USER-PTM/alloy_types.cpp +++ /dev/null @@ -1,101 +0,0 @@ -#include -#include "ptm_constants.h" -#include "initialize_data.h" - - -#define NUM_ALLOY_TYPES 3 -static uint32_t typedata[NUM_ALLOY_TYPES][3] = { - {PTM_MATCH_FCC, PTM_ALLOY_L10, 0x000001fe}, - {PTM_MATCH_FCC, PTM_ALLOY_L12_CU, 0x0000001e}, - {PTM_MATCH_FCC, PTM_ALLOY_L12_AU, 0x00001ffe}, -}; - -static bool test_pure(int num_nbrs, int32_t* numbers) -{ - for (int i=1;inum_nbrs+1;i++) - binary[i] = numbers[mapping[i]] == numbers[0] ? 0 : 1; - - for (int i=1;inum_nbrs+1;i++) - if (binary[i] != binary[0]) - return false; - - return true; -} - -static int32_t canonical_alloy_representation(const refdata_t* ref, int8_t* mapping, int32_t* numbers) -{ - int8_t binary[PTM_MAX_POINTS]; - for (int i=0;inum_nbrs+1;i++) - binary[i] = numbers[mapping[i]] == numbers[0] ? 0 : 1; - - int8_t temp[PTM_MAX_POINTS]; - uint32_t best = 0xFFFFFFFF; - for (int j=0;jnum_mappings;j++) - { - for (int i=0;inum_nbrs+1;i++) - temp[ref->mapping[j][i]] = binary[i]; - - uint32_t code = 0; - for (int i=0;inum_nbrs+1;i++) - code |= (temp[i] << i); - - best = std::min(best, code); - } - - return best; -} - -int32_t find_alloy_type(const refdata_t* ref, int8_t* mapping, int32_t* numbers) -{ - if (test_pure(ref->num_nbrs, numbers)) - return PTM_ALLOY_PURE; - - if (!test_binary(ref->num_nbrs, numbers)) - return PTM_ALLOY_NONE; - - uint32_t code = canonical_alloy_representation(ref, mapping, numbers); - for (int i=0;itype == typedata[i][0] && code == typedata[i][2]) - return typedata[i][1]; - - if (ref->type == PTM_MATCH_BCC) - if (test_shell_structure(ref, mapping, numbers, 8)) - return PTM_ALLOY_B2; - - if (ref->type == PTM_MATCH_DCUB || ref->type == PTM_MATCH_DHEX) - if (test_shell_structure(ref, mapping, numbers, 4)) - return PTM_ALLOY_SIC; - - return PTM_ALLOY_NONE; -} - diff --git a/src/USER-PTM/alloy_types.h b/src/USER-PTM/alloy_types.h deleted file mode 100644 index 1f2980593a..0000000000 --- a/src/USER-PTM/alloy_types.h +++ /dev/null @@ -1,9 +0,0 @@ -#ifndef ALLOY_TYPES_H -#define ALLOY_TYPES_H - -#include "initialize_data.h" - -int32_t find_alloy_type(const refdata_t* ref, int8_t* mapping, int32_t* numbers); - -#endif - diff --git a/src/USER-PTM/canonical_coloured.cpp b/src/USER-PTM/canonical_coloured.cpp deleted file mode 100644 index af446e1a95..0000000000 --- a/src/USER-PTM/canonical_coloured.cpp +++ /dev/null @@ -1,167 +0,0 @@ -#include -#include -#include -#include "graph_tools.h" -#include "ptm_constants.h" - - -static bool weinberg_coloured(int num_nodes, int num_edges, int8_t common[PTM_MAX_NBRS][PTM_MAX_NBRS], int8_t* colours, int8_t* best_code, int8_t* canonical_labelling, int a, int b) -{ - bool m[PTM_MAX_NBRS][PTM_MAX_NBRS]; - memset(m, 0, sizeof(bool) * PTM_MAX_NBRS * PTM_MAX_NBRS); - - int8_t index[PTM_MAX_NBRS]; - memset(index, -1, sizeof(int8_t) * PTM_MAX_NBRS); - - - int n = 0; - index[a] = colours[a] * num_nodes + n++; - if (index[a] > best_code[0]) - return false; - - bool winning = false; - if (index[a] < best_code[0]) - { - best_code[0] = index[a]; - winning = true; - } - - int c = -1; - for (int it=1;it<2*num_edges;it++) - { - bool newvertex = index[b] == -1; - - if (newvertex) - index[b] = colours[b] * num_nodes + n++; - - if (!winning && index[b] > best_code[it]) - return false; - - if (winning || index[b] < best_code[it]) - { - winning = true; - best_code[it] = index[b]; - } - - if (newvertex) - { - //When a new vertex is reached, take the right-most edge - //relative to the edge on which the vertex is reached. - - c = common[a][b]; - } - else if (m[b][a] == false) - { - //When an old vertex is reached on a new path, go back - //in the opposite direction. - - c = a; - } - else - { - //When an old vertex is reached on an old path, leave the - //vertex on the right-most edge that has not previously - //been traversed in that direction. - - c = common[a][b]; - while (m[b][c] == true) - c = common[c][b]; - } - - m[a][b] = true; - a = b; - b = c; - } - - if (winning) - { - memcpy(canonical_labelling, index, sizeof(int8_t) * num_nodes); - return true; - } - - return false; -} - -int canonical_form_coloured(int num_facets, int8_t facets[][3], int num_nodes, int8_t* degree, int8_t* colours, int8_t* canonical_labelling, int8_t* best_code, uint64_t* p_hash) -{ - int8_t common[PTM_MAX_NBRS][PTM_MAX_NBRS] = {{0}}; - int num_edges = 3 * num_facets / 2; - if (!build_facet_map(num_facets, facets, common)) - return -1; - - memset(best_code, SCHAR_MAX, sizeof(int8_t) * 2 * PTM_MAX_EDGES); - - bool equal = true; - for (int i = 1;i=0;i--) - canonical_labelling[i+1] = (canonical_labelling[i] % num_nodes) + 1; - canonical_labelling[0] = 0; - - uint64_t hash = 0; - for (int i = 0;i<2 * num_edges;i++) - { - uint64_t e = best_code[i]; - e += i % 8; - e &= 0xF; - e <<= (4 * i) % 64; - hash ^= e; - } - - *p_hash = hash; - return PTM_NO_ERROR; -} - diff --git a/src/USER-PTM/canonical_coloured.h b/src/USER-PTM/canonical_coloured.h deleted file mode 100644 index 4a7b5f5a4a..0000000000 --- a/src/USER-PTM/canonical_coloured.h +++ /dev/null @@ -1,9 +0,0 @@ -#ifndef CANONICAL_COLOURED_H -#define CANONICAL_COLOURED_H - -#include - -int canonical_form_coloured(int num_facets, int8_t facets[][3], int num_nodes, int8_t* degree, int8_t* colours, int8_t* canonical_labelling, int8_t* best_code, uint64_t* p_hash); - -#endif - diff --git a/src/USER-PTM/cell.cpp b/src/USER-PTM/cell.cpp deleted file mode 100644 index f88e310b74..0000000000 --- a/src/USER-PTM/cell.cpp +++ /dev/null @@ -1,1368 +0,0 @@ -// Voro++, a 3D cell-based Voronoi library -// -// Author : Chris H. Rycroft (LBL / UC Berkeley) -// Email : chr@alum.mit.edu -// Date : August 30th 2011 -// -// Modified by PM Larsen for use in Polyhedral Template Matching - -/** \file cell.cc - * \brief Function implementations for the voronoicell and related classes. */ - -#include -#include -#include -#include "config.h" -#include "cell.h" - -namespace voro { - -inline void voro_fatal_error(const char *p,int status) { - fprintf(stderr,"voro++: %s\n",p); - exit(status); - //return -1;//status; -} - -/** Constructs a Voronoi cell and sets up the initial memory. */ -voronoicell_base::voronoicell_base() : - current_vertices(init_vertices), current_vertex_order(init_vertex_order), - current_delete_size(init_delete_size), current_delete2_size(init_delete2_size), - ed(new int*[current_vertices]), nu(new int[current_vertices]), - pts(new double[3*current_vertices]), mem(new int[current_vertex_order]), - mec(new int[current_vertex_order]), mep(new int*[current_vertex_order]), - ds(new int[current_delete_size]), stacke(ds+current_delete_size), - ds2(new int[current_delete2_size]), stacke2(ds2+current_delete_size), - current_marginal(init_marginal), marg(new int[current_marginal]) { - int i; - for(i=0;i<3;i++) { - mem[i]=init_n_vertices;mec[i]=0; - mep[i]=new int[init_n_vertices*((i<<1)+1)]; - } - mem[3]=init_3_vertices;mec[3]=0; - mep[3]=new int[init_3_vertices*7]; - for(i=4;i=0;i--) if(mem[i]>0) delete [] mep[i]; - delete [] marg; - delete [] ds2;delete [] ds; - delete [] mep;delete [] mec; - delete [] mem;delete [] pts; - delete [] nu;delete [] ed; -} - -/** Ensures that enough memory is allocated prior to carrying out a copy. - * \param[in] vc a reference to the specialized version of the calling class. - * \param[in] vb a pointered to the class to be copied. */ -template -void voronoicell_base::check_memory_for_copy(vc_class &vc,voronoicell_base* vb) { - while(current_vertex_ordercurrent_vertex_order) add_memory_vorder(vc); - for(int i=0;imec[i]) add_memory(vc,i,ds2); - while(current_verticesp) add_memory_vertices(vc); -} - -/** Increases the memory storage for a particular vertex order, by increasing - * the size of the of the corresponding mep array. If the arrays already exist, - * their size is doubled; if they don't exist, then new ones of size - * init_n_vertices are allocated. The routine also ensures that the pointers in - * the ed array are updated, by making use of the back pointers. For the cases - * where the back pointer has been temporarily overwritten in the marginal - * vertex code, the auxiliary delete stack is scanned to find out how to update - * the ed value. If the template has been instantiated with the neighbor - * tracking turned on, then the routine also reallocates the corresponding mne - * array. - * \param[in] i the order of the vertex memory to be increased. */ -template -void voronoicell_base::add_memory(vc_class &vc,int i,int *stackp2) { - int s=(i<<1)+1; - if(mem[i]==0) { - vc.n_allocate(i,init_n_vertices); - mep[i]=new int[init_n_vertices*s]; - mem[i]=init_n_vertices; -#if VOROPP_VERBOSE >=2 - fprintf(stderr,"Order %d vertex memory created\n",i); -#endif - } else { - int j=0,k,*l; - mem[i]<<=1; - if(mem[i]>max_n_vertices) voro_fatal_error("Point memory allocation exceeded absolute maximum",VOROPP_MEMORY_ERROR); -#if VOROPP_VERBOSE >=2 - fprintf(stderr,"Order %d vertex memory scaled up to %d\n",i,mem[i]); -#endif - l=new int[s*mem[i]]; - int m=0; - vc.n_allocate_aux1(i); - while(j=0) { - ed[k]=l+j; - vc.n_set_to_aux1_offset(k,m); - } else { - int *dsp; - for(dsp=ds2;dsp=3 - fputs("Relocated dangling pointer",stderr); -#endif - } - for(k=0;k -void voronoicell_base::add_memory_vertices(vc_class &vc) { - -printf("nope: %d\n", current_vertices); -exit(3); - - int i=(current_vertices<<1),j,**pp,*pnu; - if(i>max_vertices) voro_fatal_error("Vertex memory allocation exceeded absolute maximum",VOROPP_MEMORY_ERROR); -#if VOROPP_VERBOSE >=2 - fprintf(stderr,"Vertex memory scaled up to %d\n",i); -#endif - double *ppts; - pp=new int*[i]; - for(j=0;j -void voronoicell_base::add_memory_vorder(vc_class &vc) { - int i=(current_vertex_order<<1),j,*p1,**p2; - if(i>max_vertex_order) voro_fatal_error("Vertex order memory allocation exceeded absolute maximum",VOROPP_MEMORY_ERROR); -#if VOROPP_VERBOSE >=2 - fprintf(stderr,"Vertex order memory scaled up to %d\n",i); -#endif - p1=new int[i]; - for(j=0;jmax_delete_size) voro_fatal_error("Delete stack 1 memory allocation exceeded absolute maximum",VOROPP_MEMORY_ERROR); -#if VOROPP_VERBOSE >=2 - fprintf(stderr,"Delete stack 1 memory scaled up to %d\n",current_delete_size); -#endif - int *dsn=new int[current_delete_size],*dsnp=dsn,*dsp=ds; - while(dspmax_delete2_size) voro_fatal_error("Delete stack 2 memory allocation exceeded absolute maximum",VOROPP_MEMORY_ERROR); -#if VOROPP_VERBOSE >=2 - fprintf(stderr,"Delete stack 2 memory scaled up to %d\n",current_delete2_size); -#endif - int *dsn=new int[current_delete2_size],*dsnp=dsn,*dsp=ds2; - while(dsp -inline bool voronoicell_base::search_for_outside_edge(vc_class &vc,int &up) { - int i,lp,lw,*j(ds2),*stackp2(ds2); - double l; - *(stackp2++)=up; - while(j -inline void voronoicell_base::add_to_stack(vc_class &vc,int lp,int *&stackp2) { - for(int *k(ds2);k -bool voronoicell_base::nplane(vc_class &vc,double x,double y,double z,double rsq,int p_id) { - int count=0,i,j,k,lp=up,cp,qp,rp,*stackp(ds),*stackp2(ds2),*dsp; - int us=0,ls=0,qs,iqs,cs,uw,qw,lw; - int *edp,*edd; - double u,l,r,q;bool complicated_setup=false,new_double_edge=false,double_edge=false; - - // Initialize the safe testing routine - n_marg=0;px=x;py=y;pz=z;prsq=rsq; - - // Test approximately sqrt(n)/4 points for their proximity to the plane - // and keep the one which is closest - uw=m_test(up,u); - - // Starting from an initial guess, we now move from vertex to vertex, - // to try and find an edge which intersects the cutting plane, - // or a vertex which is on the plane - try { - if(uw==1) { - - // The test point is inside the cutting plane. - us=0; - do { - lp=ed[up][us]; - lw=m_test(lp,l); - if(l=p) throw true; - u=l;up=lp; - for(us=0;us=p) throw true; - u=q;up=qp; - for(us=0;us=1 - fputs("Bailed out of convex calculation\n",stderr); -#endif - qw=1;lw=0; - for(qp=0;qp=current_vertex_order) add_memory_vorder(vc); - if(mec[nu[p]]==mem[nu[p]]) add_memory(vc,nu[p],stackp2); - vc.n_set_pointer(p,nu[p]); - ed[p]=mep[nu[p]]+((nu[p]<<1)+1)*mec[nu[p]]++; - ed[p][nu[p]<<1]=p; - - // Copy the edges of the original vertex into the new - // one. Delete the edges of the original vertex, and - // update the relational table. - us=cycle_down(i,up); - while(i=current_vertex_order) add_memory_vorder(vc); - if(mec[nu[p]]==mem[nu[p]]) add_memory(vc,nu[p],stackp2); - - // Copy the edges of the original vertex into the new - // one. Delete the edges of the original vertex, and - // update the relational table. - vc.n_set_pointer(p,nu[p]); - ed[p]=mep[nu[p]]+((nu[p]<<1)+1)*mec[nu[p]]++; - ed[p][nu[p]<<1]=p; - us=i++; - while(i0) k+=nu[j]; - } else { - if(j>0) { - - // This vertex was visited before, so - // count those vertices to the ones we - // already have. - k+=nu[j]; - - // The only time when we might make a - // duplicate edge is if the point we're - // going to move to next is also a - // marginal point, so test for that - // first. - if(lw==0) { - - // Now see whether this marginal point - // has been visited before. - i=-ed[lp][nu[lp]<<1]; - if(i>0) { - - // Now see if the last edge of that other - // marginal point actually ends up here. - if(ed[i][nu[i]-1]==j) { - new_double_edge=true; - k-=1; - } else new_double_edge=false; - } else { - - // That marginal point hasn't been visited - // before, so we probably don't have to worry - // about duplicate edges, except in the - // case when that's the way into the end - // of the facet, because that way always creates - // an edge. - if(j==rp&&lp==up&&ed[qp][nu[qp]+qs]==us) { - new_double_edge=true; - k-=1; - } else new_double_edge=false; - } - } else new_double_edge=false; - } else { - - // The vertex hasn't been visited - // before, but let's see if it's - // marginal - if(lw==0) { - - // If it is, we need to check - // for the case that it's a - // small branch, and that we're - // heading right back to where - // we came from - i=-ed[lp][nu[lp]<<1]; - if(i==cp) { - new_double_edge=true; - k-=1; - } else new_double_edge=false; - } else new_double_edge=false; - } - } - - // k now holds the number of edges of the new vertex - // we are forming. Add memory for it if it doesn't exist - // already. - while(k>=current_vertex_order) add_memory_vorder(vc); - if(mec[k]==mem[k]) add_memory(vc,k,stackp2); - - // Now create a new vertex with order k, or augment - // the existing one - if(j>0) { - - // If we're augmenting a vertex but we don't - // actually need any more edges, just skip this - // routine to avoid memory confusion - if(nu[j]!=k) { - // Allocate memory and copy the edges - // of the previous instance into it - vc.n_set_aux1(k); - edp=mep[k]+((k<<1)+1)*mec[k]++; - i=0; - while(ids) { - --p; - while(ed[p][nu[p]]==-1) { - j=nu[p]; - edp=ed[p];edd=(mep[j]+((j<<1)+1)*--mec[j]); - while(edp0) voro_fatal_error("Zero order vertex formed",VOROPP_INTERNAL_ERROR); - - // Collapse any order 2 vertices and exit - return collapse_order2(vc); -} - -/** During the creation of a new facet in the plane routine, it is possible - * that some order two vertices may arise. This routine removes them. - * Suppose an order two vertex joins c and d. If there's a edge between - * c and d already, then the order two vertex is just removed; otherwise, - * the order two vertex is removed and c and d are joined together directly. - * It is possible this process will create order two or order one vertices, - * and the routine is continually run until all of them are removed. - * \return False if the vertex removal was unsuccessful, indicative of the cell - * reducing to zero volume and disappearing; true if the vertex removal - * was successful. */ -template -inline bool voronoicell_base::collapse_order2(vc_class &vc) { - if(!collapse_order1(vc)) return false; - int a,b,i,j,k,l; - while(mec[2]>0) { - - // Pick a order 2 vertex and read in its edges - i=--mec[2]; - j=mep[2][5*i];k=mep[2][5*i+1]; - if(j==k) { -#if VOROPP_VERBOSE >=1 - fputs("Order two vertex joins itself",stderr); -#endif - return false; - } - - // Scan the edges of j to see if joins k - for(l=0;l -inline bool voronoicell_base::collapse_order1(vc_class &vc) { - int i,j,k; - while(mec[1]>0) { - up=0; -#if VOROPP_VERBOSE >=1 - fputs("Order one collapse\n",stderr); -#endif - i=--mec[1]; - j=mep[1][3*i];k=mep[1][3*i+1]; - i=mep[1][3*i+2]; - if(!delete_connection(vc,j,k,false)) return false; - --p; - if(up==i) up=0; - if(p!=i) { - if(up==p) up=i; - pts[3*i]=pts[3*p]; - pts[3*i+1]=pts[3*p+1]; - pts[3*i+2]=pts[3*p+2]; - for(k=0;k -inline bool voronoicell_base::delete_connection(vc_class &vc,int j,int k,bool hand) { - int q=hand?k:cycle_up(k,j); - int i=nu[j]-1,l,*edp,*edd,m; -#if VOROPP_VERBOSE >=1 - if(i<1) { - fputs("Zero order vertex formed\n",stderr); - return false; - } -#endif - if(mec[i]==mem[i]) add_memory(vc,i,ds2); - vc.n_set_aux1(i); - for(l=0;l &v) { - double area; - v.clear(); - int i,j,k,l,m,n; - double ux,uy,uz,vx,vy,vz,wx,wy,wz; - for(i=1;i=0) { - area=0; - ed[i][j]=-1-k; - l=cycle_up(ed[i][nu[i]+j],k); - m=ed[k][l];ed[k][l]=-1-m; - while(m!=i) { - n=cycle_up(ed[k][nu[k]+l],m); - ux=pts[3*k]-pts[3*i]; - uy=pts[3*k+1]-pts[3*i+1]; - uz=pts[3*k+2]-pts[3*i+2]; - vx=pts[3*m]-pts[3*i]; - vy=pts[3*m+1]-pts[3*i+1]; - vz=pts[3*m+2]-pts[3*i+2]; - wx=uy*vz-uz*vy; - wy=uz*vx-ux*vz; - wz=ux*vy-uy*vx; - area+=sqrt(wx*wx+wy*wy+wz*wz); - k=m;l=n; - m=ed[k][l];ed[k][l]=-1-m; - } - v.push_back(0.125*area); - } - } - reset_edges(); -} - -/** Several routines in the class that gather cell-based statistics internally - * track their progress by flipping edges to negative so that they know what - * parts of the cell have already been tested. This function resets them back - * to positive. When it is called, it assumes that every edge in the routine - * should have already been flipped to negative, and it bails out with an - * internal error if it encounters a positive edge. */ -inline void voronoicell_base::reset_edges() { - int i,j; - for(i=0;i=0) voro_fatal_error("Edge reset routine found a previously untested edge",VOROPP_INTERNAL_ERROR); - ed[i][j]=-1-ed[i][j]; - } -} - -/** Checks to see if a given vertex is inside, outside or within the test - * plane. If the point is far away from the test plane, the routine immediately - * returns whether it is inside or outside. If the routine is close the the - * plane and within the specified tolerance, then the special check_marginal() - * routine is called. - * \param[in] n the vertex to test. - * \param[out] ans the result of the scalar product used in evaluating the - * location of the point. - * \return -1 if the point is inside the plane, 1 if the point is outside the - * plane, or 0 if the point is within the plane. */ -inline int voronoicell_base::m_test(int n,double &ans) { - double *pp=pts+n+(n<<1); - ans=*(pp++)*px; - ans+=*(pp++)*py; - ans+=*pp*pz-prsq; - if(ans<-tolerance2) { - return -1; - } else if(ans>tolerance2) { - return 1; - } - return check_marginal(n,ans); -} - -/** Checks to see if a given vertex is inside, outside or within the test - * plane, for the case when the point has been detected to be very close to the - * plane. The routine ensures that the returned results are always consistent - * with previous tests, by keeping a table of any marginal results. The routine - * first sees if the vertex is in the table, and if it finds a previously - * computed result it uses that. Otherwise, it computes a result for this - * vertex and adds it the table. - * \param[in] n the vertex to test. - * \param[in] ans the result of the scalar product used in evaluating - * the location of the point. - * \return -1 if the point is inside the plane, 1 if the point is outside the - * plane, or 0 if the point is within the plane. */ -int voronoicell_base::check_marginal(int n,double &ans) { - int i; - for(i=0;imax_marginal) - voro_fatal_error("Marginal case buffer allocation exceeded absolute maximum",VOROPP_MEMORY_ERROR); -#if VOROPP_VERBOSE >=2 - fprintf(stderr,"Marginal cases buffer scaled up to %d\n",i); -#endif - int *pmarg=new int[current_marginal]; - for(int j=0;jtolerance?1:(ans<-tolerance?-1:0); - return marg[n_marg-1]; -} - -/** This initializes the class to be a rectangular box. It calls the base class - * initialization routine to set up the edge and vertex information, and then - * sets up the neighbor information, with initial faces being assigned ID - * numbers from -1 to -6. - * \param[in] (xmin,xmax) the minimum and maximum x coordinates. - * \param[in] (ymin,ymax) the minimum and maximum y coordinates. - * \param[in] (zmin,zmax) the minimum and maximum z coordinates. */ -void voronoicell_neighbor::init(double xmin,double xmax,double ymin,double ymax,double zmin,double zmax) { - init_base(xmin,xmax,ymin,ymax,zmin,zmax); - int *q=mne[3]; - *q=-5;q[1]=-3;q[2]=-1; - q[3]=-5;q[4]=-2;q[5]=-3; - q[6]=-5;q[7]=-1;q[8]=-4; - q[9]=-5;q[10]=-4;q[11]=-2; - q[12]=-6;q[13]=-1;q[14]=-3; - q[15]=-6;q[16]=-3;q[17]=-2; - q[18]=-6;q[19]=-4;q[20]=-1; - q[21]=-6;q[22]=-2;q[23]=-4; - *ne=q;ne[1]=q+3;ne[2]=q+6;ne[3]=q+9; - ne[4]=q+12;ne[5]=q+15;ne[6]=q+18;ne[7]=q+21; -} - -/** This routine checks to make sure the neighbor information of each face is - * consistent. */ -void voronoicell_neighbor::check_facets() { - int i,j,k,l,m,q; - for(i=1;i=0) { - ed[i][j]=-1-k; - q=ne[i][j]; - l=cycle_up(ed[i][nu[i]+j],k); - do { - m=ed[k][l]; - ed[k][l]=-1-m; - if(ne[k][l]!=q) fprintf(stderr,"Facet error at (%d,%d)=%d, started from (%d,%d)=%d\n",k,l,ne[k][l],i,j,q); - l=cycle_up(ed[k][nu[k]+l],m); - k=m; - } while (k!=i); - } - } - reset_edges(); -} - -/** The class constructor allocates memory for storing neighbor information. */ -voronoicell_neighbor::voronoicell_neighbor() { - int i; - mne=new int*[current_vertex_order]; - ne=new int*[current_vertices]; - for(i=0;i<3;i++) mne[i]=new int[init_n_vertices*i]; - mne[3]=new int[init_3_vertices*3]; - for(i=4;i=0;i--) if(mem[i]>0) delete [] mne[i]; - delete [] mne; - delete [] ne; -} - -/** Computes a vector list of neighbors. */ -void voronoicell_neighbor::neighbors(std::vector &v) { - v.clear(); - int i,j,k,l,m; - for(i=1;i=0) { - v.push_back(ne[i][j]); - ed[i][j]=-1-k; - l=cycle_up(ed[i][nu[i]+j],k); - do { - m=ed[k][l]; - ed[k][l]=-1-m; - l=cycle_up(ed[k][nu[k]+l],m); - k=m; - } while (k!=i); - } - } - reset_edges(); -} - -// Explicit instantiation -template bool voronoicell_base::nplane(voronoicell_neighbor&,double,double,double,double,int); -template void voronoicell_base::check_memory_for_copy(voronoicell_neighbor&,voronoicell_base*); - -} - diff --git a/src/USER-PTM/cell.h b/src/USER-PTM/cell.h deleted file mode 100644 index 51a0cbb9ef..0000000000 --- a/src/USER-PTM/cell.h +++ /dev/null @@ -1,324 +0,0 @@ -// Voro++, a 3D cell-based Voronoi library -// -// Author : Chris H. Rycroft (LBL / UC Berkeley) -// Email : chr@alum.mit.edu -// Date : August 30th 2011 -// -// Modified by PM Larsen for use in Polyhedral Template Matching - -/** \file cell.hh - * \brief Header file for the voronoicell and related classes. */ - -#ifndef VOROPP_CELL_HH -#define VOROPP_CELL_HH - -#include -#include - -#include "config.h" - -namespace voro { - -/** \brief A class representing a single Voronoi cell. - * - * This class represents a single Voronoi cell, as a collection of vertices - * that are connected by edges. The class contains routines for initializing - * the Voronoi cell to be simple shapes such as a box, tetrahedron, or octahedron. - * It the contains routines for recomputing the cell based on cutting it - * by a plane, which forms the key routine for the Voronoi cell computation. - * It contains numerous routine for computing statistics about the Voronoi cell, - * and it can output the cell in several formats. - * - * This class is not intended for direct use, but forms the base of the - * voronoicell and voronoicell_neighbor classes, which extend it based on - * whether neighboring particle ID information needs to be tracked. */ -class voronoicell_base { - public: - /** This holds the current size of the arrays ed and nu, which - * hold the vertex information. If more vertices are created - * than can fit in this array, then it is dynamically extended - * using the add_memory_vertices routine. */ - int current_vertices; - /** This holds the current maximum allowed order of a vertex, - * which sets the size of the mem, mep, and mec arrays. If a - * vertex is created with more vertices than this, the arrays - * are dynamically extended using the add_memory_vorder routine. - */ - int current_vertex_order; - /** This sets the size of the main delete stack. */ - int current_delete_size; - /** This sets the size of the auxiliary delete stack. */ - int current_delete2_size; - /** This sets the total number of vertices in the current cell. - */ - int p; - /** This is the index of particular point in the cell, which is - * used to start the tracing routines for plane intersection - * and cutting. These routines will work starting from any - * point, but it's often most efficient to start from the last - * point considered, since in many cases, the cell construction - * algorithm may consider many planes with similar vectors - * concurrently. */ - int up; - /** This is a two dimensional array that holds information - * about the edge connections of the vertices that make up the - * cell. The two dimensional array is not allocated in the - * usual method. To account for the fact the different vertices - * have different orders, and thus require different amounts of - * storage, the elements of ed[i] point to one-dimensional - * arrays in the mep[] array of different sizes. - * - * More specifically, if vertex i has order m, then ed[i] - * points to a one-dimensional array in mep[m] that has 2*m+1 - * entries. The first m elements hold the neighboring edges, so - * that the jth edge of vertex i is held in ed[i][j]. The next - * m elements hold a table of relations which is redundant but - * helps speed up the computation. It satisfies the relation - * ed[ed[i][j]][ed[i][m+j]]=i. The final entry holds a back - * pointer, so that ed[i+2*m]=i. The back pointers are used - * when rearranging the memory. */ - int **ed; - /** This array holds the order of the vertices in the Voronoi - * cell. This array is dynamically allocated, with its current - * size held by current_vertices. */ - int *nu; - /** This in an array with size 3*current_vertices for holding - * the positions of the vertices. */ - double *pts; - voronoicell_base(); - virtual ~voronoicell_base(); - void init_base(double xmin,double xmax,double ymin,double ymax,double zmin,double zmax); - void init_octahedron_base(double l); - void init_tetrahedron_base(double x0,double y0,double z0,double x1,double y1,double z1,double x2,double y2,double z2,double x3,double y3,double z3); - void translate(double x,double y,double z); - double volume(); - double max_radius_squared(); - double total_edge_distance(); - double surface_area(); - void centroid(double &cx,double &cy,double &cz); - int number_of_faces(); - int number_of_edges(); - void vertex_orders(std::vector &v); - void vertices(std::vector &v); - void vertices(double x,double y,double z,std::vector &v); - void face_areas(std::vector &v); - void face_orders(std::vector &v); - void face_freq_table(std::vector &v); - void face_vertices(std::vector &v); - void face_perimeters(std::vector &v); - void normals(std::vector &v); - template - bool nplane(vc_class &vc,double x,double y,double z,double rsq,int p_id); - bool plane_intersects(double x,double y,double z,double rsq); - bool plane_intersects_guess(double x,double y,double z,double rsq); - void construct_relations(); - void check_relations(); - void check_duplicates(); - /** Returns a list of IDs of neighboring particles - * corresponding to each face. - * \param[out] v a reference to a vector in which to return the - * results. If no neighbor information is - * available, a blank vector is returned. */ - virtual void neighbors(std::vector &v) {v.clear();} - /** This a virtual function that is overridden by a routine to - * print the neighboring particle IDs for a given vertex. By - * default, when no neighbor information is available, the - * routine does nothing. - * \param[in] i the vertex to consider. */ - /** This is a simple inline function for picking out the index - * of the next edge counterclockwise at the current vertex. - * \param[in] a the index of an edge of the current vertex. - * \param[in] p the number of the vertex. - * \return 0 if a=nu[p]-1, or a+1 otherwise. */ - inline int cycle_up(int a,int p) {return a==nu[p]-1?0:a+1;} - /** This is a simple inline function for picking out the index - * of the next edge clockwise from the current vertex. - * \param[in] a the index of an edge of the current vertex. - * \param[in] p the number of the vertex. - * \return nu[p]-1 if a=0, or a-1 otherwise. */ - inline int cycle_down(int a,int p) {return a==0?nu[p]-1:a-1;} - protected: - /** This a one dimensional array that holds the current sizes - * of the memory allocations for them mep array.*/ - int *mem; - /** This is a one dimensional array that holds the current - * number of vertices of order p that are stored in the mep[p] - * array. */ - int *mec; - /** This is a two dimensional array for holding the information - * about the edges of the Voronoi cell. mep[p] is a - * one-dimensional array for holding the edge information about - * all vertices of order p, with each vertex holding 2*p+1 - * integers of information. The total number of vertices held - * on mep[p] is stored in mem[p]. If the space runs out, the - * code allocates more using the add_memory() routine. */ - int **mep; - inline void reset_edges(); - template - void check_memory_for_copy(vc_class &vc,voronoicell_base* vb); - void copy(voronoicell_base* vb); - private: - /** This is the delete stack, used to store the vertices which - * are going to be deleted during the plane cutting procedure. - */ - int *ds,*stacke; - /** This is the auxiliary delete stack, which has size set by - * current_delete2_size. */ - int *ds2,*stacke2; - /** This stores the current memory allocation for the marginal - * cases. */ - int current_marginal; - /** This stores the total number of marginal points which are - * currently in the buffer. */ - int n_marg; - /** This array contains a list of the marginal points, and also - * the outcomes of the marginal tests. */ - int *marg; - /** The x coordinate of the normal vector to the test plane. */ - double px; - /** The y coordinate of the normal vector to the test plane. */ - double py; - /** The z coordinate of the normal vector to the test plane. */ - double pz; - /** The magnitude of the normal vector to the test plane. */ - double prsq; - template - void add_memory(vc_class &vc,int i,int *stackp2); - template - void add_memory_vertices(vc_class &vc); - template - void add_memory_vorder(vc_class &vc); - void add_memory_ds(int *&stackp); - void add_memory_ds2(int *&stackp2); - template - inline bool collapse_order1(vc_class &vc); - template - inline bool collapse_order2(vc_class &vc); - template - inline bool delete_connection(vc_class &vc,int j,int k,bool hand); - template - inline bool search_for_outside_edge(vc_class &vc,int &up); - template - inline void add_to_stack(vc_class &vc,int lp,int *&stackp2); - inline bool plane_intersects_track(double x,double y,double z,double rs,double g); - inline void normals_search(std::vector &v,int i,int j,int k); - inline bool search_edge(int l,int &m,int &k); - inline int m_test(int n,double &ans); - int check_marginal(int n,double &ans); - friend class voronoicell; - friend class voronoicell_neighbor; -}; - -/** \brief Extension of the voronoicell_base class to represent a Voronoi cell - * with neighbor information. - * - * This class is an extension of the voronoicell_base class, in cases when the - * IDs of neighboring particles associated with each face of the Voronoi cell. - * It contains additional data structures mne and ne for storing this - * information. */ -class voronoicell_neighbor : public voronoicell_base { - public: - using voronoicell_base::nplane; - /** This two dimensional array holds the neighbor information - * associated with each vertex. mne[p] is a one dimensional - * array which holds all of the neighbor information for - * vertices of order p. */ - int **mne; - /** This is a two dimensional array that holds the neighbor - * information associated with each vertex. ne[i] points to a - * one-dimensional array in mne[nu[i]]. ne[i][j] holds the - * neighbor information associated with the jth edge of vertex - * i. It is set to the ID number of the plane that made the - * face that is clockwise from the jth edge. */ - int **ne; - voronoicell_neighbor(); - ~voronoicell_neighbor(); - void operator=(voronoicell_neighbor &c); - /** Cuts the Voronoi cell by a particle whose center is at a - * separation of (x,y,z) from the cell center. The value of rsq - * should be initially set to \f$x^2+y^2+z^2\f$. - * \param[in] (x,y,z) the normal vector to the plane. - * \param[in] rsq the distance along this vector of the plane. - * \param[in] p_id the plane ID (for neighbor tracking only). - * \return False if the plane cut deleted the cell entirely, - * true otherwise. */ - inline bool nplane(double x,double y,double z,double rsq,int p_id) { - return nplane(*this,x,y,z,rsq,p_id); - } - /** This routine calculates the modulus squared of the vector - * before passing it to the main nplane() routine with full - * arguments. - * \param[in] (x,y,z) the vector to cut the cell by. - * \param[in] p_id the plane ID (for neighbor tracking only). - * \return False if the plane cut deleted the cell entirely, - * true otherwise. */ - inline bool nplane(double x,double y,double z,int p_id) { - double rsq=x*x+y*y+z*z; - return nplane(*this,x,y,z,rsq,p_id); - } - /** This version of the plane routine just makes up the plane - * ID to be zero. It will only be referenced if neighbor - * tracking is enabled. - * \param[in] (x,y,z) the vector to cut the cell by. - * \param[in] rsq the modulus squared of the vector. - * \return False if the plane cut deleted the cell entirely, - * true otherwise. */ - inline bool plane(double x,double y,double z,double rsq) { - return nplane(*this,x,y,z,rsq,0); - } - /** Cuts a Voronoi cell using the influence of a particle at - * (x,y,z), first calculating the modulus squared of this - * vector before passing it to the main nplane() routine. Zero - * is supplied as the plane ID, which will be ignored unless - * neighbor tracking is enabled. - * \param[in] (x,y,z) the vector to cut the cell by. - * \return False if the plane cut deleted the cell entirely, - * true otherwise. */ - inline bool plane(double x,double y,double z) { - double rsq=x*x+y*y+z*z; - return nplane(*this,x,y,z,rsq,0); - } - void init(double xmin,double xmax,double ymin,double ymax,double zmin,double zmax); - void check_facets(); - virtual void neighbors(std::vector &v); - - private: - int *paux1; - int *paux2; - inline void n_allocate(int i,int m) {mne[i]=new int[m*i];} - inline void n_add_memory_vertices(int i) { - int **pp=new int*[i]; - for(int j=0;j -#include -#include -#include -#include -#include "convex_hull_incremental.h" -#include "ptm_constants.h" - - -#define VISIBLE 1 -#define INVISIBLE 2 -#define BOTH 3 -#define TOLERANCE 1E-8 - -static double norm_squared(double* p) -{ - double x = p[0]; - double y = p[1]; - double z = p[2]; - - return x*x + y*y + z*z; -} - -static double dot_product(const double* a, const double* b) -{ - return a[0]*b[0] + a[1]*b[1] + a[2]*b[2]; -} - -static void cross_product(double* a, double* b, double* c) -{ - c[0] = a[1] * b[2] - a[2] * b[1]; - c[1] = a[2] * b[0] - a[0] * b[2]; - c[2] = a[0] * b[1] - a[1] * b[0]; -} - -static void calculate_plane_normal(const double (*points)[3], int a, int b, int c, double* plane_normal) -{ - double u[3] = { points[b][0] - points[a][0], - points[b][1] - points[a][1], - points[b][2] - points[a][2] }; - - double v[3] = { points[c][0] - points[a][0], - points[c][1] - points[a][1], - points[c][2] - points[a][2] }; - - cross_product(u, v, plane_normal); - double norm = sqrt(norm_squared(plane_normal)); - plane_normal[0] /= norm; - plane_normal[1] /= norm; - plane_normal[2] /= norm; -} - -static double point_plane_distance(const double* w, const double* plane_point, const double* plane_cross) -{ - return plane_cross[0] * (plane_point[0] - w[0]) - + plane_cross[1] * (plane_point[1] - w[1]) - + plane_cross[2] * (plane_point[2] - w[2]); -} - -static bool calc_max_extent(int num_points, const double (*points)[3], int* min_index, int* max_index) -{ - for (int j=0;j<3;j++) - { - double dmin = DBL_MAX, dmax = -DBL_MAX; - int imin = 0, imax = 0; - - for (int i = 0;i dmax) - { - dmax = d; - imax = i; - } - } - - if (imin == imax) - return false; //degenerate point set - - min_index[j] = imin; - max_index[j] = imax; - } - - return true; -} - -static bool find_third_point(int num_points, const double (*points)[3], int a, int b, int* p_c) -{ - const double* x1 = points[a]; - const double* x2 = points[b]; - - double x2x1[3] = {x2[0] - x1[0], x2[1] - x1[1], x2[2] - x1[2]}; - double ns_x2x1 = norm_squared(x2x1); - - int bi = -1; - double max_dist = 0.0; - for (int i = 0;i max_dist) - { - max_dist = dist; - bi = i; - } - } - - *p_c = bi; - return max_dist > TOLERANCE; -} - -static bool find_fourth_point(int num_points, const double (*points)[3], int a, int b, int c, int* p_d) -{ - double plane_normal[3]; - calculate_plane_normal(points, a, b, c, plane_normal); - - - int bi = -1; - double max_dist = 0.0; - for (int i = 0;i max_dist) - { - max_dist = dist; - bi = i; - } - } - - *p_d = bi; - return max_dist > TOLERANCE; -} - -static int initial_simplex(int num_points, const double (*points)[3], int* initial_vertices) -{ - int min_index[3] = {0}; - int max_index[3] = {0}; - if (!calc_max_extent(num_points, points, min_index, max_index)) - return -1; - - int bi = -1; - double max_dist = 0.0; - for (int i = 0;i<3;i++) - { - int a = min_index[i], b = max_index[i]; - double delta[3] = { points[a][0] - points[b][0], - points[a][1] - points[b][1], - points[a][2] - points[b][2] }; - double dist = norm_squared(delta); - if (dist > max_dist) - { - bi = i; - max_dist = dist; - } - } - - //first two points are (a, b) - int a = min_index[bi], b = max_index[bi], c = -1, d = -1; - - if (!find_third_point(num_points, points, a, b, &c)) - return -2; - - if (!find_fourth_point(num_points, points, a, b, c, &d)) - return -3; - - initial_vertices[0] = a; - initial_vertices[1] = b; - initial_vertices[2] = c; - initial_vertices[3] = d; - return 0; -} - -static bool visible(const double* w, const double* plane_point, const double* plane_normal) -{ - return point_plane_distance(w, plane_point, plane_normal) > 0; -} - -void add_facet(const double (*points)[3], int a, int b, int c, int8_t* facet, double* plane_normal, double* barycentre) -{ - calculate_plane_normal(points, a, b, c, plane_normal); - if (visible(barycentre, points[a], plane_normal)) - { - plane_normal[0] = -plane_normal[0]; - plane_normal[1] = -plane_normal[1]; - plane_normal[2] = -plane_normal[2]; - - facet[0] = b; - facet[1] = a; - facet[2] = c; - } - else - { - facet[0] = a; - facet[1] = b; - facet[2] = c; - } -} - -static int initialize_convex_hull(int num_points, const double (*points)[3], int8_t facets[][3], double plane_normal[][3], bool* processed, int* initial_vertices, double* barycentre) -{ - memset(processed, 0, PTM_MAX_POINTS * sizeof(bool)); - memset(barycentre, 0, 3 * sizeof(double)); - int ret = initial_simplex(num_points, points, initial_vertices); - if (ret != 0) - return ret; - - for (int i = 0;i<4;i++) - { - int a = initial_vertices[i]; - processed[a] = true; - - barycentre[0] += points[a][0]; - barycentre[1] += points[a][1]; - barycentre[2] += points[a][2]; - } - barycentre[0] /= 4; - barycentre[1] /= 4; - barycentre[2] /= 4; - - add_facet(points, initial_vertices[0], initial_vertices[1], initial_vertices[2], facets[0], plane_normal[0], barycentre); - add_facet(points, initial_vertices[0], initial_vertices[1], initial_vertices[3], facets[1], plane_normal[1], barycentre); - add_facet(points, initial_vertices[0], initial_vertices[2], initial_vertices[3], facets[2], plane_normal[2], barycentre); - add_facet(points, initial_vertices[1], initial_vertices[2], initial_vertices[3], facets[3], plane_normal[3], barycentre); - return 0; -} - -int get_convex_hull(int num_points, const double (*points)[3], convexhull_t* ch, int8_t simplex[][3]) -{ - assert( num_points == PTM_NUM_POINTS_FCC - || num_points == PTM_NUM_POINTS_HCP - || num_points == PTM_NUM_POINTS_BCC - || num_points == PTM_NUM_POINTS_ICO - || num_points == PTM_NUM_POINTS_SC - || num_points == PTM_NUM_POINTS_DCUB - || num_points == PTM_NUM_POINTS_DHEX); - - int ret = 0; - int num_prev = ch->num_prev; - ch->num_prev = num_points; - if (!ch->ok || 0) - { - ret = initialize_convex_hull(num_points, points, ch->facets, ch->plane_normal, ch->processed, ch->initial_vertices, ch->barycentre); - if (ret != 0) - return ret; - - ch->num_facets = 4; - num_prev = 0; - } - - for (int i = num_prev;iprocessed[i]) - continue; - ch->processed[i] = true; - - int num_to_add = 0; - int8_t to_add[PTM_MAX_FACETS][3]; - int8_t edge_visible[PTM_MAX_POINTS][PTM_MAX_POINTS]; - memset(edge_visible, 0, sizeof(int8_t) * PTM_MAX_POINTS * PTM_MAX_POINTS); - for (int j = 0;jnum_facets;j++) - { - int a = ch->facets[j][0]; - int b = ch->facets[j][1]; - int c = ch->facets[j][2]; - - int u = 0, v = 0, w = 0; - - double distance = point_plane_distance(points[i], points[a], ch->plane_normal[j]); - bool vis = distance > TOLERANCE; - if (vis) - { - u = edge_visible[a][b] |= VISIBLE; - edge_visible[b][a] |= VISIBLE; - - v = edge_visible[b][c] |= VISIBLE; - edge_visible[c][b] |= VISIBLE; - - w = edge_visible[c][a] |= VISIBLE; - edge_visible[a][c] |= VISIBLE; - - memcpy(ch->facets[j], ch->facets[ch->num_facets-1], 3 * sizeof(int8_t)); - memcpy(ch->plane_normal[j], ch->plane_normal[ch->num_facets-1], 3 * sizeof(double)); - ch->num_facets--; - j--; - } - else - { - u = edge_visible[a][b] |= INVISIBLE; - edge_visible[b][a] |= INVISIBLE; - - v = edge_visible[b][c] |= INVISIBLE; - edge_visible[c][b] |= INVISIBLE; - - w = edge_visible[c][a] |= INVISIBLE; - edge_visible[a][c] |= INVISIBLE; - } - - if (u == BOTH) - { - to_add[num_to_add][0] = i; - to_add[num_to_add][1] = a; - to_add[num_to_add][2] = b; - num_to_add++; - } - - if (v == BOTH) - { - to_add[num_to_add][0] = i; - to_add[num_to_add][1] = b; - to_add[num_to_add][2] = c; - num_to_add++; - } - - if (w == BOTH) - { - to_add[num_to_add][0] = i; - to_add[num_to_add][1] = c; - to_add[num_to_add][2] = a; - num_to_add++; - } - } - - for (int j = 0;jnum_facets >= PTM_MAX_FACETS) - return -4; - - add_facet(points, to_add[j][0], to_add[j][1], to_add[j][2], ch->facets[ch->num_facets], ch->plane_normal[ch->num_facets], ch->barycentre); ch->num_facets++; - } - } - - for (int i=0;inum_facets;i++) - { - int a = ch->facets[i][0]; - int b = ch->facets[i][1]; - int c = ch->facets[i][2]; - if (a == 0 || b == 0 || c == 0) - return 1; //central atom contained in convex hull - - simplex[i][0] = a - 1; - simplex[i][1] = b - 1; - simplex[i][2] = c - 1; - } - - return ret; -} - diff --git a/src/USER-PTM/convex_hull_incremental.h b/src/USER-PTM/convex_hull_incremental.h deleted file mode 100644 index d384a0457e..0000000000 --- a/src/USER-PTM/convex_hull_incremental.h +++ /dev/null @@ -1,27 +0,0 @@ -#ifndef CONVEX_HULL_INCREMENTAL_H -#define CONVEX_HULL_INCREMENTAL_H - - -#include -#include -#include "ptm_constants.h" - - -typedef struct -{ - int8_t facets[PTM_MAX_FACETS][3]; - double plane_normal[PTM_MAX_FACETS][3]; - bool processed[PTM_MAX_POINTS]; - int initial_vertices[4]; - double barycentre[3]; - int num_facets; - int num_prev; - bool ok; - -} convexhull_t; - -void add_facet(const double (*points)[3], int a, int b, int c, int8_t* facet, double* plane_normal, double* barycentre); -int get_convex_hull(int num_points, const double (*points)[3], convexhull_t* ch, int8_t simplex[][3]); - -#endif - diff --git a/src/USER-PTM/deformation_gradient.cpp b/src/USER-PTM/deformation_gradient.cpp deleted file mode 100644 index 9a86dff6a3..0000000000 --- a/src/USER-PTM/deformation_gradient.cpp +++ /dev/null @@ -1,37 +0,0 @@ -#include "deformation_gradient.h" - - -void calculate_deformation_gradient(int num_points, const double (*ideal_points)[3], int8_t* mapping, double (*normalized)[3], const double (*penrose)[3], double* F, double* res) -{ - for (int i = 0;i<3;i++) - { - for (int j = 0;j<3;j++) - { - double acc = 0.0; - for (int k = 0;k -#include "ptm_constants.h" - -void calculate_deformation_gradient(int num_points, const double (*ideal_points)[3], int8_t* mapping, double (*normalized)[3], const double (*penrose)[3], double* F, double* res); - -//sc -#define k_sc 0.5 -const double penrose_sc[PTM_NUM_POINTS_SC][3] = { - {0, 0, 0}, - {0, 0, -k_sc}, - {0, 0, k_sc}, - {0, -k_sc, 0}, - {0, k_sc, 0}, - {-k_sc, 0, 0}, - {k_sc, 0, 0}, - }; - -//fcc -#define k_fcc 0.17677669529663678216 -const double penrose_fcc[PTM_NUM_POINTS_FCC][3] = { - {0, 0, 0}, - {0, k_fcc, k_fcc}, - {0, -k_fcc, -k_fcc}, - {0, k_fcc, -k_fcc}, - {0, -k_fcc, k_fcc}, - {k_fcc, 0, k_fcc}, - {-k_fcc, 0, -k_fcc}, - {k_fcc, 0, -k_fcc}, - {-k_fcc, 0, k_fcc}, - {k_fcc, k_fcc, -0}, - {-k_fcc, -k_fcc, 0}, - {k_fcc, -k_fcc, 0}, - {-k_fcc, k_fcc, -0}, - }; - -//hcp -#define k_hcp 0.17677669529663678216 -const double penrose_hcp[PTM_NUM_POINTS_HCP][3] = { - {0, 0, 0}, - {k_hcp, 0, k_hcp}, - {-k_hcp/3, -4*k_hcp/3, -k_hcp/3}, - {k_hcp, k_hcp, 0}, - {-k_hcp/3, -k_hcp/3, -4*k_hcp/3}, - {0, k_hcp, k_hcp}, - {-4*k_hcp/3, -k_hcp/3, -k_hcp/3}, - {-k_hcp, k_hcp, -0}, - {0, k_hcp, -k_hcp}, - {k_hcp, 0, -k_hcp}, - {k_hcp, -k_hcp, 0}, - {-k_hcp, 0, k_hcp}, - {0, -k_hcp, k_hcp}, - }; - -//ico -#define k_ico 0.13143277802974323576 -#define phi 1.61803398874989490253 -//((1.0 + sqrt(5)) / 2) -const double penrose_ico[PTM_NUM_POINTS_ICO][3] = { - {0, 0, 0}, - {0, k_ico, phi*k_ico}, - {0, -k_ico, -phi*k_ico}, - {0, k_ico, -phi*k_ico}, - {0, -k_ico, phi*k_ico}, - {-k_ico, -phi*k_ico, -0}, - {k_ico, phi*k_ico, 0}, - {k_ico, -phi*k_ico, 0}, - {-k_ico, phi*k_ico, -0}, - {-phi*k_ico, 0, -k_ico}, - {phi*k_ico, 0, k_ico}, - {phi*k_ico, 0, -k_ico}, - {-phi*k_ico, 0, k_ico}, - }; - -//bcc -#define k_bcc 0.11543038598460284017 -const double penrose_bcc[PTM_NUM_POINTS_BCC][3] = { - {0, 0, 0}, - {-k_bcc, -k_bcc, -k_bcc}, - {k_bcc, k_bcc, k_bcc}, - {k_bcc, -k_bcc, -k_bcc}, - {-k_bcc, k_bcc, k_bcc}, - {-k_bcc, k_bcc, -k_bcc}, - {k_bcc, -k_bcc, k_bcc}, - {-k_bcc, -k_bcc, k_bcc}, - {k_bcc, k_bcc, -k_bcc}, - {0, 0, -2*k_bcc}, - {0, 0, 2*k_bcc}, - {0, -2*k_bcc, 0}, - {0, 2*k_bcc, 0}, - {-2*k_bcc, 0, 0}, - {2*k_bcc, 0, -0}, - }; - -//dcub -#define kdcub 0.07095369570691034689 -const double penrose_dcub[PTM_NUM_POINTS_DCUB][3] = { - { 0, 0, 0 }, - { -kdcub, kdcub, kdcub }, - { -kdcub, -kdcub, -kdcub }, - { kdcub, -kdcub, kdcub }, - { kdcub, kdcub, -kdcub }, - { -2 * kdcub, 0, 2 * kdcub }, - { -2 * kdcub, 2 * kdcub, 0 }, - { 0, 2 * kdcub, 2 * kdcub }, - { -2 * kdcub, -2 * kdcub, 0 }, - { -2 * kdcub, 0, -2 * kdcub }, - { 0, -2 * kdcub, -2 * kdcub }, - { 0, -2 * kdcub, 2 * kdcub }, - { 2 * kdcub, -2 * kdcub, 0 }, - { 2 * kdcub, 0, 2 * kdcub }, - { 0, 2 * kdcub, -2 * kdcub }, - { 2 * kdcub, 0, -2 * kdcub }, - { 2 * kdcub, 2 * kdcub, 0 }, - }; - - -#define kdhex 0.04730246380471011397 -const double penrose_dhex[PTM_NUM_POINTS_DHEX][3] = { - { 0, 0, 0 }, - { -kdcub, -kdcub, -kdcub }, - { kdcub, -kdcub, kdcub }, - { -kdcub, kdcub, kdcub }, - { kdcub, kdcub, -kdcub }, - { -kdhex, -4 * kdhex, -kdhex }, - { -4 * kdhex, -kdhex, -kdhex }, - { -kdhex, -kdhex, -4 * kdhex }, - { 2 * kdcub, 0, 2 * kdcub }, - { 2 * kdcub, -2 * kdcub, 0 }, - { 0, -2 * kdcub, 2 * kdcub }, - { 0, 2 * kdcub, 2 * kdcub }, - { -2 * kdcub, 2 * kdcub, 0 }, - { -2 * kdcub, 0, 2 * kdcub }, - { 2 * kdcub, 2 * kdcub, 0 }, - { 0, 2 * kdcub, -2 * kdcub }, - { 2 * kdcub, 0, -2 * kdcub }, - }; -#endif - - diff --git a/src/USER-PTM/fundamental_mappings.h b/src/USER-PTM/fundamental_mappings.h deleted file mode 100644 index 9030d3a2b2..0000000000 --- a/src/USER-PTM/fundamental_mappings.h +++ /dev/null @@ -1,180 +0,0 @@ -#ifndef FUNDAMENTAL_MAPPINGS_H -#define FUNDAMENTAL_MAPPINGS_H - -#include - -#define NUM_CUBIC_MAPPINGS 24 -#define NUM_ICO_MAPPINGS 60 -#define NUM_HEX_MAPPINGS 6 -#define NUM_DCUB_MAPPINGS 12 -#define NUM_DHEX_MAPPINGS 3 - -const int8_t mapping_sc[NUM_CUBIC_MAPPINGS][PTM_MAX_POINTS] = { - {0, 1, 2, 3, 4, 5, 6}, - {0, 2, 1, 4, 3, 5, 6}, - {0, 2, 1, 3, 4, 6, 5}, - {0, 1, 2, 4, 3, 6, 5}, - {0, 3, 4, 5, 6, 1, 2}, - {0, 5, 6, 2, 1, 4, 3}, - {0, 6, 5, 1, 2, 4, 3}, - {0, 4, 3, 5, 6, 2, 1}, - {0, 5, 6, 1, 2, 3, 4}, - {0, 4, 3, 6, 5, 1, 2}, - {0, 3, 4, 6, 5, 2, 1}, - {0, 6, 5, 2, 1, 3, 4}, - {0, 3, 4, 2, 1, 5, 6}, - {0, 6, 5, 3, 4, 1, 2}, - {0, 1, 2, 5, 6, 4, 3}, - {0, 4, 3, 1, 2, 5, 6}, - {0, 5, 6, 3, 4, 2, 1}, - {0, 1, 2, 6, 5, 3, 4}, - {0, 2, 1, 5, 6, 3, 4}, - {0, 5, 6, 4, 3, 1, 2}, - {0, 3, 4, 1, 2, 6, 5}, - {0, 2, 1, 6, 5, 4, 3}, - {0, 6, 5, 4, 3, 2, 1}, - {0, 4, 3, 2, 1, 6, 5} }; - -const int8_t mapping_fcc[NUM_CUBIC_MAPPINGS][PTM_MAX_POINTS] = { - {0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12}, - {0, 2, 1, 4, 3, 7, 8, 5, 6, 11, 12, 9, 10}, - {0, 3, 4, 1, 2, 6, 5, 8, 7, 12, 11, 10, 9}, - {0, 4, 3, 2, 1, 8, 7, 6, 5, 10, 9, 12, 11}, - {0, 9, 10, 11, 12, 1, 2, 4, 3, 5, 6, 8, 7}, - {0, 7, 8, 6, 5, 11, 12, 10, 9, 2, 1, 4, 3}, - {0, 8, 7, 5, 6, 10, 9, 11, 12, 4, 3, 2, 1}, - {0, 11, 12, 9, 10, 2, 1, 3, 4, 7, 8, 6, 5}, - {0, 5, 6, 8, 7, 9, 10, 12, 11, 1, 2, 3, 4}, - {0, 10, 9, 12, 11, 4, 3, 1, 2, 8, 7, 5, 6}, - {0, 12, 11, 10, 9, 3, 4, 2, 1, 6, 5, 7, 8}, - {0, 6, 5, 7, 8, 12, 11, 9, 10, 3, 4, 1, 2}, - {0, 3, 4, 2, 1, 9, 10, 11, 12, 7, 8, 5, 6}, - {0, 12, 11, 9, 10, 8, 7, 5, 6, 1, 2, 4, 3}, - {0, 5, 6, 7, 8, 4, 3, 2, 1, 11, 12, 10, 9}, - {0, 4, 3, 1, 2, 11, 12, 9, 10, 5, 6, 7, 8}, - {0, 9, 10, 12, 11, 7, 8, 6, 5, 3, 4, 2, 1}, - {0, 8, 7, 6, 5, 1, 2, 3, 4, 12, 11, 9, 10}, - {0, 7, 8, 5, 6, 3, 4, 1, 2, 9, 10, 12, 11}, - {0, 11, 12, 10, 9, 5, 6, 8, 7, 4, 3, 1, 2}, - {0, 1, 2, 4, 3, 12, 11, 10, 9, 8, 7, 6, 5}, - {0, 6, 5, 8, 7, 2, 1, 4, 3, 10, 9, 11, 12}, - {0, 10, 9, 11, 12, 6, 5, 7, 8, 2, 1, 3, 4}, - {0, 2, 1, 3, 4, 10, 9, 12, 11, 6, 5, 8, 7} }; - -const int8_t mapping_bcc[NUM_CUBIC_MAPPINGS][PTM_MAX_POINTS] = { - {0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14}, - {0, 4, 3, 2, 1, 7, 8, 5, 6, 10, 9, 12, 11, 13, 14}, - {0, 6, 5, 7, 8, 2, 1, 3, 4, 10, 9, 11, 12, 14, 13}, - {0, 8, 7, 5, 6, 3, 4, 2, 1, 9, 10, 12, 11, 14, 13}, - {0, 1, 2, 7, 8, 3, 4, 5, 6, 11, 12, 13, 14, 9, 10}, - {0, 4, 3, 7, 8, 5, 6, 2, 1, 13, 14, 10, 9, 12, 11}, - {0, 8, 7, 3, 4, 2, 1, 5, 6, 14, 13, 9, 10, 12, 11}, - {0, 4, 3, 5, 6, 2, 1, 7, 8, 12, 11, 13, 14, 10, 9}, - {0, 1, 2, 5, 6, 7, 8, 3, 4, 13, 14, 9, 10, 11, 12}, - {0, 8, 7, 2, 1, 5, 6, 3, 4, 12, 11, 14, 13, 9, 10}, - {0, 6, 5, 3, 4, 7, 8, 2, 1, 11, 12, 14, 13, 10, 9}, - {0, 6, 5, 2, 1, 3, 4, 7, 8, 14, 13, 10, 9, 11, 12}, - {0, 7, 8, 6, 5, 1, 2, 4, 3, 11, 12, 10, 9, 13, 14}, - {0, 3, 4, 6, 5, 8, 7, 1, 2, 14, 13, 11, 12, 9, 10}, - {0, 5, 6, 1, 2, 8, 7, 4, 3, 9, 10, 13, 14, 12, 11}, - {0, 5, 6, 8, 7, 4, 3, 1, 2, 12, 11, 9, 10, 13, 14}, - {0, 7, 8, 1, 2, 4, 3, 6, 5, 13, 14, 11, 12, 10, 9}, - {0, 3, 4, 8, 7, 1, 2, 6, 5, 9, 10, 14, 13, 11, 12}, - {0, 7, 8, 4, 3, 6, 5, 1, 2, 10, 9, 13, 14, 11, 12}, - {0, 5, 6, 4, 3, 1, 2, 8, 7, 13, 14, 12, 11, 9, 10}, - {0, 3, 4, 1, 2, 6, 5, 8, 7, 11, 12, 9, 10, 14, 13}, - {0, 2, 1, 6, 5, 4, 3, 8, 7, 10, 9, 14, 13, 12, 11}, - {0, 2, 1, 8, 7, 6, 5, 4, 3, 14, 13, 12, 11, 10, 9}, - {0, 2, 1, 4, 3, 8, 7, 6, 5, 12, 11, 10, 9, 14, 13} }; - -const int8_t mapping_ico[NUM_ICO_MAPPINGS][PTM_MAX_POINTS] = { - {0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12}, - {0, 10, 9, 8, 7, 5, 6, 2, 1, 12, 11, 3, 4}, - {0, 1, 2, 9, 10, 7, 8, 11, 12, 5, 6, 3, 4}, - {0, 4, 3, 8, 7, 2, 1, 11, 12, 9, 10, 6, 5}, - {0, 6, 5, 9, 10, 4, 3, 7, 8, 12, 11, 2, 1}, - {0, 12, 11, 3, 4, 7, 8, 10, 9, 2, 1, 6, 5}, - {0, 4, 3, 6, 5, 9, 10, 2, 1, 8, 7, 11, 12}, - {0, 8, 7, 2, 1, 4, 3, 10, 9, 5, 6, 11, 12}, - {0, 10, 9, 3, 4, 12, 11, 5, 6, 8, 7, 2, 1}, - {0, 12, 11, 6, 5, 2, 1, 7, 8, 3, 4, 10, 9}, - {0, 1, 2, 11, 12, 9, 10, 5, 6, 3, 4, 7, 8}, - {0, 8, 7, 11, 12, 5, 6, 4, 3, 2, 1, 10, 9}, - {0, 6, 5, 2, 1, 12, 11, 4, 3, 9, 10, 7, 8}, - {0, 3, 4, 5, 6, 1, 2, 10, 9, 12, 11, 7, 8}, - {0, 3, 4, 7, 8, 12, 11, 1, 2, 5, 6, 10, 9}, - {0, 6, 5, 7, 8, 9, 10, 12, 11, 2, 1, 4, 3}, - {0, 9, 10, 11, 12, 4, 3, 1, 2, 7, 8, 6, 5}, - {0, 11, 12, 9, 10, 1, 2, 4, 3, 8, 7, 5, 6}, - {0, 8, 7, 5, 6, 10, 9, 11, 12, 4, 3, 2, 1}, - {0, 10, 9, 2, 1, 8, 7, 12, 11, 3, 4, 5, 6}, - {0, 12, 11, 2, 1, 10, 9, 6, 5, 7, 8, 3, 4}, - {0, 9, 10, 6, 5, 7, 8, 4, 3, 11, 12, 1, 2}, - {0, 8, 7, 10, 9, 2, 1, 5, 6, 11, 12, 4, 3}, - {0, 6, 5, 12, 11, 7, 8, 2, 1, 4, 3, 9, 10}, - {0, 11, 12, 8, 7, 4, 3, 5, 6, 1, 2, 9, 10}, - {0, 4, 3, 11, 12, 8, 7, 9, 10, 6, 5, 2, 1}, - {0, 4, 3, 9, 10, 11, 12, 6, 5, 2, 1, 8, 7}, - {0, 12, 11, 10, 9, 3, 4, 2, 1, 6, 5, 7, 8}, - {0, 5, 6, 8, 7, 11, 12, 10, 9, 3, 4, 1, 2}, - {0, 7, 8, 6, 5, 12, 11, 9, 10, 1, 2, 3, 4}, - {0, 10, 9, 12, 11, 2, 1, 3, 4, 5, 6, 8, 7}, - {0, 7, 8, 1, 2, 9, 10, 3, 4, 12, 11, 6, 5}, - {0, 5, 6, 1, 2, 3, 4, 11, 12, 8, 7, 10, 9}, - {0, 7, 8, 12, 11, 3, 4, 6, 5, 9, 10, 1, 2}, - {0, 1, 2, 5, 6, 11, 12, 3, 4, 7, 8, 9, 10}, - {0, 11, 12, 1, 2, 5, 6, 9, 10, 4, 3, 8, 7}, - {0, 5, 6, 3, 4, 10, 9, 1, 2, 11, 12, 8, 7}, - {0, 5, 6, 10, 9, 8, 7, 3, 4, 1, 2, 11, 12}, - {0, 3, 4, 12, 11, 10, 9, 7, 8, 1, 2, 5, 6}, - {0, 9, 10, 7, 8, 1, 2, 6, 5, 4, 3, 11, 12}, - {0, 9, 10, 1, 2, 11, 12, 7, 8, 6, 5, 4, 3}, - {0, 7, 8, 3, 4, 1, 2, 12, 11, 6, 5, 9, 10}, - {0, 11, 12, 5, 6, 8, 7, 1, 2, 9, 10, 4, 3}, - {0, 1, 2, 7, 8, 3, 4, 9, 10, 11, 12, 5, 6}, - {0, 3, 4, 10, 9, 5, 6, 12, 11, 7, 8, 1, 2}, - {0, 2, 1, 4, 3, 8, 7, 6, 5, 12, 11, 10, 9}, - {0, 2, 1, 12, 11, 6, 5, 10, 9, 8, 7, 4, 3}, - {0, 9, 10, 4, 3, 6, 5, 11, 12, 1, 2, 7, 8}, - {0, 11, 12, 4, 3, 9, 10, 8, 7, 5, 6, 1, 2}, - {0, 2, 1, 10, 9, 12, 11, 8, 7, 4, 3, 6, 5}, - {0, 5, 6, 11, 12, 1, 2, 8, 7, 10, 9, 3, 4}, - {0, 10, 9, 5, 6, 3, 4, 8, 7, 2, 1, 12, 11}, - {0, 12, 11, 7, 8, 6, 5, 3, 4, 10, 9, 2, 1}, - {0, 7, 8, 9, 10, 6, 5, 1, 2, 3, 4, 12, 11}, - {0, 2, 1, 8, 7, 10, 9, 4, 3, 6, 5, 12, 11}, - {0, 8, 7, 4, 3, 11, 12, 2, 1, 10, 9, 5, 6}, - {0, 6, 5, 4, 3, 2, 1, 9, 10, 7, 8, 12, 11}, - {0, 2, 1, 6, 5, 4, 3, 12, 11, 10, 9, 8, 7}, - {0, 3, 4, 1, 2, 7, 8, 5, 6, 10, 9, 12, 11}, - {0, 4, 3, 2, 1, 6, 5, 8, 7, 11, 12, 9, 10} }; - -const int8_t mapping_hcp[NUM_HEX_MAPPINGS][PTM_MAX_POINTS] = { - {0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12}, - {0, 5, 6, 1, 2, 3, 4, 9, 10, 12, 11, 8, 7}, - {0, 3, 4, 5, 6, 1, 2, 12, 11, 7, 8, 10, 9}, - {0, 4, 3, 2, 1, 6, 5, 11, 12, 10, 9, 7, 8}, - {0, 2, 1, 6, 5, 4, 3, 8, 7, 11, 12, 9, 10}, - {0, 6, 5, 4, 3, 2, 1, 10, 9, 8, 7, 12, 11} }; - -const int8_t mapping_dcub[NUM_DCUB_MAPPINGS][PTM_MAX_POINTS] = { - {0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16}, - {0, 2, 1, 4, 3, 9, 8, 10, 6, 5, 7, 14, 16, 15, 11, 13, 12}, - {0, 4, 3, 2, 1, 15, 16, 14, 12, 13, 11, 10, 8, 9, 7, 5, 6}, - {0, 3, 4, 1, 2, 13, 12, 11, 16, 15, 14, 7, 6, 5, 10, 9, 8}, - {0, 4, 2, 1, 3, 14, 15, 16, 9, 10, 8, 6, 5, 7, 12, 11, 13}, - {0, 4, 1, 3, 2, 16, 14, 15, 7, 6, 5, 13, 11, 12, 9, 8, 10}, - {0, 1, 4, 2, 3, 6, 7, 5, 14, 16, 15, 9, 10, 8, 13, 12, 11}, - {0, 3, 1, 2, 4, 11, 13, 12, 5, 7, 6, 8, 9, 10, 16, 14, 15}, - {0, 3, 2, 4, 1, 12, 11, 13, 10, 8, 9, 15, 14, 16, 5, 6, 7}, - {0, 2, 4, 3, 1, 10, 9, 8, 15, 14, 16, 12, 13, 11, 6, 7, 5}, - {0, 1, 3, 4, 2, 7, 5, 6, 13, 11, 12, 16, 15, 14, 8, 10, 9}, - {0, 2, 3, 1, 4, 8, 10, 9, 11, 12, 13, 5, 7, 6, 15, 16, 14} }; - -const int8_t mapping_dhex[NUM_DHEX_MAPPINGS][PTM_MAX_POINTS] = { - {0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16}, - {0, 1, 3, 4, 2, 6, 7, 5, 11, 13, 12, 14, 16, 15, 8, 9, 10}, - {0, 1, 4, 2, 3, 7, 5, 6, 14, 15, 16, 8, 10, 9, 11, 13, 12} }; - -#endif - diff --git a/src/USER-PTM/graph_data.cpp b/src/USER-PTM/graph_data.cpp deleted file mode 100644 index aea2e59eac..0000000000 --- a/src/USER-PTM/graph_data.cpp +++ /dev/null @@ -1,2059 +0,0 @@ -#include "graph_data.h" - - -int8_t automorphisms[65][17] = { - { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16}, - { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, -1, -1, -1, -1}, - { 0, 4, 3, 10, 9, 5, 6, 12, 11, 8, 7, 1, 2, -1, -1, -1, -1}, - { 0, 5, 6, 11, 12, 8, 7, 2, 1, 4, 3, 10, 9, -1, -1, -1, -1}, - { 0, 8, 7, 1, 2, 4, 3, 9, 10, 5, 6, 11, 12, -1, -1, -1, -1}, - { 0, 8, 7, 10, 9, 1, 2, 6, 5, 12, 11, 3, 4, -1, -1, -1, -1}, - { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, -1, -1, -1, -1}, - { 0, 12, 3, 2, 7, 10, 8, 4, 6, 11, 5, 9, 1, -1, -1, -1, -1}, - { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, -1, -1, -1, -1}, - { 0, 4, 11, 8, 1, 9, 12, 10, 3, 5, 7, 2, 6, -1, -1, -1, -1}, - { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, -1, -1, -1, -1}, - { 0, 2, 1, 6, 5, 4, 3, 9, 8, 7, 11, 10, 12, -1, -1, -1, -1}, - { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, -1, -1, -1, -1}, - { 0, 1, 7, 10, 11, 9, 6, 4, 2, 12, 5, 8, 3, -1, -1, -1, -1}, - { 0, 1, 11, 9, 2, 3, 6, 8, 4, 10, 12, 7, 5, -1, -1, -1, -1}, - { 0, 3, 6, 1, 11, 9, 2, 10, 12, 5, 7, 4, 8, -1, -1, -1, -1}, - { 0, 3, 11, 9, 12, 8, 2, 4, 10, 1, 5, 6, 7, -1, -1, -1, -1}, - { 0, 8, 2, 3, 11, 9, 12, 1, 5, 7, 6, 10, 4, -1, -1, -1, -1}, - { 0, 9, 2, 3, 6, 1, 11, 5, 7, 8, 4, 12, 10, -1, -1, -1, -1}, - { 0, 9, 6, 1, 7, 10, 11, 12, 5, 3, 8, 2, 4, -1, -1, -1, -1}, - { 0, 9, 12, 8, 2, 3, 11, 7, 6, 4, 10, 5, 1, -1, -1, -1, -1}, - { 0, 10, 11, 9, 6, 1, 7, 3, 8, 4, 2, 5, 12, -1, -1, -1, -1}, - { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, -1, -1, -1, -1}, - { 0, 3, 2, 8, 6, 5, 12, 11, 7, 4, 9, 1, 10, -1, -1, -1, -1}, - { 0, 3, 11, 10, 6, 9, 7, 4, 2, 12, 1, 8, 5, -1, -1, -1, -1}, - { 0, 3, 12, 9, 6, 8, 11, 7, 4, 2, 10, 5, 1, -1, -1, -1, -1}, - { 0, 5, 12, 3, 2, 8, 6, 4, 9, 10, 1, 7, 11, -1, -1, -1, -1}, - { 0, 8, 6, 5, 12, 3, 2, 10, 1, 11, 7, 9, 4, -1, -1, -1, -1}, - { 0, 8, 11, 3, 12, 9, 6, 2, 10, 1, 5, 4, 7, -1, -1, -1, -1}, - { 0, 9, 6, 8, 11, 3, 12, 1, 5, 7, 4, 10, 2, -1, -1, -1, -1}, - { 0, 9, 7, 3, 11, 10, 6, 12, 1, 5, 8, 2, 4, -1, -1, -1, -1}, - { 0, 10, 6, 9, 7, 3, 11, 5, 8, 4, 2, 1, 12, -1, -1, -1, -1}, - { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, -1, -1}, - { 0, 3, 4, 6, 5, 2, 1, 9, 10, 14, 13, 11, 12, 8, 7, -1, -1}, - { 0, 4, 3, 1, 2, 5, 6, 10, 9, 13, 14, 7, 8, 12, 11, -1, -1}, - { 0, 6, 5, 1, 2, 4, 3, 14, 13, 7, 8, 11, 12, 10, 9, -1, -1}, - { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, -1, -1}, - { 0, 12, 11, 10, 9, 13, 14, 8, 7, 4, 3, 2, 1, 5, 6, -1, -1}, - { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, -1, -1}, - { 0, 9, 10, 13, 14, 11, 12, 8, 7, 1, 2, 5, 6, 3, 4, -1, -1}, - { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, -1, -1}, - { 0, 6, 5, 4, 3, 2, 1, 11, 12, 10, 9, 7, 8, 14, 13, -1, -1}, - { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, -1, -1}, - { 0, 12, 11, 10, 9, 13, 14, 8, 7, 4, 3, 2, 1, 5, 6, -1, -1}, - { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, -1, -1}, - { 0, 9, 10, 13, 14, 11, 12, 8, 7, 1, 2, 5, 6, 3, 4, -1, -1}, - { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, -1, -1}, - { 0, 3, 10, 14, 5, 9, 7, 13, 2, 8, 4, 11, 12, 1, 6, -1, -1}, - { 0, 13, 8, 1, 10, 4, 14, 6, 9, 5, 2, 11, 12, 7, 3, -1, -1}, - { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, -1, -1}, - { 0, 11, 12, 14, 13, 9, 10, 7, 8, 3, 4, 6, 5, 1, 2, -1, -1}, - { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, -1, -1}, - { 0, 13, 14, 11, 12, 5, 6, 10, 9, 1, 2, 7, 8, 4, 3, -1, -1}, - { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16}, - { 0, 4, 3, 2, 1, 15, 14, 16, 13, 12, 11, 10, 9, 8, 6, 5, 7}, - { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16}, - { 0, 4, 1, 3, 2, 15, 14, 16, 5, 7, 6, 13, 11, 12, 10, 8, 9}, - { 0, 4, 2, 1, 3, 16, 15, 14, 10, 8, 9, 5, 6, 7, 13, 12, 11}, - { 0, 4, 3, 2, 1, 14, 16, 15, 13, 12, 11, 10, 9, 8, 5, 7, 6}, - { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16}, - { 0, 3, 4, 1, 2, 12, 13, 11, 16, 14, 15, 7, 5, 6, 9, 10, 8}, - { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16}, - { 0, 4, 1, 3, 2, 16, 15, 14, 6, 5, 7, 13, 11, 12, 10, 8, 9}, - { 0, 4, 2, 1, 3, 14, 16, 15, 10, 8, 9, 6, 7, 5, 13, 12, 11}, - { 0, 4, 3, 2, 1, 15, 14, 16, 13, 12, 11, 10, 9, 8, 6, 5, 7}, -}; - -graph_t graphs_sc[NUM_SC_GRAPHS] = { - -{0, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{1,3,4},{1,3,5},{0,3,4},{0,3,5},{1,2,5},{1,2,4},{0,2,4},{0,2,5}}}, - -}; - -graph_t graphs_ico[NUM_ICO_GRAPHS] = { - -{0, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{0,5,9},{1,2,8},{0,5,7},{2,7,8},{2,5,7},{1,4,8},{1,2,10},{5,9,10},{2,5,10},{4,8,11},{7,8,11},{0,7,11},{0,3,9},{0,3,11},{3,4,11},{3,6,9},{3,4,6},{6,9,10},{1,4,6},{1,6,10}}}, - -}; - -graph_t graphs_fcc[NUM_FCC_GRAPHS] = { - -{0, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{0,4,8},{3,7,9},{2,5,11},{0,7,11},{1,5,9},{2,6,8},{3,4,10},{1,6,10},{3,4,7},{0,4,7},{0,2,11},{0,2,8},{5,7,11},{5,7,9},{1,2,6},{1,2,5},{1,3,10},{1,3,9},{4,6,10},{4,6,8}}}, - -{1, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{0,4,8},{3,7,9},{2,5,11},{0,7,11},{1,5,9},{2,6,8},{3,4,10},{1,6,10},{3,4,7},{0,4,7},{0,2,11},{0,2,8},{5,7,11},{5,7,9},{1,2,6},{1,2,5},{1,3,10},{1,3,9},{6,8,10},{4,8,10}}}, - -{2, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{0,4,8},{3,7,9},{2,5,11},{0,7,11},{1,5,9},{2,6,8},{3,4,10},{1,6,10},{3,4,7},{0,4,7},{0,2,11},{0,2,8},{5,7,11},{5,7,9},{1,2,6},{1,2,5},{3,9,10},{1,9,10},{6,8,10},{4,8,10}}}, - -{3, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{0,4,8},{3,7,9},{2,5,11},{0,7,11},{1,5,9},{2,6,8},{3,4,10},{1,6,10},{3,4,7},{0,4,7},{0,2,11},{0,2,8},{5,7,11},{5,7,9},{2,5,6},{1,5,6},{1,3,10},{1,3,9},{4,6,10},{4,6,8}}}, - -{4, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{0,4,8},{3,7,9},{2,5,11},{0,7,11},{1,5,9},{2,6,8},{3,4,10},{1,6,10},{3,4,7},{0,4,7},{0,2,11},{0,2,8},{5,7,11},{5,7,9},{2,5,6},{1,5,6},{1,3,10},{1,3,9},{6,8,10},{4,8,10}}}, - -{5, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{0,4,8},{3,7,9},{2,5,11},{0,7,11},{1,5,9},{2,6,8},{3,4,10},{1,6,10},{3,4,7},{0,4,7},{0,2,11},{0,2,8},{5,7,11},{5,7,9},{2,5,6},{1,5,6},{3,9,10},{1,9,10},{4,6,10},{4,6,8}}}, - -{6, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{0,4,8},{3,7,9},{2,5,11},{0,7,11},{1,5,9},{2,6,8},{3,4,10},{1,6,10},{3,4,7},{0,4,7},{0,2,11},{0,2,8},{7,9,11},{5,9,11},{1,2,6},{1,2,5},{3,9,10},{1,9,10},{4,6,10},{4,6,8}}}, - -{7, -0, -1, -5, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{0,4,8},{3,7,9},{2,5,11},{0,7,11},{1,5,9},{2,6,8},{3,4,10},{1,6,10},{3,4,7},{0,4,7},{0,2,11},{0,2,8},{7,9,11},{5,9,11},{2,5,6},{1,5,6},{1,3,10},{1,3,9},{6,8,10},{4,8,10}}}, - -}; - -graph_t graphs_hcp[NUM_HCP_GRAPHS] = { - -{0, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{3,8,9},{1,3,9},{2,8,9},{0,2,9},{0,10,11},{0,4,10},{2,6,7},{2,4,6}}}, - -{1, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{3,8,9},{1,3,9},{2,8,9},{0,2,9},{0,10,11},{0,4,10},{4,6,7},{2,4,7}}}, - -{2, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{3,8,9},{1,3,9},{2,8,9},{0,2,9},{4,10,11},{0,4,11},{2,6,7},{2,4,6}}}, - -{3, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{3,8,9},{1,3,9},{2,8,9},{0,2,9},{4,10,11},{0,4,11},{4,6,7},{2,4,7}}}, - -{4, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{3,8,9},{1,3,9},{0,8,9},{0,2,8},{0,10,11},{0,4,10},{2,6,7},{2,4,6}}}, - -{5, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{3,8,9},{1,3,9},{0,8,9},{0,2,8},{0,10,11},{0,4,10},{4,6,7},{2,4,7}}}, - -{6, -0, -6, -2, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{3,8,9},{1,3,9},{0,8,9},{0,2,8},{4,10,11},{0,4,11},{2,6,7},{2,4,6}}}, - -{7, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{3,8,9},{1,3,9},{0,8,9},{0,2,8},{4,10,11},{0,4,11},{4,6,7},{2,4,7}}}, - -{8, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{1,8,9},{1,3,8},{2,8,9},{0,2,9},{0,10,11},{0,4,10},{2,6,7},{2,4,6}}}, - -{9, -0, -8, -2, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{1,8,9},{1,3,8},{2,8,9},{0,2,9},{0,10,11},{0,4,10},{4,6,7},{2,4,7}}}, - -{10, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{1,8,9},{1,3,8},{2,8,9},{0,2,9},{4,10,11},{0,4,11},{4,6,7},{2,4,7}}}, - -{11, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{1,8,9},{1,3,8},{0,8,9},{0,2,8},{0,10,11},{0,4,10},{4,6,7},{2,4,7}}}, - -{12, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{1,8,9},{1,3,8},{0,8,9},{0,2,8},{4,10,11},{0,4,11},{2,6,7},{2,4,6}}}, - -{13, -0, -10, -2, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{5,6,7},{3,5,7},{3,8,9},{1,3,9},{2,8,9},{0,2,9},{0,10,11},{0,4,10},{4,6,7},{2,4,7}}}, - -{14, -0, -12, -10, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{5,6,7},{3,5,7},{3,8,9},{1,3,9},{0,8,9},{0,2,8},{4,10,11},{0,4,11},{2,6,7},{2,4,6}}}, - -{15, -0, -22, -10, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{5,10,11},{1,5,11},{3,6,7},{3,5,6},{1,8,9},{1,3,8},{2,8,9},{0,2,9},{0,10,11},{0,4,10},{4,6,7},{2,4,7}}}, - -}; - -graph_t graphs_bcc[NUM_BCC_GRAPHS] = { - -{0, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{6,9,10},{5,9,10},{4,8,12},{0,8,12},{6,10,12},{0,10,12},{7,8,13},{2,8,13},{5,10,13},{2,10,13},{2,8,10},{0,8,10}}}, - -{1, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{6,9,10},{5,9,10},{4,8,12},{0,8,12},{6,10,12},{0,10,12},{7,8,13},{2,8,13},{5,10,13},{2,10,13},{0,2,10},{0,2,8}}}, - -{2, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{6,9,10},{5,9,10},{4,8,12},{0,8,12},{6,10,12},{0,10,12},{7,8,13},{2,8,13},{2,5,13},{2,5,10},{0,2,10},{0,2,8}}}, - -{3, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{6,9,10},{5,9,10},{4,8,12},{0,8,12},{6,10,12},{0,10,12},{2,7,13},{2,7,8},{2,5,13},{2,5,10},{0,2,10},{0,2,8}}}, - -{4, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{6,9,10},{5,9,10},{4,8,12},{0,8,12},{0,6,12},{0,6,10},{7,8,13},{2,8,13},{2,5,13},{2,5,10},{2,8,10},{0,8,10}}}, - -{5, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{6,9,10},{5,9,10},{4,8,12},{0,8,12},{0,6,12},{0,6,10},{7,8,13},{2,8,13},{2,5,13},{2,5,10},{0,2,10},{0,2,8}}}, - -{6, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{6,9,10},{5,9,10},{4,8,12},{0,8,12},{0,6,12},{0,6,10},{2,7,13},{2,7,8},{5,10,13},{2,10,13},{2,8,10},{0,8,10}}}, - -{7, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{6,9,10},{5,9,10},{4,8,12},{0,8,12},{0,6,12},{0,6,10},{2,7,13},{2,7,8},{5,10,13},{2,10,13},{0,2,10},{0,2,8}}}, - -{8, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{6,9,10},{5,9,10},{4,8,12},{0,8,12},{0,6,12},{0,6,10},{2,7,13},{2,7,8},{2,5,13},{2,5,10},{2,8,10},{0,8,10}}}, - -{9, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{6,9,10},{5,9,10},{4,8,12},{0,8,12},{0,6,12},{0,6,10},{2,7,13},{2,7,8},{2,5,13},{2,5,10},{0,2,10},{0,2,8}}}, - -{10, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{6,9,10},{5,9,10},{0,4,12},{0,4,8},{6,10,12},{0,10,12},{7,8,13},{2,8,13},{2,5,13},{2,5,10},{2,8,10},{0,8,10}}}, - -{11, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{6,9,10},{5,9,10},{0,4,12},{0,4,8},{6,10,12},{0,10,12},{7,8,13},{2,8,13},{2,5,13},{2,5,10},{0,2,10},{0,2,8}}}, - -{12, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{6,9,10},{5,9,10},{0,4,12},{0,4,8},{6,10,12},{0,10,12},{2,7,13},{2,7,8},{2,5,13},{2,5,10},{2,8,10},{0,8,10}}}, - -{13, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{6,9,10},{5,9,10},{0,4,12},{0,4,8},{6,10,12},{0,10,12},{2,7,13},{2,7,8},{2,5,13},{2,5,10},{0,2,10},{0,2,8}}}, - -{14, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{6,9,10},{5,9,10},{0,4,12},{0,4,8},{0,6,12},{0,6,10},{2,7,13},{2,7,8},{2,5,13},{2,5,10},{2,8,10},{0,8,10}}}, - -{15, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{6,9,10},{5,9,10},{0,4,12},{0,4,8},{0,6,12},{0,6,10},{2,7,13},{2,7,8},{2,5,13},{2,5,10},{0,2,10},{0,2,8}}}, - -{16, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{5,6,10},{5,6,9},{4,8,12},{0,8,12},{0,6,12},{0,6,10},{7,8,13},{2,8,13},{2,5,13},{2,5,10},{0,2,10},{0,2,8}}}, - -{17, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{5,6,10},{5,6,9},{4,8,12},{0,8,12},{0,6,12},{0,6,10},{2,7,13},{2,7,8},{5,10,13},{2,10,13},{2,8,10},{0,8,10}}}, - -{18, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{5,6,10},{5,6,9},{4,8,12},{0,8,12},{0,6,12},{0,6,10},{2,7,13},{2,7,8},{5,10,13},{2,10,13},{0,2,10},{0,2,8}}}, - -{19, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{5,6,10},{5,6,9},{4,8,12},{0,8,12},{0,6,12},{0,6,10},{2,7,13},{2,7,8},{2,5,13},{2,5,10},{2,8,10},{0,8,10}}}, - -{20, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{5,6,10},{5,6,9},{4,8,12},{0,8,12},{0,6,12},{0,6,10},{2,7,13},{2,7,8},{2,5,13},{2,5,10},{0,2,10},{0,2,8}}}, - -{21, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{5,6,10},{5,6,9},{0,4,12},{0,4,8},{6,10,12},{0,10,12},{2,7,13},{2,7,8},{5,10,13},{2,10,13},{2,8,10},{0,8,10}}}, - -{22, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{5,6,10},{5,6,9},{0,4,12},{0,4,8},{6,10,12},{0,10,12},{2,7,13},{2,7,8},{5,10,13},{2,10,13},{0,2,10},{0,2,8}}}, - -{23, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{5,6,10},{5,6,9},{0,4,12},{0,4,8},{6,10,12},{0,10,12},{2,7,13},{2,7,8},{2,5,13},{2,5,10},{2,8,10},{0,8,10}}}, - -{24, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{5,6,10},{5,6,9},{0,4,12},{0,4,8},{6,10,12},{0,10,12},{2,7,13},{2,7,8},{2,5,13},{2,5,10},{0,2,10},{0,2,8}}}, - -{25, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{5,6,10},{5,6,9},{0,4,12},{0,4,8},{0,6,12},{0,6,10},{2,7,13},{2,7,8},{5,10,13},{2,10,13},{2,8,10},{0,8,10}}}, - -{26, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{5,6,10},{5,6,9},{0,4,12},{0,4,8},{0,6,12},{0,6,10},{2,7,13},{2,7,8},{5,10,13},{2,10,13},{0,2,10},{0,2,8}}}, - -{27, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{5,6,10},{5,6,9},{0,4,12},{0,4,8},{0,6,12},{0,6,10},{2,7,13},{2,7,8},{2,5,13},{2,5,10},{2,8,10},{0,8,10}}}, - 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-{196, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{1,7,13},{1,7,11},{4,7,11},{4,7,8},{1,5,13},{1,5,9},{3,6,12},{3,6,9},{5,6,10},{5,6,9},{0,4,12},{0,4,8},{6,10,12},{0,10,12},{2,7,13},{2,7,8},{5,10,13},{2,10,13},{0,2,10},{0,2,8}}}, - -{197, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{1,7,13},{1,7,11},{4,7,11},{4,7,8},{1,5,13},{1,5,9},{3,6,12},{3,6,9},{5,6,10},{5,6,9},{0,4,12},{0,4,8},{6,10,12},{0,10,12},{2,7,13},{2,7,8},{2,5,13},{2,5,10},{2,8,10},{0,8,10}}}, - -{198, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{1,7,13},{1,7,11},{4,7,11},{4,7,8},{1,5,13},{1,5,9},{3,6,12},{3,6,9},{5,6,10},{5,6,9},{0,4,12},{0,4,8},{6,10,12},{0,10,12},{2,7,13},{2,7,8},{2,5,13},{2,5,10},{0,2,10},{0,2,8}}}, - -{199, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{1,7,13},{1,7,11},{4,7,11},{4,7,8},{1,5,13},{1,5,9},{3,6,12},{3,6,9},{5,6,10},{5,6,9},{0,4,12},{0,4,8},{0,6,12},{0,6,10},{7,8,13},{2,8,13},{5,10,13},{2,10,13},{0,2,10},{0,2,8}}}, - -{200, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{1,7,13},{1,7,11},{4,7,11},{4,7,8},{1,5,13},{1,5,9},{3,6,12},{3,6,9},{5,6,10},{5,6,9},{0,4,12},{0,4,8},{0,6,12},{0,6,10},{7,8,13},{2,8,13},{2,5,13},{2,5,10},{2,8,10},{0,8,10}}}, - -{201, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{1,7,13},{1,7,11},{4,7,11},{4,7,8},{1,5,13},{1,5,9},{3,6,12},{3,6,9},{5,6,10},{5,6,9},{0,4,12},{0,4,8},{0,6,12},{0,6,10},{7,8,13},{2,8,13},{2,5,13},{2,5,10},{0,2,10},{0,2,8}}}, - -{202, -0, -40, -2, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{1,7,13},{1,7,11},{4,7,11},{4,7,8},{1,5,13},{1,5,9},{3,6,12},{3,6,9},{5,6,10},{5,6,9},{0,4,12},{0,4,8},{0,6,12},{0,6,10},{2,7,13},{2,7,8},{5,10,13},{2,10,13},{2,8,10},{0,8,10}}}, - -{203, -0, -42, -2, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{1,7,13},{1,7,11},{4,7,11},{4,7,8},{1,5,13},{1,5,9},{3,6,12},{3,6,9},{5,6,10},{5,6,9},{0,4,12},{0,4,8},{0,6,12},{0,6,10},{2,7,13},{2,7,8},{5,10,13},{2,10,13},{0,2,10},{0,2,8}}}, - -{204, -0, -44, -2, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{1,7,13},{1,7,11},{4,7,11},{4,7,8},{1,5,13},{1,5,9},{3,6,12},{3,6,9},{5,6,10},{5,6,9},{0,4,12},{0,4,8},{0,6,12},{0,6,10},{2,7,13},{2,7,8},{2,5,13},{2,5,10},{2,8,10},{0,8,10}}}, - -{205, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{1,7,13},{1,7,11},{4,7,11},{4,7,8},{1,5,13},{1,5,9},{3,6,12},{3,6,9},{5,6,10},{5,6,9},{0,4,12},{0,4,8},{0,6,12},{0,6,10},{2,7,13},{2,7,8},{2,5,13},{2,5,10},{0,2,10},{0,2,8}}}, - -{206, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{3,9,11},{1,9,11},{3,4,12},{3,4,11},{1,7,13},{1,7,11},{7,8,11},{4,8,11},{1,5,13},{1,5,9},{3,6,12},{3,6,9},{6,9,10},{5,9,10},{0,4,12},{0,4,8},{0,6,12},{0,6,10},{2,7,13},{2,7,8},{2,5,13},{2,5,10},{2,8,10},{0,8,10}}}, - -{207, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{3,9,11},{1,9,11},{3,4,12},{3,4,11},{1,7,13},{1,7,11},{7,8,11},{4,8,11},{1,5,13},{1,5,9},{3,6,12},{3,6,9},{6,9,10},{5,9,10},{0,4,12},{0,4,8},{0,6,12},{0,6,10},{2,7,13},{2,7,8},{2,5,13},{2,5,10},{0,2,10},{0,2,8}}}, - -{208, -0, -46, -3, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{3,9,11},{1,9,11},{3,4,12},{3,4,11},{1,7,13},{1,7,11},{7,8,11},{4,8,11},{1,5,13},{1,5,9},{3,6,12},{3,6,9},{5,6,10},{5,6,9},{0,4,12},{0,4,8},{6,10,12},{0,10,12},{2,7,13},{2,7,8},{5,10,13},{2,10,13},{0,2,10},{0,2,8}}}, - -{209, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{3,9,11},{1,9,11},{3,4,12},{3,4,11},{1,7,13},{1,7,11},{7,8,11},{4,8,11},{1,5,13},{1,5,9},{3,6,12},{3,6,9},{5,6,10},{5,6,9},{0,4,12},{0,4,8},{6,10,12},{0,10,12},{2,7,13},{2,7,8},{2,5,13},{2,5,10},{0,2,10},{0,2,8}}}, - -{210, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{3,9,11},{1,9,11},{3,4,12},{3,4,11},{1,7,13},{1,7,11},{7,8,11},{4,8,11},{1,5,13},{1,5,9},{3,6,12},{3,6,9},{5,6,10},{5,6,9},{0,4,12},{0,4,8},{0,6,12},{0,6,10},{2,7,13},{2,7,8},{2,5,13},{2,5,10},{0,2,10},{0,2,8}}}, - -{211, -0, -49, -2, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{3,9,11},{1,9,11},{3,4,12},{3,4,11},{1,7,13},{1,7,11},{4,7,11},{4,7,8},{1,5,13},{1,5,9},{3,6,12},{3,6,9},{5,6,10},{5,6,9},{4,8,12},{0,8,12},{0,6,12},{0,6,10},{2,7,13},{2,7,8},{5,10,13},{2,10,13},{0,2,10},{0,2,8}}}, - -{212, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{3,9,11},{1,9,11},{3,4,12},{3,4,11},{1,7,13},{1,7,11},{4,7,11},{4,7,8},{1,5,13},{1,5,9},{3,6,12},{3,6,9},{5,6,10},{5,6,9},{4,8,12},{0,8,12},{0,6,12},{0,6,10},{2,7,13},{2,7,8},{2,5,13},{2,5,10},{0,2,10},{0,2,8}}}, - -{213, -0, -51, -2, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{3,9,11},{1,9,11},{3,4,12},{3,4,11},{1,7,13},{1,7,11},{4,7,11},{4,7,8},{1,5,13},{1,5,9},{3,6,12},{3,6,9},{5,6,10},{5,6,9},{0,4,12},{0,4,8},{6,10,12},{0,10,12},{7,8,13},{2,8,13},{2,5,13},{2,5,10},{0,2,10},{0,2,8}}}, - -{214, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{3,9,11},{1,9,11},{3,4,12},{3,4,11},{1,7,13},{1,7,11},{4,7,11},{4,7,8},{1,5,13},{1,5,9},{3,6,12},{3,6,9},{5,6,10},{5,6,9},{0,4,12},{0,4,8},{6,10,12},{0,10,12},{2,7,13},{2,7,8},{2,5,13},{2,5,10},{0,2,10},{0,2,8}}}, - -{215, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{3,9,11},{1,9,11},{3,4,12},{3,4,11},{1,7,13},{1,7,11},{4,7,11},{4,7,8},{1,5,13},{1,5,9},{3,6,12},{3,6,9},{5,6,10},{5,6,9},{0,4,12},{0,4,8},{0,6,12},{0,6,10},{2,7,13},{2,7,8},{2,5,13},{2,5,10},{2,8,10},{0,8,10}}}, - -{216, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{3,9,11},{1,9,11},{3,4,12},{3,4,11},{1,7,13},{1,7,11},{4,7,11},{4,7,8},{1,5,13},{1,5,9},{3,6,12},{3,6,9},{5,6,10},{5,6,9},{0,4,12},{0,4,8},{0,6,12},{0,6,10},{2,7,13},{2,7,8},{2,5,13},{2,5,10},{0,2,10},{0,2,8}}}, - -{217, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{1,3,11},{1,3,9},{3,4,12},{3,4,11},{1,7,13},{1,7,11},{4,7,11},{4,7,8},{1,5,13},{1,5,9},{3,6,12},{3,6,9},{5,6,10},{5,6,9},{0,4,12},{0,4,8},{0,6,12},{0,6,10},{2,7,13},{2,7,8},{2,5,13},{2,5,10},{0,2,10},{0,2,8}}}, - -}; - -graph_t graphs_dcub[NUM_DCUB_GRAPHS] = { - -{0, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{4,7,10},{0,5,6},{0,4,5},{0,4,6},{2,11,12},{2,10,12},{2,10,11},{1,7,8},{1,8,9},{1,7,9},{6,12,15},{5,8,13},{3,13,15},{3,13,14},{9,11,14},{3,14,15},{5,7,8},{4,5,7},{6,10,12},{4,6,10},{7,10,11},{7,9,11},{5,13,15},{5,6,15},{9,13,14},{8,9,13},{11,14,15},{11,12,15}}}, - -{1, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{4,7,10},{0,5,6},{0,4,5},{0,4,6},{2,11,12},{2,10,12},{2,10,11},{1,7,8},{1,8,9},{1,7,9},{6,12,15},{5,8,13},{3,13,15},{3,13,14},{9,11,14},{3,14,15},{5,7,8},{4,5,7},{6,10,12},{4,6,10},{7,10,11},{7,9,11},{5,13,15},{5,6,15},{9,13,14},{8,9,13},{12,14,15},{11,12,14}}}, - -{2, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{4,7,10},{0,5,6},{0,4,5},{0,4,6},{2,11,12},{2,10,12},{2,10,11},{1,7,8},{1,8,9},{1,7,9},{6,12,15},{5,8,13},{3,13,15},{3,13,14},{9,11,14},{3,14,15},{5,7,8},{4,5,7},{6,10,12},{4,6,10},{7,10,11},{7,9,11},{5,13,15},{5,6,15},{8,13,14},{8,9,14},{11,14,15},{11,12,15}}}, - -{3, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{4,7,10},{0,5,6},{0,4,5},{0,4,6},{2,11,12},{2,10,12},{2,10,11},{1,7,8},{1,8,9},{1,7,9},{6,12,15},{5,8,13},{3,13,15},{3,13,14},{9,11,14},{3,14,15},{5,7,8},{4,5,7},{6,10,12},{4,6,10},{7,10,11},{7,9,11},{5,13,15},{5,6,15},{8,13,14},{8,9,14},{12,14,15},{11,12,14}}}, - -{4, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{4,7,10},{0,5,6},{0,4,5},{0,4,6},{2,11,12},{2,10,12},{2,10,11},{1,7,8},{1,8,9},{1,7,9},{6,12,15},{5,8,13},{3,13,15},{3,13,14},{9,11,14},{3,14,15},{5,7,8},{4,5,7},{6,10,12},{4,6,10},{7,10,11},{7,9,11},{6,13,15},{5,6,13},{9,13,14},{8,9,13},{11,14,15},{11,12,15}}}, - -{5, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{4,7,10},{0,5,6},{0,4,5},{0,4,6},{2,11,12},{2,10,12},{2,10,11},{1,7,8},{1,8,9},{1,7,9},{6,12,15},{5,8,13},{3,13,15},{3,13,14},{9,11,14},{3,14,15},{5,7,8},{4,5,7},{6,10,12},{4,6,10},{7,10,11},{7,9,11},{6,13,15},{5,6,13},{8,13,14},{8,9,14},{11,14,15},{11,12,15}}}, - -{6, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{4,7,10},{0,5,6},{0,4,5},{0,4,6},{2,11,12},{2,10,12},{2,10,11},{1,7,8},{1,8,9},{1,7,9},{6,12,15},{5,8,13},{3,13,15},{3,13,14},{9,11,14},{3,14,15},{5,7,8},{4,5,7},{6,10,12},{4,6,10},{7,10,11},{7,9,11},{6,13,15},{5,6,13},{8,13,14},{8,9,14},{12,14,15},{11,12,14}}}, - -{7, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{4,7,10},{0,5,6},{0,4,5},{0,4,6},{2,11,12},{2,10,12},{2,10,11},{1,7,8},{1,8,9},{1,7,9},{6,12,15},{5,8,13},{3,13,15},{3,13,14},{9,11,14},{3,14,15},{5,7,8},{4,5,7},{6,10,12},{4,6,10},{9,10,11},{7,9,10},{5,13,15},{5,6,15},{8,13,14},{8,9,14},{12,14,15},{11,12,14}}}, - -{8, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{4,7,10},{0,5,6},{0,4,5},{0,4,6},{2,11,12},{2,10,12},{2,10,11},{1,7,8},{1,8,9},{1,7,9},{6,12,15},{5,8,13},{3,13,15},{3,13,14},{9,11,14},{3,14,15},{5,7,8},{4,5,7},{6,10,12},{4,6,10},{9,10,11},{7,9,10},{6,13,15},{5,6,13},{9,13,14},{8,9,13},{11,14,15},{11,12,15}}}, - -{9, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{4,7,10},{0,5,6},{0,4,5},{0,4,6},{2,11,12},{2,10,12},{2,10,11},{1,7,8},{1,8,9},{1,7,9},{6,12,15},{5,8,13},{3,13,15},{3,13,14},{9,11,14},{3,14,15},{5,7,8},{4,5,7},{6,10,12},{4,6,10},{9,10,11},{7,9,10},{6,13,15},{5,6,13},{8,13,14},{8,9,14},{11,14,15},{11,12,15}}}, - -{10, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{4,7,10},{0,5,6},{0,4,5},{0,4,6},{2,11,12},{2,10,12},{2,10,11},{1,7,8},{1,8,9},{1,7,9},{6,12,15},{5,8,13},{3,13,15},{3,13,14},{9,11,14},{3,14,15},{5,7,8},{4,5,7},{4,10,12},{4,6,12},{9,10,11},{7,9,10},{6,13,15},{5,6,13},{8,13,14},{8,9,14},{11,14,15},{11,12,15}}}, - -{11, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{4,7,10},{0,5,6},{0,4,5},{0,4,6},{2,11,12},{2,10,12},{2,10,11},{1,7,8},{1,8,9},{1,7,9},{6,12,15},{5,8,13},{3,13,15},{3,13,14},{9,11,14},{3,14,15},{4,7,8},{4,5,8},{6,10,12},{4,6,10},{7,10,11},{7,9,11},{5,13,15},{5,6,15},{9,13,14},{8,9,13},{12,14,15},{11,12,14}}}, - -}; - -graph_t graphs_dhex[NUM_DHEX_GRAPHS] = { - -{0, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{5,9,12},{4,5,9},{11,13,14},{10,11,13},{6,11,14},{5,6,11},{4,8,15},{4,6,15},{7,13,15},{7,8,15}}}, - -{1, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{5,9,12},{4,5,9},{11,13,14},{10,11,13},{6,11,14},{5,6,11},{4,8,15},{4,6,15},{8,13,15},{7,8,13}}}, - -{2, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{5,9,12},{4,5,9},{11,13,14},{10,11,13},{6,11,14},{5,6,11},{6,8,15},{4,6,8},{7,13,15},{7,8,15}}}, - -{3, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{5,9,12},{4,5,9},{11,13,14},{10,11,13},{6,11,14},{5,6,11},{6,8,15},{4,6,8},{8,13,15},{7,8,13}}}, - -{4, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{5,9,12},{4,5,9},{11,13,14},{10,11,13},{5,11,14},{5,6,14},{4,8,15},{4,6,15},{8,13,15},{7,8,13}}}, - -{5, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{5,9,12},{4,5,9},{11,13,14},{10,11,13},{5,11,14},{5,6,14},{6,8,15},{4,6,8},{7,13,15},{7,8,15}}}, - -{6, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{5,9,12},{4,5,9},{11,13,14},{10,11,13},{5,11,14},{5,6,14},{6,8,15},{4,6,8},{8,13,15},{7,8,13}}}, - -{7, -0, -53, -2, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{5,9,12},{4,5,9},{10,13,14},{10,11,14},{6,11,14},{5,6,11},{4,8,15},{4,6,15},{8,13,15},{7,8,13}}}, - -{8, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{5,9,12},{4,5,9},{10,13,14},{10,11,14},{6,11,14},{5,6,11},{6,8,15},{4,6,8},{7,13,15},{7,8,15}}}, - -{9, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{5,9,12},{4,5,9},{10,13,14},{10,11,14},{6,11,14},{5,6,11},{6,8,15},{4,6,8},{8,13,15},{7,8,13}}}, - -{10, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{5,9,12},{4,5,9},{10,13,14},{10,11,14},{5,11,14},{5,6,14},{4,8,15},{4,6,15},{8,13,15},{7,8,13}}}, - -{11, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{5,9,12},{4,5,9},{10,13,14},{10,11,14},{5,11,14},{5,6,14},{6,8,15},{4,6,8},{7,13,15},{7,8,15}}}, - -{12, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{5,9,12},{4,5,9},{10,13,14},{10,11,14},{5,11,14},{5,6,14},{6,8,15},{4,6,8},{8,13,15},{7,8,13}}}, - -{13, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{4,9,12},{4,5,12},{11,13,14},{10,11,13},{5,11,14},{5,6,14},{4,8,15},{4,6,15},{8,13,15},{7,8,13}}}, - -{14, -0, -55, -4, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{4,9,12},{4,5,12},{11,13,14},{10,11,13},{5,11,14},{5,6,14},{6,8,15},{4,6,8},{7,13,15},{7,8,15}}}, - -{15, -0, -59, -2, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{4,9,12},{4,5,12},{11,13,14},{10,11,13},{5,11,14},{5,6,14},{6,8,15},{4,6,8},{8,13,15},{7,8,13}}}, - -{16, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{4,9,12},{4,5,12},{10,13,14},{10,11,14},{6,11,14},{5,6,11},{4,8,15},{4,6,15},{8,13,15},{7,8,13}}}, - -{17, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{4,9,12},{4,5,12},{10,13,14},{10,11,14},{6,11,14},{5,6,11},{6,8,15},{4,6,8},{8,13,15},{7,8,13}}}, - -{18, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{4,9,12},{4,5,12},{10,13,14},{10,11,14},{5,11,14},{5,6,14},{4,8,15},{4,6,15},{8,13,15},{7,8,13}}}, - -{19, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{4,9,12},{4,5,12},{10,13,14},{10,11,14},{5,11,14},{5,6,14},{6,8,15},{4,6,8},{8,13,15},{7,8,13}}}, - -{20, -0, -61, -4, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{7,10,12},{7,9,12},{5,9,12},{4,5,9},{10,13,14},{10,11,14},{6,11,14},{5,6,11},{4,8,15},{4,6,15},{8,13,15},{7,8,13}}}, - -{21, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{7,10,12},{7,9,12},{5,9,12},{4,5,9},{10,13,14},{10,11,14},{6,11,14},{5,6,11},{6,8,15},{4,6,8},{8,13,15},{7,8,13}}}, - -{22, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{7,10,12},{7,9,12},{5,9,12},{4,5,9},{10,13,14},{10,11,14},{5,11,14},{5,6,14},{6,8,15},{4,6,8},{8,13,15},{7,8,13}}}, - -{23, -0, -0, -1, -{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, -{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{7,10,12},{7,9,12},{4,9,12},{4,5,12},{10,13,14},{10,11,14},{5,11,14},{5,6,14},{6,8,15},{4,6,8},{8,13,15},{7,8,13}}}, - -}; - diff --git a/src/USER-PTM/graph_data.h b/src/USER-PTM/graph_data.h deleted file mode 100644 index 3a8a5c7ae7..0000000000 --- a/src/USER-PTM/graph_data.h +++ /dev/null @@ -1,37 +0,0 @@ -#ifndef GRAPH_DATA_H -#define GRAPH_DATA_H - -#include -#include "ptm_constants.h" - - -typedef struct -{ - int id; - uint64_t hash; - int automorphism_index; - int num_automorphisms; - int8_t canonical_labelling[PTM_MAX_POINTS]; - int8_t facets[PTM_MAX_FACETS][3]; -} graph_t; - -#define NUM_SC_GRAPHS 1 -#define NUM_ICO_GRAPHS 1 -#define NUM_FCC_GRAPHS 8 -#define NUM_HCP_GRAPHS 16 -#define NUM_BCC_GRAPHS 218 -#define NUM_DCUB_GRAPHS 12 -#define NUM_DHEX_GRAPHS 24 - -extern int8_t automorphisms[][PTM_MAX_POINTS]; - -extern graph_t graphs_sc[NUM_SC_GRAPHS]; -extern graph_t graphs_fcc[NUM_FCC_GRAPHS]; -extern graph_t graphs_hcp[NUM_HCP_GRAPHS]; -extern graph_t graphs_ico[NUM_ICO_GRAPHS]; -extern graph_t graphs_bcc[NUM_BCC_GRAPHS]; -extern graph_t graphs_dcub[NUM_DCUB_GRAPHS]; -extern graph_t graphs_dhex[NUM_DHEX_GRAPHS]; - -#endif - diff --git a/src/USER-PTM/graph_tools.cpp b/src/USER-PTM/graph_tools.cpp deleted file mode 100644 index 864e921b51..0000000000 --- a/src/USER-PTM/graph_tools.cpp +++ /dev/null @@ -1,52 +0,0 @@ -#include -#include -#include "graph_tools.h" -#include "ptm_constants.h" - - -bool build_facet_map(int num_facets, int8_t facets[][3], int8_t common[PTM_MAX_NBRS][PTM_MAX_NBRS]) -{ - memset(common, -1, sizeof(int8_t) * PTM_MAX_NBRS * PTM_MAX_NBRS); - - for (int i = 0;i -#include "ptm_constants.h" - -bool build_facet_map(int num_facets, int8_t facets[][3], int8_t common[PTM_MAX_NBRS][PTM_MAX_NBRS]); -int graph_degree(int num_facets, int8_t facets[][3], int num_nodes, int8_t* degree); - -#endif - diff --git a/src/USER-PTM/index_ptm.cpp b/src/USER-PTM/index_ptm.cpp deleted file mode 100644 index 2683323ac5..0000000000 --- a/src/USER-PTM/index_ptm.cpp +++ /dev/null @@ -1,218 +0,0 @@ -#include -#include -#include -#include -#include -#include -#include -#include "convex_hull_incremental.h" -#include "graph_data.h" -#include "deformation_gradient.h" -#include "alloy_types.h" -#include "neighbour_ordering.h" -#include "normalize_vertices.h" -#include "quat.h" -#include "polar.h" -#include "initialize_data.h" -#include "structure_matcher.h" -#include "ptm_functions.h" -#include "ptm_constants.h" - - -//todo: verify that c == norm(template[1]) -static double calculate_interatomic_distance(int type, double scale) -{ - assert(type >= 1 && type <= 7); - double c[8] = {0, 1, 1, (7. - 3.5 * sqrt(3)), 1, 1, sqrt(3) * 4. / (6 * sqrt(2) + sqrt(3)), sqrt(3) * 4. / (6 * sqrt(2) + sqrt(3))}; - return c[type] / scale; -} - -static double calculate_lattice_constant(int type, double interatomic_distance) -{ - assert(type >= 1 && type <= 7); - double c[8] = {0, 2 / sqrt(2), 2 / sqrt(2), 2. / sqrt(3), 2 / sqrt(2), 1, 4 / sqrt(3), 4 / sqrt(3)}; - return c[type] * interatomic_distance; -} - -static int rotate_into_fundamental_zone(int type, double* q) -{ - if (type == PTM_MATCH_SC) return rotate_quaternion_into_cubic_fundamental_zone(q); - if (type == PTM_MATCH_FCC) return rotate_quaternion_into_cubic_fundamental_zone(q); - if (type == PTM_MATCH_BCC) return rotate_quaternion_into_cubic_fundamental_zone(q); - if (type == PTM_MATCH_ICO) return rotate_quaternion_into_icosahedral_fundamental_zone(q); - if (type == PTM_MATCH_HCP) return rotate_quaternion_into_hcp_fundamental_zone(q); - if (type == PTM_MATCH_DCUB) return rotate_quaternion_into_diamond_cubic_fundamental_zone(q); - if (type == PTM_MATCH_DHEX) return rotate_quaternion_into_diamond_hexagonal_fundamental_zone(q); - return -1; -} - -static void order_points(ptm_local_handle_t local_handle, int num_points, double (*unpermuted_points)[3], int32_t* unpermuted_numbers, bool topological_ordering, - int8_t* ordering, double (*points)[3], int32_t* numbers) -{ - if (topological_ordering) - { - double normalized_points[PTM_MAX_INPUT_POINTS][3]; - normalize_vertices(num_points, unpermuted_points, normalized_points); - int ret = calculate_neighbour_ordering((void*)local_handle, num_points, (const double (*)[3])normalized_points, ordering); - if (ret != 0) - topological_ordering = false; - } - - if (!topological_ordering) - for (int i=0;iref_struct; - if (ref == NULL) - return; - - *p_type = ref->type; - if (p_alloy_type != NULL && unpermuted_numbers != NULL) - *p_alloy_type = find_alloy_type(ref, res->mapping, numbers); - - int bi = rotate_into_fundamental_zone(ref->type, res->q); - int8_t temp[PTM_MAX_POINTS]; - for (int i=0;inum_nbrs+1;i++) - temp[ref->mapping[bi][i]] = res->mapping[i]; - - memcpy(res->mapping, temp, (ref->num_nbrs+1) * sizeof(int8_t)); - - if (F != NULL && F_res != NULL) - { - double scaled_points[PTM_MAX_INPUT_POINTS][3]; - - subtract_barycentre(ref->num_nbrs + 1, points, scaled_points); - for (int i = 0;inum_nbrs + 1;i++) - { - scaled_points[i][0] *= res->scale; - scaled_points[i][1] *= res->scale; - scaled_points[i][2] *= res->scale; - } - calculate_deformation_gradient(ref->num_nbrs + 1, ref->points, res->mapping, scaled_points, ref->penrose, F, F_res); - - if (P != NULL && U != NULL) - polar_decomposition_3x3(F, false, U, P); - } - - if (mapping != NULL) - for (int i=0;inum_nbrs + 1;i++) - mapping[i] = ordering[res->mapping[i]]; - - double interatomic_distance = calculate_interatomic_distance(ref->type, res->scale); - double lattice_constant = calculate_lattice_constant(ref->type, interatomic_distance); - - if (p_interatomic_distance != NULL) - *p_interatomic_distance = interatomic_distance; - - if (p_lattice_constant != NULL) - *p_lattice_constant = lattice_constant; - - *p_rmsd = res->rmsd; - *p_scale = res->scale; - memcpy(q, res->q, 4 * sizeof(double)); -} - - -extern bool ptm_initialized; - -int ptm_index( ptm_local_handle_t local_handle, int32_t flags, - int num_points, double (*unpermuted_points)[3], int32_t* unpermuted_numbers, bool topological_ordering, - int32_t* p_type, int32_t* p_alloy_type, double* p_scale, double* p_rmsd, double* q, double* F, double* F_res, - double* U, double* P, int8_t* mapping, double* p_interatomic_distance, double* p_lattice_constant) -{ - assert(ptm_initialized); - assert(num_points <= PTM_MAX_INPUT_POINTS); - - if (flags & PTM_CHECK_SC) - assert(num_points >= PTM_NUM_POINTS_SC); - - if (flags & PTM_CHECK_BCC) - assert(num_points >= PTM_NUM_POINTS_BCC); - - if (flags & (PTM_CHECK_FCC | PTM_CHECK_HCP | PTM_CHECK_ICO)) - assert(num_points >= PTM_NUM_POINTS_FCC); - - if (flags & (PTM_CHECK_DCUB | PTM_CHECK_DHEX)) - assert(num_points >= PTM_NUM_POINTS_DCUB); - - int ret = 0; - result_t res; - res.ref_struct = NULL; - res.rmsd = INFINITY; - - int8_t ordering[PTM_MAX_INPUT_POINTS]; - double points[PTM_MAX_POINTS][3]; - int32_t numbers[PTM_MAX_POINTS]; - - int8_t dordering[PTM_MAX_INPUT_POINTS]; - double dpoints[PTM_MAX_POINTS][3]; - int32_t dnumbers[PTM_MAX_POINTS]; - - convexhull_t ch; - double ch_points[PTM_MAX_INPUT_POINTS][3]; - - if (flags & (PTM_CHECK_SC | PTM_CHECK_FCC | PTM_CHECK_HCP | PTM_CHECK_ICO | PTM_CHECK_BCC)) - { - int num_lpoints = std::min(std::min(PTM_MAX_POINTS, 20), num_points); - order_points(local_handle, num_lpoints, unpermuted_points, unpermuted_numbers, topological_ordering, ordering, points, numbers); - normalize_vertices(num_lpoints, points, ch_points); - ch.ok = false; - - if (flags & PTM_CHECK_SC) - ret = match_general(&structure_sc, ch_points, points, &ch, &res); - - if (flags & (PTM_CHECK_FCC | PTM_CHECK_HCP | PTM_CHECK_ICO)) - ret = match_fcc_hcp_ico(ch_points, points, flags, &ch, &res); - - if (flags & PTM_CHECK_BCC) - ret = match_general(&structure_bcc, ch_points, points, &ch, &res); - } - - if (flags & (PTM_CHECK_DCUB | PTM_CHECK_DHEX)) - { - ret = calculate_diamond_neighbour_ordering(num_points, unpermuted_points, unpermuted_numbers, dordering, dpoints, dnumbers); - if (ret == 0) - { - normalize_vertices(PTM_NUM_NBRS_DCUB + 1, dpoints, ch_points); - ch.ok = false; - - ret = match_dcub_dhex(ch_points, dpoints, flags, &ch, &res); - } - } - - if (res.ref_struct != NULL && (res.ref_struct->type == PTM_MATCH_DCUB || res.ref_struct->type == PTM_MATCH_DHEX)) - { - output_data( &res, num_points, unpermuted_numbers, dpoints, dnumbers, dordering, - p_type, p_alloy_type, p_scale, p_rmsd, q, F, F_res, - U, P, mapping, p_interatomic_distance, p_lattice_constant); - } - else - { - output_data( &res, num_points, unpermuted_numbers, points, numbers, ordering, - p_type, p_alloy_type, p_scale, p_rmsd, q, F, F_res, - U, P, mapping, p_interatomic_distance, p_lattice_constant); - } - - return PTM_NO_ERROR; -} - diff --git a/src/USER-PTM/initialize_data.cpp b/src/USER-PTM/initialize_data.cpp deleted file mode 100644 index 6c177bfb70..0000000000 --- a/src/USER-PTM/initialize_data.cpp +++ /dev/null @@ -1,71 +0,0 @@ -#include -#include -#include -#include -#include -#include -#include -#include "initialize_data.h" - - -static void make_facets_clockwise(int num_facets, int8_t (*facets)[3], const double (*points)[3]) -{ - double plane_normal[3]; - double origin[3] = {0, 0, 0}; - - for (int i = 0;inum_graphs;i++) - { - int8_t code[2 * PTM_MAX_EDGES]; - int8_t degree[PTM_MAX_NBRS]; - int _max_degree = graph_degree(s->num_facets, s->graphs[i].facets, s->num_nbrs, degree); - assert(_max_degree <= s->max_degree); - - make_facets_clockwise(s->num_facets, s->graphs[i].facets, &s->points[1]); - int ret = canonical_form_coloured(s->num_facets, s->graphs[i].facets, s->num_nbrs, degree, colours, s->graphs[i].canonical_labelling, (int8_t*)&code[0], &s->graphs[i].hash); - if (ret != 0) - return ret; - } - - return PTM_NO_ERROR; -} - -bool ptm_initialized = false; -int ptm_initialize_global() -{ - if (ptm_initialized) - return PTM_NO_ERROR; - - int8_t colours[PTM_MAX_POINTS] = {0}; - int8_t dcolours[PTM_MAX_POINTS] = {1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}; - - int ret = initialize_graphs(&structure_sc, colours); - ret |= initialize_graphs(&structure_fcc, colours); - ret |= initialize_graphs(&structure_hcp, colours); - ret |= initialize_graphs(&structure_ico, colours); - ret |= initialize_graphs(&structure_bcc, colours); - ret |= initialize_graphs(&structure_dcub, dcolours); - ret |= initialize_graphs(&structure_dhex, dcolours); - - if (ret == PTM_NO_ERROR) - ptm_initialized = true; - - return ret; -} - -ptm_local_handle_t ptm_initialize_local() -{ - assert(ptm_initialized); - return (ptm_local_handle_t)voronoi_initialize_local(); -} - -void ptm_uninitialize_local(ptm_local_handle_t ptr) -{ - voronoi_uninitialize_local(ptr); -} - diff --git a/src/USER-PTM/initialize_data.h b/src/USER-PTM/initialize_data.h deleted file mode 100644 index 644dfea8c4..0000000000 --- a/src/USER-PTM/initialize_data.h +++ /dev/null @@ -1,61 +0,0 @@ -#ifndef INITIALIZE_DATA_H -#define INITIALIZE_DATA_H - - -#include "graph_data.h" -#include "graph_tools.h" -#include "deformation_gradient.h" -#include "fundamental_mappings.h" -#include "neighbour_ordering.h" -#include "canonical_coloured.h" -#include "convex_hull_incremental.h" - - -typedef struct -{ - int type; - int num_nbrs; - int num_facets; - int max_degree; - int num_graphs; - int num_mappings; - graph_t* graphs; - const double (*points)[3]; - const double (*penrose)[3]; - const int8_t (*mapping)[PTM_MAX_POINTS]; -} refdata_t; - - -//refdata_t structure_sc = { .type = PTM_MATCH_SC, .num_nbrs = 6, .num_facets = 8, .max_degree = 4, .num_graphs = NUM_SC_GRAPHS, .graphs = graphs_sc, .points = ptm_template_sc, .penrose = penrose_sc , .mapping = mapping_sc }; -const refdata_t structure_sc = { PTM_MATCH_SC, 6, 8, 4, NUM_SC_GRAPHS, NUM_CUBIC_MAPPINGS, graphs_sc, ptm_template_sc, penrose_sc, mapping_sc }; -const refdata_t structure_fcc = { PTM_MATCH_FCC, 12, 20, 6, NUM_FCC_GRAPHS, NUM_CUBIC_MAPPINGS, graphs_fcc, ptm_template_fcc, penrose_fcc, mapping_fcc }; -const refdata_t structure_hcp = { PTM_MATCH_HCP, 12, 20, 6, NUM_HCP_GRAPHS, NUM_HEX_MAPPINGS, graphs_hcp, ptm_template_hcp, penrose_hcp, mapping_hcp }; -const refdata_t structure_ico = { PTM_MATCH_ICO, 12, 20, 6, NUM_ICO_GRAPHS, NUM_ICO_MAPPINGS, graphs_ico, ptm_template_ico, penrose_ico, mapping_ico }; -const refdata_t structure_bcc = { PTM_MATCH_BCC, 14, 24, 8, NUM_BCC_GRAPHS, NUM_CUBIC_MAPPINGS, graphs_bcc, ptm_template_bcc, penrose_bcc, mapping_bcc }; -const refdata_t structure_dcub = { PTM_MATCH_DCUB, 16, 28, 8, NUM_DCUB_GRAPHS, NUM_DCUB_MAPPINGS, graphs_dcub, ptm_template_dcub, penrose_dcub, mapping_dcub }; -const refdata_t structure_dhex = { PTM_MATCH_DHEX, 16, 28, 8, NUM_DHEX_GRAPHS, NUM_DHEX_MAPPINGS, graphs_dhex, ptm_template_dhex, penrose_dhex, mapping_dhex }; - - -#ifdef __cplusplus -extern "C" { -#endif - -typedef struct ptm_local_handle* ptm_local_handle_t; -ptm_local_handle_t ptm_initialize_local(); -void ptm_uninitialize_local(ptm_local_handle_t ptr); - -int ptm_initialize_global(); - -//------------------------------------ -// global initialization switch -//------------------------------------ -extern bool ptm_initialized; - - -#ifdef __cplusplus -} -#endif - - -#endif - diff --git a/src/USER-PTM/neighbour_ordering.cpp b/src/USER-PTM/neighbour_ordering.cpp deleted file mode 100644 index 8e8b016cfc..0000000000 --- a/src/USER-PTM/neighbour_ordering.cpp +++ /dev/null @@ -1,203 +0,0 @@ -#include -#include -#include -#include -#include -#include "ptm_constants.h" -#include "cell.h" -using namespace voro; - - - -typedef struct -{ - double area; - double dist; - int index; -} sorthelper_t; - -static bool sorthelper_compare(sorthelper_t const& a, sorthelper_t const& b) -{ - if (a.area > b.area) - return true; - - if (a.area < b.area) - return false; - - if (a.dist < b.dist) - return true; - - return false; -} - -//todo: change voronoi code to return errors rather than exiting -static int calculate_voronoi_face_areas(int num_points, const double (*_points)[3], double* normsq, double max_norm, voronoicell_neighbor* v, std::vector& nbr_indices, std::vector& face_areas) -{ - const double k = 1000 * max_norm; //todo: reduce this constant - v->init(-k,k,-k,k,-k,k); - - for (int i=1;inplane(x,y,z,normsq[i],i); - } - - v->neighbors(nbr_indices); - v->face_areas(face_areas); - return 0; -} - -int calculate_neighbour_ordering(void* _voronoi_handle, int num_points, const double (*_points)[3], int8_t* ordering) -{ - assert(num_points <= PTM_MAX_INPUT_POINTS); - - voronoicell_neighbor* voronoi_handle = (voronoicell_neighbor*)_voronoi_handle; - - double max_norm = 0; - double points[PTM_MAX_INPUT_POINTS][3]; - double normsq[PTM_MAX_INPUT_POINTS]; - for (int i = 0;i nbr_indices(num_points + 6); - std::vector face_areas(num_points + 6); - int ret = calculate_voronoi_face_areas(num_points, points, normsq, max_norm, voronoi_handle, nbr_indices, face_areas); - if (ret != 0) - return ret; - - double areas[PTM_MAX_INPUT_POINTS]; - memset(areas, 0, num_points * sizeof(double)); - areas[0] = INFINITY; - for (size_t i=0;i 0) - areas[index] = face_areas[i]; - } - - sorthelper_t data[PTM_MAX_INPUT_POINTS]; - for (int i=0;i= 3) - continue; - - ordering[1 + 4 + 3 * p + counts[p]] = q; - counts[p]++; - index++; - num_found++; - if (num_found >= 12) - break; - } - - if (num_found != 12) - return -1; - - for (int i=0;i - - -void subtract_barycentre(int num, double (*points)[3], double (*normalized)[3]) -{ - //calculate barycentre - double sum[3] = {0, 0, 0}; - for (int i=0;i nor the names of its contributors may be used to - * endorse or promote products derived from this software without specific prior written - * permission. - * - * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS - * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A - * PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT - * HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, - * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT - * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, - * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY - * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT - * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE - * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * Source: started anew. - * - * Change History: - * 2009/04/13 Started source - * 2010/03/28 Modified FastCalcRMSDAndRotation() to handle tiny qsqr - * If trying all rows of the adjoint still gives too small - * qsqr, then just return identity matrix. (DLT) - * 2010/06/30 Fixed prob in assigning A[9] = 0 in InnerProduct() - * invalid mem access - * 2011/02/21 Made CenterCoords use weights - * 2011/05/02 Finally changed CenterCoords declaration in qcprot.h - * Also changed some functions to static - * 2011/07/08 put in fabs() to fix taking sqrt of small neg numbers, fp error - * 2012/07/26 minor changes to comments and main.c, more info (v.1.4) - * - * 2016/05/29 QCP method adapted for polar decomposition of a 3x3 matrix, - * for use in Polyhedral Template Matching. - * - ******************************************************************************/ - -#include -#include -#include -#include "quat.h" - - -static void matmul_3x3(double* A, double* x, double* b) -{ - b[0] = A[0] * x[0] + A[1] * x[3] + A[2] * x[6]; - b[3] = A[3] * x[0] + A[4] * x[3] + A[5] * x[6]; - b[6] = A[6] * x[0] + A[7] * x[3] + A[8] * x[6]; - - b[1] = A[0] * x[1] + A[1] * x[4] + A[2] * x[7]; - b[4] = A[3] * x[1] + A[4] * x[4] + A[5] * x[7]; - b[7] = A[6] * x[1] + A[7] * x[4] + A[8] * x[7]; - - b[2] = A[0] * x[2] + A[1] * x[5] + A[2] * x[8]; - b[5] = A[3] * x[2] + A[4] * x[5] + A[5] * x[8]; - b[8] = A[6] * x[2] + A[7] * x[5] + A[8] * x[8]; -} - -static double matrix_determinant_3x3(double* A) -{ - return A[0] * (A[4]*A[8] - A[5]*A[7]) - - A[1] * (A[3]*A[8] - A[5]*A[6]) - + A[2] * (A[3]*A[7] - A[4]*A[6]); -} - -static void flip_matrix(double* A) -{ - for (int i=0;i<9;i++) - A[i] = -A[i]; -} - -static bool optimal_quaternion(double* A, bool polar, double E0, double* p_nrmsdsq, double* qopt) -{ - const double evecprec = 1e-6; - const double evalprec = 1e-11; - - double Sxx = A[0], Sxy = A[1], Sxz = A[2], - Syx = A[3], Syy = A[4], Syz = A[5], - Szx = A[6], Szy = A[7], Szz = A[8]; - - double Sxx2 = Sxx * Sxx, Syy2 = Syy * Syy, Szz2 = Szz * Szz, - Sxy2 = Sxy * Sxy, Syz2 = Syz * Syz, Sxz2 = Sxz * Sxz, - Syx2 = Syx * Syx, Szy2 = Szy * Szy, Szx2 = Szx * Szx; - - double fnorm_squared = Sxx2 + Syy2 + Szz2 + Sxy2 + Syz2 + Sxz2 + Syx2 + Szy2 + Szx2; - - double SyzSzymSyySzz2 = 2.0 * (Syz * Szy - Syy * Szz); - double Sxx2Syy2Szz2Syz2Szy2 = Syy2 + Szz2 - Sxx2 + Syz2 + Szy2; - double SxzpSzx = Sxz + Szx; - double SyzpSzy = Syz + Szy; - double SxypSyx = Sxy + Syx; - double SyzmSzy = Syz - Szy; - double SxzmSzx = Sxz - Szx; - double SxymSyx = Sxy - Syx; - double SxxpSyy = Sxx + Syy; - double SxxmSyy = Sxx - Syy; - double Sxy2Sxz2Syx2Szx2 = Sxy2 + Sxz2 - Syx2 - Szx2; - - double C[3]; - C[0] = Sxy2Sxz2Syx2Szx2 * Sxy2Sxz2Syx2Szx2 - + (Sxx2Syy2Szz2Syz2Szy2 + SyzSzymSyySzz2) * (Sxx2Syy2Szz2Syz2Szy2 - SyzSzymSyySzz2) - + (-(SxzpSzx)*(SyzmSzy)+(SxymSyx)*(SxxmSyy-Szz)) * (-(SxzmSzx)*(SyzpSzy)+(SxymSyx)*(SxxmSyy+Szz)) - + (-(SxzpSzx)*(SyzpSzy)-(SxypSyx)*(SxxpSyy-Szz)) * (-(SxzmSzx)*(SyzmSzy)-(SxypSyx)*(SxxpSyy+Szz)) - + (+(SxypSyx)*(SyzpSzy)+(SxzpSzx)*(SxxmSyy+Szz)) * (-(SxymSyx)*(SyzmSzy)+(SxzpSzx)*(SxxpSyy+Szz)) - + (+(SxypSyx)*(SyzmSzy)+(SxzmSzx)*(SxxmSyy-Szz)) * (-(SxymSyx)*(SyzpSzy)+(SxzmSzx)*(SxxpSyy-Szz)); - - C[1] = 8.0 * (Sxx*Syz*Szy + Syy*Szx*Sxz + Szz*Sxy*Syx - Sxx*Syy*Szz - Syz*Szx*Sxy - Szy*Syx*Sxz); - C[2] = -2.0 * fnorm_squared; - - //Newton-Raphson - double mxEigenV = polar ? sqrt(3 * fnorm_squared) : E0; - if (mxEigenV > evalprec) - { - for (int i=0;i<50;i++) - { - double oldg = mxEigenV; - double x2 = mxEigenV*mxEigenV; - double b = (x2 + C[2])*mxEigenV; - double a = b + C[1]; - double delta = ((a * mxEigenV + C[0]) / (2 * x2 * mxEigenV + b + a)); - mxEigenV -= delta; - if (fabs(mxEigenV - oldg) < fabs(evalprec * mxEigenV)) - break; - } - } - else - { - mxEigenV = 0.0; - } - - (*p_nrmsdsq) = std::max(0.0, 2.0 * (E0 - mxEigenV)); - - double a11 = SxxpSyy + Szz - mxEigenV; - double a12 = SyzmSzy; - double a13 = -SxzmSzx; - double a14 = SxymSyx; - - double a21 = SyzmSzy; - double a22 = SxxmSyy - Szz -mxEigenV; - double a23 = SxypSyx; - double a24 = SxzpSzx; - - double a31 = a13; - double a32 = a23; - double a33 = Syy - Sxx - Szz - mxEigenV; - double a34 = SyzpSzy; - - double a41 = a14; - double a42 = a24; - double a43 = a34; - double a44 = Szz - SxxpSyy - mxEigenV; - - double a3344_4334 = a33 * a44 - a43 * a34; - double a3244_4234 = a32 * a44 - a42 * a34; - double a3243_4233 = a32 * a43 - a42 * a33; - double a3143_4133 = a31 * a43 - a41 * a33; - double a3144_4134 = a31 * a44 - a41 * a34; - double a3142_4132 = a31 * a42 - a41 * a32; - double a1324_1423 = a13 * a24 - a14 * a23; - double a1224_1422 = a12 * a24 - a14 * a22; - double a1223_1322 = a12 * a23 - a13 * a22; - double a1124_1421 = a11 * a24 - a14 * a21; - double a1123_1321 = a11 * a23 - a13 * a21; - double a1122_1221 = a11 * a22 - a12 * a21; - - double q[4][4]; - q[0][0] = a12 * a3344_4334 - a13 * a3244_4234 + a14 * a3243_4233; - q[0][1] = -a11 * a3344_4334 + a13 * a3144_4134 - a14 * a3143_4133; - q[0][2] = a11 * a3244_4234 - a12 * a3144_4134 + a14 * a3142_4132; - q[0][3] = -a11 * a3243_4233 + a12 * a3143_4133 - a13 * a3142_4132; - - q[1][0] = a22 * a3344_4334 - a23 * a3244_4234 + a24 * a3243_4233; - q[1][1] = -a21 * a3344_4334 + a23 * a3144_4134 - a24 * a3143_4133; - q[1][2] = a21 * a3244_4234 - a22 * a3144_4134 + a24 * a3142_4132; - q[1][3] = -a21 * a3243_4233 + a22 * a3143_4133 - a23 * a3142_4132; - - q[2][0] = a32 * a1324_1423 - a33 * a1224_1422 + a34 * a1223_1322; - q[2][1] = -a31 * a1324_1423 + a33 * a1124_1421 - a34 * a1123_1321; - q[2][2] = a31 * a1224_1422 - a32 * a1124_1421 + a34 * a1122_1221; - q[2][3] = -a31 * a1223_1322 + a32 * a1123_1321 - a33 * a1122_1221; - - q[3][0] = a42 * a1324_1423 - a43 * a1224_1422 + a44 * a1223_1322; - q[3][1] = -a41 * a1324_1423 + a43 * a1124_1421 - a44 * a1123_1321; - q[3][2] = a41 * a1224_1422 - a42 * a1124_1421 + a44 * a1122_1221; - q[3][3] = -a41 * a1223_1322 + a42 * a1123_1321 - a43 * a1122_1221; - - double qsqr[4]; - for (int i=0;i<4;i++) - qsqr[i] = q[i][0]*q[i][0] + q[i][1]*q[i][1] + q[i][2]*q[i][2] + q[i][3]*q[i][3]; - - int bi = 0; - double max = 0; - for (int i=0;i<4;i++) - { - if (qsqr[i] > max) - { - bi = i; - max = qsqr[i]; - } - } - - bool too_small = false; - if (qsqr[bi] < evecprec) - { - //if qsqr is still too small, return the identity rotation. - q[bi][0] = 1; - q[bi][1] = 0; - q[bi][2] = 0; - q[bi][3] = 0; - too_small = true; - } - else - { - double normq = sqrt(qsqr[bi]); - q[bi][0] /= normq; - q[bi][1] /= normq; - q[bi][2] /= normq; - q[bi][3] /= normq; - } - - memcpy(qopt, q[bi], 4 * sizeof(double)); - return !too_small; -} - -int polar_decomposition_3x3(double* _A, bool right_sided, double* U, double* P) -{ - double A[9]; - memcpy(A, _A, 9 * sizeof(double)); - - double det = matrix_determinant_3x3(A); - if (det < 0) - flip_matrix(A); - - double q[4]; - double nrmsdsq = 0; - optimal_quaternion(A, true, -1, &nrmsdsq, q); - q[0] = -q[0]; - quaternion_to_rotation_matrix(q, U); - - if (det < 0) - flip_matrix(U); - - double UT[9] = {U[0], U[3], U[6], U[1], U[4], U[7], U[2], U[5], U[8]}; - - if (right_sided) - matmul_3x3(UT, _A, P); - else - matmul_3x3(_A, UT, P); - - return 0; -} - -void InnerProduct(double *A, int num, const double (*coords1)[3], double (*coords2)[3], int8_t* permutation) -{ - A[0] = A[1] = A[2] = A[3] = A[4] = A[5] = A[6] = A[7] = A[8] = 0.0; - - for (int i = 0; i < num; ++i) - { - double x1 = coords1[i][0]; - double y1 = coords1[i][1]; - double z1 = coords1[i][2]; - - double x2 = coords2[permutation[i]][0]; - double y2 = coords2[permutation[i]][1]; - double z2 = coords2[permutation[i]][2]; - - A[0] += x1 * x2; - A[1] += x1 * y2; - A[2] += x1 * z2; - - A[3] += y1 * x2; - A[4] += y1 * y2; - A[5] += y1 * z2; - - A[6] += z1 * x2; - A[7] += z1 * y2; - A[8] += z1 * z2; - } -} - -int FastCalcRMSDAndRotation(double *A, double E0, double *p_nrmsdsq, double *q, double* U) -{ - optimal_quaternion(A, false, E0, p_nrmsdsq, q); - quaternion_to_rotation_matrix(q, U); - return 0; -} - diff --git a/src/USER-PTM/polar.h b/src/USER-PTM/polar.h deleted file mode 100644 index 3ec025b806..0000000000 --- a/src/USER-PTM/polar.h +++ /dev/null @@ -1,12 +0,0 @@ -#ifndef POLAR_H -#define POLAR_H - -#include -#include - -int polar_decomposition_3x3(double* _A, bool right_sided, double* U, double* P); -void InnerProduct(double *A, int num, const double (*coords1)[3], double (*coords2)[3], int8_t* permutation); -int FastCalcRMSDAndRotation(double *A, double E0, double *p_nrmsdsq, double *q, double* U); - -#endif - diff --git a/src/PTM/ptm_alloy_types.cpp b/src/USER-PTM/ptm_alloy_types.cpp similarity index 100% rename from src/PTM/ptm_alloy_types.cpp rename to src/USER-PTM/ptm_alloy_types.cpp diff --git a/src/PTM/ptm_alloy_types.h b/src/USER-PTM/ptm_alloy_types.h similarity index 100% rename from src/PTM/ptm_alloy_types.h rename to src/USER-PTM/ptm_alloy_types.h diff --git a/src/PTM/ptm_canonical_coloured.cpp b/src/USER-PTM/ptm_canonical_coloured.cpp similarity index 100% rename from src/PTM/ptm_canonical_coloured.cpp rename to src/USER-PTM/ptm_canonical_coloured.cpp diff --git a/src/PTM/ptm_canonical_coloured.h b/src/USER-PTM/ptm_canonical_coloured.h similarity index 100% rename from src/PTM/ptm_canonical_coloured.h rename to src/USER-PTM/ptm_canonical_coloured.h diff --git a/src/PTM/ptm_convex_hull_incremental.cpp b/src/USER-PTM/ptm_convex_hull_incremental.cpp similarity index 100% rename from src/PTM/ptm_convex_hull_incremental.cpp rename to src/USER-PTM/ptm_convex_hull_incremental.cpp diff --git a/src/PTM/ptm_convex_hull_incremental.h b/src/USER-PTM/ptm_convex_hull_incremental.h similarity index 100% rename from src/PTM/ptm_convex_hull_incremental.h rename to src/USER-PTM/ptm_convex_hull_incremental.h diff --git a/src/PTM/ptm_deformation_gradient.cpp b/src/USER-PTM/ptm_deformation_gradient.cpp similarity index 100% rename from src/PTM/ptm_deformation_gradient.cpp rename to src/USER-PTM/ptm_deformation_gradient.cpp diff --git a/src/PTM/ptm_deformation_gradient.h b/src/USER-PTM/ptm_deformation_gradient.h similarity index 100% rename from src/PTM/ptm_deformation_gradient.h rename to src/USER-PTM/ptm_deformation_gradient.h diff --git a/src/USER-PTM/ptm_functions.h b/src/USER-PTM/ptm_functions.h index 69141a37c4..cd67d4940d 100644 --- a/src/USER-PTM/ptm_functions.h +++ b/src/USER-PTM/ptm_functions.h @@ -3,7 +3,7 @@ #include #include -#include "initialize_data.h" +#include "ptm_initialize_data.h" #include "ptm_constants.h" diff --git a/src/PTM/ptm_fundamental_mappings.h b/src/USER-PTM/ptm_fundamental_mappings.h similarity index 100% rename from src/PTM/ptm_fundamental_mappings.h rename to src/USER-PTM/ptm_fundamental_mappings.h diff --git a/src/PTM/ptm_graph_data.cpp b/src/USER-PTM/ptm_graph_data.cpp similarity index 100% rename from src/PTM/ptm_graph_data.cpp rename to src/USER-PTM/ptm_graph_data.cpp diff --git a/src/PTM/ptm_graph_data.h b/src/USER-PTM/ptm_graph_data.h similarity index 100% rename from src/PTM/ptm_graph_data.h rename to src/USER-PTM/ptm_graph_data.h diff --git a/src/PTM/ptm_graph_tools.cpp b/src/USER-PTM/ptm_graph_tools.cpp similarity index 100% rename from src/PTM/ptm_graph_tools.cpp rename to src/USER-PTM/ptm_graph_tools.cpp diff --git a/src/PTM/ptm_graph_tools.h b/src/USER-PTM/ptm_graph_tools.h similarity index 100% rename from src/PTM/ptm_graph_tools.h rename to src/USER-PTM/ptm_graph_tools.h diff --git a/src/PTM/ptm_index.cpp b/src/USER-PTM/ptm_index.cpp similarity index 100% rename from src/PTM/ptm_index.cpp rename to src/USER-PTM/ptm_index.cpp diff --git a/src/PTM/ptm_initialize_data.cpp b/src/USER-PTM/ptm_initialize_data.cpp similarity index 100% rename from src/PTM/ptm_initialize_data.cpp rename to src/USER-PTM/ptm_initialize_data.cpp diff --git a/src/PTM/ptm_initialize_data.h b/src/USER-PTM/ptm_initialize_data.h similarity index 100% rename from src/PTM/ptm_initialize_data.h rename to src/USER-PTM/ptm_initialize_data.h diff --git a/src/PTM/ptm_neighbour_ordering.cpp b/src/USER-PTM/ptm_neighbour_ordering.cpp similarity index 100% rename from src/PTM/ptm_neighbour_ordering.cpp rename to src/USER-PTM/ptm_neighbour_ordering.cpp diff --git a/src/PTM/ptm_neighbour_ordering.h b/src/USER-PTM/ptm_neighbour_ordering.h similarity index 100% rename from src/PTM/ptm_neighbour_ordering.h rename to src/USER-PTM/ptm_neighbour_ordering.h diff --git a/src/PTM/ptm_normalize_vertices.cpp b/src/USER-PTM/ptm_normalize_vertices.cpp similarity index 100% rename from src/PTM/ptm_normalize_vertices.cpp rename to src/USER-PTM/ptm_normalize_vertices.cpp diff --git a/src/PTM/ptm_normalize_vertices.h b/src/USER-PTM/ptm_normalize_vertices.h similarity index 100% rename from src/PTM/ptm_normalize_vertices.h rename to src/USER-PTM/ptm_normalize_vertices.h diff --git a/src/PTM/ptm_polar.cpp b/src/USER-PTM/ptm_polar.cpp similarity index 100% rename from src/PTM/ptm_polar.cpp rename to src/USER-PTM/ptm_polar.cpp diff --git a/src/PTM/ptm_polar.h b/src/USER-PTM/ptm_polar.h similarity index 100% rename from src/PTM/ptm_polar.h rename to src/USER-PTM/ptm_polar.h diff --git a/src/PTM/ptm_quat.cpp b/src/USER-PTM/ptm_quat.cpp similarity index 100% rename from src/PTM/ptm_quat.cpp rename to src/USER-PTM/ptm_quat.cpp diff --git a/src/PTM/ptm_quat.h b/src/USER-PTM/ptm_quat.h similarity index 100% rename from src/PTM/ptm_quat.h rename to src/USER-PTM/ptm_quat.h diff --git a/src/PTM/ptm_structure_matcher.cpp b/src/USER-PTM/ptm_structure_matcher.cpp similarity index 100% rename from src/PTM/ptm_structure_matcher.cpp rename to src/USER-PTM/ptm_structure_matcher.cpp diff --git a/src/PTM/ptm_structure_matcher.h b/src/USER-PTM/ptm_structure_matcher.h similarity index 100% rename from src/PTM/ptm_structure_matcher.h rename to src/USER-PTM/ptm_structure_matcher.h diff --git a/src/PTM/ptm_voronoi_cell.cpp b/src/USER-PTM/ptm_voronoi_cell.cpp similarity index 100% rename from src/PTM/ptm_voronoi_cell.cpp rename to src/USER-PTM/ptm_voronoi_cell.cpp diff --git a/src/PTM/ptm_voronoi_cell.h b/src/USER-PTM/ptm_voronoi_cell.h similarity index 100% rename from src/PTM/ptm_voronoi_cell.h rename to src/USER-PTM/ptm_voronoi_cell.h diff --git a/src/PTM/ptm_voronoi_config.h b/src/USER-PTM/ptm_voronoi_config.h similarity index 100% rename from src/PTM/ptm_voronoi_config.h rename to src/USER-PTM/ptm_voronoi_config.h diff --git a/src/USER-PTM/quat.cpp b/src/USER-PTM/quat.cpp deleted file mode 100644 index f55aff3d2b..0000000000 --- a/src/USER-PTM/quat.cpp +++ /dev/null @@ -1,396 +0,0 @@ -#include -#include -#include - - -#define SIGN(x) (x >= 0 ? 1 : -1) -#define MIN(X, Y) (((X) < (Y)) ? (X) : (Y)) -#define MAX(X, Y) (((X) > (Y)) ? (X) : (Y)) - - -#define SQRT_2 1.4142135623730951454746218587388284504414 -#define HALF_SQRT_2 0.7071067811865474617150084668537601828575 - -#define PHI 1.6180339887498949025257388711906969547272 -#define HALF_PHI 0.8090169943749474512628694355953484773636 - -#define INV_PHI 0.6180339887498947915034364086750429123640 -#define HALF_INV_PHI 0.3090169943749473957517182043375214561820 - -#define SQRT_5_ 2.23606797749978969640917366873127623544061835961152572427089 -#define SQRT_2_3 0.8164965809277260344600790631375275552273 -#define SQRT_1_6 0.4082482904638630172300395315687637776136 - - -double generator_cubic[24][4] = { {1, 0, 0, 0 }, - {0, 1, 0, 0 }, - {0, 0, 1, 0 }, - {0, 0, 0, 1 }, - {0.5, 0.5, 0.5, 0.5 }, - {0.5, 0.5, -0.5, 0.5 }, - {0.5, -0.5, 0.5, 0.5 }, - {0.5, -0.5, -0.5, 0.5 }, - {-0.5, 0.5, 0.5, 0.5 }, - {-0.5, 0.5, -0.5, 0.5 }, - {-0.5, -0.5, 0.5, 0.5 }, - {-0.5, -0.5, -0.5, 0.5 }, - {HALF_SQRT_2, HALF_SQRT_2, 0, 0 }, - {HALF_SQRT_2, 0, HALF_SQRT_2, 0 }, - {HALF_SQRT_2, 0, 0, HALF_SQRT_2 }, - {-HALF_SQRT_2, HALF_SQRT_2, 0, 0 }, - {-HALF_SQRT_2, 0, HALF_SQRT_2, 0 }, - {-HALF_SQRT_2, 0, 0, HALF_SQRT_2 }, - {0, HALF_SQRT_2, HALF_SQRT_2, 0 }, - {0, HALF_SQRT_2, 0, HALF_SQRT_2 }, - {0, 0, HALF_SQRT_2, HALF_SQRT_2 }, - {0, -HALF_SQRT_2, HALF_SQRT_2, 0 }, - {0, -HALF_SQRT_2, 0, HALF_SQRT_2 }, - {0, 0, -HALF_SQRT_2, HALF_SQRT_2 } }; - -double generator_diamond_cubic[12][4] = { {1, 0, 0, 0 }, - {0, 1, 0, 0 }, - {0, 0, 1, 0 }, - {0, 0, 0, 1 }, - {0.5, 0.5, 0.5, 0.5 }, - {0.5, 0.5, -0.5, 0.5 }, - {0.5, -0.5, 0.5, 0.5 }, - {0.5, -0.5, -0.5, 0.5 }, - {-0.5, 0.5, 0.5, 0.5 }, - {-0.5, 0.5, -0.5, 0.5 }, - {-0.5, -0.5, 0.5, 0.5 }, - {-0.5, -0.5, -0.5, 0.5 } }; - -double generator_hcp[6][4] = { {1, 0, 0, 0}, - {0.5, 0.5, 0.5, 0.5}, - {0.5, -0.5, -0.5, -0.5}, - {0, SQRT_2_3, -SQRT_1_6, -SQRT_1_6}, - {0, SQRT_1_6, -SQRT_2_3, SQRT_1_6}, - {0, SQRT_1_6, SQRT_1_6, -SQRT_2_3} }; - -double generator_diamond_hexagonal[3][4] = { {1, 0, 0, 0}, - {0.5, 0.5, 0.5, 0.5}, - {0.5, -0.5, -0.5, -0.5} }; - -double generator_icosahedral[60][4] = { {1, 0, 0, 0}, - {HALF_PHI, -HALF_INV_PHI, -0.5, 0}, - {HALF_PHI, 0, -HALF_INV_PHI, -0.5}, - {HALF_PHI, -0.5, 0, -HALF_INV_PHI}, - {HALF_PHI, HALF_INV_PHI, -0.5, 0}, - {HALF_PHI, 0, HALF_INV_PHI, -0.5}, - {HALF_PHI, -0.5, 0, HALF_INV_PHI}, - {HALF_PHI, 0.5, 0, -HALF_INV_PHI}, - {HALF_PHI, 0, -HALF_INV_PHI, 0.5}, - {HALF_PHI, -HALF_INV_PHI, 0.5, 0}, - {HALF_PHI, 0, HALF_INV_PHI, 0.5}, - {HALF_PHI, HALF_INV_PHI, 0.5, 0}, - {HALF_PHI, 0.5, 0, HALF_INV_PHI}, - {0.5, HALF_PHI, -HALF_INV_PHI, 0}, - {0.5, HALF_PHI, HALF_INV_PHI, 0}, - {0.5, 0.5, 0.5, 0.5}, - {0.5, 0.5, 0.5, -0.5}, - {0.5, 0.5, -0.5, 0.5}, - {0.5, 0.5, -0.5, -0.5}, - {0.5, HALF_INV_PHI, 0, HALF_PHI}, - {0.5, HALF_INV_PHI, 0, -HALF_PHI}, - {0.5, 0, HALF_PHI, -HALF_INV_PHI}, - {0.5, 0, HALF_PHI, HALF_INV_PHI}, - {0.5, 0, -HALF_PHI, -HALF_INV_PHI}, - {0.5, 0, -HALF_PHI, HALF_INV_PHI}, - {0.5, -HALF_INV_PHI, 0, HALF_PHI}, - {0.5, -HALF_INV_PHI, 0, -HALF_PHI}, - {0.5, -0.5, 0.5, 0.5}, - {0.5, -0.5, 0.5, -0.5}, - {0.5, -0.5, -0.5, 0.5}, - {0.5, -0.5, -0.5, -0.5}, - {0.5, -HALF_PHI, -HALF_INV_PHI, 0}, - {0.5, -HALF_PHI, HALF_INV_PHI, 0}, - {HALF_INV_PHI, -HALF_PHI, 0, -0.5}, - {HALF_INV_PHI, 0, -0.5, -HALF_PHI}, - {HALF_INV_PHI, -0.5, -HALF_PHI, 0}, - {HALF_INV_PHI, 0, 0.5, -HALF_PHI}, - {HALF_INV_PHI, -HALF_PHI, 0, 0.5}, - {HALF_INV_PHI, 0.5, -HALF_PHI, 0}, - {HALF_INV_PHI, HALF_PHI, 0, -0.5}, - {HALF_INV_PHI, -0.5, HALF_PHI, 0}, - {HALF_INV_PHI, 0, -0.5, HALF_PHI}, - {HALF_INV_PHI, HALF_PHI, 0, 0.5}, - {HALF_INV_PHI, 0, 0.5, HALF_PHI}, - {HALF_INV_PHI, 0.5, HALF_PHI, 0}, - {0, 1, 0, 0}, - {0, HALF_PHI, -0.5, HALF_INV_PHI}, - {0, HALF_PHI, -0.5, -HALF_INV_PHI}, - {0, HALF_PHI, 0.5, HALF_INV_PHI}, - {0, HALF_PHI, 0.5, -HALF_INV_PHI}, - {0, 0.5, HALF_INV_PHI, -HALF_PHI}, - {0, 0.5, HALF_INV_PHI, HALF_PHI}, - {0, 0.5, -HALF_INV_PHI, -HALF_PHI}, - {0, 0.5, -HALF_INV_PHI, HALF_PHI}, - {0, HALF_INV_PHI, -HALF_PHI, 0.5}, - {0, HALF_INV_PHI, -HALF_PHI, -0.5}, - {0, HALF_INV_PHI, HALF_PHI, 0.5}, - {0, HALF_INV_PHI, HALF_PHI, -0.5}, - {0, 0, 1, 0}, - {0, 0, 0, 1} }; - -static void quat_rot(double* r, double* a, double* b) -{ - b[0] = (r[0] * a[0] - r[1] * a[1] - r[2] * a[2] - r[3] * a[3]); - b[1] = (r[0] * a[1] + r[1] * a[0] + r[2] * a[3] - r[3] * a[2]); - b[2] = (r[0] * a[2] - r[1] * a[3] + r[2] * a[0] + r[3] * a[1]); - b[3] = (r[0] * a[3] + r[1] * a[2] - r[2] * a[1] + r[3] * a[0]); -} - -static int rotate_quaternion_into_fundamental_zone(int num_generators, double (*generator)[4], double* q) -{ - double max = 0.0; - int i = 0, bi = -1; - for (i=0;i max) - { - max = t; - bi = i; - } - } - - double f[4]; - quat_rot(q, generator[bi], f); - memcpy(q, &f, 4 * sizeof(double)); - if (q[0] < 0) - { - q[0] = -q[0]; - q[1] = -q[1]; - q[2] = -q[2]; - q[3] = -q[3]; - } - - return bi; -} - -int rotate_quaternion_into_cubic_fundamental_zone(double* q) -{ - return rotate_quaternion_into_fundamental_zone(24, generator_cubic, q); -} - -int rotate_quaternion_into_diamond_cubic_fundamental_zone(double* q) -{ - return rotate_quaternion_into_fundamental_zone(12, generator_diamond_cubic, q); -} - -int rotate_quaternion_into_icosahedral_fundamental_zone(double* q) -{ - return rotate_quaternion_into_fundamental_zone(60, generator_icosahedral, q); -} - -int rotate_quaternion_into_hcp_fundamental_zone(double* q) -{ - return rotate_quaternion_into_fundamental_zone(6, generator_hcp, q); -} - -int rotate_quaternion_into_diamond_hexagonal_fundamental_zone(double* q) -{ - return rotate_quaternion_into_fundamental_zone(3, generator_diamond_hexagonal, q); -} - -double quat_dot(double* a, double* b) -{ - return a[0] * b[0] - + a[1] * b[1] - + a[2] * b[2] - + a[3] * b[3]; -} - -double quat_size(double* q) -{ - return sqrt(quat_dot(q, q)); -} - -void normalize_quaternion(double* q) -{ - double size = quat_size(q); - - q[0] /= size; - q[1] /= size; - q[2] /= size; - q[3] /= size; -} - -void rotation_matrix_to_quaternion(double* u, double* q) -{ - double r11 = u[0]; - double r12 = u[1]; - double r13 = u[2]; - double r21 = u[3]; - double r22 = u[4]; - double r23 = u[5]; - double r31 = u[6]; - double r32 = u[7]; - double r33 = u[8]; - - q[0] = (1.0 + r11 + r22 + r33) / 4.0; - q[1] = (1.0 + r11 - r22 - r33) / 4.0; - q[2] = (1.0 - r11 + r22 - r33) / 4.0; - q[3] = (1.0 - r11 - r22 + r33) / 4.0; - - q[0] = sqrt(MAX(0, q[0])); - q[1] = sqrt(MAX(0, q[1])); - q[2] = sqrt(MAX(0, q[2])); - q[3] = sqrt(MAX(0, q[3])); - - double m0 = MAX(q[0], q[1]); - double m1 = MAX(q[2], q[3]); - double max = MAX(m0, m1); - - int i = 0; - for (i=0;i<4;i++) - if (q[i] == max) - break; - - if (i == 0) - { - q[1] *= SIGN(r32 - r23); - q[2] *= SIGN(r13 - r31); - q[3] *= SIGN(r21 - r12); - } - else if (i == 1) - { - q[0] *= SIGN(r32 - r23); - q[2] *= SIGN(r21 + r12); - q[3] *= SIGN(r13 + r31); - } - else if (i == 2) - { - q[0] *= SIGN(r13 - r31); - q[1] *= SIGN(r21 + r12); - q[3] *= SIGN(r32 + r23); - } - else if (i == 3) - { - q[0] *= SIGN(r21 - r12); - q[1] *= SIGN(r31 + r13); - q[2] *= SIGN(r32 + r23); - } - - normalize_quaternion(q); -} - -void quaternion_to_rotation_matrix(double* q, double* u) -{ - double a = q[0]; - double b = q[1]; - double c = q[2]; - double d = q[3]; - - u[0] = a*a + b*b - c*c - d*d; - u[1] = 2*b*c - 2*a*d; - u[2] = 2*b*d + 2*a*c; - - u[3] = 2*b*c + 2*a*d; - u[4] = a*a - b*b + c*c - d*d; - u[5] = 2*c*d - 2*a*b; - - u[6] = 2*b*d - 2*a*c; - u[7] = 2*c*d + 2*a*b; - u[8] = a*a - b*b - c*c + d*d; -} - -double quat_quick_misorientation(double* q1, double* q2) -{ - double t = quat_dot(q1, q2); - t = MIN(1, MAX(-1, t)); - return 2 * t * t - 1; -} - -double quat_misorientation(double* q1, double* q2) -{ - return acos(quat_quick_misorientation(q1, q2)); -} - - -double quat_quick_disorientation_cubic(double* q0, double* q1) -{ - double qrot[4]; - double qinv[4] = {q0[0], -q0[1], -q0[2], -q0[3]}; - quat_rot(qinv, q1, qrot); - - rotate_quaternion_into_cubic_fundamental_zone(qrot); - double t = qrot[0]; - t = MIN(1, MAX(-1, t)); - return 2 * t * t - 1; -} - -double quat_disorientation_cubic(double* q0, double* q1) -{ - return acos(quat_quick_disorientation_cubic(q0, q1)); -} - -double quat_quick_disorientation_diamond_cubic(double* q0, double* q1) -{ - double qrot[4]; - double qinv[4] = {q0[0], -q0[1], -q0[2], -q0[3]}; - quat_rot(qinv, q1, qrot); - - rotate_quaternion_into_diamond_cubic_fundamental_zone(qrot); - double t = qrot[0]; - t = MIN(1, MAX(-1, t)); - return 2 * t * t - 1; -} - -double quat_disorientation_diamond_cubic(double* q0, double* q1) -{ - return acos(quat_quick_disorientation_diamond_cubic(q0, q1)); -} - -double quat_quick_disorientation_hcp(double* q0, double* q1) -{ - double qrot[4]; - double qinv[4] = {q0[0], -q0[1], -q0[2], -q0[3]}; - quat_rot(qinv, q1, qrot); - - rotate_quaternion_into_hcp_fundamental_zone(qrot); - double t = qrot[0]; - t = MIN(1, MAX(-1, t)); - return 2 * t * t - 1; -} - -double quat_disorientation_hcp(double* q0, double* q1) -{ - return acos(quat_quick_disorientation_hcp(q0, q1)); -} - -double quat_quick_disorientation_diamond_hexagonal(double* q0, double* q1) -{ - double qrot[4]; - double qinv[4] = {q0[0], -q0[1], -q0[2], -q0[3]}; - quat_rot(qinv, q1, qrot); - - rotate_quaternion_into_diamond_hexagonal_fundamental_zone(qrot); - double t = qrot[0]; - t = MIN(1, MAX(-1, t)); - return 2 * t * t - 1; -} - -double quat_disorientation_diamond_hexagonal(double* q0, double* q1) -{ - return acos(quat_quick_disorientation_diamond_hexagonal(q0, q1)); -} - -double quat_quick_disorientation_icosahedral(double* q0, double* q1) -{ - double qrot[4]; - double qinv[4] = {q0[0], -q0[1], -q0[2], -q0[3]}; - quat_rot(qinv, q1, qrot); - - rotate_quaternion_into_icosahedral_fundamental_zone(qrot); - double t = qrot[0]; - t = MIN(1, MAX(-1, t)); - return 2 * t * t - 1; -} - -double quat_disorientation_icosahedral(double* q0, double* q1) -{ - return acos(quat_quick_disorientation_icosahedral(q0, q1)); -} - diff --git a/src/USER-PTM/quat.h b/src/USER-PTM/quat.h deleted file mode 100644 index 725086322c..0000000000 --- a/src/USER-PTM/quat.h +++ /dev/null @@ -1,32 +0,0 @@ -#ifndef QUAT_H -#define QUAT_H - -int rotate_quaternion_into_cubic_fundamental_zone(double* q); -int rotate_quaternion_into_diamond_cubic_fundamental_zone(double* q); -int rotate_quaternion_into_icosahedral_fundamental_zone(double* q); -int rotate_quaternion_into_hcp_fundamental_zone(double* q); -int rotate_quaternion_into_diamond_hexagonal_fundamental_zone(double* q); - -void normalize_quaternion(double* q); -void quaternion_to_rotation_matrix(double* q, double* U); -void rotation_matrix_to_quaternion(double* u, double* q); -double quat_dot(double* a, double* b); -double quat_quick_misorientation(double* q1, double* q2); -double quat_misorientation(double* q1, double* q2); - -double quat_quick_disorientation_cubic(double* q0, double* q1); -double quat_disorientation_cubic(double* q0, double* q1); -double quat_quick_disorientation_diamond_cubic(double* q0, double* q1); -double quat_disorientation_diamond_cubic(double* q0, double* q1); -double quat_quick_disorientation_hcp(double* q0, double* q1); -double quat_disorientation_hcp(double* q0, double* q1); -double quat_quick_disorientation_diamond_hexagonal(double* q0, double* q1); -double quat_disorientation_diamond_hexagonal(double* q0, double* q1); -double quat_quick_disorientation_icosahedral(double* q0, double* q1); -double quat_disorientation_icosahedral(double* q0, double* q1); - -#endif - - - - diff --git a/src/USER-PTM/structure_matcher.cpp b/src/USER-PTM/structure_matcher.cpp deleted file mode 100644 index dad8e3599a..0000000000 --- a/src/USER-PTM/structure_matcher.cpp +++ /dev/null @@ -1,294 +0,0 @@ -#include -#include -#include -#include -#include -#include -#include -#include "convex_hull_incremental.h" -#include "canonical_coloured.h" -#include "graph_data.h" -#include "graph_tools.h" -#include "normalize_vertices.h" -#include "polar.h" -#include "structure_matcher.h" -#include "ptm_constants.h" - - -static double calc_rmsd(int num_points, const double (*ideal_points)[3], double (*normalized)[3], int8_t* mapping, - double G1, double G2, double E0, double* q, double* p_scale) -{ - double A0[9]; - InnerProduct(A0, num_points, ideal_points, normalized, mapping); - - double nrmsdsq, rot[9]; - FastCalcRMSDAndRotation(A0, E0, &nrmsdsq, q, rot); - - double k0 = 0; - for (int i=0;inum_nbrs + 1; - const double (*ideal_points)[3] = s->points; - int8_t inverse_labelling[PTM_MAX_POINTS]; - int8_t mapping[PTM_MAX_POINTS]; - - for (int i=0; inum_graphs;i++) - { - if (hash != s->graphs[i].hash) - continue; - - graph_t* gref = &s->graphs[i]; - for (int j = 0;jnum_automorphisms;j++) - { - for (int k=0;kautomorphism_index + j][k]] = inverse_labelling[ gref->canonical_labelling[k] ]; - - double q[4], scale = 0; - double rmsd = calc_rmsd(num_points, ideal_points, normalized, mapping, G1, G2, E0, q, &scale); - if (rmsd < res->rmsd) - { - res->rmsd = rmsd; - res->scale = scale; - res->ref_struct = s; - memcpy(res->q, q, 4 * sizeof(double)); - memcpy(res->mapping, mapping, sizeof(int8_t) * num_points); - } - } - } -} - -int match_general(const refdata_t* s, double (*ch_points)[3], double (*points)[3], convexhull_t* ch, result_t* res) -{ - int8_t degree[PTM_MAX_NBRS]; - int8_t facets[PTM_MAX_FACETS][3]; - - int ret = get_convex_hull(s->num_nbrs + 1, (const double (*)[3])ch_points, ch, facets); - ch->ok = ret >= 0; - if (ret != 0) - return PTM_NO_ERROR; - - if (ch->num_facets != s->num_facets) - return PTM_NO_ERROR; //incorrect number of facets in convex hull - - int max_degree = graph_degree(s->num_facets, facets, s->num_nbrs, degree); - if (max_degree > s->max_degree) - return PTM_NO_ERROR; - - if (s->type == PTM_MATCH_SC) - for (int i = 0;inum_nbrs;i++) - if (degree[i] != 4) - return PTM_NO_ERROR; - - double normalized[PTM_MAX_POINTS][3]; - subtract_barycentre(s->num_nbrs + 1, points, normalized); - - int8_t code[2 * PTM_MAX_EDGES]; - int8_t colours[PTM_MAX_POINTS] = {0}; - int8_t canonical_labelling[PTM_MAX_POINTS]; - uint64_t hash = 0; - ret = canonical_form_coloured(s->num_facets, facets, s->num_nbrs, degree, colours, canonical_labelling, &code[0], &hash); - if (ret != PTM_NO_ERROR) - return ret; - - check_graphs(s, hash, canonical_labelling, normalized, res); - return PTM_NO_ERROR; -} - -int match_fcc_hcp_ico(double (*ch_points)[3], double (*points)[3], int32_t flags, convexhull_t* ch, result_t* res) -{ - int num_nbrs = structure_fcc.num_nbrs; - int num_facets = structure_fcc.num_facets; - int max_degree = structure_fcc.max_degree; - - int8_t degree[PTM_MAX_NBRS]; - int8_t facets[PTM_MAX_FACETS][3]; - - int ret = get_convex_hull(num_nbrs + 1, (const double (*)[3])ch_points, ch, facets); - ch->ok = ret >= 0; - if (ret != 0) - return PTM_NO_ERROR; - - if (ch->num_facets != num_facets) - return PTM_NO_ERROR; //incorrect number of facets in convex hull - - int _max_degree = graph_degree(num_facets, facets, num_nbrs, degree); - if (_max_degree > max_degree) - return PTM_NO_ERROR; - - double normalized[PTM_MAX_POINTS][3]; - subtract_barycentre(num_nbrs + 1, points, normalized); - - int8_t code[2 * PTM_MAX_EDGES]; - int8_t colours[PTM_MAX_POINTS] = {0}; - int8_t canonical_labelling[PTM_MAX_POINTS]; - uint64_t hash = 0; - ret = canonical_form_coloured(num_facets, facets, num_nbrs, degree, colours, canonical_labelling, &code[0], &hash); - if (ret != PTM_NO_ERROR) - return ret; - - if (flags & PTM_CHECK_FCC) check_graphs(&structure_fcc, hash, canonical_labelling, normalized, res); - if (flags & PTM_CHECK_HCP) check_graphs(&structure_hcp, hash, canonical_labelling, normalized, res); - if (flags & PTM_CHECK_ICO) check_graphs(&structure_ico, hash, canonical_labelling, normalized, res); - return PTM_NO_ERROR; -} - -int match_dcub_dhex(double (*ch_points)[3], double (*points)[3], int32_t flags, convexhull_t* ch, result_t* res) -{ - int num_nbrs = structure_dcub.num_nbrs; - int num_facets = structure_fcc.num_facets; - int max_degree = structure_dcub.max_degree; - - - int8_t facets[PTM_MAX_FACETS][3]; - int ret = get_convex_hull(num_nbrs + 1, (const double (*)[3])ch_points, ch, facets); - ch->ok = ret >= 0; - if (ret != 0) - return PTM_NO_ERROR; - - //check for facets with multiple inner atoms - bool inverted[4] = {false, false, false, false}; - for (int i=0;inum_facets;i++) - { - int n = 0; - for (int j=0;j<3;j++) - { - if (facets[i][j] <= 3) - { - inverted[facets[i][j]] = true; - n++; - } - } - if (n > 1) - return PTM_NO_ERROR; - } - - int num_inverted = 0; - for (int i=0;i<4;i++) - num_inverted += inverted[i] ? 1 : 0; - - if (ch->num_facets != num_facets + 2 * num_inverted) - return PTM_NO_ERROR; //incorrect number of facets in convex hull - - int8_t degree[PTM_MAX_NBRS]; - int _max_degree = graph_degree(num_facets, facets, num_nbrs, degree); - if (_max_degree > max_degree) - return PTM_NO_ERROR; - - int num_found = 0; - int8_t toadd[4][3]; - for (int i=0;inum_facets;i++) - { - int a = facets[i][0]; - int b = facets[i][1]; - int c = facets[i][2]; - if (a <= 3 || b <= 3 || c <= 3) - continue; - - int i0 = (a - 4) / 3; - int i1 = (b - 4) / 3; - int i2 = (c - 4) / 3; - - if (i0 == i1 && i0 == i2) - { - if (num_found + num_inverted >= 4) - return PTM_NO_ERROR; - - toadd[num_found][0] = a; - toadd[num_found][1] = b; - toadd[num_found][2] = c; - num_found++; - - memcpy(&facets[i], &facets[ch->num_facets - 1], 3 * sizeof(int8_t)); - ch->num_facets--; - i--; - } - } - - if (num_found + num_inverted != 4) - return PTM_NO_ERROR; - - for (int i=0;inum_facets][0] = i0; - facets[ch->num_facets][1] = b; - facets[ch->num_facets][2] = c; - ch->num_facets++; - - facets[ch->num_facets][0] = a; - facets[ch->num_facets][1] = i0; - facets[ch->num_facets][2] = c; - ch->num_facets++; - - facets[ch->num_facets][0] = a; - facets[ch->num_facets][1] = b; - facets[ch->num_facets][2] = i0; - ch->num_facets++; - } - - _max_degree = graph_degree(ch->num_facets, facets, num_nbrs, degree); - if (_max_degree > max_degree) - return PTM_NO_ERROR; - - double normalized[PTM_MAX_POINTS][3]; - subtract_barycentre(num_nbrs + 1, points, normalized); - - int8_t code[2 * PTM_MAX_EDGES]; - int8_t colours[PTM_MAX_POINTS] = {1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}; - int8_t canonical_labelling[PTM_MAX_POINTS]; - uint64_t hash = 0; - ret = canonical_form_coloured(ch->num_facets, facets, num_nbrs, degree, colours, canonical_labelling, &code[0], &hash); - if (ret != PTM_NO_ERROR) - return ret; - - if (flags & PTM_CHECK_DCUB) check_graphs(&structure_dcub, hash, canonical_labelling, normalized, res); - if (flags & PTM_CHECK_DHEX) check_graphs(&structure_dhex, hash, canonical_labelling, normalized, res); - - return PTM_NO_ERROR; -} - diff --git a/src/USER-PTM/structure_matcher.h b/src/USER-PTM/structure_matcher.h deleted file mode 100644 index 25e80a94e1..0000000000 --- a/src/USER-PTM/structure_matcher.h +++ /dev/null @@ -1,21 +0,0 @@ -#ifndef STRUCTURE_MATCHER_H -#define STRUCTURE_MATCHER_H - -#include "initialize_data.h" -#include "ptm_constants.h" - -typedef struct -{ - double rmsd; - double scale; - double q[4]; //rotation in quaternion form (rigid body transformation) - int8_t mapping[PTM_MAX_POINTS]; - const refdata_t* ref_struct; -} result_t; - -int match_general(const refdata_t* s, double (*ch_points)[3], double (*points)[3], convexhull_t* ch, result_t* res); -int match_fcc_hcp_ico(double (*ch_points)[3], double (*points)[3], int32_t flags, convexhull_t* ch, result_t* res); -int match_dcub_dhex(double (*ch_points)[3], double (*points)[3], int32_t flags, convexhull_t* ch, result_t* res); - -#endif - From 5aeba421bb8a150f109dc5ad5510e9686cd1dbb9 Mon Sep 17 00:00:00 2001 From: ckadding Date: Thu, 20 Sep 2018 09:15:43 -0400 Subject: [PATCH 182/302] Add compute_pressure_cylinder .cpp and .h files --- src/USER-MISC/compute_pressure_cylinder.cpp | 493 ++++++++++++++++++++ src/USER-MISC/compute_pressure_cylinder.h | 74 +++ 2 files changed, 567 insertions(+) create mode 100644 src/USER-MISC/compute_pressure_cylinder.cpp create mode 100644 src/USER-MISC/compute_pressure_cylinder.h diff --git a/src/USER-MISC/compute_pressure_cylinder.cpp b/src/USER-MISC/compute_pressure_cylinder.cpp new file mode 100644 index 0000000000..bae6398691 --- /dev/null +++ b/src/USER-MISC/compute_pressure_cylinder.cpp @@ -0,0 +1,493 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "math.h" +#include "string.h" +#include "stdlib.h" +#include "compute_pressure_cylinder.h" +#include "atom.h" +#include "update.h" +#include "force.h" +#include "pair.h" +#include "neighbor.h" +#include "neigh_request.h" +#include "neigh_list.h" +#include "group.h" +#include "memory.h" +#include "error.h" + +using namespace LAMMPS_NS; + +static const char cite_compute_pressure_cylinder[] = + "compute pressure/cylinder:\n\n" + "@Article{Addington,\n" + " author = {C. K. Addington, Y. Long, K. E. Gubbins},\n" + " title = {The pressure in interfaces having cylindrical geometry},\n" + " journal = {J.~Chem.~Phys.},\n" + " year = 2018,\n" + " volume = 149,\n" + " pages = {084109}\n" + "}\n\n"; + +if (lmp->citeme) lmp->citeme->add(cite_compute_pressure_cylinder); + +/*+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Calculate the configurational components of the pressure tensor in + cylindrical geometry, according to the formulation of Addington et al. (2018) + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */ + +ComputePressureCyl::ComputePressureCyl(LAMMPS *lmp, int narg, char **arg) : + Compute(lmp, narg, arg) +{ + if (narg != 7) error->all(FLERR,"Illegal compute pressure/cylinder command"); + + zlo=force->numeric(FLERR,arg[3]); + zhi=force->numeric(FLERR,arg[4]); + Rmax=force->numeric(FLERR,arg[5]); + bin_width=force->numeric(FLERR,arg[6]); + + nbins=(int)(Rmax/bin_width); + + nzbins=(int)((zhi-zlo)/bin_width); + + array_flag=1; + vector_flag=0; + extarray=0; + size_array_cols = 5; // r, number density, Pr, Pphi, Pz + size_array_rows = nbins; + + Pr_temp = new double[nbins]; + Pr_all = new double[nbins]; + Pz_temp = new double[nbins]; + Pz_all = new double[nbins]; + Pphi_temp = new double[nbins]; + Pphi_all = new double[nbins]; + R = new double[nbins]; + R2 = new double[nbins]; + PrAinv = new double[nbins]; + PzAinv = new double[nbins]; + Rinv = new double[nbins]; + binz = new double[nzbins]; + + R2kin = new double[nbins]; + density_temp = new double[nbins]; + invVbin = new double[nbins]; + density_all = new double[nbins]; + + memory->create(array,nbins,5,"PN:array"); + + nphi=360; + tangent = new double[nphi]; + ephi_x = new double[nphi]; + ephi_y = new double[nphi]; + + nktv2p = force->nktv2p; + +} + +/* ---------------------------------------------------------------------- */ + +ComputePressureCyl::~ComputePressureCyl() +{ + // count all of these for memory usage + memory->destroy(array); + delete [] R; + delete [] Rinv; + delete [] R2; + delete [] R2kin; + delete [] invVbin; + delete [] density_temp; + delete [] density_all; + delete [] tangent; + delete [] ephi_x; + delete [] ephi_y; + delete [] Pr_temp; + delete [] Pr_all; + delete [] Pz_temp; + delete [] Pz_all; + delete [] Pphi_temp; + delete [] Pphi_all; + delete [] PrAinv; + delete [] PzAinv; + delete [] binz; +} + +/* ---------------------------------------------------------------------- */ + +void ComputePressureCyl::init() +{ + if (force->pair == NULL) + error->all(FLERR,"No pair style is defined for compute pressure/cylinder"); + if (force->pair->single_enable == 0) + error->all(FLERR,"Pair style does not support compute pressure/cylinder"); + + double phi; + + for (int iphi=0;iphirequest(this,instance_me); + neighbor->requests[irequest]->pair = 0; + neighbor->requests[irequest]->compute = 1; + neighbor->requests[irequest]->occasional = 1; + + for (int zzz=0;zzzntimestep; + + int ibin; + + // clear pressures + for (ibin=0;ibinx; + tagint *tag = atom->tag; + int *type = atom->type; + int *mask = atom->mask; + int nlocal = atom->nlocal; + double *special_coul = force->special_coul; + double *special_lj = force->special_lj; + int newton_pair = force->newton_pair; + + // invoke half neighbor list (will copy or build if necessary) + neighbor->build_one(list); + + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + // calculate number density (by radius) + double temp_R2; + for (i=0;izlo) + { + temp_R2=x[i][0]*x[i][0]+x[i][1]*x[i][1]; + if (temp_R2>R2kin[nbins-1]) continue; // outside of Rmax + + for (j=0;jpair; + double **cutsq = force->pair->cutsq; + + double r1=0.0; + double r2=0.0; + double risq,rjsq; + double ri,rj,rij,fij; + double A,B,C,Bsq,A2inv,A4,D; + double alpha1,alpha2,aij; + double xi,yi,zi,dx,dy,dz; + double m,xR,yR,zR,fn; + double alpha,xL,yL,zL,L2,ftphi,ftz; + double sqrtD; + double lower_z,upper_z; + + for (ii = 0; ii < inum; ii++) + { + i = ilist[ii]; + if (!(mask[i] & groupbit)) continue; + + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + itag = tag[i]; + itype = type[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + + r1=x[i][0]*x[i][0]+x[i][1]*x[i][1]; + + for (jj = 0; jj < jnum; jj++) + { + j = jlist[jj]; + factor_lj = special_lj[sbmask(j)]; + factor_coul = special_coul[sbmask(j)]; + j &= NEIGHMASK; + + if (!(mask[j] & groupbit)) continue; + + // itag = jtag is possible for long cutoffs that include images of self + // do calculation only on appropriate processor + if (newton_pair == 0 && j >= nlocal) + { + jtag = tag[j]; + if (itag > jtag) + { + if ((itag+jtag) % 2 == 0) continue; + } + else if (itag < jtag) + { + if ((itag+jtag) % 2 == 1) continue; + } + else + { + if (x[j][2] < ztmp) continue; + if (x[j][2] == ztmp) + { + if (x[j][1] < ytmp) continue; + if (x[j][1] == ytmp && x[j][0] < xtmp) continue; + } + } + } + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + + r2=x[j][0]*x[j][0]+x[j][1]*x[j][1]; + + // ri is smaller of r1 and r2 + if (r2= cutsq[itype][jtype]) continue; + + eng = pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair); + + A=dx*dx+dy*dy; + B=2.0*(xi*dx+yi*dy); + + // normal pressure contribution P_rhorho + for (ibin=0;ibin0.0 && alpha1<1.0) + { + zR=zi+alpha1*dz; + if (zRzlo) + { + xR=xi+alpha1*dx; + yR=yi+alpha1*dy; + fn=fpair*fabs(xR*dx+yR*dy); + + Pr_temp[ibin]+=fn; + } + } + if (alpha2>0.0 && alpha2<1.0) + { + zR=zi+alpha2*dz; + if (zRzlo) + { + xR=xi+alpha2*dx; + yR=yi+alpha2*dy; + fn=fpair*fabs(xR*dx+yR*dy); + + Pr_temp[ibin]+=fn; + } + } + } + + // azimuthal pressure contribution (P_phiphi) + for (int iphi=0;iphi=1.0 || alpha<=0.0) continue; + + // no contribution (outside of averaging region) + zL=zi+alpha*dz; + if (zL>zhi || zLR2kin[nbins-1]) continue; + + ftphi=fabs(dx*ephi_x[iphi]+dy*ephi_y[iphi])*fpair; + + // add to appropriate bin + for (ibin=0;ibinbinz[zbin] && x[j][2]>binz[zbin]) continue; + if (x[i][2]R2kin[nbins-1]) continue; + + ftz=fabs(dz)*fpair; + + // add to appropriate bin + for (ibin=0;ibin Date: Thu, 20 Sep 2018 09:16:58 -0400 Subject: [PATCH 183/302] Add compute_pressure_cylinder documentation --- doc/src/compute_pressure_cylinder.txt | 64 +++++++++++++++++++++++++++ 1 file changed, 64 insertions(+) create mode 100644 doc/src/compute_pressure_cylinder.txt diff --git a/doc/src/compute_pressure_cylinder.txt b/doc/src/compute_pressure_cylinder.txt new file mode 100644 index 0000000000..c6d97e7958 --- /dev/null +++ b/doc/src/compute_pressure_cylinder.txt @@ -0,0 +1,64 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +compute pressure/cylinder command :h3 + +[Syntax:] + +compute ID group-ID pressure/cylinder zlo zhi Rmax bin_width :pre + +ID, group-ID are documented in "compute"_compute.html command +pressure/cylinder = style name of this compute command +zlo = minimum z-boundary for cylinder +zhi = maximum z-boundary for cylinder +Rmax = maximum radius to perform calculation to +bin_width = width of radial bins to use for calculation :ul + +[Examples:] + +compute 1 all pressure/cylinder -10.0 10.0 15.0 0.25 :pre + +[Description:] + +Define a computation that calculates the pressure tensor of a +system in cylindrical coordinates, as discussed in "(Addington)"_#Addington1. +This is useful for systems with a single axis of rotational symmetry, +such as cylindrical micelles or carbon nanotubes. The compute splits +the system into radial, cylindrical-shell-type bins of width bin_width, centered at x=0,y=0, +and calculates the radial (P_rhorho), azimuthal (P_phiphi), and axial (P_zz) components of the configurational pressure +tensor. The local density is also calculated for each bin, so that +the true pressure can be recovered as P_kin+P_conf=density*k*T+P_conf. +The output is a global array with 5 columns; one each for bin radius, +local number density, P_rhorho, P_phiphi, and P_zz. The number of +rows is governed by the values of Rmax and bin_width. Pressure +tensor values are output in pressure units. + +[Output info:] + +This compute calculates a global array with 5 columns and Rmax/bin_width +rows. + +The values calculated by this compute are +"intensive". The pressure values will be in pressure +"units"_units.html. The number density values will be in +inverse volume "units"_units.html. + +[Restrictions:] none + +[Related commands:] + +"compute temp"_compute_temp.html, "compute +stress/atom"_compute_stress_atom.html, +"thermo_style"_thermo_style.html, + +[Default:] none + +:line + +:link(Addington1) +[(Addington)] Addington, Long, Gubbins, J Chem Phys, 149, 084109 (2018). From 6e546ef5af0c734da053d752fe1f25e29d34ffce Mon Sep 17 00:00:00 2001 From: pmla Date: Thu, 20 Sep 2018 14:20:58 -0400 Subject: [PATCH 184/302] added ptm namespace --- src/USER-PTM/ptm_alloy_types.cpp | 3 ++ src/USER-PTM/ptm_alloy_types.h | 4 ++ src/USER-PTM/ptm_canonical_coloured.cpp | 3 ++ src/USER-PTM/ptm_canonical_coloured.h | 3 ++ src/USER-PTM/ptm_convex_hull_incremental.cpp | 3 ++ src/USER-PTM/ptm_convex_hull_incremental.h | 3 ++ src/USER-PTM/ptm_deformation_gradient.cpp | 3 ++ src/USER-PTM/ptm_deformation_gradient.h | 4 ++ src/USER-PTM/ptm_fundamental_mappings.h | 3 ++ src/USER-PTM/ptm_graph_data.cpp | 4 ++ src/USER-PTM/ptm_graph_data.h | 3 ++ src/USER-PTM/ptm_graph_tools.cpp | 4 ++ src/USER-PTM/ptm_graph_tools.h | 4 ++ src/USER-PTM/ptm_index.cpp | 44 ++++++++++---------- src/USER-PTM/ptm_initialize_data.cpp | 26 ++++++------ src/USER-PTM/ptm_initialize_data.h | 3 ++ src/USER-PTM/ptm_neighbour_ordering.cpp | 12 +++--- src/USER-PTM/ptm_neighbour_ordering.h | 4 ++ src/USER-PTM/ptm_normalize_vertices.cpp | 3 ++ src/USER-PTM/ptm_normalize_vertices.h | 4 ++ src/USER-PTM/ptm_polar.cpp | 4 ++ src/USER-PTM/ptm_polar.h | 4 ++ src/USER-PTM/ptm_quat.cpp | 4 ++ src/USER-PTM/ptm_quat.h | 7 ++-- src/USER-PTM/ptm_structure_matcher.cpp | 4 ++ src/USER-PTM/ptm_structure_matcher.h | 5 +++ src/USER-PTM/ptm_voronoi_cell.cpp | 2 +- src/USER-PTM/ptm_voronoi_cell.h | 2 +- src/USER-PTM/ptm_voronoi_config.h | 2 +- 29 files changed, 128 insertions(+), 46 deletions(-) diff --git a/src/USER-PTM/ptm_alloy_types.cpp b/src/USER-PTM/ptm_alloy_types.cpp index e14d06db99..151de3e5b8 100644 --- a/src/USER-PTM/ptm_alloy_types.cpp +++ b/src/USER-PTM/ptm_alloy_types.cpp @@ -2,6 +2,7 @@ #include "ptm_constants.h" #include "ptm_initialize_data.h" +namespace ptm { #define NUM_ALLOY_TYPES 3 static uint32_t typedata[NUM_ALLOY_TYPES][3] = { @@ -99,3 +100,5 @@ int32_t find_alloy_type(const refdata_t* ref, int8_t* mapping, int32_t* numbers) return PTM_ALLOY_NONE; } +} + diff --git a/src/USER-PTM/ptm_alloy_types.h b/src/USER-PTM/ptm_alloy_types.h index 6ea6ed1b8a..559e0a7490 100644 --- a/src/USER-PTM/ptm_alloy_types.h +++ b/src/USER-PTM/ptm_alloy_types.h @@ -3,7 +3,11 @@ #include "ptm_initialize_data.h" +namespace ptm { + int32_t find_alloy_type(const refdata_t* ref, int8_t* mapping, int32_t* numbers); +} + #endif diff --git a/src/USER-PTM/ptm_canonical_coloured.cpp b/src/USER-PTM/ptm_canonical_coloured.cpp index 551f52d7e4..ade8f23b15 100644 --- a/src/USER-PTM/ptm_canonical_coloured.cpp +++ b/src/USER-PTM/ptm_canonical_coloured.cpp @@ -4,6 +4,7 @@ #include "ptm_graph_tools.h" #include "ptm_constants.h" +namespace ptm { static bool weinberg_coloured(int num_nodes, int num_edges, int8_t common[PTM_MAX_NBRS][PTM_MAX_NBRS], int8_t* colours, int8_t* best_code, int8_t* canonical_labelling, int a, int b) { @@ -165,3 +166,5 @@ int canonical_form_coloured(int num_facets, int8_t facets[][3], int num_nodes, i return PTM_NO_ERROR; } +} + diff --git a/src/USER-PTM/ptm_canonical_coloured.h b/src/USER-PTM/ptm_canonical_coloured.h index e71bb08bfc..f8e2a7af5d 100644 --- a/src/USER-PTM/ptm_canonical_coloured.h +++ b/src/USER-PTM/ptm_canonical_coloured.h @@ -3,7 +3,10 @@ #include +namespace ptm { + int canonical_form_coloured(int num_facets, int8_t facets[][3], int num_nodes, int8_t* degree, int8_t* colours, int8_t* canonical_labelling, int8_t* best_code, uint64_t* p_hash); +} #endif diff --git a/src/USER-PTM/ptm_convex_hull_incremental.cpp b/src/USER-PTM/ptm_convex_hull_incremental.cpp index c996b17b58..7c79fd371a 100644 --- a/src/USER-PTM/ptm_convex_hull_incremental.cpp +++ b/src/USER-PTM/ptm_convex_hull_incremental.cpp @@ -6,6 +6,7 @@ #include "ptm_convex_hull_incremental.h" #include "ptm_constants.h" +namespace ptm { #define VISIBLE 1 #define INVISIBLE 2 @@ -361,3 +362,5 @@ int get_convex_hull(int num_points, const double (*points)[3], convexhull_t* ch, return ret; } +} + diff --git a/src/USER-PTM/ptm_convex_hull_incremental.h b/src/USER-PTM/ptm_convex_hull_incremental.h index 563a0c436a..6474723907 100644 --- a/src/USER-PTM/ptm_convex_hull_incremental.h +++ b/src/USER-PTM/ptm_convex_hull_incremental.h @@ -6,6 +6,7 @@ #include #include "ptm_constants.h" +namespace ptm { typedef struct { @@ -23,5 +24,7 @@ typedef struct void add_facet(const double (*points)[3], int a, int b, int c, int8_t* facet, double* plane_normal, double* barycentre); int get_convex_hull(int num_points, const double (*points)[3], convexhull_t* ch, int8_t simplex[][3]); +} + #endif diff --git a/src/USER-PTM/ptm_deformation_gradient.cpp b/src/USER-PTM/ptm_deformation_gradient.cpp index d566d5ca11..fc851920a6 100644 --- a/src/USER-PTM/ptm_deformation_gradient.cpp +++ b/src/USER-PTM/ptm_deformation_gradient.cpp @@ -1,5 +1,6 @@ #include "ptm_deformation_gradient.h" +namespace ptm { void calculate_deformation_gradient(int num_points, const double (*ideal_points)[3], int8_t* mapping, double (*normalized)[3], const double (*penrose)[3], double* F, double* res) { @@ -35,3 +36,5 @@ void calculate_deformation_gradient(int num_points, const double (*ideal_points) } } +} + diff --git a/src/USER-PTM/ptm_deformation_gradient.h b/src/USER-PTM/ptm_deformation_gradient.h index 7decab4b76..32836da44d 100644 --- a/src/USER-PTM/ptm_deformation_gradient.h +++ b/src/USER-PTM/ptm_deformation_gradient.h @@ -4,6 +4,8 @@ #include #include "ptm_constants.h" +namespace ptm { + void calculate_deformation_gradient(int num_points, const double (*ideal_points)[3], int8_t* mapping, double (*normalized)[3], const double (*penrose)[3], double* F, double* res); //sc @@ -137,6 +139,8 @@ const double penrose_dhex[PTM_NUM_POINTS_DHEX][3] = { { 0, 2 * kdcub, -2 * kdcub }, { 2 * kdcub, 0, -2 * kdcub }, }; +} + #endif diff --git a/src/USER-PTM/ptm_fundamental_mappings.h b/src/USER-PTM/ptm_fundamental_mappings.h index 3dd7c39cbb..35fae7f088 100644 --- a/src/USER-PTM/ptm_fundamental_mappings.h +++ b/src/USER-PTM/ptm_fundamental_mappings.h @@ -3,6 +3,8 @@ #include +namespace ptm { + #define NUM_CUBIC_MAPPINGS 24 #define NUM_ICO_MAPPINGS 60 #define NUM_HEX_MAPPINGS 6 @@ -175,6 +177,7 @@ const int8_t mapping_dhex[NUM_DHEX_MAPPINGS][PTM_MAX_POINTS] = { {0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16}, {0, 1, 3, 4, 2, 6, 7, 5, 11, 13, 12, 14, 16, 15, 8, 9, 10}, {0, 1, 4, 2, 3, 7, 5, 6, 14, 15, 16, 8, 10, 9, 11, 13, 12} }; +} #endif diff --git a/src/USER-PTM/ptm_graph_data.cpp b/src/USER-PTM/ptm_graph_data.cpp index a591dbf993..a742c8b339 100644 --- a/src/USER-PTM/ptm_graph_data.cpp +++ b/src/USER-PTM/ptm_graph_data.cpp @@ -1,6 +1,8 @@ #include "ptm_graph_data.h" +namespace ptm { + int8_t automorphisms[65][17] = { { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16}, { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, -1, -1, -1, -1}, @@ -2057,3 +2059,5 @@ graph_t graphs_dhex[NUM_DHEX_GRAPHS] = { }; +} + diff --git a/src/USER-PTM/ptm_graph_data.h b/src/USER-PTM/ptm_graph_data.h index 11f46a471f..251c82d2f5 100644 --- a/src/USER-PTM/ptm_graph_data.h +++ b/src/USER-PTM/ptm_graph_data.h @@ -4,6 +4,7 @@ #include #include "ptm_constants.h" +namespace ptm { typedef struct { @@ -33,5 +34,7 @@ extern graph_t graphs_bcc[NUM_BCC_GRAPHS]; extern graph_t graphs_dcub[NUM_DCUB_GRAPHS]; extern graph_t graphs_dhex[NUM_DHEX_GRAPHS]; +} + #endif diff --git a/src/USER-PTM/ptm_graph_tools.cpp b/src/USER-PTM/ptm_graph_tools.cpp index 89d07fc87a..f6fd34d097 100644 --- a/src/USER-PTM/ptm_graph_tools.cpp +++ b/src/USER-PTM/ptm_graph_tools.cpp @@ -4,6 +4,8 @@ #include "ptm_constants.h" +namespace ptm { + bool build_facet_map(int num_facets, int8_t facets[][3], int8_t common[PTM_MAX_NBRS][PTM_MAX_NBRS]) { memset(common, -1, sizeof(int8_t) * PTM_MAX_NBRS * PTM_MAX_NBRS); @@ -50,3 +52,5 @@ int graph_degree(int num_facets, int8_t facets[][3], int num_nodes, int8_t* degr return max_degree; } +} + diff --git a/src/USER-PTM/ptm_graph_tools.h b/src/USER-PTM/ptm_graph_tools.h index 78934e87c1..7befad526b 100644 --- a/src/USER-PTM/ptm_graph_tools.h +++ b/src/USER-PTM/ptm_graph_tools.h @@ -4,8 +4,12 @@ #include #include "ptm_constants.h" +namespace ptm { + bool build_facet_map(int num_facets, int8_t facets[][3], int8_t common[PTM_MAX_NBRS][PTM_MAX_NBRS]); int graph_degree(int num_facets, int8_t facets[][3], int num_nodes, int8_t* degree); +} + #endif diff --git a/src/USER-PTM/ptm_index.cpp b/src/USER-PTM/ptm_index.cpp index 7b6618848e..24998dadd0 100644 --- a/src/USER-PTM/ptm_index.cpp +++ b/src/USER-PTM/ptm_index.cpp @@ -36,13 +36,13 @@ static double calculate_lattice_constant(int type, double interatomic_distance) static int rotate_into_fundamental_zone(int type, double* q) { - if (type == PTM_MATCH_SC) return rotate_quaternion_into_cubic_fundamental_zone(q); - if (type == PTM_MATCH_FCC) return rotate_quaternion_into_cubic_fundamental_zone(q); - if (type == PTM_MATCH_BCC) return rotate_quaternion_into_cubic_fundamental_zone(q); - if (type == PTM_MATCH_ICO) return rotate_quaternion_into_icosahedral_fundamental_zone(q); - if (type == PTM_MATCH_HCP) return rotate_quaternion_into_hcp_fundamental_zone(q); - if (type == PTM_MATCH_DCUB) return rotate_quaternion_into_diamond_cubic_fundamental_zone(q); - if (type == PTM_MATCH_DHEX) return rotate_quaternion_into_diamond_hexagonal_fundamental_zone(q); + if (type == PTM_MATCH_SC) return ptm::rotate_quaternion_into_cubic_fundamental_zone(q); + if (type == PTM_MATCH_FCC) return ptm::rotate_quaternion_into_cubic_fundamental_zone(q); + if (type == PTM_MATCH_BCC) return ptm::rotate_quaternion_into_cubic_fundamental_zone(q); + if (type == PTM_MATCH_ICO) return ptm::rotate_quaternion_into_icosahedral_fundamental_zone(q); + if (type == PTM_MATCH_HCP) return ptm::rotate_quaternion_into_hcp_fundamental_zone(q); + if (type == PTM_MATCH_DCUB) return ptm::rotate_quaternion_into_diamond_cubic_fundamental_zone(q); + if (type == PTM_MATCH_DHEX) return ptm::rotate_quaternion_into_diamond_hexagonal_fundamental_zone(q); return -1; } @@ -52,8 +52,8 @@ static void order_points(ptm_local_handle_t local_handle, int num_points, double if (topological_ordering) { double normalized_points[PTM_MAX_INPUT_POINTS][3]; - normalize_vertices(num_points, unpermuted_points, normalized_points); - int ret = calculate_neighbour_ordering((void*)local_handle, num_points, (const double (*)[3])normalized_points, ordering); + ptm::normalize_vertices(num_points, unpermuted_points, normalized_points); + int ret = ptm::calculate_neighbour_ordering((void*)local_handle, num_points, (const double (*)[3])normalized_points, ordering); if (ret != 0) topological_ordering = false; } @@ -71,7 +71,7 @@ static void order_points(ptm_local_handle_t local_handle, int num_points, double } } -static void output_data(result_t* res, int num_points, int32_t* unpermuted_numbers, double (*points)[3], int32_t* numbers, int8_t* ordering, +static void output_data(ptm::result_t* res, int num_points, int32_t* unpermuted_numbers, double (*points)[3], int32_t* numbers, int8_t* ordering, int32_t* p_type, int32_t* p_alloy_type, double* p_scale, double* p_rmsd, double* q, double* F, double* F_res, double* U, double* P, int8_t* mapping, double* p_interatomic_distance, double* p_lattice_constant) { @@ -82,13 +82,13 @@ static void output_data(result_t* res, int num_points, int32_t* unpermuted_numbe if (mapping != NULL) memset(mapping, -1, num_points * sizeof(int8_t)); - const refdata_t* ref = res->ref_struct; + const ptm::refdata_t* ref = res->ref_struct; if (ref == NULL) return; *p_type = ref->type; if (p_alloy_type != NULL && unpermuted_numbers != NULL) - *p_alloy_type = find_alloy_type(ref, res->mapping, numbers); + *p_alloy_type = ptm::find_alloy_type(ref, res->mapping, numbers); int bi = rotate_into_fundamental_zone(ref->type, res->q); int8_t temp[PTM_MAX_POINTS]; @@ -101,17 +101,17 @@ static void output_data(result_t* res, int num_points, int32_t* unpermuted_numbe { double scaled_points[PTM_MAX_INPUT_POINTS][3]; - subtract_barycentre(ref->num_nbrs + 1, points, scaled_points); + ptm::subtract_barycentre(ref->num_nbrs + 1, points, scaled_points); for (int i = 0;inum_nbrs + 1;i++) { scaled_points[i][0] *= res->scale; scaled_points[i][1] *= res->scale; scaled_points[i][2] *= res->scale; } - calculate_deformation_gradient(ref->num_nbrs + 1, ref->points, res->mapping, scaled_points, ref->penrose, F, F_res); + ptm::calculate_deformation_gradient(ref->num_nbrs + 1, ref->points, res->mapping, scaled_points, ref->penrose, F, F_res); if (P != NULL && U != NULL) - polar_decomposition_3x3(F, false, U, P); + ptm::polar_decomposition_3x3(F, false, U, P); } if (mapping != NULL) @@ -156,7 +156,7 @@ int ptm_index( ptm_local_handle_t local_handle, int32_t flags, assert(num_points >= PTM_NUM_POINTS_DCUB); int ret = 0; - result_t res; + ptm::result_t res; res.ref_struct = NULL; res.rmsd = INFINITY; @@ -168,32 +168,32 @@ int ptm_index( ptm_local_handle_t local_handle, int32_t flags, double dpoints[PTM_MAX_POINTS][3]; int32_t dnumbers[PTM_MAX_POINTS]; - convexhull_t ch; + ptm::convexhull_t ch; double ch_points[PTM_MAX_INPUT_POINTS][3]; if (flags & (PTM_CHECK_SC | PTM_CHECK_FCC | PTM_CHECK_HCP | PTM_CHECK_ICO | PTM_CHECK_BCC)) { int num_lpoints = std::min(std::min(PTM_MAX_POINTS, 20), num_points); order_points(local_handle, num_lpoints, unpermuted_points, unpermuted_numbers, topological_ordering, ordering, points, numbers); - normalize_vertices(num_lpoints, points, ch_points); + ptm::normalize_vertices(num_lpoints, points, ch_points); ch.ok = false; if (flags & PTM_CHECK_SC) - ret = match_general(&structure_sc, ch_points, points, &ch, &res); + ret = match_general(&ptm::structure_sc, ch_points, points, &ch, &res); if (flags & (PTM_CHECK_FCC | PTM_CHECK_HCP | PTM_CHECK_ICO)) ret = match_fcc_hcp_ico(ch_points, points, flags, &ch, &res); if (flags & PTM_CHECK_BCC) - ret = match_general(&structure_bcc, ch_points, points, &ch, &res); + ret = match_general(&ptm::structure_bcc, ch_points, points, &ch, &res); } if (flags & (PTM_CHECK_DCUB | PTM_CHECK_DHEX)) { - ret = calculate_diamond_neighbour_ordering(num_points, unpermuted_points, unpermuted_numbers, dordering, dpoints, dnumbers); + ret = ptm::calculate_diamond_neighbour_ordering(num_points, unpermuted_points, unpermuted_numbers, dordering, dpoints, dnumbers); if (ret == 0) { - normalize_vertices(PTM_NUM_NBRS_DCUB + 1, dpoints, ch_points); + ptm::normalize_vertices(PTM_NUM_NBRS_DCUB + 1, dpoints, ch_points); ch.ok = false; ret = match_dcub_dhex(ch_points, dpoints, flags, &ch, &res); diff --git a/src/USER-PTM/ptm_initialize_data.cpp b/src/USER-PTM/ptm_initialize_data.cpp index 6157ff862f..8d96e2a2b7 100644 --- a/src/USER-PTM/ptm_initialize_data.cpp +++ b/src/USER-PTM/ptm_initialize_data.cpp @@ -14,20 +14,20 @@ static void make_facets_clockwise(int num_facets, int8_t (*facets)[3], const dou double origin[3] = {0, 0, 0}; for (int i = 0;inum_graphs;i++) { int8_t code[2 * PTM_MAX_EDGES]; int8_t degree[PTM_MAX_NBRS]; - int _max_degree = graph_degree(s->num_facets, s->graphs[i].facets, s->num_nbrs, degree); + int _max_degree = ptm::graph_degree(s->num_facets, s->graphs[i].facets, s->num_nbrs, degree); assert(_max_degree <= s->max_degree); make_facets_clockwise(s->num_facets, s->graphs[i].facets, &s->points[1]); - int ret = canonical_form_coloured(s->num_facets, s->graphs[i].facets, s->num_nbrs, degree, colours, s->graphs[i].canonical_labelling, (int8_t*)&code[0], &s->graphs[i].hash); + int ret = ptm::canonical_form_coloured(s->num_facets, s->graphs[i].facets, s->num_nbrs, degree, colours, s->graphs[i].canonical_labelling, (int8_t*)&code[0], &s->graphs[i].hash); if (ret != 0) return ret; } @@ -44,13 +44,13 @@ int ptm_initialize_global() int8_t colours[PTM_MAX_POINTS] = {0}; int8_t dcolours[PTM_MAX_POINTS] = {1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}; - int ret = initialize_graphs(&structure_sc, colours); - ret |= initialize_graphs(&structure_fcc, colours); - ret |= initialize_graphs(&structure_hcp, colours); - ret |= initialize_graphs(&structure_ico, colours); - ret |= initialize_graphs(&structure_bcc, colours); - ret |= initialize_graphs(&structure_dcub, dcolours); - ret |= initialize_graphs(&structure_dhex, dcolours); + int ret = initialize_graphs(&ptm::structure_sc, colours); + ret |= initialize_graphs(&ptm::structure_fcc, colours); + ret |= initialize_graphs(&ptm::structure_hcp, colours); + ret |= initialize_graphs(&ptm::structure_ico, colours); + ret |= initialize_graphs(&ptm::structure_bcc, colours); + ret |= initialize_graphs(&ptm::structure_dcub, dcolours); + ret |= initialize_graphs(&ptm::structure_dhex, dcolours); if (ret == PTM_NO_ERROR) ptm_initialized = true; @@ -61,11 +61,11 @@ int ptm_initialize_global() ptm_local_handle_t ptm_initialize_local() { assert(ptm_initialized); - return (ptm_local_handle_t)voronoi_initialize_local(); + return (ptm_local_handle_t)ptm::voronoi_initialize_local(); } void ptm_uninitialize_local(ptm_local_handle_t ptr) { - voronoi_uninitialize_local(ptr); + ptm::voronoi_uninitialize_local(ptr); } diff --git a/src/USER-PTM/ptm_initialize_data.h b/src/USER-PTM/ptm_initialize_data.h index f381dd864b..5374fbf7d0 100644 --- a/src/USER-PTM/ptm_initialize_data.h +++ b/src/USER-PTM/ptm_initialize_data.h @@ -11,6 +11,8 @@ #include "ptm_convex_hull_incremental.h" +namespace ptm { + typedef struct { int type; @@ -35,6 +37,7 @@ const refdata_t structure_bcc = { PTM_MATCH_BCC, 14, 24, 8, NUM_BCC_GRAPHS, N const refdata_t structure_dcub = { PTM_MATCH_DCUB, 16, 28, 8, NUM_DCUB_GRAPHS, NUM_DCUB_MAPPINGS, graphs_dcub, ptm_template_dcub, penrose_dcub, mapping_dcub }; const refdata_t structure_dhex = { PTM_MATCH_DHEX, 16, 28, 8, NUM_DHEX_GRAPHS, NUM_DHEX_MAPPINGS, graphs_dhex, ptm_template_dhex, penrose_dhex, mapping_dhex }; +} #ifdef __cplusplus extern "C" { diff --git a/src/USER-PTM/ptm_neighbour_ordering.cpp b/src/USER-PTM/ptm_neighbour_ordering.cpp index 6b5ac9601a..c77a779c68 100644 --- a/src/USER-PTM/ptm_neighbour_ordering.cpp +++ b/src/USER-PTM/ptm_neighbour_ordering.cpp @@ -5,9 +5,9 @@ #include #include "ptm_constants.h" #include "ptm_voronoi_cell.h" -using namespace voro; +namespace ptm { typedef struct { @@ -31,7 +31,7 @@ static bool sorthelper_compare(sorthelper_t const& a, sorthelper_t const& b) } //todo: change voronoi code to return errors rather than exiting -static int calculate_voronoi_face_areas(int num_points, const double (*_points)[3], double* normsq, double max_norm, voronoicell_neighbor* v, std::vector& nbr_indices, std::vector& face_areas) +static int calculate_voronoi_face_areas(int num_points, const double (*_points)[3], double* normsq, double max_norm, ptm_voro::voronoicell_neighbor* v, std::vector& nbr_indices, std::vector& face_areas) { const double k = 1000 * max_norm; //todo: reduce this constant v->init(-k,k,-k,k,-k,k); @@ -53,7 +53,7 @@ int calculate_neighbour_ordering(void* _voronoi_handle, int num_points, const do { assert(num_points <= PTM_MAX_INPUT_POINTS); - voronoicell_neighbor* voronoi_handle = (voronoicell_neighbor*)_voronoi_handle; + ptm_voro::voronoicell_neighbor* voronoi_handle = (ptm_voro::voronoicell_neighbor*)_voronoi_handle; double max_norm = 0; double points[PTM_MAX_INPUT_POINTS][3]; @@ -116,13 +116,13 @@ int calculate_neighbour_ordering(void* _voronoi_handle, int num_points, const do void* voronoi_initialize_local() { - voronoicell_neighbor* ptr = new voronoicell_neighbor; + ptm_voro::voronoicell_neighbor* ptr = new ptm_voro::voronoicell_neighbor; return (void*)ptr; } void voronoi_uninitialize_local(void* _ptr) { - voronoicell_neighbor* ptr = (voronoicell_neighbor*)_ptr; + ptm_voro::voronoicell_neighbor* ptr = (ptm_voro::voronoicell_neighbor*)_ptr; delete ptr; } @@ -201,3 +201,5 @@ int calculate_diamond_neighbour_ordering( int num_points, double (*unpermuted_po return 0; } +} + diff --git a/src/USER-PTM/ptm_neighbour_ordering.h b/src/USER-PTM/ptm_neighbour_ordering.h index ce4dfca2c0..e43ced9fd5 100644 --- a/src/USER-PTM/ptm_neighbour_ordering.h +++ b/src/USER-PTM/ptm_neighbour_ordering.h @@ -1,6 +1,8 @@ #ifndef PTM_NEIGHBOUR_ORDERING_H #define PTM_NEIGHBOUR_ORDERING_H +namespace ptm { + int calculate_neighbour_ordering(void* voronoi_handle, int num_points, const double (*_points)[3], int8_t* ordering); int calculate_diamond_neighbour_ordering( int num_points, double (*unpermuted_points)[3], int32_t* unpermuted_numbers, @@ -9,5 +11,7 @@ int calculate_diamond_neighbour_ordering( int num_points, double (*unpermuted_po void* voronoi_initialize_local(); void voronoi_uninitialize_local(void* ptr); +} + #endif diff --git a/src/USER-PTM/ptm_normalize_vertices.cpp b/src/USER-PTM/ptm_normalize_vertices.cpp index 61dca5006f..22e3c1e670 100644 --- a/src/USER-PTM/ptm_normalize_vertices.cpp +++ b/src/USER-PTM/ptm_normalize_vertices.cpp @@ -1,5 +1,6 @@ #include +namespace ptm { void subtract_barycentre(int num, double (*points)[3], double (*normalized)[3]) { @@ -53,3 +54,5 @@ double normalize_vertices(int num, double (*points)[3], double (*normalized)[3]) return scale; } +} + diff --git a/src/USER-PTM/ptm_normalize_vertices.h b/src/USER-PTM/ptm_normalize_vertices.h index 2c7b722752..dc93db94a3 100644 --- a/src/USER-PTM/ptm_normalize_vertices.h +++ b/src/USER-PTM/ptm_normalize_vertices.h @@ -1,8 +1,12 @@ #ifndef PTM_NORMALIZE_VERTICES_H #define PTM_NORMALIZE_VERTICES_H +namespace ptm { + void subtract_barycentre(int num, double (*points)[3], double (*normalized)[3]); double normalize_vertices(int num, double (*points)[3], double (*normalized)[3]); +} + #endif diff --git a/src/USER-PTM/ptm_polar.cpp b/src/USER-PTM/ptm_polar.cpp index 9089b327b9..fa199ca656 100644 --- a/src/USER-PTM/ptm_polar.cpp +++ b/src/USER-PTM/ptm_polar.cpp @@ -91,6 +91,8 @@ #include "ptm_quat.h" +namespace ptm { + static void matmul_3x3(double* A, double* x, double* b) { b[0] = A[0] * x[0] + A[1] * x[3] + A[2] * x[6]; @@ -335,3 +337,5 @@ int FastCalcRMSDAndRotation(double *A, double E0, double *p_nrmsdsq, double *q, return 0; } +} + diff --git a/src/USER-PTM/ptm_polar.h b/src/USER-PTM/ptm_polar.h index d5aa3d9540..15d1f185b7 100644 --- a/src/USER-PTM/ptm_polar.h +++ b/src/USER-PTM/ptm_polar.h @@ -4,9 +4,13 @@ #include #include +namespace ptm { + int polar_decomposition_3x3(double* _A, bool right_sided, double* U, double* P); void InnerProduct(double *A, int num, const double (*coords1)[3], double (*coords2)[3], int8_t* permutation); int FastCalcRMSDAndRotation(double *A, double E0, double *p_nrmsdsq, double *q, double* U); +} + #endif diff --git a/src/USER-PTM/ptm_quat.cpp b/src/USER-PTM/ptm_quat.cpp index f55aff3d2b..376cc74901 100644 --- a/src/USER-PTM/ptm_quat.cpp +++ b/src/USER-PTM/ptm_quat.cpp @@ -3,6 +3,8 @@ #include +namespace ptm { + #define SIGN(x) (x >= 0 ? 1 : -1) #define MIN(X, Y) (((X) < (Y)) ? (X) : (Y)) #define MAX(X, Y) (((X) > (Y)) ? (X) : (Y)) @@ -394,3 +396,5 @@ double quat_disorientation_icosahedral(double* q0, double* q1) return acos(quat_quick_disorientation_icosahedral(q0, q1)); } +} + diff --git a/src/USER-PTM/ptm_quat.h b/src/USER-PTM/ptm_quat.h index 381c3ce876..74caa2c62c 100644 --- a/src/USER-PTM/ptm_quat.h +++ b/src/USER-PTM/ptm_quat.h @@ -1,6 +1,8 @@ #ifndef PTM_QUAT_H #define PTM_QUAT_H +namespace ptm { + int rotate_quaternion_into_cubic_fundamental_zone(double* q); int rotate_quaternion_into_diamond_cubic_fundamental_zone(double* q); int rotate_quaternion_into_icosahedral_fundamental_zone(double* q); @@ -25,8 +27,7 @@ double quat_disorientation_diamond_hexagonal(double* q0, double* q1); double quat_quick_disorientation_icosahedral(double* q0, double* q1); double quat_disorientation_icosahedral(double* q0, double* q1); +} + #endif - - - diff --git a/src/USER-PTM/ptm_structure_matcher.cpp b/src/USER-PTM/ptm_structure_matcher.cpp index 7eb0a44143..a86b3670ce 100644 --- a/src/USER-PTM/ptm_structure_matcher.cpp +++ b/src/USER-PTM/ptm_structure_matcher.cpp @@ -15,6 +15,8 @@ #include "ptm_constants.h" +namespace ptm { + static double calc_rmsd(int num_points, const double (*ideal_points)[3], double (*normalized)[3], int8_t* mapping, double G1, double G2, double E0, double* q, double* p_scale) { @@ -292,3 +294,5 @@ int match_dcub_dhex(double (*ch_points)[3], double (*points)[3], int32_t flags, return PTM_NO_ERROR; } +} + diff --git a/src/USER-PTM/ptm_structure_matcher.h b/src/USER-PTM/ptm_structure_matcher.h index 4b6f969597..ffaed78e82 100644 --- a/src/USER-PTM/ptm_structure_matcher.h +++ b/src/USER-PTM/ptm_structure_matcher.h @@ -4,6 +4,9 @@ #include "ptm_initialize_data.h" #include "ptm_constants.h" + +namespace ptm { + typedef struct { double rmsd; @@ -17,5 +20,7 @@ int match_general(const refdata_t* s, double (*ch_points)[3], double (*points)[3 int match_fcc_hcp_ico(double (*ch_points)[3], double (*points)[3], int32_t flags, convexhull_t* ch, result_t* res); int match_dcub_dhex(double (*ch_points)[3], double (*points)[3], int32_t flags, convexhull_t* ch, result_t* res); +} + #endif diff --git a/src/USER-PTM/ptm_voronoi_cell.cpp b/src/USER-PTM/ptm_voronoi_cell.cpp index 6503ea16c6..ffd7a95ea2 100644 --- a/src/USER-PTM/ptm_voronoi_cell.cpp +++ b/src/USER-PTM/ptm_voronoi_cell.cpp @@ -15,7 +15,7 @@ #include "ptm_voronoi_config.h" #include "ptm_voronoi_cell.h" -namespace voro { +namespace ptm_voro { inline void voro_fatal_error(const char *p,int status) { fprintf(stderr,"voro++: %s\n",p); diff --git a/src/USER-PTM/ptm_voronoi_cell.h b/src/USER-PTM/ptm_voronoi_cell.h index 80a0501b3c..e0284bc56f 100644 --- a/src/USER-PTM/ptm_voronoi_cell.h +++ b/src/USER-PTM/ptm_voronoi_cell.h @@ -17,7 +17,7 @@ #include "ptm_voronoi_config.h" -namespace voro { +namespace ptm_voro { /** \brief A class representing a single Voronoi cell. * diff --git a/src/USER-PTM/ptm_voronoi_config.h b/src/USER-PTM/ptm_voronoi_config.h index 86257e60cc..46c5a4b915 100644 --- a/src/USER-PTM/ptm_voronoi_config.h +++ b/src/USER-PTM/ptm_voronoi_config.h @@ -12,7 +12,7 @@ #ifndef PTM_VOROPP_CONFIG_HH #define PTM_VOROPP_CONFIG_HH -namespace voro { +namespace ptm_voro { // These constants set the initial memory allocation for the Voronoi cell /** The initial memory allocation for the number of vertices. */ From 36c5fb2ec62554996193c6351449feba4e230b33 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 24 Sep 2018 10:33:26 -0400 Subject: [PATCH 185/302] update formatting --- doc/src/pair_coul_shield.txt | 3 ++- doc/src/pair_ilp_graphene_hbn.txt | 22 +++++++++++++--------- doc/src/pair_kolmogorov_crespi_full.txt | 22 ++++++++++++---------- 3 files changed, 27 insertions(+), 20 deletions(-) diff --git a/doc/src/pair_coul_shield.txt b/doc/src/pair_coul_shield.txt index 8b88d07ece..df04e76de9 100644 --- a/doc/src/pair_coul_shield.txt +++ b/doc/src/pair_coul_shield.txt @@ -38,7 +38,8 @@ charge and molecule ID information is included. Where Tap(r_ij) is the taper function which provides a continuous cutoff (up to third derivative) for inter-atomic separations larger than r_c -"(Leven1)"_#Leven3, "(Leven2)"_#Leven4 and "(Maaravi)"_#Maaravi1. Here {lambda} is the shielding parameter that +"(Leven1)"_#Leven3, "(Leven2)"_#Leven4 and "(Maaravi)"_#Maaravi1. +Here {lambda} is the shielding parameter that eliminates the short-range singularity of the classical mono-polar electrostatic interaction expression "(Maaravi)"_#Maaravi1. diff --git a/doc/src/pair_ilp_graphene_hbn.txt b/doc/src/pair_ilp_graphene_hbn.txt index b7d1c2cdb1..f048b16ccf 100644 --- a/doc/src/pair_ilp_graphene_hbn.txt +++ b/doc/src/pair_ilp_graphene_hbn.txt @@ -25,14 +25,15 @@ pair_coeff * * rebo CH.airebo NULL NULL C pair_coeff * * tersoff BNC.tersoff B N NULL pair_coeff * * ilp/graphene/hbn BNCH.ILP B N C pair_coeff 1 1 coul/shield 0.70 -pair_coeff 1 2 coul/shield 0.69498201415576216335 +pair_coeff 1 2 coul/shield 0.695 pair_coeff 2 2 coul/shield 0.69 :pre [Description:] The {ilp/graphene/hbn} style computes the registry-dependent interlayer -potential (ILP) potential as described in "(Leven1)"_#Leven1, "(Leven2)"_#Leven2 and -"(Maaravi)"_#Maaravi2. The normals are calculated in the way as described +potential (ILP) potential as described in "(Leven1)"_#Leven1, +"(Leven2)"_#Leven2 and "(Maaravi)"_#Maaravi2. +The normals are calculated in the way as described in "(Kolmogorov)"_#Kolmogorov2. :c,image(Eqs/pair_ilp_graphene_hbn.jpg) @@ -62,12 +63,15 @@ NOTE: The parameters presented in the parameter file (e.g. BNCH.ILP), are fitted with taper function by setting the cutoff equal to 16.0 Angstrom. Using different cutoff or taper function should be careful. -NOTE: Two new sets of parameters of ILP for two-dimensional hexagonal Materials are presented in "(Ouyang)"_#Ouyang. -These parameters provide a good description in both short- and long-range interaction regimes. -While the old ILP parameters published in "(Leven2)"_#Leven2 and "(Maaravi)"_#Maaravi2 are -only suitable for long-range interaction regime. This feature is essential for simulations -in high pressure regime (i.e., the interlayer distance is smaller than the equilibrium distance). -The benchmark tests and comparison of these parameters can be found in "(Ouyang)"_#Ouyang. +NOTE: Two new sets of parameters of ILP for two-dimensional hexagonal +Materials are presented in "(Ouyang)"_#Ouyang. These parameters provide +a good description in both short- and long-range interaction regimes. +While the old ILP parameters published in "(Leven2)"_#Leven2 and +"(Maaravi)"_#Maaravi2 are only suitable for long-range interaction +regime. This feature is essential for simulations in high pressure +regime (i.e., the interlayer distance is smaller than the equilibrium +distance). The benchmark tests and comparison of these parameters can +be found in "(Ouyang)"_#Ouyang. This potential must be used in combination with hybrid/overlay. Other interactions can be set to zero using pair_style {none}. diff --git a/doc/src/pair_kolmogorov_crespi_full.txt b/doc/src/pair_kolmogorov_crespi_full.txt index 1fe87dd7ee..df9a9696be 100644 --- a/doc/src/pair_kolmogorov_crespi_full.txt +++ b/doc/src/pair_kolmogorov_crespi_full.txt @@ -53,15 +53,17 @@ and {rcut} are included in the parameter file. {S} is designed to facilitate scaling of energies. {rcut} is designed to build the neighbor list for calculating the normals for each atom pair. -NOTE: Two new sets of parameters of KC potential for hydrocarbons, CH.KC (without the taper function) -and CH_taper.KC (with the taper function) are presented in "(Ouyang)"_#Ouyang1. -The energy for the KC potential with the taper function goes continuously to zero at the cutoff. -The parameters in both CH.KC and CH_taper.KC provide a good description in -both short- and long-range interaction regimes. While the original parameters (CC.KC) -published in "(Kolmogorov)"_#Kolmogorov1 are only suitable for long-range interaction regime. -This feature is essential for simulations in high pressure regime -(i.e., the interlayer distance is smaller than the equilibrium distance). -The benchmark tests and comparison of these parameters can be found in "(Ouyang)"_#Ouyang1. +NOTE: Two new sets of parameters of KC potential for hydrocarbons, CH.KC +(without the taper function) and CH_taper.KC (with the taper function) +are presented in "(Ouyang)"_#Ouyang1. The energy for the KC potential +with the taper function goes continuously to zero at the cutoff. The +parameters in both CH.KC and CH_taper.KC provide a good description in +both short- and long-range interaction regimes. While the original +parameters (CC.KC) published in "(Kolmogorov)"_#Kolmogorov1 are only +suitable for long-range interaction regime. This feature is essential +for simulations in high pressure regime (i.e., the interlayer distance +is smaller than the equilibrium distance). The benchmark tests and +comparison of these parameters can be found in "(Ouyang)"_#Ouyang1. This potential must be used in combination with hybrid/overlay. Other interactions can be set to zero using pair_style {none}. @@ -109,4 +111,4 @@ units. [(Kolmogorov)] A. N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005) :link(Ouyang1) -[(Ouyang)] W. Ouyang, D. Mandelli, M. Urbakh and O. Hod, Nano Lett. 18, 6009-6016 (2018). \ No newline at end of file +[(Ouyang)] W. Ouyang, D. Mandelli, M. Urbakh and O. Hod, Nano Lett. 18, 6009-6016 (2018). From aefdcd0f94820a2f41bee0df44bfaeaf0ce5ce43 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sebastian=20H=C3=BCtter?= Date: Tue, 25 Sep 2018 11:14:42 +0200 Subject: [PATCH 186/302] Silence some warnings --- src/USER-MEAMC/meam_dens_init.cpp | 5 ++--- src/USER-MEAMC/meam_funcs.cpp | 2 +- src/USER-MEAMC/pair_meamc.cpp | 9 +++++---- 3 files changed, 8 insertions(+), 8 deletions(-) diff --git a/src/USER-MEAMC/meam_dens_init.cpp b/src/USER-MEAMC/meam_dens_init.cpp index 4bbaa42596..0aa71125c8 100644 --- a/src/USER-MEAMC/meam_dens_init.cpp +++ b/src/USER-MEAMC/meam_dens_init.cpp @@ -101,7 +101,7 @@ MEAM::getscreen(int i, double* scrfcn, double* dscrfcn, double* fcpair, double** double xjtmp, yjtmp, zjtmp, delxik, delyik, delzik, rik2 /*,rik*/; double xktmp, yktmp, zktmp, delxjk, delyjk, delzjk, rjk2 /*,rjk*/; double xik, xjk, sij, fcij, sfcij, dfcij, sikj, dfikj, cikj; - double Cmin, Cmax, delc, /*ebound,*/ rbound, a, coef1, coef2; + double Cmin, Cmax, delc, /*ebound,*/ a, coef1, coef2; double dCikj; double rnorm, fc, dfc, drinv; @@ -129,6 +129,7 @@ MEAM::getscreen(int i, double* scrfcn, double* dscrfcn, double* fcpair, double** rij2 = delxij * delxij + delyij * delyij + delzij * delzij; rij = sqrt(rij2); + const double rbound = this->ebound_meam[elti][eltj] * rij2; if (rij > this->rc_meam) { fcij = 0.0; dfcij = 0.0; @@ -138,7 +139,6 @@ MEAM::getscreen(int i, double* scrfcn, double* dscrfcn, double* fcpair, double** sij = 1.0; // if rjk2 > ebound*rijsq, atom k is definitely outside the ellipse - const double rbound = this->ebound_meam[elti][eltj] * rij2; for (kn = 0; kn < numneigh_full; kn++) { k = firstneigh_full[kn]; eltk = fmap[type[k]]; @@ -193,7 +193,6 @@ MEAM::getscreen(int i, double* scrfcn, double* dscrfcn, double* fcpair, double** if (iszero(sfcij) || iszero(sfcij - 1.0)) goto LABEL_100; - rbound = this->ebound_meam[elti][eltj] * rij2; for (kn = 0; kn < numneigh_full; kn++) { k = firstneigh_full[kn]; if (k == j) continue; diff --git a/src/USER-MEAMC/meam_funcs.cpp b/src/USER-MEAMC/meam_funcs.cpp index 29db27fc4b..1d47dcc1f6 100644 --- a/src/USER-MEAMC/meam_funcs.cpp +++ b/src/USER-MEAMC/meam_funcs.cpp @@ -87,7 +87,7 @@ MEAM::dG_gam(const double gamma, const int ibar, double& dG) const // e.g. gsmooth_factor is 99, {: // gsmooth_switchpoint = -0.99 // G = 0.01*(-0.99/gamma)**99 - double G = 1 / (gsmooth_factor + 1) * pow((gsmooth_switchpoint / gamma), gsmooth_factor); + G = 1 / (gsmooth_factor + 1) * pow((gsmooth_switchpoint / gamma), gsmooth_factor); G = sqrt(G); dG = -gsmooth_factor * G / (2.0 * gamma); return G; diff --git a/src/USER-MEAMC/pair_meamc.cpp b/src/USER-MEAMC/pair_meamc.cpp index ff2a1180b5..b74416a46d 100644 --- a/src/USER-MEAMC/pair_meamc.cpp +++ b/src/USER-MEAMC/pair_meamc.cpp @@ -206,7 +206,7 @@ void PairMEAMC::settings(int narg, char **/*arg*/) void PairMEAMC::coeff(int narg, char **arg) { - int i,j,m,n; + int m,n; if (!allocated) allocate(); @@ -222,7 +222,7 @@ void PairMEAMC::coeff(int narg, char **arg) // elements = list of unique element names if (nelements) { - for (i = 0; i < nelements; i++) delete [] elements[i]; + for (int i = 0; i < nelements; i++) delete [] elements[i]; delete [] elements; delete [] mass; } @@ -231,7 +231,7 @@ void PairMEAMC::coeff(int narg, char **arg) elements = new char*[nelements]; mass = new double[nelements]; - for (i = 0; i < nelements; i++) { + for (int i = 0; i < nelements; i++) { n = strlen(arg[i+3]) + 1; elements[i] = new char[n]; strcpy(elements[i],arg[i+3]); @@ -247,8 +247,9 @@ void PairMEAMC::coeff(int narg, char **arg) // read args that map atom types to MEAM elements // map[i] = which element the Ith atom type is, -1 if not mapped - for (i = 4 + nelements; i < narg; i++) { + for (int i = 4 + nelements; i < narg; i++) { m = i - (4+nelements) + 1; + int j; for (j = 0; j < nelements; j++) if (strcmp(arg[i],elements[j]) == 0) break; if (j < nelements) map[m] = j; From e5ddc909adc491cfb52fe4d7a8d78979918da22b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sebastian=20H=C3=BCtter?= Date: Tue, 25 Sep 2018 14:19:26 +0200 Subject: [PATCH 187/302] Fully zero-init MEAM data structure --- src/USER-MEAMC/meam_impl.cpp | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/src/USER-MEAMC/meam_impl.cpp b/src/USER-MEAMC/meam_impl.cpp index 25c53785e4..d4a47a4f48 100644 --- a/src/USER-MEAMC/meam_impl.cpp +++ b/src/USER-MEAMC/meam_impl.cpp @@ -34,6 +34,19 @@ MEAM::MEAM(Memory* mem) maxneigh = 0; scrfcn = dscrfcn = fcpair = NULL; + + neltypes = 0; + for (int i = 0; i < maxelt; i++) { + Omega_meam[i] = Z_meam[i] = A_meam[i] = rho0_meam[i] = beta0_meam[i] = + beta1_meam[i]= beta2_meam[i] = beta3_meam[i] = + t0_meam[i] = t1_meam[i] = t2_meam[i] = t3_meam[i] = + rho_ref_meam[i] = ibar_meam[i] = ielt_meam[i] = 0.0; + for (int j = 0; j < maxelt; j++) { + lattce_meam[i][j] = FCC; + Ec_meam[i][j] = re_meam[i][j] = alpha_meam[i][j] = delta_meam[i][j] = Ec_meam[i][j] = ebound_meam[i][j] = attrac_meam[i][j] = repuls_meam[i][j] = 0.0; + nn2_meam[i][j] = zbl_meam[i][j] = eltind[i][j] = 0; + } + } } MEAM::~MEAM() From 93e56c113af8b274ea4504a9e3b284058498b5de Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 25 Sep 2018 09:18:11 -0400 Subject: [PATCH 188/302] add USER-PTM to build system --- cmake/CMakeLists.txt | 13 +++++++------ src/Makefile | 2 +- 2 files changed, 8 insertions(+), 7 deletions(-) diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index ce8de0b501..610fb5b57c 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -164,12 +164,13 @@ set(LAMMPS_DEPS) set(LAMMPS_API_DEFINES) set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE GRANULAR - KSPACE MANYBODY MC MEAM MESSAGE MISC MOLECULE PERI REAX REPLICA RIGID SHOCK SPIN SNAP - SRD KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE USER-ATC USER-AWPMD USER-BOCS - USER-CGDNA USER-MESO USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE - USER-EFF USER-FEP USER-H5MD USER-LB USER-MANIFOLD USER-MEAMC USER-MGPT USER-MISC - USER-MOFFF USER-MOLFILE USER-NETCDF USER-PHONON USER-QTB USER-REAXC USER-SCAFACOS - USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM) + KSPACE MANYBODY MC MEAM MESSAGE MISC MOLECULE PERI REAX REPLICA RIGID SHOCK + SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE USER-ATC USER-AWPMD + USER-BOCS USER-CGDNA USER-MESO USER-CGSDK USER-COLVARS USER-DIFFRACTION + USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD USER-LB USER-MANIFOLD + USER-MEAMC USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF + USER-PHONON USER-PTM USER-QTB USER-REAXC USER-SCAFACOS USER-SMD USER-SMTBQ + USER-SPH USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM) set(ACCEL_PACKAGES USER-OMP KOKKOS OPT USER-INTEL GPU) set(OTHER_PACKAGES CORESHELL QEQ) foreach(PKG ${DEFAULT_PACKAGES}) diff --git a/src/Makefile b/src/Makefile index 2ee7885562..eefc64b274 100644 --- a/src/Makefile +++ b/src/Makefile @@ -61,7 +61,7 @@ PACKUSER = user-atc user-awpmd user-bocs user-cgdna user-cgsdk user-colvars \ user-diffraction user-dpd user-drude user-eff user-fep user-h5md \ user-intel user-lb user-manifold user-meamc user-meso \ user-mgpt user-misc user-mofff user-molfile \ - user-netcdf user-omp user-phonon user-qmmm user-qtb \ + user-netcdf user-omp user-phonon user-ptm user-qmmm user-qtb \ user-quip user-reaxc user-scafacos user-smd user-smtbq \ user-sph user-tally user-uef user-vtk From 37fe03c0ab7905e11cf3b8ed9dcb4fb0b42d074d Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 25 Sep 2018 09:19:09 -0400 Subject: [PATCH 189/302] escape backslash in bibtex string for correct citeme output --- src/USER-PTM/compute_ptm_atom.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/USER-PTM/compute_ptm_atom.cpp b/src/USER-PTM/compute_ptm_atom.cpp index b6b4a9786c..eb0138de26 100644 --- a/src/USER-PTM/compute_ptm_atom.cpp +++ b/src/USER-PTM/compute_ptm_atom.cpp @@ -46,7 +46,7 @@ using namespace LAMMPS_NS; static const char cite_user_ptm_package[] = "USER-PTM package:\n\n" "@Article{larsen2016ptm,\n" - " author={Larsen, Peter Mahler and Schmidt, S{\o}ren and Schi{\o}tz, " + " author={Larsen, Peter Mahler and Schmidt, S{\\o}ren and Schi{\\o}tz, " "Jakob},\n" " title={Robust structural identification via polyhedral template " "matching},\n" From 5a6226caa5a4b6c347733b5d67ad33f33baf8bc7 Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Tue, 25 Sep 2018 10:50:43 -0600 Subject: [PATCH 190/302] jive src headers with doc page entries and example scripts --- ....txt => compute_smd_triangle_vertices.txt} | 6 +- doc/src/compute_spin.txt | 13 ++--- doc/src/fix_msst.txt | 2 +- doc/src/fix_nve_awpmd.txt | 56 +++++++++++++++++++ doc/src/fix_poems.txt | 2 +- doc/src/pair_body_nparticle.txt | 2 +- doc/src/pair_buck6d_coul_gauss.txt | 4 +- doc/src/pair_lj_expand.txt | 23 ++++++-- doc/src/pair_meam_spline.txt | 4 +- doc/src/pair_meam_sw_spline.txt | 4 +- doc/src/pair_sdk.txt | 14 +++-- doc/src/pair_spin_magelec.txt | 8 +-- doc/src/pair_spin_neel.txt | 36 ++++++------ examples/SPIN/bfo/in.spin.bfo | 2 +- examples/SPIN/cobalt_fcc/in.spin.cobalt_fcc | 2 +- examples/SPIN/cobalt_hcp/in.spin.cobalt_hcp | 2 +- examples/SPIN/iron/in.spin.iron | 2 +- examples/SPIN/nickel/in.spin.nickel | 2 +- examples/SPIN/read_restart/in.spin.read_data | 2 +- examples/SPIN/read_restart/in.spin.restart | 2 +- .../SPIN/read_restart/in.spin.write_restart | 2 +- .../fluid_structure_interaction.lmp | 2 +- src/PYTHON/fix_python_invoke.h | 2 +- src/SPIN/compute_spin.h | 2 +- src/SPIN/pair_spin.h | 7 --- ....cpp => compute_smd_triangle_vertices.cpp} | 0 ...ices.h => compute_smd_triangle_vertices.h} | 0 src/USER-SMD/compute_smd_vol.h | 2 +- src/USER-SMD/fix_smd_setvel.h | 6 +- 29 files changed, 140 insertions(+), 71 deletions(-) rename doc/src/{compute_smd_triangle_mesh_vertices.txt => compute_smd_triangle_vertices.txt} (91%) create mode 100644 doc/src/fix_nve_awpmd.txt rename src/USER-SMD/{compute_smd_triangle_mesh_vertices.cpp => compute_smd_triangle_vertices.cpp} (100%) rename src/USER-SMD/{compute_smd_triangle_mesh_vertices.h => compute_smd_triangle_vertices.h} (100%) diff --git a/doc/src/compute_smd_triangle_mesh_vertices.txt b/doc/src/compute_smd_triangle_vertices.txt similarity index 91% rename from doc/src/compute_smd_triangle_mesh_vertices.txt rename to doc/src/compute_smd_triangle_vertices.txt index cd1f8fdd9b..487b1b590b 100644 --- a/doc/src/compute_smd_triangle_mesh_vertices.txt +++ b/doc/src/compute_smd_triangle_vertices.txt @@ -6,14 +6,14 @@ :line -compute smd/triangle/mesh/vertices :h3 +compute smd/triangle/vertices command :h3 [Syntax:] -compute ID group-ID smd/triangle/mesh/vertices :pre +compute ID group-ID smd/triangle/vertices :pre ID, group-ID are documented in "compute"_compute.html command -smd/triangle/mesh/vertices = style name of this compute command :ul +smd/triangle/vertices = style name of this compute command :ul [Examples:] diff --git a/doc/src/compute_spin.txt b/doc/src/compute_spin.txt index e6185a2dd8..4edecc2408 100644 --- a/doc/src/compute_spin.txt +++ b/doc/src/compute_spin.txt @@ -10,14 +10,14 @@ compute spin command :h3 [Syntax:] -compute ID group-ID compute/spin :pre +compute ID group-ID spin :pre ID, group-ID are documented in "compute"_compute.html command -compute/spin = style name of this compute command :ul +spin = style name of this compute command :ul [Examples:] -compute out_mag all compute/spin :pre +compute out_mag all spin :pre [Description:] @@ -26,7 +26,8 @@ of atoms having spins. This compute calculates 6 magnetic quantities. -The three first quantities are the x,y and z coordinates of the total magnetization. +The three first quantities are the x,y and z coordinates of the total +magnetization. The fourth quantity is the norm of the total magnetization. @@ -39,7 +40,7 @@ The simplest way to output the results of the compute spin calculation is to define some of the quantities as variables, and to use the thermo and thermo_style commands, for example: -compute out_mag all compute/spin :pre +compute out_mag all spin :pre variable mag_z equal c_out_mag\[3\] variable mag_norm equal c_out_mag\[4\] @@ -53,7 +54,6 @@ the total magnetization, and the magnetic temperature. Three variables are assigned to those quantities. The thermo and thermo_style commands print them every 10 timesteps. - [Output info:] The array values are "intensive". The array values will be in @@ -68,7 +68,6 @@ has to be "spin" for this compute to be valid. [Related commands:] none - [Default:] none :line diff --git a/doc/src/fix_msst.txt b/doc/src/fix_msst.txt index e31f61e5f7..7f0e5512ae 100644 --- a/doc/src/fix_msst.txt +++ b/doc/src/fix_msst.txt @@ -6,7 +6,7 @@ :line - fix msst command :h3 +fix msst command :h3 [Syntax:] diff --git a/doc/src/fix_nve_awpmd.txt b/doc/src/fix_nve_awpmd.txt new file mode 100644 index 0000000000..c266d46eee --- /dev/null +++ b/doc/src/fix_nve_awpmd.txt @@ -0,0 +1,56 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +fix nve/awpmd command :h3 + +[Syntax:] + +fix ID group-ID nve/awpmd :pre + +ID, group-ID are documented in "fix"_fix.html command +nve/awpmd = style name of this fix command :ul + +[Examples:] + +fix 1 all nve/awpmd :pre + +[Description:] + +Perform constant NVE integration to update position and velocity for +nuclei and electrons in the group for the "Antisymmetrized Wave Packet +Molecular Dynamics"_pair_awpmd.html model. V is volume; E is energy. +This creates a system trajectory consistent with the microcanonical +ensemble. + +The operation of this fix is exactly like that described by the "fix +nve"_fix_nve.html command, except that the width and width-velocity of +the electron wavefunctions are also updated. + +:line + +[Restart, fix_modify, output, run start/stop, minimize info:] + +No information about this fix is written to "binary restart +files"_restart.html. None of the "fix_modify"_fix_modify.html options +are relevant to this fix. No global or per-atom quantities are stored +by this fix for access by various "output commands"_Howto_output.html. +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. + +[Restrictions:] + +This fix is part of the USER-AWPMD package. It is only enabled if +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. + +[Related commands:] + +"fix nve"_fix_nve.html + +[Default:] none diff --git a/doc/src/fix_poems.txt b/doc/src/fix_poems.txt index 52ab0ca44d..8fe793ce7f 100644 --- a/doc/src/fix_poems.txt +++ b/doc/src/fix_poems.txt @@ -6,7 +6,7 @@ :line -fix poems :h3 +fix poems command :h3 Syntax: diff --git a/doc/src/pair_body_nparticle.txt b/doc/src/pair_body_nparticle.txt index 158eb68ca8..7d841119ca 100644 --- a/doc/src/pair_body_nparticle.txt +++ b/doc/src/pair_body_nparticle.txt @@ -6,7 +6,7 @@ :line -pair_style body command :h3 +pair_style body/nparticle command :h3 [Syntax:] diff --git a/doc/src/pair_buck6d_coul_gauss.txt b/doc/src/pair_buck6d_coul_gauss.txt index d9780e0320..21de3330f4 100644 --- a/doc/src/pair_buck6d_coul_gauss.txt +++ b/doc/src/pair_buck6d_coul_gauss.txt @@ -6,8 +6,8 @@ :line -pair_style buck6d/coul/gauss/dsf :h3 -pair_style buck6d/coul/gauss/long :h3 +pair_style buck6d/coul/gauss/dsf command :h3 +pair_style buck6d/coul/gauss/long command :h3 [Syntax:] diff --git a/doc/src/pair_lj_expand.txt b/doc/src/pair_lj_expand.txt index d26c88e4f7..f37cb0fb83 100644 --- a/doc/src/pair_lj_expand.txt +++ b/doc/src/pair_lj_expand.txt @@ -9,6 +9,8 @@ pair_style lj/expand command :h3 pair_style lj/expand/gpu command :h3 pair_style lj/expand/omp command :h3 +pair_style lj/expand/coul/long command :h3 +pair_style lj/expand/coul/long/gpu command :h3 [Syntax:] @@ -22,6 +24,11 @@ pair_style lj/expand 2.5 pair_coeff * * 1.0 1.0 0.5 pair_coeff 1 1 1.0 1.0 -0.2 2.0 :pre +pair_style lj/expand/coul/long 2.5 +pair_style lj/expand/coul/long 2.5 4.0 +pair_coeff * * 1.0 1.0 0.5 +pair_coeff 1 1 1.0 1.0 -0.2 3.0 :pre + [Description:] Style {lj/expand} computes a LJ interaction with a distance shifted by @@ -34,11 +41,12 @@ formula: Rc is the cutoff which does not include the delta distance. I.e. the actual force cutoff is the sum of cutoff + delta. -The following coefficients must be defined for each pair of atoms -types via the "pair_coeff"_pair_coeff.html command as in the examples -above, or in the data file or restart files read by the -"read_data"_read_data.html or "read_restart"_read_restart.html -commands, or by mixing as described below: +For all of the {lj/expand} pair styles, the following coefficients must +be defined for each pair of atoms types via the +"pair_coeff"_pair_coeff.html command as in the examples above, or in +the data file or restart files read by the "read_data"_read_data.html +or "read_restart"_read_restart.html commands, or by mixing as +described below: epsilon (energy units) sigma (distance units) @@ -48,6 +56,11 @@ cutoff (distance units) :ul The delta values can be positive or negative. The last coefficient is optional. If not specified, the global LJ cutoff is used. +For {lj/expand/coul/long} only the LJ cutoff can be specified since a +Coulombic cutoff cannot be specified for an individual I,J type pair. +All type pairs use the same global Coulombic cutoff specified in the +pair_style command. + :line Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are diff --git a/doc/src/pair_meam_spline.txt b/doc/src/pair_meam_spline.txt index df5db81264..74adba2432 100644 --- a/doc/src/pair_meam_spline.txt +++ b/doc/src/pair_meam_spline.txt @@ -6,8 +6,8 @@ :line -pair_style meam/spline :h3 -pair_style meam/spline/omp :h3 +pair_style meam/spline command :h3 +pair_style meam/spline/omp command :h3 [Syntax:] diff --git a/doc/src/pair_meam_sw_spline.txt b/doc/src/pair_meam_sw_spline.txt index 2e8c26658a..8281315031 100644 --- a/doc/src/pair_meam_sw_spline.txt +++ b/doc/src/pair_meam_sw_spline.txt @@ -6,8 +6,8 @@ :line -pair_style meam/sw/spline :h3 -pair_style meam/sw/spline/omp :h3 +pair_style meam/sw/spline command :h3 +pair_style meam/sw/spline/omp command :h3 [Syntax:] diff --git a/doc/src/pair_sdk.txt b/doc/src/pair_sdk.txt index b977aefe88..06a0a42d5a 100644 --- a/doc/src/pair_sdk.txt +++ b/doc/src/pair_sdk.txt @@ -13,6 +13,8 @@ pair_style lj/sdk/omp command :h3 pair_style lj/sdk/coul/long command :h3 pair_style lj/sdk/coul/long/gpu command :h3 pair_style lj/sdk/coul/long/omp command :h3 +pair_style lj/sdk/coul/msm command :h3 +pair_style lj/sdk/coul/msm/omp command :h3 [Syntax:] @@ -35,6 +37,10 @@ pair_style lj/sdk/coul/long 10.0 pair_style lj/sdk/coul/long 10.0 12.0 pair_coeff 1 1 lj9_6 100.0 3.5 12.0 :pre +pair_style lj/sdk/coul/msm 10.0 +pair_style lj/sdk/coul/msm 10.0 12.0 +pair_coeff 1 1 lj9_6 100.0 3.5 12.0 :pre + [Description:] The {lj/sdk} styles compute a 9/6, 12/4, or 12/6 Lennard-Jones potential, @@ -75,10 +81,10 @@ and Coulombic interactions for this type pair. If both coefficients are specified, they are used as the LJ and Coulombic cutoffs for this type pair. -For {lj/sdk/coul/long} only the LJ cutoff can be specified since a -Coulombic cutoff cannot be specified for an individual I,J type pair. -All type pairs use the same global Coulombic cutoff specified in the -pair_style command. +For {lj/sdk/coul/long} and {lj/sdk/coul/msm} only the LJ cutoff can be +specified since a Coulombic cutoff cannot be specified for an +individual I,J type pair. All type pairs use the same global +Coulombic cutoff specified in the pair_style command. :line diff --git a/doc/src/pair_spin_magelec.txt b/doc/src/pair_spin_magelec.txt index f552c56a4b..360f440792 100644 --- a/doc/src/pair_spin_magelec.txt +++ b/doc/src/pair_spin_magelec.txt @@ -6,11 +6,11 @@ :line -pair_style spin/me command :h3 +pair_style spin/magelec command :h3 [Syntax:] -pair_style spin/me cutoff :pre +pair_style spin/magelec cutoff :pre cutoff = global cutoff pair (distance in metal units) :ulb,l @@ -18,8 +18,8 @@ cutoff = global cutoff pair (distance in metal units) :ulb,l [Examples:] -pair_style spin/me 4.5 -pair_coeff * * me 4.5 0.00109 1.0 1.0 1.0 :pre +pair_style spin/magelec 4.5 +pair_coeff * * magelec 4.5 0.00109 1.0 1.0 1.0 :pre [Description:] diff --git a/doc/src/pair_spin_neel.txt b/doc/src/pair_spin_neel.txt index fe3bb1ad14..7af71021a0 100644 --- a/doc/src/pair_spin_neel.txt +++ b/doc/src/pair_spin_neel.txt @@ -29,34 +29,36 @@ between pairs of magnetic spins: :c,image(Eqs/pair_spin_neel_interaction.jpg) -where si and sj are two neighboring magnetic spins of two particles, +where si and sj are two neighboring magnetic spins of two particles, rij = ri - rj is the inter-atomic distance between the two particles, -eij = (ri - rj)/|ri-rj| is their normalized separation vector -and g1, q1 and q2 are three functions defining the intensity of the -dipolar and quadrupolar contributions, with: +eij = (ri - rj)/|ri-rj| is their normalized separation vector and g1, +q1 and q2 are three functions defining the intensity of the dipolar +and quadrupolar contributions, with: :c,image(Eqs/pair_spin_neel_functions.jpg) -With the functions g(rij) and q(rij) defined and fitted according to the same -Bethe-Slater function used to fit the exchange interaction: +With the functions g(rij) and q(rij) defined and fitted according to +the same Bethe-Slater function used to fit the exchange interaction: :c,image(Eqs/pair_spin_exchange_function.jpg) -where a, b and d are the three constant coefficients defined in the associated -"pair_coeff" command. +where a, b and d are the three constant coefficients defined in the +associated "pair_coeff" command. -The coefficients a, b, and d need to be fitted so that the function above matches with -the values of the magneto-elastic constant of the materials at stake. +The coefficients a, b, and d need to be fitted so that the function +above matches with the values of the magneto-elastic constant of the +materials at stake. -Examples and more explanations about this function and its parametrization are reported -in "(Tranchida)"_#Tranchida6. More examples of parametrization will be provided in -future work. +Examples and more explanations about this function and its +parametrization are reported in "(Tranchida)"_#Tranchida6. More +examples of parametrization will be provided in future work. -From this DM interaction, each spin i will be submitted to a magnetic torque -omega and its associated atom to a force F (for spin-lattice calculations only). +From this DM interaction, each spin i will be submitted to a magnetic +torque omega and its associated atom to a force F (for spin-lattice +calculations only). -More details about the derivation of these torques/forces are reported in -"(Tranchida)"_#Tranchida6. +More details about the derivation of these torques/forces are reported +in "(Tranchida)"_#Tranchida6. :line diff --git a/examples/SPIN/bfo/in.spin.bfo b/examples/SPIN/bfo/in.spin.bfo index de23ba87ba..e3c88b0f06 100644 --- a/examples/SPIN/bfo/in.spin.bfo +++ b/examples/SPIN/bfo/in.spin.bfo @@ -36,7 +36,7 @@ fix 3 all nve/spin lattice no timestep 0.0002 -compute out_mag all compute/spin +compute out_mag all spin compute out_pe all pe compute out_ke all ke compute out_temp all temp diff --git a/examples/SPIN/cobalt_fcc/in.spin.cobalt_fcc b/examples/SPIN/cobalt_fcc/in.spin.cobalt_fcc index fd6833727b..ea98eeba94 100644 --- a/examples/SPIN/cobalt_fcc/in.spin.cobalt_fcc +++ b/examples/SPIN/cobalt_fcc/in.spin.cobalt_fcc @@ -40,7 +40,7 @@ timestep 0.0001 # compute and output options -compute out_mag all compute/spin +compute out_mag all spin compute out_pe all pe compute out_ke all ke compute out_temp all temp diff --git a/examples/SPIN/cobalt_hcp/in.spin.cobalt_hcp b/examples/SPIN/cobalt_hcp/in.spin.cobalt_hcp index 35aa1df86c..3ff0b1cadf 100644 --- a/examples/SPIN/cobalt_hcp/in.spin.cobalt_hcp +++ b/examples/SPIN/cobalt_hcp/in.spin.cobalt_hcp @@ -40,7 +40,7 @@ fix 3 all nve/spin lattice yes timestep 0.0001 -compute out_mag all compute/spin +compute out_mag all spin compute out_pe all pe compute out_ke all ke compute out_temp all temp diff --git a/examples/SPIN/iron/in.spin.iron b/examples/SPIN/iron/in.spin.iron index c2d5082cb6..1db5007dff 100644 --- a/examples/SPIN/iron/in.spin.iron +++ b/examples/SPIN/iron/in.spin.iron @@ -37,7 +37,7 @@ timestep 0.0001 # compute and output options -compute out_mag all compute/spin +compute out_mag all spin compute out_pe all pe compute out_ke all ke compute out_temp all temp diff --git a/examples/SPIN/nickel/in.spin.nickel b/examples/SPIN/nickel/in.spin.nickel index ba447b077f..0ed2fac410 100644 --- a/examples/SPIN/nickel/in.spin.nickel +++ b/examples/SPIN/nickel/in.spin.nickel @@ -38,7 +38,7 @@ timestep 0.0001 # compute and output options -compute out_mag all compute/spin +compute out_mag all spin compute out_pe all pe compute out_ke all ke compute out_temp all temp diff --git a/examples/SPIN/read_restart/in.spin.read_data b/examples/SPIN/read_restart/in.spin.read_data index 80de036661..17343994b5 100644 --- a/examples/SPIN/read_restart/in.spin.read_data +++ b/examples/SPIN/read_restart/in.spin.read_data @@ -25,7 +25,7 @@ timestep 0.0001 # define outputs and computes -compute out_mag all compute/spin +compute out_mag all spin compute out_pe all pe compute out_ke all ke compute out_temp all temp diff --git a/examples/SPIN/read_restart/in.spin.restart b/examples/SPIN/read_restart/in.spin.restart index a1198ccf93..39157fdac4 100644 --- a/examples/SPIN/read_restart/in.spin.restart +++ b/examples/SPIN/read_restart/in.spin.restart @@ -29,7 +29,7 @@ timestep 0.0001 # define outputs -compute out_mag all compute/spin +compute out_mag all spin compute out_pe all pe compute out_ke all ke compute out_temp all temp diff --git a/examples/SPIN/read_restart/in.spin.write_restart b/examples/SPIN/read_restart/in.spin.write_restart index 84fea24611..42f07fd316 100644 --- a/examples/SPIN/read_restart/in.spin.write_restart +++ b/examples/SPIN/read_restart/in.spin.write_restart @@ -34,7 +34,7 @@ timestep 0.0001 # compute and output options -compute out_mag all compute/spin +compute out_mag all spin compute out_pe all pe compute out_ke all ke compute out_temp all temp diff --git a/examples/USER/smd/fluid_structure_interaction/fluid_structure_interaction.lmp b/examples/USER/smd/fluid_structure_interaction/fluid_structure_interaction.lmp index 5100a52d84..0f7d726e21 100644 --- a/examples/USER/smd/fluid_structure_interaction/fluid_structure_interaction.lmp +++ b/examples/USER/smd/fluid_structure_interaction/fluid_structure_interaction.lmp @@ -129,7 +129,7 @@ compute contact_radius all smd/contact/radius compute S solids smd/tlsph/stress compute nn water smd/ulsph/num/neighs compute epl solids smd/plastic/strain -compute vol all smd/volume +compute vol all smd/vol compute rho all smd/rho dump dump_id all custom 100 dump.LAMMPS id type x y & diff --git a/src/PYTHON/fix_python_invoke.h b/src/PYTHON/fix_python_invoke.h index c277e295a1..89310eeded 100644 --- a/src/PYTHON/fix_python_invoke.h +++ b/src/PYTHON/fix_python_invoke.h @@ -13,8 +13,8 @@ #ifdef FIX_CLASS -FixStyle(python,FixPythonInvoke) FixStyle(python/invoke,FixPythonInvoke) +FixStyle(python,FixPythonInvoke) #else diff --git a/src/SPIN/compute_spin.h b/src/SPIN/compute_spin.h index b57876b7a0..c5d55b84cb 100644 --- a/src/SPIN/compute_spin.h +++ b/src/SPIN/compute_spin.h @@ -13,7 +13,7 @@ #ifdef COMPUTE_CLASS -ComputeStyle(compute/spin,ComputeSpin) +ComputeStyle(spin,ComputeSpin) #else diff --git a/src/SPIN/pair_spin.h b/src/SPIN/pair_spin.h index 100eec1732..1be8550c65 100644 --- a/src/SPIN/pair_spin.h +++ b/src/SPIN/pair_spin.h @@ -11,12 +11,6 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#ifdef PAIR_CLASS - -PairStyle(pair/spin,PairSpin) - -#else - #ifndef LMP_PAIR_SPIN_H #define LMP_PAIR_SPIN_H @@ -46,7 +40,6 @@ friend class FixNVESpin; } -#endif #endif /* ERROR/WARNING messages: diff --git a/src/USER-SMD/compute_smd_triangle_mesh_vertices.cpp b/src/USER-SMD/compute_smd_triangle_vertices.cpp similarity index 100% rename from src/USER-SMD/compute_smd_triangle_mesh_vertices.cpp rename to src/USER-SMD/compute_smd_triangle_vertices.cpp diff --git a/src/USER-SMD/compute_smd_triangle_mesh_vertices.h b/src/USER-SMD/compute_smd_triangle_vertices.h similarity index 100% rename from src/USER-SMD/compute_smd_triangle_mesh_vertices.h rename to src/USER-SMD/compute_smd_triangle_vertices.h diff --git a/src/USER-SMD/compute_smd_vol.h b/src/USER-SMD/compute_smd_vol.h index 5525ce57cb..08ad150627 100644 --- a/src/USER-SMD/compute_smd_vol.h +++ b/src/USER-SMD/compute_smd_vol.h @@ -25,7 +25,7 @@ #ifdef COMPUTE_CLASS -ComputeStyle(smd/volume,ComputeSMDVol) +ComputeStyle(smd/vol,ComputeSMDVol) #else diff --git a/src/USER-SMD/fix_smd_setvel.h b/src/USER-SMD/fix_smd_setvel.h index a3e650e682..f5fc34b4ea 100644 --- a/src/USER-SMD/fix_smd_setvel.h +++ b/src/USER-SMD/fix_smd_setvel.h @@ -24,12 +24,12 @@ #ifdef FIX_CLASS -FixStyle(smd/setvelocity,FixSMDSetVel) +FixStyle(smd/setvel,FixSMDSetVel) #else -#ifndef LMP_FIX_SMD_SET_VELOCITY_H -#define LMP_FIX_SMD_SET_VELOCITY_H +#ifndef LMP_FIX_SMD_SETVEL_H +#define LMP_FIX_SMD_SETVEL_H #include "fix.h" From a9b8a6521d15cbcf97fff4348ff15b1266f17178 Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Tue, 25 Sep 2018 13:18:54 -0600 Subject: [PATCH 191/302] more mis-matches between doc pages and src files --- doc/src/Commands_bond.txt | 2 +- doc/src/Commands_fix.txt | 2 +- doc/src/Commands_pair.txt | 2 +- doc/src/angle_sdk.txt | 25 ++++++++++++++++++++++++ doc/src/fix_property_atom.txt | 24 +++++++++++++++++++++++ doc/src/fix_surface_global.txt | 19 ------------------ doc/src/fix_wall_gran.txt | 23 ++++++++++++++++++++++ doc/src/pair_born.txt | 19 ++---------------- doc/src/pair_buck.txt | 14 +++----------- doc/src/pair_charmm.txt | 3 +++ doc/src/pair_cs.txt | 34 +++++++++++++++++++++++++++++++++ doc/src/pair_dipole.txt | 1 + doc/src/pair_edip.txt | 1 + doc/src/pair_gran.txt | 2 +- doc/src/pair_gromacs.txt | 2 ++ doc/src/pair_hybrid.txt | 3 +-- doc/src/pair_lj.txt | 2 ++ doc/src/pair_lj_expand.txt | 1 + doc/src/pair_lj_long.txt | 1 + doc/src/pair_meam_sw_spline.txt | 1 - doc/src/pair_tersoff.txt | 8 ++++---- 21 files changed, 131 insertions(+), 58 deletions(-) delete mode 100644 doc/src/fix_surface_global.txt diff --git a/doc/src/Commands_bond.txt b/doc/src/Commands_bond.txt index 0cf433d53a..773202f126 100644 --- a/doc/src/Commands_bond.txt +++ b/doc/src/Commands_bond.txt @@ -70,7 +70,7 @@ OPT. "fourier/simple (o)"_angle_fourier_simple.html, "harmonic (iko)"_angle_harmonic.html, "quartic (o)"_angle_quartic.html, -"sdk"_angle_sdk.html, +"sdk (o)"_angle_sdk.html, "table (o)"_angle_table.html :tb(c=4,ea=c) :line diff --git a/doc/src/Commands_fix.txt b/doc/src/Commands_fix.txt index e002c11770..838bcbe7a6 100644 --- a/doc/src/Commands_fix.txt +++ b/doc/src/Commands_fix.txt @@ -216,7 +216,7 @@ OPT. "wall/body/polyhedron"_fix_wall_body_polyhedron.html, "wall/colloid"_fix_wall.html, "wall/ees"_fix_wall_ees.html, -"wall/gran"_fix_wall_gran.html, +"wall/gran (o)"_fix_wall_gran.html, "wall/gran/region"_fix_wall_gran_region.html, "wall/harmonic"_fix_wall.html, "wall/lj1043"_fix_wall.html, diff --git a/doc/src/Commands_pair.txt b/doc/src/Commands_pair.txt index 33890df1fe..3b6a5f48fa 100644 --- a/doc/src/Commands_pair.txt +++ b/doc/src/Commands_pair.txt @@ -26,7 +26,7 @@ OPT. "none"_pair_none.html, "zero"_pair_zero.html, -"hybrid"_pair_hybrid.html, +"hybrid (k)"_pair_hybrid.html, "hybrid/overlay (k)"_pair_hybrid.html :tb(c=4,ea=c) "adp (o)"_pair_adp.html, diff --git a/doc/src/angle_sdk.txt b/doc/src/angle_sdk.txt index 4de1a6755d..22238880fe 100644 --- a/doc/src/angle_sdk.txt +++ b/doc/src/angle_sdk.txt @@ -7,6 +7,7 @@ :line angle_style sdk command :h3 +angle_style sdk/omp command :h3 [Syntax:] @@ -43,6 +44,30 @@ internally; hence the units of K are in energy/radian^2. The also required {lj/sdk} parameters will be extracted automatically from the pair_style. +:line + +Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. + +These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, +USER-OMP and OPT packages, respectively. They are only enabled if +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the "-suffix command-line +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. + +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. + +:line + [Restrictions:] This angle style can only be used if LAMMPS was built with the diff --git a/doc/src/fix_property_atom.txt b/doc/src/fix_property_atom.txt index 8a70cd8213..19e3b0ca40 100644 --- a/doc/src/fix_property_atom.txt +++ b/doc/src/fix_property_atom.txt @@ -7,6 +7,7 @@ :line fix property/atom command :h3 +fix property/atom/kk command :h3 [Syntax:] @@ -201,6 +202,7 @@ added classes. :line :link(isotopes) + Example for using per-atom masses with TIP4P water to study isotope effects. When setting up simulations with the "TIP4P pair styles"_Howto_tip4p.html for water, you have to provide exactly @@ -238,6 +240,28 @@ set group hwat mass 2.0141018 :pre :line +Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. + +These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, +USER-OMP and OPT packages, respectively. They are only enabled if +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the "-suffix command-line +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. + +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. + +:line + [Restart, fix_modify, output, run start/stop, minimize info:] This fix writes the per-atom values it stores to "binary restart diff --git a/doc/src/fix_surface_global.txt b/doc/src/fix_surface_global.txt deleted file mode 100644 index 2ee045141a..0000000000 --- a/doc/src/fix_surface_global.txt +++ /dev/null @@ -1,19 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix wall/surface/global command :h3 - -[Description:] - -This feature is not yet implemented. - -[Related commands:] - -"dump image"_dump_image.html - - diff --git a/doc/src/fix_wall_gran.txt b/doc/src/fix_wall_gran.txt index 0ea5b194eb..871ee2e5d1 100644 --- a/doc/src/fix_wall_gran.txt +++ b/doc/src/fix_wall_gran.txt @@ -7,6 +7,7 @@ :line fix wall/gran command :h3 +fix wall/gran/omp command :h3 [Syntax:] @@ -136,6 +137,28 @@ the clockwise direction for {vshear} > 0 or counter-clockwise for {vshear} < 0. In this case, {vshear} is the tangential velocity of the wall at whatever {radius} has been defined. +:line + +Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. + +These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, +USER-OMP and OPT packages, respectively. They are only enabled if +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the "-suffix command-line +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. + +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. + [Restart, fix_modify, output, run start/stop, minimize info:] This fix writes the shear friction state of atoms interacting with the diff --git a/doc/src/pair_born.txt b/doc/src/pair_born.txt index 195d3e6669..9cbfcffea0 100644 --- a/doc/src/pair_born.txt +++ b/doc/src/pair_born.txt @@ -11,19 +11,14 @@ pair_style born command :h3 pair_style born/omp command :h3 pair_style born/gpu command :h3 pair_style born/coul/long command :h3 -pair_style born/coul/long/cs command :h3 -pair_style born/coul/long/cs/gpu command :h3 pair_style born/coul/long/gpu command :h3 pair_style born/coul/long/omp command :h3 pair_style born/coul/msm command :h3 pair_style born/coul/msm/omp command :h3 pair_style born/coul/wolf command :h3 -pair_style born/coul/wolf/cs command :h3 -pair_style born/coul/wolf/cs/gpu command :h3 pair_style born/coul/wolf/gpu command :h3 pair_style born/coul/wolf/omp command :h3 pair_style born/coul/dsf command :h3 -pair_style born/coul/dsf/cs command :h3 [Syntax:] @@ -55,9 +50,7 @@ pair_coeff * * 6.08 0.317 2.340 24.18 11.51 pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 :pre pair_style born/coul/long 10.0 -pair_style born/coul/long/cs 10.0 -pair_style born/coul/long 10.0 8.0 -pair_style born/coul/long/cs 10.0 8.0 +pair_style born/coul/long 10.0 8. pair_coeff * * 6.08 0.317 2.340 24.18 11.51 pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 :pre @@ -68,7 +61,6 @@ pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 :pre pair_style born/coul/wolf 0.25 10.0 pair_style born/coul/wolf 0.25 10.0 9.0 -pair_style born/coul/wolf/cs 0.25 10.0 9.0 pair_coeff * * 6.08 0.317 2.340 24.18 11.51 pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 :pre @@ -107,13 +99,6 @@ Wolf potential in the "coul/wolf"_pair_coul.html pair style. The {born/coul/dsf} style computes the Coulomb contribution with the damped shifted force model as in the "coul/dsf"_pair_coul.html style. -Style {born/coul/long/cs} is identical to {born/coul/long} except that -a term is added for the "core/shell model"_Howto_coreshell.html to -allow charges on core and shell particles to be separated by r = 0.0. -The same correction is introduced for the {born/coul/dsf/cs} style -which is identical to {born/coul/dsf}. And likewise for -{born/coul/wolf/cs} style which is identical to {born/coul/wolf}. - Note that these potentials are related to the "Buckingham potential"_pair_buck.html. @@ -174,7 +159,7 @@ for the energy of the exp(), 1/r^6, and 1/r^8 portion of the pair interaction. The {born/coul/long} pair style supports the -"pair_modify"_pair_modify.html table option ti tabulate the +"pair_modify"_pair_modify.html table option to tabulate the short-range portion of the long-range Coulombic interaction. These styles support the pair_modify tail option for adding long-range diff --git a/doc/src/pair_buck.txt b/doc/src/pair_buck.txt index 5b1688e868..ec83e6b339 100644 --- a/doc/src/pair_buck.txt +++ b/doc/src/pair_buck.txt @@ -17,7 +17,6 @@ pair_style buck/coul/cut/intel command :h3 pair_style buck/coul/cut/kk command :h3 pair_style buck/coul/cut/omp command :h3 pair_style buck/coul/long command :h3 -pair_style buck/coul/long/cs command :h3 pair_style buck/coul/long/gpu command :h3 pair_style buck/coul/long/intel command :h3 pair_style buck/coul/long/kk command :h3 @@ -29,14 +28,14 @@ pair_style buck/coul/msm/omp command :h3 pair_style style args :pre -style = {buck} or {buck/coul/cut} or {buck/coul/long} or {buck/coul/long/cs} or {buck/coul/msm} +style = {buck} or {buck/coul/cut} or {buck/coul/long} or {buck/coul/msm} args = list of arguments for a particular style :ul {buck} args = cutoff cutoff = global cutoff for Buckingham interactions (distance units) {buck/coul/cut} args = cutoff (cutoff2) cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units) cutoff2 = global cutoff for Coulombic (optional) (distance units) - {buck/coul/long} or {buck/coul/long/cs} args = cutoff (cutoff2) + {buck/coul/long} args = cutoff (cutoff2) cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units) cutoff2 = global cutoff for Coulombic (optional) (distance units) {buck/coul/msm} args = cutoff (cutoff2) @@ -56,9 +55,7 @@ pair_coeff 1 1 100.0 1.5 200.0 9.0 pair_coeff 1 1 100.0 1.5 200.0 9.0 8.0 :pre pair_style buck/coul/long 10.0 -pair_style buck/coul/long/cs 10.0 pair_style buck/coul/long 10.0 8.0 -pair_style buck/coul/long/cs 10.0 8.0 pair_coeff * * 100.0 1.5 200.0 pair_coeff 1 1 100.0 1.5 200.0 9.0 :pre @@ -92,10 +89,6 @@ A,C and Coulombic terms. If two cutoffs are specified, the first is used as the cutoff for the A,C terms, and the second is the cutoff for the Coulombic term. -Style {buck/coul/long/cs} is identical to {buck/coul/long} except that -a term is added for the "core/shell model"_Howto_coreshell.html to -allow charges on core and shell particles to be separated by r = 0.0. - Note that these potentials are related to the "Born-Mayer-Huggins potential"_pair_born.html. @@ -184,8 +177,7 @@ respa"_run_style.html command. They do not support the {inner}, [Restrictions:] -The {buck/coul/long} style is part of the KSPACE package. The -{buck/coul/long/cs} style is part of the CORESHELL package. They are +The {buck/coul/long} style is part of the KSPACE package. They are only enabled if LAMMPS was built with that package. See the "Build package"_Build_package.html doc page for more info. diff --git a/doc/src/pair_charmm.txt b/doc/src/pair_charmm.txt index dfc87e1bce..131e289227 100644 --- a/doc/src/pair_charmm.txt +++ b/doc/src/pair_charmm.txt @@ -8,12 +8,15 @@ pair_style lj/charmm/coul/charmm command :h3 pair_style lj/charmm/coul/charmm/intel command :h3 +pair_style lj/charmm/coul/charmm/kk command :h3 pair_style lj/charmm/coul/charmm/omp command :h3 pair_style lj/charmm/coul/charmm/implicit command :h3 +pair_style lj/charmm/coul/charmm/implicit/kk command :h3 pair_style lj/charmm/coul/charmm/implicit/omp command :h3 pair_style lj/charmm/coul/long command :h3 pair_style lj/charmm/coul/long/gpu command :h3 pair_style lj/charmm/coul/long/intel command :h3 +pair_style lj/charmm/coul/long/kk command :h3 pair_style lj/charmm/coul/long/opt command :h3 pair_style lj/charmm/coul/long/omp command :h3 pair_style lj/charmm/coul/msm command :h3 diff --git a/doc/src/pair_cs.txt b/doc/src/pair_cs.txt index 8bd4abed68..faaea42f15 100644 --- a/doc/src/pair_cs.txt +++ b/doc/src/pair_cs.txt @@ -7,9 +7,11 @@ :line pair_style born/coul/long/cs command :h3 +pair_style born/coul/long/cs/gpu command :h3 pair_style buck/coul/long/cs command :h3 pair_style born/coul/dsf/cs command :h3 pair_style born/coul/wolf/cs command :h3 +pair_style born/coul/wolf/cs/gpu command :h3 [Syntax:] @@ -97,6 +99,38 @@ a long-range solver, thus the only correction is the addition of a minimal distance to avoid the possible r = 0.0 case for a core/shell pair. +:line + +Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. + +These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, +USER-OMP and OPT packages, respectively. They are only enabled if +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the "-suffix command-line +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. + +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. + +:line + +[Mixing, shift, table, tail correction, restart, rRESPA info]: + +See the corresponding doc pages for pair styles without the "cs" +suffix to see how mixing, shifting, tabulation, tail correction, +restarting, and rRESPA are handled by theses pair styles. + +:line + [Restrictions:] These pair styles are part of the CORESHELL package. They are only diff --git a/doc/src/pair_dipole.txt b/doc/src/pair_dipole.txt index dcb2448949..bdf37983b6 100644 --- a/doc/src/pair_dipole.txt +++ b/doc/src/pair_dipole.txt @@ -13,6 +13,7 @@ pair_style lj/sf/dipole/sf command :h3 pair_style lj/sf/dipole/sf/gpu command :h3 pair_style lj/sf/dipole/sf/omp command :h3 pair_style lj/cut/dipole/long command :h3 +pair_style lj/cut/dipole/long/gpu command :h3 pair_style lj/long/dipole/long command :h3 [Syntax:] diff --git a/doc/src/pair_edip.txt b/doc/src/pair_edip.txt index 053d43b2ba..e0e8fbb27e 100644 --- a/doc/src/pair_edip.txt +++ b/doc/src/pair_edip.txt @@ -7,6 +7,7 @@ :line pair_style edip command :h3 +pair_style edip/omp command :h3 pair_style edip/multi command :h3 [Syntax:] diff --git a/doc/src/pair_gran.txt b/doc/src/pair_gran.txt index e06d410084..5beaf30e06 100644 --- a/doc/src/pair_gran.txt +++ b/doc/src/pair_gran.txt @@ -7,7 +7,7 @@ :line pair_style gran/hooke command :h3 -pair_style gran/omp command :h3 +pair_style gran/hooke/omp command :h3 pair_style gran/hooke/history command :h3 pair_style gran/hooke/history/omp command :h3 pair_style gran/hertz/history command :h3 diff --git a/doc/src/pair_gromacs.txt b/doc/src/pair_gromacs.txt index 6a36a036c9..e50a21588c 100644 --- a/doc/src/pair_gromacs.txt +++ b/doc/src/pair_gromacs.txt @@ -8,8 +8,10 @@ pair_style lj/gromacs command :h3 pair_style lj/gromacs/gpu command :h3 +pair_style lj/gromacs/kk command :h3 pair_style lj/gromacs/omp command :h3 pair_style lj/gromacs/coul/gromacs command :h3 +pair_style lj/gromacs/coul/gromacs/kk command :h3 pair_style lj/gromacs/coul/gromacs/omp command :h3 [Syntax:] diff --git a/doc/src/pair_hybrid.txt b/doc/src/pair_hybrid.txt index 6e68e820a8..97a5972bfb 100644 --- a/doc/src/pair_hybrid.txt +++ b/doc/src/pair_hybrid.txt @@ -7,9 +7,8 @@ :line pair_style hybrid command :h3 -pair_style hybrid/omp command :h3 +pair_style hybrid/kk command :h3 pair_style hybrid/overlay command :h3 -pair_style hybrid/overlay/omp command :h3 pair_style hybrid/overlay/kk command :h3 [Syntax:] diff --git a/doc/src/pair_lj.txt b/doc/src/pair_lj.txt index b5a5726182..4939f505bb 100644 --- a/doc/src/pair_lj.txt +++ b/doc/src/pair_lj.txt @@ -14,6 +14,7 @@ pair_style lj/cut/opt command :h3 pair_style lj/cut/omp command :h3 pair_style lj/cut/coul/cut command :h3 pair_style lj/cut/coul/cut/gpu command :h3 +pair_style lj/cut/coul/cut/kk command :h3 pair_style lj/cut/coul/cut/omp command :h3 pair_style lj/cut/coul/debye command :h3 pair_style lj/cut/coul/debye/gpu command :h3 @@ -26,6 +27,7 @@ pair_style lj/cut/coul/dsf/omp command :h3 pair_style lj/cut/coul/long command :h3 pair_style lj/cut/coul/long/cs command :h3 pair_style lj/cut/coul/long/gpu command :h3 +pair_style lj/cut/coul/long/kk command :h3 pair_style lj/cut/coul/long/intel command :h3 pair_style lj/cut/coul/long/opt command :h3 pair_style lj/cut/coul/long/omp command :h3 diff --git a/doc/src/pair_lj_expand.txt b/doc/src/pair_lj_expand.txt index f37cb0fb83..178ba8d1a8 100644 --- a/doc/src/pair_lj_expand.txt +++ b/doc/src/pair_lj_expand.txt @@ -8,6 +8,7 @@ pair_style lj/expand command :h3 pair_style lj/expand/gpu command :h3 +pair_style lj/expand/kk command :h3 pair_style lj/expand/omp command :h3 pair_style lj/expand/coul/long command :h3 pair_style lj/expand/coul/long/gpu command :h3 diff --git a/doc/src/pair_lj_long.txt b/doc/src/pair_lj_long.txt index 2bc2b656ac..47a554ef4f 100644 --- a/doc/src/pair_lj_long.txt +++ b/doc/src/pair_lj_long.txt @@ -11,6 +11,7 @@ pair_style lj/long/coul/long/intel command :h3 pair_style lj/long/coul/long/omp command :h3 pair_style lj/long/coul/long/opt command :h3 pair_style lj/long/tip4p/long command :h3 +pair_style lj/long/tip4p/long/omp command :h3 [Syntax:] diff --git a/doc/src/pair_meam_sw_spline.txt b/doc/src/pair_meam_sw_spline.txt index 8281315031..77322953cf 100644 --- a/doc/src/pair_meam_sw_spline.txt +++ b/doc/src/pair_meam_sw_spline.txt @@ -7,7 +7,6 @@ :line pair_style meam/sw/spline command :h3 -pair_style meam/sw/spline/omp command :h3 [Syntax:] diff --git a/doc/src/pair_tersoff.txt b/doc/src/pair_tersoff.txt index 20744bc2a9..4b7bb0d93d 100644 --- a/doc/src/pair_tersoff.txt +++ b/doc/src/pair_tersoff.txt @@ -8,10 +8,10 @@ pair_style tersoff command :h3 pair_style tersoff/table command :h3 -pair_style tersoff/gpu :h3 -pair_style tersoff/intel :h3 -pair_style tersoff/kk :h3 -pair_style tersoff/omp :h3 +pair_style tersoff/gpu command :h3 +pair_style tersoff/intel command :h3 +pair_style tersoff/kk command :h3 +pair_style tersoff/omp command :h3 pair_style tersoff/table/omp command :h3 [Syntax:] From b07adbf98c637579bba0a4c0da89abc2c9f94c07 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 27 Sep 2018 05:49:43 -0400 Subject: [PATCH 192/302] Update installing/running LAMMPS on ubuntu for daily binary --- doc/src/Install_linux.txt | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/src/Install_linux.txt b/doc/src/Install_linux.txt index cc15ac0ae0..2eeeb6602c 100644 --- a/doc/src/Install_linux.txt +++ b/doc/src/Install_linux.txt @@ -60,10 +60,10 @@ To install LAMMPS do the following once: sudo apt-get install lammps-daily :pre -This downloads an executable named "lammps-daily" to your box, which +This downloads an executable named "lmp_daily" to your box, which can then be used in the usual way to run input scripts: -lammps-daily < in.lj :pre +lmp_daily -in in.lj :pre To update LAMMPS to the most current version, do the following: From 7987f3319ee7876f13dae302f9c949c387730e93 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 27 Sep 2018 06:05:26 -0400 Subject: [PATCH 193/302] remove outdated references to linux rpms on rpm.lammps.org --- doc/src/Install_linux.txt | 28 +--------------------------- 1 file changed, 1 insertion(+), 27 deletions(-) diff --git a/doc/src/Install_linux.txt b/doc/src/Install_linux.txt index 2eeeb6602c..d44ff2b1c7 100644 --- a/doc/src/Install_linux.txt +++ b/doc/src/Install_linux.txt @@ -9,39 +9,13 @@ Documentation"_ld - "LAMMPS Commands"_lc :c Download an executable for Linux :h3 -Binaries are available for many different versions of Linux: +Binaries are available for different versions of Linux: -"Pre-built binary RPMs for Fedora/RedHat/CentOS/openSUSE"_#rpm "Pre-built Ubuntu Linux executables"_#ubuntu "Pre-built Gentoo Linux executable"_#gentoo :all(b) :line -Pre-built binary RPMs for Fedora/RedHat/CentOS/openSUSE :h4,link(rpm) - -Pre-built LAMMPS executables for various Linux distributions -can be downloaded as binary RPM files from this site: - -"http://rpm.lammps.org"_http://rpm.lammps.org - -There are multiple package variants supporting serial, parallel and -Python wrapper versions. The LAMMPS binaries contain all optional -packages included in the source distribution except: GPU, KIM, REAX, -and USER-INTEL. - -Installation instructions for the various versions are here: - -"http://rpm.lammps.org/install.html"_http://rpm.lammps.org/install.html - -The instructions show how to enable the repository in the respective -system's package management system. Installing and updating are then -straightforward and automatic. - -Thanks to Axel Kohlmeyer (Temple U, akohlmey at gmail.com) for setting -up this RPM capability. - -:line - Pre-built Ubuntu Linux executables :h4,link(ubuntu) A pre-built LAMMPS executable suitable for running on the latest From 8e7ddff6dcd0ecf6d66f93d8e82f9cbf782ce0c5 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 27 Sep 2018 06:15:03 -0400 Subject: [PATCH 194/302] reverse order in which pdf files are created. Creating Developer.pdf first and Manual.pdf later makes any warnings from the latter step, e.g. about missing files in doc/src/lammps.book more visible. --- doc/Makefile | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/doc/Makefile b/doc/Makefile index 9069fa1d60..e4ba2fe6a1 100644 --- a/doc/Makefile +++ b/doc/Makefile @@ -38,7 +38,7 @@ OBJECTS=$(SOURCES:src/%.txt=$(RSTDIR)/%.rst) help: @echo "Please use \`make ' where is one of" @echo " html create HTML doc pages in html dir" - @echo " pdf create Manual.pdf and Developer.pdf in this dir" + @echo " pdf create Developer.pdf and Manual.pdf in this dir" @echo " old create old-style HTML doc pages in old dir" @echo " fetch fetch HTML and PDF files from LAMMPS web site" @echo " epub create ePUB format manual for e-book readers" @@ -116,17 +116,17 @@ mobi: epub pdf: utils/txt2html/txt2html.exe @(\ set -e; \ - cd src; \ + cd src/Developer; \ + pdflatex developer; \ + pdflatex developer; \ + mv developer.pdf ../../Developer.pdf; \ + cd ..; \ ../utils/txt2html/txt2html.exe -b *.txt; \ htmldoc --batch lammps.book; \ for s in `echo *.txt | sed -e 's,\.txt,\.html,g'` ; \ do grep -q $$s lammps.book || \ echo doc file $$s missing in src/lammps.book; done; \ rm *.html; \ - cd Developer; \ - pdflatex developer; \ - pdflatex developer; \ - mv developer.pdf ../../Developer.pdf; \ ) old: utils/txt2html/txt2html.exe From cf0f3b6b618e1f12456c3c41def8c48bbd1c235f Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 27 Sep 2018 06:23:59 -0400 Subject: [PATCH 195/302] Update manual for renamed or removed files --- doc/src/Commands_compute.txt | 2 +- doc/src/computes.txt | 2 +- doc/src/dump_image.txt | 7 +------ doc/src/fix_smd_move_triangulated_surface.txt | 2 +- doc/src/fix_smd_wall_surface.txt | 2 +- doc/src/fixes.txt | 2 +- doc/src/lammps.book | 4 ++-- 7 files changed, 8 insertions(+), 13 deletions(-) diff --git a/doc/src/Commands_compute.txt b/doc/src/Commands_compute.txt index 6185634187..724eeef98e 100644 --- a/doc/src/Commands_compute.txt +++ b/doc/src/Commands_compute.txt @@ -117,7 +117,7 @@ KOKKOS, o = USER-OMP, t = OPT. "smd/tlsph/strain"_compute_smd_tlsph_strain.html, "smd/tlsph/strain/rate"_compute_smd_tlsph_strain_rate.html, "smd/tlsph/stress"_compute_smd_tlsph_stress.html, -"smd/triangle/mesh/vertices"_compute_smd_triangle_mesh_vertices.html, +"smd/triangle/mesh/vertices"_compute_smd_triangle_vertices.html, "smd/ulsph/num/neighs"_compute_smd_ulsph_num_neighs.html, "smd/ulsph/strain"_compute_smd_ulsph_strain.html, "smd/ulsph/strain/rate"_compute_smd_ulsph_strain_rate.html, diff --git a/doc/src/computes.txt b/doc/src/computes.txt index a6a194ac24..e2d55605d3 100644 --- a/doc/src/computes.txt +++ b/doc/src/computes.txt @@ -91,7 +91,7 @@ Computes :h1 compute_smd_tlsph_strain compute_smd_tlsph_strain_rate compute_smd_tlsph_stress - compute_smd_triangle_mesh_vertices + compute_smd_triangle_vertices compute_smd_ulsph_num_neighs compute_smd_ulsph_strain compute_smd_ulsph_strain_rate diff --git a/doc/src/dump_image.txt b/doc/src/dump_image.txt index 9b56dd95a6..df1ff324c1 100644 --- a/doc/src/dump_image.txt +++ b/doc/src/dump_image.txt @@ -384,12 +384,7 @@ change this via the "dump_modify"_dump_modify.html command. :line The {fix} keyword can be used with a "fix"_fix.html that produces -objects to be drawn. An example is the "fix -surface/global"_fix_surface_global.html command which can draw lines -or triangles for 2d/3d simulations. - -NOTE: Aug 2016 - The fix surface/global command is not yet added to -LAMMPS. +objects to be drawn. The {fflag1} and {fflag2} settings are numerical values which are passed to the fix to affect how the drawing of its objects is done. diff --git a/doc/src/fix_smd_move_triangulated_surface.txt b/doc/src/fix_smd_move_triangulated_surface.txt index 2a998ba8c6..fca21b78f7 100644 --- a/doc/src/fix_smd_move_triangulated_surface.txt +++ b/doc/src/fix_smd_move_triangulated_surface.txt @@ -73,7 +73,7 @@ package"_Build_package.html doc page for more info. [Related commands:] -"smd/triangle_mesh_vertices"_compute_smd_triangle_mesh_vertices.html, +"smd/triangle_mesh_vertices"_compute_smd_triangle_vertices.html, "smd/wall_surface"_fix_smd_wall_surface.html [Default:] none diff --git a/doc/src/fix_smd_wall_surface.txt b/doc/src/fix_smd_wall_surface.txt index dc3625e95e..47527363a2 100644 --- a/doc/src/fix_smd_wall_surface.txt +++ b/doc/src/fix_smd_wall_surface.txt @@ -64,7 +64,7 @@ multiple objects in one file. [Related commands:] -"smd/triangle_mesh_vertices"_compute_smd_triangle_mesh_vertices.html, +"smd/triangle_mesh_vertices"_compute_smd_triangle_vertices.html, "smd/move_tri_surf"_fix_smd_move_triangulated_surface.html, "smd/tri_surface"_pair_smd_triangulated_surface.html diff --git a/doc/src/fixes.txt b/doc/src/fixes.txt index f2f257b134..7b4fdc429b 100644 --- a/doc/src/fixes.txt +++ b/doc/src/fixes.txt @@ -92,6 +92,7 @@ Fixes :h1 fix_nve fix_nve_asphere fix_nve_asphere_noforce + fix_nve_awpmd fix_nve_body fix_nve_dot fix_nve_dotc_langevin @@ -154,7 +155,6 @@ Fixes :h1 fix_srd fix_store_force fix_store_state - fix_surface_global fix_temp_berendsen fix_temp_csvr fix_temp_rescale diff --git a/doc/src/lammps.book b/doc/src/lammps.book index 0e5ceae861..972b026fde 100644 --- a/doc/src/lammps.book +++ b/doc/src/lammps.book @@ -311,6 +311,7 @@ fix_npt_sphere.html fix_nve.html fix_nve_asphere.html fix_nve_asphere_noforce.html +fix_nve_awpmd.html fix_nve_body.html fix_nve_dot.html fix_nve_dotc_langevin.html @@ -374,7 +375,6 @@ fix_spring_self.html fix_srd.html fix_store_force.html fix_store_state.html -fix_surface_global.html fix_temp_berendsen.html fix_temp_csvr.html fix_temp_rescale.html @@ -488,7 +488,7 @@ compute_smd_tlsph_shape.html compute_smd_tlsph_strain.html compute_smd_tlsph_strain_rate.html compute_smd_tlsph_stress.html -compute_smd_triangle_mesh_vertices.html +compute_smd_triangle_vertices.html compute_smd_ulsph_num_neighs.html compute_smd_ulsph_strain.html compute_smd_ulsph_strain_rate.html From 91286ddb0ebff3f652a33a7c1655110563e66e0d Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 27 Sep 2018 06:51:30 -0400 Subject: [PATCH 196/302] remove references to fix ave/spatial and ave/spatial/sphere --- doc/src/Errors_messages.txt | 62 ------------------------------------- doc/src/Errors_warnings.txt | 18 ----------- 2 files changed, 80 deletions(-) diff --git a/doc/src/Errors_messages.txt b/doc/src/Errors_messages.txt index a74182967c..695b949f7e 100644 --- a/doc/src/Errors_messages.txt +++ b/doc/src/Errors_messages.txt @@ -1092,11 +1092,6 @@ correct. :dd The specified file cannot be opened. Check that the path and name are correct. :dd -{Cannot open fix ave/spatial file %s} :dt - -The specified file cannot be opened. Check that the path and name are -correct. :dd - {Cannot open fix ave/time file %s} :dt The specified file cannot be opened. Check that the path and name are @@ -1677,10 +1672,6 @@ provided by an atom map. An atom map does not exist (by default) for non-molecular problems. Using the atom_modify map command will force an atom map to be created. :dd -{Cannot use fix ave/spatial z for 2 dimensional model} :dt - -Self-explanatory. :dd - {Cannot use fix bond/break with non-molecular systems} :dt Only systems with bonds that can be changed can be used. Atom_style @@ -2425,10 +2416,6 @@ Self-explanatory. :dd Self-explanatory. :dd -{Compute ID for fix ave/spatial does not exist} :dt - -Self-explanatory. :dd - {Compute ID for fix ave/time does not exist} :dt Self-explanatory. :dd @@ -4074,10 +4061,6 @@ Self-explanatory. :dd Self-explanatory. :dd -{Fix ID for fix ave/spatial does not exist} :dt - -Self-explanatory. :dd - {Fix ID for fix ave/time does not exist} :dt Self-explanatory. :dd @@ -4379,51 +4362,6 @@ same style. :dd Self-explanatory. :dd -{Fix ave/spatial compute does not calculate a per-atom array} :dt - -Self-explanatory. :dd - -{Fix ave/spatial compute does not calculate a per-atom vector} :dt - -A compute used by fix ave/spatial must generate per-atom values. :dd - -{Fix ave/spatial compute does not calculate per-atom values} :dt - -A compute used by fix ave/spatial must generate per-atom values. :dd - -{Fix ave/spatial compute vector is accessed out-of-range} :dt - -The index for the vector is out of bounds. :dd - -{Fix ave/spatial fix does not calculate a per-atom array} :dt - -Self-explanatory. :dd - -{Fix ave/spatial fix does not calculate a per-atom vector} :dt - -A fix used by fix ave/spatial must generate per-atom values. :dd - -{Fix ave/spatial fix does not calculate per-atom values} :dt - -A fix used by fix ave/spatial must generate per-atom values. :dd - -{Fix ave/spatial fix vector is accessed out-of-range} :dt - -The index for the vector is out of bounds. :dd - -{Fix ave/spatial for triclinic boxes requires units reduced} :dt - -Self-explanatory. :dd - -{Fix ave/spatial settings invalid with changing box size} :dt - -If the box size changes, only the units reduced option can be -used. :dd - -{Fix ave/spatial variable is not atom-style variable} :dt - -A variable used by fix ave/spatial must generate per-atom values. :dd - {Fix ave/time cannot set output array intensive/extensive from these inputs} :dt One of more of the vector inputs has individual elements which are diff --git a/doc/src/Errors_warnings.txt b/doc/src/Errors_warnings.txt index 98b66f2aa5..0980120a10 100644 --- a/doc/src/Errors_warnings.txt +++ b/doc/src/Errors_warnings.txt @@ -291,24 +291,6 @@ This may cause accuracy problems. :dd This may cause accuracy problems. :dd -{Fix thermal/conductivity comes before fix ave/spatial} :dt - -The order of these 2 fixes in your input script is such that fix -thermal/conductivity comes first. If you are using fix ave/spatial to -measure the temperature profile induced by fix viscosity, then this -may cause a glitch in the profile since you are averaging immediately -after swaps have occurred. Flipping the order of the 2 fixes -typically helps. :dd - -{Fix viscosity comes before fix ave/spatial} :dt - -The order of these 2 fixes in your input script is such that -fix viscosity comes first. If you are using fix ave/spatial -to measure the velocity profile induced by fix viscosity, then -this may cause a glitch in the profile since you are averaging -immediately after swaps have occurred. Flipping the order -of the 2 fixes typically helps. :dd - {Fixes cannot send data in Kokkos communication, switching to classic communication} :dt This is current restriction with Kokkos. :dd From 5481e99331f126baca35f1cdb14aec8bbb896dbf Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 27 Sep 2018 06:52:20 -0400 Subject: [PATCH 197/302] remove broken USER-OMP pair style --- src/USER-OMP/pair_nb3b_harmonic_omp.cpp | 170 ------------------------ src/USER-OMP/pair_nb3b_harmonic_omp.h | 49 ------- 2 files changed, 219 deletions(-) delete mode 100644 src/USER-OMP/pair_nb3b_harmonic_omp.cpp delete mode 100644 src/USER-OMP/pair_nb3b_harmonic_omp.h diff --git a/src/USER-OMP/pair_nb3b_harmonic_omp.cpp b/src/USER-OMP/pair_nb3b_harmonic_omp.cpp deleted file mode 100644 index 2ab96c43a0..0000000000 --- a/src/USER-OMP/pair_nb3b_harmonic_omp.cpp +++ /dev/null @@ -1,170 +0,0 @@ -/* ---------------------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - This software is distributed under the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -/* ---------------------------------------------------------------------- - Contributing author: Axel Kohlmeyer (Temple U) -------------------------------------------------------------------------- */ - -#include -#include "pair_nb3b_harmonic_omp.h" -#include "atom.h" -#include "comm.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" - -#include "suffix.h" -using namespace LAMMPS_NS; - -/* ---------------------------------------------------------------------- */ - -PairNb3bHarmonicOMP::PairNb3bHarmonicOMP(LAMMPS *lmp) : - PairNb3bHarmonic(lmp), ThrOMP(lmp, THR_PAIR) -{ - suffix_flag |= Suffix::OMP; - respa_enable = 0; -} - -/* ---------------------------------------------------------------------- */ - -void PairNb3bHarmonicOMP::compute(int eflag, int vflag) -{ - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; - - const int nall = atom->nlocal + atom->nghost; - const int nthreads = comm->nthreads; - const int inum = list->inum; - -#if defined(_OPENMP) -#pragma omp parallel default(none) shared(eflag,vflag) -#endif - { - int ifrom, ito, tid; - - loop_setup_thr(ifrom, ito, tid, inum, nthreads); - ThrData *thr = fix->get_thr(tid); - thr->timer(Timer::START); - ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr); - - if (evflag) { - if (eflag) { - eval<1,1>(ifrom, ito, thr); - } else { - eval<1,0>(ifrom, ito, thr); - } - } else eval<0,0>(ifrom, ito, thr); - - thr->timer(Timer::PAIR); - reduce_thr(this, eflag, vflag, thr); - } // end of omp parallel region -} - -template -void PairNb3bHarmonicOMP::eval(int iifrom, int iito, ThrData * const thr) -{ - int i,j,k,ii,jj,kk,jnum,jnumm1; - int itype,jtype,ktype,ijparam,ikparam,ijkparam; - double xtmp,ytmp,ztmp,evdwl; - double rsq1,rsq2; - double delr1[3],delr2[3],fj[3],fk[3]; - int *ilist,*jlist,*numneigh,**firstneigh; - - evdwl = 0.0; - - const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0]; - dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0]; - const int * _noalias const type = atom->type; - - ilist = list->ilist; - numneigh = list->numneigh; - firstneigh = list->firstneigh; - - double fxtmp,fytmp,fztmp; - - // loop over full neighbor list of my atoms - - for (ii = iifrom; ii < iito; ++ii) { - - i = ilist[ii]; - itype = map[type[i]]; - xtmp = x[i].x; - ytmp = x[i].y; - ztmp = x[i].z; - fxtmp = fytmp = fztmp = 0.0; - - // two-body interactions, skip half of them - - jlist = firstneigh[i]; - jnum = numneigh[i]; - jnumm1 = jnum - 1; - - for (jj = 0; jj < jnumm1; jj++) { - j = jlist[jj]; - j &= NEIGHMASK; - jtype = map[type[j]]; - ijparam = elem2param[itype][jtype][jtype]; - delr1[0] = x[j].x - xtmp; - delr1[1] = x[j].y - ytmp; - delr1[2] = x[j].z - ztmp; - rsq1 = delr1[0]*delr1[0] + delr1[1]*delr1[1] + delr1[2]*delr1[2]; - if (rsq1 > params[ijparam].cutsq) continue; - - double fjxtmp,fjytmp,fjztmp; - fjxtmp = fjytmp = fjztmp = 0.0; - - for (kk = jj+1; kk < jnum; kk++) { - k = jlist[kk]; - k &= NEIGHMASK; - ktype = map[type[k]]; - ikparam = elem2param[itype][ktype][ktype]; - ijkparam = elem2param[itype][jtype][ktype]; - - delr2[0] = x[k].x - xtmp; - delr2[1] = x[k].y - ytmp; - delr2[2] = x[k].z - ztmp; - rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2]; - if (rsq2 > params[ikparam].cutsq) continue; - - threebody(¶ms[ijparam],¶ms[ikparam],¶ms[ijkparam], - rsq1,rsq2,delr1,delr2,fj,fk,EFLAG,evdwl); - - fxtmp -= fj[0] + fk[0]; - fytmp -= fj[1] + fk[1]; - fztmp -= fj[2] + fk[2]; - fjxtmp += fj[0]; - fjytmp += fj[1]; - fjztmp += fj[2]; - f[k].x += fk[0]; - f[k].y += fk[1]; - f[k].z += fk[2]; - - if (EVFLAG) ev_tally3_thr(this,i,j,k,evdwl,0.0,fj,fk,delr1,delr2,thr); - } - f[j].x += fjxtmp; - f[j].y += fjytmp; - f[j].z += fjztmp; - } - f[i].x += fxtmp; - f[i].y += fytmp; - f[i].z += fztmp; - } -} - -/* ---------------------------------------------------------------------- */ - -double PairNb3bHarmonicOMP::memory_usage() -{ - double bytes = memory_usage_thr(); - bytes += PairNb3bHarmonic::memory_usage(); - - return bytes; -} diff --git a/src/USER-OMP/pair_nb3b_harmonic_omp.h b/src/USER-OMP/pair_nb3b_harmonic_omp.h deleted file mode 100644 index 6b8fbd8897..0000000000 --- a/src/USER-OMP/pair_nb3b_harmonic_omp.h +++ /dev/null @@ -1,49 +0,0 @@ -/* -*- c++ -*- ---------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -/* ---------------------------------------------------------------------- - Contributing author: Axel Kohlmeyer (Temple U) -------------------------------------------------------------------------- */ - -#ifdef PAIR_CLASS - -//PairStyle(nb3b/harmonic/omp,PairNb3bHarmonicOMP) -PairStyle(disabled,PairNb3bHarmonicOMP) - -#else - -#ifndef LMP_PAIR_NB3BHARMONIC_OMP_H -#define LMP_PAIR_NB3BHARMONIC_OMP_H - -#include "pair_nb3b_harmonic.h" -#include "thr_omp.h" - -namespace LAMMPS_NS { - -class PairNb3bHarmonicOMP : public PairNb3bHarmonic, public ThrOMP { - - public: - PairNb3bHarmonicOMP(class LAMMPS *); - - virtual void compute(int, int); - virtual double memory_usage(); - - private: - template - void eval(int ifrom, int ito, ThrData * const thr); -}; - -} - -#endif -#endif From e1627caf04eb20d6fcf2282964f025c866b3aad9 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 27 Sep 2018 07:20:03 -0400 Subject: [PATCH 198/302] integrate compute ptm/atom and USER-PTM into the docs --- doc/src/Commands_compute.txt | 1 + doc/src/Packages_details.txt | 20 ++++++++++++++++++++ doc/src/Packages_user.txt | 1 + doc/src/compute_ptm_atom.txt | 6 +++++- doc/src/computes.txt | 1 + doc/src/lammps.book | 1 + 6 files changed, 29 insertions(+), 1 deletion(-) diff --git a/doc/src/Commands_compute.txt b/doc/src/Commands_compute.txt index 028e274c9b..a89f3adf5d 100644 --- a/doc/src/Commands_compute.txt +++ b/doc/src/Commands_compute.txt @@ -95,6 +95,7 @@ KOKKOS, o = USER-OMP, t = OPT. "property/atom"_compute_property_atom.html, "property/chunk"_compute_property_chunk.html, "property/local"_compute_property_local.html, +"ptm/atom"_compute_ptm_atom.html "rdf"_compute_rdf.html, "reduce"_compute_reduce.html, "reduce/region"_compute_reduce.html, diff --git a/doc/src/Packages_details.txt b/doc/src/Packages_details.txt index 494f393a16..73345a2940 100644 --- a/doc/src/Packages_details.txt +++ b/doc/src/Packages_details.txt @@ -89,6 +89,7 @@ as contained in the file name. "USER-NETCDF"_#PKG-USER-NETCDF, "USER-OMP"_#PKG-USER-OMP, "USER-PHONON"_#PKG-USER-PHONON, +"USER-PTM"_#PKG-USER-PTM, "USER-QMMM"_#PKG-USER-QMMM, "USER-QTB"_#PKG-USER-QTB, "USER-QUIP"_#PKG-USER-QUIP, @@ -1744,6 +1745,25 @@ examples/USER/phonon :ul :line +USER-PTM package :link(PKG-USER-PTM),h4 + +[Contents:] + +A "compute ptm/atom"_compute_ptm.html command that calculates +local structure characterization using the Polyhedral Template +Matching methodology. + +[Author:] Peter Mahler Larsen (MIT). + +[Supporting info:] + +src/USER-PHONON: filenames -> commands +src/USER-PHONON/README +"fix phonon"_fix_phonon.html +examples/USER/phonon :ul + +:line + USER-QMMM package :link(PKG-USER-QMMM),h4 [Contents:] diff --git a/doc/src/Packages_user.txt b/doc/src/Packages_user.txt index 70ac6022b6..6d3a8f754a 100644 --- a/doc/src/Packages_user.txt +++ b/doc/src/Packages_user.txt @@ -62,6 +62,7 @@ Package, Description, Doc page, Example, Library "USER-NETCDF"_Packages_details.html#PKG-USER-NETCDF, dump output via NetCDF,"dump netcdf"_dump_netcdf.html, n/a, ext "USER-OMP"_Packages_details.html#PKG-USER-OMP, OpenMP-enabled styles,"Speed omp"_Speed_omp.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, no "USER-PHONON"_Packages_details.html#PKG-USER-PHONON, phonon dynamical matrix,"fix phonon"_fix_phonon.html, USER/phonon, no +"USER-PTM"_Packages_details.html#PKG-USER-PTM, Polyhedral Template Matching,"compute ptm/atom"_compute_ptm.html, n/a, no "USER-QMMM"_Packages_details.html#PKG-USER-QMMM, QM/MM coupling,"fix qmmm"_fix_qmmm.html, USER/qmmm, ext "USER-QTB"_Packages_details.html#PKG-USER-QTB, quantum nuclear effects,"fix qtb"_fix_qtb.html "fix qbmsst"_fix_qbmsst.html, qtb, no "USER-QUIP"_Packages_details.html#PKG-USER-QUIP, QUIP/libatoms interface,"pair_style quip"_pair_quip.html, USER/quip, ext diff --git a/doc/src/compute_ptm_atom.txt b/doc/src/compute_ptm_atom.txt index c668eb7726..6fe4d012f5 100644 --- a/doc/src/compute_ptm_atom.txt +++ b/doc/src/compute_ptm_atom.txt @@ -101,7 +101,11 @@ The (qw,qx,qy,qz) parameters represent the orientation of the local structure in quaternion form. The reference coordinates for each template (from which the orientation is determined) can be found in the {ptm_constants.h} file in the PTM source directory. -[Restrictions:] none +[Restrictions:] + +This fix is part of the USER-PTM package. It is only enabled if +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/computes.txt b/doc/src/computes.txt index 46dd30f757..aa6cf5bb64 100644 --- a/doc/src/computes.txt +++ b/doc/src/computes.txt @@ -70,6 +70,7 @@ Computes :h1 compute_property_atom compute_property_chunk compute_property_local + compute_ptm_atom compute_rdf compute_reduce compute_rigid_local diff --git a/doc/src/lammps.book b/doc/src/lammps.book index 828863ae67..ae58e66efd 100644 --- a/doc/src/lammps.book +++ b/doc/src/lammps.book @@ -467,6 +467,7 @@ compute_pressure_uef.html compute_property_atom.html compute_property_chunk.html compute_property_local.html +compute_ptm_atom.html compute_rdf.html compute_reduce.html compute_rigid_local.html From f23b638d471e3e76f23b82a229cb9a62a8638cf3 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 27 Sep 2018 07:23:38 -0400 Subject: [PATCH 199/302] include USER-PTM into git management --- .github/CODEOWNERS | 1 + src/.gitignore | 5 +++++ 2 files changed, 6 insertions(+) diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS index 4f561a4c19..164bc05d60 100644 --- a/.github/CODEOWNERS +++ b/.github/CODEOWNERS @@ -30,6 +30,7 @@ src/USER-MOFFF/* @hheenen src/USER-MOLFILE/* @akohlmey src/USER-NETCDF/* @pastewka src/USER-PHONON/* @lingtikong +src/USER-PTM/* @pmla src/USER-OMP/* @akohlmey src/USER-QMMM/* @akohlmey src/USER-REAXC/* @hasanmetin diff --git a/src/.gitignore b/src/.gitignore index df3a22a5cd..13a8622fe1 100644 --- a/src/.gitignore +++ b/src/.gitignore @@ -41,6 +41,11 @@ /pair_meamc.cpp /pair_meamc.h +/ptm_*.cpp +/ptm_*.h +/compute_ptm.cpp +/compute_ptm.h + /fix_qeq*.cpp /fix_qeq*.h From 9ae6cb5c4fde9ad598aa7eecd8d2a92937b1a0c9 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 27 Sep 2018 07:28:44 -0400 Subject: [PATCH 200/302] add recently renamed file to purge list --- src/Purge.list | 3 +++ 1 file changed, 3 insertions(+) diff --git a/src/Purge.list b/src/Purge.list index c70392c935..6cfc580c25 100644 --- a/src/Purge.list +++ b/src/Purge.list @@ -24,6 +24,9 @@ style_nstencil.h style_ntopo.h # other auto-generated files lmpinstalledpkgs.h +# renamed on 25 September 2018 +compute_smd_triangle_mesh_vertices.h +compute_smd_triangle_mesh_vertices.cpp # renamed on 6 September 2018 pair_cdeam_omp.h pair_cdeam_omp.cpp From f58aa05e02129c0d125b1acb9700d0756ab73c42 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 27 Sep 2018 07:44:54 -0400 Subject: [PATCH 201/302] remove references to USER-OMP version of pair style nb3b/harmonic --- doc/src/Commands_pair.txt | 2 +- doc/src/pair_nb3b_harmonic.txt | 23 ----------------------- 2 files changed, 1 insertion(+), 24 deletions(-) diff --git a/doc/src/Commands_pair.txt b/doc/src/Commands_pair.txt index 3b6a5f48fa..ae115dd904 100644 --- a/doc/src/Commands_pair.txt +++ b/doc/src/Commands_pair.txt @@ -167,7 +167,7 @@ OPT. "morse/soft"_pair_morse.html, "multi/lucy"_pair_multi_lucy.html, "multi/lucy/rx (k)"_pair_multi_lucy_rx.html, -"nb3b/harmonic (o)"_pair_nb3b_harmonic.html, +"nb3b/harmonic"_pair_nb3b_harmonic.html, "nm/cut (o)"_pair_nm.html, "nm/cut/coul/cut (o)"_pair_nm.html, "nm/cut/coul/long (o)"_pair_nm.html, diff --git a/doc/src/pair_nb3b_harmonic.txt b/doc/src/pair_nb3b_harmonic.txt index 6a119d74e1..2b2152a873 100644 --- a/doc/src/pair_nb3b_harmonic.txt +++ b/doc/src/pair_nb3b_harmonic.txt @@ -7,7 +7,6 @@ :line pair_style nb3b/harmonic command :h3 -pair_style nb3b/harmonic/omp command :h3 [Syntax:] @@ -89,28 +88,6 @@ a particular simulation; LAMMPS ignores those entries. :line -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - [Restrictions:] This pair style can only be used if LAMMPS was built with the MANYBODY From 2da999d864800a839e42163100f3af0e09880a56 Mon Sep 17 00:00:00 2001 From: Christoph Junghans Date: Thu, 27 Sep 2018 12:18:43 -0600 Subject: [PATCH 202/302] cmake: prevent in-source build --- cmake/CMakeLists.txt | 2 ++ cmake/Modules/PreventInSourceBuilds.cmake | 22 ++++++++++++++++++++++ 2 files changed, 24 insertions(+) create mode 100644 cmake/Modules/PreventInSourceBuilds.cmake diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index ce8de0b501..20a2c2729d 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -69,6 +69,8 @@ get_lammps_version(${LAMMPS_SOURCE_DIR}/version.h LAMMPS_VERSION) # Cmake modules/macros are in a subdirectory to keep this file cleaner set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/Modules) +include(PreventInSourceBuilds) + if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CXX_FLAGS) #release comes with -O3 by default set(CMAKE_BUILD_TYPE Release CACHE STRING "Choose the type of build, options are: None Debug Release RelWithDebInfo MinSizeRel." FORCE) diff --git a/cmake/Modules/PreventInSourceBuilds.cmake b/cmake/Modules/PreventInSourceBuilds.cmake new file mode 100644 index 0000000000..20d9d25590 --- /dev/null +++ b/cmake/Modules/PreventInSourceBuilds.cmake @@ -0,0 +1,22 @@ +# - Prevent in-source builds. +# https://stackoverflow.com/questions/1208681/with-cmake-how-would-you-disable-in-source-builds/ + +function(prevent_in_source_builds) + # make sure the user doesn't play dirty with symlinks + get_filename_component(srcdir "${CMAKE_SOURCE_DIR}" REALPATH) + get_filename_component(srcdir2 "${CMAKE_SOURCE_DIR}/.." REALPATH) + get_filename_component(bindir "${CMAKE_BINARY_DIR}" REALPATH) + + # disallow in-source builds + if("${srcdir}" STREQUAL "${bindir}" OR "${srcdir2}" STREQUAL "${bindir}") + message(FATAL_ERROR "\ + +CMake must not to be run in the source directory. \ +Rather create a dedicated build directory and run CMake there. \ +To clean up after this aborted in-place compilation: + rm -r CMakeCache.txt CMakeFiles +") + endif() +endfunction() + +prevent_in_source_builds() From 21c59d4cf0762bceefaab1e96284ce8a244a6ec6 Mon Sep 17 00:00:00 2001 From: dilkins Date: Fri, 28 Sep 2018 12:46:11 +0200 Subject: [PATCH 203/302] Fast-forward Langevin functionality included --- doc/src/fix_ffl.txt | 129 ++++++++++ src/USER-MISC/README | 1 + src/USER-MISC/fix_ffl.cpp | 527 ++++++++++++++++++++++++++++++++++++++ src/USER-MISC/fix_ffl.h | 67 +++++ 4 files changed, 724 insertions(+) create mode 100644 doc/src/fix_ffl.txt create mode 100644 src/USER-MISC/fix_ffl.cpp create mode 100644 src/USER-MISC/fix_ffl.h diff --git a/doc/src/fix_ffl.txt b/doc/src/fix_ffl.txt new file mode 100644 index 0000000000..8d6b243142 --- /dev/null +++ b/doc/src/fix_ffl.txt @@ -0,0 +1,129 @@ + + + +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +fix ffl command :h3 + +[Syntax:] + +fix ID id-group ffl tau Tstart Tstop seed \[flip-type\] :pre + +ID, group-ID are documented in "fix"_fix.html command :ulb,l +ffl = style name of this fix command :l +tau = thermostat parameter (positive real) :l +Tstart, Tstop = temperature ramp during the run :l +seed = random number seed to use for generating noise (positive integer) :l +one more value may be appended :l + flip-type = determines the flipping type, can be chosen between rescale - no_flip - hard - soft, if no flip type is given, rescale will be chosen by default :pre +:ule + +[Examples:] + +fix 3 boundary ffl 10 300 300 31415 +fix 1 all ffl 100 500 500 9265 soft :pre + +[Description:] + +Apply a Fast-Forward Langevin Equation (FFL) thermostat as described +in "(Hijazi)"_#Hijazi. Contrary to +"fix langevin"_fix_langevin.html, this fix performs both +thermostatting and evolution of the Hamiltonian equations of motion, so it +should not be used together with "fix nve"_fix_nve.html -- at least not +on the same atom groups. + +The time-evolution of a single particle undergoing Langevin dynamics is described +by the equations + +\begin\{equation\} \frac \{dq\}\{dt\} = \frac\{p\}\{m\}, \end\{equation\} + +\begin\{equation\} \frac \{dp\}\{dt\} = -\gamma p + W + F, \end\{equation\} + +where \(F\) is the physical force, \(\gamma\) is the friction coefficient, and \(W\) is a +Gaussian random force. + +The friction coefficient is the inverse of the thermostat parameter : \(\gamma = 1/\tau\), with \(\tau\) the thermostat parameter {tau}. +The thermostat parameter is given in the time units, \(\gamma\) is in inverse time units. + +Equilibrium sampling a temperature T is obtained by specifying the +target value as the {Tstart} and {Tstop} arguments, so that the internal +constants depending on the temperature are computed automatically. + +The random number {seed} must be a positive integer. A Marsaglia random +number generator is used. Each processor uses the input seed to +generate its own unique seed and its own stream of random numbers. +Thus the dynamics of the system will not be identical on two runs on +different numbers of processors. + +The flipping type {flip-type} can be chosen between 4 types described in +"(Hijazi)"_#Hijazi. The flipping operation occurs during the thermostatting +step and it flips the momenta of the atoms. If no_flip is chosen, no flip +will be executed and the integration will be the same as a standard +Langevin thermostat "(Bussi)"_#Bussi. The other flipping types are : rescale - hard - soft. + +[Restart, fix_modify, output, run start/stop, minimize info:] + +The instantaneous values of the extended variables are written to +"binary restart files"_restart.html. Because the state of the random +number generator is not saved in restart files, this means you cannot +do "exact" restarts with this fix, where the simulation continues on +the same as if no restart had taken place. However, in a statistical +sense, a restarted simulation should produce the same behavior. +Note however that you should use a different seed each time you +restart, otherwise the same sequence of random numbers will be used +each time, which might lead to stochastic synchronization and +subtle artefacts in the sampling. + +This fix can ramp its target temperature over multiple runs, using the +{start} and {stop} keywords of the "run"_run.html command. See the +"run"_run.html command for details of how to do this. + +The "fix_modify"_fix_modify.html {energy} option is supported by this +fix to add the energy change induced by Langevin thermostatting to the +system's potential energy as part of "thermodynamic +output"_thermo_style.html. + +This fix computes a global scalar which can be accessed by various +"output commands"_Section_howto.html#howto_15. The scalar is the +cumulative energy change due to this fix. The scalar value +calculated by this fix is "extensive". + +[Restrictions:] + +The GLE thermostat in its current implementation should not be used +with rigid bodies, SHAKE or RATTLE. It is expected that all the +thermostatted degrees of freedom are fully flexible, and the sampled +ensemble will not be correct otherwise. + +In order to perform constant-pressure simulations please use +"fix press/berendsen"_fix_press_berendsen.html, rather than +"fix npt"_fix_nh.html, to avoid duplicate integration of the +equations of motion. + +This fix is part of the USER-MISC package. It is only enabled if LAMMPS +was built with that package. See the "Making +LAMMPS"_Section_start.html#start_3 section for more info. + +[Related commands:] + +"fix nvt"_fix_nh.html, "fix temp/rescale"_fix_temp_rescale.html, "fix +viscous"_fix_viscous.html, "fix nvt"_fix_nh.html, "pair_style +dpd/tstat"_pair_dpd.html, "fix gld"_fix_gld.html, "fix gle"_fix_gle.html + +:line + +:link(Hijazi) +[(Hijazi)] M. Hijazi, D. M. Wilkins, M. Ceriotti, J. Chem. Phys. 148, 184109 (2018) +:link(Bussi) +[(Bussi)] G. Bussi, M. Parrinello, Phs. Rev. E 75, 056707 (2007) + diff --git a/src/USER-MISC/README b/src/USER-MISC/README index eb221c07db..b3c3e85948 100644 --- a/src/USER-MISC/README +++ b/src/USER-MISC/README @@ -44,6 +44,7 @@ dihedral_style table/cut, Mike Salerno, ksalerno@pha.jhu.edu, 11 May 18 fix addtorque, Laurent Joly (U Lyon), ljoly.ulyon at gmail.com, 8 Aug 11 fix ave/correlate/long, Jorge Ramirez (UPM Madrid), jorge.ramirez at upm.es, 21 Oct 2015 fix bond/react, Jacob Gissinger (CU Boulder), info at disarmmd.org, 24 Feb 2018 +fix ffl, David Wilkins (EPFL Lausanne), david.wilkins @ epfl.ch, 28 Sep 2018 fix filter/corotate, Lukas Fath (KIT), lukas.fath at kit.edu, 15 Mar 2017 fix flow/gauss, Joel Eaves (CU Boulder), Joel.Eaves@Colorado.edu, 23 Aug 2016 fix gle, Michele Ceriotti (EPFL Lausanne), michele.ceriotti at gmail.com, 24 Nov 2014 diff --git a/src/USER-MISC/fix_ffl.cpp b/src/USER-MISC/fix_ffl.cpp new file mode 100644 index 0000000000..54e5c03a62 --- /dev/null +++ b/src/USER-MISC/fix_ffl.cpp @@ -0,0 +1,527 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Fast-forward Langevin thermostat, see + M. Hijazi, D. M. Wilkins, M. Ceriotti, J. Chem. Phys. 148, 184109 (2018) +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing authors: Lionel Constantin (EPFL), David M. Wilkins (EPFL), + Michele Ceriotti (EPFL) +------------------------------------------------------------------------- */ + +#include +#include +#include +#include +#include "fix_ffl.h" +#include "math_extra.h" +#include "atom.h" +#include "atom_vec_ellipsoid.h" +#include "force.h" +#include "update.h" +#include "modify.h" +#include "compute.h" +#include "domain.h" +#include "region.h" +#include "respa.h" +#include "comm.h" +#include "input.h" +#include "variable.h" +#include "random_mars.h" +#include "memory.h" +#include "error.h" +#include "group.h" + +using namespace LAMMPS_NS; +using namespace FixConst; + +enum {NOBIAS,BIAS}; +enum {CONSTANT,EQUAL,ATOM}; +//#define FFL_DEBUG 1 + +#define MAXLINE 1024 + +/* syntax for fix_ffl: + * fix nfix id-group ffl tau Tstart Tstop seed [flip_type] + * + * */ + +/* ---------------------------------------------------------------------- */ + + +FixFFL::FixFFL(LAMMPS *lmp, int narg, char **arg) : + Fix(lmp, narg, arg) +{ + + + if (narg < 7) + error->all(FLERR,"Illegal fix ffl command. Expecting: fix " + " ffl "); + + restart_peratom = 1; + time_integrate = 1; + scalar_flag = 1; + + //gamma = 1/ time constant(tau) + if (force->numeric(FLERR,arg[3]) <= 0) + error->all(FLERR,"Illegal fix ffl tau value, should be greater than 0"); + gamma = 1.0/force->numeric(FLERR,arg[3]); + ffl_every=1; + ffl_step=0; + + // start temperature (t ramp) + t_start = force->numeric(FLERR,arg[4]); + + // final temperature (t ramp) + t_stop = force->numeric(FLERR,arg[5]); + + // PRNG seed + int seed = force->inumeric(FLERR,arg[6]); + + // Flip type used, uses rescale if no flip is given + if (narg == 8) strcpy(flip_type,arg[7]); + else strcpy(flip_type,"rescale"); + + + // Tests if the flip type is valid + if ( strcmp(flip_type,"rescale") && strcmp(flip_type,"hard") + && strcmp(flip_type,"soft") && strcmp(flip_type,"no_flip") ) + error->all(FLERR,"Illegal fix ffl flip type, only accepts : rescale - hard - soft - no_flip"); + + if ( strcmp(flip_type,"no_flip") == 0 ) flip_int = 0; + if ( strcmp(flip_type,"rescale") == 0 ) flip_int = 1; + if ( strcmp(flip_type,"hard") == 0 ) flip_int = 2; + if ( strcmp(flip_type,"soft") == 0 ) flip_int = 3; + + t_target=t_start; + const double kT = t_target * force->boltz / force->mvv2e; + + + // initialize Marsaglia RNG with processor-unique seed + // NB: this means runs will not be the same with different numbers of processors + if (seed <= 0) error->all(FLERR,"Illegal fix ffl command"); + random = new RanMars(lmp,seed + comm->me); + + // allocate per-type arrays for mass-scaling + sqrt_m=NULL; + memory->grow(sqrt_m, atom->ntypes+1,"ffl:sqrt_m"); + + // allocates space for temporaries + ffl_tmp1=ffl_tmp2=NULL; + + grow_arrays(atom->nmax); + + // add callbacks to enable restarts + atom->add_callback(0); + atom->add_callback(1); + + energy = 0.0; +} + + +/* --- Frees up memory used by temporaries and buffers ------------------ */ + +FixFFL::~FixFFL() +{ + delete random; + + memory->destroy(sqrt_m); + memory->destroy(ffl_tmp1); + memory->destroy(ffl_tmp2); +} + +/* ---------------------------------------------------------------------- */ + +int FixFFL::setmask() +{ + int mask = 0; + + mask |= INITIAL_INTEGRATE; + mask |= FINAL_INTEGRATE; + mask |= INITIAL_INTEGRATE_RESPA; + mask |= FINAL_INTEGRATE_RESPA; + mask |= THERMO_ENERGY; + + + return mask; +} + +/* ------- Initializes one-time quantities for FFL ---------------------- */ + +void FixFFL::init() +{ + doffl = 1; + dtv = update->dt; + dtf = 0.5 * update->dt * force->ftm2v; + + // set force prefactors + if (!atom->rmass) + { + for (int i = 1; i <= atom->ntypes; i++) + { + sqrt_m[i] = sqrt(atom->mass[i]); + } + } + + if (strstr(update->integrate_style,"respa")) + { + nlevels_respa = ((Respa *) update->integrate)->nlevels; + step_respa = ((Respa *) update->integrate)->step; + } + + init_ffl(); +} + +/* ------- Initializes constants for FFL (change with T and dt) ------- */ + +void FixFFL::init_ffl() +{ + const double kT = t_target * force->boltz / force->mvv2e; + + // compute constants for FFL + + c1 = exp ( - gamma * 0.5 * dtv ); + c2 = sqrt( (1.0 - c1*c1)* kT ); //without the mass term + + +} + + + +/* ---------------------------------------------------------------------- */ + +void FixFFL::setup(int vflag) +{ + if (strstr(update->integrate_style,"verlet")) + post_force(vflag); + else + { + ((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1); + post_force_respa(vflag,nlevels_respa-1,0); + ((Respa *) update->integrate)->copy_f_flevel(nlevels_respa-1); + } +} + +void FixFFL::ffl_integrate() +{ + double **v = atom->v; + double *rmass = atom->rmass, smi, ismi; + double factor; + int *type = atom->type; + int *mask = atom->mask; + int nlocal = atom->nlocal; + if (igroup == atom->firstgroup) nlocal = atom->nfirst; + + // loads momentum data (mass-scaled) into the temporary vectors for the propagation + int nk=0; + double deltae=0.0; + for (int i = 0; i < nlocal; i++) + { + if (mask[i] & groupbit) + { + if (rmass) smi = sqrt(rmass[i]); + else smi = sqrt_m[type[i]]; + + for (int k = 0; k<3; k++) + { + // first loads velocities and accumulates conserved quantity + ffl_tmp2[nk] = v[i][k] * smi; + deltae += ffl_tmp2[nk] * ffl_tmp2[nk]; + nk++; + } + } + } + + //fills up a vector of random numbers + for (int i = 0; i < nk; i++) ffl_tmp1[i] = random->gaussian(); + + + // unloads momentum data (mass-scaled) from the temporary vectors + nk=0; + for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) + { + if (rmass) ismi = 1.0 / sqrt(rmass[i]); + else ismi = 1.0/ sqrt_m[type[i]]; + + for (int k = 0; k<3; k++) + { + // fetches new velocities and completes computation of the conserved quantity change + v[i][k]= c1*v[i][k] + c2*ffl_tmp1[nk]*ismi; + + deltae-= v[i][k]*v[i][k] /ismi /ismi; + + //flips the sign of the momentum (HARD FLIP) + if ( flip_int == 2) + { + if (v[i][k]*ffl_tmp2[nk] < 0.0) v[i][k] = -v[i][k]; + } + + nk++; + } + } + + //rescale operation (RESCALE FLIP) + if (flip_int == 1) + { + nk=0; + for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) + { + factor = sqrt ((v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) / + (ffl_tmp2[nk]*ffl_tmp2[nk] + ffl_tmp2[nk+1]*ffl_tmp2[nk+1] + + ffl_tmp2[nk+2]*ffl_tmp2[nk+2])); + + for (int k = 0; k<3; k++) + { + v[i][k]= factor * ffl_tmp2[nk]; + nk++; + } + } + } + + + //soft flip operation (SOFT FLIP) + if (flip_int == 3) + { + nk=0; + for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) + { + factor = v[i][0]*ffl_tmp2[nk] + v[i][1]*ffl_tmp2[nk+1] + v[i][2]*ffl_tmp2[nk+2]; + if (factor < 0) + { + factor = factor / (ffl_tmp2[nk]*ffl_tmp2[nk] + ffl_tmp2[nk+1]*ffl_tmp2[nk+1] + + ffl_tmp2[nk+2]*ffl_tmp2[nk+2]); + + for (int k = 0; k<3; k++) + { + v[i][k] -= 2.0 * factor * ffl_tmp2[nk]; + nk++; + } + } + else + nk += 3; + } + } + + energy += deltae*0.5*force->mvv2e; + +} + +void FixFFL::initial_integrate(int vflag) +{ + double dtfm; + + // update v and x of atoms in group + double **x = atom->x; + double **v = atom->v; + double **f = atom->f; + double *rmass = atom->rmass; + double *mass = atom->mass; + int *type = atom->type; + int *mask = atom->mask; + int nlocal = atom->nlocal; + if (igroup == atom->firstgroup) nlocal = atom->nfirst; + + ffl_step--; + if (doffl && ffl_step<1) ffl_integrate(); + + if (rmass) + { + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) + { + dtfm = dtf / rmass[i]; + v[i][0] += dtfm * f[i][0]; + v[i][1] += dtfm * f[i][1]; + v[i][2] += dtfm * f[i][2]; + x[i][0] += dtv * v[i][0]; + x[i][1] += dtv * v[i][1]; + x[i][2] += dtv * v[i][2]; + } + + } + else + { + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) + { + dtfm = dtf / mass[type[i]]; + v[i][0] += dtfm * f[i][0]; + v[i][1] += dtfm * f[i][1]; + v[i][2] += dtfm * f[i][2]; + x[i][0] += dtv * v[i][0]; + x[i][1] += dtv * v[i][1]; + x[i][2] += dtv * v[i][2]; + } + } +} + +void FixFFL::final_integrate() +{ + double dtfm; + + // update v of atoms in group + + double **v = atom->v; + double **f = atom->f; + double *rmass = atom->rmass; + double *mass = atom->mass; + int *type = atom->type; + int *mask = atom->mask; + int nlocal = atom->nlocal; + if (igroup == atom->firstgroup) nlocal = atom->nfirst; + + if (rmass) + { + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) + { + dtfm = dtf / rmass[i]; + v[i][0] += dtfm * f[i][0]; + v[i][1] += dtfm * f[i][1]; + v[i][2] += dtfm * f[i][2]; + } + + } + else + { + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) + { + dtfm = dtf / mass[type[i]]; + v[i][0] += dtfm * f[i][0]; + v[i][1] += dtfm * f[i][1]; + v[i][2] += dtfm * f[i][2]; + } + } + + if (doffl && ffl_step<1) + { + ffl_integrate(); + ffl_step = ffl_every; + } + + // Change the temperature for the next step + double delta = update->ntimestep - update->beginstep; + delta /= update->endstep - update->beginstep; + t_target = t_start + delta * (t_stop - t_start); + if (t_stop != t_start) + { + // only updates if it is really necessary + init_ffl(); + } + +} +/* ---------------------------------------------------------------------- */ + +void FixFFL::initial_integrate_respa(int vflag, int ilevel, int iloop) +{ + dtv = step_respa[ilevel]; + dtf = 0.5 * step_respa[ilevel] * force->ftm2v; + + // innermost level - NVE update of v and x + // all other levels - NVE update of v + + if (ilevel==nlevels_respa-1) ffl_integrate(); + doffl=0; + if (ilevel == 0) initial_integrate(vflag); + else + { + final_integrate(); + } +} + +void FixFFL::final_integrate_respa(int ilevel, int iloop) +{ + + dtv = step_respa[ilevel]; + dtf = 0.5 * step_respa[ilevel] * force->ftm2v; + doffl=0; + final_integrate(); + if (ilevel==nlevels_respa-1) ffl_integrate(); +} + + +double FixFFL::compute_scalar() +{ + + double energy_me = energy; + double energy_all; + MPI_Allreduce(&energy_me,&energy_all,1,MPI_DOUBLE,MPI_SUM,world); + + return energy_all; +} + +/* ---------------------------------------------------------------------- + extract thermostat properties +------------------------------------------------------------------------- */ + +void *FixFFL::extract(const char *str, int &dim) +{ + dim = 0; + if (strcmp(str,"t_target") == 0) + { + return &t_target; + } + return NULL; +} + + +/* ---------------------------------------------------------------------- + Called when a change to the target temperature is requested mid-run +------------------------------------------------------------------------- */ + +void FixFFL::reset_target(double t_new) +{ + + t_target = t_start = t_stop = t_new; +} + +/* ---------------------------------------------------------------------- + Called when a change to the timestep is requested mid-run +------------------------------------------------------------------------- */ + +void FixFFL::reset_dt() +{ + // set the time integration constants + dtv = update->dt; + dtf = 0.5 * update->dt * (force->ftm2v); + init_ffl(); +} + +/* ---------------------------------------------------------------------- + memory usage of local atom-based arrays +------------------------------------------------------------------------- */ + +double FixFFL::memory_usage() +{ + double bytes = atom->nmax*(3*2)*sizeof(double); + return bytes; +} + + +/* ---------------------------------------------------------------------- + allocate local atom-based arrays +------------------------------------------------------------------------- */ + +void FixFFL::grow_arrays(int nmax) +{ + memory->grow(ffl_tmp1, nmax*3,"ffl:tmp1"); + memory->grow(ffl_tmp2, nmax*3,"ffl:tmp2"); + //zeroes out temporary buffers + for (int i=0; i< nmax*3; ++i) ffl_tmp1[i] = 0.0; + for (int i=0; i< nmax*3; ++i) ffl_tmp2[i] = 0.0; +} + + diff --git a/src/USER-MISC/fix_ffl.h b/src/USER-MISC/fix_ffl.h new file mode 100644 index 0000000000..1225d25989 --- /dev/null +++ b/src/USER-MISC/fix_ffl.h @@ -0,0 +1,67 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef FIX_CLASS + +FixStyle(ffl,FixFFL) + +#else + +#ifndef LMP_FIX_FFL_H +#define LMP_FIX_FFL_H + +#include "fix.h" + +namespace LAMMPS_NS { + +class FixFFL : public Fix { + public: + FixFFL(class LAMMPS *, int, char **); + virtual ~FixFFL(); + int setmask(); + void init(); + void setup(int); + void ffl_integrate(); + void initial_integrate_respa(int vflag, int ilevel, int iloop); + void final_integrate_respa(int ilevel, int iloop); + void initial_integrate(int vflag); + void final_integrate(); + double compute_scalar(); + void reset_target(double); + virtual void reset_dt(); + double memory_usage(); + void grow_arrays(int); + + virtual void *extract(const char *, int &); + + void init_ffl(); + protected: + double *ffl_tmp1, *ffl_tmp2; + double t_start, t_stop, t_target; + double dtv, dtf, c1, c2, gamma; + char flip_type[10]; + + int doffl, ffl_every, ffl_step, flip_int; + class RanMars *random; + double *sqrt_m; + double *step_respa; + double energy; + int nlevels_respa; + + double **vaux; +}; + +} + +#endif +#endif From 497af2ebb959acf56a71ceea08969760c1fb3d8c Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 28 Sep 2018 13:44:42 +0200 Subject: [PATCH 204/302] document eam/cd/old --- doc/src/Commands_pair.txt | 1 + doc/src/pair_eam.txt | 10 ++++++++-- 2 files changed, 9 insertions(+), 2 deletions(-) diff --git a/doc/src/Commands_pair.txt b/doc/src/Commands_pair.txt index ae115dd904..5715c0123b 100644 --- a/doc/src/Commands_pair.txt +++ b/doc/src/Commands_pair.txt @@ -81,6 +81,7 @@ OPT. "eam (gikot)"_pair_eam.html, "eam/alloy (gikot)"_pair_eam.html, "eam/cd (o)"_pair_eam.html, +"eam/cd/old (o)"_pair_eam.html, "eam/fs (gikot)"_pair_eam.html, "edip (o)"_pair_edip.html, "edip/multi"_pair_edip.html, diff --git a/doc/src/pair_eam.txt b/doc/src/pair_eam.txt index 6c3793cb61..ed1378b6fd 100644 --- a/doc/src/pair_eam.txt +++ b/doc/src/pair_eam.txt @@ -20,6 +20,8 @@ pair_style eam/alloy/omp command :h3 pair_style eam/alloy/opt command :h3 pair_style eam/cd command :h3 pair_style eam/cd/omp command :h3 +pair_style eam/cd/old command :h3 +pair_style eam/cd/old/omp command :h3 pair_style eam/fs command :h3 pair_style eam/fs/gpu command :h3 pair_style eam/fs/intel command :h3 @@ -31,7 +33,7 @@ pair_style eam/fs/opt command :h3 pair_style style :pre -style = {eam} or {eam/alloy} or {eam/cd} or {eam/fs} :ul +style = {eam} or {eam/alloy} or {eam/cd} or {eam/cd/old} or {eam/fs} :ul [Examples:] @@ -268,7 +270,8 @@ Style {eam/cd} is similar to the {eam/alloy} style, except that it computes alloy pairwise interactions using the concentration-dependent embedded-atom method (CD-EAM). This model can reproduce the enthalpy of mixing of alloys over the full composition range, as described in -"(Stukowski)"_#Stukowski. +"(Stukowski)"_#Stukowski. Style {eam/cd/old} is an older, slightly +different and slower two-site formulation of the model "(Caro)"_#Caro. The pair_coeff command is specified the same as for the {eam/alloy} style. However the DYNAMO {setfl} file must has two @@ -442,3 +445,6 @@ Daw, Baskes, Phys Rev B, 29, 6443 (1984). :link(Stukowski) [(Stukowski)] Stukowski, Sadigh, Erhart, Caro; Modeling Simulation Materials Science & Engineering, 7, 075005 (2009). + +:link(Caro) +[(Caro)] A Caro, DA Crowson, M Caro; Phys Rev Lett, 95, 075702 (2005) From 12d2dd201a149b9ecd862af47b6134699095a85b Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 28 Sep 2018 15:47:56 +0200 Subject: [PATCH 205/302] update description of RPM based LAMMPS packages with info from @junghans this fixes #1135 --- doc/src/Install_linux.txt | 77 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 77 insertions(+) diff --git a/doc/src/Install_linux.txt b/doc/src/Install_linux.txt index d44ff2b1c7..bd22de057c 100644 --- a/doc/src/Install_linux.txt +++ b/doc/src/Install_linux.txt @@ -12,6 +12,9 @@ Download an executable for Linux :h3 Binaries are available for different versions of Linux: "Pre-built Ubuntu Linux executables"_#ubuntu +"Pre-built Fedora Linux executables"_#fedora +"Pre-built EPEL Linux executables (RHEL, CentOS)"_#epel +"Pre-built OpenSuse Linux executables"_#opensuse "Pre-built Gentoo Linux executable"_#gentoo :all(b) :line @@ -73,6 +76,80 @@ Ubuntu package capability. :line +Pre-built Fedora Linux executables :h4,link(fedora) + +Pre-built LAMMPS packages for stable releases are available +in the Fedora Linux distribution as of version 28. The packages +can be installed via the dnf package manager. There are 3 basic +varieties (lammps = no MPI, lammps-mpich = MPICH MPI library, +lammps-openmpi = OpenMPI MPI library) and for each support for +linking to the C library interface (lammps-devel, lammps-mpich-devel, +lammps-openmpi-devel), the header for compiling programs using +the C library interface (lammps-headers), and the LAMMPS python +module for Python 3. All packages can be installed at the same +time and the name of the LAMMPS executable is {lmp} in all 3 cases. +By default, {lmp} will refer to the serial executable, unless +one of the MPI environment modules is loaded +("module load mpi/mpich-x86_64" or "module load mpi/openmpi-x86_64"). +Then the corresponding parallel LAMMPS executable is used. +The same mechanism applies when loading the LAMMPS python module. + +To install LAMMPS with OpenMPI and run an input in.lj with 2 CPUs do: + +dnf install lammps-openmpi +module load mpi/openmpi-x86_64 +mpirun -np 2 lmp -in in.lj :pre + +The "dnf install" command is needed only once. In case of a new LAMMPS +stable release, "dnf update" will automatically update to the newer +version as soon at the RPM files are built and uploaded to the download +mirrors. The "module load" command is needed once per (shell) session +or shell terminal instance, unless it is automatically loaded from the +shell profile. + +Please use "lmp -help" to see which compilation options, packages, +and styles are included in the binary. + +Thanks to Christoph Junghans (LANL) for making LAMMPS available in Fedora. + +:line + +Pre-built EPEL Linux executable :h4,link(epel) + +Pre-built LAMMPS packages for stable releases are available +in the "Extra Packages for Enterprise Linux (EPEL) repository"_https://fedoraproject.org/wiki/EPEL +for use with Red Hat Enterprise Linux (RHEL) or CentOS version 7.x +and compatible Linux distributions. Names of packages, executable, +and content are the same as described above for Fedora Linux. +But RHEL/CentOS 7.x uses the "yum" package manager instead of "dnf" +in Fedora 28. + +Please use "lmp -help" to see which compilation options, packages, +and styles are included in the binary. + +Thanks to Christoph Junghans (LANL) for making LAMMPS available in EPEL. + +:line + +Pre-built OpenSuse Linux executable :h4,link(opensuse) + +A pre-built LAMMPS package for stable releases is available +in OpenSuse as of Leap 15.0. You can install the package with: + +zypper install lammps :pre + +This includes support for OpenMPI. The name of the LAMMPS executable +is {lmp}. Thus to run an input in parallel on 2 CPUs you would do: + +mpirun -np 2 lmp -in in.lj :pre + +Please use "lmp -help" to see which compilation options, packages, +and styles are included in the binary. + +Thanks to Christoph Junghans (LANL) for making LAMMPS available in OpenSuse. + +:line + Pre-built Gentoo Linux executable :h4,link(gentoo) LAMMPS is part of Gentoo's main package tree and can be installed by From a333fdac307dce61d997adf44afe1f7ec2964930 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 28 Sep 2018 18:02:13 +0200 Subject: [PATCH 206/302] correct some documentation issues with the recently added USER-PTM package --- doc/src/Commands_compute.txt | 2 +- doc/src/Packages_details.txt | 9 ++++----- doc/src/Packages_user.txt | 2 +- doc/src/compute_ptm_atom.txt | 4 ++-- 4 files changed, 8 insertions(+), 9 deletions(-) diff --git a/doc/src/Commands_compute.txt b/doc/src/Commands_compute.txt index 99c46eed4a..81b618a6e2 100644 --- a/doc/src/Commands_compute.txt +++ b/doc/src/Commands_compute.txt @@ -96,7 +96,7 @@ KOKKOS, o = USER-OMP, t = OPT. "property/atom"_compute_property_atom.html, "property/chunk"_compute_property_chunk.html, "property/local"_compute_property_local.html, -"ptm/atom"_compute_ptm_atom.html +"ptm/atom"_compute_ptm_atom.html, "rdf"_compute_rdf.html, "reduce"_compute_reduce.html, "reduce/chunk"_compute_reduce_chunk.html, diff --git a/doc/src/Packages_details.txt b/doc/src/Packages_details.txt index 73345a2940..6efcfd5f62 100644 --- a/doc/src/Packages_details.txt +++ b/doc/src/Packages_details.txt @@ -1749,7 +1749,7 @@ USER-PTM package :link(PKG-USER-PTM),h4 [Contents:] -A "compute ptm/atom"_compute_ptm.html command that calculates +A "compute ptm/atom"_compute_ptm_atom.html command that calculates local structure characterization using the Polyhedral Template Matching methodology. @@ -1757,10 +1757,9 @@ Matching methodology. [Supporting info:] -src/USER-PHONON: filenames -> commands -src/USER-PHONON/README -"fix phonon"_fix_phonon.html -examples/USER/phonon :ul +src/USER-PTM: filename starting with ptm_ -> supporting code, other filenames -> commands +src/USER-PTM/LICENSE +"compute ptm/atom"_compute_ptm_atom.html :ul :line diff --git a/doc/src/Packages_user.txt b/doc/src/Packages_user.txt index 6d3a8f754a..6e363b28f7 100644 --- a/doc/src/Packages_user.txt +++ b/doc/src/Packages_user.txt @@ -62,7 +62,7 @@ Package, Description, Doc page, Example, Library "USER-NETCDF"_Packages_details.html#PKG-USER-NETCDF, dump output via NetCDF,"dump netcdf"_dump_netcdf.html, n/a, ext "USER-OMP"_Packages_details.html#PKG-USER-OMP, OpenMP-enabled styles,"Speed omp"_Speed_omp.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, no "USER-PHONON"_Packages_details.html#PKG-USER-PHONON, phonon dynamical matrix,"fix phonon"_fix_phonon.html, USER/phonon, no -"USER-PTM"_Packages_details.html#PKG-USER-PTM, Polyhedral Template Matching,"compute ptm/atom"_compute_ptm.html, n/a, no +"USER-PTM"_Packages_details.html#PKG-USER-PTM, Polyhedral Template Matching,"compute ptm/atom"_compute_ptm_atom.html, n/a, no "USER-QMMM"_Packages_details.html#PKG-USER-QMMM, QM/MM coupling,"fix qmmm"_fix_qmmm.html, USER/qmmm, ext "USER-QTB"_Packages_details.html#PKG-USER-QTB, quantum nuclear effects,"fix qtb"_fix_qtb.html "fix qbmsst"_fix_qbmsst.html, qtb, no "USER-QUIP"_Packages_details.html#PKG-USER-QUIP, QUIP/libatoms interface,"pair_style quip"_pair_quip.html, USER/quip, ext diff --git a/doc/src/compute_ptm_atom.txt b/doc/src/compute_ptm_atom.txt index 6fe4d012f5..2e22e4e9fb 100644 --- a/doc/src/compute_ptm_atom.txt +++ b/doc/src/compute_ptm_atom.txt @@ -80,9 +80,9 @@ too frequently or to have multiple compute/dump commands, each with a [Output info:] -This compute calculates a per-atom array, which can be accessed by +This compute calculates a per-atom arry, which can be accessed by any command that uses per-atom values from a compute as input. See -"Section 6.15"_Section_howto.html#howto_15 for an overview of +the "Howto output"_Howto_output.html doc page for an overview of LAMMPS output options. Results are stored in the per-atom array in the following order: From 799ffc58d914d3335d4ebb18fb8f58dd670bfd71 Mon Sep 17 00:00:00 2001 From: dilkins Date: Mon, 1 Oct 2018 17:13:56 +0200 Subject: [PATCH 207/302] C++ system headers included and enumeration of flip_int used;documentation corrected --- doc/src/fix_ffl.txt | 5 ----- src/USER-MISC/fix_ffl.cpp | 31 ++++++++++++++++++------------- 2 files changed, 18 insertions(+), 18 deletions(-) diff --git a/doc/src/fix_ffl.txt b/doc/src/fix_ffl.txt index 8d6b243142..b8e745eddd 100644 --- a/doc/src/fix_ffl.txt +++ b/doc/src/fix_ffl.txt @@ -100,11 +100,6 @@ calculated by this fix is "extensive". [Restrictions:] -The GLE thermostat in its current implementation should not be used -with rigid bodies, SHAKE or RATTLE. It is expected that all the -thermostatted degrees of freedom are fully flexible, and the sampled -ensemble will not be correct otherwise. - In order to perform constant-pressure simulations please use "fix press/berendsen"_fix_press_berendsen.html, rather than "fix npt"_fix_nh.html, to avoid duplicate integration of the diff --git a/src/USER-MISC/fix_ffl.cpp b/src/USER-MISC/fix_ffl.cpp index 54e5c03a62..29fce9b8ff 100644 --- a/src/USER-MISC/fix_ffl.cpp +++ b/src/USER-MISC/fix_ffl.cpp @@ -22,9 +22,9 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include +#include +#include +#include #include "fix_ffl.h" #include "math_extra.h" #include "atom.h" @@ -91,19 +91,24 @@ FixFFL::FixFFL(LAMMPS *lmp, int narg, char **arg) : int seed = force->inumeric(FLERR,arg[6]); // Flip type used, uses rescale if no flip is given - if (narg == 8) strcpy(flip_type,arg[7]); - else strcpy(flip_type,"rescale"); + if (narg == 8) { + if (strcmp(arg[7],"no_flip") == 0) {flip_int = 0;} + else if ((strcmp(arg[7],"rescale") == 0) {flip_int = 1;} + else if ((strcmp(arg[7],"hard") == 0) {flip_int = 2;} + else if ((strcmp(arg[7],"soft") == 0) {flip_int = 3;} + else { + error->all(FLERR,"Illegal fix ffl flip type, only accepts : rescale - hard - soft - no_flip"); + } + } else { + flip_int = 1; + } - // Tests if the flip type is valid - if ( strcmp(flip_type,"rescale") && strcmp(flip_type,"hard") - && strcmp(flip_type,"soft") && strcmp(flip_type,"no_flip") ) - error->all(FLERR,"Illegal fix ffl flip type, only accepts : rescale - hard - soft - no_flip"); - if ( strcmp(flip_type,"no_flip") == 0 ) flip_int = 0; - if ( strcmp(flip_type,"rescale") == 0 ) flip_int = 1; - if ( strcmp(flip_type,"hard") == 0 ) flip_int = 2; - if ( strcmp(flip_type,"soft") == 0 ) flip_int = 3; +// if ( strcmp(flip_type,"no_flip") == 0 ) flip_int = 0; + // if ( strcmp(flip_type,"rescale") == 0 ) flip_int = 1; + // if ( strcmp(flip_type,"hard") == 0 ) flip_int = 2; + // if ( strcmp(flip_type,"soft") == 0 ) flip_int = 3; t_target=t_start; const double kT = t_target * force->boltz / force->mvv2e; From 14251948f31eb678597c641b3fee51f1718fb61d Mon Sep 17 00:00:00 2001 From: dilkins Date: Tue, 2 Oct 2018 10:18:40 +0200 Subject: [PATCH 208/302] LAMMPS coding conventions --- src/USER-MISC/fix_ffl.cpp | 626 ++++++++++++++++++-------------------- 1 file changed, 288 insertions(+), 338 deletions(-) diff --git a/src/USER-MISC/fix_ffl.cpp b/src/USER-MISC/fix_ffl.cpp index 29fce9b8ff..f6cf1b268e 100644 --- a/src/USER-MISC/fix_ffl.cpp +++ b/src/USER-MISC/fix_ffl.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- - Contributing authors: Lionel Constantin (EPFL), David M. Wilkins (EPFL), + Contributing authors: Lionel Constantin (EPFL), David M. Wilkins (EPFL), Michele Ceriotti (EPFL) ------------------------------------------------------------------------- */ @@ -62,143 +62,132 @@ enum {CONSTANT,EQUAL,ATOM}; FixFFL::FixFFL(LAMMPS *lmp, int narg, char **arg) : - Fix(lmp, narg, arg) -{ + Fix(lmp, narg, arg) { - if (narg < 7) - error->all(FLERR,"Illegal fix ffl command. Expecting: fix " - " ffl "); + if (narg < 7) + error->all(FLERR,"Illegal fix ffl command. Expecting: fix " + " ffl "); - restart_peratom = 1; - time_integrate = 1; - scalar_flag = 1; + restart_peratom = 1; + time_integrate = 1; + scalar_flag = 1; - //gamma = 1/ time constant(tau) - if (force->numeric(FLERR,arg[3]) <= 0) - error->all(FLERR,"Illegal fix ffl tau value, should be greater than 0"); - gamma = 1.0/force->numeric(FLERR,arg[3]); - ffl_every=1; - ffl_step=0; + //gamma = 1/ time constant(tau) + if (force->numeric(FLERR,arg[3]) <= 0) + error->all(FLERR,"Illegal fix ffl tau value, should be greater than 0"); + gamma = 1.0/force->numeric(FLERR,arg[3]); + ffl_every=1; + ffl_step=0; - // start temperature (t ramp) - t_start = force->numeric(FLERR,arg[4]); + // start temperature (t ramp) + t_start = force->numeric(FLERR,arg[4]); - // final temperature (t ramp) - t_stop = force->numeric(FLERR,arg[5]); + // final temperature (t ramp) + t_stop = force->numeric(FLERR,arg[5]); - // PRNG seed - int seed = force->inumeric(FLERR,arg[6]); + // PRNG seed + int seed = force->inumeric(FLERR,arg[6]); - // Flip type used, uses rescale if no flip is given - if (narg == 8) { - if (strcmp(arg[7],"no_flip") == 0) {flip_int = 0;} - else if ((strcmp(arg[7],"rescale") == 0) {flip_int = 1;} - else if ((strcmp(arg[7],"hard") == 0) {flip_int = 2;} - else if ((strcmp(arg[7],"soft") == 0) {flip_int = 3;} - else { - error->all(FLERR,"Illegal fix ffl flip type, only accepts : rescale - hard - soft - no_flip"); - } + // Flip type used, uses rescale if no flip is given + if (narg == 8) { + if (strcmp(arg[7],"no_flip") == 0) { + flip_int = 0; + } else if (strcmp(arg[7],"rescale") == 0) { + flip_int = 1; + } else if (strcmp(arg[7],"hard") == 0) { + flip_int = 2; + } else if (strcmp(arg[7],"soft") == 0) { + flip_int = 3; } else { - flip_int = 1; + error->all(FLERR,"Illegal fix ffl flip type, only accepts : rescale - hard - soft - no_flip"); } + } else { + flip_int = 1; + } + + t_target=t_start; + const double kT = t_target * force->boltz / force->mvv2e; + // initialize Marsaglia RNG with processor-unique seed + // NB: this means runs will not be the same with different numbers of processors + if (seed <= 0) error->all(FLERR,"Illegal fix ffl command"); + random = new RanMars(lmp,seed + comm->me); -// if ( strcmp(flip_type,"no_flip") == 0 ) flip_int = 0; - // if ( strcmp(flip_type,"rescale") == 0 ) flip_int = 1; - // if ( strcmp(flip_type,"hard") == 0 ) flip_int = 2; - // if ( strcmp(flip_type,"soft") == 0 ) flip_int = 3; + // allocate per-type arrays for mass-scaling + sqrt_m=NULL; + memory->grow(sqrt_m, atom->ntypes+1,"ffl:sqrt_m"); - t_target=t_start; - const double kT = t_target * force->boltz / force->mvv2e; + // allocates space for temporaries + ffl_tmp1=ffl_tmp2=NULL; + grow_arrays(atom->nmax); - // initialize Marsaglia RNG with processor-unique seed - // NB: this means runs will not be the same with different numbers of processors - if (seed <= 0) error->all(FLERR,"Illegal fix ffl command"); - random = new RanMars(lmp,seed + comm->me); + // add callbacks to enable restarts + atom->add_callback(0); + atom->add_callback(1); - // allocate per-type arrays for mass-scaling - sqrt_m=NULL; - memory->grow(sqrt_m, atom->ntypes+1,"ffl:sqrt_m"); - - // allocates space for temporaries - ffl_tmp1=ffl_tmp2=NULL; - - grow_arrays(atom->nmax); - - // add callbacks to enable restarts - atom->add_callback(0); - atom->add_callback(1); - - energy = 0.0; + energy = 0.0; } /* --- Frees up memory used by temporaries and buffers ------------------ */ -FixFFL::~FixFFL() -{ - delete random; +FixFFL::~FixFFL() { + delete random; - memory->destroy(sqrt_m); - memory->destroy(ffl_tmp1); - memory->destroy(ffl_tmp2); + memory->destroy(sqrt_m); + memory->destroy(ffl_tmp1); + memory->destroy(ffl_tmp2); } /* ---------------------------------------------------------------------- */ -int FixFFL::setmask() -{ - int mask = 0; +int FixFFL::setmask() { + int mask = 0; - mask |= INITIAL_INTEGRATE; - mask |= FINAL_INTEGRATE; - mask |= INITIAL_INTEGRATE_RESPA; - mask |= FINAL_INTEGRATE_RESPA; - mask |= THERMO_ENERGY; + mask |= INITIAL_INTEGRATE; + mask |= FINAL_INTEGRATE; + mask |= INITIAL_INTEGRATE_RESPA; + mask |= FINAL_INTEGRATE_RESPA; + mask |= THERMO_ENERGY; - return mask; + return mask; } /* ------- Initializes one-time quantities for FFL ---------------------- */ -void FixFFL::init() -{ - doffl = 1; - dtv = update->dt; - dtf = 0.5 * update->dt * force->ftm2v; +void FixFFL::init() { + doffl = 1; + dtv = update->dt; + dtf = 0.5 * update->dt * force->ftm2v; - // set force prefactors - if (!atom->rmass) - { - for (int i = 1; i <= atom->ntypes; i++) - { - sqrt_m[i] = sqrt(atom->mass[i]); - } + // set force prefactors + if (!atom->rmass) { + for (int i = 1; i <= atom->ntypes; i++) { + sqrt_m[i] = sqrt(atom->mass[i]); } + } - if (strstr(update->integrate_style,"respa")) - { - nlevels_respa = ((Respa *) update->integrate)->nlevels; - step_respa = ((Respa *) update->integrate)->step; - } + if (strstr(update->integrate_style,"respa")) { + nlevels_respa = ((Respa *) update->integrate)->nlevels; + step_respa = ((Respa *) update->integrate)->step; + } - init_ffl(); + init_ffl(); } /* ------- Initializes constants for FFL (change with T and dt) ------- */ -void FixFFL::init_ffl() -{ - const double kT = t_target * force->boltz / force->mvv2e; +void FixFFL::init_ffl() { + const double kT = t_target * force->boltz / force->mvv2e; - // compute constants for FFL + // compute constants for FFL - c1 = exp ( - gamma * 0.5 * dtv ); - c2 = sqrt( (1.0 - c1*c1)* kT ); //without the mass term + c1 = exp ( - gamma * 0.5 * dtv ); + c2 = sqrt( (1.0 - c1*c1)* kT ); //without the mass term } @@ -207,279 +196,244 @@ void FixFFL::init_ffl() /* ---------------------------------------------------------------------- */ -void FixFFL::setup(int vflag) -{ - if (strstr(update->integrate_style,"verlet")) - post_force(vflag); - else - { - ((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1); - post_force_respa(vflag,nlevels_respa-1,0); - ((Respa *) update->integrate)->copy_f_flevel(nlevels_respa-1); - } +void FixFFL::setup(int vflag) { + if (strstr(update->integrate_style,"verlet")) + post_force(vflag); + else { + ((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1); + post_force_respa(vflag,nlevels_respa-1,0); + ((Respa *) update->integrate)->copy_f_flevel(nlevels_respa-1); + } } -void FixFFL::ffl_integrate() -{ - double **v = atom->v; - double *rmass = atom->rmass, smi, ismi; - double factor; - int *type = atom->type; - int *mask = atom->mask; - int nlocal = atom->nlocal; - if (igroup == atom->firstgroup) nlocal = atom->nfirst; +void FixFFL::ffl_integrate() { + double **v = atom->v; + double *rmass = atom->rmass, smi, ismi; + double factor; + int *type = atom->type; + int *mask = atom->mask; + int nlocal = atom->nlocal; + if (igroup == atom->firstgroup) nlocal = atom->nfirst; - // loads momentum data (mass-scaled) into the temporary vectors for the propagation - int nk=0; - double deltae=0.0; - for (int i = 0; i < nlocal; i++) - { - if (mask[i] & groupbit) - { - if (rmass) smi = sqrt(rmass[i]); - else smi = sqrt_m[type[i]]; + // loads momentum data (mass-scaled) into the temporary vectors for the propagation + int nk=0; + double deltae=0.0; + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + if (rmass) smi = sqrt(rmass[i]); + else smi = sqrt_m[type[i]]; - for (int k = 0; k<3; k++) - { - // first loads velocities and accumulates conserved quantity - ffl_tmp2[nk] = v[i][k] * smi; - deltae += ffl_tmp2[nk] * ffl_tmp2[nk]; - nk++; - } + for (int k = 0; k<3; k++) { + // first loads velocities and accumulates conserved quantity + ffl_tmp2[nk] = v[i][k] * smi; + deltae += ffl_tmp2[nk] * ffl_tmp2[nk]; + nk++; + } + } + } + + //fills up a vector of random numbers + for (int i = 0; i < nk; i++) ffl_tmp1[i] = random->gaussian(); + + + // unloads momentum data (mass-scaled) from the temporary vectors + nk=0; + for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) { + if (rmass) ismi = 1.0 / sqrt(rmass[i]); + else ismi = 1.0/ sqrt_m[type[i]]; + + for (int k = 0; k<3; k++) { + // fetches new velocities and completes computation of the conserved quantity change + v[i][k]= c1*v[i][k] + c2*ffl_tmp1[nk]*ismi; + + deltae-= v[i][k]*v[i][k] /ismi /ismi; + + //flips the sign of the momentum (HARD FLIP) + if ( flip_int == 2) { + if (v[i][k]*ffl_tmp2[nk] < 0.0) v[i][k] = -v[i][k]; } + + nk++; + } } - //fills up a vector of random numbers - for (int i = 0; i < nk; i++) ffl_tmp1[i] = random->gaussian(); - - - // unloads momentum data (mass-scaled) from the temporary vectors + //rescale operation (RESCALE FLIP) + if (flip_int == 1) { nk=0; - for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) - { - if (rmass) ismi = 1.0 / sqrt(rmass[i]); - else ismi = 1.0/ sqrt_m[type[i]]; + for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) { + factor = sqrt ((v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) / + (ffl_tmp2[nk]*ffl_tmp2[nk] + ffl_tmp2[nk+1]*ffl_tmp2[nk+1] + + ffl_tmp2[nk+2]*ffl_tmp2[nk+2])); - for (int k = 0; k<3; k++) - { - // fetches new velocities and completes computation of the conserved quantity change - v[i][k]= c1*v[i][k] + c2*ffl_tmp1[nk]*ismi; + for (int k = 0; k<3; k++) { + v[i][k]= factor * ffl_tmp2[nk]; + nk++; + } + } + } - deltae-= v[i][k]*v[i][k] /ismi /ismi; - //flips the sign of the momentum (HARD FLIP) - if ( flip_int == 2) - { - if (v[i][k]*ffl_tmp2[nk] < 0.0) v[i][k] = -v[i][k]; - } + //soft flip operation (SOFT FLIP) + if (flip_int == 3) { + nk=0; + for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) { + factor = v[i][0]*ffl_tmp2[nk] + v[i][1]*ffl_tmp2[nk+1] + v[i][2]*ffl_tmp2[nk+2]; + if (factor < 0) { + factor = factor / (ffl_tmp2[nk]*ffl_tmp2[nk] + ffl_tmp2[nk+1]*ffl_tmp2[nk+1] + + ffl_tmp2[nk+2]*ffl_tmp2[nk+2]); - nk++; - } + for (int k = 0; k<3; k++) { + v[i][k] -= 2.0 * factor * ffl_tmp2[nk]; + nk++; } - - //rescale operation (RESCALE FLIP) - if (flip_int == 1) - { - nk=0; - for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) - { - factor = sqrt ((v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) / - (ffl_tmp2[nk]*ffl_tmp2[nk] + ffl_tmp2[nk+1]*ffl_tmp2[nk+1] - + ffl_tmp2[nk+2]*ffl_tmp2[nk+2])); - - for (int k = 0; k<3; k++) - { - v[i][k]= factor * ffl_tmp2[nk]; - nk++; - } - } + } else { + nk += 3; + } } + } - //soft flip operation (SOFT FLIP) - if (flip_int == 3) - { - nk=0; - for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) - { - factor = v[i][0]*ffl_tmp2[nk] + v[i][1]*ffl_tmp2[nk+1] + v[i][2]*ffl_tmp2[nk+2]; - if (factor < 0) - { - factor = factor / (ffl_tmp2[nk]*ffl_tmp2[nk] + ffl_tmp2[nk+1]*ffl_tmp2[nk+1] - + ffl_tmp2[nk+2]*ffl_tmp2[nk+2]); - - for (int k = 0; k<3; k++) - { - v[i][k] -= 2.0 * factor * ffl_tmp2[nk]; - nk++; - } - } - else - nk += 3; - } - } - - energy += deltae*0.5*force->mvv2e; + energy += deltae*0.5*force->mvv2e; } -void FixFFL::initial_integrate(int vflag) -{ - double dtfm; +void FixFFL::initial_integrate(int vflag) { + double dtfm; - // update v and x of atoms in group - double **x = atom->x; - double **v = atom->v; - double **f = atom->f; - double *rmass = atom->rmass; - double *mass = atom->mass; - int *type = atom->type; - int *mask = atom->mask; - int nlocal = atom->nlocal; - if (igroup == atom->firstgroup) nlocal = atom->nfirst; + // update v and x of atoms in group + double **x = atom->x; + double **v = atom->v; + double **f = atom->f; + double *rmass = atom->rmass; + double *mass = atom->mass; + int *type = atom->type; + int *mask = atom->mask; + int nlocal = atom->nlocal; + if (igroup == atom->firstgroup) nlocal = atom->nfirst; - ffl_step--; - if (doffl && ffl_step<1) ffl_integrate(); + ffl_step--; + if (doffl && ffl_step<1) ffl_integrate(); - if (rmass) - { - for (int i = 0; i < nlocal; i++) - if (mask[i] & groupbit) - { - dtfm = dtf / rmass[i]; - v[i][0] += dtfm * f[i][0]; - v[i][1] += dtfm * f[i][1]; - v[i][2] += dtfm * f[i][2]; - x[i][0] += dtv * v[i][0]; - x[i][1] += dtv * v[i][1]; - x[i][2] += dtv * v[i][2]; - } + if (rmass) { + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) { + dtfm = dtf / rmass[i]; + v[i][0] += dtfm * f[i][0]; + v[i][1] += dtfm * f[i][1]; + v[i][2] += dtfm * f[i][2]; + x[i][0] += dtv * v[i][0]; + x[i][1] += dtv * v[i][1]; + x[i][2] += dtv * v[i][2]; + } - } - else - { - for (int i = 0; i < nlocal; i++) - if (mask[i] & groupbit) - { - dtfm = dtf / mass[type[i]]; - v[i][0] += dtfm * f[i][0]; - v[i][1] += dtfm * f[i][1]; - v[i][2] += dtfm * f[i][2]; - x[i][0] += dtv * v[i][0]; - x[i][1] += dtv * v[i][1]; - x[i][2] += dtv * v[i][2]; - } - } + } else { + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) { + dtfm = dtf / mass[type[i]]; + v[i][0] += dtfm * f[i][0]; + v[i][1] += dtfm * f[i][1]; + v[i][2] += dtfm * f[i][2]; + x[i][0] += dtv * v[i][0]; + x[i][1] += dtv * v[i][1]; + x[i][2] += dtv * v[i][2]; + } + } } -void FixFFL::final_integrate() -{ - double dtfm; +void FixFFL::final_integrate() { + double dtfm; - // update v of atoms in group + // update v of atoms in group - double **v = atom->v; - double **f = atom->f; - double *rmass = atom->rmass; - double *mass = atom->mass; - int *type = atom->type; - int *mask = atom->mask; - int nlocal = atom->nlocal; - if (igroup == atom->firstgroup) nlocal = atom->nfirst; + double **v = atom->v; + double **f = atom->f; + double *rmass = atom->rmass; + double *mass = atom->mass; + int *type = atom->type; + int *mask = atom->mask; + int nlocal = atom->nlocal; + if (igroup == atom->firstgroup) nlocal = atom->nfirst; - if (rmass) - { - for (int i = 0; i < nlocal; i++) - if (mask[i] & groupbit) - { - dtfm = dtf / rmass[i]; - v[i][0] += dtfm * f[i][0]; - v[i][1] += dtfm * f[i][1]; - v[i][2] += dtfm * f[i][2]; - } + if (rmass) { + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) { + dtfm = dtf / rmass[i]; + v[i][0] += dtfm * f[i][0]; + v[i][1] += dtfm * f[i][1]; + v[i][2] += dtfm * f[i][2]; + } - } - else - { - for (int i = 0; i < nlocal; i++) - if (mask[i] & groupbit) - { - dtfm = dtf / mass[type[i]]; - v[i][0] += dtfm * f[i][0]; - v[i][1] += dtfm * f[i][1]; - v[i][2] += dtfm * f[i][2]; - } - } + } else { + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) { + dtfm = dtf / mass[type[i]]; + v[i][0] += dtfm * f[i][0]; + v[i][1] += dtfm * f[i][1]; + v[i][2] += dtfm * f[i][2]; + } + } - if (doffl && ffl_step<1) - { - ffl_integrate(); - ffl_step = ffl_every; - } + if (doffl && ffl_step<1) { + ffl_integrate(); + ffl_step = ffl_every; + } - // Change the temperature for the next step - double delta = update->ntimestep - update->beginstep; - delta /= update->endstep - update->beginstep; - t_target = t_start + delta * (t_stop - t_start); - if (t_stop != t_start) - { - // only updates if it is really necessary - init_ffl(); - } + // Change the temperature for the next step + double delta = update->ntimestep - update->beginstep; + delta /= update->endstep - update->beginstep; + t_target = t_start + delta * (t_stop - t_start); + if (t_stop != t_start) { + // only updates if it is really necessary + init_ffl(); + } } /* ---------------------------------------------------------------------- */ -void FixFFL::initial_integrate_respa(int vflag, int ilevel, int iloop) -{ - dtv = step_respa[ilevel]; - dtf = 0.5 * step_respa[ilevel] * force->ftm2v; +void FixFFL::initial_integrate_respa(int vflag, int ilevel, int iloop) { + dtv = step_respa[ilevel]; + dtf = 0.5 * step_respa[ilevel] * force->ftm2v; - // innermost level - NVE update of v and x - // all other levels - NVE update of v + // innermost level - NVE update of v and x + // all other levels - NVE update of v - if (ilevel==nlevels_respa-1) ffl_integrate(); - doffl=0; - if (ilevel == 0) initial_integrate(vflag); - else - { - final_integrate(); - } -} - -void FixFFL::final_integrate_respa(int ilevel, int iloop) -{ - - dtv = step_respa[ilevel]; - dtf = 0.5 * step_respa[ilevel] * force->ftm2v; - doffl=0; + if (ilevel==nlevels_respa-1) ffl_integrate(); + doffl=0; + if (ilevel == 0) initial_integrate(vflag); + else { final_integrate(); - if (ilevel==nlevels_respa-1) ffl_integrate(); + } +} + +void FixFFL::final_integrate_respa(int ilevel, int iloop) { + + dtv = step_respa[ilevel]; + dtf = 0.5 * step_respa[ilevel] * force->ftm2v; + doffl=0; + final_integrate(); + if (ilevel==nlevels_respa-1) ffl_integrate(); } -double FixFFL::compute_scalar() -{ +double FixFFL::compute_scalar() { - double energy_me = energy; - double energy_all; - MPI_Allreduce(&energy_me,&energy_all,1,MPI_DOUBLE,MPI_SUM,world); + double energy_me = energy; + double energy_all; + MPI_Allreduce(&energy_me,&energy_all,1,MPI_DOUBLE,MPI_SUM,world); - return energy_all; + return energy_all; } /* ---------------------------------------------------------------------- extract thermostat properties ------------------------------------------------------------------------- */ -void *FixFFL::extract(const char *str, int &dim) -{ - dim = 0; - if (strcmp(str,"t_target") == 0) - { - return &t_target; - } - return NULL; +void *FixFFL::extract(const char *str, int &dim) { + dim = 0; + if (strcmp(str,"t_target") == 0) { + return &t_target; + } + return NULL; } @@ -487,32 +441,29 @@ void *FixFFL::extract(const char *str, int &dim) Called when a change to the target temperature is requested mid-run ------------------------------------------------------------------------- */ -void FixFFL::reset_target(double t_new) -{ +void FixFFL::reset_target(double t_new) { - t_target = t_start = t_stop = t_new; + t_target = t_start = t_stop = t_new; } /* ---------------------------------------------------------------------- Called when a change to the timestep is requested mid-run ------------------------------------------------------------------------- */ -void FixFFL::reset_dt() -{ - // set the time integration constants - dtv = update->dt; - dtf = 0.5 * update->dt * (force->ftm2v); - init_ffl(); +void FixFFL::reset_dt() { + // set the time integration constants + dtv = update->dt; + dtf = 0.5 * update->dt * (force->ftm2v); + init_ffl(); } /* ---------------------------------------------------------------------- memory usage of local atom-based arrays ------------------------------------------------------------------------- */ -double FixFFL::memory_usage() -{ - double bytes = atom->nmax*(3*2)*sizeof(double); - return bytes; +double FixFFL::memory_usage() { + double bytes = atom->nmax*(3*2)*sizeof(double); + return bytes; } @@ -520,13 +471,12 @@ double FixFFL::memory_usage() allocate local atom-based arrays ------------------------------------------------------------------------- */ -void FixFFL::grow_arrays(int nmax) -{ - memory->grow(ffl_tmp1, nmax*3,"ffl:tmp1"); - memory->grow(ffl_tmp2, nmax*3,"ffl:tmp2"); - //zeroes out temporary buffers - for (int i=0; i< nmax*3; ++i) ffl_tmp1[i] = 0.0; - for (int i=0; i< nmax*3; ++i) ffl_tmp2[i] = 0.0; +void FixFFL::grow_arrays(int nmax) { + memory->grow(ffl_tmp1, nmax*3,"ffl:tmp1"); + memory->grow(ffl_tmp2, nmax*3,"ffl:tmp2"); + //zeroes out temporary buffers + for (int i=0; i< nmax*3; ++i) ffl_tmp1[i] = 0.0; + for (int i=0; i< nmax*3; ++i) ffl_tmp2[i] = 0.0; } From d5e71e709913271d5d192c0904c216e2741b3323 Mon Sep 17 00:00:00 2001 From: dilkins Date: Tue, 2 Oct 2018 10:41:55 +0200 Subject: [PATCH 209/302] enumeration of flip types --- src/USER-MISC/fix_ffl.cpp | 17 +++++++++-------- 1 file changed, 9 insertions(+), 8 deletions(-) diff --git a/src/USER-MISC/fix_ffl.cpp b/src/USER-MISC/fix_ffl.cpp index f6cf1b268e..e2fb0166a2 100644 --- a/src/USER-MISC/fix_ffl.cpp +++ b/src/USER-MISC/fix_ffl.cpp @@ -49,6 +49,7 @@ using namespace FixConst; enum {NOBIAS,BIAS}; enum {CONSTANT,EQUAL,ATOM}; +enum {NO_FLIP, FLIP_RESCALE, FLIP_HARD, FLIP_SOFT}; //#define FFL_DEBUG 1 #define MAXLINE 1024 @@ -92,18 +93,18 @@ FixFFL::FixFFL(LAMMPS *lmp, int narg, char **arg) : // Flip type used, uses rescale if no flip is given if (narg == 8) { if (strcmp(arg[7],"no_flip") == 0) { - flip_int = 0; + flip_int = NO_FLIP; } else if (strcmp(arg[7],"rescale") == 0) { - flip_int = 1; + flip_int = FLIP_RESCALE; } else if (strcmp(arg[7],"hard") == 0) { - flip_int = 2; + flip_int = FLIP_HARD; } else if (strcmp(arg[7],"soft") == 0) { - flip_int = 3; + flip_int = FLIP_SOFT; } else { error->all(FLERR,"Illegal fix ffl flip type, only accepts : rescale - hard - soft - no_flip"); } } else { - flip_int = 1; + flip_int = FLIP_RESCALE; } t_target=t_start; @@ -249,7 +250,7 @@ void FixFFL::ffl_integrate() { deltae-= v[i][k]*v[i][k] /ismi /ismi; //flips the sign of the momentum (HARD FLIP) - if ( flip_int == 2) { + if ( flip_int == FLIP_HARD) { if (v[i][k]*ffl_tmp2[nk] < 0.0) v[i][k] = -v[i][k]; } @@ -258,7 +259,7 @@ void FixFFL::ffl_integrate() { } //rescale operation (RESCALE FLIP) - if (flip_int == 1) { + if (flip_int == FLIP_RESCALE) { nk=0; for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) { factor = sqrt ((v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) / @@ -274,7 +275,7 @@ void FixFFL::ffl_integrate() { //soft flip operation (SOFT FLIP) - if (flip_int == 3) { + if (flip_int == FLIP_SOFT) { nk=0; for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) { factor = v[i][0]*ffl_tmp2[nk] + v[i][1]*ffl_tmp2[nk+1] + v[i][2]*ffl_tmp2[nk+2]; From 990a93f9d98b78991d99e1aa340e551daf3c34bd Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 2 Oct 2018 10:58:28 +0200 Subject: [PATCH 210/302] fix typo in example input --- doc/src/dihedral_nharmonic.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/src/dihedral_nharmonic.txt b/doc/src/dihedral_nharmonic.txt index 7a8bf6cdb7..660bbb3f1f 100644 --- a/doc/src/dihedral_nharmonic.txt +++ b/doc/src/dihedral_nharmonic.txt @@ -16,7 +16,7 @@ dihedral_style nharmonic :pre [Examples:] dihedral_style nharmonic -dihedral_coeff 3 10.0 20.0 30.0 :pre +dihedral_coeff * 3 10.0 20.0 30.0 :pre [Description:] From 66bfdd20d4275e09480f0429115c2e0546223a8b Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 2 Oct 2018 11:24:45 +0200 Subject: [PATCH 211/302] fully integrate fix ffl docs into the manual system --- doc/src/Commands_fix.txt | 1 + doc/src/fix_ffl.txt | 12 ++++++------ doc/src/fixes.txt | 1 + doc/src/lammps.book | 1 + 4 files changed, 9 insertions(+), 6 deletions(-) diff --git a/doc/src/Commands_fix.txt b/doc/src/Commands_fix.txt index e002c11770..2b6f4a3080 100644 --- a/doc/src/Commands_fix.txt +++ b/doc/src/Commands_fix.txt @@ -65,6 +65,7 @@ OPT. "eos/table/rx (k)"_fix_eos_table_rx.html, "evaporate"_fix_evaporate.html, "external"_fix_external.html, +"ffl"_fix_ffl.html, "filter/corotate"_fix_filter_corotate.html, "flow/gauss"_fix_flow_gauss.html, "freeze"_fix_freeze.html, diff --git a/doc/src/fix_ffl.txt b/doc/src/fix_ffl.txt index b8e745eddd..8b874fb3b7 100644 --- a/doc/src/fix_ffl.txt +++ b/doc/src/fix_ffl.txt @@ -94,9 +94,9 @@ system's potential energy as part of "thermodynamic output"_thermo_style.html. This fix computes a global scalar which can be accessed by various -"output commands"_Section_howto.html#howto_15. The scalar is the -cumulative energy change due to this fix. The scalar value -calculated by this fix is "extensive". +"output commands"_Howto_output.html. The scalar is the cumulative +energy change due to this fix. The scalar value calculated by this +fix is "extensive". [Restrictions:] @@ -105,9 +105,9 @@ In order to perform constant-pressure simulations please use "fix npt"_fix_nh.html, to avoid duplicate integration of the equations of motion. -This fix is part of the USER-MISC package. It is only enabled if LAMMPS -was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +This fix is part of the USER-MISC package. It is only enabled if +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/fixes.txt b/doc/src/fixes.txt index f2f257b134..9ab299465b 100644 --- a/doc/src/fixes.txt +++ b/doc/src/fixes.txt @@ -46,6 +46,7 @@ Fixes :h1 fix_eos_table_rx fix_evaporate fix_external + fix_ffl fix_filter_corotate fix_flow_gauss fix_freeze diff --git a/doc/src/lammps.book b/doc/src/lammps.book index 0e5ceae861..110ae3876c 100644 --- a/doc/src/lammps.book +++ b/doc/src/lammps.book @@ -266,6 +266,7 @@ fix_eos_table.html fix_eos_table_rx.html fix_evaporate.html fix_external.html +fix_ffl.html fix_filter_corotate.html fix_flow_gauss.html fix_freeze.html From 4b4f7d6ee037013a448b2a0037a09dd7a12c4aa7 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 2 Oct 2018 11:25:12 +0200 Subject: [PATCH 212/302] implement conventions for unique links in docs --- doc/src/fix_ffl.txt | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/src/fix_ffl.txt b/doc/src/fix_ffl.txt index 8b874fb3b7..ea33dc432f 100644 --- a/doc/src/fix_ffl.txt +++ b/doc/src/fix_ffl.txt @@ -69,7 +69,7 @@ The flipping type {flip-type} can be chosen between 4 types described in "(Hijazi)"_#Hijazi. The flipping operation occurs during the thermostatting step and it flips the momenta of the atoms. If no_flip is chosen, no flip will be executed and the integration will be the same as a standard -Langevin thermostat "(Bussi)"_#Bussi. The other flipping types are : rescale - hard - soft. +Langevin thermostat "(Bussi)"_#Bussi3. The other flipping types are : rescale - hard - soft. [Restart, fix_modify, output, run start/stop, minimize info:] @@ -119,6 +119,6 @@ dpd/tstat"_pair_dpd.html, "fix gld"_fix_gld.html, "fix gle"_fix_gle.html :link(Hijazi) [(Hijazi)] M. Hijazi, D. M. Wilkins, M. Ceriotti, J. Chem. Phys. 148, 184109 (2018) -:link(Bussi) +:link(Bussi3) [(Bussi)] G. Bussi, M. Parrinello, Phs. Rev. E 75, 056707 (2007) From ca3a64ea3e26c8a62db4f9b1b1faef7f722289d3 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 2 Oct 2018 11:25:39 +0200 Subject: [PATCH 213/302] fully integrate fix ffl in conventional build processing --- src/.gitignore | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/.gitignore b/src/.gitignore index 3a6ba21426..d7cfae2ffb 100644 --- a/src/.gitignore +++ b/src/.gitignore @@ -424,6 +424,8 @@ /fix_eos_table.h /fix_evaporate.cpp /fix_evaporate.h +/fix_ffl.cpp +/fix_ffl.h /fix_filter_corotate.cpp /fix_filter_corotate.h /fix_viscosity.cpp From 3a0cfc1d57869c51309e8828f48a2a7597357481 Mon Sep 17 00:00:00 2001 From: ckadding Date: Tue, 2 Oct 2018 09:32:26 -0400 Subject: [PATCH 214/302] Modifying headers --- src/USER-MISC/compute_pressure_cylinder.cpp | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/src/USER-MISC/compute_pressure_cylinder.cpp b/src/USER-MISC/compute_pressure_cylinder.cpp index bae6398691..4c3b227842 100644 --- a/src/USER-MISC/compute_pressure_cylinder.cpp +++ b/src/USER-MISC/compute_pressure_cylinder.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "math.h" -#include "string.h" -#include "stdlib.h" +#include +#include +#include #include "compute_pressure_cylinder.h" #include "atom.h" #include "update.h" @@ -25,6 +25,7 @@ #include "group.h" #include "memory.h" #include "error.h" +#include "citeme.h" using namespace LAMMPS_NS; From 89c0655809998f498a172c4018f46337cb7d3087 Mon Sep 17 00:00:00 2001 From: ckadding Date: Tue, 2 Oct 2018 09:46:53 -0400 Subject: [PATCH 215/302] Add input validation --- src/USER-MISC/compute_pressure_cylinder.cpp | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/src/USER-MISC/compute_pressure_cylinder.cpp b/src/USER-MISC/compute_pressure_cylinder.cpp index 4c3b227842..a40e105b5a 100644 --- a/src/USER-MISC/compute_pressure_cylinder.cpp +++ b/src/USER-MISC/compute_pressure_cylinder.cpp @@ -26,6 +26,7 @@ #include "memory.h" #include "error.h" #include "citeme.h" +#include "domain.h" using namespace LAMMPS_NS; @@ -56,10 +57,19 @@ ComputePressureCyl::ComputePressureCyl(LAMMPS *lmp, int narg, char **arg) : zhi=force->numeric(FLERR,arg[4]); Rmax=force->numeric(FLERR,arg[5]); bin_width=force->numeric(FLERR,arg[6]); + + if (bin_width<0.0 || bin_widthall(FLERR,"Illegal compute pressure/cylinder command"); + if (zhiall(FLERR,"Illegal compute pressure/cylinder command"); + if (zhi>domain->boxhi[2] || zloboxlo[2]) + error->all(FLERR,"Illegal compute pressure/cylinder command"); nbins=(int)(Rmax/bin_width); - nzbins=(int)((zhi-zlo)/bin_width); + + if (nbins<1 or nzbins<1) + error->all(FLERR,"Illegal compute pressure/cylinder command"); array_flag=1; vector_flag=0; From af5ac6bcdf9b97e2eeeb124edd86426f423aa8a2 Mon Sep 17 00:00:00 2001 From: ckadding Date: Tue, 2 Oct 2018 09:55:37 -0400 Subject: [PATCH 216/302] Add NULL pointers to constructor init --- src/USER-MISC/compute_pressure_cylinder.cpp | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/src/USER-MISC/compute_pressure_cylinder.cpp b/src/USER-MISC/compute_pressure_cylinder.cpp index a40e105b5a..cb8f841ac3 100644 --- a/src/USER-MISC/compute_pressure_cylinder.cpp +++ b/src/USER-MISC/compute_pressure_cylinder.cpp @@ -49,7 +49,11 @@ if (lmp->citeme) lmp->citeme->add(cite_compute_pressure_cylinder); +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */ ComputePressureCyl::ComputePressureCyl(LAMMPS *lmp, int narg, char **arg) : - Compute(lmp, narg, arg) + Compute(lmp, narg, arg), + R(NULL), Rinv(NULL), R2(NULL), R2kin(NULL), invVbin(NULL), + density_temp(NULL), density_all(NULL), tangent(NULL), ephi_x(NULL), + ephi_y(NULL), Pr_temp(NULL), Pr_all(NULL), Pz_temp(NULL), Pz_all(NULL), + Pphi_temp(NULL), Pphi_all(NULL), PrAinv(NULL) PzAinv(NULL), binz(NULL) { if (narg != 7) error->all(FLERR,"Illegal compute pressure/cylinder command"); From 69c3ff560eb96c57b510b80f98962129954c0426 Mon Sep 17 00:00:00 2001 From: ckadding Date: Tue, 2 Oct 2018 10:11:57 -0400 Subject: [PATCH 217/302] Clarify restrictions and output --- doc/src/compute_pressure_cylinder.txt | 13 +++++++++++-- 1 file changed, 11 insertions(+), 2 deletions(-) diff --git a/doc/src/compute_pressure_cylinder.txt b/doc/src/compute_pressure_cylinder.txt index c6d97e7958..e73ac5b53d 100644 --- a/doc/src/compute_pressure_cylinder.txt +++ b/doc/src/compute_pressure_cylinder.txt @@ -41,14 +41,23 @@ tensor values are output in pressure units. [Output info:] This compute calculates a global array with 5 columns and Rmax/bin_width -rows. +rows. The output columns are: R (distance units), number density (inverse +volume units), configurational radial pressure (pressure units), +configurational azimuthal pressure (pressure units), and configurational +axial pressure (pressure units). The values calculated by this compute are "intensive". The pressure values will be in pressure "units"_units.html. The number density values will be in inverse volume "units"_units.html. -[Restrictions:] none +[Restrictions:] This compute currently calculates the pressure +tensor contributions for pair styles only (i.e. no bond, dihedral, etc.) +and requires pair force +calculations not available for many manybody pair styles. K-space +calculations are also excluded. Note that the pressure outputs +are the configurational terms only; the kinetic contribution may +be calculated from the number density output by P_kin=density*k*T. [Related commands:] From b481af51d64e1e795db06907adf559e2917f5135 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 2 Oct 2018 16:26:20 +0200 Subject: [PATCH 218/302] add pair_style deprecated and some tweaks for fix style --- src/fix_deprecated.cpp | 10 +++++ src/fix_deprecated.h | 1 + src/modify.cpp | 11 +++--- src/pair_deprecated.cpp | 53 ++++++++++++++++++++++++++ src/pair_deprecated.h | 84 +++++++++++++++++++++++++++++++++++++++++ 5 files changed, 154 insertions(+), 5 deletions(-) create mode 100644 src/pair_deprecated.cpp create mode 100644 src/pair_deprecated.h diff --git a/src/fix_deprecated.cpp b/src/fix_deprecated.cpp index d0a63b0096..666ec41734 100644 --- a/src/fix_deprecated.cpp +++ b/src/fix_deprecated.cpp @@ -23,6 +23,16 @@ using namespace LAMMPS_NS; FixDeprecated::FixDeprecated(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg) { + if (strcmp(style,"deprecated") == 0) { + const char *message = "\n" + "NOTE: The fix style 'deprecated' is a dummy fix style that was added to\n" + "LAMMPS in order to print suitable error messages for deleted features.\n\n"; + + if (comm->me == 0) { + if (screen) fputs(message,screen); + if (logfile) fputs(message,logfile); + } + } if (strncmp(style,"ave/spatial",11) == 0) { const char *message = "\n" "NOTE: The fix styles 'ave/spatial' and 'ave/spatial/sphere' have been replaced\n" diff --git a/src/fix_deprecated.h b/src/fix_deprecated.h index e11e283f37..f4e76c47e8 100644 --- a/src/fix_deprecated.h +++ b/src/fix_deprecated.h @@ -15,6 +15,7 @@ // list all deprecated and removed fix styles here +FixStyle(deprecated,FixDeprecated) FixStyle(ave/spatial,FixDeprecated) FixStyle(ave/spatial/sphere,FixDeprecated) diff --git a/src/modify.cpp b/src/modify.cpp index 8a0d1afa2c..547fc4a251 100644 --- a/src/modify.cpp +++ b/src/modify.cpp @@ -785,16 +785,17 @@ void Modify::add_fix(int narg, char **arg, int trysuffix) // but can't think of better way // too late if instantiate fix, then check flag set in fix constructor, // since some fixes access domain settings in their constructor - // MUST change NEXCEPT above when add new fix to this list + // NULL must be last entry in this list - const char *exceptions[NEXCEPT] = - {"GPU","OMP","INTEL","property/atom","cmap","cmap3","rx"}; + const char *exceptions[] = + {"GPU", "OMP", "INTEL", "property/atom", "cmap", "cmap3", "rx", + "deprecated", NULL}; if (domain->box_exist == 0) { int m; - for (m = 0; m < NEXCEPT; m++) + for (m = 0; exceptions[m] != NULL; m++) if (strcmp(arg[2],exceptions[m]) == 0) break; - if (m == NEXCEPT) + if (exceptions[m] == NULL) error->all(FLERR,"Fix command before simulation box is defined"); } diff --git a/src/pair_deprecated.cpp b/src/pair_deprecated.cpp new file mode 100644 index 0000000000..a383f390cf --- /dev/null +++ b/src/pair_deprecated.cpp @@ -0,0 +1,53 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Axel Kohlmeyer (Temple U) +------------------------------------------------------------------------- */ + +#include "pair_deprecated.h" +#include "pair_hybrid.h" +#include "comm.h" +#include "force.h" +#include "error.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +PairDeprecated::PairDeprecated(LAMMPS *lmp) : Pair(lmp) +{ + if (strcmp(force->pair_style,"deprecated") == 0) { + const char *message = "\n" + "NOTE: The pair style 'deprecated' is a dummy fix style that was added to\n" + "LAMMPS in order to print suitable error messages for deleted features.\n\n"; + + if (comm->me == 0) { + if (screen) fputs(message,screen); + if (logfile) fputs(message,logfile); + } + } + if (strncmp(force->pair_style,"reax",11) == 0) { + const char *message = "\n" + "NOTE: The pair style 'reax' has been removed from LAMMPS after the\n" + "## November 2018 stable release. Its functionality has long before\n" + "been superseded by pair styles 'reax/c' and 'reax/c/kk'\n\n"; + + if (comm->me == 0) { + if (screen) fputs(message,screen); + if (logfile) fputs(message,logfile); + } + } + error->all(FLERR,"This pair_style command has been removed from LAMMPS"); +} + diff --git a/src/pair_deprecated.h b/src/pair_deprecated.h new file mode 100644 index 0000000000..4201b3453d --- /dev/null +++ b/src/pair_deprecated.h @@ -0,0 +1,84 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS + +PairStyle(deprecated,PairDeprecated) + +#else + +#ifndef LMP_PAIR_DEPRECATED_H +#define LMP_PAIR_DEPRECATED_H + +#include "pair.h" + +namespace LAMMPS_NS { + +class PairDeprecated : public Pair { + public: + PairDeprecated(class LAMMPS *); + virtual ~PairDeprecated() {}; + + virtual void compute(int, int) {}; + virtual void settings(int, char **) {}; + virtual void coeff(int, char **) {}; + +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Not all pairs processed in pair_style list + +Not all interacting pairs for which coefficients were found. This can be intentional +and then you need to set the 'nocheck' option. If not, it usually means that the +communication cutoff is too small. This can be ameliorated by either increasing +the cutoff in the pair_style command or the communication cutoff. + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: Cannot open pair list file + +Self-explanatory. The file with the list of pairs cannot be open for reading. +Check the path and permissions. + +E: Incorrectly formatted ... + +Self-explanatory. The content of the pair list file does not match the documented +format. Please re-read the documentation and carefully compare it to your file. + +E: Unknown pair list potential style + +Self-explanatory. You requested a potential type that is not yet implemented or have a typo. + +E: Incorrect args for pair coefficients + +Self-explanatory. Check the input script or data file. + +E: Pair style list requires atom IDs + +Self-explanatory. The pairs in the list are identified via atom IDs, so they need to be present. + +E: Pair style list requires an atom map + +Self-explanatory. Atoms are looked up via an atom map. Create one using the atom_style map command. + +*/ From b5a5270f4a858bdda3c733d51fb76d011c0f6464 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 2 Oct 2018 16:29:18 +0200 Subject: [PATCH 219/302] fix typos in compute msd/chunk as reported by @evoyiatzis the example is incorrect, but also a mention of the compute a few lines above. --- doc/src/compute_msd_chunk.txt | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/src/compute_msd_chunk.txt b/doc/src/compute_msd_chunk.txt index 264f38d5fd..7ff57c9844 100644 --- a/doc/src/compute_msd_chunk.txt +++ b/doc/src/compute_msd_chunk.txt @@ -90,12 +90,12 @@ This is so that the fix this compute creates to store per-chunk quantities will also have the same ID, and thus be initialized correctly with chunk reference positions from the restart file. -The simplest way to output the results of the compute com/msd +The simplest way to output the results of the compute msd/chunk calculation to a file is to use the "fix ave/time"_fix_ave_time.html command, for example: compute cc1 all chunk/atom molecule -compute myChunk all com/msd cc1 +compute myChunk all msd/chunk cc1 fix 1 all ave/time 100 1 100 c_myChunk\[*\] file tmp.out mode vector :pre [Output info:] From ac658a17fc612c73267e9678139c4daf84d982d7 Mon Sep 17 00:00:00 2001 From: ckadding Date: Tue, 2 Oct 2018 10:34:08 -0400 Subject: [PATCH 220/302] Update compute_pressure_cylinder.cpp --- src/USER-MISC/compute_pressure_cylinder.cpp | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/src/USER-MISC/compute_pressure_cylinder.cpp b/src/USER-MISC/compute_pressure_cylinder.cpp index cb8f841ac3..cbef2941a8 100644 --- a/src/USER-MISC/compute_pressure_cylinder.cpp +++ b/src/USER-MISC/compute_pressure_cylinder.cpp @@ -40,9 +40,7 @@ static const char cite_compute_pressure_cylinder[] = " volume = 149,\n" " pages = {084109}\n" "}\n\n"; - -if (lmp->citeme) lmp->citeme->add(cite_compute_pressure_cylinder); - + /*+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Calculate the configurational components of the pressure tensor in cylindrical geometry, according to the formulation of Addington et al. (2018) @@ -55,6 +53,7 @@ ComputePressureCyl::ComputePressureCyl(LAMMPS *lmp, int narg, char **arg) : ephi_y(NULL), Pr_temp(NULL), Pr_all(NULL), Pz_temp(NULL), Pz_all(NULL), Pphi_temp(NULL), Pphi_all(NULL), PrAinv(NULL) PzAinv(NULL), binz(NULL) { + if (lmp->citeme) lmp->citeme->add(cite_compute_pressure_cylinder); if (narg != 7) error->all(FLERR,"Illegal compute pressure/cylinder command"); zlo=force->numeric(FLERR,arg[3]); From c7c0defa7715d7a0d8a1d3cbe0f99de609a8590c Mon Sep 17 00:00:00 2001 From: ckadding Date: Tue, 2 Oct 2018 10:45:43 -0400 Subject: [PATCH 221/302] Insert a comma --- src/USER-MISC/compute_pressure_cylinder.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/USER-MISC/compute_pressure_cylinder.cpp b/src/USER-MISC/compute_pressure_cylinder.cpp index cbef2941a8..ebe28d848a 100644 --- a/src/USER-MISC/compute_pressure_cylinder.cpp +++ b/src/USER-MISC/compute_pressure_cylinder.cpp @@ -51,7 +51,7 @@ ComputePressureCyl::ComputePressureCyl(LAMMPS *lmp, int narg, char **arg) : R(NULL), Rinv(NULL), R2(NULL), R2kin(NULL), invVbin(NULL), density_temp(NULL), density_all(NULL), tangent(NULL), ephi_x(NULL), ephi_y(NULL), Pr_temp(NULL), Pr_all(NULL), Pz_temp(NULL), Pz_all(NULL), - Pphi_temp(NULL), Pphi_all(NULL), PrAinv(NULL) PzAinv(NULL), binz(NULL) + Pphi_temp(NULL), Pphi_all(NULL), PrAinv(NULL), PzAinv(NULL), binz(NULL) { if (lmp->citeme) lmp->citeme->add(cite_compute_pressure_cylinder); if (narg != 7) error->all(FLERR,"Illegal compute pressure/cylinder command"); From 57b2f605564bcb073d4a3aee2e35cec851cc260e Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Tue, 2 Oct 2018 09:45:13 -0600 Subject: [PATCH 222/302] Fix bug in Kokkos EAM --- src/KOKKOS/pair_eam_alloy_kokkos.cpp | 3 +++ src/KOKKOS/pair_eam_fs_kokkos.cpp | 3 +++ src/KOKKOS/pair_eam_kokkos.cpp | 3 +++ 3 files changed, 9 insertions(+) diff --git a/src/KOKKOS/pair_eam_alloy_kokkos.cpp b/src/KOKKOS/pair_eam_alloy_kokkos.cpp index 49e1313c26..e198ddb85a 100644 --- a/src/KOKKOS/pair_eam_alloy_kokkos.cpp +++ b/src/KOKKOS/pair_eam_alloy_kokkos.cpp @@ -165,6 +165,9 @@ void PairEAMAlloyKokkos::compute(int eflag_in, int vflag_in) } } + if (need_dup) + Kokkos::Experimental::contribute(d_rho, dup_rho); + // communicate and sum densities (on the host) if (newton_pair) { diff --git a/src/KOKKOS/pair_eam_fs_kokkos.cpp b/src/KOKKOS/pair_eam_fs_kokkos.cpp index ee0a799826..f5e4445db3 100644 --- a/src/KOKKOS/pair_eam_fs_kokkos.cpp +++ b/src/KOKKOS/pair_eam_fs_kokkos.cpp @@ -165,6 +165,9 @@ void PairEAMFSKokkos::compute(int eflag_in, int vflag_in) } } + if (need_dup) + Kokkos::Experimental::contribute(d_rho, dup_rho); + // communicate and sum densities (on the host) if (newton_pair) { diff --git a/src/KOKKOS/pair_eam_kokkos.cpp b/src/KOKKOS/pair_eam_kokkos.cpp index a1431334b4..6ef3d99ac3 100644 --- a/src/KOKKOS/pair_eam_kokkos.cpp +++ b/src/KOKKOS/pair_eam_kokkos.cpp @@ -159,6 +159,9 @@ void PairEAMKokkos::compute(int eflag_in, int vflag_in) } } + if (need_dup) + Kokkos::Experimental::contribute(d_rho, dup_rho); + // communicate and sum densities (on the host) if (newton_pair) { From f81836d605e8516713d16dae62f8d1f3f28cb4f6 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 2 Oct 2018 11:51:23 -0400 Subject: [PATCH 223/302] reformat compute pressure/cylinder docs and integrate it into the manual --- doc/src/compute_pressure_cylinder.txt | 44 ++++++++++++++++----------- doc/src/computes.txt | 1 + doc/src/lammps.book | 1 + 3 files changed, 28 insertions(+), 18 deletions(-) diff --git a/doc/src/compute_pressure_cylinder.txt b/doc/src/compute_pressure_cylinder.txt index e73ac5b53d..4865fe8a79 100644 --- a/doc/src/compute_pressure_cylinder.txt +++ b/doc/src/compute_pressure_cylinder.txt @@ -25,18 +25,19 @@ compute 1 all pressure/cylinder -10.0 10.0 15.0 0.25 :pre [Description:] -Define a computation that calculates the pressure tensor of a -system in cylindrical coordinates, as discussed in "(Addington)"_#Addington1. +Define a computation that calculates the pressure tensor of a system in +cylindrical coordinates, as discussed in "(Addington)"_#Addington1. This is useful for systems with a single axis of rotational symmetry, -such as cylindrical micelles or carbon nanotubes. The compute splits -the system into radial, cylindrical-shell-type bins of width bin_width, centered at x=0,y=0, -and calculates the radial (P_rhorho), azimuthal (P_phiphi), and axial (P_zz) components of the configurational pressure -tensor. The local density is also calculated for each bin, so that -the true pressure can be recovered as P_kin+P_conf=density*k*T+P_conf. -The output is a global array with 5 columns; one each for bin radius, -local number density, P_rhorho, P_phiphi, and P_zz. The number of -rows is governed by the values of Rmax and bin_width. Pressure -tensor values are output in pressure units. +such as cylindrical micelles or carbon nanotubes. The compute splits the +system into radial, cylindrical-shell-type bins of width bin_width, +centered at x=0,y=0, and calculates the radial (P_rhorho), azimuthal +(P_phiphi), and axial (P_zz) components of the configurational pressure +tensor. The local density is also calculated for each bin, so that the +true pressure can be recovered as P_kin+P_conf=density*k*T+P_conf. The +output is a global array with 5 columns; one each for bin radius, local +number density, P_rhorho, P_phiphi, and P_zz. The number of rows is +governed by the values of Rmax and bin_width. Pressure tensor values are +output in pressure units. [Output info:] @@ -51,13 +52,20 @@ The values calculated by this compute are "units"_units.html. The number density values will be in inverse volume "units"_units.html. -[Restrictions:] This compute currently calculates the pressure -tensor contributions for pair styles only (i.e. no bond, dihedral, etc.) -and requires pair force -calculations not available for many manybody pair styles. K-space -calculations are also excluded. Note that the pressure outputs -are the configurational terms only; the kinetic contribution may -be calculated from the number density output by P_kin=density*k*T. +[Restrictions:] + +This compute currently calculates the pressure tensor contributions +for pair styles only (i.e. no bond, angle, dihedral, etc. contributions +and in the presence of bonded interactions, the result will be incorrect +due to exclusions for special bonds) and requires pair-wise force +calculations not available for most manybody pair styles. K-space +calculations are also excluded. Note that this pressure compute outputs +the configurational terms only; the kinetic contribution is not included +and may be calculated from the number density output by P_kin=density*k*T. + +This compute is part of the USER-MISC package. It is only enabled +if LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/computes.txt b/doc/src/computes.txt index a6a194ac24..bdd6455541 100644 --- a/doc/src/computes.txt +++ b/doc/src/computes.txt @@ -67,6 +67,7 @@ Computes :h1 compute_pe_atom compute_plasticity_atom compute_pressure + compute_pressure_cylinder compute_pressure_uef compute_property_atom compute_property_chunk diff --git a/doc/src/lammps.book b/doc/src/lammps.book index 0e5ceae861..4bb4394062 100644 --- a/doc/src/lammps.book +++ b/doc/src/lammps.book @@ -464,6 +464,7 @@ compute_pe.html compute_pe_atom.html compute_plasticity_atom.html compute_pressure.html +compute_pressure_cylinder.html compute_pressure_uef.html compute_property_atom.html compute_property_chunk.html From 13d3903e8dc36a696c889b4835f55feb821c6f8a Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 2 Oct 2018 11:56:29 -0400 Subject: [PATCH 224/302] integrate compute pressure/cylinder into build and README --- src/.gitignore | 2 ++ src/USER-MISC/README | 1 + 2 files changed, 3 insertions(+) diff --git a/src/.gitignore b/src/.gitignore index 3a6ba21426..323b63693c 100644 --- a/src/.gitignore +++ b/src/.gitignore @@ -296,6 +296,8 @@ /compute_plasticity_atom.h /compute_pressure_bocs.cpp /compute_pressure_bocs.h +/compute_pressure_cylinder.cpp +/compute_pressure_cylinder.h /compute_pressure_grem.cpp /compute_pressure_grem.h /compute_rigid_local.cpp diff --git a/src/USER-MISC/README b/src/USER-MISC/README index eb221c07db..30431a704b 100644 --- a/src/USER-MISC/README +++ b/src/USER-MISC/README @@ -30,6 +30,7 @@ compute ackland/atom, Gerolf Ziegenhain, gerolf at ziegenhain.com, 4 Oct 2007 compute basal/atom, Christopher Barrett, cdb333 at cavs.msstate.edu, 3 Mar 2013 compute cnp/atom, Paulo Branicio (USC), branicio at usc.edu, 31 May 2017 compute entropy/atom, Pablo Piaggi (EPFL), pablo.piaggi at epfl.ch, 15 June 2018 +compute pressure/cylinder, Cody K. Addington (NCSU), , 2 Oct 2018 compute stress/mop, Romain Vermorel (U Pau) & Laurent Joly (U Lyon), romain.vermorel at univ-pau.fr & ljoly.ulyon at gmail.com, 5 Sep 18 compute stress/mop/profile, Romain Vermorel (U Pau) & Laurent Joly (U Lyon), romain.vermorel at univ-pau.fr & ljoly.ulyon at gmail.com, 5 Sep 18 compute temp/rotate, Laurent Joly (U Lyon), ljoly.ulyon at gmail.com, 8 Aug 11 From ff7449b29af0010cc124ef65f64b0856bbf37e07 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 2 Oct 2018 12:27:05 -0400 Subject: [PATCH 225/302] ensure, that we have no division by zero and add an upper limit for bins --- src/USER-MISC/compute_pressure_cylinder.cpp | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/src/USER-MISC/compute_pressure_cylinder.cpp b/src/USER-MISC/compute_pressure_cylinder.cpp index ebe28d848a..04767eb4c3 100644 --- a/src/USER-MISC/compute_pressure_cylinder.cpp +++ b/src/USER-MISC/compute_pressure_cylinder.cpp @@ -61,17 +61,20 @@ ComputePressureCyl::ComputePressureCyl(LAMMPS *lmp, int narg, char **arg) : Rmax=force->numeric(FLERR,arg[5]); bin_width=force->numeric(FLERR,arg[6]); - if (bin_width<0.0 || bin_widthall(FLERR,"Illegal compute pressure/cylinder command"); - if (zhiall(FLERR,"Illegal compute pressure/cylinder command"); - if (zhi>domain->boxhi[2] || zloboxlo[2]) + if ((zhi > domain->boxhi[2]) || (zlo < domain->boxlo[2])) error->all(FLERR,"Illegal compute pressure/cylinder command"); nbins=(int)(Rmax/bin_width); nzbins=(int)((zhi-zlo)/bin_width); - - if (nbins<1 or nzbins<1) + + // NOTE: at 2^22 = 4.2M bins, we will be close to exhausting allocatable + // memory on a 32-bit environment. so we use this as an upper limit. + + if ((nbins < 1) || (nzbins < 1) || (nbins > 2>>22) || (nbins > 2>>22)) error->all(FLERR,"Illegal compute pressure/cylinder command"); array_flag=1; From e3b80e734a5e77c25d5a185460a4b4544fdced4d Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 2 Oct 2018 12:37:13 -0400 Subject: [PATCH 226/302] remove trailing whitespace --- src/USER-MISC/compute_pressure_cylinder.cpp | 50 ++++++++++----------- 1 file changed, 25 insertions(+), 25 deletions(-) diff --git a/src/USER-MISC/compute_pressure_cylinder.cpp b/src/USER-MISC/compute_pressure_cylinder.cpp index 04767eb4c3..03331a1b98 100644 --- a/src/USER-MISC/compute_pressure_cylinder.cpp +++ b/src/USER-MISC/compute_pressure_cylinder.cpp @@ -40,16 +40,16 @@ static const char cite_compute_pressure_cylinder[] = " volume = 149,\n" " pages = {084109}\n" "}\n\n"; - + /*+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ - Calculate the configurational components of the pressure tensor in + Calculate the configurational components of the pressure tensor in cylindrical geometry, according to the formulation of Addington et al. (2018) +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */ ComputePressureCyl::ComputePressureCyl(LAMMPS *lmp, int narg, char **arg) : Compute(lmp, narg, arg), R(NULL), Rinv(NULL), R2(NULL), R2kin(NULL), invVbin(NULL), - density_temp(NULL), density_all(NULL), tangent(NULL), ephi_x(NULL), + density_temp(NULL), density_all(NULL), tangent(NULL), ephi_x(NULL), ephi_y(NULL), Pr_temp(NULL), Pr_all(NULL), Pz_temp(NULL), Pz_all(NULL), Pphi_temp(NULL), Pphi_all(NULL), PrAinv(NULL), PzAinv(NULL), binz(NULL) { @@ -60,8 +60,8 @@ ComputePressureCyl::ComputePressureCyl(LAMMPS *lmp, int narg, char **arg) : zhi=force->numeric(FLERR,arg[4]); Rmax=force->numeric(FLERR,arg[5]); bin_width=force->numeric(FLERR,arg[6]); - - if ((bin_width <= 0.0) || (bin_width < Rmax)) + + if ((bin_width <= 0.0) || (bin_width < Rmax)) error->all(FLERR,"Illegal compute pressure/cylinder command"); if ((zhi < zlo) || ((zhi-zlo) < bin_width)) error->all(FLERR,"Illegal compute pressure/cylinder command"); @@ -73,8 +73,8 @@ ComputePressureCyl::ComputePressureCyl(LAMMPS *lmp, int narg, char **arg) : // NOTE: at 2^22 = 4.2M bins, we will be close to exhausting allocatable // memory on a 32-bit environment. so we use this as an upper limit. - - if ((nbins < 1) || (nzbins < 1) || (nbins > 2>>22) || (nbins > 2>>22)) + + if ((nbins < 1) || (nzbins < 1) || (nbins > 2>>22) || (nbins > 2>>22)) error->all(FLERR,"Illegal compute pressure/cylinder command"); array_flag=1; @@ -109,7 +109,7 @@ ComputePressureCyl::ComputePressureCyl(LAMMPS *lmp, int narg, char **arg) : ephi_y = new double[nphi]; nktv2p = force->nktv2p; - + } /* ---------------------------------------------------------------------- */ @@ -170,8 +170,8 @@ void ComputePressureCyl::init() PphiAinv=1.0/((zhi-zlo)*bin_width*2.0*(double)nphi); invVbin[0]=1.0/((zhi-zlo)*3.14159*R2kin[0]); - PzAinv[0]=1.0/(3.14159*R2kin[0]*((double)nzbins)); - for (int jq=1;jqntimestep; + invoked_array = update->ntimestep; int ibin; // clear pressures - for (ibin=0;ibin= nlocal) + if (newton_pair == 0 && j >= nlocal) { jtag = tag[j]; - if (itag > jtag) + if (itag > jtag) { if ((itag+jtag) % 2 == 0) continue; - } - else if (itag < jtag) + } + else if (itag < jtag) { if ((itag+jtag) % 2 == 1) continue; - } - else + } + else { if (x[j][2] < ztmp) continue; - if (x[j][2] == ztmp) + if (x[j][2] == ztmp) { if (x[j][1] < ytmp) continue; if (x[j][1] == ytmp && x[j][0] < xtmp) continue; @@ -458,7 +458,7 @@ void ComputePressureCyl::compute_array() xL=xi+alpha*dx; yL=yi+alpha*dy; - L2=xL*xL+yL*yL; + L2=xL*xL+yL*yL; if (L2>R2kin[nbins-1]) continue; @@ -475,7 +475,7 @@ void ComputePressureCyl::compute_array() } // calculate pressure (force over area) - for (ibin=0;ibin Date: Tue, 2 Oct 2018 14:33:49 -0400 Subject: [PATCH 227/302] Use MathConst namespace --- src/USER-MISC/compute_pressure_cylinder.cpp | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/src/USER-MISC/compute_pressure_cylinder.cpp b/src/USER-MISC/compute_pressure_cylinder.cpp index 03331a1b98..917ef75a4a 100644 --- a/src/USER-MISC/compute_pressure_cylinder.cpp +++ b/src/USER-MISC/compute_pressure_cylinder.cpp @@ -27,8 +27,10 @@ #include "error.h" #include "citeme.h" #include "domain.h" +#include "math_const.h" using namespace LAMMPS_NS; +using namespace MathConst; static const char cite_compute_pressure_cylinder[] = "compute pressure/cylinder:\n\n" @@ -152,7 +154,7 @@ void ComputePressureCyl::init() for (int iphi=0;iphi Date: Tue, 2 Oct 2018 14:54:09 -0400 Subject: [PATCH 228/302] Apply uniform LAMMPS formatting --- src/USER-MISC/compute_pressure_cylinder.cpp | 99 ++++++++------------- 1 file changed, 38 insertions(+), 61 deletions(-) diff --git a/src/USER-MISC/compute_pressure_cylinder.cpp b/src/USER-MISC/compute_pressure_cylinder.cpp index 917ef75a4a..bdffa32af1 100644 --- a/src/USER-MISC/compute_pressure_cylinder.cpp +++ b/src/USER-MISC/compute_pressure_cylinder.cpp @@ -152,16 +152,14 @@ void ComputePressureCyl::init() double phi; - for (int iphi=0;iphirequests[irequest]->compute = 1; neighbor->requests[irequest]->occasional = 1; - for (int zzz=0;zzzzlo) - { + for (i = 0; i < nlocal; i++) if ((x[i][2] < zhi) && (x[i][2] > zlo)) { temp_R2=x[i][0]*x[i][0]+x[i][1]*x[i][1]; - if (temp_R2>R2kin[nbins-1]) continue; // outside of Rmax + if (temp_R2 > R2kin[nbins-1]) continue; // outside of Rmax - for (j=0;j= nlocal) - { + if (newton_pair == 0 && j >= nlocal) { jtag = tag[j]; - if (itag > jtag) - { + if (itag > jtag) { if ((itag+jtag) % 2 == 0) continue; } - else if (itag < jtag) - { + else if (itag < jtag) { if ((itag+jtag) % 2 == 1) continue; } - else - { + else { if (x[j][2] < ztmp) continue; - if (x[j][2] == ztmp) - { + if (x[j][2] == ztmp) { if (x[j][1] < ytmp) continue; if (x[j][1] == ytmp && x[j][0] < xtmp) continue; } @@ -344,8 +333,7 @@ void ComputePressureCyl::compute_array() r2=x[j][0]*x[j][0]+x[j][1]*x[j][1]; // ri is smaller of r1 and r2 - if (r20.0 && alpha1<1.0) - { + if ((alpha1 > 0.0) && (alpha1 < 1.0)) { zR=zi+alpha1*dz; - if (zRzlo) + if ((zR < zhi) && (zR > zlo)) { xR=xi+alpha1*dx; yR=yi+alpha1*dy; @@ -404,11 +389,9 @@ void ComputePressureCyl::compute_array() Pr_temp[ibin]+=fn; } } - if (alpha2>0.0 && alpha2<1.0) - { + if ((alpha2 > 0.0) && (alpha2 < 1.0)) { zR=zi+alpha2*dz; - if (zRzlo) - { + if ((zR < zhi) && (zR > zlo)) { xR=xi+alpha2*dx; yR=yi+alpha2*dy; fn=fpair*fabs(xR*dx+yR*dy); @@ -419,16 +402,15 @@ void ComputePressureCyl::compute_array() } // azimuthal pressure contribution (P_phiphi) - for (int iphi=0;iphi=1.0 || alpha<=0.0) continue; + if ((alpha >= 1.0) || (alpha <= 0.0)) continue; // no contribution (outside of averaging region) zL=zi+alpha*dz; - if (zL>zhi || zL zhi) || (zL < zlo)) continue; xL=xi+alpha*dx; yL=yi+alpha*dy; @@ -436,24 +418,22 @@ void ComputePressureCyl::compute_array() L2=xL*xL+yL*yL; // no intersection (outside of Rmax) - if (L2>R2kin[nbins-1]) continue; + if (L2 > R2kin[nbins-1]) continue; ftphi=fabs(dx*ephi_x[iphi]+dy*ephi_y[iphi])*fpair; // add to appropriate bin - for (ibin=0;ibinbinz[zbin] && x[j][2]>binz[zbin]) continue; - if (x[i][2] binz[zbin]) && (x[j][2] > binz[zbin])) continue; + if ((x[i][2] < binz[zbin]) && (x[j][2] < binz[zbin])) continue; alpha=(binz[zbin]-zi)/dz; @@ -462,13 +442,12 @@ void ComputePressureCyl::compute_array() L2=xL*xL+yL*yL; - if (L2>R2kin[nbins-1]) continue; + if (L2 > R2kin[nbins-1]) continue; ftz=fabs(dz)*fpair; // add to appropriate bin - for (ibin=0;ibin Date: Tue, 2 Oct 2018 15:17:11 -0400 Subject: [PATCH 229/302] convert more system headers to c++ style --- src/USER-MISC/compute_pressure_cylinder.cpp | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/USER-MISC/compute_pressure_cylinder.cpp b/src/USER-MISC/compute_pressure_cylinder.cpp index bdffa32af1..b35e851e4b 100644 --- a/src/USER-MISC/compute_pressure_cylinder.cpp +++ b/src/USER-MISC/compute_pressure_cylinder.cpp @@ -12,8 +12,8 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include #include "compute_pressure_cylinder.h" #include "atom.h" #include "update.h" From a549752764a34219f6e07232a886c227d1a6b285 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 2 Oct 2018 15:18:06 -0400 Subject: [PATCH 230/302] reduce compiler warnings and some more whitespace adjustments --- src/USER-MISC/compute_pressure_cylinder.cpp | 35 +++++++++------------ 1 file changed, 15 insertions(+), 20 deletions(-) diff --git a/src/USER-MISC/compute_pressure_cylinder.cpp b/src/USER-MISC/compute_pressure_cylinder.cpp index b35e851e4b..6fcd343e38 100644 --- a/src/USER-MISC/compute_pressure_cylinder.cpp +++ b/src/USER-MISC/compute_pressure_cylinder.cpp @@ -50,10 +50,10 @@ static const char cite_compute_pressure_cylinder[] = ComputePressureCyl::ComputePressureCyl(LAMMPS *lmp, int narg, char **arg) : Compute(lmp, narg, arg), - R(NULL), Rinv(NULL), R2(NULL), R2kin(NULL), invVbin(NULL), - density_temp(NULL), density_all(NULL), tangent(NULL), ephi_x(NULL), - ephi_y(NULL), Pr_temp(NULL), Pr_all(NULL), Pz_temp(NULL), Pz_all(NULL), - Pphi_temp(NULL), Pphi_all(NULL), PrAinv(NULL), PzAinv(NULL), binz(NULL) + Pr_temp(NULL), Pr_all(NULL), Pz_temp(NULL), Pz_all(NULL), Pphi_temp(NULL), + Pphi_all(NULL), R(NULL), Rinv(NULL), R2(NULL), PrAinv(NULL), PzAinv(NULL), + R2kin(NULL), density_temp(NULL), invVbin(NULL), density_all(NULL), + tangent(NULL), ephi_x(NULL), ephi_y(NULL), binz(NULL) { if (lmp->citeme) lmp->citeme->add(cite_compute_pressure_cylinder); if (narg != 7) error->all(FLERR,"Illegal compute pressure/cylinder command"); @@ -171,7 +171,7 @@ void ComputePressureCyl::init() invVbin[0]=1.0/((zhi-zlo)*MY_PI*R2kin[0]); PzAinv[0]=1.0/(MY_PI*R2kin[0]*((double)nzbins)); - + for (int jq = 1; jq < nbins; jq++) { invVbin[jq]=1.0/((zhi-zlo)*MY_PI*(R2kin[jq]-R2kin[jq-1])); PzAinv[jq]=1.0/(MY_PI*(R2kin[jq]-R2kin[jq-1])*((double)nzbins)); @@ -189,7 +189,7 @@ void ComputePressureCyl::init() /* ---------------------------------------------------------------------- */ -void ComputePressureCyl::init_list(int id, NeighList *ptr) +void ComputePressureCyl::init_list(int /* id */, NeighList *ptr) { list = ptr; } @@ -226,10 +226,10 @@ void ComputePressureCyl::compute_array() int me; MPI_Comm_rank(world,&me); - int i,j,n,ii,jj,inum,jnum,itype,jtype; + int i,j,ii,jj,inum,jnum,itype,jtype; tagint itag,jtag; double xtmp,ytmp,ztmp,delx,dely,delz; - double rsq,eng,fpair,factor_coul,factor_lj; + double rsq,fpair,factor_coul,factor_lj; int *ilist,*jlist,*numneigh,**firstneigh; double **x = atom->x; @@ -276,14 +276,12 @@ void ComputePressureCyl::compute_array() double r1=0.0; double r2=0.0; double risq,rjsq; - double ri,rj,rij,fij; - double A,B,C,Bsq,A2inv,A4,D; - double alpha1,alpha2,aij; + double A,B,C,D; + double alpha1,alpha2; double xi,yi,zi,dx,dy,dz; - double m,xR,yR,zR,fn; + double xR,yR,zR,fn; double alpha,xL,yL,zL,L2,ftphi,ftz; double sqrtD; - double lower_z,upper_z; for (ii = 0; ii < inum; ii++) { i = ilist[ii]; @@ -313,11 +311,9 @@ void ComputePressureCyl::compute_array() jtag = tag[j]; if (itag > jtag) { if ((itag+jtag) % 2 == 0) continue; - } - else if (itag < jtag) { + } else if (itag < jtag) { if ((itag+jtag) % 2 == 1) continue; - } - else { + } else { if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { if (x[j][1] < ytmp) continue; @@ -342,8 +338,7 @@ void ComputePressureCyl::compute_array() dx=x[i][0]-x[j][0]; dy=x[i][1]-x[j][1]; dz=x[i][2]-x[j][2]; - } - else { + } else { risq=r1; rjsq=r2; xi=x[i][0]; @@ -358,7 +353,7 @@ void ComputePressureCyl::compute_array() jtype = type[j]; if (rsq >= cutsq[itype][jtype]) continue; - eng = pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair); + pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair); A=dx*dx+dy*dy; B=2.0*(xi*dx+yi*dy); From 9e9b97231cfbf6d912c937b49677f4e93d85867a Mon Sep 17 00:00:00 2001 From: Aidan Thompson Date: Tue, 2 Oct 2018 16:56:27 -0600 Subject: [PATCH 231/302] Fixed sign error on mu for semigrand variant --- src/MC/fix_atom_swap.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/MC/fix_atom_swap.cpp b/src/MC/fix_atom_swap.cpp index 3e981c5609..12b5d65f4a 100644 --- a/src/MC/fix_atom_swap.cpp +++ b/src/MC/fix_atom_swap.cpp @@ -377,7 +377,7 @@ int FixAtomSwap::attempt_semi_grand() int success = 0; if (i >= 0) if (random_unequal->uniform() < - exp(-beta*(energy_after - energy_before + exp(beta*(energy_before - energy_after + mu[jtype] - mu[itype]))) success = 1; int success_all = 0; From c3abf13af1ec4c54f660b4365b372ac175001a52 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 4 Oct 2018 12:18:01 +0200 Subject: [PATCH 232/302] don't allow hybrid/overlay as hybrid substyle as well --- src/pair_hybrid.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/pair_hybrid.cpp b/src/pair_hybrid.cpp index 03747e1de3..2b2304718c 100644 --- a/src/pair_hybrid.cpp +++ b/src/pair_hybrid.cpp @@ -281,7 +281,7 @@ void PairHybrid::settings(int narg, char **arg) iarg = 0; nstyles = 0; while (iarg < narg) { - if (strcmp(arg[iarg],"hybrid") == 0) + if (strncmp(arg[iarg],"hybrid",6) == 0) error->all(FLERR,"Pair style hybrid cannot have hybrid as an argument"); if (strcmp(arg[iarg],"none") == 0) error->all(FLERR,"Pair style hybrid cannot have none as an argument"); From a1a9f34c1857c842e3033b0628b8fa1dfa8630df Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 4 Oct 2018 12:18:28 +0200 Subject: [PATCH 233/302] pair style deprecated now functional and compatible with hybrid pair styles --- src/pair_deprecated.cpp | 56 +++++++++++++++++++++++------------------ src/pair_deprecated.h | 10 ++++---- src/pair_hybrid.h | 1 + 3 files changed, 38 insertions(+), 29 deletions(-) diff --git a/src/pair_deprecated.cpp b/src/pair_deprecated.cpp index a383f390cf..e64c4913e4 100644 --- a/src/pair_deprecated.cpp +++ b/src/pair_deprecated.cpp @@ -23,31 +23,39 @@ using namespace LAMMPS_NS; -/* ---------------------------------------------------------------------- */ - -PairDeprecated::PairDeprecated(LAMMPS *lmp) : Pair(lmp) +static void writemsg(LAMMPS *lmp, const char *msg, int abend=1) { - if (strcmp(force->pair_style,"deprecated") == 0) { - const char *message = "\n" - "NOTE: The pair style 'deprecated' is a dummy fix style that was added to\n" - "LAMMPS in order to print suitable error messages for deleted features.\n\n"; - - if (comm->me == 0) { - if (screen) fputs(message,screen); - if (logfile) fputs(message,logfile); - } + if (lmp->comm->me == 0) { + if (lmp->screen) fputs(msg,lmp->screen); + if (lmp->logfile) fputs(msg,lmp->logfile); } - if (strncmp(force->pair_style,"reax",11) == 0) { - const char *message = "\n" - "NOTE: The pair style 'reax' has been removed from LAMMPS after the\n" - "## November 2018 stable release. Its functionality has long before\n" - "been superseded by pair styles 'reax/c' and 'reax/c/kk'\n\n"; - - if (comm->me == 0) { - if (screen) fputs(message,screen); - if (logfile) fputs(message,logfile); - } - } - error->all(FLERR,"This pair_style command has been removed from LAMMPS"); + if (abend) + lmp->error->all(FLERR,"This pair_style is no longer available"); } + +/* ---------------------------------------------------------------------- */ + +void PairDeprecated::settings(int, char **) +{ + const char *my_style = force->pair_style; + + // hybrid substyles are created in PairHybrid::settings(), so when this is + // called, our style was just added at the end of the list of substyles + if (strncmp(my_style,"hybrid",6) == 0) { + PairHybrid *hybrid = (PairHybrid *)force->pair; + my_style = hybrid->keywords[hybrid->nstyles]; + } + + if (strcmp(my_style,"deprecated") == 0) { + writemsg(lmp,"\nPair style 'deprecated' is a dummy pair style\n\n",0); + + } else if (strcmp(my_style,"reax") == 0) { + writemsg(lmp, "\nPair style 'reax' has been removed from LAMMPS " + "after the\n## November 2018 stable release. Its " + "functionality has long before\nbeen superseded by pair " + "styles 'reax/c' and 'reax/c/kk'\n\n"); + } +} + + diff --git a/src/pair_deprecated.h b/src/pair_deprecated.h index 4201b3453d..163b2a8f1b 100644 --- a/src/pair_deprecated.h +++ b/src/pair_deprecated.h @@ -26,12 +26,12 @@ namespace LAMMPS_NS { class PairDeprecated : public Pair { public: - PairDeprecated(class LAMMPS *); - virtual ~PairDeprecated() {}; + PairDeprecated(class LAMMPS *lmp) : Pair(lmp) {} + virtual ~PairDeprecated() {} - virtual void compute(int, int) {}; - virtual void settings(int, char **) {}; - virtual void coeff(int, char **) {}; + virtual void compute(int, int) {} + virtual void settings(int, char **); + virtual void coeff(int, char **) {} }; diff --git a/src/pair_hybrid.h b/src/pair_hybrid.h index 08f5a574df..e313e16f18 100644 --- a/src/pair_hybrid.h +++ b/src/pair_hybrid.h @@ -32,6 +32,7 @@ class PairHybrid : public Pair { friend class Force; friend class Respa; friend class Info; + friend class PairDeprecated; public: PairHybrid(class LAMMPS *); virtual ~PairHybrid(); From b02d3b1b94dc333edc6ac241f42c931eed85de01 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 4 Oct 2018 12:24:46 +0200 Subject: [PATCH 234/302] cosmetic change --- src/pair_deprecated.cpp | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/src/pair_deprecated.cpp b/src/pair_deprecated.cpp index e64c4913e4..9045b3f2a8 100644 --- a/src/pair_deprecated.cpp +++ b/src/pair_deprecated.cpp @@ -53,8 +53,7 @@ void PairDeprecated::settings(int, char **) } else if (strcmp(my_style,"reax") == 0) { writemsg(lmp, "\nPair style 'reax' has been removed from LAMMPS " "after the\n## November 2018 stable release. Its " - "functionality has long before\nbeen superseded by pair " - "styles 'reax/c' and 'reax/c/kk'\n\n"); + "functionality has\nbeen superseded by pair style 'reax/c'.\n\n"); } } From fd20eb93b2e7f63b2fb1efda2b81e494b1cdc994 Mon Sep 17 00:00:00 2001 From: jrgissing Date: Thu, 4 Oct 2018 21:30:34 -0600 Subject: [PATCH 235/302] remove listing of extinct special_bonds 'extra' keyword --- doc/src/special_bonds.txt | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/src/special_bonds.txt b/doc/src/special_bonds.txt index 283aad6c2d..e90535e65f 100644 --- a/doc/src/special_bonds.txt +++ b/doc/src/special_bonds.txt @@ -13,7 +13,7 @@ special_bonds command :h3 special_bonds keyword values ... :pre one or more keyword/value pairs may be appended :ulb,l -keyword = {amber} or {charmm} or {dreiding} or {fene} or {lj/coul} or {lj} or {coul} or {angle} or {dihedral} or {extra} :l +keyword = {amber} or {charmm} or {dreiding} or {fene} or {lj/coul} or {lj} or {coul} or {angle} or {dihedral} :l {amber} values = none {charmm} values = none {dreiding} values = none @@ -219,7 +219,7 @@ each time the command is issued. [Default:] All 3 Lennard-Jones and 3 Coulombic weighting coefficients = 0.0, -angle = no, dihedral = no, and extra = 0. +angle = no, dihedral = no. :line From 7f8302b65b44f7e7f6ee5bfa7827b2defab79bd9 Mon Sep 17 00:00:00 2001 From: jrgissing Date: Thu, 4 Oct 2018 22:08:43 -0600 Subject: [PATCH 236/302] replace extra_special with maxspecial in restarts --- src/read_restart.cpp | 6 +++--- src/write_restart.cpp | 4 ++-- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/src/read_restart.cpp b/src/read_restart.cpp index 9be035e1a1..a57831a5b2 100644 --- a/src/read_restart.cpp +++ b/src/read_restart.cpp @@ -64,7 +64,7 @@ enum{VERSION,SMALLINT,TAGINT,BIGINT, ATOM_ID,ATOM_MAP_STYLE,ATOM_MAP_USER,ATOM_SORTFREQ,ATOM_SORTBIN, COMM_MODE,COMM_CUTOFF,COMM_VEL,NO_PAIR, EXTRA_BOND_PER_ATOM,EXTRA_ANGLE_PER_ATOM,EXTRA_DIHEDRAL_PER_ATOM, - EXTRA_IMPROPER_PER_ATOM,EXTRA_SPECIAL_PER_ATOM}; + EXTRA_IMPROPER_PER_ATOM,MAXSPECIAL}; #define LB_FACTOR 1.1 @@ -924,8 +924,8 @@ void ReadRestart::header(int incompatible) atom->extra_dihedral_per_atom = read_int(); } else if (flag == EXTRA_IMPROPER_PER_ATOM) { atom->extra_improper_per_atom = read_int(); - } else if (flag == EXTRA_SPECIAL_PER_ATOM) { - force->special_extra = read_int(); + } else if (flag == MAXSPECIAL) { + atom->maxspecial = read_int(); } else error->all(FLERR,"Invalid flag in header section of restart file"); diff --git a/src/write_restart.cpp b/src/write_restart.cpp index edb6dfa7e8..6e01ab2997 100644 --- a/src/write_restart.cpp +++ b/src/write_restart.cpp @@ -63,7 +63,7 @@ enum{VERSION,SMALLINT,TAGINT,BIGINT, ATOM_ID,ATOM_MAP_STYLE,ATOM_MAP_USER,ATOM_SORTFREQ,ATOM_SORTBIN, COMM_MODE,COMM_CUTOFF,COMM_VEL,NO_PAIR, EXTRA_BOND_PER_ATOM,EXTRA_ANGLE_PER_ATOM,EXTRA_DIHEDRAL_PER_ATOM, - EXTRA_IMPROPER_PER_ATOM,EXTRA_SPECIAL_PER_ATOM}; + EXTRA_IMPROPER_PER_ATOM,MAXSPECIAL}; /* ---------------------------------------------------------------------- */ @@ -533,7 +533,7 @@ void WriteRestart::header() write_int(EXTRA_ANGLE_PER_ATOM,atom->extra_angle_per_atom); write_int(EXTRA_DIHEDRAL_PER_ATOM,atom->extra_dihedral_per_atom); write_int(EXTRA_IMPROPER_PER_ATOM,atom->extra_improper_per_atom); - write_int(EXTRA_SPECIAL_PER_ATOM,force->special_extra); + write_int(MAXSPECIAL,atom->maxspecial); // -1 flag signals end of header From 17853aef202c668b4abd976e6fa1d82e74629836 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 5 Oct 2018 09:47:47 +0200 Subject: [PATCH 237/302] modify restart changes, so it stays backward compatible and does not result in unexpected behavior when reading old restarts. also use consistent naming conventions for enum entries --- src/read_restart.cpp | 6 ++++-- src/write_restart.cpp | 4 ++-- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/src/read_restart.cpp b/src/read_restart.cpp index a57831a5b2..252c48d251 100644 --- a/src/read_restart.cpp +++ b/src/read_restart.cpp @@ -64,7 +64,7 @@ enum{VERSION,SMALLINT,TAGINT,BIGINT, ATOM_ID,ATOM_MAP_STYLE,ATOM_MAP_USER,ATOM_SORTFREQ,ATOM_SORTBIN, COMM_MODE,COMM_CUTOFF,COMM_VEL,NO_PAIR, EXTRA_BOND_PER_ATOM,EXTRA_ANGLE_PER_ATOM,EXTRA_DIHEDRAL_PER_ATOM, - EXTRA_IMPROPER_PER_ATOM,MAXSPECIAL}; + EXTRA_IMPROPER_PER_ATOM,EXTRA_SPECIAL_PER_ATOM,ATOM_MAXSPECIAL}; #define LB_FACTOR 1.1 @@ -924,7 +924,9 @@ void ReadRestart::header(int incompatible) atom->extra_dihedral_per_atom = read_int(); } else if (flag == EXTRA_IMPROPER_PER_ATOM) { atom->extra_improper_per_atom = read_int(); - } else if (flag == MAXSPECIAL) { + } else if (flag == EXTRA_SPECIAL_PER_ATOM) { + force->special_extra = read_int(); + } else if (flag == ATOM_MAXSPECIAL) { atom->maxspecial = read_int(); } else error->all(FLERR,"Invalid flag in header section of restart file"); diff --git a/src/write_restart.cpp b/src/write_restart.cpp index 6e01ab2997..e0e17cd292 100644 --- a/src/write_restart.cpp +++ b/src/write_restart.cpp @@ -63,7 +63,7 @@ enum{VERSION,SMALLINT,TAGINT,BIGINT, ATOM_ID,ATOM_MAP_STYLE,ATOM_MAP_USER,ATOM_SORTFREQ,ATOM_SORTBIN, COMM_MODE,COMM_CUTOFF,COMM_VEL,NO_PAIR, EXTRA_BOND_PER_ATOM,EXTRA_ANGLE_PER_ATOM,EXTRA_DIHEDRAL_PER_ATOM, - EXTRA_IMPROPER_PER_ATOM,MAXSPECIAL}; + EXTRA_IMPROPER_PER_ATOM,EXTRA_SPECIAL_PER_ATOM,ATOM_MAXSPECIAL}; /* ---------------------------------------------------------------------- */ @@ -533,7 +533,7 @@ void WriteRestart::header() write_int(EXTRA_ANGLE_PER_ATOM,atom->extra_angle_per_atom); write_int(EXTRA_DIHEDRAL_PER_ATOM,atom->extra_dihedral_per_atom); write_int(EXTRA_IMPROPER_PER_ATOM,atom->extra_improper_per_atom); - write_int(MAXSPECIAL,atom->maxspecial); + write_int(ATOM_MAXSPECIAL,atom->maxspecial); // -1 flag signals end of header From 61e2cd3f61fc18850e26326eecb86b03576a841c Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 5 Oct 2018 16:03:11 +0200 Subject: [PATCH 238/302] avoid requesting threaded neighbor lists that are both threaded via USER-OMP and USER-INTEL --- src/USER-INTEL/fix_intel.cpp | 7 ++++++- src/USER-OMP/fix_omp.cpp | 5 ++++- 2 files changed, 10 insertions(+), 2 deletions(-) diff --git a/src/USER-INTEL/fix_intel.cpp b/src/USER-INTEL/fix_intel.cpp index 3a67b60632..37212928df 100644 --- a/src/USER-INTEL/fix_intel.cpp +++ b/src/USER-INTEL/fix_intel.cpp @@ -532,8 +532,13 @@ void FixIntel::check_neighbor_intel() _offload_noghost = 0; } #endif + + // avoid flagging a neighbor list as both USER-INTEL and USER-OMP + if (neighbor->requests[i]->intel) + neighbor->requests[i]->omp = 0; + if (neighbor->requests[i]->skip) - error->all(FLERR, "Cannot yet use hybrid styles with Intel package."); + error->all(FLERR, "Hybrid styles with Intel package are unsupported."); } } diff --git a/src/USER-OMP/fix_omp.cpp b/src/USER-OMP/fix_omp.cpp index 8d54d5b451..8be54caada 100644 --- a/src/USER-OMP/fix_omp.cpp +++ b/src/USER-OMP/fix_omp.cpp @@ -318,8 +318,11 @@ void FixOMP::set_neighbor_omp() const int neigh_omp = _neighbor ? 1 : 0; const int nrequest = neighbor->nrequest; + // flag *all* neighbor list requests as USER-OMP threaded, + // but skip lists already flagged as USER-INTEL threaded for (int i = 0; i < nrequest; ++i) - neighbor->requests[i]->omp = neigh_omp; + if (! neighbor->requests[i]->intel) + neighbor->requests[i]->omp = neigh_omp; } /* ---------------------------------------------------------------------- */ From 43ae9656d7bf87f95e3b25baf1b799f671e0ae8b Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 5 Oct 2018 17:23:09 +0200 Subject: [PATCH 239/302] add a "deprecated" command style for flagging future removed commands --- src/deprecated.cpp | 48 ++++++++++++++++++++++++++++ src/deprecated.h | 70 +++++++++++++++++++++++++++++++++++++++++ src/input.h | 6 +++- src/pair_deprecated.cpp | 1 + 4 files changed, 124 insertions(+), 1 deletion(-) create mode 100644 src/deprecated.cpp create mode 100644 src/deprecated.h diff --git a/src/deprecated.cpp b/src/deprecated.cpp new file mode 100644 index 0000000000..ed9a9e6de4 --- /dev/null +++ b/src/deprecated.cpp @@ -0,0 +1,48 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing authors: Axel Kohlmeyer (Temple U), +------------------------------------------------------------------------- */ + +#include +#include "deprecated.h" +#include "comm.h" +#include "force.h" +#include "error.h" +#include "input.h" + +using namespace LAMMPS_NS; + +static void writemsg(LAMMPS *lmp, const char *msg, int abend=1) +{ + if (lmp->comm->me == 0) { + if (lmp->screen) fputs(msg,lmp->screen); + if (lmp->logfile) fputs(msg,lmp->logfile); + } + if (abend) + lmp->error->all(FLERR,"This command is no longer available"); +} + +/* ---------------------------------------------------------------------- */ + +void Deprecated::command(int narg, char **arg) +{ + if (strcmp(input->command,"deprecated") == 0) { + writemsg(lmp,"\nCommand 'deprecated' is a dummy command\n\n",0); + + } else if (strcmp(input->command,"XXX") == 0) { + writemsg(lmp, "\nCommand 'XXX' has been removed from LAMMPS " + "after the\n## XXX 20## stable release.\n\n"); + } +} diff --git a/src/deprecated.h b/src/deprecated.h new file mode 100644 index 0000000000..9835579245 --- /dev/null +++ b/src/deprecated.h @@ -0,0 +1,70 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef COMMAND_CLASS + +CommandStyle(deprecated,Deprecated) +CommandStyle(XXX,Deprecated) + +#else + +#ifndef LMP_DEPRECATED_H +#define LMP_DEPRECATED_H + +#include "pointers.h" + +namespace LAMMPS_NS { + +class Deprecated : protected Pointers { + public: + Deprecated(class LAMMPS *lmp) : Pointers(lmp) {}; + void command(int, char **); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +W: Ignoring unknown or incorrect info command flag + +Self-explanatory. An unknown argument was given to the info command. +Compare your input with the documentation. + +E: Unknown name for info package category + +Self-explanatory. + +E: Unknown name for info newton category + +Self-explanatory. + +E: Unknown name for info pair category + +Self-explanatory. + +E: Unknown category for info is_active() + +Self-explanatory. + +E: Unknown category for info is_available() + +Self-explanatory. + +E: Unknown category for info is_defined() + +Self-explanatory. + +*/ diff --git a/src/input.h b/src/input.h index 80b3e8c7da..be320a41ec 100644 --- a/src/input.h +++ b/src/input.h @@ -24,6 +24,8 @@ namespace LAMMPS_NS { class Input : protected Pointers { friend class Info; friend class Error; + friend class Deprecated; + public: int narg; // # of command args char **arg; // parsed args for command @@ -38,9 +40,11 @@ class Input : protected Pointers { // substitute for variables in a string int expand_args(int, char **, int, char **&); // expand args due to wildcard + protected: + char *command; // ptr to current command + private: int me; // proc ID - char *command; // ptr to current command int maxarg; // max # of args in arg char *line,*copy,*work; // input line & copy and work string int maxline,maxcopy,maxwork; // max lengths of char strings diff --git a/src/pair_deprecated.cpp b/src/pair_deprecated.cpp index 9045b3f2a8..143cfd46f4 100644 --- a/src/pair_deprecated.cpp +++ b/src/pair_deprecated.cpp @@ -15,6 +15,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ +#include #include "pair_deprecated.h" #include "pair_hybrid.h" #include "comm.h" From 0c1ff5ac3ef689e25a10f222c91bcfe64bff5b89 Mon Sep 17 00:00:00 2001 From: Denis Taniguchi Date: Fri, 5 Oct 2018 17:10:31 +0100 Subject: [PATCH 240/302] Fixing issues with AtomVecSphereKokkos not correctly handling cases with varying and constant radius. --- src/KOKKOS/atom_vec_sphere_kokkos.cpp | 530 +++++++++++++++++--------- src/KOKKOS/atom_vec_sphere_kokkos.h | 2 + 2 files changed, 344 insertions(+), 188 deletions(-) diff --git a/src/KOKKOS/atom_vec_sphere_kokkos.cpp b/src/KOKKOS/atom_vec_sphere_kokkos.cpp index 76582086df..476091ff41 100644 --- a/src/KOKKOS/atom_vec_sphere_kokkos.cpp +++ b/src/KOKKOS/atom_vec_sphere_kokkos.cpp @@ -278,78 +278,78 @@ int AtomVecSphereKokkos::pack_comm_kokkos( sync(Host,X_MASK|RADIUS_MASK|RMASS_MASK); if(pbc_flag) { if(domain->triclinic) { - struct AtomVecSphereKokkos_PackComm f( - atomKK->k_x, - atomKK->k_radius,atomKK->k_rmass, - buf,list,iswap, - domain->xprd,domain->yprd,domain->zprd, - domain->xy,domain->xz,domain->yz,pbc); - Kokkos::parallel_for(n,f); - } else { - struct AtomVecSphereKokkos_PackComm f( + struct AtomVecSphereKokkos_PackComm f( atomKK->k_x, - atomKK->k_radius,atomKK->k_rmass, - buf,list,iswap, - domain->xprd,domain->yprd,domain->zprd, - domain->xy,domain->xz,domain->yz,pbc); - Kokkos::parallel_for(n,f); + atomKK->k_radius,atomKK->k_rmass, + buf,list,iswap, + domain->xprd,domain->yprd,domain->zprd, + domain->xy,domain->xz,domain->yz,pbc); + Kokkos::parallel_for(n,f); + } else { + struct AtomVecSphereKokkos_PackComm f( + atomKK->k_x, + atomKK->k_radius,atomKK->k_rmass, + buf,list,iswap, + domain->xprd,domain->yprd,domain->zprd, + domain->xy,domain->xz,domain->yz,pbc); + Kokkos::parallel_for(n,f); } } else { if(domain->triclinic) { - struct AtomVecSphereKokkos_PackComm f( + struct AtomVecSphereKokkos_PackComm f( atomKK->k_x, - atomKK->k_radius,atomKK->k_rmass, - buf,list,iswap, - domain->xprd,domain->yprd,domain->zprd, - domain->xy,domain->xz,domain->yz,pbc); - Kokkos::parallel_for(n,f); + atomKK->k_radius,atomKK->k_rmass, + buf,list,iswap, + domain->xprd,domain->yprd,domain->zprd, + domain->xy,domain->xz,domain->yz,pbc); + Kokkos::parallel_for(n,f); } else { - struct AtomVecSphereKokkos_PackComm f( + struct AtomVecSphereKokkos_PackComm f( atomKK->k_x, - atomKK->k_radius,atomKK->k_rmass, - buf,list,iswap, - domain->xprd,domain->yprd,domain->zprd, - domain->xy,domain->xz,domain->yz,pbc); - Kokkos::parallel_for(n,f); + atomKK->k_radius,atomKK->k_rmass, + buf,list,iswap, + domain->xprd,domain->yprd,domain->zprd, + domain->xy,domain->xz,domain->yz,pbc); + Kokkos::parallel_for(n,f); } } } else { sync(Device,X_MASK|RADIUS_MASK|RMASS_MASK); if(pbc_flag) { if(domain->triclinic) { - struct AtomVecSphereKokkos_PackComm f( + struct AtomVecSphereKokkos_PackComm f( atomKK->k_x, - atomKK->k_radius,atomKK->k_rmass, - buf,list,iswap, - domain->xprd,domain->yprd,domain->zprd, - domain->xy,domain->xz,domain->yz,pbc); - Kokkos::parallel_for(n,f); + atomKK->k_radius,atomKK->k_rmass, + buf,list,iswap, + domain->xprd,domain->yprd,domain->zprd, + domain->xy,domain->xz,domain->yz,pbc); + Kokkos::parallel_for(n,f); } else { - struct AtomVecSphereKokkos_PackComm f( + struct AtomVecSphereKokkos_PackComm f( atomKK->k_x, - atomKK->k_radius,atomKK->k_rmass, - buf,list,iswap, - domain->xprd,domain->yprd,domain->zprd, - domain->xy,domain->xz,domain->yz,pbc); - Kokkos::parallel_for(n,f); + atomKK->k_radius,atomKK->k_rmass, + buf,list,iswap, + domain->xprd,domain->yprd,domain->zprd, + domain->xy,domain->xz,domain->yz,pbc); + Kokkos::parallel_for(n,f); } } else { if(domain->triclinic) { - struct AtomVecSphereKokkos_PackComm f( + struct AtomVecSphereKokkos_PackComm f( atomKK->k_x, - atomKK->k_radius,atomKK->k_rmass, - buf,list,iswap, - domain->xprd,domain->yprd,domain->zprd, - domain->xy,domain->xz,domain->yz,pbc); - Kokkos::parallel_for(n,f); + atomKK->k_radius,atomKK->k_rmass, + buf,list,iswap, + domain->xprd,domain->yprd,domain->zprd, + domain->xy,domain->xz,domain->yz,pbc); + Kokkos::parallel_for(n,f); } else { - struct AtomVecSphereKokkos_PackComm f( + struct AtomVecSphereKokkos_PackComm f( atomKK->k_x, - atomKK->k_radius,atomKK->k_rmass, - buf,list,iswap, - domain->xprd,domain->yprd,domain->zprd, - domain->xy,domain->xz,domain->yz,pbc); - Kokkos::parallel_for(n,f); + atomKK->k_radius,atomKK->k_rmass, + buf,list,iswap, + domain->xprd,domain->yprd,domain->zprd, + domain->xy,domain->xz,domain->yz,pbc); + Kokkos::parallel_for(n,f); } } } @@ -358,7 +358,7 @@ int AtomVecSphereKokkos::pack_comm_kokkos( /* ---------------------------------------------------------------------- */ -template +template struct AtomVecSphereKokkos_PackCommVel { typedef DeviceType device_type; @@ -399,7 +399,7 @@ struct AtomVecSphereKokkos_PackCommVel { _xy(xy),_xz(xz),_yz(yz), _deform_vremap(deform_vremap) { - const size_t elements = 11; + const size_t elements = 9 + 2 * RADVARY; const int maxsend = (buf.template view().extent(0)*buf.template view().extent(1))/elements; _buf = typename ArrayTypes::t_xfloat_2d_um(buf.view().data(),maxsend,elements); _pbc[0] = pbc[0]; _pbc[1] = pbc[1]; _pbc[2] = pbc[2]; @@ -426,26 +426,28 @@ struct AtomVecSphereKokkos_PackCommVel { _buf(i,2) = _x(j,2) + _pbc[2]*_zprd; } } - _buf(i,3) = _radius(j); - _buf(i,4) = _rmass(j); if (DEFORM_VREMAP == 0) { - _buf(i,5) = _v(j,0); - _buf(i,6) = _v(j,1); - _buf(i,7) = _v(j,2); + _buf(i,3) = _v(j,0); + _buf(i,4) = _v(j,1); + _buf(i,5) = _v(j,2); } else { if (_mask(i) & _deform_vremap) { - _buf(i,5) = _v(j,0) + _pbc[0]*_h_rate[0] + _pbc[5]*_h_rate[5] + _pbc[4]*_h_rate[4]; - _buf(i,6) = _v(j,1) + _pbc[1]*_h_rate[1] + _pbc[3]*_h_rate[3]; - _buf(i,7) = _v(j,2) + _pbc[2]*_h_rate[2]; + _buf(i,3) = _v(j,0) + _pbc[0]*_h_rate[0] + _pbc[5]*_h_rate[5] + _pbc[4]*_h_rate[4]; + _buf(i,4) = _v(j,1) + _pbc[1]*_h_rate[1] + _pbc[3]*_h_rate[3]; + _buf(i,5) = _v(j,2) + _pbc[2]*_h_rate[2]; } else { - _buf(i,5) = _v(j,0); - _buf(i,6) = _v(j,1); - _buf(i,7) = _v(j,2); + _buf(i,3) = _v(j,0); + _buf(i,4) = _v(j,1); + _buf(i,5) = _v(j,2); } } - _buf(i,8) = _omega(j,0); - _buf(i,9) = _omega(j,1); - _buf(i,10) = _omega(j,2); + _buf(i,6) = _omega(j,0); + _buf(i,7) = _omega(j,1); + _buf(i,8) = _omega(j,2); + if (RADVARY) { + _buf(i,9) = _radius(j); + _buf(i,10) = _rmass(j); + } } }; @@ -464,64 +466,130 @@ int AtomVecSphereKokkos::pack_comm_vel_kokkos( if(pbc_flag) { if(deform_vremap) { if(domain->triclinic) { - struct AtomVecSphereKokkos_PackCommVel f( - atomKK->k_x,atomKK->k_mask, - atomKK->k_radius,atomKK->k_rmass, - atomKK->k_v,atomKK->k_omega, - buf,list,iswap, - domain->xprd,domain->yprd,domain->zprd, - domain->xy,domain->xz,domain->yz,pbc,h_rate,deform_vremap); - Kokkos::parallel_for(n,f); + if (radvary == 0) { + struct AtomVecSphereKokkos_PackCommVel f( + atomKK->k_x,atomKK->k_mask, + atomKK->k_radius,atomKK->k_rmass, + atomKK->k_v,atomKK->k_omega, + buf,list,iswap, + domain->xprd,domain->yprd,domain->zprd, + domain->xy,domain->xz,domain->yz,pbc,h_rate,deform_vremap); + Kokkos::parallel_for(n,f); + } else { + struct AtomVecSphereKokkos_PackCommVel f( + atomKK->k_x,atomKK->k_mask, + atomKK->k_radius,atomKK->k_rmass, + atomKK->k_v,atomKK->k_omega, + buf,list,iswap, + domain->xprd,domain->yprd,domain->zprd, + domain->xy,domain->xz,domain->yz,pbc,h_rate,deform_vremap); + Kokkos::parallel_for(n,f); + } } else { - struct AtomVecSphereKokkos_PackCommVel f( - atomKK->k_x,atomKK->k_mask, - atomKK->k_radius,atomKK->k_rmass, - atomKK->k_v,atomKK->k_omega, - buf,list,iswap, - domain->xprd,domain->yprd,domain->zprd, - domain->xy,domain->xz,domain->yz,pbc,h_rate,deform_vremap); - Kokkos::parallel_for(n,f); + if (radvary == 0) { + struct AtomVecSphereKokkos_PackCommVel f( + atomKK->k_x,atomKK->k_mask, + atomKK->k_radius,atomKK->k_rmass, + atomKK->k_v,atomKK->k_omega, + buf,list,iswap, + domain->xprd,domain->yprd,domain->zprd, + domain->xy,domain->xz,domain->yz,pbc,h_rate,deform_vremap); + Kokkos::parallel_for(n,f); + } else { + struct AtomVecSphereKokkos_PackCommVel f( + atomKK->k_x,atomKK->k_mask, + atomKK->k_radius,atomKK->k_rmass, + atomKK->k_v,atomKK->k_omega, + buf,list,iswap, + domain->xprd,domain->yprd,domain->zprd, + domain->xy,domain->xz,domain->yz,pbc,h_rate,deform_vremap); + Kokkos::parallel_for(n,f); + } } } else { if(domain->triclinic) { - struct AtomVecSphereKokkos_PackCommVel f( - atomKK->k_x,atomKK->k_mask, - atomKK->k_radius,atomKK->k_rmass, - atomKK->k_v,atomKK->k_omega, - buf,list,iswap, - domain->xprd,domain->yprd,domain->zprd, - domain->xy,domain->xz,domain->yz,pbc,h_rate,deform_vremap); - Kokkos::parallel_for(n,f); + if (radvary == 0) { + struct AtomVecSphereKokkos_PackCommVel f( + atomKK->k_x,atomKK->k_mask, + atomKK->k_radius,atomKK->k_rmass, + atomKK->k_v,atomKK->k_omega, + buf,list,iswap, + domain->xprd,domain->yprd,domain->zprd, + domain->xy,domain->xz,domain->yz,pbc,h_rate,deform_vremap); + Kokkos::parallel_for(n,f); + } else { + struct AtomVecSphereKokkos_PackCommVel f( + atomKK->k_x,atomKK->k_mask, + atomKK->k_radius,atomKK->k_rmass, + atomKK->k_v,atomKK->k_omega, + buf,list,iswap, + domain->xprd,domain->yprd,domain->zprd, + domain->xy,domain->xz,domain->yz,pbc,h_rate,deform_vremap); + Kokkos::parallel_for(n,f); + } } else { - struct AtomVecSphereKokkos_PackCommVel f( - atomKK->k_x,atomKK->k_mask, - atomKK->k_radius,atomKK->k_rmass, - atomKK->k_v,atomKK->k_omega, - buf,list,iswap, - domain->xprd,domain->yprd,domain->zprd, - domain->xy,domain->xz,domain->yz,pbc,h_rate,deform_vremap); - Kokkos::parallel_for(n,f); + if (radvary == 0) { + struct AtomVecSphereKokkos_PackCommVel f( + atomKK->k_x,atomKK->k_mask, + atomKK->k_radius,atomKK->k_rmass, + atomKK->k_v,atomKK->k_omega, + buf,list,iswap, + domain->xprd,domain->yprd,domain->zprd, + domain->xy,domain->xz,domain->yz,pbc,h_rate,deform_vremap); + Kokkos::parallel_for(n,f); + } else { + struct AtomVecSphereKokkos_PackCommVel f( + atomKK->k_x,atomKK->k_mask, + atomKK->k_radius,atomKK->k_rmass, + atomKK->k_v,atomKK->k_omega, + buf,list,iswap, + domain->xprd,domain->yprd,domain->zprd, + domain->xy,domain->xz,domain->yz,pbc,h_rate,deform_vremap); + Kokkos::parallel_for(n,f); + } } } } else { if(domain->triclinic) { - struct AtomVecSphereKokkos_PackCommVel f( - atomKK->k_x,atomKK->k_mask, - atomKK->k_radius,atomKK->k_rmass, - atomKK->k_v,atomKK->k_omega, - buf,list,iswap, - domain->xprd,domain->yprd,domain->zprd, - domain->xy,domain->xz,domain->yz,pbc,h_rate,deform_vremap); - Kokkos::parallel_for(n,f); + if (radvary == 0) { + struct AtomVecSphereKokkos_PackCommVel f( + atomKK->k_x,atomKK->k_mask, + atomKK->k_radius,atomKK->k_rmass, + atomKK->k_v,atomKK->k_omega, + buf,list,iswap, + domain->xprd,domain->yprd,domain->zprd, + domain->xy,domain->xz,domain->yz,pbc,h_rate,deform_vremap); + Kokkos::parallel_for(n,f); + } else { + struct AtomVecSphereKokkos_PackCommVel f( + atomKK->k_x,atomKK->k_mask, + atomKK->k_radius,atomKK->k_rmass, + atomKK->k_v,atomKK->k_omega, + buf,list,iswap, + domain->xprd,domain->yprd,domain->zprd, + domain->xy,domain->xz,domain->yz,pbc,h_rate,deform_vremap); + Kokkos::parallel_for(n,f); + } } else { - struct AtomVecSphereKokkos_PackCommVel f( - atomKK->k_x,atomKK->k_mask, - atomKK->k_radius,atomKK->k_rmass, - atomKK->k_v,atomKK->k_omega, - buf,list,iswap, - domain->xprd,domain->yprd,domain->zprd, - domain->xy,domain->xz,domain->yz,pbc,h_rate,deform_vremap); - Kokkos::parallel_for(n,f); + if (radvary == 0) { + struct AtomVecSphereKokkos_PackCommVel f( + atomKK->k_x,atomKK->k_mask, + atomKK->k_radius,atomKK->k_rmass, + atomKK->k_v,atomKK->k_omega, + buf,list,iswap, + domain->xprd,domain->yprd,domain->zprd, + domain->xy,domain->xz,domain->yz,pbc,h_rate,deform_vremap); + Kokkos::parallel_for(n,f); + } else { + struct AtomVecSphereKokkos_PackCommVel f( + atomKK->k_x,atomKK->k_mask, + atomKK->k_radius,atomKK->k_rmass, + atomKK->k_v,atomKK->k_omega, + buf,list,iswap, + domain->xprd,domain->yprd,domain->zprd, + domain->xy,domain->xz,domain->yz,pbc,h_rate,deform_vremap); + Kokkos::parallel_for(n,f); + } } } } else { @@ -529,68 +597,134 @@ int AtomVecSphereKokkos::pack_comm_vel_kokkos( if(pbc_flag) { if(deform_vremap) { if(domain->triclinic) { - struct AtomVecSphereKokkos_PackCommVel f( - atomKK->k_x,atomKK->k_mask, - atomKK->k_radius,atomKK->k_rmass, - atomKK->k_v,atomKK->k_omega, - buf,list,iswap, - domain->xprd,domain->yprd,domain->zprd, - domain->xy,domain->xz,domain->yz,pbc,h_rate,deform_vremap); - Kokkos::parallel_for(n,f); + if (radvary == 0) { + struct AtomVecSphereKokkos_PackCommVel f( + atomKK->k_x,atomKK->k_mask, + atomKK->k_radius,atomKK->k_rmass, + atomKK->k_v,atomKK->k_omega, + buf,list,iswap, + domain->xprd,domain->yprd,domain->zprd, + domain->xy,domain->xz,domain->yz,pbc,h_rate,deform_vremap); + Kokkos::parallel_for(n,f); + } else { + struct AtomVecSphereKokkos_PackCommVel f( + atomKK->k_x,atomKK->k_mask, + atomKK->k_radius,atomKK->k_rmass, + atomKK->k_v,atomKK->k_omega, + buf,list,iswap, + domain->xprd,domain->yprd,domain->zprd, + domain->xy,domain->xz,domain->yz,pbc,h_rate,deform_vremap); + Kokkos::parallel_for(n,f); + } } else { - struct AtomVecSphereKokkos_PackCommVel f( - atomKK->k_x,atomKK->k_mask, - atomKK->k_radius,atomKK->k_rmass, - atomKK->k_v,atomKK->k_omega, - buf,list,iswap, - domain->xprd,domain->yprd,domain->zprd, - domain->xy,domain->xz,domain->yz,pbc,h_rate,deform_vremap); - Kokkos::parallel_for(n,f); + if (radvary == 0) { + struct AtomVecSphereKokkos_PackCommVel f( + atomKK->k_x,atomKK->k_mask, + atomKK->k_radius,atomKK->k_rmass, + atomKK->k_v,atomKK->k_omega, + buf,list,iswap, + domain->xprd,domain->yprd,domain->zprd, + domain->xy,domain->xz,domain->yz,pbc,h_rate,deform_vremap); + Kokkos::parallel_for(n,f); + } else { + struct AtomVecSphereKokkos_PackCommVel f( + atomKK->k_x,atomKK->k_mask, + atomKK->k_radius,atomKK->k_rmass, + atomKK->k_v,atomKK->k_omega, + buf,list,iswap, + domain->xprd,domain->yprd,domain->zprd, + domain->xy,domain->xz,domain->yz,pbc,h_rate,deform_vremap); + Kokkos::parallel_for(n,f); + } } } else { if(domain->triclinic) { - struct AtomVecSphereKokkos_PackCommVel f( - atomKK->k_x,atomKK->k_mask, - atomKK->k_radius,atomKK->k_rmass, - atomKK->k_v,atomKK->k_omega, - buf,list,iswap, - domain->xprd,domain->yprd,domain->zprd, - domain->xy,domain->xz,domain->yz,pbc,h_rate,deform_vremap); - Kokkos::parallel_for(n,f); + if (radvary == 0) { + struct AtomVecSphereKokkos_PackCommVel f( + atomKK->k_x,atomKK->k_mask, + atomKK->k_radius,atomKK->k_rmass, + atomKK->k_v,atomKK->k_omega, + buf,list,iswap, + domain->xprd,domain->yprd,domain->zprd, + domain->xy,domain->xz,domain->yz,pbc,h_rate,deform_vremap); + Kokkos::parallel_for(n,f); + } else { + struct AtomVecSphereKokkos_PackCommVel f( + atomKK->k_x,atomKK->k_mask, + atomKK->k_radius,atomKK->k_rmass, + atomKK->k_v,atomKK->k_omega, + buf,list,iswap, + domain->xprd,domain->yprd,domain->zprd, + domain->xy,domain->xz,domain->yz,pbc,h_rate,deform_vremap); + Kokkos::parallel_for(n,f); + } } else { - struct AtomVecSphereKokkos_PackCommVel f( - atomKK->k_x,atomKK->k_mask, - atomKK->k_radius,atomKK->k_rmass, - atomKK->k_v,atomKK->k_omega, - buf,list,iswap, - domain->xprd,domain->yprd,domain->zprd, - domain->xy,domain->xz,domain->yz,pbc,h_rate,deform_vremap); - Kokkos::parallel_for(n,f); + if (radvary == 0) { + struct AtomVecSphereKokkos_PackCommVel f( + atomKK->k_x,atomKK->k_mask, + atomKK->k_radius,atomKK->k_rmass, + atomKK->k_v,atomKK->k_omega, + buf,list,iswap, + domain->xprd,domain->yprd,domain->zprd, + domain->xy,domain->xz,domain->yz,pbc,h_rate,deform_vremap); + Kokkos::parallel_for(n,f); + } else { + struct AtomVecSphereKokkos_PackCommVel f( + atomKK->k_x,atomKK->k_mask, + atomKK->k_radius,atomKK->k_rmass, + atomKK->k_v,atomKK->k_omega, + buf,list,iswap, + domain->xprd,domain->yprd,domain->zprd, + domain->xy,domain->xz,domain->yz,pbc,h_rate,deform_vremap); + Kokkos::parallel_for(n,f); + } } } } else { if(domain->triclinic) { - struct AtomVecSphereKokkos_PackCommVel f( - atomKK->k_x,atomKK->k_mask, - atomKK->k_radius,atomKK->k_rmass, - atomKK->k_v,atomKK->k_omega, - buf,list,iswap, - domain->xprd,domain->yprd,domain->zprd, - domain->xy,domain->xz,domain->yz,pbc,h_rate,deform_vremap); - Kokkos::parallel_for(n,f); + if (radvary == 0) { + struct AtomVecSphereKokkos_PackCommVel f( + atomKK->k_x,atomKK->k_mask, + atomKK->k_radius,atomKK->k_rmass, + atomKK->k_v,atomKK->k_omega, + buf,list,iswap, + domain->xprd,domain->yprd,domain->zprd, + domain->xy,domain->xz,domain->yz,pbc,h_rate,deform_vremap); + Kokkos::parallel_for(n,f); + } else { + struct AtomVecSphereKokkos_PackCommVel f( + atomKK->k_x,atomKK->k_mask, + atomKK->k_radius,atomKK->k_rmass, + atomKK->k_v,atomKK->k_omega, + buf,list,iswap, + domain->xprd,domain->yprd,domain->zprd, + domain->xy,domain->xz,domain->yz,pbc,h_rate,deform_vremap); + Kokkos::parallel_for(n,f); + } } else { - struct AtomVecSphereKokkos_PackCommVel f( - atomKK->k_x,atomKK->k_mask, - atomKK->k_radius,atomKK->k_rmass, - atomKK->k_v,atomKK->k_omega, - buf,list,iswap, - domain->xprd,domain->yprd,domain->zprd, - domain->xy,domain->xz,domain->yz,pbc,h_rate,deform_vremap); - Kokkos::parallel_for(n,f); + if (radvary == 0) { + struct AtomVecSphereKokkos_PackCommVel f( + atomKK->k_x,atomKK->k_mask, + atomKK->k_radius,atomKK->k_rmass, + atomKK->k_v,atomKK->k_omega, + buf,list,iswap, + domain->xprd,domain->yprd,domain->zprd, + domain->xy,domain->xz,domain->yz,pbc,h_rate,deform_vremap); + Kokkos::parallel_for(n,f); + } else { + struct AtomVecSphereKokkos_PackCommVel f( + atomKK->k_x,atomKK->k_mask, + atomKK->k_radius,atomKK->k_rmass, + atomKK->k_v,atomKK->k_omega, + buf,list,iswap, + domain->xprd,domain->yprd,domain->zprd, + domain->xy,domain->xz,domain->yz,pbc,h_rate,deform_vremap); + Kokkos::parallel_for(n,f); + } } } } - return n*11; + return n*(size_forward+size_velocity); } /* ---------------------------------------------------------------------- */ @@ -739,7 +873,7 @@ int AtomVecSphereKokkos::pack_comm_self( } } } - return n*3; + return n*size_forward; } /* ---------------------------------------------------------------------- */ @@ -808,7 +942,7 @@ void AtomVecSphereKokkos::unpack_comm_kokkos( /* ---------------------------------------------------------------------- */ -template +template struct AtomVecSphereKokkos_UnpackCommVel { typedef DeviceType device_type; @@ -833,7 +967,7 @@ struct AtomVecSphereKokkos_UnpackCommVel { _omega(omega.view()), _first(first) { - const size_t elements = 11; + const size_t elements = 9 + 2 * RADVARY; const int maxsend = (buf.template view().extent(0)*buf.template view().extent(1))/elements; buffer_view(_buf,buf,maxsend,elements); }; @@ -843,14 +977,16 @@ struct AtomVecSphereKokkos_UnpackCommVel { _x(i+_first,0) = _buf(i,0); _x(i+_first,1) = _buf(i,1); _x(i+_first,2) = _buf(i,2); - _radius(i+_first) = _buf(i,3); - _rmass(i+_first) = _buf(i,4); - _v(i+_first,0) = _buf(i,5); - _v(i+_first,1) = _buf(i,6); - _v(i+_first,2) = _buf(i,7); - _omega(i+_first,0) = _buf(i,8); - _omega(i+_first,1) = _buf(i,9); - _omega(i+_first,2) = _buf(i,10); + _v(i+_first,0) = _buf(i,3); + _v(i+_first,1) = _buf(i,4); + _v(i+_first,2) = _buf(i,5); + _omega(i+_first,0) = _buf(i,6); + _omega(i+_first,1) = _buf(i,7); + _omega(i+_first,2) = _buf(i,8); + if (RADVARY) { + _radius(i+_first) = _buf(i,9); + _rmass(i+_first) = _buf(i,10); + } } }; @@ -861,20 +997,38 @@ void AtomVecSphereKokkos::unpack_comm_vel_kokkos( const DAT::tdual_xfloat_2d &buf ) { if(commKK->forward_comm_on_host) { modified(Host,X_MASK|RADIUS_MASK|RMASS_MASK|V_MASK|OMEGA_MASK); - struct AtomVecSphereKokkos_UnpackCommVel f( - atomKK->k_x, - atomKK->k_radius,atomKK->k_rmass, - atomKK->k_v,atomKK->k_omega, - buf,first); - Kokkos::parallel_for(n,f); + if (radvary == 0) { + struct AtomVecSphereKokkos_UnpackCommVel f( + atomKK->k_x, + atomKK->k_radius,atomKK->k_rmass, + atomKK->k_v,atomKK->k_omega, + buf,first); + Kokkos::parallel_for(n,f); + } else { + struct AtomVecSphereKokkos_UnpackCommVel f( + atomKK->k_x, + atomKK->k_radius,atomKK->k_rmass, + atomKK->k_v,atomKK->k_omega, + buf,first); + Kokkos::parallel_for(n,f); + } } else { modified(Device,X_MASK|RADIUS_MASK|RMASS_MASK|V_MASK|OMEGA_MASK); - struct AtomVecSphereKokkos_UnpackCommVel f( - atomKK->k_x, - atomKK->k_radius,atomKK->k_rmass, - atomKK->k_v,atomKK->k_omega, - buf,first); - Kokkos::parallel_for(n,f); + if (radvary == 0) { + struct AtomVecSphereKokkos_UnpackCommVel f( + atomKK->k_x, + atomKK->k_radius,atomKK->k_rmass, + atomKK->k_v,atomKK->k_omega, + buf,first); + Kokkos::parallel_for(n,f); + } else { + struct AtomVecSphereKokkos_UnpackCommVel f( + atomKK->k_x, + atomKK->k_radius,atomKK->k_rmass, + atomKK->k_v,atomKK->k_omega, + buf,first); + Kokkos::parallel_for(n,f); + } } } @@ -1381,7 +1535,7 @@ int AtomVecSphereKokkos::pack_border_kokkos( Kokkos::parallel_for(n,f); } } - return n*8; + return n*size_border; } /* ---------------------------------------------------------------------- */ @@ -1609,7 +1763,7 @@ int AtomVecSphereKokkos::pack_border_vel_kokkos( } } - return n*14; + return n*(size_border + size_velocity); } /* ---------------------------------------------------------------------- */ diff --git a/src/KOKKOS/atom_vec_sphere_kokkos.h b/src/KOKKOS/atom_vec_sphere_kokkos.h index d9fc061ada..28c8a3c8f6 100644 --- a/src/KOKKOS/atom_vec_sphere_kokkos.h +++ b/src/KOKKOS/atom_vec_sphere_kokkos.h @@ -14,6 +14,8 @@ #ifdef ATOM_CLASS AtomStyle(sphere/kk,AtomVecSphereKokkos) +AtomStyle(sphere/kk/device,AtomVecSphereKokkos) +AtomStyle(sphere/kk/host,AtomVecSphereKokkos) #else From 1e9778b81e2e3f58bcd06414a8097b9e33af028f Mon Sep 17 00:00:00 2001 From: mkanski Date: Fri, 5 Oct 2018 20:34:12 +0200 Subject: [PATCH 241/302] Extend compute pair to handle multiple instances of a given pair style --- doc/src/compute_pair.txt | 33 +++++++++++++++++++++++---------- src/compute_pair.cpp | 32 +++++++++++++++++++++++--------- src/compute_pair.h | 2 +- 3 files changed, 47 insertions(+), 20 deletions(-) diff --git a/doc/src/compute_pair.txt b/doc/src/compute_pair.txt index b309019e30..751ea2c340 100644 --- a/doc/src/compute_pair.txt +++ b/doc/src/compute_pair.txt @@ -10,17 +10,22 @@ compute pair command :h3 [Syntax:] -compute ID group-ID pair pstyle evalue :pre +compute ID group-ID pair pstyle keyword value :pre -ID, group-ID are documented in "compute"_compute.html command -pair = style name of this compute command -pstyle = style name of a pair style that calculates additional values -evalue = {epair} or {evdwl} or {ecoul} or blank (optional setting) :ul +ID, group-ID are documented in "compute"_compute.html command :ulb,l +pair = style name of this compute command :l +pstyle = style name of a pair style that calculates additional values :l +zero or more keyword/value pairs may be appended :l +keyword = {evalue} or {nsub} + {evalue} arg = {epair} or {evdwl} or {ecoul} + {nsub} n = use {n}-th instance of a sub-style in a pair_style hybrid or hybrid/overlay command :pre +:ule [Examples:] compute 1 all pair gauss -compute 1 all pair lj/cut/coul/cut ecoul +compute 1 all pair lj/cut/coul/cut evalue ecoul +compute 1 all pair tersoff nsub 2 compute 1 all pair reax :pre [Description:] @@ -33,15 +38,23 @@ NOTE: The group specified for this command is [ignored]. The specified {pstyle} must be a pair style used in your simulation either by itself or as a sub-style in a "pair_style hybrid or -hybrid/overlay"_pair_hybrid.html command. +hybrid/overlay"_pair_hybrid.html command. If the sub-style is +used more than once, additional keyword {nsub} has to be specified in +order to choose a single instance. -The {evalue} setting is optional; it may be left off the command. All +NOTE: The {nsub} keyword should be used only if the sub-style occurs +multiple times. Its value must be an integer from 1 to M, where M is +the number of times the sub-style is listed in the "pair_style hybrid +or hybrid/overlay"_pair_hybrid.html" command. If the pair style is +used once, {nsub} must remain zero. + +The {evalue} setting is optional. All pair styles tally a potential energy {epair} which may be broken into two parts: {evdwl} and {ecoul} such that {epair} = {evdwl} + {ecoul}. If the pair style calculates Coulombic interactions, their energy will be tallied in {ecoul}. Everything else (whether it is a Lennard-Jones style van der Waals interaction or not) is tallied in {evdwl}. If -{evalue} is specified as {epair} or left out, then {epair} is stored +{evalue} is specified as {epair}, then {epair} is stored as a global scalar by this compute. This is useful when using "pair_style hybrid"_pair_hybrid.html if you want to know the portion of the total energy contributed by one sub-style. If {evalue} is @@ -82,4 +95,4 @@ the doc page for the pair style for details. [Default:] -The default for {evalue} is {epair}. +The keyword defaults are {evalue} = {epair}, nsub = 0. diff --git a/src/compute_pair.cpp b/src/compute_pair.cpp index 444395bae5..6129f192e2 100644 --- a/src/compute_pair.cpp +++ b/src/compute_pair.cpp @@ -29,7 +29,7 @@ ComputePair::ComputePair(LAMMPS *lmp, int narg, char **arg) : Compute(lmp, narg, arg), pstyle(NULL), pair(NULL), one(NULL) { - if (narg < 4 || narg > 5) error->all(FLERR,"Illegal compute pair command"); + if (narg < 4) error->all(FLERR,"Illegal compute pair command"); scalar_flag = 1; extscalar = 1; @@ -41,19 +41,33 @@ ComputePair::ComputePair(LAMMPS *lmp, int narg, char **arg) : pstyle = new char[n]; strcpy(pstyle,arg[3]); - if (narg == 5) { - if (strcmp(arg[4],"epair") == 0) evalue = EPAIR; - if (strcmp(arg[4],"evdwl") == 0) evalue = EVDWL; - if (strcmp(arg[4],"ecoul") == 0) evalue = ECOUL; - } else evalue = EPAIR; + int iarg = 4; + nsub = 0; + + while (iarg < narg) { + if (strcmp(arg[iarg],"evalue") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal compute pair command"); + if (strcmp(arg[iarg+1],"epair") == 0) evalue = EPAIR; + else if (strcmp(arg[iarg+1],"evdwl") == 0) evalue = EVDWL; + else if (strcmp(arg[iarg+1],"ecoul") == 0) evalue = ECOUL; + else error->all(FLERR, "Unrecognized energy type"); + iarg += 2; + } else if (strcmp(arg[iarg],"nsub") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal compute pair command"); + nsub = force->inumeric(FLERR,arg[iarg+1]); + iarg += 2; + } else error->all(FLERR,"Illegal compute pair command"); + + } + // check if pair style with and without suffix exists - pair = force->pair_match(pstyle,1); + pair = force->pair_match(pstyle,1,nsub); if (!pair && lmp->suffix) { strcat(pstyle,"/"); strcat(pstyle,lmp->suffix); - pair = force->pair_match(pstyle,1); + pair = force->pair_match(pstyle,1,nsub); } if (!pair) @@ -84,7 +98,7 @@ void ComputePair::init() { // recheck for pair style in case it has been deleted - pair = force->pair_match(pstyle,1); + pair = force->pair_match(pstyle,1,nsub); if (!pair) error->all(FLERR,"Unrecognized pair style in compute pair command"); } diff --git a/src/compute_pair.h b/src/compute_pair.h index 9f2678aaab..57d52a5bab 100644 --- a/src/compute_pair.h +++ b/src/compute_pair.h @@ -33,7 +33,7 @@ class ComputePair : public Compute { void compute_vector(); private: - int evalue,npair; + int evalue,npair,nsub; char *pstyle; class Pair *pair; double *one; From 8960774b166119fbdf58d54b65cbca142e9e0c29 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 5 Oct 2018 14:55:18 -0400 Subject: [PATCH 242/302] correct typo in USER-SMD introduced by doc-adjust PR --- src/USER-SMD/compute_smd_triangle_vertices.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/USER-SMD/compute_smd_triangle_vertices.cpp b/src/USER-SMD/compute_smd_triangle_vertices.cpp index 67ec27778a..b24223b8b5 100644 --- a/src/USER-SMD/compute_smd_triangle_vertices.cpp +++ b/src/USER-SMD/compute_smd_triangle_vertices.cpp @@ -28,7 +28,7 @@ #include #include #include -#include "compute_smd_triangle_mesh_vertices.h" +#include "compute_smd_triangle_vertices.h" #include "atom.h" #include "update.h" #include "modify.h" From 8b944e06f015a391c2d9b773768488d950edfe5e Mon Sep 17 00:00:00 2001 From: mkanski Date: Fri, 5 Oct 2018 21:08:18 +0200 Subject: [PATCH 243/302] Small changes in doc file --- doc/src/compute_pair.txt | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/doc/src/compute_pair.txt b/doc/src/compute_pair.txt index 751ea2c340..1a3ec06508 100644 --- a/doc/src/compute_pair.txt +++ b/doc/src/compute_pair.txt @@ -18,7 +18,7 @@ pstyle = style name of a pair style that calculates additional values :l zero or more keyword/value pairs may be appended :l keyword = {evalue} or {nsub} {evalue} arg = {epair} or {evdwl} or {ecoul} - {nsub} n = use {n}-th instance of a sub-style in a pair_style hybrid or hybrid/overlay command :pre + {nsub} n = use the {n}-th instance of a sub-style in a pair_style hybrid or hybrid/overlay command :pre :ule [Examples:] @@ -39,14 +39,15 @@ NOTE: The group specified for this command is [ignored]. The specified {pstyle} must be a pair style used in your simulation either by itself or as a sub-style in a "pair_style hybrid or hybrid/overlay"_pair_hybrid.html command. If the sub-style is -used more than once, additional keyword {nsub} has to be specified in -order to choose a single instance. +used more than once, an additional keyword {nsub} has to be +specified in order to choose which instance of the sub-style will +be used by the compute. NOTE: The {nsub} keyword should be used only if the sub-style occurs multiple times. Its value must be an integer from 1 to M, where M is the number of times the sub-style is listed in the "pair_style hybrid or hybrid/overlay"_pair_hybrid.html" command. If the pair style is -used once, {nsub} must remain zero. +used only once, {nsub} must remain zero. The {evalue} setting is optional. All pair styles tally a potential energy {epair} which may be broken into From 3c41295e7077b592351676c19e0ff45779553f91 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 8 Oct 2018 17:23:22 +0200 Subject: [PATCH 244/302] change implementation to be consistent with pair_coeff and remain backward compatible --- doc/src/compute_pair.txt | 27 ++++++++++----------------- src/compute_pair.cpp | 32 +++++++++++++++++--------------- 2 files changed, 27 insertions(+), 32 deletions(-) diff --git a/doc/src/compute_pair.txt b/doc/src/compute_pair.txt index 1a3ec06508..b36d61f71c 100644 --- a/doc/src/compute_pair.txt +++ b/doc/src/compute_pair.txt @@ -10,22 +10,20 @@ compute pair command :h3 [Syntax:] -compute ID group-ID pair pstyle keyword value :pre +compute ID group-ID pair pstyle \[nstyle\] \[evalue\] :pre ID, group-ID are documented in "compute"_compute.html command :ulb,l pair = style name of this compute command :l pstyle = style name of a pair style that calculates additional values :l -zero or more keyword/value pairs may be appended :l -keyword = {evalue} or {nsub} - {evalue} arg = {epair} or {evdwl} or {ecoul} - {nsub} n = use the {n}-th instance of a sub-style in a pair_style hybrid or hybrid/overlay command :pre +nsub = {n}-instance of a substyle, if a pair style is used multiple times in a hybrid style :l +{evalue} = {epair} or {evdwl} or {ecoul} or blank (optional) :l :ule [Examples:] compute 1 all pair gauss -compute 1 all pair lj/cut/coul/cut evalue ecoul -compute 1 all pair tersoff nsub 2 +compute 1 all pair lj/cut/coul/cut ecoul +compute 1 all pair tersoff 2 epair compute 1 all pair reax :pre [Description:] @@ -39,15 +37,10 @@ NOTE: The group specified for this command is [ignored]. The specified {pstyle} must be a pair style used in your simulation either by itself or as a sub-style in a "pair_style hybrid or hybrid/overlay"_pair_hybrid.html command. If the sub-style is -used more than once, an additional keyword {nsub} has to be -specified in order to choose which instance of the sub-style will -be used by the compute. - -NOTE: The {nsub} keyword should be used only if the sub-style occurs -multiple times. Its value must be an integer from 1 to M, where M is -the number of times the sub-style is listed in the "pair_style hybrid -or hybrid/overlay"_pair_hybrid.html" command. If the pair style is -used only once, {nsub} must remain zero. +used more than once, an additional number {nsub} has to be specified +in order to choose which instance of the sub-style will be used by +the compute. Not specifying the number in this case will cause the +compute to fail. The {evalue} setting is optional. All pair styles tally a potential energy {epair} which may be broken into @@ -55,7 +48,7 @@ two parts: {evdwl} and {ecoul} such that {epair} = {evdwl} + {ecoul}. If the pair style calculates Coulombic interactions, their energy will be tallied in {ecoul}. Everything else (whether it is a Lennard-Jones style van der Waals interaction or not) is tallied in {evdwl}. If -{evalue} is specified as {epair}, then {epair} is stored +{evalue} is blank or specified as {epair}, then {epair} is stored as a global scalar by this compute. This is useful when using "pair_style hybrid"_pair_hybrid.html if you want to know the portion of the total energy contributed by one sub-style. If {evalue} is diff --git a/src/compute_pair.cpp b/src/compute_pair.cpp index 6129f192e2..9690f140c5 100644 --- a/src/compute_pair.cpp +++ b/src/compute_pair.cpp @@ -13,6 +13,7 @@ #include #include +#include #include "compute_pair.h" #include "update.h" #include "force.h" @@ -43,23 +44,24 @@ ComputePair::ComputePair(LAMMPS *lmp, int narg, char **arg) : int iarg = 4; nsub = 0; + evalue = NPAIR; - while (iarg < narg) { - if (strcmp(arg[iarg],"evalue") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal compute pair command"); - if (strcmp(arg[iarg+1],"epair") == 0) evalue = EPAIR; - else if (strcmp(arg[iarg+1],"evdwl") == 0) evalue = EVDWL; - else if (strcmp(arg[iarg+1],"ecoul") == 0) evalue = ECOUL; - else error->all(FLERR, "Unrecognized energy type"); - iarg += 2; - } else if (strcmp(arg[iarg],"nsub") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal compute pair command"); - nsub = force->inumeric(FLERR,arg[iarg+1]); - iarg += 2; - } else error->all(FLERR,"Illegal compute pair command"); - + if (narg > iarg) { + if (isdigit(arg[iarg][0])) { + nsub = force->inumeric(FLERR,arg[iarg]); + ++iarg; + if (nsub <= 0) + error->all(FLERR,"Illegal compute pair command"); + } + } + + if (narg > iarg) { + if (strcmp(arg[iarg],"epair") == 0) evalue = EPAIR; + else if (strcmp(arg[iarg],"evdwl") == 0) evalue = EVDWL; + else if (strcmp(arg[iarg],"ecoul") == 0) evalue = ECOUL; + else error->all(FLERR, "Illegal compute pair command"); + ++iarg; } - // check if pair style with and without suffix exists From dc6123fafcb63d1dab91b7e831d91d7cd5fa8464 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 8 Oct 2018 17:26:21 +0200 Subject: [PATCH 245/302] fix stupid typo --- src/compute_pair.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/compute_pair.cpp b/src/compute_pair.cpp index 9690f140c5..df4f3a1ddb 100644 --- a/src/compute_pair.cpp +++ b/src/compute_pair.cpp @@ -44,7 +44,7 @@ ComputePair::ComputePair(LAMMPS *lmp, int narg, char **arg) : int iarg = 4; nsub = 0; - evalue = NPAIR; + evalue = EPAIR; if (narg > iarg) { if (isdigit(arg[iarg][0])) { From 70bee266418851e036fb47c952d2d855218cc006 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 9 Oct 2018 12:59:12 -0400 Subject: [PATCH 246/302] update version number --- doc/src/Manual.txt | 4 ++-- src/version.h | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/doc/src/Manual.txt b/doc/src/Manual.txt index ecee17269a..dab2ea385e 100644 --- a/doc/src/Manual.txt +++ b/doc/src/Manual.txt @@ -1,7 +1,7 @@ LAMMPS Users Manual - + @@ -21,7 +21,7 @@ :line LAMMPS Documentation :c,h1 -18 Sep 2018 version :c,h2 +10 Oct 2018 version :c,h2 "What is a LAMMPS version?"_Manual_version.html diff --git a/src/version.h b/src/version.h index 469d74fed7..d9d93cac0e 100644 --- a/src/version.h +++ b/src/version.h @@ -1 +1 @@ -#define LAMMPS_VERSION "18 Sep 2018" +#define LAMMPS_VERSION "10 Oct 2018" From 2def00d4c9007ecb3ac86b59a5e2b5dc38882ca2 Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Wed, 10 Oct 2018 14:18:00 -0600 Subject: [PATCH 247/302] Add missing files to .gitignore --- src/.gitignore | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/src/.gitignore b/src/.gitignore index 5699a87089..4f517af3af 100644 --- a/src/.gitignore +++ b/src/.gitignore @@ -269,6 +269,8 @@ /compute_dpd.h /compute_dpd_atom.cpp /compute_dpd_atom.h +/compute_entropy_atom.cpp +/compute_entropy_atom.h /compute_erotate_asphere.cpp /compute_erotate_asphere.h /compute_erotate_rigid.cpp @@ -311,8 +313,8 @@ /compute_spec_atom.h /compute_stress_mop.cpp /compute_stress_mop.h -/compute_stress_mop.profile.cpp -/compute_stress_mop.profile.h +/compute_stress_mop_profile.cpp +/compute_stress_mop_profile.h /compute_stress_tally.cpp /compute_stress_tally.h /compute_temp_asphere.cpp @@ -746,6 +748,8 @@ /pair_eam_cd.h /pair_eam_fs.cpp /pair_eam_fs.h +/pair_lj_expand_coul_long.cpp +/pair_lj_expand_coul_long.h /pair_edip.cpp /pair_edip.h /pair_edip_multi.cpp From 7cce002cf992a5f430239772da5af587a48d1b59 Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Wed, 10 Oct 2018 14:18:24 -0600 Subject: [PATCH 248/302] Makefile fix from the mailing list --- src/Makefile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/Makefile b/src/Makefile index eefc64b274..7d31c81c75 100644 --- a/src/Makefile +++ b/src/Makefile @@ -74,7 +74,7 @@ PACKSYS = compress mpiio python user-lb PACKINT = gpu kokkos meam message poems reax user-atc user-awpmd user-colvars -PACKEXT = kim mscg voronoi \ +PACKEXT = kim latte mscg voronoi \ user-h5md user-molfile user-netcdf user-qmmm user-quip \ user-smd user-vtk From a1266a1a1ec95a3a6eb5a440edc8e27d97f48f48 Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Wed, 10 Oct 2018 14:19:23 -0600 Subject: [PATCH 249/302] Fix compile error with copysign function --- src/USER-MISC/compute_stress_mop.cpp | 6 +++--- src/USER-MISC/compute_stress_mop_profile.cpp | 2 +- src/USER-SMD/smd_math.h | 2 +- 3 files changed, 5 insertions(+), 5 deletions(-) diff --git a/src/USER-MISC/compute_stress_mop.cpp b/src/USER-MISC/compute_stress_mop.cpp index f764e0ee7e..e63dff507f 100644 --- a/src/USER-MISC/compute_stress_mop.cpp +++ b/src/USER-MISC/compute_stress_mop.cpp @@ -397,13 +397,13 @@ void ComputeStressMop::compute_pairs() // at each timestep, must check atoms going through the // image of the plane that is closest to the box - double pos_temp = pos+copysign(1,domain->prd_half[dir]-pos)*domain->prd[dir]; + double pos_temp = pos+copysign(1.0,domain->prd_half[dir]-pos)*domain->prd[dir]; if (fabs(xi[dir]-pos) limit) { // limit delVdotDelR to a fraction of speed of sound - x = limit * copysign(1, x); + x = limit * copysign(1.0, x); } } From c142288eb3b4c99c52feed7e1b123289fc2defa4 Mon Sep 17 00:00:00 2001 From: Aidan Thompson Date: Wed, 10 Oct 2018 17:24:14 -0600 Subject: [PATCH 250/302] Fixed a segfault introduced by memory-leak fix --- src/SNAP/compute_snad_atom.cpp | 3 ++- src/SNAP/compute_snav_atom.cpp | 3 ++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/src/SNAP/compute_snad_atom.cpp b/src/SNAP/compute_snad_atom.cpp index da56555055..b0395d5317 100644 --- a/src/SNAP/compute_snad_atom.cpp +++ b/src/SNAP/compute_snad_atom.cpp @@ -113,7 +113,8 @@ ComputeSNADAtom::ComputeSNADAtom(LAMMPS *lmp, int narg, char **arg) : } else error->all(FLERR,"Illegal compute snad/atom command"); } - snaptr = new SNA*[comm->nthreads]; + nthreads = comm->nthreads; + snaptr = new SNA*[nthreads]; #if defined(_OPENMP) #pragma omp parallel default(none) shared(lmp,rfac0,twojmax,rmin0,switchflag,bzeroflag) #endif diff --git a/src/SNAP/compute_snav_atom.cpp b/src/SNAP/compute_snav_atom.cpp index 27bfc1bef0..b2d555f713 100644 --- a/src/SNAP/compute_snav_atom.cpp +++ b/src/SNAP/compute_snav_atom.cpp @@ -109,7 +109,8 @@ ComputeSNAVAtom::ComputeSNAVAtom(LAMMPS *lmp, int narg, char **arg) : } else error->all(FLERR,"Illegal compute snav/atom command"); } - snaptr = new SNA*[comm->nthreads]; + nthreads = comm->nthreads; + snaptr = new SNA*[nthreads]; #if defined(_OPENMP) #pragma omp parallel default(none) shared(lmp,rfac0,twojmax,rmin0,switchflag,bzeroflag) #endif From c37deebffab781c1b727b80f3299d59c9c4c323f Mon Sep 17 00:00:00 2001 From: Michael Brown Date: Thu, 11 Oct 2018 05:12:00 -0700 Subject: [PATCH 251/302] Adding full hybrid support to USER-INTEL package and fixing bug with EAM parameter initialization. --- doc/src/Speed_intel.txt | 2 +- src/USER-INTEL/angle_harmonic_intel.cpp | 2 +- src/USER-INTEL/bond_fene_intel.cpp | 2 +- src/USER-INTEL/dihedral_opls_intel.cpp | 2 +- src/USER-INTEL/fix_intel.cpp | 107 ++++++-- src/USER-INTEL/fix_intel.h | 63 +++-- src/USER-INTEL/improper_cvff_intel.cpp | 2 +- src/USER-INTEL/intel_buffers.cpp | 130 +++++++--- src/USER-INTEL/intel_buffers.h | 58 +++-- src/USER-INTEL/intel_preprocess.h | 5 +- src/USER-INTEL/intel_simd.h | 6 + src/USER-INTEL/nbin_intel.cpp | 1 - src/USER-INTEL/npair_full_bin_ghost_intel.cpp | 24 +- src/USER-INTEL/npair_full_bin_intel.cpp | 3 +- .../npair_half_bin_newton_intel.cpp | 2 +- .../npair_half_bin_newton_tri_intel.cpp | 2 +- src/USER-INTEL/npair_halffull_newtoff_intel.h | 47 ++++ .../npair_halffull_newton_intel.cpp | 233 ++++++++++++++++++ src/USER-INTEL/npair_halffull_newton_intel.h | 72 ++++++ src/USER-INTEL/npair_intel.cpp | 100 ++++++-- src/USER-INTEL/npair_intel.h | 6 +- src/USER-INTEL/npair_skip_intel.cpp | 230 +++++++++++++++++ src/USER-INTEL/npair_skip_intel.h | 69 ++++++ src/USER-INTEL/pair_airebo_intel.cpp | 74 +++--- src/USER-INTEL/pair_airebo_intel.h | 6 + src/USER-INTEL/pair_buck_coul_cut_intel.cpp | 42 ++-- src/USER-INTEL/pair_buck_coul_long_intel.cpp | 42 ++-- src/USER-INTEL/pair_buck_intel.cpp | 41 ++- src/USER-INTEL/pair_dpd_intel.cpp | 55 ++--- src/USER-INTEL/pair_eam_intel.cpp | 57 ++--- src/USER-INTEL/pair_gayberne_intel.cpp | 41 ++- .../pair_lj_charmm_coul_charmm_intel.cpp | 41 ++- .../pair_lj_charmm_coul_long_intel.cpp | 71 +++--- .../pair_lj_charmm_coul_long_intel.h | 2 +- .../pair_lj_cut_coul_long_intel.cpp | 41 ++- src/USER-INTEL/pair_lj_cut_intel.cpp | 50 ++-- src/USER-INTEL/pair_sw_intel.cpp | 190 +++++++------- src/USER-INTEL/pair_sw_intel.h | 6 +- src/USER-INTEL/pair_tersoff_intel.cpp | 61 +++-- src/USER-INTEL/pppm_intel.cpp | 12 + src/memory.cpp | 4 +- src/pair.h | 4 + 42 files changed, 1442 insertions(+), 566 deletions(-) create mode 100644 src/USER-INTEL/npair_halffull_newtoff_intel.h create mode 100644 src/USER-INTEL/npair_halffull_newton_intel.cpp create mode 100644 src/USER-INTEL/npair_halffull_newton_intel.h create mode 100644 src/USER-INTEL/npair_skip_intel.cpp create mode 100644 src/USER-INTEL/npair_skip_intel.h diff --git a/doc/src/Speed_intel.txt b/doc/src/Speed_intel.txt index bf078fb576..d35a311f46 100644 --- a/doc/src/Speed_intel.txt +++ b/doc/src/Speed_intel.txt @@ -499,7 +499,7 @@ MPI task. When offloading to a coprocessor, "hybrid"_pair_hybrid.html styles that require skip lists for neighbor builds cannot be offloaded. Using "hybrid/overlay"_pair_hybrid.html is allowed. Only one intel -accelerated style may be used with hybrid styles. +accelerated style may be used with hybrid styles when offloading. "Special_bonds"_special_bonds.html exclusion lists are not currently supported with offload, however, the same effect can often be accomplished by setting cutoffs for excluded atom types to 0. None of diff --git a/src/USER-INTEL/angle_harmonic_intel.cpp b/src/USER-INTEL/angle_harmonic_intel.cpp index 5777dad947..6d8901a5ee 100644 --- a/src/USER-INTEL/angle_harmonic_intel.cpp +++ b/src/USER-INTEL/angle_harmonic_intel.cpp @@ -314,7 +314,7 @@ void AngleHarmonicIntel::init_style() template void AngleHarmonicIntel::pack_force_const(ForceConst &fc, - IntelBuffers * /*buffers*/) + IntelBuffers * /*buffers*/) { const int bp1 = atom->nangletypes + 1; fc.set_ntypes(bp1,memory); diff --git a/src/USER-INTEL/bond_fene_intel.cpp b/src/USER-INTEL/bond_fene_intel.cpp index 9d54269c05..bff3722a44 100644 --- a/src/USER-INTEL/bond_fene_intel.cpp +++ b/src/USER-INTEL/bond_fene_intel.cpp @@ -291,7 +291,7 @@ void BondFENEIntel::init_style() template void BondFENEIntel::pack_force_const(ForceConst &fc, - IntelBuffers * /*buffers*/) + IntelBuffers * /*buffers*/) { const int bp1 = atom->nbondtypes + 1; fc.set_ntypes(bp1,memory); diff --git a/src/USER-INTEL/dihedral_opls_intel.cpp b/src/USER-INTEL/dihedral_opls_intel.cpp index ef95cc75bb..7a60b62cae 100644 --- a/src/USER-INTEL/dihedral_opls_intel.cpp +++ b/src/USER-INTEL/dihedral_opls_intel.cpp @@ -416,7 +416,7 @@ void DihedralOPLSIntel::init_style() template void DihedralOPLSIntel::pack_force_const(ForceConst &fc, - IntelBuffers * /*buffers*/) + IntelBuffers * /*buffers*/) { const int bp1 = atom->ndihedraltypes + 1; fc.set_ntypes(bp1,memory); diff --git a/src/USER-INTEL/fix_intel.cpp b/src/USER-INTEL/fix_intel.cpp index 37212928df..e0865f0431 100644 --- a/src/USER-INTEL/fix_intel.cpp +++ b/src/USER-INTEL/fix_intel.cpp @@ -65,6 +65,7 @@ FixIntel::FixIntel(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg) _nbor_pack_width = 1; _three_body_neighbor = 0; + _hybrid_nonpair = 0; _precision_mode = PREC_MODE_MIXED; _offload_balance = -1.0; @@ -266,8 +267,7 @@ FixIntel::~FixIntel() double *time1 = off_watch_pair(); double *time2 = off_watch_neighbor(); int *overflow = get_off_overflow_flag(); - if (_offload_balance != 0.0 && time1 != NULL && time2 != NULL && - overflow != NULL) { + if (_offload_balance != 0.0) { #pragma offload_transfer target(mic:_cop) \ nocopy(time1,time2,overflow:alloc_if(0) free_if(1)) } @@ -314,34 +314,63 @@ void FixIntel::init() int nstyles = 0; if (force->pair_match("hybrid", 1) != NULL) { + _pair_hybrid_flag = 1; PairHybrid *hybrid = (PairHybrid *) force->pair; for (int i = 0; i < hybrid->nstyles; i++) if (strstr(hybrid->keywords[i], "/intel") != NULL) nstyles++; + if (force->newton_pair != 0 && force->pair->no_virial_fdotr_compute) + error->all(FLERR, + "Intel package requires fdotr virial with newton on."); } else if (force->pair_match("hybrid/overlay", 1) != NULL) { + _pair_hybrid_flag = 1; PairHybridOverlay *hybrid = (PairHybridOverlay *) force->pair; for (int i = 0; i < hybrid->nstyles; i++) if (strstr(hybrid->keywords[i], "/intel") != NULL) nstyles++; - else - force->pair->no_virial_fdotr_compute = 1; + if (force->newton_pair != 0 && force->pair->no_virial_fdotr_compute) + error->all(FLERR, + "Intel package requires fdotr virial with newton on."); + } else + _pair_hybrid_flag = 0; + + if (nstyles > 1 && _pair_hybrid_flag) _pair_hybrid_flag = 2; + else if (force->newton_pair == 0) _pair_hybrid_flag = 0; + + _pair_hybrid_zero = 0; + _zero_master = 0; + + if (_pair_hybrid_flag && _hybrid_nonpair) + if (_pair_hybrid_flag > 1 || force->newton_pair == 0) + _pair_hybrid_zero = 1; + _hybrid_nonpair = 0; + + #ifdef _LMP_INTEL_OFFLOAD + if (offload_balance() != 0.0) { + _pair_hybrid_zero = 0; + if (force->newton_pair == 0) _pair_hybrid_flag = 0; + if (nstyles > 1) + error->all(FLERR, + "Currently, cannot offload more than one intel style with hybrid."); } - if (nstyles > 1) - error->all(FLERR, - "Currently, cannot use more than one intel style with hybrid."); + #endif check_neighbor_intel(); + int off_mode = 0; if (_offload_balance != 0.0) off_mode = 1; if (_precision_mode == PREC_MODE_SINGLE) { _single_buffers->zero_ev(); _single_buffers->grow_ncache(off_mode,_nthreads); + _single_buffers->free_list_ptrs(); } else if (_precision_mode == PREC_MODE_MIXED) { _mixed_buffers->zero_ev(); _mixed_buffers->grow_ncache(off_mode,_nthreads); + _mixed_buffers->free_list_ptrs(); } else { _double_buffers->zero_ev(); _double_buffers->grow_ncache(off_mode,_nthreads); + _double_buffers->free_list_ptrs(); } _need_reduce = 0; @@ -349,7 +378,7 @@ void FixIntel::init() /* ---------------------------------------------------------------------- */ -void FixIntel::setup(int /*vflag*/) +void FixIntel::setup(int vflag) { if (neighbor->style != Neighbor::BIN) error->all(FLERR, @@ -395,8 +424,7 @@ void FixIntel::pair_init_check(const bool cdmessage) double *time1 = off_watch_pair(); double *time2 = off_watch_neighbor(); int *overflow = get_off_overflow_flag(); - if (_offload_balance !=0.0 && time1 != NULL && time2 != NULL && - overflow != NULL) { + if (_offload_balance !=0.0) { #pragma offload_transfer target(mic:_cop) \ nocopy(time1,time2:length(1) alloc_if(1) free_if(0)) \ in(overflow:length(5) alloc_if(1) free_if(0)) @@ -419,6 +447,21 @@ void FixIntel::pair_init_check(const bool cdmessage) #endif } + #ifndef LMP_INTEL_NBOR_COMPAT + if (force->pair->manybody_flag && atom->molecular) { + int flag = 0; + if (atom->nbonds > 0 && force->special_lj[1] == 0.0 && + force->special_coul[1] == 0.0) flag = 1; + if (atom->nangles > 0 && force->special_lj[2] == 0.0 && + force->special_coul[2] == 0.0) flag = 1; + if (atom->ndihedrals > 0 && force->special_lj[3] == 0.0 && + force->special_coul[3] == 0.0) flag = 1; + if (flag) + error->all(FLERR,"Add -DLMP_INTEL_NBOR_COMPAT to build for special_bond" + "exclusions with Intel"); + } + #endif + int need_tag = 0; if (atom->molecular) need_tag = 1; @@ -477,11 +520,13 @@ void FixIntel::bond_init_check() if (force->pair_match("/intel", 0) != NULL) intel_pair = 1; else if (force->pair_match("hybrid", 1) != NULL) { + _hybrid_nonpair = 1; PairHybrid *hybrid = (PairHybrid *) force->pair; for (int i = 0; i < hybrid->nstyles; i++) if (strstr(hybrid->keywords[i], "/intel") != NULL) intel_pair = 1; } else if (force->pair_match("hybrid/overlay", 1) != NULL) { + _hybrid_nonpair = 1; PairHybridOverlay *hybrid = (PairHybridOverlay *) force->pair; for (int i = 0; i < hybrid->nstyles; i++) if (strstr(hybrid->keywords[i], "/intel") != NULL) @@ -501,11 +546,13 @@ void FixIntel::kspace_init_check() if (force->pair_match("/intel", 0) != NULL) intel_pair = 1; else if (force->pair_match("hybrid", 1) != NULL) { + _hybrid_nonpair = 1; PairHybrid *hybrid = (PairHybrid *) force->pair; for (int i = 0; i < hybrid->nstyles; i++) if (strstr(hybrid->keywords[i], "/intel") != NULL) intel_pair = 1; } else if (force->pair_match("hybrid/overlay", 1) != NULL) { + _hybrid_nonpair = 1; PairHybridOverlay *hybrid = (PairHybridOverlay *) force->pair; for (int i = 0; i < hybrid->nstyles; i++) if (strstr(hybrid->keywords[i], "/intel") != NULL) @@ -522,51 +569,60 @@ void FixIntel::check_neighbor_intel() { #ifdef _LMP_INTEL_OFFLOAD _full_host_list = 0; - #endif - const int nrequest = neighbor->nrequest; + const int nrequest = neighbor->nrequest; for (int i = 0; i < nrequest; ++i) { - #ifdef _LMP_INTEL_OFFLOAD if (_offload_balance != 0.0 && neighbor->requests[i]->intel == 0) { _full_host_list = 1; _offload_noghost = 0; } - #endif + if (neighbor->requests[i]->skip && _offload_balance != 0.0) + error->all(FLERR, "Cannot yet use hybrid styles with Intel offload."); // avoid flagging a neighbor list as both USER-INTEL and USER-OMP if (neighbor->requests[i]->intel) neighbor->requests[i]->omp = 0; - - if (neighbor->requests[i]->skip) - error->all(FLERR, "Hybrid styles with Intel package are unsupported."); } + #else + // avoid flagging a neighbor list as both USER-INTEL and USER-OMP + const int nrequest = neighbor->nrequest; + for (int i = 0; i < nrequest; ++i) + if (neighbor->requests[i]->intel) + neighbor->requests[i]->omp = 0; + #endif } /* ---------------------------------------------------------------------- */ -void FixIntel::pre_reverse(int /*eflag*/, int /*vflag*/) +void FixIntel::_sync_main_arrays(const int prereverse) { + if (!prereverse) _zero_master = 1; + int done_this_step = prereverse; + if (_pair_hybrid_zero == 0) done_this_step = 1; if (_force_array_m != 0) { if (_need_reduce) { reduce_results(&_force_array_m[0].x); _need_reduce = 0; } add_results(_force_array_m, _ev_array_d, _results_eatom, _results_vatom,0); - _force_array_m = 0; + if (done_this_step) _force_array_m = 0; + else _ev_array_d = 0; } else if (_force_array_d != 0) { if (_need_reduce) { reduce_results(&_force_array_d[0].x); _need_reduce = 0; } add_results(_force_array_d, _ev_array_d, _results_eatom, _results_vatom,0); - _force_array_d = 0; + if (done_this_step) _force_array_d = 0; + else _ev_array_d = 0; } else if (_force_array_s != 0) { if (_need_reduce) { reduce_results(&_force_array_s[0].x); _need_reduce = 0; } add_results(_force_array_s, _ev_array_s, _results_eatom, _results_vatom,0); - _force_array_s = 0; + if (done_this_step) _force_array_s = 0; + else _ev_array_s = 0; } #ifdef _LMP_INTEL_OFFLOAD @@ -576,6 +632,13 @@ void FixIntel::pre_reverse(int /*eflag*/, int /*vflag*/) /* ---------------------------------------------------------------------- */ +void FixIntel::pre_reverse(int /*eflag*/, int /*vflag*/) +{ + _sync_main_arrays(1); +} + +/* ---------------------------------------------------------------------- */ + template void FixIntel::reduce_results(acc_t * _noalias const f_scalar) { @@ -657,7 +720,7 @@ template void FixIntel::add_results(const ft * _noalias const f_in, const acc_t * _noalias const ev_global, const int eatom, const int vatom, - const int /*offload*/) { + const int offload) { start_watch(TIME_PACK); int f_length; #ifdef _LMP_INTEL_OFFLOAD diff --git a/src/USER-INTEL/fix_intel.h b/src/USER-INTEL/fix_intel.h index e6e09be503..81dd0b5d97 100644 --- a/src/USER-INTEL/fix_intel.h +++ b/src/USER-INTEL/fix_intel.h @@ -74,11 +74,12 @@ class FixIntel : public Fix { inline int nbor_pack_width() const { return _nbor_pack_width; } inline void nbor_pack_width(const int w) { _nbor_pack_width = w; } inline int three_body_neighbor() { return _three_body_neighbor; } - inline void three_body_neighbor(const int /*i*/) { _three_body_neighbor = 1; } + inline void three_body_neighbor(const int i) { _three_body_neighbor = i; } inline int need_zero(const int tid) { if (_need_reduce == 0 && tid > 0) return 1; - return 0; + else if (_zero_master && tid == 0) { _zero_master = 0; return 1; } + else return 0; } inline void set_reduce_flag() { if (_nthreads > 1) _need_reduce = 1; } inline int lrt() { @@ -100,7 +101,10 @@ class FixIntel : public Fix { IntelBuffers *_double_buffers; int _precision_mode, _nthreads, _nbor_pack_width, _three_body_neighbor; - + int _pair_hybrid_flag; + // These should be removed in subsequent update w/ simpler hybrid arch + int _pair_hybrid_zero, _hybrid_nonpair, _zero_master; + public: inline int* get_overflow_flag() { return _overflow_flag; } inline int* get_off_overflow_flag() { return _off_overflow_flag; } @@ -210,6 +214,8 @@ class FixIntel : public Fix { _alignvar(double _stopwatch_offload_neighbor[1],64); _alignvar(double _stopwatch_offload_pair[1],64); + void _sync_main_arrays(const int prereverse); + template void reduce_results(ft * _noalias const f_in); @@ -238,7 +244,7 @@ class FixIntel : public Fix { /* ---------------------------------------------------------------------- */ -void FixIntel::get_buffern(const int /*offload*/, int &nlocal, int &nall, +void FixIntel::get_buffern(const int offload, int &nlocal, int &nall, int &minlocal) { #ifdef _LMP_INTEL_OFFLOAD if (_separate_buffers) { @@ -273,7 +279,7 @@ void FixIntel::get_buffern(const int /*offload*/, int &nlocal, int &nall, /* ---------------------------------------------------------------------- */ void FixIntel::add_result_array(IntelBuffers::vec3_acc_t *f_in, - double *ev_in, const int /*offload*/, + double *ev_in, const int offload, const int eatom, const int vatom, const int rflag) { #ifdef _LMP_INTEL_OFFLOAD @@ -282,6 +288,8 @@ void FixIntel::add_result_array(IntelBuffers::vec3_acc_t *f_in, _off_results_vatom = vatom; _off_force_array_d = f_in; _off_ev_array_d = ev_in; + if (_pair_hybrid_flag && force->pair->fdotr_is_set()) + _sync_main_arrays(1); return; } #endif @@ -296,12 +304,15 @@ void FixIntel::add_result_array(IntelBuffers::vec3_acc_t *f_in, if (_overflow_flag[LMP_OVERFLOW]) error->one(FLERR, "Neighbor list overflow, boost neigh_modify one"); + + if (_pair_hybrid_flag > 1 || + (_pair_hybrid_flag && force->pair->fdotr_is_set())) _sync_main_arrays(0); } /* ---------------------------------------------------------------------- */ void FixIntel::add_result_array(IntelBuffers::vec3_acc_t *f_in, - double *ev_in, const int /*offload*/, + double *ev_in, const int offload, const int eatom, const int vatom, const int rflag) { #ifdef _LMP_INTEL_OFFLOAD @@ -310,6 +321,8 @@ void FixIntel::add_result_array(IntelBuffers::vec3_acc_t *f_in, _off_results_vatom = vatom; _off_force_array_m = f_in; _off_ev_array_d = ev_in; + if (_pair_hybrid_flag && force->pair->fdotr_is_set()) + _sync_main_arrays(1); return; } #endif @@ -324,12 +337,16 @@ void FixIntel::add_result_array(IntelBuffers::vec3_acc_t *f_in, if (_overflow_flag[LMP_OVERFLOW]) error->one(FLERR, "Neighbor list overflow, boost neigh_modify one"); + + if (_pair_hybrid_flag > 1 || + (_pair_hybrid_flag && force->pair->fdotr_is_set())) + _sync_main_arrays(0); } /* ---------------------------------------------------------------------- */ void FixIntel::add_result_array(IntelBuffers::vec3_acc_t *f_in, - float *ev_in, const int /*offload*/, + float *ev_in, const int offload, const int eatom, const int vatom, const int rflag) { #ifdef _LMP_INTEL_OFFLOAD @@ -338,6 +355,8 @@ void FixIntel::add_result_array(IntelBuffers::vec3_acc_t *f_in, _off_results_vatom = vatom; _off_force_array_s = f_in; _off_ev_array_s = ev_in; + if (_pair_hybrid_flag && force->pair->fdotr_is_set()) + _sync_main_arrays(1); return; } #endif @@ -352,6 +371,10 @@ void FixIntel::add_result_array(IntelBuffers::vec3_acc_t *f_in, if (_overflow_flag[LMP_OVERFLOW]) error->one(FLERR, "Neighbor list overflow, boost neigh_modify one"); + + if (_pair_hybrid_flag > 1 || + (_pair_hybrid_flag && force->pair->fdotr_is_set())) + _sync_main_arrays(0); } /* ---------------------------------------------------------------------- */ @@ -487,16 +510,16 @@ The compiler version used to build LAMMPS is not supported when using offload to a coprocessor. There could be performance or correctness issues. Please use 14.0.1.106 or 15.1.133 or later. -E: Currently, cannot use more than one intel style with hybrid. +E: Currently, cannot offload more than one intel style with hybrid. -Currently, hybrid pair styles can only use the intel suffix for one of the -pair styles. +Currently, when using offload, hybrid pair styles can only use the intel +suffix for one of the pair styles. -E: Cannot yet use hybrid styles with Intel package. +E: Cannot yet use hybrid styles with Intel offload. -The hybrid pair style configuration is not yet supported by the Intel -package. Support is limited to hybrid/overlay or a hybrid style that does -not require a skip list. +The hybrid pair style configuration is not yet supported when using offload +within the Intel package. Support is limited to hybrid/overlay or a hybrid +style that does not require a skip list. W: Leaving a core/node free can improve performance for offload @@ -538,4 +561,16 @@ E: Too few atoms for load balancing offload. When using offload to a coprocessor, each MPI task must have at least 2 atoms throughout the simulation. +E: Intel package requires fdotr virial with newton on. + +This error can occur with a hybrid pair style that mixes styles that are +incompatible with the newton pair setting turned on. Try turning the +newton pair setting off. + +E: Add -DLMP_INTEL_NBOR_COMPAT to build for special_bond exclusions with Intel + +When using a manybody pair style, bonds/angles/dihedrals, and special_bond +exclusions, LAMMPS should be built with the above compile flag for compatible +results. + */ diff --git a/src/USER-INTEL/improper_cvff_intel.cpp b/src/USER-INTEL/improper_cvff_intel.cpp index c20c004657..03bd134b40 100644 --- a/src/USER-INTEL/improper_cvff_intel.cpp +++ b/src/USER-INTEL/improper_cvff_intel.cpp @@ -428,7 +428,7 @@ void ImproperCvffIntel::init_style() template void ImproperCvffIntel::pack_force_const(ForceConst &fc, - IntelBuffers * /*buffers*/) + IntelBuffers * /*buffers*/) { const int bp1 = atom->nimpropertypes + 1; fc.set_ntypes(bp1,memory); diff --git a/src/USER-INTEL/intel_buffers.cpp b/src/USER-INTEL/intel_buffers.cpp index 05176e1fd1..b7026f90b7 100644 --- a/src/USER-INTEL/intel_buffers.cpp +++ b/src/USER-INTEL/intel_buffers.cpp @@ -24,7 +24,9 @@ using namespace LAMMPS_NS; template IntelBuffers::IntelBuffers(class LAMMPS *lmp_in) : lmp(lmp_in), _x(0), _q(0), _quat(0), _f(0), _off_threads(0), - _buf_size(0), _buf_local_size(0) { + _buf_size(0), _buf_local_size(0), _n_list_ptrs(1), _max_list_ptrs(4) { + _neigh_list_ptrs = new IntelNeighListPtrs[_max_list_ptrs]; + _neigh_list_ptrs[0].cnumneigh = 0; _list_alloc_atoms = 0; _ntypes = 0; _off_map_listlocal = 0; @@ -55,6 +57,7 @@ IntelBuffers::~IntelBuffers() free_all_nbor_buffers(); free_ccache(); set_ntypes(0); + delete []_neigh_list_ptrs; } /* ---------------------------------------------------------------------- */ @@ -109,7 +112,7 @@ void IntelBuffers::free_buffers() template void IntelBuffers::_grow(const int nall, const int nlocal, const int nthreads, - const int /*offload_end*/) + const int offload_end) { free_buffers(); _buf_size = static_cast(nall) * 1.1 + 1; @@ -186,11 +189,9 @@ void IntelBuffers::free_nmax() const int * tag = _off_map_tag; const int * special = _off_map_special; const int * nspecial = _off_map_nspecial; - if (tag != 0 && special != 0 && nspecial !=0) { - #pragma offload_transfer target(mic:_cop) \ - nocopy(tag:alloc_if(0) free_if(1)) \ - nocopy(special,nspecial:alloc_if(0) free_if(1)) - } + #pragma offload_transfer target(mic:_cop) \ + nocopy(tag:alloc_if(0) free_if(1)) \ + nocopy(special,nspecial:alloc_if(0) free_if(1)) _off_map_nmax = 0; _host_nmax = 0; } @@ -200,7 +201,7 @@ void IntelBuffers::free_nmax() /* ---------------------------------------------------------------------- */ template -void IntelBuffers::_grow_nmax(const int /*offload_end*/) +void IntelBuffers::_grow_nmax(const int offload_end) { #ifdef _LMP_INTEL_OFFLOAD free_nmax(); @@ -243,46 +244,117 @@ template void IntelBuffers::free_list_local() { if (_off_map_listlocal > 0) { - int * cnumneigh = _cnumneigh; + if (_neigh_list_ptrs[0].cnumneigh) { + int * cnumneigh = _neigh_list_ptrs[0].cnumneigh; + _neigh_list_ptrs[0].cnumneigh = 0; + #ifdef _LMP_INTEL_OFFLOAD + if (_off_map_ilist != NULL) { + #pragma offload_transfer target(mic:_cop) \ + nocopy(cnumneigh:alloc_if(0) free_if(1)) + } + #endif + lmp->memory->destroy(cnumneigh); + } + #ifdef _LMP_INTEL_OFFLOAD if (_off_map_ilist != NULL) { const int * ilist = _off_map_ilist; const int * numneigh = _off_map_numneigh; + const int ** firstneigh = (const int **)_off_map_firstneigh; _off_map_ilist = NULL; - if (numneigh != 0 && ilist != 0) { - #pragma offload_transfer target(mic:_cop) \ - nocopy(ilist,numneigh,cnumneigh:alloc_if(0) free_if(1)) - } + #pragma offload_transfer target(mic:_cop) \ + nocopy(ilist,firstneigh,numneigh:alloc_if(0) free_if(1)) } #endif - lmp->memory->destroy(cnumneigh); _off_map_listlocal = 0; } } /* ---------------------------------------------------------------------- */ +template +void IntelBuffers::free_list_ptrs() +{ + for (int list_num = 1; list_num < _n_list_ptrs; list_num++) { + if (_neigh_list_ptrs[list_num].size) { + lmp->memory->destroy(_neigh_list_ptrs[list_num].cnumneigh); + lmp->memory->destroy(_neigh_list_ptrs[list_num].numneighhalf); + } + _neigh_list_ptrs[list_num].size = 0; + _neigh_list_ptrs[list_num].list_ptr = 0; + } + _n_list_ptrs = 1; +} + +/* ---------------------------------------------------------------------- */ + +template +void IntelBuffers::grow_data3(NeighList *list, + int *&numneighhalf, + int *&cnumneigh) +{ + const int size = list->get_maxlocal(); + int list_num; + for (list_num = 0; list_num < _n_list_ptrs; list_num++) + if (_neigh_list_ptrs[list_num].list_ptr == (void*)list) break; + if (list_num == _n_list_ptrs) { + if (_n_list_ptrs == _max_list_ptrs) { + _max_list_ptrs *= 2; + IntelNeighListPtrs *new_list = new IntelNeighListPtrs[_max_list_ptrs]; + for (int i = 0; i < _n_list_ptrs; i++) new_list[i] = _neigh_list_ptrs[i]; + delete []_neigh_list_ptrs; + _neigh_list_ptrs = new_list; + } + _neigh_list_ptrs[list_num].list_ptr = (void *)list; + _neigh_list_ptrs[list_num].size = 0; + _n_list_ptrs++; + } + if (size > _neigh_list_ptrs[list_num].size) { + if (_neigh_list_ptrs[list_num].size) { + lmp->memory->destroy(_neigh_list_ptrs[list_num].cnumneigh); + lmp->memory->destroy(_neigh_list_ptrs[list_num].numneighhalf); + } + lmp->memory->create(_neigh_list_ptrs[list_num].cnumneigh, size, + "_cnumneigh"); + lmp->memory->create(_neigh_list_ptrs[list_num].numneighhalf, size, + "_cnumneigh"); + _neigh_list_ptrs[list_num].size = size; + } + numneighhalf = _neigh_list_ptrs[list_num].numneighhalf; + cnumneigh = _neigh_list_ptrs[list_num].cnumneigh; +} + +/* ---------------------------------------------------------------------- */ + template void IntelBuffers::_grow_list_local(NeighList *list, - const int /*offload_end*/) + const int three_body, + const int offload_end) { free_list_local(); int size = list->get_maxlocal(); - lmp->memory->create(_cnumneigh, size, "_cnumneigh"); _off_map_listlocal = size; + if (three_body) + lmp->memory->create(_neigh_list_ptrs[0].cnumneigh, size, "_cnumneigh"); #ifdef _LMP_INTEL_OFFLOAD if (offload_end > 0) { + int tb_size = size; + if (three_body == 0) { + lmp->memory->create(_neigh_list_ptrs[0].cnumneigh, 16, "_cnumneigh"); + tb_size = 16; + } + int ** firstneigh = list->firstneigh; int * numneigh = list->numneigh; int * ilist = list->ilist; - int * cnumneigh = _cnumneigh; - if (cnumneigh != 0) { - #pragma offload_transfer target(mic:_cop) \ - nocopy(ilist:length(size) alloc_if(1) free_if(0)) \ - nocopy(numneigh:length(size) alloc_if(1) free_if(0)) \ - nocopy(cnumneigh:length(size) alloc_if(1) free_if(0)) - } + int * cnumneigh = _neigh_list_ptrs[0].cnumneigh; + #pragma offload_transfer target(mic:_cop) \ + nocopy(ilist:length(size) alloc_if(1) free_if(0)) \ + nocopy(firstneigh:length(size) alloc_if(1) free_if(0)) \ + nocopy(numneigh:length(size) alloc_if(1) free_if(0)) \ + nocopy(cnumneigh:length(tb_size) alloc_if(1) free_if(0)) _off_map_ilist = ilist; + _off_map_firstneigh = firstneigh; _off_map_numneigh = numneigh; } #endif @@ -313,7 +385,7 @@ template void IntelBuffers::_grow_nbor_list(NeighList * /*list*/, const int nlocal, const int nthreads, - const int /*offload_end*/, + const int offload_end, const int pack_width) { free_nbor_list(); @@ -382,7 +454,7 @@ void IntelBuffers::free_ccache() /* ---------------------------------------------------------------------- */ template -void IntelBuffers::grow_ccache(const int /*off_flag*/, +void IntelBuffers::grow_ccache(const int off_flag, const int nthreads, const int width) { @@ -481,7 +553,7 @@ void IntelBuffers::free_ncache() /* ---------------------------------------------------------------------- */ template -void IntelBuffers::grow_ncache(const int /*off_flag*/, +void IntelBuffers::grow_ncache(const int off_flag, const int nthreads) { const int nsize = get_max_nbors() * 3; @@ -576,12 +648,12 @@ void IntelBuffers::set_ntypes(const int ntypes, if (_ntypes > 0) { #ifdef _LMP_INTEL_OFFLOAD flt_t * cutneighsqo = _cutneighsq[0]; - if (_off_threads > 0 && cutneighsqo != 0) { + if (_off_threads > 0) { #pragma offload_transfer target(mic:_cop) \ nocopy(cutneighsqo:alloc_if(0) free_if(1)) } flt_t * cutneighghostsqo; - if (_cutneighghostsq && _off_threads > 0 && cutneighghostsqo != 0) { + if (_cutneighghostsq && _off_threads > 0) { cutneighghostsqo = _cutneighghostsq[0]; #pragma offload_transfer target(mic:_cop) \ nocopy(cutneighghostsqo:alloc_if(0) free_if(1)) @@ -637,6 +709,8 @@ double IntelBuffers::memory_usage(const int nthreads) tmem += (_list_alloc_atoms + _off_threads) * get_max_nbors() * sizeof(int); tmem += _ntypes * _ntypes * sizeof(int); + tmem += _buf_local_size + (_n_list_ptrs - 1) * _buf_local_size * 2; + return tmem; } diff --git a/src/USER-INTEL/intel_buffers.h b/src/USER-INTEL/intel_buffers.h index e8225a4a30..276b87ec5f 100644 --- a/src/USER-INTEL/intel_buffers.h +++ b/src/USER-INTEL/intel_buffers.h @@ -33,12 +33,20 @@ namespace LAMMPS_NS { #define QUAT_T typename IntelBuffers::quat_t #define FORCE_T typename IntelBuffers::vec3_acc_t +struct IntelNeighListPtrs { + void * list_ptr; + int *cnumneigh; + int *numneighhalf; + int size; +}; + // May not need a separate force array for mixed/double template class IntelBuffers { public: typedef struct { flt_t x,y,z; int w; } atom_t; typedef struct { flt_t w,i,j,k; } quat_t; + typedef struct { flt_t x,y; } vec2_t; typedef struct { flt_t x,y,z,w; } vec3_t; typedef struct { flt_t x,y,z,w; } vec4_t; typedef struct { acc_t x,y,z,w; } vec3_acc_t; @@ -62,8 +70,12 @@ class IntelBuffers { void free_buffers(); void free_nmax(); - inline void set_bininfo(int *atombin, int *binpacked) - { _atombin = atombin; _binpacked = binpacked; } + inline void set_bininfo(int *atombin, int *binpacked) { + _atombin = atombin; + _binpacked = binpacked; + _neigh_list_ptrs[0].numneighhalf = atombin; + } + inline void grow(const int nall, const int nlocal, const int nthreads, const int offload_end) { if (nall >= _buf_size || nlocal >= _buf_local_size) @@ -79,18 +91,22 @@ class IntelBuffers { free_nmax(); free_list_local(); free_ncache(); + free_list_ptrs(); } inline void grow_list(NeighList *list, const int nlocal, const int nthreads, - const int offload_end, const int pack_width=1) { - grow_list_local(list, offload_end); + const int three_body, const int offload_end, + const int pack_width=1) { + grow_list_local(list, three_body, offload_end); grow_nbor_list(list, nlocal, nthreads, offload_end, pack_width); } void free_list_local(); - inline void grow_list_local(NeighList *list, const int offload_end) { + inline void grow_list_local(NeighList *list, const int three_body, + const int offload_end) { + _neigh_list_ptrs[0].list_ptr = (void *)list; if (list->get_maxlocal() > _off_map_listlocal) - _grow_list_local(list, offload_end); + _grow_list_local(list, three_body, offload_end); } void free_ccache(); @@ -133,26 +149,36 @@ class IntelBuffers { _grow_nbor_list(list, nlocal, nthreads, offload_end, pack_width); } - void set_ntypes(const int ntypes, const int use_ghost_cut = 0); + void set_ntypes(const int ntypes, const int use_ghost_cut = 1); - inline int * firstneigh(const NeighList * /*list*/) { return _list_alloc; } - inline int * cnumneigh(const NeighList * /*list*/) { return _cnumneigh; } + inline int * intel_list(const NeighList * /*list*/) { return _list_alloc; } inline int * get_atombin() { return _atombin; } inline int * get_binpacked() { return _binpacked; } + inline int * cnumneigh() { return _neigh_list_ptrs[0].cnumneigh; } + inline void get_list_data3(const NeighList *list, int *&numneighhalf, + int *&cnumneigh) { + for (int i = 0; i < _n_list_ptrs; i++) + if ((void *)list == _neigh_list_ptrs[i].list_ptr) { + numneighhalf = _neigh_list_ptrs[i].numneighhalf; + cnumneigh = _neigh_list_ptrs[i].cnumneigh; + } + } + void grow_data3(NeighList *list, int *&numneighhalf, int *&cnumneigh); + void free_list_ptrs(); - inline atom_t * get_x(const int /*offload*/ = 1) { + inline atom_t * get_x(const int offload = 1) { #ifdef _LMP_INTEL_OFFLOAD if (_separate_buffers && offload == 0) return _host_x; #endif return _x; } - inline flt_t * get_q(const int /*offload*/ = 1) { + inline flt_t * get_q(const int offload = 1) { #ifdef _LMP_INTEL_OFFLOAD if (_separate_buffers && offload == 0) return _host_q; #endif return _q; } - inline quat_t * get_quat(const int /*offload*/ = 1) { + inline quat_t * get_quat(const int offload = 1) { #ifdef _LMP_INTEL_OFFLOAD if (_separate_buffers && offload == 0) return _host_quat; #endif @@ -298,6 +324,9 @@ class IntelBuffers { int _list_alloc_atoms; int *_list_alloc, *_cnumneigh, *_atombin, *_binpacked; + IntelNeighListPtrs *_neigh_list_ptrs; + int _n_list_ptrs, _max_list_ptrs; + flt_t **_cutneighsq, **_cutneighghostsq; int _ntypes; @@ -325,7 +354,7 @@ class IntelBuffers { int _off_map_nmax, _cop, _off_ccache, _off_ncache; int *_off_map_ilist; int *_off_map_special, *_off_map_nspecial, *_off_map_tag; - int *_off_map_numneigh; + int **_off_map_firstneigh, *_off_map_numneigh; bool _off_list_alloc; #endif @@ -336,7 +365,8 @@ class IntelBuffers { void _grow(const int nall, const int nlocal, const int nthreads, const int offload_end); void _grow_nmax(const int offload_end); - void _grow_list_local(NeighList *list, const int offload_end); + void _grow_list_local(NeighList *list, const int three_body, + const int offload_end); void _grow_nbor_list(NeighList *list, const int nlocal, const int nthreads, const int offload_end, const int pack_width); }; diff --git a/src/USER-INTEL/intel_preprocess.h b/src/USER-INTEL/intel_preprocess.h index 2f1b02a49f..178a20c6e1 100644 --- a/src/USER-INTEL/intel_preprocess.h +++ b/src/USER-INTEL/intel_preprocess.h @@ -20,6 +20,9 @@ #if (__INTEL_COMPILER_BUILD_DATE > 20160720) #define LMP_INTEL_USE_SIMDOFF #endif +#pragma warning (disable:3948) +#pragma warning (disable:3949) +#pragma warning (disable:13200) #endif #ifdef __INTEL_OFFLOAD @@ -606,7 +609,7 @@ inline double MIC_Wtime() { if (newton) \ f_stride = buffers->get_stride(nall); \ else \ - f_stride = buffers->get_stride(inum); \ + f_stride = buffers->get_stride(nlocal); \ } #define IP_PRE_get_buffers(offload, buffers, fix, tc, f_start, \ diff --git a/src/USER-INTEL/intel_simd.h b/src/USER-INTEL/intel_simd.h index e9d5d92995..75fc9828b9 100644 --- a/src/USER-INTEL/intel_simd.h +++ b/src/USER-INTEL/intel_simd.h @@ -213,6 +213,12 @@ namespace ip_simd { _MM_SCALE_8); } + inline SIMD_int SIMD_gatherz(const SIMD_mask &m, const int *p, + const SIMD_int &i) { + return _mm512_mask_i32gather_epi32( _mm512_set1_epi32(0), m, i, p, + _MM_SCALE_4); + } + inline SIMD_float SIMD_gatherz(const SIMD_mask &m, const float *p, const SIMD_int &i) { return _mm512_mask_i32gather_ps( _mm512_set1_ps((float)0), m, i, p, diff --git a/src/USER-INTEL/nbin_intel.cpp b/src/USER-INTEL/nbin_intel.cpp index 789fa35b42..8359587eb2 100644 --- a/src/USER-INTEL/nbin_intel.cpp +++ b/src/USER-INTEL/nbin_intel.cpp @@ -192,7 +192,6 @@ void NBinIntel::bin_atoms(IntelBuffers * buffers) { // ---------- Bin Atoms ------------- _fix->start_watch(TIME_HOST_NEIGHBOR); - //const ATOM_T * _noalias const x = buffers->get_x(); int * _noalias const atombin = this->_atombin; int * _noalias const binpacked = this->_binpacked; diff --git a/src/USER-INTEL/npair_full_bin_ghost_intel.cpp b/src/USER-INTEL/npair_full_bin_ghost_intel.cpp index 74a04f0e7d..5149b26f2f 100644 --- a/src/USER-INTEL/npair_full_bin_ghost_intel.cpp +++ b/src/USER-INTEL/npair_full_bin_ghost_intel.cpp @@ -86,7 +86,7 @@ void NPairFullBinGhostIntel::fbi(NeighList * list, // only uses offload_end_neighbor to check whether we are doing offloading // at all, no need to correct this later - buffers->grow_list(list, nall, comm->nthreads, off_end, + buffers->grow_list(list, nall, comm->nthreads, 0, off_end, _fix->nbor_pack_width()); int need_ic = 0; @@ -106,7 +106,7 @@ void NPairFullBinGhostIntel::fbi(NeighList * list, /* ---------------------------------------------------------------------- */ template -void NPairFullBinGhostIntel::fbi(const int /*offload*/, NeighList * list, +void NPairFullBinGhostIntel::fbi(const int offload, NeighList * list, IntelBuffers * buffers, const int pstart, const int pend) { if (pend-pstart == 0) return; @@ -116,7 +116,8 @@ void NPairFullBinGhostIntel::fbi(const int /*offload*/, NeighList * list, const int aend = nall; const ATOM_T * _noalias const x = buffers->get_x(); - int * _noalias const firstneigh = buffers->firstneigh(list); + int * _noalias const intel_list = buffers->intel_list(list); + int ** _noalias const firstneigh = list->firstneigh; const int e_nall = nall_t; const int molecular = atom->molecular; @@ -140,7 +141,6 @@ void NPairFullBinGhostIntel::fbi(const int /*offload*/, NeighList * list, int * _noalias const ilist = list->ilist; int * _noalias numneigh = list->numneigh; - int * _noalias const cnumneigh = buffers->cnumneigh(list); const int nstencil = this->nstencil; const int * _noalias const stencil = this->stencil; const flt_t * _noalias const cutneighsq = buffers->get_cutneighsq()[0]; @@ -228,7 +228,7 @@ void NPairFullBinGhostIntel::fbi(const int /*offload*/, NeighList * list, in(cutneighsq:length(0) alloc_if(0) free_if(0)) \ in(cutneighghostsq:length(0) alloc_if(0) free_if(0)) \ in(firstneigh:length(0) alloc_if(0) free_if(0)) \ - in(cnumneigh:length(0) alloc_if(0) free_if(0)) \ + in(intel_list:length(0) alloc_if(0) free_if(0)) \ in(numneigh:length(0) alloc_if(0) free_if(0)) \ in(ilist:length(0) alloc_if(0) free_if(0)) \ in(atombin:length(aend) alloc_if(0) free_if(0)) \ @@ -295,7 +295,7 @@ void NPairFullBinGhostIntel::fbi(const int /*offload*/, NeighList * list, int pack_offset = maxnbors; int ct = (ifrom + tid * 2) * maxnbors; - int *neighptr = firstneigh + ct; + int *neighptr = intel_list + ct; const int obound = pack_offset + maxnbors * 2; const int toffs = tid * ncache_stride; @@ -528,12 +528,12 @@ void NPairFullBinGhostIntel::fbi(const int /*offload*/, NeighList * list, if (ns > maxnbors) *overflow = 1; ilist[i] = i; - cnumneigh[i] = ct; + firstneigh[i] = intel_list + ct; numneigh[i] = ns; ct += ns; IP_PRE_edge_align(ct, sizeof(int)); - neighptr = firstneigh + ct; + neighptr = intel_list + ct; if (ct + obound > list_size) { if (i < ito - 1) { *overflow = 1; @@ -564,13 +564,12 @@ void NPairFullBinGhostIntel::fbi(const int /*offload*/, NeighList * list, if (offload) { _fix->stop_watch(TIME_OFFLOAD_LATENCY); _fix->start_watch(TIME_HOST_NEIGHBOR); + firstneigh[0] = intel_list; for (int n = 0; n < aend; n++) { ilist[n] = n; numneigh[n] = 0; } } else { - for (int i = 0; i < aend; i++) - list->firstneigh[i] = firstneigh + cnumneigh[i]; if (separate_buffers) { _fix->start_watch(TIME_PACK); _fix->set_neighbor_host_sizes(); @@ -581,10 +580,5 @@ void NPairFullBinGhostIntel::fbi(const int /*offload*/, NeighList * list, _fix->stop_watch(TIME_PACK); } } - #else - #pragma vector aligned - #pragma simd - for (int i = 0; i < aend; i++) - list->firstneigh[i] = firstneigh + cnumneigh[i]; #endif } diff --git a/src/USER-INTEL/npair_full_bin_intel.cpp b/src/USER-INTEL/npair_full_bin_intel.cpp index 60b912d796..4ef84be75f 100644 --- a/src/USER-INTEL/npair_full_bin_intel.cpp +++ b/src/USER-INTEL/npair_full_bin_intel.cpp @@ -70,7 +70,8 @@ fbi(NeighList *list, IntelBuffers *buffers) { int offload_noghost = _fix->offload_noghost(); #endif - buffers->grow_list(list, atom->nlocal, comm->nthreads, off_end, + buffers->grow_list(list, atom->nlocal, comm->nthreads, + _fix->three_body_neighbor(), off_end, _fix->nbor_pack_width()); int need_ic = 0; diff --git a/src/USER-INTEL/npair_half_bin_newton_intel.cpp b/src/USER-INTEL/npair_half_bin_newton_intel.cpp index 8c024a4604..799ba2b57b 100644 --- a/src/USER-INTEL/npair_half_bin_newton_intel.cpp +++ b/src/USER-INTEL/npair_half_bin_newton_intel.cpp @@ -71,7 +71,7 @@ hbni(NeighList *list, IntelBuffers *buffers) { int offload_noghost = _fix->offload_noghost(); #endif - buffers->grow_list(list, atom->nlocal, comm->nthreads, off_end); + buffers->grow_list(list, atom->nlocal, comm->nthreads, 0, off_end); int need_ic = 0; if (atom->molecular) diff --git a/src/USER-INTEL/npair_half_bin_newton_tri_intel.cpp b/src/USER-INTEL/npair_half_bin_newton_tri_intel.cpp index 653a951394..1f859cb5f1 100644 --- a/src/USER-INTEL/npair_half_bin_newton_tri_intel.cpp +++ b/src/USER-INTEL/npair_half_bin_newton_tri_intel.cpp @@ -71,7 +71,7 @@ hbnti(NeighList *list, IntelBuffers *buffers) { int offload_noghost = _fix->offload_noghost(); #endif - buffers->grow_list(list, atom->nlocal, comm->nthreads, off_end); + buffers->grow_list(list, atom->nlocal, comm->nthreads, 0, off_end); int need_ic = 0; if (atom->molecular) diff --git a/src/USER-INTEL/npair_halffull_newtoff_intel.h b/src/USER-INTEL/npair_halffull_newtoff_intel.h new file mode 100644 index 0000000000..c4c41a85a1 --- /dev/null +++ b/src/USER-INTEL/npair_halffull_newtoff_intel.h @@ -0,0 +1,47 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: W. Michael Brown (Intel) +------------------------------------------------------------------------- */ + +// Only used for hybrid to generate list for non-intel style. Use +// standard routines. + +#ifdef NPAIR_CLASS + +NPairStyle(halffull/newtoff/intel, + NPairHalffullNewtoff, + NP_HALF_FULL | NP_NEWTOFF | NP_NSQ | NP_BIN | NP_MULTI | NP_HALF | + NP_ORTHO | NP_TRI | NP_INTEL) + +NPairStyle(halffull/newtoff/skip/intel, + NPairHalffullNewtoff, + NP_HALF_FULL | NP_NEWTOFF | NP_NSQ | NP_BIN | NP_MULTI | NP_HALF | + NP_ORTHO | NP_TRI | NP_SKIP | NP_INTEL) + +NPairStyle(halffull/newtoff/ghost/intel, + NPairHalffullNewtoff, + NP_HALF_FULL | NP_NEWTOFF | NP_NSQ | NP_BIN | NP_MULTI | NP_HALF | + NP_ORTHO | NP_TRI | NP_GHOST | NP_INTEL) + +NPairStyle(halffull/newtoff/skip/ghost/intel, + NPairHalffullNewtoff, + NP_HALF_FULL | NP_NEWTOFF | NP_NSQ | NP_BIN | NP_MULTI | NP_HALF | + NP_ORTHO | NP_TRI | NP_SKIP | NP_GHOST | NP_INTEL) + +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/USER-INTEL/npair_halffull_newton_intel.cpp b/src/USER-INTEL/npair_halffull_newton_intel.cpp new file mode 100644 index 0000000000..93a1a97923 --- /dev/null +++ b/src/USER-INTEL/npair_halffull_newton_intel.cpp @@ -0,0 +1,233 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: W. Michael Brown (Intel) +------------------------------------------------------------------------- */ + +#include "npair_halffull_newton_intel.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "atom.h" +#include "atom_vec.h" +#include "comm.h" +#include "modify.h" +#include "molecule.h" +#include "domain.h" +#include "my_page.h" +#include "error.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +NPairHalffullNewtonIntel::NPairHalffullNewtonIntel(LAMMPS *lmp) : NPair(lmp) { + int ifix = modify->find_fix("package_intel"); + if (ifix < 0) + error->all(FLERR, + "The 'package intel' command is required for /intel styles"); + _fix = static_cast(modify->fix[ifix]); +} + +/* ---------------------------------------------------------------------- + build half list from full list + pair stored once if i,j are both owned and i < j + if j is ghost, only store if j coords are "above and to the right" of i + works if full list is a skip list +------------------------------------------------------------------------- */ + +template +void NPairHalffullNewtonIntel::build_t(NeighList *list, + IntelBuffers *buffers) +{ + const int inum_full = list->listfull->inum; + const int nlocal = atom->nlocal; + const int e_nall = nlocal + atom->nghost; + const ATOM_T * _noalias const x = buffers->get_x(); + int * _noalias const ilist = list->ilist; + int * _noalias const numneigh = list->numneigh; + int ** _noalias const firstneigh = list->firstneigh; + const int * _noalias const ilist_full = list->listfull->ilist; + const int * _noalias const numneigh_full = list->listfull->numneigh; + const int ** _noalias const firstneigh_full = + (const int ** const)list->listfull->firstneigh; + + #if defined(_OPENMP) + #pragma omp parallel + #endif + { + int tid, ifrom, ito; + IP_PRE_omp_range_id(ifrom, ito, tid, inum_full, comm->nthreads); + + // each thread has its own page allocator + MyPage &ipage = list->ipage[tid]; + ipage.reset(); + + // loop over parent full list + for (int ii = ifrom; ii < ito; ii++) { + int n = 0; + int *neighptr = ipage.vget(); + + const int i = ilist_full[ii]; + const flt_t xtmp = x[i].x; + const flt_t ytmp = x[i].y; + const flt_t ztmp = x[i].z; + + // loop over full neighbor list + + const int * _noalias const jlist = firstneigh_full[i]; + const int jnum = numneigh_full[i]; + + #if defined(LMP_SIMD_COMPILER) + #pragma vector aligned + #pragma ivdep + #endif + for (int jj = 0; jj < jnum; jj++) { + const int joriginal = jlist[jj]; + const int j = joriginal & NEIGHMASK; + int addme = 1; + if (j < nlocal) { + if (i > j) addme = 0; + } else { + if (x[j].z < ztmp) addme = 0; + if (x[j].z == ztmp) { + if (x[j].y < ytmp) addme = 0; + if (x[j].y == ytmp && x[j].x < xtmp) addme = 0; + } + } + if (addme) + neighptr[n++] = joriginal; + } + + ilist[ii] = i; + firstneigh[i] = neighptr; + numneigh[i] = n; + + int pad_end = n; + IP_PRE_neighbor_pad(pad_end, 0); + #if defined(LMP_SIMD_COMPILER) + #pragma vector aligned + #pragma loop_count min=1, max=INTEL_COMPILE_WIDTH-1, \ + avg=INTEL_COMPILE_WIDTH/2 + #endif + for ( ; n < pad_end; n++) + neighptr[n] = e_nall; + + ipage.vgot(n); + if (ipage.status()) + error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); + } + } + list->inum = inum_full; +} + +/* ---------------------------------------------------------------------- + build half list from full 3-body list + half list is already stored as first part of 3-body list +------------------------------------------------------------------------- */ + +template +void NPairHalffullNewtonIntel::build_t3(NeighList *list, int *numhalf) +{ + const int inum_full = list->listfull->inum; + const int e_nall = atom->nlocal + atom->nghost; + int * _noalias const ilist = list->ilist; + int * _noalias const numneigh = list->numneigh; + int ** _noalias const firstneigh = list->firstneigh; + const int * _noalias const ilist_full = list->listfull->ilist; + const int * _noalias const numneigh_full = numhalf; + const int ** _noalias const firstneigh_full = + (const int ** const)list->listfull->firstneigh; + + int packthreads = 1; + if (comm->nthreads > INTEL_HTHREADS) packthreads = comm->nthreads; + + #if defined(_OPENMP) + #pragma omp parallel if(packthreads > 1) + #endif + { + int tid, ifrom, ito; + IP_PRE_omp_range_id(ifrom, ito, tid, inum_full, packthreads); + + // each thread has its own page allocator + MyPage &ipage = list->ipage[tid]; + ipage.reset(); + + // loop over parent full list + for (int ii = ifrom; ii < ito; ii++) { + int n = 0; + int *neighptr = ipage.vget(); + + const int i = ilist_full[ii]; + + // loop over full neighbor list + + const int * _noalias const jlist = firstneigh_full[i]; + const int jnum = numneigh_full[ii]; + + #if defined(LMP_SIMD_COMPILER) + #pragma vector aligned + #pragma ivdep + #endif + for (int jj = 0; jj < jnum; jj++) { + const int joriginal = jlist[jj]; + neighptr[n++] = joriginal; + } + + ilist[ii] = i; + firstneigh[i] = neighptr; + numneigh[i] = n; + + int pad_end = n; + IP_PRE_neighbor_pad(pad_end, 0); + #if defined(LMP_SIMD_COMPILER) + #pragma vector aligned + #pragma loop_count min=1, max=INTEL_COMPILE_WIDTH-1, \ + avg=INTEL_COMPILE_WIDTH/2 + #endif + for ( ; n < pad_end; n++) + neighptr[n] = e_nall; + + ipage.vgot(n); + if (ipage.status()) + error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); + } + } + list->inum = inum_full; +} + +/* ---------------------------------------------------------------------- */ + +void NPairHalffullNewtonIntel::build(NeighList *list) +{ + if (_fix->three_body_neighbor() == 0) { + if (_fix->precision() == FixIntel::PREC_MODE_MIXED) + build_t(list, _fix->get_mixed_buffers()); + else if (_fix->precision() == FixIntel::PREC_MODE_DOUBLE) + build_t(list, _fix->get_double_buffers()); + else + build_t(list, _fix->get_single_buffers()); + } else { + int *nhalf, *cnum; + if (_fix->precision() == FixIntel::PREC_MODE_MIXED) { + _fix->get_mixed_buffers()->get_list_data3(list->listfull, nhalf, cnum); + build_t3(list, nhalf); + } else if (_fix->precision() == FixIntel::PREC_MODE_DOUBLE) { + _fix->get_double_buffers()->get_list_data3(list->listfull, nhalf, cnum); + build_t3(list, nhalf); + } else { + _fix->get_single_buffers()->get_list_data3(list->listfull, nhalf, cnum); + build_t3(list, nhalf); + } + } +} diff --git a/src/USER-INTEL/npair_halffull_newton_intel.h b/src/USER-INTEL/npair_halffull_newton_intel.h new file mode 100644 index 0000000000..b3069d8074 --- /dev/null +++ b/src/USER-INTEL/npair_halffull_newton_intel.h @@ -0,0 +1,72 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: W. Michael Brown (Intel) +------------------------------------------------------------------------- */ + +#ifdef NPAIR_CLASS + +NPairStyle(halffull/newton/intel, + NPairHalffullNewtonIntel, + NP_HALF_FULL | NP_NEWTON | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI | + NP_ORTHO | NP_TRI| NP_INTEL) + +NPairStyle(halffull/newton/skip/intel, + NPairHalffullNewtonIntel, + NP_HALF_FULL | NP_NEWTON | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI | + NP_ORTHO | NP_TRI | NP_SKIP | NP_INTEL) + +#else + +#ifndef LMP_NPAIR_HALFFULL_NEWTON_INTEL_H +#define LMP_NPAIR_HALFFULL_NEWTON_INTEL_H + +#include "npair.h" +#include "fix_intel.h" + +#if defined(_OPENMP) +#include +#endif + + +namespace LAMMPS_NS { + +class NPairHalffullNewtonIntel : public NPair { + public: + NPairHalffullNewtonIntel(class LAMMPS *); + ~NPairHalffullNewtonIntel() {} + void build(class NeighList *); + + protected: + FixIntel *_fix; + + template + void build_t(NeighList *, IntelBuffers *); + + template + void build_t3(NeighList *, int *); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: The 'package intel' command is required for /intel styles + +Self explanatory. + +*/ diff --git a/src/USER-INTEL/npair_intel.cpp b/src/USER-INTEL/npair_intel.cpp index 6d4529752a..a1c0785d4c 100644 --- a/src/USER-INTEL/npair_intel.cpp +++ b/src/USER-INTEL/npair_intel.cpp @@ -52,12 +52,61 @@ NPairIntel::~NPairIntel() { /* ---------------------------------------------------------------------- */ +void NPairIntel::copy_neighbor_info() +{ + NPair::copy_neighbor_info(); + if (_fix->precision() == FixIntel::PREC_MODE_MIXED) + copy_cutsq_info(_fix->get_mixed_buffers()); + else if (_fix->precision() == FixIntel::PREC_MODE_DOUBLE) + copy_cutsq_info(_fix->get_double_buffers()); + else + copy_cutsq_info(_fix->get_single_buffers()); +} + +/* ---------------------------------------------------------------------- */ + +template +void NPairIntel::copy_cutsq_info(IntelBuffers *buffers) { + int tp1 = atom->ntypes + 1; + int use_ghost_cut = 0; + if (cutneighghostsq) + use_ghost_cut = 1; + buffers->set_ntypes(tp1, use_ghost_cut); + + flt_t **cutneighsqb = buffers->get_cutneighsq(); + for (int i = 1; i <= atom->ntypes; i++) + for (int j = 1; j <= atom->ntypes; j++) + cutneighsqb[i][j] = cutneighsq[i][j]; + + flt_t **cutneighghostsqb; + if (use_ghost_cut) { + cutneighghostsqb = buffers->get_cutneighghostsq(); + for (int i = 1; i <= atom->ntypes; i++) + for (int j = 1; j <= atom->ntypes; j++) + cutneighghostsqb[i][j] = cutneighghostsq[i][j]; + } + + #ifdef _LMP_INTEL_OFFLOAD + if (_cop < 0) return; + int tp1sq = tp1 * tp1; + flt_t * ocutneighsq = cutneighsqb[0]; + #pragma offload_transfer target(mic:_cop) in(ocutneighsq: length(tp1sq)) + if (use_ghost_cut) { + flt_t * ocutneighghostsq = cutneighghostsqb[0]; + #pragma offload_transfer target(mic:_cop) \ + in(ocutneighghostsq: length(tp1sq)) + } + #endif +} + +/* ---------------------------------------------------------------------- */ + template -void NPairIntel::bin_newton(const int /*offload*/, NeighList *list, +void NPairIntel::bin_newton(const int offload, NeighList *list, IntelBuffers *buffers, const int astart, const int aend, - const int /*offload_end*/) { + const int offload_end) { if (aend-astart == 0) return; @@ -71,7 +120,7 @@ void NPairIntel::bin_newton(const int /*offload*/, NeighList *list, const int pack_width = _fix->nbor_pack_width(); const ATOM_T * _noalias const x = buffers->get_x(); - int * _noalias const firstneigh = buffers->firstneigh(list); + int * _noalias const intel_list = buffers->intel_list(list); const int e_nall = nall_t; const int molecular = atom->molecular; @@ -94,8 +143,10 @@ void NPairIntel::bin_newton(const int /*offload*/, NeighList *list, const tagint * _noalias const tag = atom->tag; int * _noalias const ilist = list->ilist; - int * _noalias numneigh = list->numneigh; - int * _noalias const cnumneigh = buffers->cnumneigh(list); + int ** _noalias const firstneigh = list->firstneigh; + int * _noalias const numneigh = list->numneigh; + int * _noalias const cnumneigh = buffers->cnumneigh(); + const int nstencil = this->nstencil; const int * _noalias const stencil = this->stencil; const flt_t * _noalias const cutneighsq = buffers->get_cutneighsq()[0]; @@ -168,6 +219,7 @@ void NPairIntel::bin_newton(const int /*offload*/, NeighList *list, in(binhead:length(mbins+1) alloc_if(0) free_if(0)) \ in(cutneighsq:length(0) alloc_if(0) free_if(0)) \ in(firstneigh:length(0) alloc_if(0) free_if(0)) \ + in(intel_list:length(0) alloc_if(0) free_if(0)) \ in(cnumneigh:length(0) alloc_if(0) free_if(0)) \ out(numneigh:length(0) alloc_if(0) free_if(0)) \ in(ilist:length(0) alloc_if(0) free_if(0)) \ @@ -178,7 +230,7 @@ void NPairIntel::bin_newton(const int /*offload*/, NeighList *list, in(ncache_stride,maxnbors,nthreads,maxspecial,nstencil,e_nall,offload) \ in(offload_end,separate_buffers,astart,aend,nlocal,molecular) \ in(ntypes,xperiodic,yperiodic,zperiodic,xprd_half,yprd_half,zprd_half) \ - in(pack_width,special_bound) \ + in(pack_width,special_bound) \ out(overflow:length(5) alloc_if(0) free_if(0)) \ out(timer_compute:length(1) alloc_if(0) free_if(0)) \ signal(tag) @@ -212,7 +264,7 @@ void NPairIntel::bin_newton(const int /*offload*/, NeighList *list, #if defined(_OPENMP) #pragma omp parallel default(none) \ - shared(numneigh, overflow, nstencilp, binstart, binend) + shared(overflow, nstencilp, binstart, binend) #endif { #ifdef _LMP_INTEL_OFFLOAD @@ -246,7 +298,7 @@ void NPairIntel::bin_newton(const int /*offload*/, NeighList *list, const int obound = maxnbors * 3; #endif int ct = (ifrom + tid * 2) * maxnbors; - int *neighptr = firstneigh + ct; + int *neighptr = intel_list + ct; int *neighptr2; if (THREE) neighptr2 = neighptr; @@ -605,12 +657,24 @@ void NPairIntel::bin_newton(const int /*offload*/, NeighList *list, if (n > maxnbors) *overflow = 1; ilist[i] = i; - cnumneigh[i] = ct; + firstneigh[i] = intel_list + ct; if (THREE) { + numneigh[i] = ns; + cnumneigh[i] = ct; #ifdef LMP_INTEL_3BODY_FAST cnumneigh[i] += lane; + #else + // Pad anyways just in case we have hybrid with 2-body and newton off + int pad_end = ns; + IP_PRE_neighbor_pad(pad_end, offload); + #if defined(LMP_SIMD_COMPILER) + #pragma vector aligned + #pragma loop_count min=1, max=INTEL_COMPILE_WIDTH-1, \ + avg=INTEL_COMPILE_WIDTH/2 + #endif + for ( ; ns < pad_end; ns++) + neighptr[n++] = e_nall; #endif - numneigh[i] = ns; } else { numneigh[i] = n; int pad_end = n; @@ -631,7 +695,7 @@ void NPairIntel::bin_newton(const int /*offload*/, NeighList *list, if (lane == pack_width) { ct += max_chunk * pack_width; IP_PRE_edge_align(ct, sizeof(int)); - neighptr = firstneigh + ct; + neighptr = intel_list + ct; neighptr2 = neighptr; max_chunk = 0; lane = 0; @@ -647,7 +711,7 @@ void NPairIntel::bin_newton(const int /*offload*/, NeighList *list, { ct += n; //IP_PRE_edge_align(ct, sizeof(int)); - neighptr = firstneigh + ct; + neighptr = intel_list + ct; if (THREE) neighptr2 = neighptr; if (ct + obound > list_size) { if (i < ito - 1) { @@ -667,7 +731,7 @@ void NPairIntel::bin_newton(const int /*offload*/, NeighList *list, int ghost_offset = 0, nall_offset = e_nall; if (separate_buffers) { for (int i = ifrom; i < ito; ++i) { - int * _noalias jlist = firstneigh + cnumneigh[i]; + int * _noalias jlist = firstneigh[i]; int jnum = numneigh[i]; if (!THREE) IP_PRE_neighbor_pad(jnum, offload); #if __INTEL_COMPILER+0 > 1499 @@ -712,7 +776,7 @@ void NPairIntel::bin_newton(const int /*offload*/, NeighList *list, } for (int i = ifrom; i < ito; ++i) { - int * _noalias jlist = firstneigh + cnumneigh[i]; + int * _noalias jlist = firstneigh[i]; int jnum = numneigh[i]; if (!THREE) IP_PRE_neighbor_pad(jnum, offload); int jj = 0; @@ -739,13 +803,12 @@ void NPairIntel::bin_newton(const int /*offload*/, NeighList *list, if (offload) { _fix->stop_watch(TIME_OFFLOAD_LATENCY); _fix->start_watch(TIME_HOST_NEIGHBOR); + firstneigh[0] = intel_list; for (int n = 0; n < aend; n++) { ilist[n] = n; numneigh[n] = 0; } } else { - for (int i = astart; i < aend; i++) - list->firstneigh[i] = firstneigh + cnumneigh[i]; if (separate_buffers) { _fix->start_watch(TIME_PACK); _fix->set_neighbor_host_sizes(); @@ -756,11 +819,6 @@ void NPairIntel::bin_newton(const int /*offload*/, NeighList *list, _fix->stop_watch(TIME_PACK); } } - #else - #pragma vector aligned - #pragma simd - for (int i = astart; i < aend; i++) - list->firstneigh[i] = firstneigh + cnumneigh[i]; #endif } diff --git a/src/USER-INTEL/npair_intel.h b/src/USER-INTEL/npair_intel.h index 55a529b2cb..e47687abea 100644 --- a/src/USER-INTEL/npair_intel.h +++ b/src/USER-INTEL/npair_intel.h @@ -75,7 +75,8 @@ class NPairIntel : public NPair { public: NPairIntel(class LAMMPS *); ~NPairIntel(); - + virtual void copy_neighbor_info(); + #ifdef _LMP_INTEL_OFFLOAD void grow_stencil(); #endif @@ -83,6 +84,9 @@ class NPairIntel : public NPair { protected: FixIntel *_fix; + template + void copy_cutsq_info(IntelBuffers *); + template void bin_newton(const int, NeighList *, IntelBuffers *, const int, const int, const int offload_end = 0); diff --git a/src/USER-INTEL/npair_skip_intel.cpp b/src/USER-INTEL/npair_skip_intel.cpp new file mode 100644 index 0000000000..3d2463a0b9 --- /dev/null +++ b/src/USER-INTEL/npair_skip_intel.cpp @@ -0,0 +1,230 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: W. Michael Brown (Intel) +------------------------------------------------------------------------- */ + +#include "npair_skip_intel.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "atom.h" +#include "atom_vec.h" +#include "comm.h" +#include "modify.h" +#include "molecule.h" +#include "neigh_request.h" +#include "domain.h" +#include "my_page.h" +#include "error.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +NPairSkipIntel::NPairSkipIntel(LAMMPS *lmp) : NPair(lmp) { + int ifix = modify->find_fix("package_intel"); + if (ifix < 0) + error->all(FLERR, + "The 'package intel' command is required for /intel styles"); + _fix = static_cast(modify->fix[ifix]); + _inum_starts = new int[comm->nthreads]; + _inum_counts = new int[comm->nthreads]; + _full_props = 0; +} + +/* ---------------------------------------------------------------------- */ + +NPairSkipIntel::~NPairSkipIntel() { + delete []_inum_starts; + delete []_inum_counts; + if (_full_props) delete []_full_props; +} + +/* ---------------------------------------------------------------------- */ + +void NPairSkipIntel::copy_neighbor_info() +{ + NPair::copy_neighbor_info(); + if (_full_props) delete []_full_props; + _full_props = new int[neighbor->nlist]; + for (int i = 0; i < neighbor->nlist; i++) + _full_props[i] = neighbor->requests[i]->full; +} + +/* ---------------------------------------------------------------------- + build skip list for subset of types from parent list + works for half and full lists + works for owned (non-ghost) list, also for ghost list + iskip and ijskip flag which atom types and type pairs to skip + if ghost, also store neighbors of ghost atoms & set inum,gnum correctly +------------------------------------------------------------------------- */ + +template +void NPairSkipIntel::build_t(NeighList *list, int *numhalf, int *cnumneigh, + int *numhalf_skip) +{ + const int nlocal = atom->nlocal; + const int e_nall = nlocal + atom->nghost; + const int * _noalias const type = atom->type; + int * _noalias const ilist = list->ilist; + int * _noalias const numneigh = list->numneigh; + int ** _noalias const firstneigh = (int ** const)list->firstneigh; + const int * _noalias const ilist_skip = list->listskip->ilist; + const int * _noalias const numneigh_skip = list->listskip->numneigh; + const int ** _noalias const firstneigh_skip = + (const int ** const)list->listskip->firstneigh; + const int * _noalias const iskip = list->iskip; + const int ** _noalias const ijskip = (const int ** const)list->ijskip; + + int num_skip = list->listskip->inum; + if (list->ghost) num_skip += list->listskip->gnum; + + int packthreads; + if (comm->nthreads > INTEL_HTHREADS && THREE==0) + packthreads = comm->nthreads; + else + packthreads = 1; + + #if defined(_OPENMP) + #pragma omp parallel if(packthreads > 1) + #endif + { + int tid, ifrom, ito; + IP_PRE_omp_range_id(ifrom, ito, tid, num_skip, packthreads); + + // each thread has its own page allocator + MyPage &ipage = list->ipage[tid]; + ipage.reset(); + + int my_inum = ifrom; + _inum_starts[tid] = ifrom; + + // loop over parent full list + for (int ii = ifrom; ii < ito; ii++) { + const int i = ilist_skip[ii]; + const int itype = type[i]; + if (iskip[itype]) continue; + + int n = 0; + int *neighptr = ipage.vget(); + + // loop over parent non-skip list + + const int * _noalias const jlist = firstneigh_skip[i]; + const int jnum = numneigh_skip[i]; + + if (THREE) { + const int jnumhalf = numhalf_skip[ii]; + for (int jj = 0; jj < jnumhalf; jj++) { + const int joriginal = jlist[jj]; + const int j = joriginal & NEIGHMASK; + if (!ijskip[itype][type[j]]) neighptr[n++] = joriginal; + } + numhalf[my_inum] = n; + + for (int jj = jnumhalf; jj < jnum; jj++) { + const int joriginal = jlist[jj]; + const int j = joriginal & NEIGHMASK; + if (!ijskip[itype][type[j]]) neighptr[n++] = joriginal; + } + } else { + #if defined(LMP_SIMD_COMPILER) + #pragma vector aligned + #pragma ivdep + #endif + for (int jj = 0; jj < jnum; jj++) { + const int joriginal = jlist[jj]; + const int j = joriginal & NEIGHMASK; + if (!ijskip[itype][type[j]]) neighptr[n++] = joriginal; + } + } + + ilist[my_inum++] = i; + firstneigh[i] = neighptr; + numneigh[i] = n; + + int pad_end = n; + IP_PRE_neighbor_pad(pad_end, 0); + #if defined(LMP_SIMD_COMPILER) + #pragma vector aligned + #pragma loop_count min=1, max=INTEL_COMPILE_WIDTH-1, \ + avg=INTEL_COMPILE_WIDTH/2 + #endif + for ( ; n < pad_end; n++) + neighptr[n] = e_nall; + + ipage.vgot(n); + if (ipage.status()) + error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); + } + + int last_inum = 0, loop_end; + _inum_counts[tid] = my_inum; + } + int inum = _inum_counts[0]; + for (int tid = 1; tid < packthreads; tid++) { + for (int i = _inum_starts[tid]; i < _inum_counts[tid]; i++) { + if (THREE) numhalf[inum] = numhalf[i]; + ilist[inum++] = ilist[i]; + } + } + list->inum = inum; + + if (THREE && num_skip > 0) { + int * const list_start = firstneigh[ilist[0]]; + for (int ii = 0; ii < inum; ii++) { + int i = ilist[ii]; + cnumneigh[ii] = static_cast(firstneigh[i] - list_start); + } + } + if (list->ghost) { + int num = 0; + int my_inum = list->inum; + for (int i = 0; i < my_inum; i++) + if (ilist[i] < nlocal) num++; + else break; + list->inum = num; + list->gnum = my_inum - num; + } +} + +/* ---------------------------------------------------------------------- */ + +void NPairSkipIntel::build(NeighList *list) +{ + if (_fix->three_body_neighbor()==0 || + _full_props[list->listskip->index] == 0) { + if (_fix->precision() == FixIntel::PREC_MODE_MIXED) + build_t(list, 0, 0, 0); + else if (_fix->precision() == FixIntel::PREC_MODE_DOUBLE) + build_t(list, 0, 0, 0); + else + build_t(list, 0, 0, 0); + } else { + int *nhalf, *cnumneigh, *nhalf_skip, *u; + if (_fix->precision() == FixIntel::PREC_MODE_MIXED) { + _fix->get_mixed_buffers()->get_list_data3(list->listskip,nhalf_skip,u); + _fix->get_mixed_buffers()->grow_data3(list, nhalf, cnumneigh); + build_t(list, nhalf, cnumneigh, nhalf_skip); + } else if (_fix->precision() == FixIntel::PREC_MODE_DOUBLE) { + _fix->get_double_buffers()->get_list_data3(list->listskip,nhalf_skip,u); + _fix->get_double_buffers()->grow_data3(list, nhalf, cnumneigh); + build_t(list, nhalf, cnumneigh, nhalf_skip); + } else { + _fix->get_single_buffers()->get_list_data3(list->listskip,nhalf_skip,u); + _fix->get_single_buffers()->grow_data3(list,nhalf,cnumneigh); + build_t(list, nhalf, cnumneigh, nhalf_skip); + } + } +} diff --git a/src/USER-INTEL/npair_skip_intel.h b/src/USER-INTEL/npair_skip_intel.h new file mode 100644 index 0000000000..e3277708d5 --- /dev/null +++ b/src/USER-INTEL/npair_skip_intel.h @@ -0,0 +1,69 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef NPAIR_CLASS + +NPairStyle(skip/intel, + NPairSkipIntel, + NP_SKIP | NP_HALF | NP_FULL | + NP_NSQ | NP_BIN | NP_MULTI | + NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_INTEL) + +NPairStyle(skip/ghost/intel, + NPairSkipIntel, + NP_SKIP | NP_HALF | NP_FULL | + NP_NSQ | NP_BIN | NP_MULTI | + NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_GHOST | NP_INTEL) + +#else + +#ifndef LMP_NPAIR_SKIP_INTEL_H +#define LMP_NPAIR_SKIP_INTEL_H + +#include "npair.h" +#include "fix_intel.h" + +#if defined(_OPENMP) +#include +#endif + + +namespace LAMMPS_NS { + +class NPairSkipIntel : public NPair { + public: + NPairSkipIntel(class LAMMPS *); + ~NPairSkipIntel(); + virtual void copy_neighbor_info(); + void build(class NeighList *); + + protected: + FixIntel *_fix; + int *_inum_starts, *_inum_counts, *_full_props; + + template + void build_t(NeighList *, int *numhalf, int *cnumneigh, int *numhalf_skip); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: The 'package intel' command is required for /intel styles + +Self explanatory. + +*/ diff --git a/src/USER-INTEL/pair_airebo_intel.cpp b/src/USER-INTEL/pair_airebo_intel.cpp index 601144a3c0..198f8798fa 100644 --- a/src/USER-INTEL/pair_airebo_intel.cpp +++ b/src/USER-INTEL/pair_airebo_intel.cpp @@ -97,6 +97,13 @@ struct LAMMPS_NS::PairAIREBOIntelParam { namespace { +struct NeighListLMPAIREBO { + int * num; /* num_all */ + int * num_half; /* num_all */ + int * offset; /* num_all */ + int ** entries; /* num_all * num_neighs_per_atom */ +}; + struct NeighListAIREBO { int * num; /* num_all */ int * num_half; /* num_all */ @@ -125,7 +132,7 @@ struct KernelArgsAIREBOT { int neigh_from_atom, neigh_to_atom; int rebuild_flag; flt_t skin; - struct NeighListAIREBO neigh_lmp; + struct NeighListLMPAIREBO neigh_lmp; struct NeighListAIREBO neigh_rebo; PairAIREBOIntelParam params; struct AtomAIREBOT * x; /* num_all */ @@ -176,6 +183,11 @@ void PairAIREBOIntel::init_style() PairAIREBO::init_style(); neighbor->requests[neighbor->nrequest-1]->intel = 1; + const int nrequest = neighbor->nrequest; + for (int i = 0; i < nrequest; ++i) + if (neighbor->requests[i]->skip) + error->all(FLERR, "Cannot yet use airebo/intel with hybrid."); + int ifix = modify->find_fix("package_intel"); if (ifix < 0) error->all(FLERR, @@ -399,8 +411,7 @@ void PairAIREBOIntel::eval( ATOM_T * _noalias const x = buffers->get_x(offload); const int * _noalias const numneighhalf = buffers->get_atombin(); const int * _noalias const numneigh = list->numneigh; - const int * _noalias const cnumneigh = buffers->cnumneigh(list); - const int * _noalias const firstneigh = buffers->firstneigh(list); + const int ** _noalias const firstneigh = (const int **)list->firstneigh; tagint * const tag = atom->tag; const int ntypes = atom->ntypes + 1; @@ -441,7 +452,6 @@ void PairAIREBOIntel::eval( #pragma offload target(mic:_cop) if(offload) \ in(firstneigh:length(0) alloc_if(0) free_if(0)) \ - in(cnumneigh:length(0) alloc_if(0) free_if(0)) \ in(numneigh:length(0) alloc_if(0) free_if(0)) \ in(numneighhalf:length(0) alloc_if(0) free_if(0)) \ in(x:length(x_size) alloc_if(0) free_if(0)) \ @@ -472,10 +482,8 @@ void PairAIREBOIntel::eval( f_stride, x, 0/*q*/); acc_t oevdwl, oecoul, ov0, ov1, ov2, ov3, ov4, ov5; - if (EVFLAG) { - oevdwl = oecoul = (acc_t)0; - if (vflag) ov0 = ov1 = ov2 = ov3 = ov4 = ov5 = (acc_t)0; - } + if (EVFLAG) + oevdwl = oecoul = ov0 = ov1 = ov2 = ov3 = ov4 = ov5 = (acc_t)0; // loop over neighbors of my atoms #if defined(_OPENMP) @@ -508,8 +516,7 @@ void PairAIREBOIntel::eval( args.skin = skin; args.neigh_lmp.num = const_cast(numneigh); args.neigh_lmp.num_half = const_cast(numneighhalf); - args.neigh_lmp.offset = const_cast(cnumneigh); - args.neigh_lmp.entries = const_cast(firstneigh); + args.neigh_lmp.entries = const_cast(firstneigh); args.neigh_rebo.num = REBO_numneigh; args.neigh_rebo.num_half = REBO_num_skin; args.neigh_rebo.offset = REBO_cnumneigh; @@ -543,18 +550,14 @@ void PairAIREBOIntel::eval( IP_PRE_fdotr_reduce(1, nall, nthreads, f_stride, vflag, ov0, ov1, ov2, ov3, ov4, ov5); if (EVFLAG) { - if (EFLAG) { - ev_global[0] = oevdwl; - ev_global[1] = oecoul; - } - if (vflag) { - ev_global[2] = ov0; - ev_global[3] = ov1; - ev_global[4] = ov2; - ev_global[5] = ov3; - ev_global[6] = ov4; - ev_global[7] = ov5; - } + ev_global[0] = oevdwl; + ev_global[1] = oecoul; + ev_global[2] = ov0; + ev_global[3] = ov1; + ev_global[4] = ov2; + ev_global[5] = ov3; + ev_global[6] = ov4; + ev_global[7] = ov5; } #if defined(__MIC__) && defined(_LMP_INTEL_OFFLOAD) *timer_compute = MIC_Wtime() - *timer_compute; @@ -578,28 +581,20 @@ template void PairAIREBOIntel::pack_force_const(IntelBuffers * buffers) { int tp1 = atom->ntypes + 1; - buffers->set_ntypes(tp1,1); - flt_t **cutneighsq = buffers->get_cutneighsq(); - flt_t **cutneighghostsq = buffers->get_cutneighghostsq(); - // Repeat cutsq calculation because done after call to init_style - double cut, cutneigh; for (int i = 1; i <= atom->ntypes; i++) { for (int j = i; j <= atom->ntypes; j++) { - if (setflag[i][j] != 0 || (setflag[i][i] != 0 && setflag[j][j] != 0)) { + double cut; + if (setflag[i][j] != 0 || (setflag[i][i] != 0 && setflag[j][j] != 0)) cut = init_one(i, j); - cutneigh = cut + neighbor->skin; - cutsq[i][j] = cutsq[j][i] = cut*cut; - cutneighsq[i][j] = cutneighsq[j][i] = cutneigh * cutneigh; - cut = cutghost[i][j] + neighbor->skin; - cutneighghostsq[i][j] = cutneighghostsq[j][i] = cut*cut; - } + else + cut = 0.0; + cutsq[i][j] = cutsq[j][i] = cut*cut; } } #ifdef _LMP_INTEL_OFFLOAD if (_cop < 0) return; - flt_t * ocutneighsq = cutneighsq[0]; size_t VL = 512 / 8 / sizeof(flt_t); int ntypes = tp1; int tp1sq = tp1 * tp1; @@ -607,7 +602,6 @@ void PairAIREBOIntel::pack_force_const(IntelBuffers * buffers) { // it might not be freed if this method is called more than once int * map = this->map; #pragma offload_transfer target(mic:_cop) \ - in(ocutneighsq: length(tp1sq) alloc_if(0) free_if(0)) \ in(map: length(tp1) alloc_if(1) free_if(0)) #endif @@ -1580,7 +1574,7 @@ void ref_rebo_neigh(KernelArgsAIREBOT * ka) { ka->nC[i] = 0; ka->nH[i] = 0; for (int j = 0; j < ka->neigh_lmp.num[i]; j++) { - int ji = ka->neigh_lmp.entries[ka->neigh_lmp.offset[i] + j]; + int ji = ka->neigh_lmp.entries[i][j]; flt_t delx = ka->x[i].x - ka->x[ji].x; flt_t dely = ka->x[i].y - ka->x[ji].y; flt_t delz = ka->x[i].z - ka->x[ji].z; @@ -2168,7 +2162,7 @@ void ref_lennard_jones_single_atom(KernelArgsAIREBOT * ka, int i, int morseflag) { AtomAIREBOT * x = ka->x; int jj; - int * neighs = ka->neigh_lmp.entries + ka->neigh_lmp.offset[i]; + int * neighs = ka->neigh_lmp.entries[i]; int jnum = ka->neigh_lmp.num_half[i]; for (jj = 0; jj < jnum; jj++) { int j = neighs[jj]; @@ -2332,7 +2326,7 @@ static void aut_rebo_neigh(KernelArgsAIREBOT * ka) { int jnum = ka->rebuild_flag ? ka->neigh_lmp.num[i] : ka->neigh_rebo.num_half[i]; int * neighs = ka->rebuild_flag ? - &ka->neigh_lmp.entries[ka->neigh_lmp.offset[i]] : + ka->neigh_lmp.entries[i] : &ka->neigh_rebo.entries[ka->neigh_rebo.offset[i]+jnum]; int * skin_target = &ka->neigh_rebo.entries[offset+ka->num_neighs_per_atom]; int n = 0; @@ -4554,7 +4548,7 @@ static void aut_lennard_jones(KernelArgsAIREBOT * ka) { fvec p_lj40 = fvec::set1(ka->params.lj4[itype][0]); fvec p_lj41 = fvec::set1(ka->params.lj4[itype][1]); - int * neighs = ka->neigh_lmp.entries + ka->neigh_lmp.offset[i]; + int * neighs = ka->neigh_lmp.entries[i]; int jnum = ka->neigh_lmp.num_half[i]; bool tap_success = aut_airebo_lj_test_all_paths(ka, i, &test_path_result); diff --git a/src/USER-INTEL/pair_airebo_intel.h b/src/USER-INTEL/pair_airebo_intel.h index 2d32925f68..8a319536de 100644 --- a/src/USER-INTEL/pair_airebo_intel.h +++ b/src/USER-INTEL/pair_airebo_intel.h @@ -107,4 +107,10 @@ E: Cannot open AIREBO potential file %s The specified AIREBO potential file cannot be opened. Check that the path and name are correct. +E: Cannot yet use airebo/intel with hybrid. + +Pair style airebo/intel cannot currently be used as part of a hybrid +pair style (with the exception of hybrid/overlay). + + */ diff --git a/src/USER-INTEL/pair_buck_coul_cut_intel.cpp b/src/USER-INTEL/pair_buck_coul_cut_intel.cpp index 39fa9014db..3954d559e1 100644 --- a/src/USER-INTEL/pair_buck_coul_cut_intel.cpp +++ b/src/USER-INTEL/pair_buck_coul_cut_intel.cpp @@ -144,8 +144,7 @@ void PairBuckCoulCutIntel::eval(const int offload, const int vflag, const int * _noalias const ilist = list->ilist; const int * _noalias const numneigh = list->numneigh; - const int * _noalias const cnumneigh = buffers->cnumneigh(list); - const int * _noalias const firstneigh = buffers->firstneigh(list); + const int ** _noalias const firstneigh = (const int **)list->firstneigh; const flt_t * _noalias const special_coul = fc.special_coul; const flt_t * _noalias const special_lj = fc.special_lj; @@ -182,7 +181,6 @@ void PairBuckCoulCutIntel::eval(const int offload, const int vflag, in(special_lj,special_coul:length(0) alloc_if(0) free_if(0)) \ in(c_force, c_energy, c_cut:length(0) alloc_if(0) free_if(0)) \ in(firstneigh:length(0) alloc_if(0) free_if(0)) \ - in(cnumneigh:length(0) alloc_if(0) free_if(0)) \ in(numneigh:length(0) alloc_if(0) free_if(0)) \ in(x:length(x_size) alloc_if(0) free_if(0)) \ in(q:length(q_size) alloc_if(0) free_if(0)) \ @@ -204,8 +202,10 @@ void PairBuckCoulCutIntel::eval(const int offload, const int vflag, f_stride, x, q); acc_t oevdwl, oecoul, ov0, ov1, ov2, ov3, ov4, ov5; - if (EFLAG) oevdwl = oecoul = (acc_t)0; - if (vflag) ov0 = ov1 = ov2 = ov3 = ov4 = ov5 = (acc_t)0; + if (EFLAG || vflag) + oevdwl = oecoul = ov0 = ov1 = ov2 = ov3 = ov4 = ov5 = (acc_t)0; + if (NEWTON_PAIR == 0 && inum != nlocal) + memset(f_start, 0, f_stride * sizeof(FORCE_T)); // loop over neighbors of my atoms #if defined(_OPENMP) @@ -231,8 +231,8 @@ void PairBuckCoulCutIntel::eval(const int offload, const int vflag, const C_FORCE_T * _noalias const c_forcei = c_force + ptr_off; const C_ENERGY_T * _noalias const c_energyi = c_energy + ptr_off; const C_CUT_T * _noalias const c_cuti = c_cut + ptr_off; - const int * _noalias const jlist = firstneigh + cnumneigh[ii]; - int jnum = numneigh[ii]; + const int * _noalias const jlist = firstneigh[i]; + int jnum = numneigh[i]; IP_PRE_neighbor_pad(jnum, offload); acc_t fxtmp,fytmp,fztmp,fwtmp; @@ -361,13 +361,10 @@ void PairBuckCoulCutIntel::eval(const int offload, const int vflag, IP_PRE_fdotr_reduce(NEWTON_PAIR, nall, nthreads, f_stride, vflag, ov0, ov1, ov2, ov3, ov4, ov5); - if (EFLAG) { - if (NEWTON_PAIR == 0) oevdwl *= (acc_t)0.5; - ev_global[0] = oevdwl; - ev_global[1] = oecoul; - } - if (vflag) { + if (EFLAG || vflag) { if (NEWTON_PAIR == 0) { + oevdwl *= (acc_t)0.5; + oecoul *= (acc_t)0.5; ov0 *= (acc_t)0.5; ov1 *= (acc_t)0.5; ov2 *= (acc_t)0.5; @@ -375,6 +372,8 @@ void PairBuckCoulCutIntel::eval(const int offload, const int vflag, ov4 *= (acc_t)0.5; ov5 *= (acc_t)0.5; } + ev_global[0] = oevdwl; + ev_global[1] = oecoul; ev_global[2] = ov0; ev_global[3] = ov1; ev_global[4] = ov2; @@ -439,19 +438,16 @@ void PairBuckCoulCutIntel::pack_force_const(ForceConst &fc, for (int i = 0; i < ncoultablebits; i++) ntable *= 2; fc.set_ntypes(tp1, ntable, memory, _cop); - buffers->set_ntypes(tp1); - flt_t **cutneighsq = buffers->get_cutneighsq(); // Repeat cutsq calculation because done after call to init_style - double cut, cutneigh; for (int i = 1; i <= atom->ntypes; i++) { for (int j = i; j <= atom->ntypes; j++) { - if (setflag[i][j] != 0 || (setflag[i][i] != 0 && setflag[j][j] != 0)) { + double cut; + if (setflag[i][j] != 0 || (setflag[i][i] != 0 && setflag[j][j] != 0)) cut = init_one(i, j); - cutneigh = cut + neighbor->skin; - cutsq[i][j] = cutsq[j][i] = cut*cut; - cutneighsq[i][j] = cutneighsq[j][i] = cutneigh * cutneigh; - } + else + cut = 0.0; + cutsq[i][j] = cutsq[j][i] = cut*cut; } } @@ -483,12 +479,10 @@ void PairBuckCoulCutIntel::pack_force_const(ForceConst &fc, C_FORCE_T * c_force = fc.c_force[0]; C_ENERGY_T * c_energy = fc.c_energy[0]; C_CUT_T * c_cut = fc.c_cut[0]; - flt_t * ocutneighsq = cutneighsq[0]; int tp1sq = tp1 * tp1; #pragma offload_transfer target(mic:_cop) \ in(special_lj, special_coul: length(4) alloc_if(0) free_if(0)) \ - in(c_force, c_energy, c_cut: length(tp1sq) alloc_if(0) free_if(0)) \ - in(ocutneighsq: length(tp1sq) alloc_if(0) free_if(0)) + in(c_force, c_energy, c_cut: length(tp1sq) alloc_if(0) free_if(0)) #endif } diff --git a/src/USER-INTEL/pair_buck_coul_long_intel.cpp b/src/USER-INTEL/pair_buck_coul_long_intel.cpp index fe4d408a13..059413c3d9 100644 --- a/src/USER-INTEL/pair_buck_coul_long_intel.cpp +++ b/src/USER-INTEL/pair_buck_coul_long_intel.cpp @@ -144,8 +144,7 @@ void PairBuckCoulLongIntel::eval(const int offload, const int vflag, const int * _noalias const ilist = list->ilist; const int * _noalias const numneigh = list->numneigh; - const int * _noalias const cnumneigh = buffers->cnumneigh(list); - const int * _noalias const firstneigh = buffers->firstneigh(list); + const int ** _noalias const firstneigh = (const int **)list->firstneigh; const flt_t * _noalias const special_coul = fc.special_coul; const flt_t * _noalias const special_lj = fc.special_lj; @@ -206,7 +205,6 @@ void PairBuckCoulLongIntel::eval(const int offload, const int vflag, in(c_force, c_energy:length(0) alloc_if(0) free_if(0)) \ in(rho_inv:length(0) alloc_if(0) free_if(0)) \ in(firstneigh:length(0) alloc_if(0) free_if(0)) \ - in(cnumneigh:length(0) alloc_if(0) free_if(0)) \ in(numneigh:length(0) alloc_if(0) free_if(0)) \ in(x:length(x_size) alloc_if(0) free_if(0)) \ in(q:length(q_size) alloc_if(0) free_if(0)) \ @@ -230,8 +228,10 @@ void PairBuckCoulLongIntel::eval(const int offload, const int vflag, f_stride, x, q); acc_t oevdwl, oecoul, ov0, ov1, ov2, ov3, ov4, ov5; - if (EFLAG) oevdwl = oecoul = (acc_t)0; - if (vflag) ov0 = ov1 = ov2 = ov3 = ov4 = ov5 = (acc_t)0; + if (EFLAG || vflag) + oevdwl = oecoul = ov0 = ov1 = ov2 = ov3 = ov4 = ov5 = (acc_t)0; + if (NEWTON_PAIR == 0 && inum != nlocal) + memset(f_start, 0, f_stride * sizeof(FORCE_T)); // loop over neighbors of my atoms #if defined(_OPENMP) @@ -265,8 +265,8 @@ void PairBuckCoulLongIntel::eval(const int offload, const int vflag, const C_ENERGY_T * _noalias const c_energyi = c_energy + ptr_off; const flt_t * _noalias const rho_invi = rho_inv + ptr_off; - const int * _noalias const jlist = firstneigh + cnumneigh[ii]; - int jnum = numneigh[ii]; + const int * _noalias const jlist = firstneigh[i]; + int jnum = numneigh[i]; IP_PRE_neighbor_pad(jnum, offload); acc_t fxtmp,fytmp,fztmp,fwtmp; @@ -437,13 +437,10 @@ void PairBuckCoulLongIntel::eval(const int offload, const int vflag, IP_PRE_fdotr_reduce(NEWTON_PAIR, nall, nthreads, f_stride, vflag, ov0, ov1, ov2, ov3, ov4, ov5); - if (EFLAG) { - if (NEWTON_PAIR == 0) oevdwl *= (acc_t)0.5; - ev_global[0] = oevdwl; - ev_global[1] = oecoul; - } - if (vflag) { + if (EFLAG || vflag) { if (NEWTON_PAIR == 0) { + oevdwl *= (acc_t)0.5; + oecoul *= (acc_t)0.5; ov0 *= (acc_t)0.5; ov1 *= (acc_t)0.5; ov2 *= (acc_t)0.5; @@ -451,6 +448,8 @@ void PairBuckCoulLongIntel::eval(const int offload, const int vflag, ov4 *= (acc_t)0.5; ov5 *= (acc_t)0.5; } + ev_global[0] = oevdwl; + ev_global[1] = oecoul; ev_global[2] = ov0; ev_global[3] = ov1; ev_global[4] = ov2; @@ -523,19 +522,16 @@ void PairBuckCoulLongIntel::pack_force_const(ForceConst &fc, for (int i = 0; i < ncoultablebits; i++) ntable *= 2; fc.set_ntypes(tp1, ntable, memory, _cop); - buffers->set_ntypes(tp1); - flt_t **cutneighsq = buffers->get_cutneighsq(); // Repeat cutsq calculation because done after call to init_style - double cut, cutneigh; for (int i = 1; i <= atom->ntypes; i++) { for (int j = i; j <= atom->ntypes; j++) { - if (setflag[i][j] != 0 || (setflag[i][i] != 0 && setflag[j][j] != 0)) { + double cut; + if (setflag[i][j] != 0 || (setflag[i][i] != 0 && setflag[j][j] != 0)) cut = init_one(i, j); - cutneigh = cut + neighbor->skin; - cutsq[i][j] = cutsq[j][i] = cut*cut; - cutneighsq[i][j] = cutneighsq[j][i] = cutneigh * cutneigh; - } + else + cut = 0.0; + cutsq[i][j] = cutsq[j][i] = cut*cut; } } @@ -591,15 +587,13 @@ void PairBuckCoulLongIntel::pack_force_const(ForceConst &fc, flt_t * detable = fc.detable; flt_t * ctable = fc.ctable; flt_t * dctable = fc.dctable; - flt_t * ocutneighsq = cutneighsq[0]; int tp1sq = tp1 * tp1; #pragma offload_transfer target(mic:_cop) \ in(special_lj, special_coul: length(4) alloc_if(0) free_if(0)) \ in(c_force, c_energy: length(tp1sq) alloc_if(0) free_if(0)) \ in(rho_inv: length(tp1sq) alloc_if(0) free_if(0)) \ in(table: length(ntable) alloc_if(0) free_if(0)) \ - in(etable,detable,ctable,dctable: length(ntable) alloc_if(0) free_if(0)) \ - in(ocutneighsq: length(tp1sq) alloc_if(0) free_if(0)) + in(etable,detable,ctable,dctable: length(ntable) alloc_if(0) free_if(0)) #endif } diff --git a/src/USER-INTEL/pair_buck_intel.cpp b/src/USER-INTEL/pair_buck_intel.cpp index 8ce3d121e0..0e0bd0f56f 100644 --- a/src/USER-INTEL/pair_buck_intel.cpp +++ b/src/USER-INTEL/pair_buck_intel.cpp @@ -135,8 +135,7 @@ void PairBuckIntel::eval(const int offload, const int vflag, const int * _noalias const ilist = list->ilist; const int * _noalias const numneigh = list->numneigh; - const int * _noalias const cnumneigh = buffers->cnumneigh(list); - const int * _noalias const firstneigh = buffers->firstneigh(list); + const int ** _noalias const firstneigh = (const int **)list->firstneigh; const flt_t * _noalias const special_lj = fc.special_lj; const C_FORCE_T * _noalias const c_force = fc.c_force[0]; @@ -167,7 +166,6 @@ void PairBuckIntel::eval(const int offload, const int vflag, in(special_lj:length(0) alloc_if(0) free_if(0)) \ in(c_force, c_energy:length(0) alloc_if(0) free_if(0)) \ in(firstneigh:length(0) alloc_if(0) free_if(0)) \ - in(cnumneigh:length(0) alloc_if(0) free_if(0)) \ in(numneigh:length(0) alloc_if(0) free_if(0)) \ in(x:length(x_size) alloc_if(0) free_if(0)) \ in(ilist:length(0) alloc_if(0) free_if(0)) \ @@ -188,8 +186,10 @@ void PairBuckIntel::eval(const int offload, const int vflag, f_stride, x, 0); acc_t oevdwl, ov0, ov1, ov2, ov3, ov4, ov5; - if (EFLAG) oevdwl = (acc_t)0; - if (vflag) ov0 = ov1 = ov2 = ov3 = ov4 = ov5 = (acc_t)0; + if (EFLAG || vflag) + oevdwl = ov0 = ov1 = ov2 = ov3 = ov4 = ov5 = (acc_t)0; + if (NEWTON_PAIR == 0 && inum != nlocal) + memset(f_start, 0, f_stride * sizeof(FORCE_T)); // loop over neighbors of my atoms #if defined(_OPENMP) @@ -214,8 +214,8 @@ void PairBuckIntel::eval(const int offload, const int vflag, const int ptr_off = itype * ntypes; const C_FORCE_T * _noalias const c_forcei = c_force + ptr_off; const C_ENERGY_T * _noalias const c_energyi = c_energy + ptr_off; - const int * _noalias const jlist = firstneigh + cnumneigh[ii]; - int jnum = numneigh[ii]; + const int * _noalias const jlist = firstneigh[i]; + int jnum = numneigh[i]; IP_PRE_neighbor_pad(jnum, offload); acc_t fxtmp,fytmp,fztmp,fwtmp; @@ -324,13 +324,9 @@ void PairBuckIntel::eval(const int offload, const int vflag, IP_PRE_fdotr_reduce(NEWTON_PAIR, nall, nthreads, f_stride, vflag, ov0, ov1, ov2, ov3, ov4, ov5); - if (EFLAG) { - if (NEWTON_PAIR == 0) oevdwl *= (acc_t)0.5; - ev_global[0] = oevdwl; - ev_global[1] = (acc_t)0; - } - if (vflag) { + if (EFLAG || vflag) { if (NEWTON_PAIR == 0) { + oevdwl *= (acc_t)0.5; ov0 *= (acc_t)0.5; ov1 *= (acc_t)0.5; ov2 *= (acc_t)0.5; @@ -338,6 +334,8 @@ void PairBuckIntel::eval(const int offload, const int vflag, ov4 *= (acc_t)0.5; ov5 *= (acc_t)0.5; } + ev_global[0] = oevdwl; + ev_global[1] = (acc_t)0; ev_global[2] = ov0; ev_global[3] = ov1; ev_global[4] = ov2; @@ -396,19 +394,16 @@ void PairBuckIntel::pack_force_const(ForceConst &fc, int tp1 = atom->ntypes + 1; fc.set_ntypes(tp1, memory, _cop); - buffers->set_ntypes(tp1); - flt_t **cutneighsq = buffers->get_cutneighsq(); // Repeat cutsq calculation because done after call to init_style - double cut, cutneigh; for (int i = 1; i <= atom->ntypes; i++) { for (int j = i; j <= atom->ntypes; j++) { - if (setflag[i][j] != 0 || (setflag[i][i] != 0 && setflag[j][j] != 0)) { + double cut; + if (setflag[i][j] != 0 || (setflag[i][i] != 0 && setflag[j][j] != 0)) cut = init_one(i, j); - cutneigh = cut + neighbor->skin; - cutsq[i][j] = cutsq[j][i] = cut*cut; - cutneighsq[i][j] = cutneighsq[j][i] = cutneigh * cutneigh; - } + else + cut = 0.0; + cutsq[i][j] = cutsq[j][i] = cut*cut; } } @@ -434,12 +429,10 @@ void PairBuckIntel::pack_force_const(ForceConst &fc, flt_t * special_lj = fc.special_lj; C_FORCE_T * c_force = fc.c_force[0]; C_ENERGY_T * c_energy = fc.c_energy[0]; - flt_t * ocutneighsq = cutneighsq[0]; int tp1sq = tp1 * tp1; #pragma offload_transfer target(mic:_cop) \ in(special_lj: length(4) alloc_if(0) free_if(0)) \ - in(c_force, c_energy: length(tp1sq) alloc_if(0) free_if(0)) \ - in(ocutneighsq: length(tp1sq) alloc_if(0) free_if(0)) + in(c_force, c_energy: length(tp1sq) alloc_if(0) free_if(0)) #endif } diff --git a/src/USER-INTEL/pair_dpd_intel.cpp b/src/USER-INTEL/pair_dpd_intel.cpp index 7c33ed21d3..9baa64e8e0 100644 --- a/src/USER-INTEL/pair_dpd_intel.cpp +++ b/src/USER-INTEL/pair_dpd_intel.cpp @@ -173,8 +173,7 @@ void PairDPDIntel::eval(const int offload, const int vflag, const int * _noalias const ilist = list->ilist; const int * _noalias const numneigh = list->numneigh; - const int * _noalias const cnumneigh = buffers->cnumneigh(list); - const int * _noalias const firstneigh = buffers->firstneigh(list); + const int ** _noalias const firstneigh = (const int **)list->firstneigh; const FC_PACKED1_T * _noalias const param = fc.param[0]; const flt_t * _noalias const special_lj = fc.special_lj; int * _noalias const rngi_thread = fc.rngi; @@ -204,8 +203,10 @@ void PairDPDIntel::eval(const int offload, const int vflag, f_stride, x, 0); acc_t oevdwl, ov0, ov1, ov2, ov3, ov4, ov5; - if (EFLAG) oevdwl = (acc_t)0; - if (vflag) ov0 = ov1 = ov2 = ov3 = ov4 = ov5 = (acc_t)0; + if (EFLAG || vflag) + oevdwl = ov0 = ov1 = ov2 = ov3 = ov4 = ov5 = (acc_t)0; + if (NEWTON_PAIR == 0 && inum != nlocal) + memset(f_start, 0, f_stride * sizeof(FORCE_T)); // loop over neighbors of my atoms #if defined(_OPENMP) @@ -233,10 +234,10 @@ void PairDPDIntel::eval(const int offload, const int vflag, flt_t icut, a0, gamma, sigma; if (ONETYPE) { - icut = param[3].icut; - a0 = param[3].a0; - gamma = param[3].gamma; - sigma = param[3].sigma; + icut = param[_onetype].icut; + a0 = param[_onetype].a0; + gamma = param[_onetype].gamma; + sigma = param[_onetype].sigma; } for (int ii = iifrom; ii < iito; ii += iip) { const int i = ilist[ii]; @@ -248,8 +249,8 @@ void PairDPDIntel::eval(const int offload, const int vflag, parami = param + ptr_off; } - const int * _noalias const jlist = firstneigh + cnumneigh[ii]; - int jnum = numneigh[ii]; + const int * _noalias const jlist = firstneigh[i]; + int jnum = numneigh[i]; IP_PRE_neighbor_pad(jnum, offload); acc_t fxtmp, fytmp, fztmp, fwtmp; @@ -379,13 +380,9 @@ void PairDPDIntel::eval(const int offload, const int vflag, IP_PRE_fdotr_reduce(NEWTON_PAIR, nall, nthreads, f_stride, vflag, ov0, ov1, ov2, ov3, ov4, ov5); - if (EFLAG) { - if (NEWTON_PAIR == 0) oevdwl *= (acc_t)0.5; - ev_global[0] = oevdwl; - ev_global[1] = (acc_t)0.0; - } - if (vflag) { + if (EFLAG || vflag) { if (NEWTON_PAIR == 0) { + oevdwl *= (acc_t)0.5; ov0 *= (acc_t)0.5; ov1 *= (acc_t)0.5; ov2 *= (acc_t)0.5; @@ -393,6 +390,8 @@ void PairDPDIntel::eval(const int offload, const int vflag, ov4 *= (acc_t)0.5; ov5 *= (acc_t)0.5; } + ev_global[0] = oevdwl; + ev_global[1] = (acc_t)0.0; ev_global[2] = ov0; ev_global[3] = ov1; ev_global[4] = ov2; @@ -503,32 +502,26 @@ void PairDPDIntel::pack_force_const(ForceConst &fc, IntelBuffers *buffers) { _onetype = 0; - if (atom->ntypes == 1 && !atom->molecular) _onetype = 1; int tp1 = atom->ntypes + 1; fc.set_ntypes(tp1,comm->nthreads,buffers->get_max_nbors(),memory,_cop); - buffers->set_ntypes(tp1); - flt_t **cutneighsq = buffers->get_cutneighsq(); // Repeat cutsq calculation because done after call to init_style - double cut, cutneigh; + int mytypes = 0; for (int i = 1; i <= atom->ntypes; i++) { for (int j = i; j <= atom->ntypes; j++) { if (setflag[i][j] != 0 || (setflag[i][i] != 0 && setflag[j][j] != 0)) { - cut = init_one(i,j); - cutneigh = cut + neighbor->skin; - cutsq[i][j] = cutsq[j][i] = cut*cut; - cutneighsq[i][j] = cutneighsq[j][i] = cutneigh * cutneigh; - double icut = 1.0 / cut; - fc.param[i][j].icut = fc.param[j][i].icut = icut; - } else { - cut = init_one(i,j); - double icut = 1.0 / cut; - fc.param[i][j].icut = fc.param[j][i].icut = icut; + mytypes++; + _onetype = i * tp1 + j; } + double cut = init_one(i,j); + cutsq[i][j] = cutsq[j][i] = cut*cut; + double icut = 1.0 / cut; + fc.param[i][j].icut = fc.param[j][i].icut = icut; } } - + if (mytypes > 1 || atom->molecular) _onetype = 0; + for (int i = 0; i < 4; i++) { fc.special_lj[i] = force->special_lj[i]; fc.special_lj[0] = 1.0; diff --git a/src/USER-INTEL/pair_eam_intel.cpp b/src/USER-INTEL/pair_eam_intel.cpp index ce9ede69d6..95d0272d33 100644 --- a/src/USER-INTEL/pair_eam_intel.cpp +++ b/src/USER-INTEL/pair_eam_intel.cpp @@ -193,8 +193,7 @@ void PairEAMIntel::eval(const int offload, const int vflag, const int * _noalias const ilist = list->ilist; const int * _noalias const numneigh = list->numneigh; - const int * _noalias const cnumneigh = buffers->cnumneigh(list); - const int * _noalias const firstneigh = buffers->firstneigh(list); + const int ** _noalias const firstneigh = (const int **)list->firstneigh; const FC_PACKED1_T * _noalias const rhor_spline_f = fc.rhor_spline_f; const FC_PACKED1_T * _noalias const rhor_spline_e = fc.rhor_spline_e; const FC_PACKED2_T * _noalias const z2r_spline_t = fc.z2r_spline_t; @@ -243,8 +242,10 @@ void PairEAMIntel::eval(const int offload, const int vflag, f_stride, x, 0); acc_t oevdwl, ov0, ov1, ov2, ov3, ov4, ov5; - if (EFLAG) oevdwl = (acc_t)0; - if (vflag) ov0 = ov1 = ov2 = ov3 = ov4 = ov5 = (acc_t)0; + if (EFLAG || vflag) + oevdwl = ov0 = ov1 = ov2 = ov3 = ov4 = ov5 = (acc_t)0; + if (NEWTON_PAIR == 0 && inum != nlocal) + memset(f_start, 0, f_stride * sizeof(FORCE_T)); // loop over neighbors of my atoms #if defined(_OPENMP) @@ -293,8 +294,8 @@ void PairEAMIntel::eval(const int offload, const int vflag, itype = x[i].w; rhor_ioff = istride * itype; } - const int * _noalias const jlist = firstneigh + cnumneigh[ii]; - int jnum = numneigh[ii]; + const int * _noalias const jlist = firstneigh[i]; + int jnum = numneigh[i]; IP_PRE_neighbor_pad(jnum, offload); const flt_t xtmp = x[i].x; @@ -450,8 +451,7 @@ void PairEAMIntel::eval(const int offload, const int vflag, if (tid == 0) comm->forward_comm_pair(this); - if (NEWTON_PAIR) - memset(f + minlocal, 0, f_stride * sizeof(FORCE_T)); + if (NEWTON_PAIR) memset(f + minlocal, 0, f_stride * sizeof(FORCE_T)); #if defined(_OPENMP) #pragma omp barrier @@ -469,8 +469,8 @@ void PairEAMIntel::eval(const int offload, const int vflag, rhor_ioff = istride * itype; scale_fi = scale_f + itype*ntypes; } - const int * _noalias const jlist = firstneigh + cnumneigh[ii]; - int jnum = numneigh[ii]; + const int * _noalias const jlist = firstneigh[i]; + int jnum = numneigh[i]; IP_PRE_neighbor_pad(jnum, offload); acc_t fxtmp, fytmp, fztmp, fwtmp; @@ -597,11 +597,7 @@ void PairEAMIntel::eval(const int offload, const int vflag, IP_PRE_fdotr_reduce(NEWTON_PAIR, nall, nthreads, f_stride, vflag, ov0, ov1, ov2, ov3, ov4, ov5); - if (EFLAG) { - ev_global[0] = oevdwl; - ev_global[1] = (acc_t)0.0; - } - if (vflag) { + if (EFLAG || vflag) { if (NEWTON_PAIR == 0) { ov0 *= (acc_t)0.5; ov1 *= (acc_t)0.5; @@ -610,6 +606,8 @@ void PairEAMIntel::eval(const int offload, const int vflag, ov4 *= (acc_t)0.5; ov5 *= (acc_t)0.5; } + ev_global[0] = oevdwl; + ev_global[1] = (acc_t)0.0; ev_global[2] = ov0; ev_global[3] = ov1; ev_global[4] = ov2; @@ -682,19 +680,16 @@ void PairEAMIntel::pack_force_const(ForceConst &fc, int tp1 = atom->ntypes + 1; fc.set_ntypes(tp1,nr,nrho,memory,_cop); - buffers->set_ntypes(tp1); - flt_t **cutneighsq = buffers->get_cutneighsq(); // Repeat cutsq calculation because done after call to init_style - double cut, cutneigh; for (int i = 1; i <= atom->ntypes; i++) { for (int j = i; j <= atom->ntypes; j++) { - if (setflag[i][j] != 0 || (setflag[i][i] != 0 && setflag[j][j] != 0)) { + double cut; + if (setflag[i][j] != 0 || (setflag[i][i] != 0 && setflag[j][j] != 0)) cut = init_one(i,j); - cutneigh = cut + neighbor->skin; - cutsq[i][j] = cutsq[j][i] = cut*cut; - cutneighsq[i][j] = cutneighsq[j][i] = cutneigh * cutneigh; - } + else + cut = 0.0; + cutsq[i][j] = cutsq[j][i] = cut*cut; } } @@ -733,13 +728,13 @@ void PairEAMIntel::pack_force_const(ForceConst &fc, fc.rhor_spline_e[joff + k].b=rhor_spline[type2rhor[j][i]][k][4]; fc.rhor_spline_e[joff + k].c=rhor_spline[type2rhor[j][i]][k][5]; fc.rhor_spline_e[joff + k].d=rhor_spline[type2rhor[j][i]][k][6]; - fc.z2r_spline_t[joff + k].a=z2r_spline[type2rhor[j][i]][k][0]; - fc.z2r_spline_t[joff + k].b=z2r_spline[type2rhor[j][i]][k][1]; - fc.z2r_spline_t[joff + k].c=z2r_spline[type2rhor[j][i]][k][2]; - fc.z2r_spline_t[joff + k].d=z2r_spline[type2rhor[j][i]][k][3]; - fc.z2r_spline_t[joff + k].e=z2r_spline[type2rhor[j][i]][k][4]; - fc.z2r_spline_t[joff + k].f=z2r_spline[type2rhor[j][i]][k][5]; - fc.z2r_spline_t[joff + k].g=z2r_spline[type2rhor[j][i]][k][6]; + fc.z2r_spline_t[joff + k].a=z2r_spline[type2z2r[j][i]][k][0]; + fc.z2r_spline_t[joff + k].b=z2r_spline[type2z2r[j][i]][k][1]; + fc.z2r_spline_t[joff + k].c=z2r_spline[type2z2r[j][i]][k][2]; + fc.z2r_spline_t[joff + k].d=z2r_spline[type2z2r[j][i]][k][3]; + fc.z2r_spline_t[joff + k].e=z2r_spline[type2z2r[j][i]][k][4]; + fc.z2r_spline_t[joff + k].f=z2r_spline[type2z2r[j][i]][k][5]; + fc.z2r_spline_t[joff + k].g=z2r_spline[type2z2r[j][i]][k][6]; } } } @@ -754,7 +749,7 @@ void PairEAMIntel::ForceConst::set_ntypes(const int ntypes, const int nr, const int nrho, Memory *memory, const int cop) { - if (ntypes != _ntypes || nr > _nr || nrho > _nrho) { + if (ntypes != _ntypes || nr + 1 > _nr || nrho + 1 > _nrho) { if (_ntypes > 0) { _memory->destroy(rhor_spline_f); _memory->destroy(rhor_spline_e); diff --git a/src/USER-INTEL/pair_gayberne_intel.cpp b/src/USER-INTEL/pair_gayberne_intel.cpp index 30941a7594..51524355d5 100644 --- a/src/USER-INTEL/pair_gayberne_intel.cpp +++ b/src/USER-INTEL/pair_gayberne_intel.cpp @@ -228,8 +228,7 @@ void PairGayBerneIntel::eval(const int offload, const int vflag, const int * _noalias const ilist = list->ilist; const int * _noalias const numneigh = list->numneigh; - const int * _noalias const cnumneigh = buffers->cnumneigh(list); - const int * _noalias const firstneigh = buffers->firstneigh(list); + const int ** _noalias const firstneigh = (const int **)list->firstneigh; const flt_t * _noalias const special_lj = fc.special_lj; const FC_PACKED1_T * _noalias const ijc = fc.ijc[0]; @@ -283,7 +282,6 @@ void PairGayBerneIntel::eval(const int offload, const int vflag, in(rsq_formi, delx_formi, dely_formi: length(0) alloc_if(0) free_if(0)) \ in(delz_formi, jtype_formi, jlist_formi: length(0) alloc_if(0) free_if(0))\ in(firstneigh:length(0) alloc_if(0) free_if(0)) \ - in(cnumneigh:length(0) alloc_if(0) free_if(0)) \ in(numneigh:length(0) alloc_if(0) free_if(0)) \ in(x:length(x_size) alloc_if(0) free_if(0)) \ in(quat:length(nall+1) alloc_if(0) free_if(0)) \ @@ -337,9 +335,11 @@ void PairGayBerneIntel::eval(const int offload, const int vflag, #endif acc_t oevdwl, ov0, ov1, ov2, ov3, ov4, ov5; - if (EFLAG) oevdwl = (acc_t)0.0; - if (vflag) ov0 = ov1 = ov2 = ov3 = ov4 = ov5 = (acc_t)0.0; + if (EFLAG || vflag) + oevdwl = ov0 = ov1 = ov2 = ov3 = ov4 = ov5 = (acc_t)0.0; if (NEWTON_PAIR == 0) f_start[1].w = 0; + if (NEWTON_PAIR == 0 && inum != nlocal) + memset(f_start, 0, f_stride * sizeof(FORCE_T)); // loop over neighbors of my atoms #if defined(_OPENMP) @@ -372,8 +372,8 @@ void PairGayBerneIntel::eval(const int offload, const int vflag, const FC_PACKED1_T * _noalias const ijci = ijc + ptr_off; const FC_PACKED2_T * _noalias const lj34i = lj34 + ptr_off; - const int * _noalias const jlist = firstneigh + cnumneigh[ii]; - int jnum = numneigh[ii]; + const int * _noalias const jlist = firstneigh[i]; + int jnum = numneigh[i]; IP_PRE_neighbor_pad(jnum, offload); const flt_t xtmp = x[i].x; @@ -833,13 +833,9 @@ void PairGayBerneIntel::eval(const int offload, const int vflag, f_start[1].w = ierror; } // omp - if (EFLAG) { - if (NEWTON_PAIR == 0) oevdwl *= (acc_t)0.5; - ev_global[0] = oevdwl; - ev_global[1] = (acc_t)0.0; - } - if (vflag) { + if (EFLAG || vflag) { if (NEWTON_PAIR == 0) { + oevdwl *= (acc_t)0.5; ov0 *= (acc_t)-0.5; ov1 *= (acc_t)-0.5; ov2 *= (acc_t)-0.5; @@ -847,6 +843,8 @@ void PairGayBerneIntel::eval(const int offload, const int vflag, ov4 *= (acc_t)-0.5; ov5 *= (acc_t)-0.5; } + ev_global[0] = oevdwl; + ev_global[1] = (acc_t)0.0; ev_global[2] = ov0; ev_global[3] = ov1; ev_global[4] = ov2; @@ -914,19 +912,16 @@ void PairGayBerneIntel::pack_force_const(ForceConst &fc, if (mthreads < buffers->get_off_threads()) mthreads = buffers->get_off_threads(); fc.set_ntypes(tp1, _max_nbors, mthreads, memory, _cop); - buffers->set_ntypes(tp1); - flt_t **cutneighsq = buffers->get_cutneighsq(); // Repeat cutsq calculation because done after call to init_style - double cut, cutneigh; for (int i = 1; i <= atom->ntypes; i++) { for (int j = i; j <= atom->ntypes; j++) { - if (setflag[i][j] != 0 || (setflag[i][i] != 0 && setflag[j][j] != 0)) { + double cut; + if (setflag[i][j] != 0 || (setflag[i][i] != 0 && setflag[j][j] != 0)) cut = init_one(i,j); - cutneigh = cut + neighbor->skin; - cutsq[i][j] = cutsq[j][i] = cut*cut; - cutneighsq[i][j] = cutneighsq[j][i] = cutneigh * cutneigh; - } + else + cut = 0.0; + cutsq[i][j] = cutsq[j][i] = cut*cut; } } @@ -963,14 +958,12 @@ void PairGayBerneIntel::pack_force_const(ForceConst &fc, FC_PACKED1_T *oijc = fc.ijc[0]; FC_PACKED2_T *olj34 = fc.lj34[0]; FC_PACKED3_T *oic = fc.ic; - flt_t * ocutneighsq = cutneighsq[0]; int tp1sq = tp1 * tp1; if (oijc != NULL && oic != NULL) { #pragma offload_transfer target(mic:_cop) \ in(special_lj: length(4) alloc_if(0) free_if(0)) \ in(oijc,olj34: length(tp1sq) alloc_if(0) free_if(0)) \ - in(oic: length(tp1) alloc_if(0) free_if(0)) \ - in(ocutneighsq: length(tp1sq)) + in(oic: length(tp1) alloc_if(0) free_if(0)) } #endif } diff --git a/src/USER-INTEL/pair_lj_charmm_coul_charmm_intel.cpp b/src/USER-INTEL/pair_lj_charmm_coul_charmm_intel.cpp index 8e6395c388..0b6ac3ffa5 100644 --- a/src/USER-INTEL/pair_lj_charmm_coul_charmm_intel.cpp +++ b/src/USER-INTEL/pair_lj_charmm_coul_charmm_intel.cpp @@ -138,8 +138,7 @@ void PairLJCharmmCoulCharmmIntel::eval(const int offload, const int vflag, const int * _noalias const ilist = list->ilist; const int * _noalias const numneigh = list->numneigh; - const int * _noalias const cnumneigh = buffers->cnumneigh(list); - const int * _noalias const firstneigh = buffers->firstneigh(list); + const int ** _noalias const firstneigh = (const int **)list->firstneigh; const flt_t * _noalias const special_coul = fc.special_coul; const flt_t * _noalias const special_lj = fc.special_lj; @@ -186,7 +185,6 @@ void PairLJCharmmCoulCharmmIntel::eval(const int offload, const int vflag, in(special_lj,special_coul:length(0) alloc_if(0) free_if(0)) \ in(cutsq,lj:length(0) alloc_if(0) free_if(0)) \ in(firstneigh:length(0) alloc_if(0) free_if(0)) \ - in(cnumneigh:length(0) alloc_if(0) free_if(0)) \ in(numneigh:length(0) alloc_if(0) free_if(0)) \ in(x:length(x_size) alloc_if(0) free_if(0)) \ in(q:length(q_size) alloc_if(0) free_if(0)) \ @@ -212,8 +210,10 @@ void PairLJCharmmCoulCharmmIntel::eval(const int offload, const int vflag, f_stride, x, q); acc_t oevdwl, oecoul, ov0, ov1, ov2, ov3, ov4, ov5; - if (EFLAG) oevdwl = oecoul = (acc_t)0; - if (vflag) ov0 = ov1 = ov2 = ov3 = ov4 = ov5 = (acc_t)0; + if (EFLAG || vflag) + oevdwl = oecoul = ov0 = ov1 = ov2 = ov3 = ov4 = ov5 = (acc_t)0; + if (NEWTON_PAIR == 0 && inum != nlocal) + memset(f_start, 0, f_stride * sizeof(FORCE_T)); // loop over neighbors of my atoms #if defined(_OPENMP) @@ -248,8 +248,8 @@ void PairLJCharmmCoulCharmmIntel::eval(const int offload, const int vflag, const flt_t * _noalias const cutsqi = cutsq + ptr_off; const LJ_T * _noalias const lji = lj + ptr_off; - const int * _noalias const jlist = firstneigh + cnumneigh[ii]; - int jnum = numneigh[ii]; + const int * _noalias const jlist = firstneigh[i]; + int jnum = numneigh[i]; IP_PRE_neighbor_pad(jnum, offload); acc_t fxtmp,fytmp,fztmp,fwtmp; @@ -403,16 +403,10 @@ void PairLJCharmmCoulCharmmIntel::eval(const int offload, const int vflag, IP_PRE_fdotr_reduce(NEWTON_PAIR, nall, nthreads, f_stride, vflag, ov0, ov1, ov2, ov3, ov4, ov5); - if (EFLAG) { + if (EFLAG || vflag) { if (NEWTON_PAIR == 0) { oevdwl *= (acc_t)0.5; oecoul *= (acc_t)0.5; - } - ev_global[0] = oevdwl; - ev_global[1] = oecoul; - } - if (vflag) { - if (NEWTON_PAIR == 0) { ov0 *= (acc_t)0.5; ov1 *= (acc_t)0.5; ov2 *= (acc_t)0.5; @@ -420,6 +414,8 @@ void PairLJCharmmCoulCharmmIntel::eval(const int offload, const int vflag, ov4 *= (acc_t)0.5; ov5 *= (acc_t)0.5; } + ev_global[0] = oevdwl; + ev_global[1] = oecoul; ev_global[2] = ov0; ev_global[3] = ov1; ev_global[4] = ov2; @@ -487,22 +483,19 @@ void PairLJCharmmCoulCharmmIntel::pack_force_const(ForceConst &fc, int tp1 = atom->ntypes + 1; fc.set_ntypes(tp1, memory, _cop); - buffers->set_ntypes(tp1); - flt_t **cutneighsq = buffers->get_cutneighsq(); // Repeat cutsq calculation because done after call to init_style - double cut, cutneigh; if (cut_lj > cut_coul) error->all(FLERR, "Intel varient of lj/charmm/coul/long expects lj cutoff<=coulombic"); for (int i = 1; i <= atom->ntypes; i++) { for (int j = i; j <= atom->ntypes; j++) { - if (setflag[i][j] != 0 || (setflag[i][i] != 0 && setflag[j][j] != 0)) { + double cut; + if (setflag[i][j] != 0 || (setflag[i][i] != 0 && setflag[j][j] != 0)) cut = init_one(i, j); - cutneigh = cut + neighbor->skin; - cutsq[i][j] = cutsq[j][i] = cut*cut; - cutneighsq[i][j] = cutneighsq[j][i] = cutneigh * cutneigh; - } + else + cut = 0.0; + cutsq[i][j] = cutsq[j][i] = cut*cut; } } @@ -540,12 +533,10 @@ void PairLJCharmmCoulCharmmIntel::pack_force_const(ForceConst &fc, flt_t * special_coul = fc.special_coul; flt_t * cutsq = fc.cutsq[0]; LJ_T * lj = fc.lj[0]; - flt_t * ocutneighsq = cutneighsq[0]; int tp1sq = tp1 * tp1; #pragma offload_transfer target(mic:_cop) \ in(special_lj, special_coul: length(4) alloc_if(0) free_if(0)) \ - in(cutsq,lj: length(tp1sq) alloc_if(0) free_if(0)) \ - in(ocutneighsq: length(tp1sq) alloc_if(0) free_if(0)) + in(cutsq,lj: length(tp1sq) alloc_if(0) free_if(0)) #endif } diff --git a/src/USER-INTEL/pair_lj_charmm_coul_long_intel.cpp b/src/USER-INTEL/pair_lj_charmm_coul_long_intel.cpp index a01a4688a5..753a9afdd9 100644 --- a/src/USER-INTEL/pair_lj_charmm_coul_long_intel.cpp +++ b/src/USER-INTEL/pair_lj_charmm_coul_long_intel.cpp @@ -28,7 +28,7 @@ #include "suffix.h" using namespace LAMMPS_NS; -#define LJ_T typename IntelBuffers::vec4_t +#define LJ_T typename IntelBuffers::vec2_t #define TABLE_T typename ForceConst::table_t /* ---------------------------------------------------------------------- */ @@ -142,8 +142,7 @@ void PairLJCharmmCoulLongIntel::eval(const int offload, const int vflag, const int * _noalias const ilist = list->ilist; const int * _noalias const numneigh = list->numneigh; - const int * _noalias const cnumneigh = buffers->cnumneigh(list); - const int * _noalias const firstneigh = buffers->firstneigh(list); + const int ** _noalias const firstneigh = (const int **)list->firstneigh; const flt_t * _noalias const special_coul = fc.special_coul; const flt_t * _noalias const special_lj = fc.special_lj; @@ -207,7 +206,6 @@ void PairLJCharmmCoulLongIntel::eval(const int offload, const int vflag, in(special_lj,special_coul:length(0) alloc_if(0) free_if(0)) \ in(cutsq,lj:length(0) alloc_if(0) free_if(0)) \ in(firstneigh:length(0) alloc_if(0) free_if(0)) \ - in(cnumneigh:length(0) alloc_if(0) free_if(0)) \ in(numneigh:length(0) alloc_if(0) free_if(0)) \ in(x:length(x_size) alloc_if(0) free_if(0)) \ in(q:length(q_size) alloc_if(0) free_if(0)) \ @@ -232,8 +230,10 @@ void PairLJCharmmCoulLongIntel::eval(const int offload, const int vflag, f_stride, x, q); acc_t oevdwl, oecoul, ov0, ov1, ov2, ov3, ov4, ov5; - if (EFLAG) oevdwl = oecoul = (acc_t)0; - if (vflag) ov0 = ov1 = ov2 = ov3 = ov4 = ov5 = (acc_t)0; + if (EFLAG || vflag) + oevdwl = oecoul = ov0 = ov1 = ov2 = ov3 = ov4 = ov5 = (acc_t)0; + if (NEWTON_PAIR == 0 && inum != nlocal) + memset(f_start, 0, f_stride * sizeof(FORCE_T)); // loop over neighbors of my atoms #if defined(_OPENMP) @@ -268,8 +268,8 @@ void PairLJCharmmCoulLongIntel::eval(const int offload, const int vflag, const flt_t * _noalias const cutsqi = cutsq + ptr_off; const LJ_T * _noalias const lji = lj + ptr_off; - const int * _noalias const jlist = firstneigh + cnumneigh[ii]; - int jnum = numneigh[ii]; + const int * _noalias const jlist = firstneigh[i]; + int jnum = numneigh[i]; IP_PRE_neighbor_pad(jnum, offload); acc_t fxtmp,fytmp,fztmp,fwtmp; @@ -376,8 +376,14 @@ void PairLJCharmmCoulLongIntel::eval(const int offload, const int vflag, if (rsq < cut_ljsq) { #endif flt_t r6inv = r2inv * r2inv * r2inv; - forcelj = r6inv * (lji[jtype].x * r6inv - lji[jtype].y); - if (EFLAG) evdwl = r6inv*(lji[jtype].z * r6inv - lji[jtype].w); + flt_t eps4 = lji[jtype].x; + flt_t sigp6 = lji[jtype].y; + flt_t lj4 = eps4 * sigp6; + flt_t lj3 = lj4 * sigp6; + flt_t lj2 = (flt_t)6.0 * lj4; + flt_t lj1 = (flt_t)12.0 * lj3; + forcelj = r6inv * (lj1 * r6inv - lj2); + if (EFLAG) evdwl = r6inv*(lj3 * r6inv - lj4); #ifdef INTEL_VMASK if (rsq > cut_lj_innersq) { @@ -397,8 +403,7 @@ void PairLJCharmmCoulLongIntel::eval(const int offload, const int vflag, } #endif } else { - const flt_t philj = r6inv * (lji[jtype].z*r6inv - - lji[jtype].w); + const flt_t philj = r6inv * (lj3 * r6inv - lj4); #ifndef INTEL_VMASK if (rsq > cut_lj_innersq) #endif @@ -463,16 +468,10 @@ void PairLJCharmmCoulLongIntel::eval(const int offload, const int vflag, IP_PRE_fdotr_reduce(NEWTON_PAIR, nall, nthreads, f_stride, vflag, ov0, ov1, ov2, ov3, ov4, ov5); - if (EFLAG) { + if (EFLAG || vflag) { if (NEWTON_PAIR == 0) { oevdwl *= (acc_t)0.5; oecoul *= (acc_t)0.5; - } - ev_global[0] = oevdwl; - ev_global[1] = oecoul; - } - if (vflag) { - if (NEWTON_PAIR == 0) { ov0 *= (acc_t)0.5; ov1 *= (acc_t)0.5; ov2 *= (acc_t)0.5; @@ -480,6 +479,8 @@ void PairLJCharmmCoulLongIntel::eval(const int offload, const int vflag, ov4 *= (acc_t)0.5; ov5 *= (acc_t)0.5; } + ev_global[0] = oevdwl; + ev_global[1] = oecoul; ev_global[2] = ov0; ev_global[3] = ov1; ev_global[4] = ov2; @@ -552,22 +553,19 @@ void PairLJCharmmCoulLongIntel::pack_force_const(ForceConst &fc, for (int i = 0; i < ncoultablebits; i++) ntable *= 2; fc.set_ntypes(tp1, ntable, memory, _cop); - buffers->set_ntypes(tp1); - flt_t **cutneighsq = buffers->get_cutneighsq(); // Repeat cutsq calculation because done after call to init_style - double cut, cutneigh; if (cut_lj > cut_coul) error->all(FLERR, "Intel varient of lj/charmm/coul/long expects lj cutoff<=coulombic"); for (int i = 1; i <= atom->ntypes; i++) { for (int j = i; j <= atom->ntypes; j++) { - if (setflag[i][j] != 0 || (setflag[i][i] != 0 && setflag[j][j] != 0)) { + double cut; + if (setflag[i][j] != 0 || (setflag[i][i] != 0 && setflag[j][j] != 0)) cut = init_one(i, j); - cutneigh = cut + neighbor->skin; - cutsq[i][j] = cutsq[j][i] = cut*cut; - cutneighsq[i][j] = cutneighsq[j][i] = cutneigh * cutneigh; - } + else + cut = 0.0; + cutsq[i][j] = cutsq[j][i] = cut*cut; } } @@ -591,10 +589,13 @@ void PairLJCharmmCoulLongIntel::pack_force_const(ForceConst &fc, for (int i = 1; i < tp1; i++) { for (int j = 1; j < tp1; j++) { - fc.lj[i][j].x = lj1[i][j]; - fc.lj[i][j].y = lj2[i][j]; - fc.lj[i][j].z = lj3[i][j]; - fc.lj[i][j].w = lj4[i][j]; + if (i <= j) { + fc.lj[i][j].x = epsilon[i][j] * 4.0; + fc.lj[i][j].y = pow(sigma[i][j],6.0); + } else { + fc.lj[i][j].x = epsilon[j][i] * 4.0; + fc.lj[i][j].y = pow(sigma[j][i],6.0); + } fc.cutsq[i][j] = cutsq[i][j]; } } @@ -623,14 +624,12 @@ void PairLJCharmmCoulLongIntel::pack_force_const(ForceConst &fc, flt_t * detable = fc.detable; flt_t * ctable = fc.ctable; flt_t * dctable = fc.dctable; - flt_t * ocutneighsq = cutneighsq[0]; int tp1sq = tp1 * tp1; #pragma offload_transfer target(mic:_cop) \ in(special_lj, special_coul: length(4) alloc_if(0) free_if(0)) \ in(cutsq,lj: length(tp1sq) alloc_if(0) free_if(0)) \ in(table: length(ntable) alloc_if(0) free_if(0)) \ - in(etable,detable,ctable,dctable: length(ntable) alloc_if(0) free_if(0)) \ - in(ocutneighsq: length(tp1sq) alloc_if(0) free_if(0)) + in(etable,detable,ctable,dctable: length(ntable) alloc_if(0) free_if(0)) #endif } @@ -647,7 +646,7 @@ void PairLJCharmmCoulLongIntel::ForceConst::set_ntypes(const int ntypes, flt_t * ospecial_lj = special_lj; flt_t * ospecial_coul = special_coul; flt_t * ocutsq = cutsq[0]; - typename IntelBuffers::vec4_t * olj = lj[0]; + typename IntelBuffers::vec2_t * olj = lj[0]; table_t * otable = table; flt_t * oetable = etable; flt_t * odetable = detable; @@ -687,7 +686,7 @@ void PairLJCharmmCoulLongIntel::ForceConst::set_ntypes(const int ntypes, flt_t * ospecial_lj = special_lj; flt_t * ospecial_coul = special_coul; flt_t * ocutsq = cutsq[0]; - typename IntelBuffers::vec4_t * olj = lj[0]; + typename IntelBuffers::vec2_t * olj = lj[0]; table_t * otable = table; flt_t * oetable = etable; flt_t * odetable = detable; diff --git a/src/USER-INTEL/pair_lj_charmm_coul_long_intel.h b/src/USER-INTEL/pair_lj_charmm_coul_long_intel.h index 1b13d78497..0066745078 100644 --- a/src/USER-INTEL/pair_lj_charmm_coul_long_intel.h +++ b/src/USER-INTEL/pair_lj_charmm_coul_long_intel.h @@ -69,7 +69,7 @@ class PairLJCharmmCoulLongIntel : public PairLJCharmmCoulLong { flt_t cut_lj_innersq; table_t *table; flt_t *etable, *detable, *ctable, *dctable; - typename IntelBuffers::vec4_t **lj; + typename IntelBuffers::vec2_t **lj; ForceConst() : _ntypes(0), _ntable(0) {} ~ForceConst() { set_ntypes(0,0,NULL,_cop); } diff --git a/src/USER-INTEL/pair_lj_cut_coul_long_intel.cpp b/src/USER-INTEL/pair_lj_cut_coul_long_intel.cpp index ab0b5b3d55..35ed9061ce 100644 --- a/src/USER-INTEL/pair_lj_cut_coul_long_intel.cpp +++ b/src/USER-INTEL/pair_lj_cut_coul_long_intel.cpp @@ -141,8 +141,7 @@ void PairLJCutCoulLongIntel::eval(const int offload, const int vflag, const int * _noalias const ilist = list->ilist; const int * _noalias const numneigh = list->numneigh; - const int * _noalias const cnumneigh = buffers->cnumneigh(list); - const int * _noalias const firstneigh = buffers->firstneigh(list); + const int ** _noalias const firstneigh = (const int **)list->firstneigh; const flt_t * _noalias const special_coul = fc.special_coul; const flt_t * _noalias const special_lj = fc.special_lj; @@ -201,7 +200,6 @@ void PairLJCutCoulLongIntel::eval(const int offload, const int vflag, in(special_lj,special_coul:length(0) alloc_if(0) free_if(0)) \ in(c_force, c_energy:length(0) alloc_if(0) free_if(0)) \ in(firstneigh:length(0) alloc_if(0) free_if(0)) \ - in(cnumneigh:length(0) alloc_if(0) free_if(0)) \ in(numneigh:length(0) alloc_if(0) free_if(0)) \ in(x:length(x_size) alloc_if(0) free_if(0)) \ in(q:length(q_size) alloc_if(0) free_if(0)) \ @@ -225,8 +223,10 @@ void PairLJCutCoulLongIntel::eval(const int offload, const int vflag, f_stride, x, q); acc_t oevdwl, oecoul, ov0, ov1, ov2, ov3, ov4, ov5; - if (EFLAG) oevdwl = oecoul = (acc_t)0; - if (vflag) ov0 = ov1 = ov2 = ov3 = ov4 = ov5 = (acc_t)0; + if (EFLAG || vflag) + oevdwl = oecoul = ov0 = ov1 = ov2 = ov3 = ov4 = ov5 = (acc_t)0; + if (NEWTON_PAIR == 0 && inum != nlocal) + memset(f_start, 0, f_stride * sizeof(FORCE_T)); // loop over neighbors of my atoms #if defined(_OPENMP) @@ -260,8 +260,8 @@ void PairLJCutCoulLongIntel::eval(const int offload, const int vflag, const C_FORCE_T * _noalias const c_forcei = c_force + ptr_off; const C_ENERGY_T * _noalias const c_energyi = c_energy + ptr_off; - const int * _noalias const jlist = firstneigh + cnumneigh[ii]; - int jnum = numneigh[ii]; + const int * _noalias const jlist = firstneigh[i]; + int jnum = numneigh[i]; IP_PRE_neighbor_pad(jnum, offload); acc_t fxtmp,fytmp,fztmp,fwtmp; @@ -433,16 +433,10 @@ void PairLJCutCoulLongIntel::eval(const int offload, const int vflag, IP_PRE_fdotr_reduce(NEWTON_PAIR, nall, nthreads, f_stride, vflag, ov0, ov1, ov2, ov3, ov4, ov5); - if (EFLAG) { + if (EFLAG || vflag) { if (NEWTON_PAIR == 0) { oevdwl *= (acc_t)0.5; oecoul *= (acc_t)0.5; - } - ev_global[0] = oevdwl; - ev_global[1] = oecoul; - } - if (vflag) { - if (NEWTON_PAIR == 0) { ov0 *= (acc_t)0.5; ov1 *= (acc_t)0.5; ov2 *= (acc_t)0.5; @@ -450,6 +444,8 @@ void PairLJCutCoulLongIntel::eval(const int offload, const int vflag, ov4 *= (acc_t)0.5; ov5 *= (acc_t)0.5; } + ev_global[0] = oevdwl; + ev_global[1] = oecoul; ev_global[2] = ov0; ev_global[3] = ov1; ev_global[4] = ov2; @@ -522,19 +518,16 @@ void PairLJCutCoulLongIntel::pack_force_const(ForceConst &fc, for (int i = 0; i < ncoultablebits; i++) ntable *= 2; fc.set_ntypes(tp1, ntable, memory, _cop); - buffers->set_ntypes(tp1); - flt_t **cutneighsq = buffers->get_cutneighsq(); // Repeat cutsq calculation because done after call to init_style - double cut, cutneigh; for (int i = 1; i <= atom->ntypes; i++) { for (int j = i; j <= atom->ntypes; j++) { - if (setflag[i][j] != 0 || (setflag[i][i] != 0 && setflag[j][j] != 0)) { + double cut; + if (setflag[i][j] != 0 || (setflag[i][i] != 0 && setflag[j][j] != 0)) cut = init_one(i, j); - cutneigh = cut + neighbor->skin; - cutsq[i][j] = cutsq[j][i] = cut*cut; - cutneighsq[i][j] = cutneighsq[j][i] = cutneigh * cutneigh; - } + else + cut = 0.0; + cutsq[i][j] = cutsq[j][i] = cut*cut; } } @@ -587,14 +580,12 @@ void PairLJCutCoulLongIntel::pack_force_const(ForceConst &fc, flt_t * detable = fc.detable; flt_t * ctable = fc.ctable; flt_t * dctable = fc.dctable; - flt_t * ocutneighsq = cutneighsq[0]; int tp1sq = tp1 * tp1; #pragma offload_transfer target(mic:_cop) \ in(special_lj, special_coul: length(4) alloc_if(0) free_if(0)) \ in(c_force, c_energy: length(tp1sq) alloc_if(0) free_if(0)) \ in(table: length(ntable) alloc_if(0) free_if(0)) \ - in(etable,detable,ctable,dctable: length(ntable) alloc_if(0) free_if(0)) \ - in(ocutneighsq: length(tp1sq) alloc_if(0) free_if(0)) + in(etable,detable,ctable,dctable: length(ntable) alloc_if(0) free_if(0)) #endif } diff --git a/src/USER-INTEL/pair_lj_cut_intel.cpp b/src/USER-INTEL/pair_lj_cut_intel.cpp index c973639709..94133a7f47 100644 --- a/src/USER-INTEL/pair_lj_cut_intel.cpp +++ b/src/USER-INTEL/pair_lj_cut_intel.cpp @@ -150,8 +150,7 @@ void PairLJCutIntel::eval(const int offload, const int vflag, const int * _noalias const ilist = list->ilist; const int * _noalias const numneigh = list->numneigh; - const int * _noalias const cnumneigh = buffers->cnumneigh(list); - const int * _noalias const firstneigh = buffers->firstneigh(list); + const int ** _noalias const firstneigh = (const int **)list->firstneigh; const flt_t * _noalias const special_lj = fc.special_lj; const FC_PACKED1_T * _noalias const ljc12o = fc.ljc12o[0]; const FC_PACKED2_T * _noalias const lj34 = fc.lj34[0]; @@ -180,8 +179,10 @@ void PairLJCutIntel::eval(const int offload, const int vflag, f_stride, x, 0); acc_t oevdwl, ov0, ov1, ov2, ov3, ov4, ov5; - if (EFLAG) oevdwl = (acc_t)0; - if (vflag) ov0 = ov1 = ov2 = ov3 = ov4 = ov5 = (acc_t)0; + if (EFLAG || vflag) + oevdwl = ov0 = ov1 = ov2 = ov3 = ov4 = ov5 = (acc_t)0; + if (NEWTON_PAIR == 0 && inum != nlocal) + memset(f_start, 0, f_stride * sizeof(FORCE_T)); // loop over neighbors of my atoms #if defined(_OPENMP) @@ -201,12 +202,12 @@ void PairLJCutIntel::eval(const int offload, const int vflag, flt_t cutsq, lj1, lj2, lj3, lj4, offset; if (ONETYPE) { - cutsq = ljc12o[3].cutsq; - lj1 = ljc12o[3].lj1; - lj2 = ljc12o[3].lj2; - lj3 = lj34[3].lj3; - lj4 = lj34[3].lj4; - offset = ljc12o[3].offset; + cutsq = ljc12o[_onetype].cutsq; + lj1 = ljc12o[_onetype].lj1; + lj2 = ljc12o[_onetype].lj2; + lj3 = lj34[_onetype].lj3; + lj4 = lj34[_onetype].lj4; + offset = ljc12o[_onetype].offset; } for (int ii = iifrom; ii < iito; ii += iip) { const int i = ilist[ii]; @@ -219,8 +220,8 @@ void PairLJCutIntel::eval(const int offload, const int vflag, ljc12oi = ljc12o + ptr_off; lj34i = lj34 + ptr_off; } - const int * _noalias const jlist = firstneigh + cnumneigh[ii]; - int jnum = numneigh[ii]; + const int * _noalias const jlist = firstneigh[i]; + int jnum = numneigh[i]; IP_PRE_neighbor_pad(jnum, offload); acc_t fxtmp, fytmp, fztmp, fwtmp; @@ -338,13 +339,9 @@ void PairLJCutIntel::eval(const int offload, const int vflag, IP_PRE_fdotr_reduce(NEWTON_PAIR, nall, nthreads, f_stride, vflag, ov0, ov1, ov2, ov3, ov4, ov5); - if (EFLAG) { - if (NEWTON_PAIR == 0) oevdwl *= (acc_t)0.5; - ev_global[0] = oevdwl; - ev_global[1] = (acc_t)0.0; - } - if (vflag) { + if (EFLAG || vflag) { if (NEWTON_PAIR == 0) { + oevdwl *= (acc_t)0.5; ov0 *= (acc_t)0.5; ov1 *= (acc_t)0.5; ov2 *= (acc_t)0.5; @@ -352,6 +349,8 @@ void PairLJCutIntel::eval(const int offload, const int vflag, ov4 *= (acc_t)0.5; ov5 *= (acc_t)0.5; } + ev_global[0] = oevdwl; + ev_global[1] = (acc_t)0.0; ev_global[2] = ov0; ev_global[3] = ov1; ev_global[4] = ov2; @@ -414,25 +413,26 @@ void PairLJCutIntel::pack_force_const(ForceConst &fc, IntelBuffers *buffers) { _onetype = 0; - if (atom->ntypes == 1 && !atom->molecular) _onetype = 1; int tp1 = atom->ntypes + 1; fc.set_ntypes(tp1,memory,_cop); - buffers->set_ntypes(tp1); - flt_t **cutneighsq = buffers->get_cutneighsq(); // Repeat cutsq calculation because done after call to init_style - double cut, cutneigh; + int mytypes = 0; for (int i = 1; i <= atom->ntypes; i++) { for (int j = i; j <= atom->ntypes; j++) { + double cut; if (setflag[i][j] != 0 || (setflag[i][i] != 0 && setflag[j][j] != 0)) { cut = init_one(i,j); - cutneigh = cut + neighbor->skin; - cutsq[i][j] = cutsq[j][i] = cut*cut; - cutneighsq[i][j] = cutneighsq[j][i] = cutneigh * cutneigh; + mytypes++; + _onetype = i * tp1 + j; + } else { + cut = 0.0; } + cutsq[i][j] = cutsq[j][i] = cut*cut; } } + if (mytypes > 1 || atom->molecular) _onetype = 0; for (int i = 0; i < 4; i++) { fc.special_lj[i] = force->special_lj[i]; diff --git a/src/USER-INTEL/pair_sw_intel.cpp b/src/USER-INTEL/pair_sw_intel.cpp index aff8ba88a7..9e00516087 100644 --- a/src/USER-INTEL/pair_sw_intel.cpp +++ b/src/USER-INTEL/pair_sw_intel.cpp @@ -130,37 +130,37 @@ void PairSWIntel::compute(int eflag, int vflag, if (_onetype) { if (_spq) { if (eflag) { - eval<1,1,1>(1, ovflag, buffers, fc, 0, offload_end, _offload_pad); - eval<1,1,1>(0, ovflag, buffers, fc, host_start, inum, _host_pad); + eval<1,1,1>(1, ovflag, buffers, fc, 0, offload_end); + eval<1,1,1>(0, ovflag, buffers, fc, host_start, inum); } else { - eval<1,1,0>(1, ovflag, buffers, fc, 0, offload_end, _offload_pad); - eval<1,1,0>(0, ovflag, buffers, fc, host_start, inum, _host_pad); + eval<1,1,0>(1, ovflag, buffers, fc, 0, offload_end); + eval<1,1,0>(0, ovflag, buffers, fc, host_start, inum); } } else { if (eflag) { - eval<0,1,1>(1, ovflag, buffers, fc, 0, offload_end, _offload_pad); - eval<0,1,1>(0, ovflag, buffers, fc, host_start, inum, _host_pad); + eval<0,1,1>(1, ovflag, buffers, fc, 0, offload_end); + eval<0,1,1>(0, ovflag, buffers, fc, host_start, inum); } else { - eval<0,1,0>(1, ovflag, buffers, fc, 0, offload_end, _offload_pad); - eval<0,1,0>(0, ovflag, buffers, fc, host_start, inum, _host_pad); + eval<0,1,0>(1, ovflag, buffers, fc, 0, offload_end); + eval<0,1,0>(0, ovflag, buffers, fc, host_start, inum); } } } else { if (_spq) { if (eflag) { - eval<1,0,1>(1, ovflag, buffers, fc, 0, offload_end, _offload_pad); - eval<1,0,1>(0, ovflag, buffers, fc, host_start, inum, _host_pad); + eval<1,0,1>(1, ovflag, buffers, fc, 0, offload_end); + eval<1,0,1>(0, ovflag, buffers, fc, host_start, inum); } else { - eval<1,0,0>(1, ovflag, buffers, fc, 0, offload_end, _offload_pad); - eval<1,0,0>(0, ovflag, buffers, fc, host_start, inum, _host_pad); + eval<1,0,0>(1, ovflag, buffers, fc, 0, offload_end); + eval<1,0,0>(0, ovflag, buffers, fc, host_start, inum); } } else { if (eflag) { - eval<0,0,1>(1, ovflag, buffers, fc, 0, offload_end, _offload_pad); - eval<0,0,1>(0, ovflag, buffers, fc, host_start, inum, _host_pad); + eval<0,0,1>(1, ovflag, buffers, fc, 0, offload_end); + eval<0,0,1>(0, ovflag, buffers, fc, host_start, inum); } else { - eval<0,0,0>(1, ovflag, buffers, fc, 0, offload_end, _offload_pad); - eval<0,0,0>(0, ovflag, buffers, fc, host_start, inum, _host_pad); + eval<0,0,0>(1, ovflag, buffers, fc, 0, offload_end); + eval<0,0,0>(0, ovflag, buffers, fc, host_start, inum); } } } @@ -173,7 +173,7 @@ template void PairSWIntel::eval(const int offload, const int vflag, IntelBuffers *buffers, const ForceConst &fc, const int astart, - const int aend, const int /*pad_width*/) + const int aend) { const int inum = aend - astart; if (inum == 0) return; @@ -185,10 +185,13 @@ void PairSWIntel::eval(const int offload, const int vflag, ATOM_T * _noalias const x = buffers->get_x(offload); const int * _noalias const ilist = list->ilist; - const int * _noalias const numneighhalf = buffers->get_atombin(); const int * _noalias const numneigh = list->numneigh; - const int * _noalias const cnumneigh = buffers->cnumneigh(list); - const int * _noalias const firstneigh = buffers->firstneigh(list); + const int * _noalias const firstneigh = list->firstneigh[ilist[0]]; + + int *nhalf, *cnum; + buffers->get_list_data3(list, nhalf, cnum); + const int * _noalias const numneighhalf = nhalf; + const int * _noalias const cnumneigh = cnum; const FC_PACKED0_T * _noalias const p2 = fc.p2[0]; const FC_PACKED1_T * _noalias const p2f = fc.p2f[0]; @@ -206,6 +209,8 @@ void PairSWIntel::eval(const int offload, const int vflag, const int ntypes = atom->ntypes + 1; const int eatom = this->eflag_atom; + const int onetype = _onetype; + const int onetype3 = _onetype3; // Determine how much data to transfer int x_size, q_size, f_stride, ev_size, separate_flag; @@ -235,8 +240,8 @@ void PairSWIntel::eval(const int offload, const int vflag, in(overflow:length(0) alloc_if(0) free_if(0)) \ in(ccachex,ccachey,ccachez,ccachew:length(0) alloc_if(0) free_if(0)) \ in(ccachei,ccachej:length(0) alloc_if(0) free_if(0)) \ - in(ccache_stride,nthreads,inum,nall,ntypes,vflag,eatom,offload) \ - in(astart,nlocal,f_stride,minlocal,separate_flag,pad_width) \ + in(ccache_stride,nthreads,inum,nall,ntypes,vflag,eatom,offload,onetype3) \ + in(astart,nlocal,f_stride,minlocal,separate_flag,onetype) \ out(f_start:length(f_stride) alloc_if(0) free_if(0)) \ out(ev_global:length(ev_size) alloc_if(0) free_if(0)) \ out(timer_compute:length(1) alloc_if(0) free_if(0)) \ @@ -251,8 +256,8 @@ void PairSWIntel::eval(const int offload, const int vflag, f_stride, x, 0); acc_t oevdwl, ov0, ov1, ov2, ov3, ov4, ov5; - if (EFLAG) oevdwl = (acc_t)0; - if (vflag) ov0 = ov1 = ov2 = ov3 = ov4 = ov5 = (acc_t)0; + if (EFLAG || vflag) + oevdwl = ov0 = ov1 = ov2 = ov3 = ov4 = ov5 = (acc_t)0; #if defined(_OPENMP) #pragma omp parallel reduction(+:oevdwl,ov0,ov1,ov2,ov3,ov4,ov5) @@ -278,24 +283,24 @@ void PairSWIntel::eval(const int offload, const int vflag, flt_t cutsq, cut, powerp, powerq, sigma, c1, c2, c3, c4, c5, c6; flt_t sigma_gamma, costheta, lambda_epsilon, lambda_epsilon2; if (ONETYPE) { - cutsq = p2[3].cutsq; - cut = p2f[3].cut; - sigma = p2f[3].sigma; - c1 = p2f2[3].c1; - c2 = p2f2[3].c2; - c3 = p2f2[3].c3; - c4 = p2f2[3].c4; - sigma_gamma = p2[3].sigma_gamma; - costheta = p3[7].costheta; - lambda_epsilon = p3[7].lambda_epsilon; - lambda_epsilon2 = p3[7].lambda_epsilon2; + cutsq = p2[onetype].cutsq; + cut = p2f[onetype].cut; + sigma = p2f[onetype].sigma; + c1 = p2f2[onetype].c1; + c2 = p2f2[onetype].c2; + c3 = p2f2[onetype].c3; + c4 = p2f2[onetype].c4; + sigma_gamma = p2[onetype].sigma_gamma; + costheta = p3[onetype3].costheta; + lambda_epsilon = p3[onetype3].lambda_epsilon; + lambda_epsilon2 = p3[onetype3].lambda_epsilon2; if (SPQ == 0) { - powerp = p2f[3].powerp; - powerq = p2f[3].powerq; + powerp = p2f[onetype].powerp; + powerq = p2f[onetype].powerq; } if (EFLAG) { - c5 = p2e[3].c5; - c6 = p2e[3].c6; + c5 = p2e[onetype].c5; + c6 = p2e[onetype].c6; } } @@ -312,7 +317,7 @@ void PairSWIntel::eval(const int offload, const int vflag, } const int * _noalias const jlist = firstneigh + cnumneigh[ii]; - const int jnum = numneigh[ii]; + const int jnum = numneigh[i]; const int jnumhalf = numneighhalf[ii]; acc_t fxtmp, fytmp, fztmp, fwtmp; @@ -541,11 +546,9 @@ void PairSWIntel::eval(const int offload, const int vflag, IP_PRE_fdotr_reduce(1, nall, nthreads, f_stride, vflag, ov0, ov1, ov2, ov3, ov4, ov5); - if (EFLAG) { + if (EFLAG || vflag) { ev_global[0] = oevdwl; ev_global[1] = (acc_t)0.0; - } - if (vflag) { ev_global[2] = ov0; ev_global[3] = ov1; ev_global[4] = ov2; @@ -585,7 +588,7 @@ template void PairSWIntel::eval(const int offload, const int vflag, IntelBuffers *buffers, const ForceConst &fc, const int astart, - const int aend, const int pad_width) + const int aend) { typedef typename SIMD_type::SIMD_vec SIMD_flt_t; typedef typename SIMD_type::SIMD_vec SIMD_acc_t; @@ -601,10 +604,13 @@ void PairSWIntel::eval(const int offload, const int vflag, ATOM_T * _noalias const x = buffers->get_x(offload); const int * _noalias const ilist = list->ilist; - const int * _noalias const numneighhalf = buffers->get_atombin(); const int * _noalias const numneigh = list->numneigh; - const int * _noalias const cnumneigh = buffers->cnumneigh(list); - const int * _noalias const firstneigh = buffers->firstneigh(list); + const int * _noalias const firstneigh = list->firstneigh[ilist[0]]; + + int *nhalf, *cnum; + buffers->get_list_data3(list, nhalf, cnum); + const int * _noalias const numneighhalf = nhalf; + const int * _noalias const cnumneigh = cnum; const FC_PACKED0_T * _noalias const p2 = fc.p2[0]; const FC_PACKED1_T * _noalias const p2f = fc.p2f[0]; @@ -654,7 +660,7 @@ void PairSWIntel::eval(const int offload, const int vflag, in(ccachex,ccachey,ccachez,ccachew:length(0) alloc_if(0) free_if(0)) \ in(ccachei,ccachej,ccachef:length(0) alloc_if(0) free_if(0)) \ in(ccache_stride,nthreads,inum,nall,ntypes,vflag,eatom,offload) \ - in(astart,nlocal,f_stride,minlocal,separate_flag,pad_width) \ + in(astart,nlocal,f_stride,minlocal,separate_flag) \ in(ccache_stride3) \ out(f_start:length(f_stride) alloc_if(0) free_if(0)) \ out(ev_global:length(ev_size) alloc_if(0) free_if(0)) \ @@ -670,8 +676,8 @@ void PairSWIntel::eval(const int offload, const int vflag, f_stride, x, 0); acc_t oevdwl, ov0, ov1, ov2, ov3, ov4, ov5; - if (EFLAG) oevdwl = (acc_t)0; - if (vflag) ov0 = ov1 = ov2 = ov3 = ov4 = ov5 = (acc_t)0; + if (EFLAG || vflag) + oevdwl = ov0 = ov1 = ov2 = ov3 = ov4 = ov5 = (acc_t)0; #if defined(_OPENMP) #pragma omp parallel reduction(+:oevdwl,ov0,ov1,ov2,ov3,ov4,ov5) @@ -701,34 +707,38 @@ void PairSWIntel::eval(const int offload, const int vflag, SIMD_flt_t cutsq, cut, powerp, powerq, sigma, c1, c2, c3,c4, c5, c6; SIMD_flt_t sigma_gamma, costheta, lambda_epsilon, lambda_epsilon2; if (ONETYPE) { - cutsq = SIMD_set(p2[3].cutsq); - cut = SIMD_set(p2f[3].cut); - sigma = SIMD_set(p2f[3].sigma); - c1 = SIMD_set(p2f2[3].c1); - c2 = SIMD_set(p2f2[3].c2); - c3 = SIMD_set(p2f2[3].c3); - c4 = SIMD_set(p2f2[3].c4); - sigma_gamma = SIMD_set(p2[3].sigma_gamma); - costheta = SIMD_set(p3[7].costheta); - lambda_epsilon = SIMD_set(p3[7].lambda_epsilon); - lambda_epsilon2 = SIMD_set(p3[7].lambda_epsilon2); + cutsq = SIMD_set(p2[_onetype].cutsq); + cut = SIMD_set(p2f[_onetype].cut); + sigma = SIMD_set(p2f[_onetype].sigma); + c1 = SIMD_set(p2f2[_onetype].c1); + c2 = SIMD_set(p2f2[_onetype].c2); + c3 = SIMD_set(p2f2[_onetype].c3); + c4 = SIMD_set(p2f2[_onetype].c4); + sigma_gamma = SIMD_set(p2[_onetype].sigma_gamma); + costheta = SIMD_set(p3[_onetype3].costheta); + lambda_epsilon = SIMD_set(p3[_onetype3].lambda_epsilon); + lambda_epsilon2 = SIMD_set(p3[_onetype3].lambda_epsilon2); if (SPQ == 0) { - powerp = SIMD_set(p2f[3].powerp); - powerq = SIMD_set(p2f[3].powerq); + powerp = SIMD_set(p2f[_onetype].powerp); + powerq = SIMD_set(p2f[_onetype].powerq); } if (EFLAG) { - c5 = SIMD_set(p2e[3].c5); - c6 = SIMD_set(p2e[3].c6); + c5 = SIMD_set(p2e[_onetype].c5); + c6 = SIMD_set(p2e[_onetype].c6); } } - const SIMD_int goffset = SIMD_set(0,16,32,48,64,80,96,112,128, - 144,160,176,192,208,224,240); acc_t * const dforce = &(f[0].x); for (int i = iifrom; i < iito; i += iip) { SIMD_int ilistv = SIMD_load(ilist + i); SIMD_int goffset = ilistv * 16; - SIMD_mask imask = ilistv < iito; + SIMD_mask imask; + if (swidth == 16) + imask = 0xFFFF; + else + imask = 0xFF; + const int rem = iito - i; + if (rem < swidth) imask = imask >> (swidth - rem); SIMD_flt_t xtmp, ytmp, ztmp; SIMD_int itype, itype_offset; @@ -741,11 +751,12 @@ void PairSWIntel::eval(const int offload, const int vflag, #ifdef LMP_INTEL_3BODY_FAST const int* ng = firstneigh + cnumneigh[i] - swidth; + const SIMD_int jnum = SIMD_loadz(imask, numneigh + i); #else SIMD_int ng = SIMD_load(cnumneigh + i); + const SIMD_int jnum = SIMD_gatherz(imask, numneigh, ilistv); ng = ng - 1; #endif - const SIMD_int jnum = SIMD_loadz(imask, numneigh + i); const SIMD_int jnumhalf = SIMD_loadz(imask, numneighhalf + i); const int jnum_max = SIMD_max(jnum); @@ -1051,11 +1062,9 @@ void PairSWIntel::eval(const int offload, const int vflag, IP_PRE_fdotr_reduce(1, nall, nthreads, f_stride, vflag, ov0, ov1, ov2, ov3, ov4, ov5); - if (EFLAG) { + if (EFLAG || vflag) { ev_global[0] = oevdwl; ev_global[1] = (acc_t)0.0; - } - if (vflag) { ev_global[2] = ov0; ev_global[3] = ov1; ev_global[4] = ov2; @@ -1162,26 +1171,22 @@ void PairSWIntel::pack_force_const(ForceConst &fc, int tp1 = atom->ntypes + 1; fc.set_ntypes(tp1,memory,_cop); - buffers->set_ntypes(tp1); - flt_t **cutneighsq = buffers->get_cutneighsq(); // Repeat cutsq calculation because done after call to init_style - double cut, cutneigh; for (int i = 1; i <= atom->ntypes; i++) { for (int j = i; j <= atom->ntypes; j++) { - if (setflag[i][j] != 0 || (setflag[i][i] != 0 && setflag[j][j] != 0)) { + double cut; + if (setflag[i][j] != 0 || (setflag[i][i] != 0 && setflag[j][j] != 0)) cut = init_one(i,j); - cutneigh = cut + neighbor->skin; - cutsq[i][j] = cutsq[j][i] = cut*cut; - cutneighsq[i][j] = cutneighsq[j][i] = cutneigh * cutneigh; - } + else + cut = 0.0; + cutsq[i][j] = cutsq[j][i] = cut*cut; } } _onetype = 0; - if (atom->ntypes == 1) _onetype = 1; - _spq = 1; + int mytypes = 0; for (int ii = 0; ii < tp1; ii++) { int i = map[ii]; for (int jj = 0; jj < tp1; jj++) { @@ -1231,6 +1236,9 @@ void PairSWIntel::pack_force_const(ForceConst &fc, fc.p3[ii][jj][kk].lambda_epsilon = 0; fc.p3[ii][jj][kk].lambda_epsilon2 = 0; } else { + mytypes++; + _onetype = ii * tp1 + jj; + _onetype3 = ii * tp1 * tp1 + jj * tp1 + kk; int ijkparam = elem2param[i][j][k]; fc.p3[ii][jj][kk].costheta = params[ijkparam].costheta; fc.p3[ii][jj][kk].lambda_epsilon = params[ijkparam].lambda_epsilon; @@ -1239,12 +1247,7 @@ void PairSWIntel::pack_force_const(ForceConst &fc, } } } - - _host_pad = 1; - _offload_pad = 1; - - if (INTEL_NBOR_PAD > 1) - _host_pad = INTEL_NBOR_PAD * sizeof(float) / sizeof(flt_t); + if (mytypes > 1) _onetype = 0; #ifdef _LMP_INTEL_OFFLOAD if (_cop < 0) return; @@ -1253,16 +1256,11 @@ void PairSWIntel::pack_force_const(ForceConst &fc, FC_PACKED1p2_T *op2f2 = fc.p2f2[0]; FC_PACKED2_T *op2e = fc.p2e[0]; FC_PACKED3_T *op3 = fc.p3[0][0]; - flt_t * ocutneighsq = cutneighsq[0]; int tp1sq = tp1 * tp1; int tp1cu = tp1sq * tp1; - if (op2 != NULL && op2f != NULL && op2f2 != NULL && op2e != NULL && - op3 != NULL && ocutneighsq != NULL) { - #pragma offload_transfer target(mic:_cop) \ - in(op2,op2f,op2f2,op2e: length(tp1sq) alloc_if(0) free_if(0)) \ - in(op3: length(tp1cu) alloc_if(0) free_if(0)) \ - in(ocutneighsq: length(tp1sq)) - } + #pragma offload_transfer target(mic:_cop) \ + in(op2,op2f,op2f2,op2e: length(tp1sq) alloc_if(0) free_if(0)) \ + in(op3: length(tp1cu) alloc_if(0) free_if(0)) #endif } diff --git a/src/USER-INTEL/pair_sw_intel.h b/src/USER-INTEL/pair_sw_intel.h index ffcf9a6fb6..36e39e3e85 100644 --- a/src/USER-INTEL/pair_sw_intel.h +++ b/src/USER-INTEL/pair_sw_intel.h @@ -49,13 +49,13 @@ class PairSWIntel : public PairSW { template void eval(const int offload, const int vflag, IntelBuffers * buffers, const ForceConst &fc, - const int astart, const int aend, const int pad_width); + const int astart, const int aend); template void pack_force_const(ForceConst &fc, IntelBuffers *buffers); - int _ccache_stride, _host_pad, _offload_pad, _spq, _onetype; + int _ccache_stride, _spq, _onetype, _onetype3; #ifdef LMP_USE_AVXCD int _ccache_stride3; #endif @@ -75,7 +75,7 @@ class PairSWIntel : public PairSW { flt_t c1, c2, c3, c4; } fc_packed1p2; typedef struct { - flt_t c5, c6; + flt_t c5, c6, d1, d2; } fc_packed2; typedef struct { flt_t costheta, lambda_epsilon, lambda_epsilon2, pad; diff --git a/src/USER-INTEL/pair_tersoff_intel.cpp b/src/USER-INTEL/pair_tersoff_intel.cpp index 584b371784..5d4c5f2cb6 100644 --- a/src/USER-INTEL/pair_tersoff_intel.cpp +++ b/src/USER-INTEL/pair_tersoff_intel.cpp @@ -220,7 +220,7 @@ struct IntelKernelTersoff : public lmp_intel::vector_routines static void kernel_step( int eatom, int vflag, const int * _noalias const numneigh, - const int * _noalias const cnumneigh, + iarr vcnumneigh, const int * _noalias const firstneigh, int ntypes, typename IntelBuffers::atom_t * _noalias const x, @@ -241,7 +241,8 @@ struct IntelKernelTersoff : public lmp_intel::vector_routines const c_inner_t * _noalias const c_inner, const c_outer_t * _noalias const c_outer, typename IntelBuffers::vec3_acc_t * _noalias const f, - avec *vsevdwl, int compress_idx, int i, iarr js, bvec vmask_repulsive + avec *vsevdwl, int compress_idx, int ii, int i, iarr js, + bvec vmask_repulsive ); }; @@ -274,9 +275,12 @@ void PairTersoffIntel::eval(const int offload, const int vflag, const int * _noalias const ilist = list->ilist; const int * _noalias const numneigh = list->numneigh; - const int * _noalias const cnumneigh = buffers->cnumneigh(list); - const int * _noalias const numneighhalf = buffers->get_atombin(); - const int * _noalias const firstneigh = buffers->firstneigh(list); + const int * _noalias const firstneigh = list->firstneigh[ilist[0]]; + + int *nhalf, *cnum; + buffers->get_list_data3(list, nhalf, cnum); + const int * _noalias const numneighhalf = nhalf; + const int * _noalias const cnumneigh = cnum; typedef typename ForceConst::c_inner_t c_inner_t; typedef typename ForceConst::c_outer_t c_outer_t; @@ -332,13 +336,13 @@ void PairTersoffIntel::eval(const int offload, const int vflag, IP_PRE_repack_for_offload(1, separate_flag, nlocal, nall, f_stride, x, 0); - acc_t oevdwl, oecoul, ov0, ov1, ov2, ov3, ov4, ov5; - if (EFLAG) oevdwl = oecoul = (acc_t)0; - if (vflag) ov0 = ov1 = ov2 = ov3 = ov4 = ov5 = (acc_t)0; + acc_t oevdwl, ov0, ov1, ov2, ov3, ov4, ov5; + if (EFLAG || vflag) + oevdwl = ov0 = ov1 = ov2 = ov3 = ov4 = ov5 = (acc_t)0; // loop over neighbors of my atoms #if defined(_OPENMP) - #pragma omp parallel reduction(+:oevdwl,oecoul,ov0,ov1,ov2,ov3,ov4,ov5) + #pragma omp parallel reduction(+:oevdwl,ov0,ov1,ov2,ov3,ov4,ov5) #endif { int iifrom, iito, tid; @@ -379,11 +383,9 @@ void PairTersoffIntel::eval(const int offload, const int vflag, IP_PRE_fdotr_reduce(1, nall, nthreads, f_stride, vflag, ov0, ov1, ov2, ov3, ov4, ov5); - if (EFLAG) { + if (EFLAG || vflag) { ev_global[0] = oevdwl; ev_global[1] = 0.0; - } - if (vflag) { ev_global[2] = ov0; ev_global[3] = ov1; ev_global[4] = ov2; @@ -461,19 +463,16 @@ void PairTersoffIntel::pack_force_const(ForceConst &fc, int tp1 = atom->ntypes + 1; fc.set_ntypes(tp1, memory, _cop); - buffers->set_ntypes(tp1); - flt_t **cutneighsq = buffers->get_cutneighsq(); // Repeat cutsq calculation because done after call to init_style - double cut, cutneigh; for (int i = 1; i <= atom->ntypes; i++) { for (int j = i; j <= atom->ntypes; j++) { - if (setflag[i][j] != 0 || (setflag[i][i] != 0 && setflag[j][j] != 0)) { + double cut; + if (setflag[i][j] != 0 || (setflag[i][i] != 0 && setflag[j][j] != 0)) cut = init_one(i, j); - cutneigh = cut + neighbor->skin; - cutsq[i][j] = cutsq[j][i] = cut*cut; - cutneighsq[i][j] = cutneighsq[j][i] = cutneigh * cutneigh; - } + else + cut = 0.0; + cutsq[i][j] = cutsq[j][i] = cut*cut; } } @@ -547,7 +546,6 @@ void PairTersoffIntel::pack_force_const(ForceConst &fc, typename ForceConst::c_inner_loop_t * c_inner_loop = fc.c_inner_loop[0][0]; typename ForceConst::c_cutoff_t * c_cutoff_inner = fc.c_cutoff_inner[0][0]; typename ForceConst::c_inner_t * c_inner = fc.c_inner[0][0]; - flt_t * ocutneighsq = cutneighsq[0]; size_t VL = 512 / 8 / sizeof(flt_t); int ntypes = tp1; int ntypes_pad = ntypes + VL - ntypes % VL; @@ -557,8 +555,7 @@ void PairTersoffIntel::pack_force_const(ForceConst &fc, #pragma offload_transfer target(mic:_cop) \ in(c_first_loop, c_second_loop, c_cutoff_outer, c_outer : length(tp1sq) alloc_if(0) free_if(0)) \ in(c_inner : length(tp1cb) alloc_if(0) free_if(0)) \ - in(c_cutoff_inner : length(tp1cb_pad) alloc_if(0) free_if(0)) \ - in(ocutneighsq: length(tp1sq) alloc_if(0) free_if(0)) + in(c_cutoff_inner : length(tp1cb_pad) alloc_if(0) free_if(0)) #endif } @@ -647,7 +644,7 @@ template template void IntelKernelTersoff::kernel_step( int eatom, int vflag, - const int * _noalias const numneigh, const int * _noalias const cnumneigh, + const int * _noalias const numneigh, iarr vcnumneigh, const int * _noalias const firstneigh, int ntypes, typename IntelBuffers::atom_t * _noalias const x, const typename PairTersoffIntel::ForceConst::c_inner_t * _noalias const c_inner, @@ -681,6 +678,7 @@ void IntelKernelTersoff::kernel_step( // TDO: We could extract this from the driver routine ivec vis = v::int_mullo(v_i4floats, v::int_load_vl(is)); ivec vjs = v::int_mullo(v_i4floats, v::int_load_vl(js)); + ivec vcnumneigh_i = v::int_load_vl(vcnumneigh); bvec vmask = v::mask_enable_lower(compress_idx); fvec vx_i = v::zero(), vy_i = v::zero(), vz_i = v::zero(); ivec vw_i = v_i0; @@ -692,7 +690,6 @@ void IntelKernelTersoff::kernel_step( fvec vrijsq = vdx_ij * vdx_ij + vdy_ij * vdy_ij + vdz_ij * vdz_ij; fvec vrij = sqrt(vrijsq); ivec vis_orig = v::int_load_vl(is); - ivec vcnumneigh_i = v::int_gather<4>(v_i0, vmask, vis_orig, cnumneigh); ivec vnumneigh_i = v::int_gather<4>(v_i0, vmask, vis_orig, numneigh); ivec vc_idx_ij = v::int_mullo(v_i4floats, vw_j + v::int_mullo(v_i_ntypes, vw_i)); @@ -930,6 +927,7 @@ void IntelKernelTersoff::kernel_step_const_i( typename IntelBuffers::vec3_acc_t * _noalias const f, avec *vsevdwl, int compress_idx, + int ii, int i, iarr js, bvec vmask_repulsive @@ -970,7 +968,7 @@ void IntelKernelTersoff::kernel_step_const_i( fvec vrijsq = vdx_ij * vdx_ij + vdy_ij * vdy_ij + vdz_ij * vdz_ij; fvec vrij = sqrt(vrijsq); - int cnumneigh_i = cnumneigh[i]; + int cnumneigh_i = cnumneigh[ii]; int numneigh_i = numneigh[i]; ivec vc_idx_j = v::int_mullo(v_i4floats, vw_j); ivec vc_idx_j_ntypes = v::int_mullo(v_i_ntypes, vc_idx_j); @@ -1147,7 +1145,7 @@ void IntelKernelTersoff::kernel( ) { int compress_idx = 0; int ii, jj; - iarr is, js; + iarr is, js, vc; avec vsevdwl = v::acc_zero(); ivec v_i4floats(static_cast(sizeof(typename v::fscal) * 4)); ivec vj, v_NEIGHMASK(NEIGHMASK); @@ -1166,7 +1164,7 @@ void IntelKernelTersoff::kernel( flt_t y_i = x[i].y; flt_t z_i = x[i].z; int jlist_off_i = cnumneigh[ii]; - int jnum = numneigh[ii]; + int jnum = numneigh[i]; for (jj = 0; jj < jnum; jj++) { int j = firstneigh[jlist_off_i + jj] & NEIGHMASK; int w_j = x[j].w; @@ -1178,6 +1176,7 @@ void IntelKernelTersoff::kernel( if (rsq < cutsq) { is[compress_idx] = ii; js[compress_idx] = j; + vc[compress_idx] = jlist_off_i; if (jj < numneighhalf[ii]) repulsive_flag[compress_idx] = 1; compress_idx += 1; @@ -1187,7 +1186,7 @@ void IntelKernelTersoff::kernel( vmask_repulsive = v::int_cmpneq(v::int_load_vl(repulsive_flag), ivec(0)); kernel_step( eatom, vflag, - numneigh, cnumneigh, firstneigh, ntypes, + numneigh, vc, firstneigh, ntypes, x, c_inner, c_outer, f, &vsevdwl, compress_idx, is, js, vmask_repulsive @@ -1203,7 +1202,7 @@ void IntelKernelTersoff::kernel( numneigh, cnumneigh, firstneigh, ntypes, x, c_inner, c_outer, f, &vsevdwl, compress_idx, - i, js, vmask_repulsive + ii, i, js, vmask_repulsive ); compress_idx = 0; v::int_clear_arr(repulsive_flag); @@ -1215,7 +1214,7 @@ void IntelKernelTersoff::kernel( vmask_repulsive = v::int_cmpneq(v::int_load_vl(repulsive_flag), ivec(0)); IntelKernelTersoff::kernel_step( eatom, vflag, - numneigh, cnumneigh, firstneigh, ntypes, + numneigh, vc, firstneigh, ntypes, x, c_inner, c_outer, f, &vsevdwl, compress_idx, is, js, vmask_repulsive diff --git a/src/USER-INTEL/pppm_intel.cpp b/src/USER-INTEL/pppm_intel.cpp index e5540e6377..537a573f23 100644 --- a/src/USER-INTEL/pppm_intel.cpp +++ b/src/USER-INTEL/pppm_intel.cpp @@ -581,6 +581,12 @@ void PPPMIntel::fieldforce_ik(IntelBuffers *buffers) else nthr = comm->nthreads; + if (fix->need_zero(0)) { + int zl = nlocal; + if (force->newton_pair) zl += atom->nghost; + memset(f, 0, zl * sizeof(FORCE_T)); + } + #if defined(_OPENMP) #pragma omp parallel default(none) \ shared(nlocal, nthr) if(!_use_lrt) @@ -726,6 +732,12 @@ void PPPMIntel::fieldforce_ad(IntelBuffers *buffers) FFT_SCALAR * _noalias const particle_eky = this->particle_eky; FFT_SCALAR * _noalias const particle_ekz = this->particle_ekz; + if (fix->need_zero(0)) { + int zl = nlocal; + if (force->newton_pair) zl += atom->nghost; + memset(f, 0, zl * sizeof(FORCE_T)); + } + #if defined(_OPENMP) #pragma omp parallel default(none) \ shared(nlocal, nthr) if(!_use_lrt) diff --git a/src/memory.cpp b/src/memory.cpp index 7a23a23079..971de3dce6 100644 --- a/src/memory.cpp +++ b/src/memory.cpp @@ -79,7 +79,9 @@ void *Memory::srealloc(void *ptr, bigint nbytes, const char *name) #if defined(LMP_USE_TBB_ALLOCATOR) ptr = scalable_aligned_realloc(ptr, nbytes, LAMMPS_MEMALIGN); -#elif defined(LMP_INTEL_NO_TBB) && defined(LAMMPS_MEMALIGN) +#elif defined(LMP_INTEL_NO_TBB) && defined(LAMMPS_MEMALIGN) && \ + defined(__INTEL_COMPILER) + ptr = realloc(ptr, nbytes); uintptr_t offset = ((uintptr_t)(const void *)(ptr)) % LAMMPS_MEMALIGN; if (offset) { diff --git a/src/pair.h b/src/pair.h index 844bc0cdc7..c1a9e6eef8 100644 --- a/src/pair.h +++ b/src/pair.h @@ -207,6 +207,10 @@ class Pair : protected Pointers { typedef union {int i; float f;} union_int_float_t; + // Accessor for the user-intel package to determine virial calc for hybrid + + inline int fdotr_is_set() const { return vflag_fdotr; } + protected: int vflag_fdotr; int maxeatom,maxvatom; From 8cbee78725c92f8059331ad8e5932c2418a425de Mon Sep 17 00:00:00 2001 From: Michael Brown Date: Thu, 11 Oct 2018 05:46:40 -0700 Subject: [PATCH 252/302] Changes to intel Makefiles to make use of MKL consistent. --- src/MAKE/OPTIONS/Makefile.intel_cpu | 7 +++---- src/MAKE/OPTIONS/Makefile.intel_cpu_intelmpi | 7 +++---- src/MAKE/OPTIONS/Makefile.intel_cpu_mpich | 6 +++--- src/MAKE/OPTIONS/Makefile.intel_cpu_openmpi | 6 +++--- 4 files changed, 12 insertions(+), 14 deletions(-) diff --git a/src/MAKE/OPTIONS/Makefile.intel_cpu b/src/MAKE/OPTIONS/Makefile.intel_cpu index efd8ac288d..831b16d854 100644 --- a/src/MAKE/OPTIONS/Makefile.intel_cpu +++ b/src/MAKE/OPTIONS/Makefile.intel_cpu @@ -15,8 +15,8 @@ SHFLAGS = -fPIC DEPFLAGS = -M LINK = mpiicpc -LINKFLAGS = -qopenmp $(OPTFLAGS) -LIB = -ltbbmalloc +LINKFLAGS = -qopenmp $(OPTFLAGS) -L$(MKLROOT)/lib/intel64/ +LIB = -ltbbmalloc -lmkl_intel_ilp64 -lmkl_sequential -lmkl_core SIZE = size ARCHIVE = ar @@ -55,8 +55,7 @@ MPI_LIB = FFT_INC = -DFFT_MKL -DFFT_SINGLE FFT_PATH = -FFT_LIB = -L$(MKLROOT)/lib/intel64/ -lmkl_intel_ilp64 \ - -lmkl_sequential -lmkl_core +FFT_LIB = # JPEG and/or PNG library # see discussion in Section 2.2 (step 7) of manual diff --git a/src/MAKE/OPTIONS/Makefile.intel_cpu_intelmpi b/src/MAKE/OPTIONS/Makefile.intel_cpu_intelmpi index 9d425bf22a..926518f354 100644 --- a/src/MAKE/OPTIONS/Makefile.intel_cpu_intelmpi +++ b/src/MAKE/OPTIONS/Makefile.intel_cpu_intelmpi @@ -15,8 +15,8 @@ SHFLAGS = -fPIC DEPFLAGS = -M LINK = mpiicpc -LINKFLAGS = -qopenmp $(OPTFLAGS) -LIB = -ltbbmalloc +LINKFLAGS = -qopenmp $(OPTFLAGS) -L$(MKLROOT)/lib/intel64/ +LIB = -ltbbmalloc -lmkl_intel_ilp64 -lmkl_sequential -lmkl_core SIZE = size ARCHIVE = ar @@ -55,8 +55,7 @@ MPI_LIB = FFT_INC = -DFFT_MKL -DFFT_SINGLE FFT_PATH = -FFT_LIB = -L$(MKLROOT)/lib/intel64/ -lmkl_intel_ilp64 \ - -lmkl_sequential -lmkl_core +FFT_LIB = # JPEG and/or PNG library # see discussion in Section 2.2 (step 7) of manual diff --git a/src/MAKE/OPTIONS/Makefile.intel_cpu_mpich b/src/MAKE/OPTIONS/Makefile.intel_cpu_mpich index 102e66f8bb..61934b69b4 100644 --- a/src/MAKE/OPTIONS/Makefile.intel_cpu_mpich +++ b/src/MAKE/OPTIONS/Makefile.intel_cpu_mpich @@ -15,8 +15,8 @@ SHFLAGS = -fPIC DEPFLAGS = -M LINK = mpicxx -cxx=icc -LINKFLAGS = -qopenmp $(OPTFLAGS) -LIB = -ltbbmalloc +LINKFLAGS = -qopenmp $(OPTFLAGS) -L$(MKLROOT)/lib/intel64/ +LIB = -ltbbmalloc -lmkl_intel_ilp64 -lmkl_sequential -lmkl_core SIZE = size ARCHIVE = ar @@ -53,7 +53,7 @@ MPI_LIB = -lmpich -lmpl -lpthread # PATH = path for FFT library # LIB = name of FFT library -FFT_INC = +FFT_INC = -DFFT_MKL -DFFT_SINGLE FFT_PATH = FFT_LIB = diff --git a/src/MAKE/OPTIONS/Makefile.intel_cpu_openmpi b/src/MAKE/OPTIONS/Makefile.intel_cpu_openmpi index a0dea06aac..ee26443f7d 100644 --- a/src/MAKE/OPTIONS/Makefile.intel_cpu_openmpi +++ b/src/MAKE/OPTIONS/Makefile.intel_cpu_openmpi @@ -16,8 +16,8 @@ SHFLAGS = -fPIC DEPFLAGS = -M LINK = mpicxx -LINKFLAGS = -qopenmp $(OPTFLAGS) -LIB = -ltbbmalloc +LINKFLAGS = -qopenmp $(OPTFLAGS) -L$(MKLROOT)/lib/intel64/ +LIB = -ltbbmalloc -lmkl_intel_ilp64 -lmkl_sequential -lmkl_core SIZE = size ARCHIVE = ar @@ -54,7 +54,7 @@ MPI_LIB = # PATH = path for FFT library # LIB = name of FFT library -FFT_INC = +FFT_INC = -DFFT_MKL -DFFT_SINGLE FFT_PATH = FFT_LIB = From 8eb74d8fb37dd865ba7e2b70102d9e288f683f72 Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Thu, 11 Oct 2018 13:21:44 -0600 Subject: [PATCH 253/302] Add missing Kokkos pack/unpack comm vel functions --- src/KOKKOS/atom_vec_kokkos.cpp | 271 +++++++++++++++++++++++++++++++++ src/KOKKOS/atom_vec_kokkos.h | 4 +- 2 files changed, 273 insertions(+), 2 deletions(-) diff --git a/src/KOKKOS/atom_vec_kokkos.cpp b/src/KOKKOS/atom_vec_kokkos.cpp index f2c04bec1b..555bb2e747 100644 --- a/src/KOKKOS/atom_vec_kokkos.cpp +++ b/src/KOKKOS/atom_vec_kokkos.cpp @@ -305,6 +305,277 @@ void AtomVecKokkos::unpack_comm_kokkos(const int &n, const int &first, } } + +/* ---------------------------------------------------------------------- */ + +template +struct AtomVecKokkos_PackCommVel { + typedef DeviceType device_type; + + typename ArrayTypes::t_x_array_randomread _x; + typename ArrayTypes::t_int_1d _mask; + typename ArrayTypes::t_v_array _v; + typename ArrayTypes::t_xfloat_2d_um _buf; + typename ArrayTypes::t_int_2d_const _list; + const int _iswap; + X_FLOAT _xprd,_yprd,_zprd,_xy,_xz,_yz; + X_FLOAT _pbc[6]; + X_FLOAT _h_rate[6]; + const int _deform_vremap; + + AtomVecKokkos_PackCommVel( + const typename DAT::tdual_x_array &x, + const typename DAT::tdual_int_1d &mask, + const typename DAT::tdual_v_array &v, + const typename DAT::tdual_xfloat_2d &buf, + const typename DAT::tdual_int_2d &list, + const int &iswap, + const X_FLOAT &xprd, const X_FLOAT &yprd, const X_FLOAT &zprd, + const X_FLOAT &xy, const X_FLOAT &xz, const X_FLOAT &yz, const int* const pbc, + const double * const h_rate, + const int &deform_vremap): + _x(x.view()), + _mask(mask.view()), + _v(v.view()), + _list(list.view()),_iswap(iswap), + _xprd(xprd),_yprd(yprd),_zprd(zprd), + _xy(xy),_xz(xz),_yz(yz), + _deform_vremap(deform_vremap) + { + const size_t elements = 6; + const int maxsend = (buf.template view().extent(0)*buf.template view().extent(1))/elements; + _buf = typename ArrayTypes::t_xfloat_2d_um(buf.view().data(),maxsend,elements); + _pbc[0] = pbc[0]; _pbc[1] = pbc[1]; _pbc[2] = pbc[2]; + _pbc[3] = pbc[3]; _pbc[4] = pbc[4]; _pbc[5] = pbc[5]; + _h_rate[0] = h_rate[0]; _h_rate[1] = h_rate[1]; _h_rate[2] = h_rate[2]; + _h_rate[3] = h_rate[3]; _h_rate[4] = h_rate[4]; _h_rate[5] = h_rate[5]; + } + + KOKKOS_INLINE_FUNCTION + void operator() (const int& i) const { + const int j = _list(_iswap,i); + if (PBC_FLAG == 0) { + _buf(i,0) = _x(j,0); + _buf(i,1) = _x(j,1); + _buf(i,2) = _x(j,2); + _buf(i,3) = _v(j,0); + _buf(i,4) = _v(j,1); + _buf(i,5) = _v(j,2); + } else { + if (TRICLINIC == 0) { + _buf(i,0) = _x(j,0) + _pbc[0]*_xprd; + _buf(i,1) = _x(j,1) + _pbc[1]*_yprd; + _buf(i,2) = _x(j,2) + _pbc[2]*_zprd; + } else { + _buf(i,0) = _x(j,0) + _pbc[0]*_xprd + _pbc[5]*_xy + _pbc[4]*_xz; + _buf(i,1) = _x(j,1) + _pbc[1]*_yprd + _pbc[3]*_yz; + _buf(i,2) = _x(j,2) + _pbc[2]*_zprd; + } + + if (DEFORM_VREMAP == 0) { + _buf(i,3) = _v(j,0); + _buf(i,4) = _v(j,1); + _buf(i,5) = _v(j,2); + } else { + if (_mask(i) & _deform_vremap) { + _buf(i,3) = _v(j,0) + _pbc[0]*_h_rate[0] + _pbc[5]*_h_rate[5] + _pbc[4]*_h_rate[4]; + _buf(i,4) = _v(j,1) + _pbc[1]*_h_rate[1] + _pbc[3]*_h_rate[3]; + _buf(i,5) = _v(j,2) + _pbc[2]*_h_rate[2]; + } else { + _buf(i,3) = _v(j,0); + _buf(i,4) = _v(j,1); + _buf(i,5) = _v(j,2); + } + } + } + } +}; + +/* ---------------------------------------------------------------------- */ + +int AtomVecKokkos::pack_comm_vel_kokkos( + const int &n, + const DAT::tdual_int_2d &list, + const int & iswap, + const DAT::tdual_xfloat_2d &buf, + const int &pbc_flag, + const int* const pbc) +{ + if(commKK->forward_comm_on_host) { + sync(Host,X_MASK|V_MASK); + if (pbc_flag) { + if (deform_vremap) { + if (domain->triclinic) { + struct AtomVecKokkos_PackCommVel f( + atomKK->k_x,atomKK->k_mask, + atomKK->k_v, + buf,list,iswap, + domain->xprd,domain->yprd,domain->zprd, + domain->xy,domain->xz,domain->yz,pbc,h_rate,deform_vremap); + Kokkos::parallel_for(n,f); + } else { + struct AtomVecKokkos_PackCommVel f( + atomKK->k_x,atomKK->k_mask, + atomKK->k_v, + buf,list,iswap, + domain->xprd,domain->yprd,domain->zprd, + domain->xy,domain->xz,domain->yz,pbc,h_rate,deform_vremap); + Kokkos::parallel_for(n,f); + } + } else { + if(domain->triclinic) { + struct AtomVecKokkos_PackCommVel f( + atomKK->k_x,atomKK->k_mask, + atomKK->k_v, + buf,list,iswap, + domain->xprd,domain->yprd,domain->zprd, + domain->xy,domain->xz,domain->yz,pbc,h_rate,deform_vremap); + Kokkos::parallel_for(n,f); + } else { + struct AtomVecKokkos_PackCommVel f( + atomKK->k_x,atomKK->k_mask, + atomKK->k_v, + buf,list,iswap, + domain->xprd,domain->yprd,domain->zprd, + domain->xy,domain->xz,domain->yz,pbc,h_rate,deform_vremap); + Kokkos::parallel_for(n,f); + } + } + } else { + if(domain->triclinic) { + struct AtomVecKokkos_PackCommVel f( + atomKK->k_x,atomKK->k_mask, + atomKK->k_v, + buf,list,iswap, + domain->xprd,domain->yprd,domain->zprd, + domain->xy,domain->xz,domain->yz,pbc,h_rate,deform_vremap); + Kokkos::parallel_for(n,f); + } else { + struct AtomVecKokkos_PackCommVel f( + atomKK->k_x,atomKK->k_mask, + atomKK->k_v, + buf,list,iswap, + domain->xprd,domain->yprd,domain->zprd, + domain->xy,domain->xz,domain->yz,pbc,h_rate,deform_vremap); + Kokkos::parallel_for(n,f); + } + } + } else { + sync(Device,X_MASK|V_MASK); + if(pbc_flag) { + if(deform_vremap) { + if(domain->triclinic) { + struct AtomVecKokkos_PackCommVel f( + atomKK->k_x,atomKK->k_mask, + atomKK->k_v, + buf,list,iswap, + domain->xprd,domain->yprd,domain->zprd, + domain->xy,domain->xz,domain->yz,pbc,h_rate,deform_vremap); + Kokkos::parallel_for(n,f); + } else { + struct AtomVecKokkos_PackCommVel f( + atomKK->k_x,atomKK->k_mask, + atomKK->k_v, + buf,list,iswap, + domain->xprd,domain->yprd,domain->zprd, + domain->xy,domain->xz,domain->yz,pbc,h_rate,deform_vremap); + Kokkos::parallel_for(n,f); + } + } else { + if(domain->triclinic) { + struct AtomVecKokkos_PackCommVel f( + atomKK->k_x,atomKK->k_mask, + atomKK->k_v, + buf,list,iswap, + domain->xprd,domain->yprd,domain->zprd, + domain->xy,domain->xz,domain->yz,pbc,h_rate,deform_vremap); + Kokkos::parallel_for(n,f); + } else { + struct AtomVecKokkos_PackCommVel f( + atomKK->k_x,atomKK->k_mask, + atomKK->k_v, + buf,list,iswap, + domain->xprd,domain->yprd,domain->zprd, + domain->xy,domain->xz,domain->yz,pbc,h_rate,deform_vremap); + Kokkos::parallel_for(n,f); + } + } + } else { + if(domain->triclinic) { + struct AtomVecKokkos_PackCommVel f( + atomKK->k_x,atomKK->k_mask, + atomKK->k_v, + buf,list,iswap, + domain->xprd,domain->yprd,domain->zprd, + domain->xy,domain->xz,domain->yz,pbc,h_rate,deform_vremap); + Kokkos::parallel_for(n,f); + } else { + struct AtomVecKokkos_PackCommVel f( + atomKK->k_x,atomKK->k_mask, + atomKK->k_v, + buf,list,iswap, + domain->xprd,domain->yprd,domain->zprd, + domain->xy,domain->xz,domain->yz,pbc,h_rate,deform_vremap); + Kokkos::parallel_for(n,f); + } + } + } + return n*6; +} + +/* ---------------------------------------------------------------------- */ + +template +struct AtomVecKokkos_UnpackCommVel { + typedef DeviceType device_type; + + typename ArrayTypes::t_x_array _x; + typename ArrayTypes::t_v_array _v; + typename ArrayTypes::t_xfloat_2d_const _buf; + int _first; + + AtomVecKokkos_UnpackCommVel( + const typename DAT::tdual_x_array &x, + const typename DAT::tdual_v_array &v, + const typename DAT::tdual_xfloat_2d &buf, + const int& first): + _x(x.view()), + _v(v.view()), + _first(first) + { + const size_t elements = 6; + const int maxsend = (buf.template view().extent(0)*buf.template view().extent(1))/elements; + buffer_view(_buf,buf,maxsend,elements); + }; + + KOKKOS_INLINE_FUNCTION + void operator() (const int& i) const { + _x(i+_first,0) = _buf(i,0); + _x(i+_first,1) = _buf(i,1); + _x(i+_first,2) = _buf(i,2); + _v(i+_first,0) = _buf(i,3); + _v(i+_first,1) = _buf(i,4); + _v(i+_first,2) = _buf(i,5); + } +}; + +/* ---------------------------------------------------------------------- */ + +void AtomVecKokkos::unpack_comm_vel_kokkos(const int &n, const int &first, + const DAT::tdual_xfloat_2d &buf ) { + if(commKK->forward_comm_on_host) { + sync(Host,X_MASK|V_MASK); + modified(Host,X_MASK|V_MASK); + struct AtomVecKokkos_UnpackCommVel f(atomKK->k_x,atomKK->k_v,buf,first); + Kokkos::parallel_for(n,f); + } else { + sync(Device,X_MASK|V_MASK); + modified(Device,X_MASK|V_MASK); + struct AtomVecKokkos_UnpackCommVel f(atomKK->k_x,atomKK->k_v,buf,first); + Kokkos::parallel_for(n,f); + } +} + /* ---------------------------------------------------------------------- */ int AtomVecKokkos::pack_comm(int n, int *list, double *buf, diff --git a/src/KOKKOS/atom_vec_kokkos.h b/src/KOKKOS/atom_vec_kokkos.h index 38ffed9d37..e1d626ac1b 100644 --- a/src/KOKKOS/atom_vec_kokkos.h +++ b/src/KOKKOS/atom_vec_kokkos.h @@ -63,11 +63,11 @@ class AtomVecKokkos : public AtomVec { virtual int pack_comm_vel_kokkos(const int &n, const DAT::tdual_int_2d &list, const int & iswap, const DAT::tdual_xfloat_2d &buf, - const int &pbc_flag, const int pbc[]) { return 0; } + const int &pbc_flag, const int pbc[]); virtual void unpack_comm_vel_kokkos(const int &n, const int &nfirst, - const DAT::tdual_xfloat_2d &buf) {} + const DAT::tdual_xfloat_2d &buf); virtual int unpack_reverse_self(const int &n, const DAT::tdual_int_2d &list, From a223338b47d2495e81fa4ec187faf80d6f703f48 Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Thu, 11 Oct 2018 16:32:00 -0600 Subject: [PATCH 254/302] Fix hang with Kokkos and USER-DPD examples --- src/KOKKOS/atom_vec_dpd_kokkos.cpp | 4 +++- src/KOKKOS/atom_vec_hybrid_kokkos.cpp | 5 ++++- src/KOKKOS/atom_vec_kokkos.cpp | 3 +++ src/KOKKOS/atom_vec_kokkos.h | 2 ++ src/KOKKOS/atom_vec_sphere_kokkos.cpp | 2 ++ src/KOKKOS/comm_kokkos.cpp | 6 +++++- 6 files changed, 19 insertions(+), 3 deletions(-) diff --git a/src/KOKKOS/atom_vec_dpd_kokkos.cpp b/src/KOKKOS/atom_vec_dpd_kokkos.cpp index 24b23c6ccf..217929b332 100644 --- a/src/KOKKOS/atom_vec_dpd_kokkos.cpp +++ b/src/KOKKOS/atom_vec_dpd_kokkos.cpp @@ -37,7 +37,7 @@ AtomVecDPDKokkos::AtomVecDPDKokkos(LAMMPS *lmp) : AtomVecKokkos(lmp) size_forward = 7; size_reverse = 3; size_border = 12; - size_velocity = 3; + size_velocity = 10; size_data_atom = 6; size_data_vel = 4; xcol_data = 4; @@ -48,6 +48,8 @@ AtomVecDPDKokkos::AtomVecDPDKokkos(LAMMPS *lmp) : AtomVecKokkos(lmp) k_count = DAT::tdual_int_1d("atom::k_count",1); atomKK = (AtomKokkos *) atom; commKK = (CommKokkos *) comm; + + no_comm_vel_flag = 1; } /* ---------------------------------------------------------------------- diff --git a/src/KOKKOS/atom_vec_hybrid_kokkos.cpp b/src/KOKKOS/atom_vec_hybrid_kokkos.cpp index 7e1cc200d3..ce36f59053 100644 --- a/src/KOKKOS/atom_vec_hybrid_kokkos.cpp +++ b/src/KOKKOS/atom_vec_hybrid_kokkos.cpp @@ -26,7 +26,10 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -AtomVecHybridKokkos::AtomVecHybridKokkos(LAMMPS *lmp) : AtomVecKokkos(lmp) {} +AtomVecHybridKokkos::AtomVecHybridKokkos(LAMMPS *lmp) : AtomVecKokkos(lmp) { + no_comm_vel_flag = 1; + no_border_vel_flag = 1; +} /* ---------------------------------------------------------------------- */ diff --git a/src/KOKKOS/atom_vec_kokkos.cpp b/src/KOKKOS/atom_vec_kokkos.cpp index 555bb2e747..83af437eba 100644 --- a/src/KOKKOS/atom_vec_kokkos.cpp +++ b/src/KOKKOS/atom_vec_kokkos.cpp @@ -26,6 +26,9 @@ AtomVecKokkos::AtomVecKokkos(LAMMPS *lmp) : AtomVec(lmp) kokkosable = 1; buffer = NULL; buffer_size = 0; + + no_comm_vel_flag = 0; + no_border_vel_flag = 1; } /* ---------------------------------------------------------------------- */ diff --git a/src/KOKKOS/atom_vec_kokkos.h b/src/KOKKOS/atom_vec_kokkos.h index e1d626ac1b..efe55c47ad 100644 --- a/src/KOKKOS/atom_vec_kokkos.h +++ b/src/KOKKOS/atom_vec_kokkos.h @@ -113,6 +113,8 @@ class AtomVecKokkos : public AtomVec { ExecutionSpace space) = 0; + int no_comm_vel_flag,no_border_vel_flag; + protected: HAT::t_x_array h_x; diff --git a/src/KOKKOS/atom_vec_sphere_kokkos.cpp b/src/KOKKOS/atom_vec_sphere_kokkos.cpp index 476091ff41..3dfbc5efdc 100644 --- a/src/KOKKOS/atom_vec_sphere_kokkos.cpp +++ b/src/KOKKOS/atom_vec_sphere_kokkos.cpp @@ -57,6 +57,8 @@ AtomVecSphereKokkos::AtomVecSphereKokkos(LAMMPS *lmp) : AtomVecKokkos(lmp) k_count = DAT::tdual_int_1d("atom::k_count",1); atomKK = (AtomKokkos *) atom; commKK = (CommKokkos *) comm; + + no_border_vel_flag = 0; } /* ---------------------------------------------------------------------- */ diff --git a/src/KOKKOS/comm_kokkos.cpp b/src/KOKKOS/comm_kokkos.cpp index a9a26c0a3c..f40156aabc 100644 --- a/src/KOKKOS/comm_kokkos.cpp +++ b/src/KOKKOS/comm_kokkos.cpp @@ -136,6 +136,9 @@ void CommKokkos::init() if (!comm_f_only) // not all Kokkos atom_vec styles have reverse pack/unpack routines yet reverse_comm_classic = true; + + if (ghost_velocity && ((AtomVecKokkos*)atom->avec)->no_comm_vel_flag) // not all Kokkos atom_vec styles have comm vel pack/unpack routines yet + forward_comm_classic = true; } /* ---------------------------------------------------------------------- @@ -725,7 +728,8 @@ void CommKokkos::borders() if (!exchange_comm_classic) { static int print = 1; - if (mode != Comm::SINGLE || bordergroup) { + if (mode != Comm::SINGLE || bordergroup || + (ghost_velocity && ((AtomVecKokkos*)atom->avec)->no_border_vel_flag)) { if (print && comm->me==0) { error->warning(FLERR,"Required border comm not yet implemented in Kokkos communication, " "switching to classic communication"); From 8224c89f932d14c9c02a84b525e8fbe99bf3bd3e Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Thu, 11 Oct 2018 16:38:44 -0600 Subject: [PATCH 255/302] Revert size_velocity change in atom_vec_dpd_kokkos --- src/KOKKOS/atom_vec_dpd_kokkos.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/KOKKOS/atom_vec_dpd_kokkos.cpp b/src/KOKKOS/atom_vec_dpd_kokkos.cpp index 217929b332..30db76e723 100644 --- a/src/KOKKOS/atom_vec_dpd_kokkos.cpp +++ b/src/KOKKOS/atom_vec_dpd_kokkos.cpp @@ -37,7 +37,7 @@ AtomVecDPDKokkos::AtomVecDPDKokkos(LAMMPS *lmp) : AtomVecKokkos(lmp) size_forward = 7; size_reverse = 3; size_border = 12; - size_velocity = 10; + size_velocity = 3; size_data_atom = 6; size_data_vel = 4; xcol_data = 4; From bea0a3091d0b77bead59ca25b23926bd4acbb09b Mon Sep 17 00:00:00 2001 From: Michael Brown Date: Mon, 15 Oct 2018 10:25:39 -0700 Subject: [PATCH 256/302] Fix to allow suffix and pair hybrid to work together with USER-INTEL. --- src/USER-INTEL/fix_intel.cpp | 37 +++++++++++------------------------- src/USER-INTEL/fix_intel.h | 2 +- 2 files changed, 12 insertions(+), 27 deletions(-) diff --git a/src/USER-INTEL/fix_intel.cpp b/src/USER-INTEL/fix_intel.cpp index e0865f0431..b305590729 100644 --- a/src/USER-INTEL/fix_intel.cpp +++ b/src/USER-INTEL/fix_intel.cpp @@ -65,6 +65,7 @@ FixIntel::FixIntel(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg) _nbor_pack_width = 1; _three_body_neighbor = 0; + _pair_intel_count = 0; _hybrid_nonpair = 0; _precision_mode = PREC_MODE_MIXED; @@ -312,22 +313,14 @@ void FixIntel::init() } #endif - int nstyles = 0; + const int nstyles = _pair_intel_count; if (force->pair_match("hybrid", 1) != NULL) { _pair_hybrid_flag = 1; - PairHybrid *hybrid = (PairHybrid *) force->pair; - for (int i = 0; i < hybrid->nstyles; i++) - if (strstr(hybrid->keywords[i], "/intel") != NULL) - nstyles++; if (force->newton_pair != 0 && force->pair->no_virial_fdotr_compute) error->all(FLERR, "Intel package requires fdotr virial with newton on."); } else if (force->pair_match("hybrid/overlay", 1) != NULL) { _pair_hybrid_flag = 1; - PairHybridOverlay *hybrid = (PairHybridOverlay *) force->pair; - for (int i = 0; i < hybrid->nstyles; i++) - if (strstr(hybrid->keywords[i], "/intel") != NULL) - nstyles++; if (force->newton_pair != 0 && force->pair->no_virial_fdotr_compute) error->all(FLERR, "Intel package requires fdotr virial with newton on."); @@ -345,6 +338,8 @@ void FixIntel::init() _pair_hybrid_zero = 1; _hybrid_nonpair = 0; + _pair_intel_count = 0; + #ifdef _LMP_INTEL_OFFLOAD if (offload_balance() != 0.0) { _pair_hybrid_zero = 0; @@ -458,7 +453,7 @@ void FixIntel::pair_init_check(const bool cdmessage) force->special_coul[3] == 0.0) flag = 1; if (flag) error->all(FLERR,"Add -DLMP_INTEL_NBOR_COMPAT to build for special_bond" - "exclusions with Intel"); + " exclusions with Intel"); } #endif @@ -478,6 +473,8 @@ void FixIntel::pair_init_check(const bool cdmessage) get_double_buffers()->need_tag(need_tag); } + _pair_intel_count++; + #ifdef _LMP_INTEL_OFFLOAD set_offload_affinity(); #endif @@ -521,16 +518,10 @@ void FixIntel::bond_init_check() intel_pair = 1; else if (force->pair_match("hybrid", 1) != NULL) { _hybrid_nonpair = 1; - PairHybrid *hybrid = (PairHybrid *) force->pair; - for (int i = 0; i < hybrid->nstyles; i++) - if (strstr(hybrid->keywords[i], "/intel") != NULL) - intel_pair = 1; + if (_pair_intel_count) intel_pair = 1; } else if (force->pair_match("hybrid/overlay", 1) != NULL) { _hybrid_nonpair = 1; - PairHybridOverlay *hybrid = (PairHybridOverlay *) force->pair; - for (int i = 0; i < hybrid->nstyles; i++) - if (strstr(hybrid->keywords[i], "/intel") != NULL) - intel_pair = 1; + if (_pair_intel_count) intel_pair = 1; } if (intel_pair == 0) @@ -547,16 +538,10 @@ void FixIntel::kspace_init_check() intel_pair = 1; else if (force->pair_match("hybrid", 1) != NULL) { _hybrid_nonpair = 1; - PairHybrid *hybrid = (PairHybrid *) force->pair; - for (int i = 0; i < hybrid->nstyles; i++) - if (strstr(hybrid->keywords[i], "/intel") != NULL) - intel_pair = 1; + if (_pair_intel_count) intel_pair = 1; } else if (force->pair_match("hybrid/overlay", 1) != NULL) { _hybrid_nonpair = 1; - PairHybridOverlay *hybrid = (PairHybridOverlay *) force->pair; - for (int i = 0; i < hybrid->nstyles; i++) - if (strstr(hybrid->keywords[i], "/intel") != NULL) - intel_pair = 1; + if (_pair_intel_count) intel_pair = 1; } if (intel_pair == 0) diff --git a/src/USER-INTEL/fix_intel.h b/src/USER-INTEL/fix_intel.h index 81dd0b5d97..a01ed18bfe 100644 --- a/src/USER-INTEL/fix_intel.h +++ b/src/USER-INTEL/fix_intel.h @@ -101,7 +101,7 @@ class FixIntel : public Fix { IntelBuffers *_double_buffers; int _precision_mode, _nthreads, _nbor_pack_width, _three_body_neighbor; - int _pair_hybrid_flag; + int _pair_intel_count, _pair_hybrid_flag; // These should be removed in subsequent update w/ simpler hybrid arch int _pair_hybrid_zero, _hybrid_nonpair, _zero_master; From 2273604533fde75f8b05f9b38bf38ad50b593da8 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 16 Oct 2018 13:49:06 -0400 Subject: [PATCH 257/302] resolve portability issues to windows w.r.t. fixed width integer types --- src/USER-PTM/ptm_neighbour_ordering.cpp | 1 + src/USER-PTM/ptm_neighbour_ordering.h | 2 ++ src/USER-PTM/ptm_polar.cpp | 1 + src/USER-PTM/ptm_polar.h | 1 + src/library.h | 1 + 5 files changed, 6 insertions(+) diff --git a/src/USER-PTM/ptm_neighbour_ordering.cpp b/src/USER-PTM/ptm_neighbour_ordering.cpp index c77a779c68..d5948b9dc6 100644 --- a/src/USER-PTM/ptm_neighbour_ordering.cpp +++ b/src/USER-PTM/ptm_neighbour_ordering.cpp @@ -5,6 +5,7 @@ #include #include "ptm_constants.h" #include "ptm_voronoi_cell.h" +#include "ptm_neighbour_ordering.h" namespace ptm { diff --git a/src/USER-PTM/ptm_neighbour_ordering.h b/src/USER-PTM/ptm_neighbour_ordering.h index e43ced9fd5..78bf4d533b 100644 --- a/src/USER-PTM/ptm_neighbour_ordering.h +++ b/src/USER-PTM/ptm_neighbour_ordering.h @@ -1,6 +1,8 @@ #ifndef PTM_NEIGHBOUR_ORDERING_H #define PTM_NEIGHBOUR_ORDERING_H +#include + namespace ptm { int calculate_neighbour_ordering(void* voronoi_handle, int num_points, const double (*_points)[3], int8_t* ordering); diff --git a/src/USER-PTM/ptm_polar.cpp b/src/USER-PTM/ptm_polar.cpp index fa199ca656..2c255f386b 100644 --- a/src/USER-PTM/ptm_polar.cpp +++ b/src/USER-PTM/ptm_polar.cpp @@ -89,6 +89,7 @@ #include #include #include "ptm_quat.h" +#include "ptm_polar.h" namespace ptm { diff --git a/src/USER-PTM/ptm_polar.h b/src/USER-PTM/ptm_polar.h index 15d1f185b7..e1980f974a 100644 --- a/src/USER-PTM/ptm_polar.h +++ b/src/USER-PTM/ptm_polar.h @@ -3,6 +3,7 @@ #include #include +#include namespace ptm { diff --git a/src/library.h b/src/library.h index 82071f673b..f6f8d9d75c 100644 --- a/src/library.h +++ b/src/library.h @@ -17,6 +17,7 @@ */ #include +#include /* for int64_t */ /* ifdefs allow this file to be included in a C program */ From b71f530bd0c75a8c7aa3beb19ddae155605b113e Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 17 Oct 2018 16:04:52 -0400 Subject: [PATCH 258/302] make default style name for deprecated styles uppercase, so it is considered internal also consolidate the writeout message across styles into a single convenience function --- src/deprecated.cpp | 7 ++----- src/deprecated.h | 3 +-- src/fix_deprecated.cpp | 46 ++++++++++++++++++++--------------------- src/fix_deprecated.h | 2 +- src/pair_deprecated.cpp | 12 ++++------- src/pair_deprecated.h | 2 +- 6 files changed, 31 insertions(+), 41 deletions(-) diff --git a/src/deprecated.cpp b/src/deprecated.cpp index ed9a9e6de4..2f2282f07c 100644 --- a/src/deprecated.cpp +++ b/src/deprecated.cpp @@ -38,11 +38,8 @@ static void writemsg(LAMMPS *lmp, const char *msg, int abend=1) void Deprecated::command(int narg, char **arg) { - if (strcmp(input->command,"deprecated") == 0) { - writemsg(lmp,"\nCommand 'deprecated' is a dummy command\n\n",0); + if (strcmp(input->command,"DEPRECATED") == 0) { + writemsg(lmp,"\nCommand 'DEPRECATED' is a dummy command\n\n",0); - } else if (strcmp(input->command,"XXX") == 0) { - writemsg(lmp, "\nCommand 'XXX' has been removed from LAMMPS " - "after the\n## XXX 20## stable release.\n\n"); } } diff --git a/src/deprecated.h b/src/deprecated.h index 9835579245..97a77591c5 100644 --- a/src/deprecated.h +++ b/src/deprecated.h @@ -13,8 +13,7 @@ #ifdef COMMAND_CLASS -CommandStyle(deprecated,Deprecated) -CommandStyle(XXX,Deprecated) +CommandStyle(DEPRECATED,Deprecated) #else diff --git a/src/fix_deprecated.cpp b/src/fix_deprecated.cpp index 666ec41734..7db27152ba 100644 --- a/src/fix_deprecated.cpp +++ b/src/fix_deprecated.cpp @@ -18,35 +18,33 @@ using namespace LAMMPS_NS; +static void writemsg(LAMMPS *lmp, const char *msg, int abend=1) +{ + if (lmp->comm->me == 0) { + if (lmp->screen) fputs(msg,lmp->screen); + if (lmp->logfile) fputs(msg,lmp->logfile); + } + if (abend) + lmp->error->all(FLERR,"This fix style is no longer available"); +} + /* ---------------------------------------------------------------------- */ FixDeprecated::FixDeprecated(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg) { - if (strcmp(style,"deprecated") == 0) { - const char *message = "\n" - "NOTE: The fix style 'deprecated' is a dummy fix style that was added to\n" - "LAMMPS in order to print suitable error messages for deleted features.\n\n"; + if (strcmp(style,"DEPRECATED") == 0) { + writemsg(lmp,"\nFix style 'DEPRECATED' is a dummy style\n\n",0); - if (comm->me == 0) { - if (screen) fputs(message,screen); - if (logfile) fputs(message,logfile); - } + } else if (strncmp(style,"ave/spatial",11) == 0) { + writemsg(lmp,"\nFix styles 'ave/spatial' and 'ave/spatial/sphere' have " + "been replaced\nby the more general fix ave/chunk and compute " + "chunk/atom commands.\nAll ave/spatial and ave/spatial/sphere " + "functionality is available in these\nnew commands. These " + "ave/spatial keywords & options are part of fix ave/chunk:\n" + " Nevery, Nrepeat, Nfreq, input values, norm, ave, file, " + "overwrite, title123\nThese ave/spatial keywords & options for " + "binning are part of compute chunk/atom:\n dim, origin, delta," + " region, bound, discard, units\n\n"); } - if (strncmp(style,"ave/spatial",11) == 0) { - const char *message = "\n" - "NOTE: The fix styles 'ave/spatial' and 'ave/spatial/sphere' have been replaced\n" - "by the more general fix ave/chunk and compute chunk/atom commands.\n" - "All ave/spatial and ave/spatial/sphere functionality is available in these\n" - "new commands. These ave/spatial keywords & options are part of fix ave/chunk:\n" - " Nevery, Nrepeat, Nfreq, input values, norm, ave, file, overwrite, title123\n" - "These ave/spatial keywords & options for binning are part of compute chunk/atom:\n" - " dim, origin, delta, region, bound, discard, units\n\n"; - - if (comm->me == 0) { - if (screen) fputs(message,screen); - if (logfile) fputs(message,logfile); - } - } - error->all(FLERR,"This fix command has been removed from LAMMPS"); } diff --git a/src/fix_deprecated.h b/src/fix_deprecated.h index f4e76c47e8..a7267be04b 100644 --- a/src/fix_deprecated.h +++ b/src/fix_deprecated.h @@ -15,7 +15,7 @@ // list all deprecated and removed fix styles here -FixStyle(deprecated,FixDeprecated) +FixStyle(DEPRECATED,FixDeprecated) FixStyle(ave/spatial,FixDeprecated) FixStyle(ave/spatial/sphere,FixDeprecated) diff --git a/src/pair_deprecated.cpp b/src/pair_deprecated.cpp index 143cfd46f4..20b5c9775b 100644 --- a/src/pair_deprecated.cpp +++ b/src/pair_deprecated.cpp @@ -31,10 +31,9 @@ static void writemsg(LAMMPS *lmp, const char *msg, int abend=1) if (lmp->logfile) fputs(msg,lmp->logfile); } if (abend) - lmp->error->all(FLERR,"This pair_style is no longer available"); + lmp->error->all(FLERR,"This pair style is no longer available"); } - /* ---------------------------------------------------------------------- */ void PairDeprecated::settings(int, char **) @@ -43,18 +42,15 @@ void PairDeprecated::settings(int, char **) // hybrid substyles are created in PairHybrid::settings(), so when this is // called, our style was just added at the end of the list of substyles + if (strncmp(my_style,"hybrid",6) == 0) { PairHybrid *hybrid = (PairHybrid *)force->pair; my_style = hybrid->keywords[hybrid->nstyles]; } - if (strcmp(my_style,"deprecated") == 0) { - writemsg(lmp,"\nPair style 'deprecated' is a dummy pair style\n\n",0); + if (strcmp(my_style,"DEPRECATED") == 0) { + writemsg(lmp,"\nPair style 'DEPRECATED' is a dummy style\n\n",0); - } else if (strcmp(my_style,"reax") == 0) { - writemsg(lmp, "\nPair style 'reax' has been removed from LAMMPS " - "after the\n## November 2018 stable release. Its " - "functionality has\nbeen superseded by pair style 'reax/c'.\n\n"); } } diff --git a/src/pair_deprecated.h b/src/pair_deprecated.h index 163b2a8f1b..779dedee9a 100644 --- a/src/pair_deprecated.h +++ b/src/pair_deprecated.h @@ -13,7 +13,7 @@ #ifdef PAIR_CLASS -PairStyle(deprecated,PairDeprecated) +PairStyle(DEPRECATED,PairDeprecated) #else From 65ebbdada3943eeb68d1e9592a631e45f76117f0 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 17 Oct 2018 16:05:10 -0400 Subject: [PATCH 259/302] add DEPRECATED compute style --- src/compute_deprecated.cpp | 39 +++++++++++++++++++++++++++++++ src/compute_deprecated.h | 47 ++++++++++++++++++++++++++++++++++++++ 2 files changed, 86 insertions(+) create mode 100644 src/compute_deprecated.cpp create mode 100644 src/compute_deprecated.h diff --git a/src/compute_deprecated.cpp b/src/compute_deprecated.cpp new file mode 100644 index 0000000000..069fa73437 --- /dev/null +++ b/src/compute_deprecated.cpp @@ -0,0 +1,39 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include +#include "compute_deprecated.h" +#include "comm.h" +#include "error.h" + +using namespace LAMMPS_NS; + +static void writemsg(LAMMPS *lmp, const char *msg, int abend=1) +{ + if (lmp->comm->me == 0) { + if (lmp->screen) fputs(msg,lmp->screen); + if (lmp->logfile) fputs(msg,lmp->logfile); + } + if (abend) + lmp->error->all(FLERR,"This compute style is no longer available"); +} + +/* ---------------------------------------------------------------------- */ + +ComputeDeprecated::ComputeDeprecated(LAMMPS *lmp, int narg, char **arg) : + Compute(lmp, narg, arg) +{ + if (strcmp(style,"DEPRECATED") == 0) { + writemsg(lmp,"\nCompute style 'DEPRECATED' is a dummy style\n\n",0); + } +} diff --git a/src/compute_deprecated.h b/src/compute_deprecated.h new file mode 100644 index 0000000000..35c114c542 --- /dev/null +++ b/src/compute_deprecated.h @@ -0,0 +1,47 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef COMPUTE_CLASS + +// list all deprecated and removed compute styles here + +ComputeStyle(DEPRECATED,ComputeDeprecated) + +#else + +#ifndef LMP_COMPUTE_DEPRECATED_H +#define LMP_COMPUTE_DEPRECATED_H + +#include "compute.h" + +namespace LAMMPS_NS { + +class ComputeDeprecated : public Compute { + public: + ComputeDeprecated(class LAMMPS *, int, char **); + ~ComputeDeprecated() {} + void init() {} +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: This compute command has been removed from LAMMPS + +UNDOCUMENTED + +*/ From 2b0e474729edf2038de610df74c2edf4a45ae33e Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 17 Oct 2018 16:26:20 -0400 Subject: [PATCH 260/302] implement deprecated styles for bond, angle, dihedral, and improper --- src/angle_deprecated.cpp | 57 +++++++++++++++++++++++++++++++++++++ src/angle_deprecated.h | 48 +++++++++++++++++++++++++++++++ src/bond_deprecated.cpp | 57 +++++++++++++++++++++++++++++++++++++ src/bond_deprecated.h | 48 +++++++++++++++++++++++++++++++ src/dihedral_deprecated.cpp | 57 +++++++++++++++++++++++++++++++++++++ src/dihedral_deprecated.h | 46 ++++++++++++++++++++++++++++++ src/improper_deprecated.cpp | 57 +++++++++++++++++++++++++++++++++++++ src/improper_deprecated.h | 46 ++++++++++++++++++++++++++++++ src/pair_deprecated.h | 39 ------------------------- 9 files changed, 416 insertions(+), 39 deletions(-) create mode 100644 src/angle_deprecated.cpp create mode 100644 src/angle_deprecated.h create mode 100644 src/bond_deprecated.cpp create mode 100644 src/bond_deprecated.h create mode 100644 src/dihedral_deprecated.cpp create mode 100644 src/dihedral_deprecated.h create mode 100644 src/improper_deprecated.cpp create mode 100644 src/improper_deprecated.h diff --git a/src/angle_deprecated.cpp b/src/angle_deprecated.cpp new file mode 100644 index 0000000000..66efbfacbc --- /dev/null +++ b/src/angle_deprecated.cpp @@ -0,0 +1,57 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Axel Kohlmeyer (Temple U) +------------------------------------------------------------------------- */ + +#include +#include "angle_deprecated.h" +#include "angle_hybrid.h" +#include "comm.h" +#include "force.h" +#include "error.h" + +using namespace LAMMPS_NS; + +static void writemsg(LAMMPS *lmp, const char *msg, int abend=1) +{ + if (lmp->comm->me == 0) { + if (lmp->screen) fputs(msg,lmp->screen); + if (lmp->logfile) fputs(msg,lmp->logfile); + } + if (abend) + lmp->error->all(FLERR,"This angle style is no longer available"); +} + +/* ---------------------------------------------------------------------- */ + +void AngleDeprecated::settings(int, char **) +{ + const char *my_style = force->angle_style; + + // hybrid substyles are created in AngleHybrid::settings(), so when this is + // called, our style was just added at the end of the list of substyles + + if (strncmp(my_style,"hybrid",6) == 0) { + AngleHybrid *hybrid = (AngleHybrid *)force->angle; + my_style = hybrid->keywords[hybrid->nstyles]; + } + + if (strcmp(my_style,"DEPRECATED") == 0) { + writemsg(lmp,"\nAngle style 'DEPRECATED' is a dummy style\n\n",0); + + } +} + + diff --git a/src/angle_deprecated.h b/src/angle_deprecated.h new file mode 100644 index 0000000000..631df37da2 --- /dev/null +++ b/src/angle_deprecated.h @@ -0,0 +1,48 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef ANGLE_CLASS + +AngleStyle(DEPRECATED,AngleDeprecated) + +#else + +#ifndef LMP_ANGLE_DEPRECATED_H +#define LMP_ANGLE_DEPRECATED_H + +#include "angle.h" + +namespace LAMMPS_NS { + +class AngleDeprecated : public Angle { + public: + AngleDeprecated(class LAMMPS *lmp) : Angle(lmp) {} + virtual ~AngleDeprecated() {} + + virtual void compute(int, int) {} + virtual void settings(int, char **); + virtual void coeff(int, char **) {} + virtual double equilibrium_angle(int) { return 0.0; } + virtual void write_restart(FILE *) {} + virtual void read_restart(FILE *) {} + virtual double single(int, int, int, int) { return 0.0; } +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/bond_deprecated.cpp b/src/bond_deprecated.cpp new file mode 100644 index 0000000000..e7d91df7b5 --- /dev/null +++ b/src/bond_deprecated.cpp @@ -0,0 +1,57 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Axel Kohlmeyer (Temple U) +------------------------------------------------------------------------- */ + +#include +#include "bond_deprecated.h" +#include "bond_hybrid.h" +#include "comm.h" +#include "force.h" +#include "error.h" + +using namespace LAMMPS_NS; + +static void writemsg(LAMMPS *lmp, const char *msg, int abend=1) +{ + if (lmp->comm->me == 0) { + if (lmp->screen) fputs(msg,lmp->screen); + if (lmp->logfile) fputs(msg,lmp->logfile); + } + if (abend) + lmp->error->all(FLERR,"This bond style is no longer available"); +} + +/* ---------------------------------------------------------------------- */ + +void BondDeprecated::settings(int, char **) +{ + const char *my_style = force->bond_style; + + // hybrid substyles are created in BondHybrid::settings(), so when this is + // called, our style was just added at the end of the list of substyles + + if (strncmp(my_style,"hybrid",6) == 0) { + BondHybrid *hybrid = (BondHybrid *)force->bond; + my_style = hybrid->keywords[hybrid->nstyles]; + } + + if (strcmp(my_style,"DEPRECATED") == 0) { + writemsg(lmp,"\nBond style 'DEPRECATED' is a dummy style\n\n",0); + + } +} + + diff --git a/src/bond_deprecated.h b/src/bond_deprecated.h new file mode 100644 index 0000000000..e81b7a5b27 --- /dev/null +++ b/src/bond_deprecated.h @@ -0,0 +1,48 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef BOND_CLASS + +BondStyle(DEPRECATED,BondDeprecated) + +#else + +#ifndef LMP_BOND_DEPRECATED_H +#define LMP_BOND_DEPRECATED_H + +#include "bond.h" + +namespace LAMMPS_NS { + +class BondDeprecated : public Bond { + public: + BondDeprecated(class LAMMPS *lmp) : Bond(lmp) {} + virtual ~BondDeprecated() {} + + virtual void compute(int, int) {} + virtual void settings(int, char **); + virtual void coeff(int, char **) {} + virtual double equilibrium_distance(int) { return 0.0; } + virtual void write_restart(FILE *) {} + virtual void read_restart(FILE *) {} + virtual double single(int, double, int, int, double &) { return 0.0; } +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/dihedral_deprecated.cpp b/src/dihedral_deprecated.cpp new file mode 100644 index 0000000000..138d0971a8 --- /dev/null +++ b/src/dihedral_deprecated.cpp @@ -0,0 +1,57 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Axel Kohlmeyer (Temple U) +------------------------------------------------------------------------- */ + +#include +#include "dihedral_deprecated.h" +#include "dihedral_hybrid.h" +#include "comm.h" +#include "force.h" +#include "error.h" + +using namespace LAMMPS_NS; + +static void writemsg(LAMMPS *lmp, const char *msg, int abend=1) +{ + if (lmp->comm->me == 0) { + if (lmp->screen) fputs(msg,lmp->screen); + if (lmp->logfile) fputs(msg,lmp->logfile); + } + if (abend) + lmp->error->all(FLERR,"This dihedral style is no longer available"); +} + +/* ---------------------------------------------------------------------- */ + +void DihedralDeprecated::settings(int, char **) +{ + const char *my_style = force->dihedral_style; + + // hybrid substyles are created in DihedralHybrid::settings(), so when this is + // called, our style was just added at the end of the list of substyles + + if (strncmp(my_style,"hybrid",6) == 0) { + DihedralHybrid *hybrid = (DihedralHybrid *)force->dihedral; + my_style = hybrid->keywords[hybrid->nstyles]; + } + + if (strcmp(my_style,"DEPRECATED") == 0) { + writemsg(lmp,"\nDihedral style 'DEPRECATED' is a dummy style\n\n",0); + + } +} + + diff --git a/src/dihedral_deprecated.h b/src/dihedral_deprecated.h new file mode 100644 index 0000000000..216791f623 --- /dev/null +++ b/src/dihedral_deprecated.h @@ -0,0 +1,46 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef DIHEDRAL_CLASS + +DihedralStyle(DEPRECATED,DihedralDeprecated) + +#else + +#ifndef LMP_DIHEDRAL_DEPRECATED_H +#define LMP_DIHEDRAL_DEPRECATED_H + +#include "dihedral.h" + +namespace LAMMPS_NS { + +class DihedralDeprecated : public Dihedral { + public: + DihedralDeprecated(class LAMMPS *lmp) : Dihedral(lmp) {} + virtual ~DihedralDeprecated() {} + + virtual void compute(int, int) {} + virtual void settings(int, char **); + virtual void coeff(int, char **) {} + virtual void write_restart(FILE *) {} + virtual void read_restart(FILE *) {} +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/improper_deprecated.cpp b/src/improper_deprecated.cpp new file mode 100644 index 0000000000..e03fd785a7 --- /dev/null +++ b/src/improper_deprecated.cpp @@ -0,0 +1,57 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Axel Kohlmeyer (Temple U) +------------------------------------------------------------------------- */ + +#include +#include "improper_deprecated.h" +#include "improper_hybrid.h" +#include "comm.h" +#include "force.h" +#include "error.h" + +using namespace LAMMPS_NS; + +static void writemsg(LAMMPS *lmp, const char *msg, int abend=1) +{ + if (lmp->comm->me == 0) { + if (lmp->screen) fputs(msg,lmp->screen); + if (lmp->logfile) fputs(msg,lmp->logfile); + } + if (abend) + lmp->error->all(FLERR,"This improper style is no longer available"); +} + +/* ---------------------------------------------------------------------- */ + +void ImproperDeprecated::settings(int, char **) +{ + const char *my_style = force->improper_style; + + // hybrid substyles are created in ImproperHybrid::settings(), so when this is + // called, our style was just added at the end of the list of substyles + + if (strncmp(my_style,"hybrid",6) == 0) { + ImproperHybrid *hybrid = (ImproperHybrid *)force->improper; + my_style = hybrid->keywords[hybrid->nstyles]; + } + + if (strcmp(my_style,"DEPRECATED") == 0) { + writemsg(lmp,"\nImproper style 'DEPRECATED' is a dummy style\n\n",0); + + } +} + + diff --git a/src/improper_deprecated.h b/src/improper_deprecated.h new file mode 100644 index 0000000000..04ecfeeb98 --- /dev/null +++ b/src/improper_deprecated.h @@ -0,0 +1,46 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef IMPROPER_CLASS + +ImproperStyle(DEPRECATED,ImproperDeprecated) + +#else + +#ifndef LMP_IMPROPER_DEPRECATED_H +#define LMP_IMPROPER_DEPRECATED_H + +#include "improper.h" + +namespace LAMMPS_NS { + +class ImproperDeprecated : public Improper { + public: + ImproperDeprecated(class LAMMPS *lmp) : Improper(lmp) {} + virtual ~ImproperDeprecated() {} + + virtual void compute(int, int) {} + virtual void settings(int, char **); + virtual void coeff(int, char **) {} + virtual void write_restart(FILE *) {} + virtual void read_restart(FILE *) {} +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/pair_deprecated.h b/src/pair_deprecated.h index 779dedee9a..29d6efffaf 100644 --- a/src/pair_deprecated.h +++ b/src/pair_deprecated.h @@ -42,43 +42,4 @@ class PairDeprecated : public Pair { /* ERROR/WARNING messages: -E: Not all pairs processed in pair_style list - -Not all interacting pairs for which coefficients were found. This can be intentional -and then you need to set the 'nocheck' option. If not, it usually means that the -communication cutoff is too small. This can be ameliorated by either increasing -the cutoff in the pair_style command or the communication cutoff. - -E: Illegal ... command - -Self-explanatory. Check the input script syntax and compare to the -documentation for the command. You can use -echo screen as a -command-line option when running LAMMPS to see the offending line. - -E: Cannot open pair list file - -Self-explanatory. The file with the list of pairs cannot be open for reading. -Check the path and permissions. - -E: Incorrectly formatted ... - -Self-explanatory. The content of the pair list file does not match the documented -format. Please re-read the documentation and carefully compare it to your file. - -E: Unknown pair list potential style - -Self-explanatory. You requested a potential type that is not yet implemented or have a typo. - -E: Incorrect args for pair coefficients - -Self-explanatory. Check the input script or data file. - -E: Pair style list requires atom IDs - -Self-explanatory. The pairs in the list are identified via atom IDs, so they need to be present. - -E: Pair style list requires an atom map - -Self-explanatory. Atoms are looked up via an atom map. Create one using the atom_style map command. - */ From 7bb5821baff4cb94bdc97224a3012e23fb9d520c Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 17 Oct 2018 18:13:12 -0400 Subject: [PATCH 261/302] add deprecated dump and region styles --- src/dump_deprecated.cpp | 40 +++++++++++++++++++++++++++++++ src/dump_deprecated.h | 50 +++++++++++++++++++++++++++++++++++++++ src/region_deprecated.cpp | 40 +++++++++++++++++++++++++++++++ src/region_deprecated.h | 50 +++++++++++++++++++++++++++++++++++++++ 4 files changed, 180 insertions(+) create mode 100644 src/dump_deprecated.cpp create mode 100644 src/dump_deprecated.h create mode 100644 src/region_deprecated.cpp create mode 100644 src/region_deprecated.h diff --git a/src/dump_deprecated.cpp b/src/dump_deprecated.cpp new file mode 100644 index 0000000000..f0999f4276 --- /dev/null +++ b/src/dump_deprecated.cpp @@ -0,0 +1,40 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include +#include "dump_deprecated.h" +#include "comm.h" +#include "error.h" + +using namespace LAMMPS_NS; + +static void writemsg(LAMMPS *lmp, const char *msg, int abend=1) +{ + if (lmp->comm->me == 0) { + if (lmp->screen) fputs(msg,lmp->screen); + if (lmp->logfile) fputs(msg,lmp->logfile); + } + if (abend) + lmp->error->all(FLERR,"This dump style is no longer available"); +} + +/* ---------------------------------------------------------------------- */ + +DumpDeprecated::DumpDeprecated(LAMMPS *lmp, int narg, char **arg) : + Dump(lmp, narg, arg) +{ + if (strcmp(style,"DEPRECATED") == 0) { + writemsg(lmp,"\nDump style 'DEPRECATED' is a dummy style\n\n",0); + + } +} diff --git a/src/dump_deprecated.h b/src/dump_deprecated.h new file mode 100644 index 0000000000..51235ba4e4 --- /dev/null +++ b/src/dump_deprecated.h @@ -0,0 +1,50 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef DUMP_CLASS + +// list all deprecated and removed dump styles here + +DumpStyle(DEPRECATED,DumpDeprecated) + +#else + +#ifndef LMP_DUMP_DEPRECATED_H +#define LMP_DUMP_DEPRECATED_H + +#include "dump.h" + +namespace LAMMPS_NS { + +class DumpDeprecated : public Dump { + public: + DumpDeprecated(class LAMMPS *, int, char **); + ~DumpDeprecated() {} + virtual void init_style() {} + virtual void write_header(bigint) {} + virtual void pack(tagint *) {} + virtual void write_data(int, double *) {} + }; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: This dump style has been removed from LAMMPS + +UNDOCUMENTED + +*/ diff --git a/src/region_deprecated.cpp b/src/region_deprecated.cpp new file mode 100644 index 0000000000..87225959fa --- /dev/null +++ b/src/region_deprecated.cpp @@ -0,0 +1,40 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include +#include "region_deprecated.h" +#include "comm.h" +#include "error.h" + +using namespace LAMMPS_NS; + +static void writemsg(LAMMPS *lmp, const char *msg, int abend=1) +{ + if (lmp->comm->me == 0) { + if (lmp->screen) fputs(msg,lmp->screen); + if (lmp->logfile) fputs(msg,lmp->logfile); + } + if (abend) + lmp->error->all(FLERR,"This region style is no longer available"); +} + +/* ---------------------------------------------------------------------- */ + +RegionDeprecated::RegionDeprecated(LAMMPS *lmp, int narg, char **arg) : + Region(lmp, narg, arg) +{ + if (strcmp(style,"DEPRECATED") == 0) { + writemsg(lmp,"\nRegion style 'DEPRECATED' is a dummy style\n\n",0); + + } +} diff --git a/src/region_deprecated.h b/src/region_deprecated.h new file mode 100644 index 0000000000..d7e0d20330 --- /dev/null +++ b/src/region_deprecated.h @@ -0,0 +1,50 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef REGION_CLASS + +// list all deprecated and removed region styles here + +RegionStyle(DEPRECATED,RegionDeprecated) + +#else + +#ifndef LMP_REGION_DEPRECATED_H +#define LMP_REGION_DEPRECATED_H + +#include "region.h" + +namespace LAMMPS_NS { + +class RegionDeprecated : public Region { + public: + RegionDeprecated(class LAMMPS *, int, char **); + ~RegionDeprecated() {} + virtual void init() {} + virtual int inside(double, double, double) { return 0; } + virtual int surface_interior(double *, double) { return 0; } + virtual int surface_exterior(double *, double) { return 0; } + }; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: This region command has been removed from LAMMPS + +UNDOCUMENTED + +*/ From dcde84eb5384725a55c49d364b47c9418544324d Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Thu, 18 Oct 2018 11:22:51 -0600 Subject: [PATCH 262/302] bug fix for create_atoms single remap and triclinic --- src/create_atoms.cpp | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/src/create_atoms.cpp b/src/create_atoms.cpp index dcc36aa5d4..383c60f1cd 100644 --- a/src/create_atoms.cpp +++ b/src/create_atoms.cpp @@ -569,10 +569,20 @@ void CreateAtoms::add_single() } // if triclinic, convert to lamda coords (0-1) + // with remapflag set and periodic dims, + // resulting coord must satisfy 0.0 <= coord < 1.0 double lamda[3],*coord; if (triclinic) { domain->x2lamda(xone,lamda); + if (remapflag) { + if (domain->xperiodic && (lamda[0] < 0.0 || lamda[0] >= 1.0)) + lamda[0] = 0.0; + if (domain->yperiodic && (lamda[1] < 0.0 || lamda[1] >= 1.0)) + lamda[1] = 0.0; + if (domain->zperiodic && (lamda[2] < 0.0 || lamda[2] >= 1.0)) + lamda[2] = 0.0; + } coord = lamda; } else coord = xone; From d9dd80b3684cf11c297c1e28e009135dd0af65c3 Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Thu, 18 Oct 2018 14:24:48 -0600 Subject: [PATCH 263/302] added -restart2dump command-line option --- doc/src/Run_options.txt | 102 ++++++++++++++++++++++++++++------------ src/lammps.cpp | 80 ++++++++++++++++++++----------- 2 files changed, 126 insertions(+), 56 deletions(-) diff --git a/doc/src/Run_options.txt b/doc/src/Run_options.txt index 1fc00bc2e3..db5a7baa6e 100644 --- a/doc/src/Run_options.txt +++ b/doc/src/Run_options.txt @@ -24,8 +24,9 @@ letter abbreviation can be used: "-p or -partition"_#partition "-pl or -plog"_#plog "-ps or -pscreen"_#pscreen -"-r or -restart"_#restart "-ro or -reorder"_#reorder +"-r2data or -restart2data"_#restart2data +"-r2dump or -restart2dump"_#restart2dump "-sc or -screen"_#screen "-sf or -suffix"_#suffix "-v or -var"_#var :ul @@ -280,34 +281,6 @@ specified by the -screen command-line option. :line -[-restart restartfile {remap} datafile keyword value ...] :link(restart) - -Convert the restart file into a data file and immediately exit. This -is the same operation as if the following 2-line input script were -run: - -read_restart restartfile {remap} -write_data datafile keyword value ... :pre - -Note that the specified restartfile and datafile can have wild-card -characters ("*",%") as described by the -"read_restart"_read_restart.html and "write_data"_write_data.html -commands. But a filename such as file.* will need to be enclosed in -quotes to avoid shell expansion of the "*" character. - -Note that following restartfile, the optional flag {remap} can be -used. This has the same effect as adding it to the -"read_restart"_read_restart.html command, as explained on its doc -page. This is only useful if the reading of the restart file triggers -an error that atoms have been lost. In that case, use of the remap -flag should allow the data file to still be produced. - -Also note that following datafile, the same optional keyword/value -pairs can be listed as used by the "write_data"_write_data.html -command. - -:line - [-reorder] :link(reorder) This option has 2 forms: @@ -381,6 +354,77 @@ the LAMMPS simulation domain. :line +[-restart2data restartfile (remap) datafile keyword value ...] :link(restart2data) + +Convert the restart file into a data file and immediately exit. This +is the same operation as if the following 2-line input script were +run: + +read_restart restartfile (remap) +write_data datafile keyword value ... :pre + +Note that the specified restartfile and/or datafile can have the +wild-card character "*". The restartfile can also have the wild-card +character "%". The meaning of these characters is explained on the +"read_restart"_read_restart.html and "write_data"_write_data.html doc +pages. The use of "%" means that a parallel restart file can be read. +Note that a filename such as file.* will need to be enclosed in quotes +to avoid shell expansion of the "*" character. + +Note that following restartfile, the optional word "remap" can be +used. This has the effect of adding it to the +"read_restart"_read_restart.html command, as explained on its doc +page. This is useful if reading the restart file triggers an error +that atoms have been lost. In that case, use of the remap flag should +allow the data file to still be produced. + +The syntax following restartfile (or remap), namely + +datafile keyword value ... :pre + +is identical to the arguments of the "write_data"_write_data.html +command. See its doc page for details. This includes its +optional keyword/value settings. + +:line + +[-restart2dump restartfile {remap} group-ID dumpstyle dumpfile arg1 arg2 ...] :link(restart2dump) + +Convert the restart file into a dump file and immediately exit. This +is the same operation as if the following 2-line input script were +run: + +read_restart restartfile (remap) +write_dump group-ID dumpstyle dumpfile arg1 arg2 ... :pre + +Note that the specified restartfile and dumpfile can have wild-card +characters ("*","%") as explained on the +"read_restart"_read_restart.html and "write_dump"_write_dump.html doc +pages. The use of "%" means that a parallel restart file and/or +parallel dump file can be read and/or written. Note that a filename +such as file.* will need to be enclosed in quotes to avoid shell +expansion of the "*" character. + +Note that following restartfile, the optional word "remap" can be +used. This has the effect as adding it to the +"read_restart"_read_restart.html command, as explained on its doc +page. This is useful if reading the restart file triggers an error +that atoms have been lost. In that case, use of the remap flag should +allow the dump file to still be produced. + +The syntax following restartfile (or remap), namely + +group-ID dumpstyle dumpfile arg1 arg2 ... :pre + +is identical to the arguments of the "write_dump"_write_dump.html +command. See its doc page for details. This includes what per-atom +fields are written to the dump file and optional dump_modify settings, +including ones that affect how parallel dump files are written, e.g. +the {nfile} and {fileper} keywords. See the +"dump_modify"_dump_modify.html doc page for details. + +:line + [-screen file] :link(screen) Specify a file for LAMMPS to write its screen information to. In diff --git a/src/lammps.cpp b/src/lammps.cpp index 04d8daa478..c6d8b7c967 100644 --- a/src/lammps.cpp +++ b/src/lammps.cpp @@ -121,8 +121,9 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) int partscreenflag = 0; int partlogflag = 0; int kokkosflag = 0; - int restartflag = 0; - int restartremapflag = 0; + int restart2data = 0; + int restart2dump = 0; + int restartremap = 0; int citeflag = 1; int helpflag = 0; @@ -132,9 +133,8 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) else exename = NULL; packargs = NULL; num_package = 0; - char *rfile = NULL; - char *dfile = NULL; - int wdfirst,wdlast; + char *restartfile = NULL; + int wfirst,wlast; int kkfirst,kklast; int npack = 0; @@ -248,26 +248,49 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) universe->reorder(arg[iarg+1],arg[iarg+2]); iarg += 3; - } else if (strcmp(arg[iarg],"-restart") == 0 || - strcmp(arg[iarg],"-r") == 0) { + } else if (strcmp(arg[iarg],"-restart2data") == 0 || + strcmp(arg[iarg],"-r2data") == 0) { if (iarg+3 > narg) error->universe_all(FLERR,"Invalid command-line argument"); - restartflag = 1; - rfile = arg[iarg+1]; - dfile = arg[iarg+2]; + if (restart2dump) + error->universe_all(FLERR, + "Cannot use both -restart2data and -restart2dump"); + restart2data = 1; + restartfile = arg[iarg+1]; // check for restart remap flag - if (strcmp(dfile,"remap") == 0) { + if (strcmp(arg[iarg+2],"remap") == 0) { if (iarg+4 > narg) error->universe_all(FLERR,"Invalid command-line argument"); - restartremapflag = 1; - dfile = arg[iarg+3]; + restartremap = 1; iarg++; } - iarg += 3; - // delimit any extra args for the write_data command - wdfirst = iarg; + iarg += 2; + // delimit args for the write_data command + wfirst = iarg; while (iarg < narg && arg[iarg][0] != '-') iarg++; - wdlast = iarg; + wlast = iarg; + + } else if (strcmp(arg[iarg],"-restart2dump") == 0 || + strcmp(arg[iarg],"-r2dump") == 0) { + if (iarg+3 > narg) + error->universe_all(FLERR,"Invalid command-line argument"); + if (restart2data) + error->universe_all(FLERR, + "Cannot use both -restart2data and -restart2dump"); + restart2dump = 1; + restartfile = arg[iarg+1]; + // check for restart remap flag + if (strcmp(arg[iarg+2],"remap") == 0) { + if (iarg+4 > narg) + error->universe_all(FLERR,"Invalid command-line argument"); + restartremap = 1; + iarg++; + } + iarg += 2; + // delimit args for the write_dump command + wfirst = iarg; + while (iarg < narg && arg[iarg][0] != '-') iarg++; + wlast = iarg; } else if (strcmp(arg[iarg],"-screen") == 0 || strcmp(arg[iarg],"-sc") == 0) { @@ -547,6 +570,7 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) input = new Input(this,narg,arg); // copy package cmdline arguments + if (npack > 0) { num_package = npack; packargs = new char**[npack]; @@ -573,19 +597,21 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) error->done(0); } - // if restartflag set, invoke 2 commands and quit - // add args between wdfirst and wdlast to write_data command - // also add "noinit" to prevent write_data from doing system init + // if either restart conversion option was used, invoke 2 commands and quit + // add args between wfirst and wlast to write_data or write_data command + // add "noinit" to write_data to prevent a system init + // write_dump will just give a warning message about no init - if (restartflag) { - char cmd[128]; - snprintf(cmd,128,"read_restart %s\n",rfile); - if (restartremapflag) strcat(cmd," remap\n"); + if (restart2data || restart2dump) { + char cmd[256]; + snprintf(cmd,256,"read_restart %s\n",restartfile); + if (restartremap) strcat(cmd," remap\n"); input->one(cmd); - snprintf(cmd,128,"write_data %s",dfile); - for (iarg = wdfirst; iarg < wdlast; iarg++) + if (restart2data) snprintf(cmd,256,"write_data"); + else snprintf(cmd,256,"write_dump"); + for (iarg = wfirst; iarg < wlast; iarg++) sprintf(&cmd[strlen(cmd)]," %s",arg[iarg]); - strcat(cmd," noinit\n"); + if (restart2data) strcat(cmd," noinit\n"); input->one(cmd); error->done(0); } From 7deb1df2b6a32fe4e94eff28eda76e708fb9b212 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 18 Oct 2018 16:30:45 -0400 Subject: [PATCH 264/302] split kspace style constructor into plain constructor and settings() method --- src/force.cpp | 30 +++++++++++++++--------------- src/force.h | 8 ++++---- src/input.cpp | 3 ++- src/kspace.cpp | 2 +- src/kspace.h | 3 ++- 5 files changed, 24 insertions(+), 22 deletions(-) diff --git a/src/force.cpp b/src/force.cpp index 91fccd7197..2bfd809451 100644 --- a/src/force.cpp +++ b/src/force.cpp @@ -665,14 +665,14 @@ Improper *Force::improper_match(const char *style) new kspace style ------------------------------------------------------------------------- */ -void Force::create_kspace(int narg, char **arg, int trysuffix) +void Force::create_kspace(const char *style, int trysuffix) { delete [] kspace_style; if (kspace) delete kspace; int sflag; - kspace = new_kspace(narg,arg,trysuffix,sflag); - store_style(kspace_style,arg[0],sflag); + kspace = new_kspace(style,trysuffix,sflag); + store_style(kspace_style,style,sflag); if (comm->style == 1 && !kspace_match("ewald",0)) error->all(FLERR, @@ -683,39 +683,39 @@ void Force::create_kspace(int narg, char **arg, int trysuffix) generate a kspace class ------------------------------------------------------------------------- */ -KSpace *Force::new_kspace(int narg, char **arg, int trysuffix, int &sflag) +KSpace *Force::new_kspace(const char *style, int trysuffix, int &sflag) { if (trysuffix && lmp->suffix_enable) { if (lmp->suffix) { sflag = 1; char estyle[256]; - sprintf(estyle,"%s/%s",arg[0],lmp->suffix); + sprintf(estyle,"%s/%s",style,lmp->suffix); if (kspace_map->find(estyle) != kspace_map->end()) { KSpaceCreator kspace_creator = (*kspace_map)[estyle]; - return kspace_creator(lmp, narg-1, &arg[1]); + return kspace_creator(lmp); } } if (lmp->suffix2) { sflag = 1; char estyle[256]; - sprintf(estyle,"%s/%s",arg[0],lmp->suffix2); + sprintf(estyle,"%s/%s",style,lmp->suffix2); if (kspace_map->find(estyle) != kspace_map->end()) { KSpaceCreator kspace_creator = (*kspace_map)[estyle]; - return kspace_creator(lmp, narg-1, &arg[1]); + return kspace_creator(lmp); } } } sflag = 0; - if (strcmp(arg[0],"none") == 0) return NULL; - if (kspace_map->find(arg[0]) != kspace_map->end()) { - KSpaceCreator kspace_creator = (*kspace_map)[arg[0]]; - return kspace_creator(lmp, narg-1, &arg[1]); + if (strcmp(style,"none") == 0) return NULL; + if (kspace_map->find(style) != kspace_map->end()) { + KSpaceCreator kspace_creator = (*kspace_map)[style]; + return kspace_creator(lmp); } char str[128]; - sprintf(str,"Unknown kspace style %s",arg[0]); + sprintf(str,"Unknown kspace style %s",style); error->all(FLERR,str); return NULL; @@ -726,9 +726,9 @@ KSpace *Force::new_kspace(int narg, char **arg, int trysuffix, int &sflag) ------------------------------------------------------------------------- */ template -KSpace *Force::kspace_creator(LAMMPS *lmp, int narg, char ** arg) +KSpace *Force::kspace_creator(LAMMPS *lmp) { - return new T(lmp, narg, arg); + return new T(lmp); } /* ---------------------------------------------------------------------- diff --git a/src/force.h b/src/force.h index ce593fa518..e4bb0f990e 100644 --- a/src/force.h +++ b/src/force.h @@ -72,7 +72,7 @@ class Force : protected Pointers { typedef Angle *(*AngleCreator)(LAMMPS *); typedef Dihedral *(*DihedralCreator)(LAMMPS *); typedef Improper *(*ImproperCreator)(LAMMPS *); - typedef KSpace *(*KSpaceCreator)(LAMMPS *,int,char**); + typedef KSpace *(*KSpaceCreator)(LAMMPS *); typedef std::map PairCreatorMap; typedef std::map BondCreatorMap; @@ -123,8 +123,8 @@ class Force : protected Pointers { class Improper *new_improper(const char *, int, int &); class Improper *improper_match(const char *); - void create_kspace(int, char **, int); - class KSpace *new_kspace(int, char **, int, int &); + void create_kspace(const char *, int); + class KSpace *new_kspace(const char *, int, int &); class KSpace *kspace_match(const char *, int); void store_style(char *&, const char *, int); @@ -148,7 +148,7 @@ class Force : protected Pointers { template static Angle *angle_creator(LAMMPS *); template static Dihedral *dihedral_creator(LAMMPS *); template static Improper *improper_creator(LAMMPS *); - template static KSpace *kspace_creator(LAMMPS *, int, char **); + template static KSpace *kspace_creator(LAMMPS *); }; } diff --git a/src/input.cpp b/src/input.cpp index 2834e36913..f9dd1ec314 100644 --- a/src/input.cpp +++ b/src/input.cpp @@ -1633,7 +1633,8 @@ void Input::kspace_modify() void Input::kspace_style() { - force->create_kspace(narg,arg,1); + force->create_kspace(arg[0],1); + if (force->kspace) force->kspace->settings(narg-1,&arg[1]); } /* ---------------------------------------------------------------------- */ diff --git a/src/kspace.cpp b/src/kspace.cpp index b92cd1e9dc..25491cd964 100644 --- a/src/kspace.cpp +++ b/src/kspace.cpp @@ -30,7 +30,7 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -KSpace::KSpace(LAMMPS *lmp, int /*narg*/, char **/*arg*/) : Pointers(lmp) +KSpace::KSpace(LAMMPS *lmp) : Pointers(lmp) { order_allocated = 0; energy = 0.0; diff --git a/src/kspace.h b/src/kspace.h index c25dc93f45..3917a0a72f 100644 --- a/src/kspace.h +++ b/src/kspace.h @@ -92,7 +92,7 @@ class KSpace : protected Pointers { double splittol; // tolerance for when to truncate splitting - KSpace(class LAMMPS *, int, char **); + KSpace(class LAMMPS *); virtual ~KSpace(); void triclinic_check(); void modify_params(int, char **); @@ -112,6 +112,7 @@ class KSpace : protected Pointers { // general child-class methods + virtual void settings(int, char **) {}; virtual void init() = 0; virtual void setup() = 0; virtual void setup_grid() {}; From 9090fd0255fe2423a79311af089e4efe8d891ebe Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 18 Oct 2018 16:31:17 -0400 Subject: [PATCH 265/302] propagate the kspace change to a the first few kspace styles --- src/KSPACE/ewald.cpp | 13 +++++++++---- src/KSPACE/ewald.h | 3 ++- src/KSPACE/ewald_disp.cpp | 12 ++++++++---- src/KSPACE/ewald_disp.h | 3 ++- src/KSPACE/msm.cpp | 14 +++++++++----- src/KSPACE/msm.h | 3 ++- 6 files changed, 32 insertions(+), 16 deletions(-) diff --git a/src/KSPACE/ewald.cpp b/src/KSPACE/ewald.cpp index 0ced09eb93..c9c10ab738 100644 --- a/src/KSPACE/ewald.cpp +++ b/src/KSPACE/ewald.cpp @@ -40,7 +40,7 @@ using namespace MathConst; /* ---------------------------------------------------------------------- */ -Ewald::Ewald(LAMMPS *lmp, int narg, char **arg) : KSpace(lmp, narg, arg), +Ewald::Ewald(LAMMPS *lmp) : KSpace(lmp), kxvecs(NULL), kyvecs(NULL), kzvecs(NULL), ug(NULL), eg(NULL), vg(NULL), ek(NULL), sfacrl(NULL), sfacim(NULL), sfacrl_all(NULL), sfacim_all(NULL), cs(NULL), sn(NULL), sfacrl_A(NULL), sfacim_A(NULL), sfacrl_A_all(NULL), @@ -49,12 +49,10 @@ Ewald::Ewald(LAMMPS *lmp, int narg, char **arg) : KSpace(lmp, narg, arg), { group_allocate_flag = 0; kmax_created = 0; - if (narg != 1) error->all(FLERR,"Illegal kspace_style ewald command"); - ewaldflag = 1; group_group_enable = 1; - accuracy_relative = fabs(force->numeric(FLERR,arg[0])); + accuracy_relative = 0.0; kmax = 0; kxvecs = kyvecs = kzvecs = NULL; @@ -69,6 +67,13 @@ Ewald::Ewald(LAMMPS *lmp, int narg, char **arg) : KSpace(lmp, narg, arg), kcount = 0; } +void Ewald::settings(int narg, char **arg) +{ + if (narg != 1) error->all(FLERR,"Illegal kspace_style ewald command"); + + accuracy_relative = fabs(force->numeric(FLERR,arg[0])); +} + /* ---------------------------------------------------------------------- free all memory ------------------------------------------------------------------------- */ diff --git a/src/KSPACE/ewald.h b/src/KSPACE/ewald.h index d9ff68dd08..7d520b3ab0 100644 --- a/src/KSPACE/ewald.h +++ b/src/KSPACE/ewald.h @@ -26,10 +26,11 @@ namespace LAMMPS_NS { class Ewald : public KSpace { public: - Ewald(class LAMMPS *, int, char **); + Ewald(class LAMMPS *); virtual ~Ewald(); void init(); void setup(); + virtual void settings(int, char **); virtual void compute(int, int); double memory_usage(); diff --git a/src/KSPACE/ewald_disp.cpp b/src/KSPACE/ewald_disp.cpp index 78d7b38e4d..0ff8acff6e 100644 --- a/src/KSPACE/ewald_disp.cpp +++ b/src/KSPACE/ewald_disp.cpp @@ -43,14 +43,11 @@ using namespace MathSpecial; /* ---------------------------------------------------------------------- */ -EwaldDisp::EwaldDisp(LAMMPS *lmp, int narg, char **arg) : KSpace(lmp, narg, arg), +EwaldDisp::EwaldDisp(LAMMPS *lmp) : KSpace(lmp), kenergy(NULL), kvirial(NULL), energy_self_peratom(NULL), virial_self_peratom(NULL), ekr_local(NULL), hvec(NULL), kvec(NULL), B(NULL), cek_local(NULL), cek_global(NULL) { - if (narg!=1) error->all(FLERR,"Illegal kspace_style ewald/n command"); - ewaldflag = dispersionflag = dipoleflag = 1; - accuracy_relative = fabs(force->numeric(FLERR,arg[0])); memset(function, 0, EWALD_NFUNCS*sizeof(int)); kenergy = kvirial = NULL; @@ -68,6 +65,13 @@ EwaldDisp::EwaldDisp(LAMMPS *lmp, int narg, char **arg) : KSpace(lmp, narg, arg) M2 = 0; } +void EwaldDisp::settings(int narg, char **arg) +{ + if (narg!=1) error->all(FLERR,"Illegal kspace_style ewald/n command"); + accuracy_relative = fabs(force->numeric(FLERR,arg[0])); +} + + /* ---------------------------------------------------------------------- */ EwaldDisp::~EwaldDisp() diff --git a/src/KSPACE/ewald_disp.h b/src/KSPACE/ewald_disp.h index 946b40b193..a8dfb5bb20 100644 --- a/src/KSPACE/ewald_disp.h +++ b/src/KSPACE/ewald_disp.h @@ -36,10 +36,11 @@ typedef struct kvector { long x, y, z; } kvector; class EwaldDisp : public KSpace { public: - EwaldDisp(class LAMMPS *, int, char **); + EwaldDisp(class LAMMPS *); ~EwaldDisp(); void init(); void setup(); + void settings(int, char **); void compute(int, int); double memory_usage() {return bytes;} diff --git a/src/KSPACE/msm.cpp b/src/KSPACE/msm.cpp index efa2c87296..9583ed4ef5 100644 --- a/src/KSPACE/msm.cpp +++ b/src/KSPACE/msm.cpp @@ -44,7 +44,7 @@ enum{REVERSE_RHO,REVERSE_AD,REVERSE_AD_PERATOM}; enum{FORWARD_RHO,FORWARD_AD,FORWARD_AD_PERATOM}; /* ---------------------------------------------------------------------- */ -MSM::MSM(LAMMPS *lmp, int narg, char **arg) : KSpace(lmp, narg, arg), +MSM::MSM(LAMMPS *lmp) : KSpace(lmp), factors(NULL), delxinv(NULL), delyinv(NULL), delzinv(NULL), nx_msm(NULL), ny_msm(NULL), nz_msm(NULL), nxlo_in(NULL), nylo_in(NULL), nzlo_in(NULL), nxhi_in(NULL), nyhi_in(NULL), nzhi_in(NULL), nxlo_out(NULL), nylo_out(NULL), @@ -58,12 +58,8 @@ MSM::MSM(LAMMPS *lmp, int narg, char **arg) : KSpace(lmp, narg, arg), phi1d(NULL), dphi1d(NULL), procneigh_levels(NULL), cg(NULL), cg_peratom(NULL), cg_all(NULL), cg_peratom_all(NULL), part2grid(NULL), boxlo(NULL) { - if (narg < 1) error->all(FLERR,"Illegal kspace_style msm command"); - msmflag = 1; - accuracy_relative = fabs(force->numeric(FLERR,arg[0])); - nfactors = 1; factors = new int[nfactors]; factors[0] = 2; @@ -115,6 +111,14 @@ MSM::MSM(LAMMPS *lmp, int narg, char **arg) : KSpace(lmp, narg, arg), order = 10; } + +void MSM::settings(int narg, char **arg) +{ + if (narg < 1) error->all(FLERR,"Illegal kspace_style msm command"); + accuracy_relative = fabs(force->numeric(FLERR,arg[0])); +} + + /* ---------------------------------------------------------------------- free all memory ------------------------------------------------------------------------- */ diff --git a/src/KSPACE/msm.h b/src/KSPACE/msm.h index 6a0b7d0eeb..0f81eb9c3f 100644 --- a/src/KSPACE/msm.h +++ b/src/KSPACE/msm.h @@ -29,10 +29,11 @@ namespace LAMMPS_NS { class MSM : public KSpace { public: - MSM(class LAMMPS *, int, char **); + MSM(class LAMMPS *); virtual ~MSM(); void init(); void setup(); + virtual void settings(int, char **); virtual void compute(int, int); protected: From cc6f1be82df383758cc7fe040ae7d1d5206f1fa9 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 19 Oct 2018 07:26:49 -0400 Subject: [PATCH 266/302] first attempt to port fix halt to minimizations --- doc/src/fix_halt.txt | 3 +-- src/fix_halt.cpp | 7 +++++++ src/fix_halt.h | 1 + 3 files changed, 9 insertions(+), 2 deletions(-) diff --git a/doc/src/fix_halt.txt b/doc/src/fix_halt.txt index ec117518d2..87ad97accf 100644 --- a/doc/src/fix_halt.txt +++ b/doc/src/fix_halt.txt @@ -135,8 +135,7 @@ files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various "output commands"_Howto_output.html. No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. +the "run"_run.html command. [Restrictions:] none diff --git a/src/fix_halt.cpp b/src/fix_halt.cpp index 983f993ae8..8acc08b107 100644 --- a/src/fix_halt.cpp +++ b/src/fix_halt.cpp @@ -143,6 +143,13 @@ void FixHalt::init() /* ---------------------------------------------------------------------- */ +void FixHalt::min_step(double, double *) +{ + if ((update->ntimestep % nevery) == 0) end_of_step(); +} + +/* ---------------------------------------------------------------------- */ + void FixHalt::end_of_step() { // variable evaluation may invoke computes so wrap with clear/add diff --git a/src/fix_halt.h b/src/fix_halt.h index d3b39cc1e2..1bc49bbe1c 100644 --- a/src/fix_halt.h +++ b/src/fix_halt.h @@ -32,6 +32,7 @@ class FixHalt : public Fix { int setmask(); void init(); void end_of_step(); + void min_step(double, double *); void post_run(); private: From 80e0dddae072acd04e29d93941018e91751f154d Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 19 Oct 2018 14:08:25 -0400 Subject: [PATCH 267/302] use min_post_force() method to hook fix halt into minimization --- src/fix_halt.cpp | 6 +++++- src/fix_halt.h | 4 ++-- 2 files changed, 7 insertions(+), 3 deletions(-) diff --git a/src/fix_halt.cpp b/src/fix_halt.cpp index 8acc08b107..5fda4c30d6 100644 --- a/src/fix_halt.cpp +++ b/src/fix_halt.cpp @@ -119,6 +119,7 @@ int FixHalt::setmask() int mask = 0; mask |= END_OF_STEP; mask |= POST_RUN; + mask |= MIN_POST_FORCE; return mask; } @@ -138,14 +139,17 @@ void FixHalt::init() // settings used by TLIMIT nextstep = (update->ntimestep/nevery)*nevery + nevery; + thisstep = -1; tratio = 0.5; } /* ---------------------------------------------------------------------- */ -void FixHalt::min_step(double, double *) +void FixHalt::min_post_force(int /* vflag */) { + if (update->ntimestep == thisstep) return; if ((update->ntimestep % nevery) == 0) end_of_step(); + thisstep = update->ntimestep; } /* ---------------------------------------------------------------------- */ diff --git a/src/fix_halt.h b/src/fix_halt.h index 1bc49bbe1c..372c915a7f 100644 --- a/src/fix_halt.h +++ b/src/fix_halt.h @@ -32,12 +32,12 @@ class FixHalt : public Fix { int setmask(); void init(); void end_of_step(); - void min_step(double, double *); + void min_post_force(int); void post_run(); private: int attribute,operation,eflag,msgflag,ivar; - bigint nextstep; + bigint nextstep,thisstep; double value,tratio; char *idvar; From 2f52eee6bfc1945b09800fb97cfca988d4d2b337 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 19 Oct 2018 15:11:37 -0400 Subject: [PATCH 268/302] kspace refactor compiles for KSPACE and USER-OMP --- src/KSPACE/fix_tune_kspace.cpp | 3 ++- src/KSPACE/msm.cpp | 2 +- src/KSPACE/msm_cg.cpp | 17 +++++++++++++---- src/KSPACE/msm_cg.h | 3 ++- src/KSPACE/pppm.cpp | 14 +++++++++----- src/KSPACE/pppm.h | 3 ++- src/KSPACE/pppm_cg.cpp | 17 +++++++++++++---- src/KSPACE/pppm_cg.h | 3 ++- src/KSPACE/pppm_disp.cpp | 13 +++++++++---- src/KSPACE/pppm_disp.h | 3 ++- src/KSPACE/pppm_disp_tip4p.cpp | 3 +-- src/KSPACE/pppm_disp_tip4p.h | 2 +- src/KSPACE/pppm_stagger.cpp | 5 ++--- src/KSPACE/pppm_stagger.h | 2 +- src/KSPACE/pppm_tip4p.cpp | 3 +-- src/KSPACE/pppm_tip4p.h | 2 +- src/USER-OMP/ewald_omp.cpp | 3 +-- src/USER-OMP/ewald_omp.h | 2 +- src/USER-OMP/msm_cg_omp.cpp | 15 +++++++++++---- src/USER-OMP/msm_cg_omp.h | 3 ++- src/USER-OMP/msm_omp.cpp | 3 +-- src/USER-OMP/msm_omp.h | 4 ++-- src/USER-OMP/pppm_cg_omp.cpp | 3 +-- src/USER-OMP/pppm_cg_omp.h | 2 +- src/USER-OMP/pppm_disp_omp.cpp | 3 +-- src/USER-OMP/pppm_disp_omp.h | 2 +- src/USER-OMP/pppm_disp_tip4p_omp.cpp | 4 ++-- src/USER-OMP/pppm_disp_tip4p_omp.h | 2 +- src/USER-OMP/pppm_omp.cpp | 3 +-- src/USER-OMP/pppm_omp.h | 2 +- src/USER-OMP/pppm_tip4p_omp.cpp | 4 ++-- src/USER-OMP/pppm_tip4p_omp.h | 2 +- 32 files changed, 92 insertions(+), 60 deletions(-) diff --git a/src/KSPACE/fix_tune_kspace.cpp b/src/KSPACE/fix_tune_kspace.cpp index 399e551b57..a3ac5e1e83 100644 --- a/src/KSPACE/fix_tune_kspace.cpp +++ b/src/KSPACE/fix_tune_kspace.cpp @@ -273,7 +273,8 @@ void FixTuneKspace::update_kspace_style(char *new_kspace_style, // delete old kspace style and create new one - force->create_kspace(narg,arg,1); + force->create_kspace(arg[0],1); + force->kspace->settings(narg-1,&arg[1]); force->kspace->differentiation_flag = old_differentiation_flag; force->kspace->slabflag = old_slabflag; force->kspace->slab_volfactor = old_slab_volfactor; diff --git a/src/KSPACE/msm.cpp b/src/KSPACE/msm.cpp index 9583ed4ef5..ed4abcf077 100644 --- a/src/KSPACE/msm.cpp +++ b/src/KSPACE/msm.cpp @@ -111,6 +111,7 @@ MSM::MSM(LAMMPS *lmp) : KSpace(lmp), order = 10; } +/* ---------------------------------------------------------------------- */ void MSM::settings(int narg, char **arg) { @@ -118,7 +119,6 @@ void MSM::settings(int narg, char **arg) accuracy_relative = fabs(force->numeric(FLERR,arg[0])); } - /* ---------------------------------------------------------------------- free all memory ------------------------------------------------------------------------- */ diff --git a/src/KSPACE/msm_cg.cpp b/src/KSPACE/msm_cg.cpp index 3ae3d62725..1139ce4957 100644 --- a/src/KSPACE/msm_cg.cpp +++ b/src/KSPACE/msm_cg.cpp @@ -42,18 +42,27 @@ enum{FORWARD_RHO,FORWARD_AD,FORWARD_AD_PERATOM}; /* ---------------------------------------------------------------------- */ -MSMCG::MSMCG(LAMMPS *lmp, int narg, char **arg) : MSM(lmp, narg, arg), +MSMCG::MSMCG(LAMMPS *lmp) : MSM(lmp), is_charged(NULL) +{ + triclinic_support = 0; + + num_charged = -1; +} + +/* ---------------------------------------------------------------------- */ + +void MSMCG::settings(int narg, char **arg) { if ((narg < 1) || (narg > 2)) error->all(FLERR,"Illegal kspace_style msm/cg command"); - triclinic_support = 0; + // first argument is processed in parent class + + MSM::settings(narg,arg); if (narg == 2) smallq = fabs(force->numeric(FLERR,arg[1])); else smallq = SMALLQ; - - num_charged = -1; } /* ---------------------------------------------------------------------- diff --git a/src/KSPACE/msm_cg.h b/src/KSPACE/msm_cg.h index 2f68e46461..7a27e3b83a 100644 --- a/src/KSPACE/msm_cg.h +++ b/src/KSPACE/msm_cg.h @@ -26,8 +26,9 @@ namespace LAMMPS_NS { class MSMCG : public MSM { public: - MSMCG(class LAMMPS *, int, char **); + MSMCG(class LAMMPS *); virtual ~MSMCG(); + virtual void settings(int, char **); virtual void compute(int, int); virtual double memory_usage(); diff --git a/src/KSPACE/pppm.cpp b/src/KSPACE/pppm.cpp index 132389b7d6..57e030f255 100644 --- a/src/KSPACE/pppm.cpp +++ b/src/KSPACE/pppm.cpp @@ -64,7 +64,7 @@ enum{FORWARD_IK,FORWARD_AD,FORWARD_IK_PERATOM,FORWARD_AD_PERATOM}; /* ---------------------------------------------------------------------- */ -PPPM::PPPM(LAMMPS *lmp, int narg, char **arg) : KSpace(lmp, narg, arg), +PPPM::PPPM(LAMMPS *lmp) : KSpace(lmp), factors(NULL), density_brick(NULL), vdx_brick(NULL), vdy_brick(NULL), vdz_brick(NULL), u_brick(NULL), v0_brick(NULL), v1_brick(NULL), v2_brick(NULL), v3_brick(NULL), v4_brick(NULL), v5_brick(NULL), greensfn(NULL), vg(NULL), fkx(NULL), fky(NULL), @@ -78,14 +78,10 @@ PPPM::PPPM(LAMMPS *lmp, int narg, char **arg) : KSpace(lmp, narg, arg), peratom_allocate_flag = 0; group_allocate_flag = 0; - if (narg < 1) error->all(FLERR,"Illegal kspace_style pppm command"); - pppmflag = 1; group_group_enable = 1; triclinic = domain->triclinic; - accuracy_relative = fabs(force->numeric(FLERR,arg[0])); - nfactors = 3; factors = new int[nfactors]; factors[0] = 2; @@ -161,6 +157,14 @@ PPPM::PPPM(LAMMPS *lmp, int narg, char **arg) : KSpace(lmp, narg, arg), acons[7][6] = 4887769399.0 / 37838389248.0; } +/* ---------------------------------------------------------------------- */ + +void PPPM::settings(int narg, char **arg) +{ + if (narg < 1) error->all(FLERR,"Illegal kspace_style pppm command"); + accuracy_relative = fabs(force->numeric(FLERR,arg[0])); +} + /* ---------------------------------------------------------------------- free all memory ------------------------------------------------------------------------- */ diff --git a/src/KSPACE/pppm.h b/src/KSPACE/pppm.h index 9cb6bebb25..20ba7c3ff1 100644 --- a/src/KSPACE/pppm.h +++ b/src/KSPACE/pppm.h @@ -37,8 +37,9 @@ namespace LAMMPS_NS { class PPPM : public KSpace { public: - PPPM(class LAMMPS *, int, char **); + PPPM(class LAMMPS *); virtual ~PPPM(); + virtual void settings(int, char **); virtual void init(); virtual void setup(); void setup_grid(); diff --git a/src/KSPACE/pppm_cg.cpp b/src/KSPACE/pppm_cg.cpp index ca7abc9b5a..fa73588363 100644 --- a/src/KSPACE/pppm_cg.cpp +++ b/src/KSPACE/pppm_cg.cpp @@ -48,17 +48,26 @@ enum{FORWARD_IK,FORWARD_AD,FORWARD_IK_PERATOM,FORWARD_AD_PERATOM}; /* ---------------------------------------------------------------------- */ -PPPMCG::PPPMCG(LAMMPS *lmp, int narg, char **arg) : PPPM(lmp, narg, arg), +PPPMCG::PPPMCG(LAMMPS *lmp) : PPPM(lmp), is_charged(NULL) +{ + num_charged = -1; + group_group_enable = 1; +} + +/* ---------------------------------------------------------------------- */ + +void PPPMCG::settings(int narg, char **arg) { if ((narg < 1) || (narg > 2)) error->all(FLERR,"Illegal kspace_style pppm/cg command"); + // first argument is processed in parent class + + PPPM::settings(narg,arg); + if (narg == 2) smallq = fabs(force->numeric(FLERR,arg[1])); else smallq = SMALLQ; - - num_charged = -1; - group_group_enable = 1; } /* ---------------------------------------------------------------------- diff --git a/src/KSPACE/pppm_cg.h b/src/KSPACE/pppm_cg.h index 09824f9a41..8b5e26deca 100644 --- a/src/KSPACE/pppm_cg.h +++ b/src/KSPACE/pppm_cg.h @@ -26,8 +26,9 @@ namespace LAMMPS_NS { class PPPMCG : public PPPM { public: - PPPMCG(class LAMMPS *, int, char **); + PPPMCG(class LAMMPS *); virtual ~PPPMCG(); + virtual void settings(int, char **); virtual void compute(int, int); virtual double memory_usage(); diff --git a/src/KSPACE/pppm_disp.cpp b/src/KSPACE/pppm_disp.cpp index b8cd52c5fe..9fcfb7d769 100644 --- a/src/KSPACE/pppm_disp.cpp +++ b/src/KSPACE/pppm_disp.cpp @@ -63,7 +63,7 @@ enum{FORWARD_IK, FORWARD_AD, FORWARD_IK_PERATOM, FORWARD_AD_PERATOM, /* ---------------------------------------------------------------------- */ -PPPMDisp::PPPMDisp(LAMMPS *lmp, int narg, char **arg) : KSpace(lmp, narg, arg), +PPPMDisp::PPPMDisp(LAMMPS *lmp) : KSpace(lmp), factors(NULL), csumi(NULL), cii(NULL), B(NULL), density_brick(NULL), vdx_brick(NULL), vdy_brick(NULL), vdz_brick(NULL), density_fft(NULL), u_brick(NULL), v0_brick(NULL), v1_brick(NULL), v2_brick(NULL), v3_brick(NULL), v4_brick(NULL), v5_brick(NULL), @@ -106,11 +106,8 @@ PPPMDisp::PPPMDisp(LAMMPS *lmp, int narg, char **arg) : KSpace(lmp, narg, arg), fft2_6(NULL), remap(NULL), remap_6(NULL), cg(NULL), cg_peratom(NULL), cg_6(NULL), cg_peratom_6(NULL), part2grid(NULL), part2grid_6(NULL), boxlo(NULL) { - if (narg < 1) error->all(FLERR,"Illegal kspace_style pppm/disp command"); - triclinic_support = 0; pppmflag = dispersionflag = 1; - accuracy_relative = fabs(force->numeric(FLERR,arg[0])); nfactors = 3; factors = new int[nfactors]; @@ -225,6 +222,14 @@ PPPMDisp::PPPMDisp(LAMMPS *lmp, int narg, char **arg) : KSpace(lmp, narg, arg), memset(function, 0, EWALD_FUNCS*sizeof(int)); } +/* ---------------------------------------------------------------------- */ + +void PPPMDisp::settings(int narg, char **arg) +{ + if (narg < 1) error->all(FLERR,"Illegal kspace_style pppm/disp command"); + accuracy_relative = fabs(force->numeric(FLERR,arg[0])); +} + /* ---------------------------------------------------------------------- free all memory ------------------------------------------------------------------------- */ diff --git a/src/KSPACE/pppm_disp.h b/src/KSPACE/pppm_disp.h index 89df3d947e..8a3fb700e6 100644 --- a/src/KSPACE/pppm_disp.h +++ b/src/KSPACE/pppm_disp.h @@ -41,11 +41,12 @@ namespace LAMMPS_NS { class PPPMDisp : public KSpace { public: - PPPMDisp(class LAMMPS *, int, char **); + PPPMDisp(class LAMMPS *); virtual ~PPPMDisp(); virtual void init(); virtual void setup(); void setup_grid(); + virtual void settings(int, char **); virtual void compute(int, int); virtual int timing_1d(int, double &); virtual int timing_3d(int, double &); diff --git a/src/KSPACE/pppm_disp_tip4p.cpp b/src/KSPACE/pppm_disp_tip4p.cpp index 1a25b300fc..2bc63a84bb 100644 --- a/src/KSPACE/pppm_disp_tip4p.cpp +++ b/src/KSPACE/pppm_disp_tip4p.cpp @@ -41,8 +41,7 @@ using namespace MathConst; /* ---------------------------------------------------------------------- */ -PPPMDispTIP4P::PPPMDispTIP4P(LAMMPS *lmp, int narg, char **arg) : - PPPMDisp(lmp, narg, arg) +PPPMDispTIP4P::PPPMDispTIP4P(LAMMPS *lmp) : PPPMDisp(lmp) { triclinic_support = 0; tip4pflag = 1; diff --git a/src/KSPACE/pppm_disp_tip4p.h b/src/KSPACE/pppm_disp_tip4p.h index 7b3c24db8b..596be5f60b 100644 --- a/src/KSPACE/pppm_disp_tip4p.h +++ b/src/KSPACE/pppm_disp_tip4p.h @@ -26,7 +26,7 @@ namespace LAMMPS_NS { class PPPMDispTIP4P : public PPPMDisp { public: - PPPMDispTIP4P(class LAMMPS *, int, char **); + PPPMDispTIP4P(class LAMMPS *); virtual ~PPPMDispTIP4P () {}; void init(); diff --git a/src/KSPACE/pppm_stagger.cpp b/src/KSPACE/pppm_stagger.cpp index 6d3308a05b..ca369cf260 100644 --- a/src/KSPACE/pppm_stagger.cpp +++ b/src/KSPACE/pppm_stagger.cpp @@ -51,11 +51,10 @@ enum{FORWARD_IK,FORWARD_AD,FORWARD_IK_PERATOM,FORWARD_AD_PERATOM}; /* ---------------------------------------------------------------------- */ -PPPMStagger::PPPMStagger(LAMMPS *lmp, int narg, char **arg) : - PPPM(lmp, narg, arg), +PPPMStagger::PPPMStagger(LAMMPS *lmp) : + PPPM(lmp), gf_b2(NULL) { - if (narg < 1) error->all(FLERR,"Illegal kspace_style pppm/stagger command"); stagger_flag = 1; group_group_enable = 0; diff --git a/src/KSPACE/pppm_stagger.h b/src/KSPACE/pppm_stagger.h index c096d3b0ac..80161a3707 100644 --- a/src/KSPACE/pppm_stagger.h +++ b/src/KSPACE/pppm_stagger.h @@ -26,7 +26,7 @@ namespace LAMMPS_NS { class PPPMStagger : public PPPM { public: - PPPMStagger(class LAMMPS *, int, char **); + PPPMStagger(class LAMMPS *); virtual ~PPPMStagger(); virtual void init(); virtual void compute(int, int); diff --git a/src/KSPACE/pppm_tip4p.cpp b/src/KSPACE/pppm_tip4p.cpp index 08fc8c711c..b9fe3e6488 100644 --- a/src/KSPACE/pppm_tip4p.cpp +++ b/src/KSPACE/pppm_tip4p.cpp @@ -39,8 +39,7 @@ using namespace MathConst; /* ---------------------------------------------------------------------- */ -PPPMTIP4P::PPPMTIP4P(LAMMPS *lmp, int narg, char **arg) : - PPPM(lmp, narg, arg) +PPPMTIP4P::PPPMTIP4P(LAMMPS *lmp) : PPPM(lmp) { triclinic_support = 1; tip4pflag = 1; diff --git a/src/KSPACE/pppm_tip4p.h b/src/KSPACE/pppm_tip4p.h index 88a5707f2d..440bc46fa6 100644 --- a/src/KSPACE/pppm_tip4p.h +++ b/src/KSPACE/pppm_tip4p.h @@ -26,7 +26,7 @@ namespace LAMMPS_NS { class PPPMTIP4P : public PPPM { public: - PPPMTIP4P(class LAMMPS *, int, char **); + PPPMTIP4P(class LAMMPS *); virtual ~PPPMTIP4P () {}; void init(); diff --git a/src/USER-OMP/ewald_omp.cpp b/src/USER-OMP/ewald_omp.cpp index a26d5cf27d..1fece5c31b 100644 --- a/src/USER-OMP/ewald_omp.cpp +++ b/src/USER-OMP/ewald_omp.cpp @@ -34,8 +34,7 @@ using namespace MathConst; /* ---------------------------------------------------------------------- */ -EwaldOMP::EwaldOMP(LAMMPS *lmp, int narg, char **arg) - : Ewald(lmp, narg, arg), ThrOMP(lmp, THR_KSPACE) +EwaldOMP::EwaldOMP(LAMMPS *lmp) : Ewald(lmp), ThrOMP(lmp, THR_KSPACE) { triclinic_support = 0; suffix_flag |= Suffix::OMP; diff --git a/src/USER-OMP/ewald_omp.h b/src/USER-OMP/ewald_omp.h index 222806f15a..d06b634c43 100644 --- a/src/USER-OMP/ewald_omp.h +++ b/src/USER-OMP/ewald_omp.h @@ -27,7 +27,7 @@ namespace LAMMPS_NS { class EwaldOMP : public Ewald, public ThrOMP { public: - EwaldOMP(class LAMMPS *, int, char **); + EwaldOMP(class LAMMPS *); virtual ~EwaldOMP() { }; virtual void allocate(); virtual void compute(int, int); diff --git a/src/USER-OMP/msm_cg_omp.cpp b/src/USER-OMP/msm_cg_omp.cpp index 226083deb4..eaff373742 100644 --- a/src/USER-OMP/msm_cg_omp.cpp +++ b/src/USER-OMP/msm_cg_omp.cpp @@ -44,18 +44,25 @@ enum{FORWARD_RHO,FORWARD_AD,FORWARD_AD_PERATOM}; /* ---------------------------------------------------------------------- */ -MSMCGOMP::MSMCGOMP(LAMMPS *lmp, int narg, char **arg) : MSMOMP(lmp, narg, arg), +MSMCGOMP::MSMCGOMP(LAMMPS *lmp) : MSMOMP(lmp), is_charged(NULL) +{ + triclinic_support = 0; + + num_charged = -1; +} + +/* ---------------------------------------------------------------------- */ + +void MSMCGOMP::settings(int narg, char **arg) { if ((narg < 1) || (narg > 2)) error->all(FLERR,"Illegal kspace_style msm/cg/omp command"); - triclinic_support = 0; + MSMOMP::settings(narg,arg); if (narg == 2) smallq = fabs(force->numeric(FLERR,arg[1])); else smallq = SMALLQ; - - num_charged = -1; } /* ---------------------------------------------------------------------- diff --git a/src/USER-OMP/msm_cg_omp.h b/src/USER-OMP/msm_cg_omp.h index 1036db134f..e5842aaa28 100644 --- a/src/USER-OMP/msm_cg_omp.h +++ b/src/USER-OMP/msm_cg_omp.h @@ -26,8 +26,9 @@ namespace LAMMPS_NS { class MSMCGOMP : public MSMOMP { public: - MSMCGOMP(class LAMMPS *, int, char **); + MSMCGOMP(class LAMMPS *); virtual ~MSMCGOMP(); + virtual void settings(int, char **); virtual void compute(int, int); virtual double memory_usage(); diff --git a/src/USER-OMP/msm_omp.cpp b/src/USER-OMP/msm_omp.cpp index 3bc7ddb1cd..74cbb56be7 100644 --- a/src/USER-OMP/msm_omp.cpp +++ b/src/USER-OMP/msm_omp.cpp @@ -35,8 +35,7 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -MSMOMP::MSMOMP(LAMMPS *lmp, int narg, char **arg) : - MSM(lmp, narg, arg), ThrOMP(lmp, THR_KSPACE) +MSMOMP::MSMOMP(LAMMPS *lmp) : MSM(lmp), ThrOMP(lmp, THR_KSPACE) { triclinic_support = 0; suffix_flag |= Suffix::OMP; diff --git a/src/USER-OMP/msm_omp.h b/src/USER-OMP/msm_omp.h index 0dc6776c22..400772acf1 100644 --- a/src/USER-OMP/msm_omp.h +++ b/src/USER-OMP/msm_omp.h @@ -27,7 +27,7 @@ namespace LAMMPS_NS { class MSMOMP : public MSM, public ThrOMP { public: - MSMOMP(class LAMMPS *, int, char **); + MSMOMP(class LAMMPS *); virtual ~MSMOMP () {}; protected: @@ -51,4 +51,4 @@ E: Must use 'kspace_modify pressure/scalar no' with kspace_style msm/omp The kspace scalar pressure option is not compatible with kspace_style msm/omp. -*/ \ No newline at end of file +*/ diff --git a/src/USER-OMP/pppm_cg_omp.cpp b/src/USER-OMP/pppm_cg_omp.cpp index 990c50932e..2b4619f685 100644 --- a/src/USER-OMP/pppm_cg_omp.cpp +++ b/src/USER-OMP/pppm_cg_omp.cpp @@ -46,8 +46,7 @@ using namespace MathSpecial; /* ---------------------------------------------------------------------- */ -PPPMCGOMP::PPPMCGOMP(LAMMPS *lmp, int narg, char **arg) : - PPPMCG(lmp, narg, arg), ThrOMP(lmp, THR_KSPACE) +PPPMCGOMP::PPPMCGOMP(LAMMPS *lmp) : PPPMCG(lmp), ThrOMP(lmp, THR_KSPACE) { triclinic_support = 0; suffix_flag |= Suffix::OMP; diff --git a/src/USER-OMP/pppm_cg_omp.h b/src/USER-OMP/pppm_cg_omp.h index 057f86099d..b421d6b525 100644 --- a/src/USER-OMP/pppm_cg_omp.h +++ b/src/USER-OMP/pppm_cg_omp.h @@ -27,7 +27,7 @@ namespace LAMMPS_NS { class PPPMCGOMP : public PPPMCG, public ThrOMP { public: - PPPMCGOMP(class LAMMPS *, int, char **); + PPPMCGOMP(class LAMMPS *); virtual ~PPPMCGOMP (); virtual void compute(int, int); diff --git a/src/USER-OMP/pppm_disp_omp.cpp b/src/USER-OMP/pppm_disp_omp.cpp index 97bb909a2c..435341a31c 100644 --- a/src/USER-OMP/pppm_disp_omp.cpp +++ b/src/USER-OMP/pppm_disp_omp.cpp @@ -43,8 +43,7 @@ using namespace MathConst; /* ---------------------------------------------------------------------- */ -PPPMDispOMP::PPPMDispOMP(LAMMPS *lmp, int narg, char **arg) : - PPPMDisp(lmp, narg, arg), ThrOMP(lmp, THR_KSPACE) +PPPMDispOMP::PPPMDispOMP(LAMMPS *lmp) : PPPMDisp(lmp), ThrOMP(lmp, THR_KSPACE) { triclinic_support = 0; suffix_flag |= Suffix::OMP; diff --git a/src/USER-OMP/pppm_disp_omp.h b/src/USER-OMP/pppm_disp_omp.h index ac4a54c9f8..33dc9a308c 100644 --- a/src/USER-OMP/pppm_disp_omp.h +++ b/src/USER-OMP/pppm_disp_omp.h @@ -27,7 +27,7 @@ namespace LAMMPS_NS { class PPPMDispOMP : public PPPMDisp, public ThrOMP { public: - PPPMDispOMP(class LAMMPS *, int, char **); + PPPMDispOMP(class LAMMPS *); virtual ~PPPMDispOMP (); virtual void compute(int, int); diff --git a/src/USER-OMP/pppm_disp_tip4p_omp.cpp b/src/USER-OMP/pppm_disp_tip4p_omp.cpp index 2f7fbbea55..a53c5b2ac5 100644 --- a/src/USER-OMP/pppm_disp_tip4p_omp.cpp +++ b/src/USER-OMP/pppm_disp_tip4p_omp.cpp @@ -43,8 +43,8 @@ using namespace MathSpecial; /* ---------------------------------------------------------------------- */ -PPPMDispTIP4POMP::PPPMDispTIP4POMP(LAMMPS *lmp, int narg, char **arg) : - PPPMDispTIP4P(lmp, narg, arg), ThrOMP(lmp, THR_KSPACE) +PPPMDispTIP4POMP::PPPMDispTIP4POMP(LAMMPS *lmp) : + PPPMDispTIP4P(lmp), ThrOMP(lmp, THR_KSPACE) { triclinic_support = 0; tip4pflag = 1; diff --git a/src/USER-OMP/pppm_disp_tip4p_omp.h b/src/USER-OMP/pppm_disp_tip4p_omp.h index 8f499e2964..442c36c31a 100644 --- a/src/USER-OMP/pppm_disp_tip4p_omp.h +++ b/src/USER-OMP/pppm_disp_tip4p_omp.h @@ -27,7 +27,7 @@ namespace LAMMPS_NS { class PPPMDispTIP4POMP : public PPPMDispTIP4P, public ThrOMP { public: - PPPMDispTIP4POMP(class LAMMPS *, int, char **); + PPPMDispTIP4POMP(class LAMMPS *); virtual ~PPPMDispTIP4POMP (); protected: diff --git a/src/USER-OMP/pppm_omp.cpp b/src/USER-OMP/pppm_omp.cpp index e9c24a000c..66190b3f51 100644 --- a/src/USER-OMP/pppm_omp.cpp +++ b/src/USER-OMP/pppm_omp.cpp @@ -43,8 +43,7 @@ using namespace MathSpecial; /* ---------------------------------------------------------------------- */ -PPPMOMP::PPPMOMP(LAMMPS *lmp, int narg, char **arg) : - PPPM(lmp, narg, arg), ThrOMP(lmp, THR_KSPACE) +PPPMOMP::PPPMOMP(LAMMPS *lmp) : PPPM(lmp), ThrOMP(lmp, THR_KSPACE) { triclinic_support = 0; suffix_flag |= Suffix::OMP; diff --git a/src/USER-OMP/pppm_omp.h b/src/USER-OMP/pppm_omp.h index c447003605..bbaaaa00ef 100644 --- a/src/USER-OMP/pppm_omp.h +++ b/src/USER-OMP/pppm_omp.h @@ -27,7 +27,7 @@ namespace LAMMPS_NS { class PPPMOMP : public PPPM, public ThrOMP { public: - PPPMOMP(class LAMMPS *, int, char **); + PPPMOMP(class LAMMPS *); virtual ~PPPMOMP (); virtual void compute(int, int); diff --git a/src/USER-OMP/pppm_tip4p_omp.cpp b/src/USER-OMP/pppm_tip4p_omp.cpp index 29966216da..5fe44d2b71 100644 --- a/src/USER-OMP/pppm_tip4p_omp.cpp +++ b/src/USER-OMP/pppm_tip4p_omp.cpp @@ -44,8 +44,8 @@ using namespace MathSpecial; /* ---------------------------------------------------------------------- */ -PPPMTIP4POMP::PPPMTIP4POMP(LAMMPS *lmp, int narg, char **arg) : - PPPMTIP4P(lmp, narg, arg), ThrOMP(lmp, THR_KSPACE) +PPPMTIP4POMP::PPPMTIP4POMP(LAMMPS *lmp) : + PPPMTIP4P(lmp), ThrOMP(lmp, THR_KSPACE) { triclinic_support = 1; suffix_flag |= Suffix::OMP; diff --git a/src/USER-OMP/pppm_tip4p_omp.h b/src/USER-OMP/pppm_tip4p_omp.h index 1060f73c07..de130030f9 100644 --- a/src/USER-OMP/pppm_tip4p_omp.h +++ b/src/USER-OMP/pppm_tip4p_omp.h @@ -27,7 +27,7 @@ namespace LAMMPS_NS { class PPPMTIP4POMP : public PPPMTIP4P, public ThrOMP { public: - PPPMTIP4POMP(class LAMMPS *, int, char **); + PPPMTIP4POMP(class LAMMPS *); virtual ~PPPMTIP4POMP (); virtual void compute(int, int); From da84138475a5600df6f9c7903bf41a4d5b8ff8d7 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 19 Oct 2018 15:31:53 -0400 Subject: [PATCH 269/302] correct scafacos input example --- examples/USER/scafacos/in.scafacos | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/examples/USER/scafacos/in.scafacos b/examples/USER/scafacos/in.scafacos index 9a1f0f321e..d86112f203 100644 --- a/examples/USER/scafacos/in.scafacos +++ b/examples/USER/scafacos/in.scafacos @@ -1,7 +1,7 @@ # Point dipoles in a 2d box units lj -atom_style full +atom_style charge read_data data.NaCl @@ -29,7 +29,7 @@ pair_coeff * * #fix 2 all scafacos p3m tolerance field 0.001 kspace_style scafacos p3m 0.001 -kspace_style scafacos tolerance field +#kspace_style scafacos tolerance field timestep 0.005 thermo 10 From 3a4bef351c020f06d8369bea3928b383c6cc046b Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 19 Oct 2018 15:32:29 -0400 Subject: [PATCH 270/302] refactor kspace style in USER-SCAFACOS and fix uninitialized handle bug --- src/USER-SCAFACOS/scafacos.cpp | 47 ++++++++++++++++------------------ src/USER-SCAFACOS/scafacos.h | 3 ++- 2 files changed, 24 insertions(+), 26 deletions(-) diff --git a/src/USER-SCAFACOS/scafacos.cpp b/src/USER-SCAFACOS/scafacos.cpp index 52bb0e46c4..482a5586c7 100644 --- a/src/USER-SCAFACOS/scafacos.cpp +++ b/src/USER-SCAFACOS/scafacos.cpp @@ -36,7 +36,21 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -Scafacos::Scafacos(LAMMPS *lmp, int narg, char **arg) : KSpace(lmp, narg, arg) +Scafacos::Scafacos(LAMMPS *lmp) : KSpace(lmp) +{ + me = comm->me; + initialized = 0; + + maxatom = 0; + xpbc = NULL; + epot = NULL; + efield = NULL; + fcs = NULL; +} + +/* ---------------------------------------------------------------------- */ + +void Scafacos::settings(int narg, char **arg) { if (narg != 2) error->all(FLERR,"Illegal scafacos command"); @@ -48,35 +62,18 @@ Scafacos::Scafacos(LAMMPS *lmp, int narg, char **arg) : KSpace(lmp, narg, arg) // optional ScaFaCoS library setting defaults // choose the correct default tolerance type for chosen method // throw an error if a not yet supported solver is chosen - if (strcmp(method,"fmm") == 0) - { + if (strcmp(method,"fmm") == 0) { tolerance_type = FCS_TOLERANCE_TYPE_ENERGY; fmm_tuning_flag = 0; - } - else if (strcmp(method,"p3m") == 0 || - strcmp(method,"p2nfft") == 0 || - strcmp(method,"ewald") == 0) - { + } else if (strcmp(method,"p3m") == 0 || + strcmp(method,"p2nfft") == 0 || + strcmp(method,"ewald") == 0) { tolerance_type = FCS_TOLERANCE_TYPE_FIELD; - } - else if (strcmp(method,"direct") == 0) - { - // direct summation has no tolerance type - } - else - { + } else if (strcmp(method,"direct") == 0) { + ; // direct summation has no tolerance type + } else { error->all(FLERR,"Unsupported ScaFaCoS method"); } - - // initializations - - me = comm->me; - initialized = 0; - - maxatom = 0; - xpbc = NULL; - epot = NULL; - efield = NULL; } /* ---------------------------------------------------------------------- */ diff --git a/src/USER-SCAFACOS/scafacos.h b/src/USER-SCAFACOS/scafacos.h index fdf15739a6..33e714e136 100644 --- a/src/USER-SCAFACOS/scafacos.h +++ b/src/USER-SCAFACOS/scafacos.h @@ -27,10 +27,11 @@ namespace LAMMPS_NS { class Scafacos : public KSpace { public: - Scafacos(class LAMMPS *, int, char **); + Scafacos(class LAMMPS *); ~Scafacos(); void init(); void setup() {} + void settings(int, char **); void compute(int, int); int modify_param(int, char **); double memory_usage(); From 83c830fd8af8120add5ab8043b5a13d9a7eaa133 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 19 Oct 2018 15:47:00 -0400 Subject: [PATCH 271/302] port kspace refactor to GPU and KOKKOS package --- src/GPU/pppm_gpu.cpp | 4 +--- src/GPU/pppm_gpu.h | 2 +- src/KOKKOS/pppm_kokkos.cpp | 13 ++++++++----- src/KOKKOS/pppm_kokkos.h | 3 ++- 4 files changed, 12 insertions(+), 10 deletions(-) diff --git a/src/GPU/pppm_gpu.cpp b/src/GPU/pppm_gpu.cpp index 1f7c4239f8..4b460b1280 100644 --- a/src/GPU/pppm_gpu.cpp +++ b/src/GPU/pppm_gpu.cpp @@ -89,10 +89,8 @@ void PPPM_GPU_API(forces)(double **f); /* ---------------------------------------------------------------------- */ -PPPMGPU::PPPMGPU(LAMMPS *lmp, int narg, char **arg) : PPPM(lmp, narg, arg) +PPPMGPU::PPPMGPU(LAMMPS *lmp) : PPPM(lmp) { - if (narg != 1) error->all(FLERR,"Illegal kspace_style pppm/gpu command"); - triclinic_support = 0; density_brick_gpu = vd_brick = NULL; kspace_split = false; diff --git a/src/GPU/pppm_gpu.h b/src/GPU/pppm_gpu.h index 5f2ec96231..737d6c1816 100644 --- a/src/GPU/pppm_gpu.h +++ b/src/GPU/pppm_gpu.h @@ -26,7 +26,7 @@ namespace LAMMPS_NS { class PPPMGPU : public PPPM { public: - PPPMGPU(class LAMMPS *, int, char **); + PPPMGPU(class LAMMPS *); virtual ~PPPMGPU(); void init(); void setup(); diff --git a/src/KOKKOS/pppm_kokkos.cpp b/src/KOKKOS/pppm_kokkos.cpp index 13683d148f..5ec454f783 100644 --- a/src/KOKKOS/pppm_kokkos.cpp +++ b/src/KOKKOS/pppm_kokkos.cpp @@ -64,10 +64,8 @@ enum{FORWARD_IK,FORWARD_IK_PERATOM}; /* ---------------------------------------------------------------------- */ template -PPPMKokkos::PPPMKokkos(LAMMPS *lmp, int narg, char **arg) : PPPM(lmp, narg, arg) +PPPMKokkos::PPPMKokkos(LAMMPS *lmp) : PPPM(lmp) { - if (narg < 1) error->all(FLERR,"Illegal kspace_style pppm command"); - atomKK = (AtomKokkos *) atom; execution_space = ExecutionSpaceFromDevice::space; datamask_read = X_MASK | F_MASK | TYPE_MASK | Q_MASK; @@ -77,8 +75,6 @@ PPPMKokkos::PPPMKokkos(LAMMPS *lmp, int narg, char **arg) : PPPM(lmp group_group_enable = 0; triclinic_support = 0; - accuracy_relative = fabs(force->numeric(FLERR,arg[0])); - nfactors = 3; //factors = new int[nfactors]; factors[0] = 2; @@ -148,6 +144,13 @@ PPPMKokkos::PPPMKokkos(LAMMPS *lmp, int narg, char **arg) : PPPM(lmp k_flag = DAT::tdual_int_scalar("PPPM:flag"); } +template +void PPPMKokkos::settings(int narg, char **arg) +{ + if (narg < 1) error->all(FLERR,"Illegal kspace_style pppm/kk command"); + accuracy_relative = fabs(force->numeric(FLERR,arg[0])); +} + /* ---------------------------------------------------------------------- free all memory ------------------------------------------------------------------------- */ diff --git a/src/KOKKOS/pppm_kokkos.h b/src/KOKKOS/pppm_kokkos.h index 2d2b94bb49..db5b8f7ae6 100644 --- a/src/KOKKOS/pppm_kokkos.h +++ b/src/KOKKOS/pppm_kokkos.h @@ -92,11 +92,12 @@ class PPPMKokkos : public PPPM, public KokkosBase { typedef DeviceType device_type; typedef ArrayTypes AT; - PPPMKokkos(class LAMMPS *, int, char **); + PPPMKokkos(class LAMMPS *); virtual ~PPPMKokkos(); virtual void init(); virtual void setup(); void setup_grid(); + virtual void settings(int, char **); virtual void compute(int, int); virtual int timing_1d(int, double &); virtual int timing_3d(int, double &); From 0ec94b2ad63c757e98b9bce9913237e6a9b2d5b4 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 19 Oct 2018 16:01:13 -0400 Subject: [PATCH 272/302] replace non-ASCII character --- src/kspace.h | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/kspace.h b/src/kspace.h index 3917a0a72f..f29659d0e8 100644 --- a/src/kspace.h +++ b/src/kspace.h @@ -133,7 +133,7 @@ class KSpace : protected Pointers { /* ---------------------------------------------------------------------- compute gamma for MSM and pair styles - see Eq 4 from Parallel Computing 35 (2009) 164–177 + see Eq 4 from Parallel Computing 35 (2009) 164-177 ------------------------------------------------------------------------- */ double gamma(const double &rho) const From 9d7c4ac5f2e27d3356ac9d7f59fde616f288657e Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 19 Oct 2018 16:01:26 -0400 Subject: [PATCH 273/302] add depreacted kspace style --- src/kspace_deprecated.cpp | 49 +++++++++++++++++++++++++++++++++++++++ src/kspace_deprecated.h | 44 +++++++++++++++++++++++++++++++++++ 2 files changed, 93 insertions(+) create mode 100644 src/kspace_deprecated.cpp create mode 100644 src/kspace_deprecated.h diff --git a/src/kspace_deprecated.cpp b/src/kspace_deprecated.cpp new file mode 100644 index 0000000000..f783139d1b --- /dev/null +++ b/src/kspace_deprecated.cpp @@ -0,0 +1,49 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Axel Kohlmeyer (Temple U) +------------------------------------------------------------------------- */ + +#include +#include "kspace_deprecated.h" +#include "kspace_hybrid.h" +#include "comm.h" +#include "force.h" +#include "error.h" + +using namespace LAMMPS_NS; + +static void writemsg(LAMMPS *lmp, const char *msg, int abend=1) +{ + if (lmp->comm->me == 0) { + if (lmp->screen) fputs(msg,lmp->screen); + if (lmp->logfile) fputs(msg,lmp->logfile); + } + if (abend) + lmp->error->all(FLERR,"This kspace style is no longer available"); +} + +/* ---------------------------------------------------------------------- */ + +void KspaceDeprecated::settings(int, char **) +{ + const char *my_style = force->kspace_style; + + if (strcmp(my_style,"DEPRECATED") == 0) { + writemsg(lmp,"\nKspace style 'DEPRECATED' is a dummy style\n\n",0); + + } +} + + diff --git a/src/kspace_deprecated.h b/src/kspace_deprecated.h new file mode 100644 index 0000000000..c43d8f6869 --- /dev/null +++ b/src/kspace_deprecated.h @@ -0,0 +1,44 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef KSPACE_CLASS + +KspaceStyle(DEPRECATED,KspaceDeprecated) + +#else + +#ifndef LMP_KSPACE_DEPRECATED_H +#define LMP_KSPACE_DEPRECATED_H + +#include "kspace.h" + +namespace LAMMPS_NS { + +class KspaceDeprecated : public Kspace { + public: + KspaceDeprecated(class LAMMPS *lmp) : Kspace(lmp) {} + virtual ~KspaceDeprecated() {} + + virtual void init() {} + virtual void setup() {} + virtual void compute(int, int) {} +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ From db32373b329e4679a4ce2da213c93c7a09ae90cd Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 19 Oct 2018 16:11:13 -0400 Subject: [PATCH 274/302] fix some typos caused by trusting emacs' smart case-preserving replace too much --- src/kspace_deprecated.cpp | 7 +++---- src/kspace_deprecated.h | 9 +++++---- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/src/kspace_deprecated.cpp b/src/kspace_deprecated.cpp index f783139d1b..1d62de2692 100644 --- a/src/kspace_deprecated.cpp +++ b/src/kspace_deprecated.cpp @@ -17,7 +17,6 @@ #include #include "kspace_deprecated.h" -#include "kspace_hybrid.h" #include "comm.h" #include "force.h" #include "error.h" @@ -36,14 +35,14 @@ static void writemsg(LAMMPS *lmp, const char *msg, int abend=1) /* ---------------------------------------------------------------------- */ -void KspaceDeprecated::settings(int, char **) +void KSpaceDeprecated::settings(int, char **) { const char *my_style = force->kspace_style; if (strcmp(my_style,"DEPRECATED") == 0) { - writemsg(lmp,"\nKspace style 'DEPRECATED' is a dummy style\n\n",0); + writemsg(lmp,"\nKSpace style 'DEPRECATED' is a dummy style\n\n",0); } -} +} diff --git a/src/kspace_deprecated.h b/src/kspace_deprecated.h index c43d8f6869..ca5205b9e3 100644 --- a/src/kspace_deprecated.h +++ b/src/kspace_deprecated.h @@ -13,7 +13,7 @@ #ifdef KSPACE_CLASS -KspaceStyle(DEPRECATED,KspaceDeprecated) +KSpaceStyle(DEPRECATED,KSpaceDeprecated) #else @@ -24,12 +24,13 @@ KspaceStyle(DEPRECATED,KspaceDeprecated) namespace LAMMPS_NS { -class KspaceDeprecated : public Kspace { +class KSpaceDeprecated : public KSpace { public: - KspaceDeprecated(class LAMMPS *lmp) : Kspace(lmp) {} - virtual ~KspaceDeprecated() {} + KSpaceDeprecated(class LAMMPS *lmp) : KSpace(lmp) {} + virtual ~KSpaceDeprecated() {} virtual void init() {} + virtual void settings(int, char**); virtual void setup() {} virtual void compute(int, int) {} }; From 709013be5ab1c2f0b731c318e108bc226155285f Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 19 Oct 2018 16:48:37 -0400 Subject: [PATCH 275/302] harden code against buffer overflows --- src/lammps.cpp | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/src/lammps.cpp b/src/lammps.cpp index c6d8b7c967..8273016e8a 100644 --- a/src/lammps.cpp +++ b/src/lammps.cpp @@ -604,14 +604,15 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) if (restart2data || restart2dump) { char cmd[256]; - snprintf(cmd,256,"read_restart %s\n",restartfile); + snprintf(cmd,248,"read_restart %s\n",restartfile); if (restartremap) strcat(cmd," remap\n"); input->one(cmd); - if (restart2data) snprintf(cmd,256,"write_data"); - else snprintf(cmd,256,"write_dump"); + if (restart2data) strcpy(cmd,"write_data"); + else strcpy(cmd,"write_dump"); for (iarg = wfirst; iarg < wlast; iarg++) - sprintf(&cmd[strlen(cmd)]," %s",arg[iarg]); + snprintf(&cmd[strlen(cmd)],246-strlen(cmd)," %s",arg[iarg]); if (restart2data) strcat(cmd," noinit\n"); + else strcat(cmd,"\n"); input->one(cmd); error->done(0); } From 01c3ab5979c001453b24164cb4446b0a353ffc73 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 19 Oct 2018 16:49:06 -0400 Subject: [PATCH 276/302] update embedded command line help summary string for new feature --- src/lammps.cpp | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/src/lammps.cpp b/src/lammps.cpp index 8273016e8a..699efe37a3 100644 --- a/src/lammps.cpp +++ b/src/lammps.cpp @@ -912,7 +912,9 @@ void LAMMPS::help() "-partition size1 size2 ... : assign partition sizes (-p)\n" "-plog basename : basename for partition logs (-pl)\n" "-pscreen basename : basename for partition screens (-ps)\n" - "-restart rfile dfile ... : convert restart to data file (-r)\n" + "-restart2data rfile dfile ... : convert restart to data file (-r2data)\n" + "-restart2dump rfile dgroup dstyle dfile ... \n" + " : convert restart to dump file (-r2dump)\n" "-reorder topology-specs : processor reordering (-r)\n" "-screen none/filename : where to send screen output (-sc)\n" "-suffix gpu/intel/opt/omp : style suffix to apply (-sf)\n" From 27a46cec8ce39cdc7861218bfb1754c78dfa7a81 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Fri, 19 Oct 2018 17:25:18 -0400 Subject: [PATCH 277/302] Add src directory to PreventInSourceBuilds checks --- cmake/Modules/PreventInSourceBuilds.cmake | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/cmake/Modules/PreventInSourceBuilds.cmake b/cmake/Modules/PreventInSourceBuilds.cmake index 20d9d25590..31f2376aa1 100644 --- a/cmake/Modules/PreventInSourceBuilds.cmake +++ b/cmake/Modules/PreventInSourceBuilds.cmake @@ -5,10 +5,11 @@ function(prevent_in_source_builds) # make sure the user doesn't play dirty with symlinks get_filename_component(srcdir "${CMAKE_SOURCE_DIR}" REALPATH) get_filename_component(srcdir2 "${CMAKE_SOURCE_DIR}/.." REALPATH) + get_filename_component(srcdir3 "${CMAKE_SOURCE_DIR}/../src" REALPATH) get_filename_component(bindir "${CMAKE_BINARY_DIR}" REALPATH) # disallow in-source builds - if("${srcdir}" STREQUAL "${bindir}" OR "${srcdir2}" STREQUAL "${bindir}") + if("${srcdir}" STREQUAL "${bindir}" OR "${srcdir2}" STREQUAL "${bindir}" OR "${srcdir3}" STREQUAL "${bindir}") message(FATAL_ERROR "\ CMake must not to be run in the source directory. \ From 8cd70f7d78cf2b1b33dfce6f1672cfcf17fc846d Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Fri, 19 Oct 2018 15:27:38 -0600 Subject: [PATCH 278/302] fix triclinic rounding bug for lib interface as well --- src/domain.cpp | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/src/domain.cpp b/src/domain.cpp index 8238ab7eea..beaf5fc08e 100644 --- a/src/domain.cpp +++ b/src/domain.cpp @@ -1623,8 +1623,14 @@ int Domain::ownatom(int /*id*/, double *x, imageint *image, int shrinkexceed) if (image) remap(x,*image); else remap(x); + // if triclinic, convert to lamda coords (0-1) + // for periodic dims, resulting coord must satisfy 0.0 <= coord < 1.0 + if (triclinic) { x2lamda(x,lamda); + if (xperiodic && (lamda[0] < 0.0 || lamda[0] >= 1.0)) lamda[0] = 0.0; + if (yperiodic && (lamda[1] < 0.0 || lamda[1] >= 1.0)) lamda[1] = 0.0; + if (zperiodic && (lamda[2] < 0.0 || lamda[2] >= 1.0)) lamda[2] = 0.0; coord = lamda; } else coord = x; From 04a4a29fcf0bc6c54b63e8bedfd7965a4ae1ee46 Mon Sep 17 00:00:00 2001 From: Aidan Thompson Date: Fri, 19 Oct 2018 18:36:11 -0600 Subject: [PATCH 279/302] Creatd new compute ADF for angular distribution function --- doc/src/compute_adf.txt | 207 ++++++++++++++ src/compute_adf.cpp | 580 ++++++++++++++++++++++++++++++++++++++++ src/compute_adf.h | 89 ++++++ 3 files changed, 876 insertions(+) create mode 100644 doc/src/compute_adf.txt create mode 100644 src/compute_adf.cpp create mode 100644 src/compute_adf.h diff --git a/doc/src/compute_adf.txt b/doc/src/compute_adf.txt new file mode 100644 index 0000000000..9c0540b746 --- /dev/null +++ b/doc/src/compute_adf.txt @@ -0,0 +1,207 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +compute adf command :h3 + +[Syntax:] + +compute ID group-ID adf Nbin itype1 jtype1 ktype1 Rjinner1 Rjouter1 Rkinner1 Rkouter1 ... :pre + +ID, group-ID are documented in "compute"_compute.html command :ulb,l +adf = style name of this compute command :l +Nbin = number of ADF bins :l +itypeN = central atom type for Nth ADF histogram (see asterisk form below) :l +jtypeN = J atom type for Nth ADF histogram (see asterisk form below) :l +ktypeN = K atom type for Nth ADF histogram (see asterisk form below) :l +RjinnerN = inner radius of J atom shell for Nth ADF histogram (distance units) :l +RjouterN = outer radius of J atom shell for Nth ADF histogram (distance units) :l +RkinnerN = inner radius of K atom shell for Nth ADF histogram (distance units) :l +RkouterN = outer radius of K atom shell for Nth ADF histogram (distance units) :l + +zero or one keyword/value pairs may be appended :l +keyword = {ordinate} :l + {ordinate} value = {degree} or {radian} or {cosine} + Choose the ordinate parameter for the histogram :pre +:ule + +[Examples:] + +compute 1 fluid adf 32 1 1 1 0.0 1.2 0.0 1.2 & + 1 1 2 0.0 1.2 0.0 1.5 & + 1 2 2 0.0 1.5 0.0 1.5 & + 2 1 1 0.0 1.2 0.0 1.2 & + 2 1 2 0.0 1.5 2.0 3.5 & + 2 2 2 2.0 3.5 2.0 3.5 +compute 1 fluid adf 32 1*2 1*2 1*2 0.5 3.5 +compute 1 fluid adf 32 :pre + +[Description:] + +Define a computation that calculates one or more angular distribution functions +(ADF) for a group of particles. Each ADF is calculated in histogram form +by measuring the angle formed by a central atom and two neighbor atoms and +binning these angles into {Nbin} bins. +Only neighbors for which {Rinner} < {R} < {Router} are counted, where +{Rinner} and {Router} are specified separately for the first and second +neighbor atom in each requested ADF. + +NOTE: If you have a bonded system, then the settings of +"special_bonds"_special_bonds.html command can remove pairwise +interactions between atoms in the same bond, angle, or dihedral. This +is the default setting for the "special_bonds"_special_bonds.html +command, and means those pairwise interactions do not appear in the +neighbor list. Because this fix uses a neighbor list, it also means +those pairs will not be included in the ADF. This does not apply when +using long-range coulomb interactions ({coul/long}, {coul/msm}, +{coul/wolf} or similar. One way to get around this would be to set +special_bond scaling factors to very tiny numbers that are not exactly +zero (e.g. 1.0e-50). Another workaround is to write a dump file, and +use the "rerun"_rerun.html command to compute the ADF for snapshots in +the dump file. The rerun script can use a +"special_bonds"_special_bonds.html command that includes all pairs in +the neighbor list. + +NOTE: If you request any outer cutoff {Router} > force cutoff, or if no +pair style is defined, e.g. the "rerun"_rerun.html command is being used to +post-process a dump file of snapshots you must insure ghost atom information +out to the largest value of {Router} + {skin} is communicated, via the +"comm_modify cutoff"_comm_modify.html command, else the ADF computation +cannot be performed, and LAMMPS will give an error message. The {skin} value +is what is specified with the "neighbor"_neighbor.html command. + +The {itypeN},{jtypeN},{ktypeN} settings can be specified in one of two +ways. An explicit numeric value can be used, as in the 1st example +above. Or a wild-card asterisk can be used to specify a range of atom +types as in the 2nd example above. +This takes the form "*" or "*n" or "n*" or "m*n". If N = the +number of atom types, then an asterisk with no numeric values means +all types from 1 to N. A leading asterisk means all types from 1 to n +(inclusive). A trailing asterisk means all types from n to N +(inclusive). A middle asterisk means all types from m to n +(inclusive). + +If {itypeN}, {jtypeN}, and {ktypeN} are single values, as in the 1st example +above, this means that the ADF is computed where atoms of type {itypeN} +are the central atom, and neighbor atoms of type {jtypeN} and {ktypeN} +are forming the angle. If any of {itypeN}, {jtypeN}, or {ktypeN} +represent a range of values via +the wild-card asterisk, as in the 2nd example above, this means that the +ADF is computed where atoms of any of the range of types represented +by {itypeN} are the central atom, and the angle is formed by two neighbors, +one neighbor in the range of types represented by {jtypeN} and another neighbor +in the range of types represented by {ktypeN}. + +If no {itypeN}, {jtypeN}, {ktypeN} settings are specified, then +LAMMPS will generate a single ADF for all atoms in the group. +The inner cutoff is set to zero and the outer cutoff is set +to the force cutoff. If no pair_style is specified, there is no +force cutoff and LAMMPS will give an error message. Note that +in most cases, generating an ADF for all atoms is not a good thing. +Such an ADF is both uninformative and +extremely expensive to compute. For example, with liquid water +with a 10 A force cutoff, there are 80,000 angles per atom. +In addition, most of the interesting angular structure occurs for +neighbors that are the closest to the central atom, involving +just a few dozen angles. + +Angles for each ADF are generated by double-looping over the list of +neighbors of each central atom I, +just as they would be in the force calculation for +a threebody potential such as "Stillinger-Weber"_pair_sw.html. +The angle formed by central atom I and neighbor atoms J and K is included in an +ADF if the following criteria are met: + +atoms I,J,K are all in the specified compute group +the distance between atoms I,J is between Rjinner and Rjouter +the distance between atoms I,K is between Rkinner and Rkouter +the type of the I atom matches itypeN (one or a range of types) +atoms I,J,K are distinct +the type of the J atom matches jtypeN (one or a range of types) +the type of the K atom matches ktypeN (one or a range of types) :ul + +Each unique angle satisfying the above criteria is counted only once, regardless +of whether either or both of the neighbor atoms making up the +angle appear in both the J and K lists. +It is OK if a particular angle is included in more than +one individual histogram, due to the way the {itypeN}, {jtypeN}, {ktypeN} +arguments are specified. + +The first ADF value for a bin is calculated from the histogram count by +dividing by the total number of triples satisfying the criteria, +so that the integral of the ADF w.r.t. angle is one i.e. the ADF +is a probability density function. + +The second ADF value is reported as a cumulative sum of +all bins up to the current bins, averaged +over atoms of type {itypeN}. It represents the +number of angles per central atom with angle less +than or equal to the angle of the current bin, +analogous to the coordination +number radial distribution function. + +The {ordinate} optional keyword determines +whether the bins are of uniform angular size from zero +to 180 ({degree}), zero to Pi ({radian}), or the +cosine of the angle uniform in the range \[-1,1\] ({cosine}). +Regardless of which is chosen, the first ADF will be normalized +so that the integral w.r.t. the ordinate is one. + +The simplest way to output the results of the compute adf calculation +to a file is to use the "fix ave/time"_fix_ave_time.html command, for +example: + +compute myADF all adf 32 2 2 2 0.5 3.5 0.5 3.5 +fix 1 all ave/time 100 1 100 c_myADF\[*\] file tmp.adf mode vector :pre + +[Output info:] + +This compute calculates a global array with the number of rows = +{Nbins}, and the number of columns = 1 + 2*Ntriples, where Ntriples is the +number of I,J,K triples specified. The first column has the bin +coordinate (angle-related ordinate at midpoint of bin). Each subsequent column has +the two ADF values for a specific set of ({itypeN},{jtypeN},{ktypeN}) +interactions, as described above. These values can be used +by any command that uses a global values from a compute as input. See +"Section 6.15"_Section_howto.html#howto_15 for an overview of +LAMMPS output options. + +The array values calculated by this compute are all "intensive". + +The first column of array values is the angle-related ordinate, either +the angle in degrees or radians, or the cosine of the angle. Each +subsequent pair of columns gives the first and second kinds of ADF +for a specific set of ({itypeN},{jtypeN},{ktypeN}). The values +in the first ADF column are normalized numbers >= 0.0, +whose integral w.r.t. the ordinate is one, +i.e. the first ADF is a normalized probability distribution. +The values in the second ADF column are also numbers >= 0.0. +They are the cumulative density distribution of angles per atom. +By definition, this ADF is monotonically increasing from zero to +a maximum value equal to the average total number of +angles per atom satisfying the ADF criteria. + +[Restrictions:] + +The ADF is not computed for neighbors outside the force cutoff, +since processors (in parallel) don't know about atom coordinates for +atoms further away than that distance. If you want an ADF for larger +distances, you can use the "rerun"_rerun.html command to post-process +a dump file and set the cutoff for the potential to be longer in the +rerun script. Note that in the rerun context, the force cutoff is +arbitrary, since you aren't running dynamics and thus are not changing +your model. + +[Related commands:] + +"compute rdf"_compute_rdf.html, "fix ave/time"_fix_ave_time.html, "compute_modify"_compute_modify.html + +[Default:] + +The keyword default is ordinate = degree. + + diff --git a/src/compute_adf.cpp b/src/compute_adf.cpp new file mode 100644 index 0000000000..5639d073db --- /dev/null +++ b/src/compute_adf.cpp @@ -0,0 +1,580 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing authors: Aidan P. Thompson (SNL) +------------------------------------------------------------------------- */ + +#include +#include +#include +#include +#include "compute_adf.h" +#include "atom.h" +#include "update.h" +#include "force.h" +#include "pair.h" +#include "domain.h" +#include "neighbor.h" +#include "neigh_request.h" +#include "neigh_list.h" +#include "group.h" +#include "math_const.h" +#include "memory.h" +#include "error.h" +#include "comm.h" + +using namespace LAMMPS_NS; +using namespace MathConst; + +enum{DEGREE, RADIAN, COSINE}; + +/* ---------------------------------------------------------------------- + compute angular distribution functions for I, J, K atoms + ---------------------------------------------------------------------- */ + +ComputeADF::ComputeADF(LAMMPS *lmp, int narg, char **arg) : + Compute(lmp, narg, arg), + ilo(NULL), ihi(NULL), jlo(NULL), jhi(NULL), klo(NULL), khi(NULL), + iatomcount(NULL), iatomcountall(NULL), + hist(NULL), histall(NULL), + iatomflag(NULL), + jatomflag(NULL), rcutinnerj(NULL), rcutouterj(NULL), + katomflag(NULL), rcutinnerk(NULL), rcutouterk(NULL), + maxjatom(NULL), numjatom(NULL), neighjatom(NULL), + maxkatom(NULL), numkatom(NULL), neighkatom(NULL), + maxjkatom(NULL), numjkatom(NULL), neighjkatom(NULL), bothjkatom(NULL) +{ + int nargsperadf = 7; + + if (narg < 4 ) error->all(FLERR,"Illegal compute adf command"); + + array_flag = 1; + extarray = 0; + + // default values + + ordinate_style = DEGREE; + cutflag = 0; + + nbin = force->inumeric(FLERR,arg[3]); + if (nbin < 1) error->all(FLERR,"Illegal compute adf command"); + + // optional args + // nargtriple = # of triplewise args, starting at iarg = 4 + + int iarg; + for (iarg = 4; iarg < narg; iarg++) + if (strcmp(arg[iarg],"ordinate") == 0) break; + + int nargtriple = iarg - 4; + + // loop over keywords + + while (iarg < narg) { + if (strcmp(arg[iarg],"ordinate") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal compute adf command"); + if (strcmp(arg[iarg+1],"degree") == 0) ordinate_style = DEGREE; + else if (strcmp(arg[iarg+1],"radian") == 0) ordinate_style = RADIAN; + else if (strcmp(arg[iarg+1],"cosine") == 0) ordinate_style = COSINE; + else error->all(FLERR,"Illegal compute adf command"); + iarg += 2; + } else error->all(FLERR,"Illegal compute adf command"); + } + + // triplewise args + + if (!nargtriple) ntriples = 1; + else { + if (nargtriple % nargsperadf) + error->all(FLERR,"Illegal compute adf command"); + ntriples = nargtriple/nargsperadf; + } + + size_array_rows = nbin; + size_array_cols = 1 + 2*ntriples; + + int ntypes = atom->ntypes; + memory->create(iatomflag,ntriples,ntypes+1, + "adf:iatomflag"); + memory->create(jatomflag,ntriples,ntypes+1, + "adf:jatomflag"); + memory->create(katomflag,ntriples,ntypes+1, + "adf:katomflag"); + + ilo = new int[ntriples]; + ihi = new int[ntriples]; + jlo = new int[ntriples]; + jhi = new int[ntriples]; + klo = new int[ntriples]; + khi = new int[ntriples]; + iatomcount = new int[ntriples]; + iatomcountall = new int[ntriples]; + + rcutinnerj = new double[ntriples]; + rcutouterj = new double[ntriples]; + rcutinnerk = new double[ntriples]; + rcutouterk = new double[ntriples]; + + if (!nargtriple) { + ilo[0] = 1; ihi[0] = ntypes; + jlo[0] = 1; jhi[0] = ntypes; + klo[0] = 1; khi[0] = ntypes; + } else { + cutflag = 1; + iarg = 4; + for (int itriple = 0; itriple < ntriples; itriple++) { + force->bounds(FLERR,arg[iarg],atom->ntypes,ilo[itriple],ihi[itriple]); + force->bounds(FLERR,arg[iarg+1],atom->ntypes,jlo[itriple],jhi[itriple]); + force->bounds(FLERR,arg[iarg+2],atom->ntypes,klo[itriple],khi[itriple]); + if (ilo[itriple] > ihi[itriple] || + jlo[itriple] > jhi[itriple] || + klo[itriple] > khi[itriple]) + error->all(FLERR,"Illegal compute adf command"); + rcutinnerj[itriple] = force->numeric(FLERR,arg[iarg+3]); + rcutouterj[itriple] = force->numeric(FLERR,arg[iarg+4]); + if (rcutinnerj[itriple] < 0.0 || rcutinnerj[itriple] >= rcutouterj[itriple]) + error->all(FLERR,"Illegal compute adf command"); + rcutinnerk[itriple] = force->numeric(FLERR,arg[iarg+5]); + rcutouterk[itriple] = force->numeric(FLERR,arg[iarg+6]); + if (rcutinnerk[itriple] < 0.0 || rcutinnerk[itriple] >= rcutouterk[itriple]) + error->all(FLERR,"Illegal compute adf command"); + iarg += nargsperadf; + } + } + + // identify central atom types + + int i,j,k; + + for (int m = 0; m < ntriples; m++) { + for (i = 1; i <= ntypes; i++) + iatomflag[m][i] = 0; + for (i = ilo[m]; i <= ihi[m]; i++) + iatomflag[m][i] = 1; + } + + // identify j atom types + + for (int m = 0; m < ntriples; m++) { + for (j = 1; j <= ntypes; j++) + jatomflag[m][j] = 0; + for (j = jlo[m]; j <= jhi[m]; j++) + jatomflag[m][j] = 1; + } + + // identify k atom types + + for (int m = 0; m < ntriples; m++) { + for (k = 1; k <= ntypes; k++) + katomflag[m][k] = 0; + for (k = klo[m]; k <= khi[m]; k++) + katomflag[m][k] = 1; + } + + memory->create(hist,ntriples,nbin,"adf:hist"); + memory->create(histall,ntriples,nbin,"adf:histall"); + memory->create(array,nbin,1+2*ntriples,"adf:array"); + + // initialize list of jatom neighbor lists + + maxjatom = new int[ntriples]; + numjatom = new int[ntriples]; + neighjatom = new int*[ntriples]; + for (int m = 0; m < ntriples; m++) { + maxjatom[m] = 10; + memory->create(neighjatom[m],maxjatom[m],"adf:neighjatom"); + } + + // initialize list of katom neighbor lists + + maxkatom = new int[ntriples]; + numkatom = new int[ntriples]; + neighkatom = new int*[ntriples]; + for (int m = 0; m < ntriples; m++) { + maxkatom[m] = 10; + memory->create(neighkatom[m],maxkatom[m],"adf:neighkatom"); + } + + // initialize list of short neighbor lists + + maxjkatom = new int[ntriples]; + numjkatom = new int[ntriples]; + neighjkatom = new int*[ntriples]; + bothjkatom = new int*[ntriples]; + delrjkatom = new double**[ntriples]; + for (int m = 0; m < ntriples; m++) { + maxjkatom[m] = 10; + memory->create(neighjkatom[m],maxjkatom[m],"adf:neighjkatom"); + memory->create(bothjkatom[m],maxjkatom[m],"adf:bothjkatom"); + memory->create(delrjkatom[m],maxjkatom[m],4,"adf:delrjkatom"); + } + + rad2deg = 180.0 / MY_PI; +} + +/* ---------------------------------------------------------------------- */ + +ComputeADF::~ComputeADF() +{ + memory->destroy(iatomflag); + delete [] ilo; + delete [] ihi; + delete [] jlo; + delete [] jhi; + delete [] klo; + delete [] khi; + delete [] iatomcount; + delete [] iatomcountall; + memory->destroy(hist); + memory->destroy(histall); + memory->destroy(array); + + memory->destroy(jatomflag); + delete [] rcutinnerj; + delete [] rcutouterj; + delete [] maxjatom; + delete [] numjatom; + for (int m = 0; m < ntriples; m++) + memory->destroy(neighjatom[m]); + delete [] neighjatom; + + memory->destroy(katomflag); + delete [] rcutinnerk; + delete [] rcutouterk; + delete [] maxkatom; + delete [] numkatom; + for (int m = 0; m < ntriples; m++) + memory->destroy(neighkatom[m]); + delete [] neighkatom; + + delete [] maxjkatom; + delete [] numjkatom; + for (int m = 0; m < ntriples; m++) + memory->destroy(neighjkatom[m]); + delete [] neighjkatom; + for (int m = 0; m < ntriples; m++) + memory->destroy(bothjkatom[m]); + delete [] bothjkatom; + for (int m = 0; m < ntriples; m++) + memory->destroy(delrjkatom[m]); + delete [] delrjkatom; +} + +/* ---------------------------------------------------------------------- */ + +void ComputeADF::init() +{ + double mycutneigh; + double maxouter; + + if (!cutflag) { + if (!force->pair) + error->all(FLERR,"Compute adf requires a pair style be defined " + "or outer cutoff specified"); + rcutinnerj[0] = 0.0; + rcutinnerk[0] = 0.0; + rcutouterj[0] = force->pair->cutforce; + rcutouterk[0] = force->pair->cutforce; + maxouter = force->pair->cutforce;; + } else { + maxouter = 0.0; + for (int m = 0; m < ntriples; m++) { + maxouter = MAX(rcutouterj[m],maxouter); + maxouter = MAX(rcutouterk[m],maxouter); + } + } + + // specify mycutneigh if force cutoff too small or non-existent + + if (!(force->pair) || maxouter > force->pair->cutforce) { + double skin = neighbor->skin; + mycutneigh = maxouter + skin; + if (mycutneigh > comm->cutghostuser) + error->all(FLERR,"Compute adf outer cutoff exceeds ghost atom range - " + "use comm_modify cutoff command"); + } + + // assign ordinate values to 1st column of output array + + int x0; + if (ordinate_style == DEGREE) { + deltax = MY_PI / nbin * rad2deg; + deltaxinv = nbin / MY_PI; + x0 = 0.0; + + } else if (ordinate_style == RADIAN) { + deltax = MY_PI / nbin; + deltaxinv = nbin / MY_PI; + x0 = 0.0; + + } else if (ordinate_style == COSINE) { + deltax = 2.0 / nbin; + deltaxinv = 1.0/deltax; + x0 = -1.0; + } + + for (int i = 0; i < nbin; i++) + array[i][0] = x0 + (i+0.5) * deltax; + + // need an occasional full neighbor list + // if mycutneigh specified, request a cutoff = maxouter + skin + // skin is included b/c Neighbor uses this value similar + // to its cutneighmax = force cutoff + skin + // also, this NeighList may be used by this compute for multiple steps + // (until next reneighbor), so it needs to contain atoms further + // than maxouter apart, just like a normal neighbor list does + + int irequest = neighbor->request(this,instance_me); + neighbor->requests[irequest]->half = 0; + neighbor->requests[irequest]->full = 1; + neighbor->requests[irequest]->pair = 0; + neighbor->requests[irequest]->compute = 1; + neighbor->requests[irequest]->occasional = 1; + if (mycutneigh > 0.0) { + neighbor->requests[irequest]->cut = 1; + neighbor->requests[irequest]->cutoff = mycutneigh; + } +} + +/* ---------------------------------------------------------------------- */ + +void ComputeADF::init_list(int /*id*/, NeighList *ptr) +{ + list = ptr; +} + +/* ---------------------------------------------------------------------- */ + +void ComputeADF::compute_array() +{ + int i,j,k,m,ii,jj,jatom,katom,jk,jjj,kkk; + int inum,jnum,itype,jtype,ibin,ihisto; + double xtmp,ytmp,ztmp,delx,dely,delz,rsq; + int *ilist,*jlist,*klist,*numneigh,**firstneigh; + double factor_lj,factor_coul; + double delr1[3],delr2[3],rinv1,rinv2,rinv12,cs,theta; + + invoked_array = update->ntimestep; + + // invoke full neighbor list (will copy or build if necessary) + + neighbor->build_one(list); + + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + // zero the histogram counts + + for (i = 0; i < ntriples; i++) + for (j = 0; j < nbin; j++) + hist[i][j] = 0.0; + + // zero the central atom counts + + for (i = 0; i < ntriples; i++) + iatomcount[m] = 0; + + // tally the ADFs + // all three atoms i, j, and k must be in fix group + // tally I,J,K triple only if I is central atom + // and J,K matches unordered neighbor types (JJ,KK) + + double **x = atom->x; + int *type = atom->type; + int *mask = atom->mask; + int nlocal = atom->nlocal; + + double *special_coul = force->special_coul; + double *special_lj = force->special_lj; + int newton_pair = force->newton_pair; + + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + if (!(mask[i] & groupbit)) continue; + itype = type[i]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + + // count atom i in each matching ADF + // zero the jatom, katom neighbor list counts + + for (m = 0; m < ntriples; m++) { + if (iatomflag[m][itype]) { + iatomcount[m]++; + } + numjatom[m] = 0; + numkatom[m] = 0; + numjkatom[m] = 0; + } + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + factor_lj = special_lj[sbmask(j)]; + factor_coul = special_coul[sbmask(j)]; + j &= NEIGHMASK; + + // if both weighting factors are 0, skip this pair + // could be 0 and still be in neigh list for long-range Coulombics + // want consistency with non-charged triples which wouldn't be in list + + if (factor_lj == 0.0 && factor_coul == 0.0) continue; + + if (!(mask[j] & groupbit)) continue; + jtype = type[j]; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + + for (m = 0; m < ntriples; m++) { + + // check if itype, jtype, ktype match this ADF definition + // if yes, add j to jatom, katom, and jkatom lists + + if (!iatomflag[m][itype]) continue; + + int jflag = 0; + if (jatomflag[m][jtype] && + rsq >= rcutinnerj[m]*rcutinnerj[m] && + rsq <= rcutouterj[m]*rcutouterj[m]) { + jflag = 1; + jatom = numjatom[m]++; + neighjatom[m][jatom] = numjkatom[m]; + if (numjatom[m] >= maxjatom[m]) { + maxjatom[m] += maxjatom[m]/2; + memory->grow(neighjatom[m],maxjatom[m],"adf:neighjatom"); + } + } + + int kflag = 0; + if (katomflag[m][jtype] && + rsq >= rcutinnerk[m]*rcutinnerk[m] && + rsq <= rcutouterk[m]*rcutouterk[m]) { + kflag = 1; + katom = numkatom[m]++; + neighkatom[m][katom] = numjkatom[m]; + if (numkatom[m] >= maxkatom[m]) { + maxkatom[m] += maxkatom[m]/2; + memory->grow(neighkatom[m],maxkatom[m],"adf:neighkatom"); + } + } + + // if atom in either list, add to jklist + + if (jflag || kflag) { + jk = numjkatom[m]++; + neighjkatom[m][jk] = j; + delrjkatom[m][jk][0] = delx; + delrjkatom[m][jk][1] = dely; + delrjkatom[m][jk][2] = delz; + delrjkatom[m][jk][3] = 1.0/sqrt(rsq); + if (numjkatom[m] >= maxjkatom[m]) { + maxjkatom[m] += maxjkatom[m]/2; + memory->grow(neighjkatom[m],maxjkatom[m],"adf:neighjkatom"); + memory->grow(bothjkatom[m],maxjkatom[m],"adf:bothjkatom"); + memory->grow(delrjkatom[m],maxjkatom[m],4,"adf:delrjkatom"); + } + + // indicate if atom in both lists + + if (jflag && kflag) + bothjkatom[m][jk] = 1; + else + bothjkatom[m][jk] = 0; + } + } + } + + // loop over ADFs + + for (m = 0; m < ntriples; m++) { + + // loop over (j,k) pairs + + for (jatom = 0; jatom < numjatom[m]; jatom++) { + jjj = neighjatom[m][jatom]; + j = neighjkatom[m][jjj]; + + delr1[0] = delrjkatom[m][jjj][0]; + delr1[1] = delrjkatom[m][jjj][1]; + delr1[2] = delrjkatom[m][jjj][2]; + rinv1 = delrjkatom[m][jjj][3]; + + for (katom = 0; katom < numkatom[m]; katom++) { + kkk = neighkatom[m][katom]; + k = neighjkatom[m][kkk]; + + // skip if j==k, or j > k and both are in both lists + + if (k == j || (j > k && bothjkatom[m][jjj] && bothjkatom[m][kkk])) continue; + + delr2[0] = delrjkatom[m][kkk][0]; + delr2[1] = delrjkatom[m][kkk][1]; + delr2[2] = delrjkatom[m][kkk][2]; + rinv2 = delrjkatom[m][kkk][3]; + rinv12 = rinv1*rinv2; + cs = (delr1[0]*delr2[0] + delr1[1]*delr2[1] + delr1[2]*delr2[2]) * rinv12; + + if (ordinate_style == COSINE) { + ibin = static_cast ((cs+1.0)*deltaxinv); + if (ibin >= nbin || ibin < 0) continue; + hist[m][ibin] += 1.0; + } else { + if (cs > 1.0) cs = 1.0; + if (cs < -1.0) cs = -1.0; + theta = acos(cs); + ibin = static_cast (theta*deltaxinv); + if (ibin >= nbin || ibin < 0) continue; + hist[m][ibin] += 1.0; + } + } + } + } + } + + // sum histograms across procs + + MPI_Allreduce(hist[0],histall[0],ntriples*nbin,MPI_DOUBLE,MPI_SUM,world); + MPI_Allreduce(iatomcount,iatomcountall,ntriples,MPI_INT,MPI_SUM,world); + + // convert counts to pdf(theta) and adf(theta) + // copy into output array + + for (m = 0; m < ntriples; m++) { + + double count = 0; + for (ibin = 0; ibin < nbin; ibin++) + count += histall[m][ibin]; + + double normfac1, pdftheta, normfac2, adftheta; + if (count > 0.0) normfac1 = deltaxinv/count; + else normfac1 = 0.0; + if (iatomcountall[m] > 0.0) normfac2 = 1.0/iatomcountall[m]; + else normfac2 = 0.0; + adftheta = 0.0; + for (ibin = 0; ibin < nbin; ibin++) { + pdftheta = histall[m][ibin] * normfac1; + adftheta += histall[m][ibin] * normfac2; + array[ibin][1+2*m] = pdftheta; + array[ibin][2+2*m] = adftheta; + } + } + +} diff --git a/src/compute_adf.h b/src/compute_adf.h new file mode 100644 index 0000000000..4c9e13707b --- /dev/null +++ b/src/compute_adf.h @@ -0,0 +1,89 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef COMPUTE_CLASS + +ComputeStyle(adf,ComputeADF) + +#else + +#ifndef LMP_COMPUTE_ADF_H +#define LMP_COMPUTE_ADF_H + +#include +#include "compute.h" + +namespace LAMMPS_NS { + +class ComputeADF : public Compute { + public: + ComputeADF(class LAMMPS *, int, char **); + ~ComputeADF(); + void init(); + void init_list(int, class NeighList *); + void compute_array(); + + private: + int nbin; // # of adf bins + int ntriples; // # of adf triples + double deltax,deltaxinv; // bin width and inverse-width + int *ilo,*ihi,*jlo,*jhi,*klo,*khi; + double **hist; // histogram bins + double **histall; // summed histogram bins across all procs + + double *rcutinnerj, *rcutinnerk; // list of inner cutoffs + double *rcutouterj, *rcutouterk; // list of outer cutoffs + + class NeighList *list; // full neighbor list + + int *iatomcount; // local number of central atoms + int *iatomcountall; // total number of central atoms + int **iatomflag; // 1 if type is central atom in ADF + int *maxjatom, *maxkatom; // allocated size jatom, katom neighlist + int *numjatom, *numkatom; // actual size of jatom, katom neighlist + int **neighjatom, **neighkatom;// list of short neighbor lists + int **jatomflag, **katomflag; // 1 if type is neighbor atom in ADF + + int *maxjkatom; // allocated size short neighlist + int *numjkatom; // actual size of short neighlist + int **neighjkatom; // list of short neighbor lists + int **bothjkatom; // 1 if atom is in both jatom and katom lists + double ***delrjkatom; // list of 4-vectors: delx, dely, delx, and 1/r + + double rad2deg; // conversion factor from radians to degrees + int ordinate_style; // DEGREE, RADIAN, or COSINE + int cutflag; // 1 if at least one outer cutoff specified +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: Compute adf requires a pair style be defined or outer cutoff specified + +Self-explanatory. + +E: Compute adf cutoff exceeds ghost atom range - use comm_modify cutoff command + +Self-explanatary. + +*/ From 3a735d15d41a898962e730a2bc9859882399e884 Mon Sep 17 00:00:00 2001 From: Aidan Thompson Date: Fri, 19 Oct 2018 18:43:04 -0600 Subject: [PATCH 280/302] Added compute_rdf.cpp --- src/compute_rdf.cpp | 40 ++++++++++++++++++++++------------------ 1 file changed, 22 insertions(+), 18 deletions(-) diff --git a/src/compute_rdf.cpp b/src/compute_rdf.cpp index 0a0e8fb684..0809cc8b8e 100644 --- a/src/compute_rdf.cpp +++ b/src/compute_rdf.cpp @@ -45,7 +45,7 @@ ComputeRDF::ComputeRDF(LAMMPS *lmp, int narg, char **arg) : hist(NULL), histall(NULL), typecount(NULL), icount(NULL), jcount(NULL), duplicates(NULL) { - if (narg < 4 || (narg-4) % 2) error->all(FLERR,"Illegal compute rdf command"); + if (narg < 4) error->all(FLERR,"Illegal compute rdf command"); array_flag = 1; extarray = 0; @@ -77,7 +77,10 @@ ComputeRDF::ComputeRDF(LAMMPS *lmp, int narg, char **arg) : // pairwise args if (nargpair == 0) npairs = 1; - else npairs = nargpair/2; + else { + if (nargpair % 2) error->all(FLERR,"Illegal compute rdf command"); + npairs = nargpair/2; + } size_array_rows = nbin; size_array_cols = 1 + 2*npairs; @@ -93,17 +96,13 @@ ComputeRDF::ComputeRDF(LAMMPS *lmp, int narg, char **arg) : if (nargpair == 0) { ilo[0] = 1; ihi[0] = ntypes; jlo[0] = 1; jhi[0] = ntypes; - npairs = 1; - } else { - npairs = 0; iarg = 4; - while (iarg < 4+nargpair) { - force->bounds(FLERR,arg[iarg],atom->ntypes,ilo[npairs],ihi[npairs]); - force->bounds(FLERR,arg[iarg+1],atom->ntypes,jlo[npairs],jhi[npairs]); - if (ilo[npairs] > ihi[npairs] || jlo[npairs] > jhi[npairs]) + for (int ipair = 0; ipair < npairs; ipair++) { + force->bounds(FLERR,arg[iarg],atom->ntypes,ilo[ipair],ihi[ipair]); + force->bounds(FLERR,arg[iarg+1],atom->ntypes,jlo[ipair],jhi[ipair]); + if (ilo[ipair] > ihi[ipair] || jlo[ipair] > jhi[ipair]) error->all(FLERR,"Illegal compute rdf command"); - npairs++; iarg += 2; } } @@ -113,10 +112,13 @@ ComputeRDF::ComputeRDF(LAMMPS *lmp, int narg, char **arg) : for (j = 1; j <= ntypes; j++) nrdfpair[i][j] = 0; + int ihisto; for (int m = 0; m < npairs; m++) for (i = ilo[m]; i <= ihi[m]; i++) - for (j = jlo[m]; j <= jhi[m]; j++) - rdfpair[nrdfpair[i][j]++][i][j] = m; + for (j = jlo[m]; j <= jhi[m]; j++) { + ihisto = nrdfpair[i][j]++; + rdfpair[ihisto][i][j] = m; + } memory->create(hist,npairs,nbin,"rdf:hist"); memory->create(histall,npairs,nbin,"rdf:histall"); @@ -347,13 +349,15 @@ void ComputeRDF::compute_array() ibin = static_cast (r*delrinv); if (ibin >= nbin) continue; - if (ipair) - for (ihisto = 0; ihisto < ipair; ihisto++) - hist[rdfpair[ihisto][itype][jtype]][ibin] += 1.0; + for (ihisto = 0; ihisto < ipair; ihisto++) { + m = rdfpair[ihisto][itype][jtype]; + hist[m][ibin] += 1.0; + } if (newton_pair || j < nlocal) { - if (jpair) - for (ihisto = 0; ihisto < jpair; ihisto++) - hist[rdfpair[ihisto][jtype][itype]][ibin] += 1.0; + for (ihisto = 0; ihisto < jpair; ihisto++) { + m = rdfpair[ihisto][jtype][itype]; + hist[m][ibin] += 1.0; + } } } } From 0783f8ad2fa522726ec14e14e7d7c9090789b64b Mon Sep 17 00:00:00 2001 From: Aidan Thompson Date: Fri, 19 Oct 2018 18:43:58 -0600 Subject: [PATCH 281/302] Added compute_rdf.txt --- doc/src/compute_rdf.txt | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/doc/src/compute_rdf.txt b/doc/src/compute_rdf.txt index d11ae9e3bf..17fa68e526 100644 --- a/doc/src/compute_rdf.txt +++ b/doc/src/compute_rdf.txt @@ -191,7 +191,8 @@ via "compute_modify dynamic yes"_compute_modify.html [Related commands:] -"fix ave/time"_fix_ave_time.html, "compute_modify"_compute_modify.html +"fix ave/time"_fix_ave_time.html, "compute_modify"_compute_modify.html, +"compute adf"_compute_adf.html [Default:] From 348febdf4b082a3396654679f120e441d64999c8 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 20 Oct 2018 02:54:48 -0400 Subject: [PATCH 282/302] work around for parallel_for() compilation issue with newer compilers apparently, data items used inside parallel_for() constructs have rather strict requirements on const-ness, which is enforced by newer GNU compilers. As a workaround we construct explicit const copies of those class instances. This closes #1045 --- src/KOKKOS/fix_momentum_kokkos.cpp | 16 +++++++++------- 1 file changed, 9 insertions(+), 7 deletions(-) diff --git a/src/KOKKOS/fix_momentum_kokkos.cpp b/src/KOKKOS/fix_momentum_kokkos.cpp index 9af7e79da8..493dffc3d9 100644 --- a/src/KOKKOS/fix_momentum_kokkos.cpp +++ b/src/KOKKOS/fix_momentum_kokkos.cpp @@ -111,8 +111,9 @@ void FixMomentumKokkos::end_of_step() /* this is needed because Group is not Kokkos-aware ! */ atomKK->sync(ExecutionSpaceFromDevice::space, V_MASK | MASK_MASK | TYPE_MASK | RMASS_MASK); - Few vcm; - group->vcm(igroup,masstotal,&vcm[0]); + Few tmpvcm; + group->vcm(igroup,masstotal,&tmpvcm[0]); + const Few vcm(tmpvcm); // adjust velocities by vcm to zero linear momentum // only adjust a component if flag is set @@ -132,19 +133,20 @@ void FixMomentumKokkos::end_of_step() } if (angular) { - Few xcm, angmom, omega; + Few tmpxcm, tmpangmom, tmpomega; double inertia[3][3]; /* syncs for each Kokkos-unaware Group method */ atomKK->sync(ExecutionSpaceFromDevice::space, X_MASK | MASK_MASK | TYPE_MASK | IMAGE_MASK | RMASS_MASK); - group->xcm(igroup,masstotal,&xcm[0]); + group->xcm(igroup,masstotal,&tmpxcm[0]); atomKK->sync(ExecutionSpaceFromDevice::space, X_MASK | V_MASK | MASK_MASK | TYPE_MASK | IMAGE_MASK | RMASS_MASK); - group->angmom(igroup,&xcm[0],&angmom[0]); + group->angmom(igroup,&tmpxcm[0],&tmpangmom[0]); atomKK->sync(ExecutionSpaceFromDevice::space, X_MASK | MASK_MASK | TYPE_MASK | IMAGE_MASK | RMASS_MASK); - group->inertia(igroup,&xcm[0],inertia); - group->omega(&angmom[0],inertia,&omega[0]); + group->inertia(igroup,&tmpxcm[0],inertia); + group->omega(&tmpangmom[0],inertia,&tmpomega[0]); + const Few xcm(tmpxcm), angmom(tmpangmom), omega(tmpomega); // adjust velocities to zero omega // vnew_i = v_i - w x r_i From 79da210dc4594593c6a6839d613889921fb4c9e9 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 20 Oct 2018 06:45:28 -0400 Subject: [PATCH 283/302] integrate compute adf into manual build infrastructure --- doc/src/Commands_compute.txt | 1 + doc/src/computes.txt | 1 + doc/src/lammps.book | 1 + 3 files changed, 3 insertions(+) diff --git a/doc/src/Commands_compute.txt b/doc/src/Commands_compute.txt index 81b618a6e2..769f99d64b 100644 --- a/doc/src/Commands_compute.txt +++ b/doc/src/Commands_compute.txt @@ -25,6 +25,7 @@ additional letters in parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT. "ackland/atom"_compute_ackland_atom.html, +"adf"_compute_adf.html, "aggregate/atom"_compute_cluster_atom.html, "angle"_compute_angle.html, "angle/local"_compute_angle_local.html, diff --git a/doc/src/computes.txt b/doc/src/computes.txt index c836fb6cb1..926b8da222 100644 --- a/doc/src/computes.txt +++ b/doc/src/computes.txt @@ -6,6 +6,7 @@ Computes :h1 :maxdepth: 1 compute_ackland_atom + compute_adf compute_angle compute_angle_local compute_angmom_chunk diff --git a/doc/src/lammps.book b/doc/src/lammps.book index c006e77d65..f739712f08 100644 --- a/doc/src/lammps.book +++ b/doc/src/lammps.book @@ -404,6 +404,7 @@ lammps_commands_compute.html compute.html compute_modify.html compute_ackland_atom.html +compute_adf.html compute_angle.html compute_angle_local.html compute_angmom_chunk.html From fb6f019a117e7f90a473d2efb6c546997ac902ce Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 20 Oct 2018 06:45:57 -0400 Subject: [PATCH 284/302] correct link to output options --- doc/src/compute_adf.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/src/compute_adf.txt b/doc/src/compute_adf.txt index 9c0540b746..5748d93328 100644 --- a/doc/src/compute_adf.txt +++ b/doc/src/compute_adf.txt @@ -167,7 +167,7 @@ coordinate (angle-related ordinate at midpoint of bin). Each subsequent column h the two ADF values for a specific set of ({itypeN},{jtypeN},{ktypeN}) interactions, as described above. These values can be used by any command that uses a global values from a compute as input. See -"Section 6.15"_Section_howto.html#howto_15 for an overview of +the "Howto output"_Howto_output.html doc page for an overview of LAMMPS output options. The array values calculated by this compute are all "intensive". From 2140caa6f53cac2e9c65b7b8a3dcb7fe750f0e4d Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 20 Oct 2018 08:12:02 -0400 Subject: [PATCH 285/302] add an example for RDF and ADF computation with water molecules --- examples/rdf-adf/data.spce | 9029 +++++++++++++++++++++ examples/rdf-adf/in.spce | 43 + examples/rdf-adf/log.10Oct2018.spce.g++.2 | 202 + examples/rdf-adf/spce-adf.dat.ref | 49 + examples/rdf-adf/spce-rdf.dat.ref | 104 + 5 files changed, 9427 insertions(+) create mode 100644 examples/rdf-adf/data.spce create mode 100644 examples/rdf-adf/in.spce create mode 100644 examples/rdf-adf/log.10Oct2018.spce.g++.2 create mode 100644 examples/rdf-adf/spce-adf.dat.ref create mode 100644 examples/rdf-adf/spce-rdf.dat.ref diff --git a/examples/rdf-adf/data.spce b/examples/rdf-adf/data.spce new file mode 100644 index 0000000000..1e8a4a0913 --- /dev/null +++ b/examples/rdf-adf/data.spce @@ -0,0 +1,9029 @@ +LAMMPS Atom File + + 4500 atoms + 3000 bonds + 1500 angles + 0 dihedrals + 0 impropers + + 2 atom types + 1 bond types + 1 angle types + + 0.02645 35.53280 xlo xhi + 0.02645 35.53280 ylo yhi + 0.02641 35.47360 zlo zhi + +Masses + + 1 15.9994 + 2 1.00794 + +Atoms + + 1 1 1 -0.8472 12.12456 28.09298 22.27452 0 1 0 + 2 1 2 0.4236 12.53683 28.75606 22.89928 0 1 0 + 3 1 2 0.4236 11.49482 28.56390 21.65678 0 1 0 + 4 2 1 -0.8472 1.17079 29.37777 23.72984 1 -1 0 + 5 2 2 0.4236 1.91804 29.48483 23.07399 1 -1 0 + 6 2 2 0.4236 0.40074 28.91964 23.28586 1 -1 0 + 7 3 1 -0.8472 29.68313 14.73733 21.62793 -1 0 0 + 8 3 2 0.4236 30.54284 14.93741 21.15800 -1 0 0 + 9 3 2 0.4236 29.73135 15.07344 22.56848 -1 0 0 + 10 4 1 -0.8472 10.87272 7.00153 35.10920 0 1 0 + 11 4 2 0.4236 11.11057 6.21663 34.53712 0 1 0 + 12 4 2 0.4236 9.95658 7.32301 34.86983 0 1 0 + 13 5 1 -0.8472 9.46588 6.43648 19.79899 0 1 0 + 14 5 2 0.4236 9.04840 6.32936 18.89668 0 1 0 + 15 5 2 0.4236 10.31722 5.91326 19.83657 0 1 0 + 16 6 1 -0.8472 3.17905 29.69801 22.11922 0 0 0 + 17 6 2 0.4236 3.19240 30.63289 21.76465 0 0 0 + 18 6 2 0.4236 3.38651 29.05797 21.37944 0 0 0 + 19 7 1 -0.8472 23.38618 11.29979 30.78238 0 0 0 + 20 7 2 0.4236 23.69882 10.46688 31.23897 0 0 0 + 21 7 2 0.4236 24.17354 11.79208 30.41132 0 0 0 + 22 8 1 -0.8472 11.03761 10.46106 30.14741 0 1 0 + 23 8 2 0.4236 10.94682 11.45112 30.25464 0 1 0 + 24 8 2 0.4236 11.60678 10.09680 30.88450 0 1 0 + 25 9 1 -0.8472 26.24001 25.40937 21.06754 0 0 0 + 26 9 2 0.4236 25.67045 26.09258 21.52442 0 0 0 + 27 9 2 0.4236 26.22311 25.56759 20.08030 0 0 0 + 28 10 1 -0.8472 10.84087 35.33915 19.78347 0 -1 0 + 29 10 2 0.4236 10.20697 0.54421 19.48018 0 0 0 + 30 10 2 0.4236 11.06253 34.74012 19.01405 0 -1 0 + 31 11 1 -0.8472 20.07383 4.95885 33.62365 0 1 0 + 32 11 2 0.4236 19.77359 5.87080 33.90322 0 1 0 + 33 11 2 0.4236 20.68149 4.57954 34.32139 0 1 0 + 34 12 1 -0.8472 12.43897 28.56656 17.39837 0 0 0 + 35 12 2 0.4236 12.80348 27.99505 18.13354 0 0 0 + 36 12 2 0.4236 11.63887 28.12177 16.99597 0 0 0 + 37 13 1 -0.8472 14.80338 7.14199 1.42116 0 0 0 + 38 13 2 0.4236 14.86001 6.68442 0.53382 0 0 0 + 39 13 2 0.4236 14.13589 6.67036 1.99737 0 0 0 + 40 14 1 -0.8472 15.87968 22.18330 24.13468 1 -1 0 + 41 14 2 0.4236 15.97100 22.71526 23.29285 1 -1 0 + 42 14 2 0.4236 16.69618 22.30846 24.69826 1 -1 0 + 43 15 1 -0.8472 13.29194 18.30473 12.37157 1 0 0 + 44 15 2 0.4236 12.55838 18.63231 12.96701 1 0 0 + 45 15 2 0.4236 13.24823 18.78335 11.49467 1 0 0 + 46 16 1 -0.8472 20.27409 23.94157 15.50212 0 0 0 + 47 16 2 0.4236 20.17851 24.67734 14.83167 0 0 0 + 48 16 2 0.4236 20.62006 23.12024 15.04857 0 0 0 + 49 17 1 -0.8472 30.10203 10.78182 14.24321 1 0 0 + 50 17 2 0.4236 29.40171 11.00523 13.56532 1 0 0 + 51 17 2 0.4236 29.70120 10.21329 14.96159 1 0 0 + 52 18 1 -0.8472 19.71525 12.98975 25.40578 0 0 0 + 53 18 2 0.4236 20.21522 13.35852 26.18938 0 0 0 + 54 18 2 0.4236 18.75253 12.87297 25.64962 0 0 0 + 55 19 1 -0.8472 4.22362 18.99305 32.62946 1 0 0 + 56 19 2 0.4236 4.05067 18.17865 32.07556 1 0 0 + 57 19 2 0.4236 3.38513 19.53353 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+pair_style lj/cut/coul/long 12.0 12.0 +pair_coeff * * 0.0 1.0 +pair_coeff 1 1 0.15535 3.166 +kspace_style pppm 1.0e-6 + +bond_style harmonic +angle_style harmonic +dihedral_style none +improper_style none + +bond_coeff 1 1000.00 1.000 +angle_coeff 1 100.0 109.47 + +# need to set bond/angle inclusion to > 0.0 +# so that intramolecular pairs are included in neighbor lists (required for second ADF) +special_bonds lj/coul 1.0e-100 1.0e-100 1.0 + +neighbor 2.0 bin +timestep 2.0 +neigh_modify every 1 delay 2 check yes + +fix 1 all shake 0.0001 20 0 b 1 a 1 +fix 2 all nvt temp 300.0 300.0 100.0 + +velocity all create 300.0 6244325 + +thermo 100 +run 500 + +reset_timestep 0 + +compute gofr all rdf 100 1 1 2 2 1 2 # O-O, H-H, O-H +compute gofa all adf 45 1 1 1 2.0 3.5 2.0 3.5 & + 1 2 1 0.0 1.2 1.5 2.5 +fix rdf all ave/time 100 10 1000 c_gofr[*] file spce-rdf.dat mode vector +fix adf all ave/time 10 100 1000 c_gofa[*] file spce-adf.dat mode vector + +run 1000 diff --git a/examples/rdf-adf/log.10Oct2018.spce.g++.2 b/examples/rdf-adf/log.10Oct2018.spce.g++.2 new file mode 100644 index 0000000000..d19e69a031 --- /dev/null +++ b/examples/rdf-adf/log.10Oct2018.spce.g++.2 @@ -0,0 +1,202 @@ +LAMMPS (10 Oct 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +units real +atom_style full + +read_data data.spce + orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736) + 1 by 2 by 1 MPI processor grid + reading atoms ... + 4500 atoms + scanning bonds ... + 2 = max bonds/atom + scanning angles ... + 1 = max angles/atom + reading bonds ... + 3000 bonds + reading angles ... + 1500 angles + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + +pair_style lj/cut/coul/long 12.0 12.0 +pair_coeff * * 0.0 1.0 +pair_coeff 1 1 0.15535 3.166 +kspace_style pppm 1.0e-6 + +bond_style harmonic +angle_style harmonic +dihedral_style none +improper_style none + +bond_coeff 1 1000.00 1.000 +angle_coeff 1 100.0 109.47 + +# need to set bond/angle inclusion to > 0.0 +# so that intramolecular pairs are included in neighbor lists (required for second ADF) +special_bonds lj/coul 1.0e-100 1.0e-100 1.0 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 2 = max # of special neighbors + +neighbor 2.0 bin +timestep 2.0 +neigh_modify every 1 delay 2 check yes + +fix 1 all shake 0.0001 20 0 b 1 a 1 + 0 = # of size 2 clusters + 0 = # of size 3 clusters + 0 = # of size 4 clusters + 1500 = # of frozen angles +fix 2 all nvt temp 300.0 300.0 100.0 + +velocity all create 300.0 6244325 + +thermo 100 +run 500 +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) + G vector (1/distance) = 0.279652 + grid = 40 40 40 + stencil order = 5 + estimated absolute RMS force accuracy = 0.000394674 + estimated relative force accuracy = 1.18855e-06 + using double precision FFTs + 3d grid and FFT values/proc = 59643 32000 +Neighbor list info ... + update every 1 steps, delay 2 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 25.06 | 25.25 | 25.44 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 300 -16692.369 0 -14010.534 -112.83562 + 100 283.44729 -17008.717 0 -14474.854 -162.06374 + 200 298.75279 -16765.544 0 -14094.858 428.79127 + 300 296.6501 -16589.155 0 -13937.267 547.40768 + 400 303.83151 -16625.028 0 -13908.942 237.9775 + 500 298.01615 -16717.015 0 -14052.915 230.7095 +Loop time of 21.4041 on 2 procs for 500 steps with 4500 atoms + +Performance: 4.037 ns/day, 5.946 hours/ns, 23.360 timesteps/s +94.8% CPU use with 2 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 14.892 | 15.034 | 15.176 | 3.7 | 70.24 +Bond | 0.00056624 | 0.00059342 | 0.0006206 | 0.0 | 0.00 +Kspace | 3.987 | 4.1321 | 4.2773 | 7.1 | 19.31 +Neigh | 1.7494 | 1.7496 | 1.7497 | 0.0 | 8.17 +Comm | 0.20554 | 0.20637 | 0.2072 | 0.2 | 0.96 +Output | 0.00015688 | 0.00036144 | 0.00056601 | 0.0 | 0.00 +Modify | 0.25707 | 0.2606 | 0.26413 | 0.7 | 1.22 +Other | | 0.02059 | | | 0.10 + +Nlocal: 2250 ave 2258 max 2242 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Nghost: 16319 ave 16381 max 16257 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Neighs: 1.30073e+06 ave 1.32386e+06 max 1.2776e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 2601457 +Ave neighs/atom = 578.102 +Ave special neighs/atom = 2 +Neighbor list builds = 45 +Dangerous builds = 0 + +reset_timestep 0 + +compute gofr all rdf 100 1 1 2 2 1 2 # O-O, H-H, O-H +compute gofa all adf 45 1 1 1 2.0 3.5 2.0 3.5 1 2 1 0.0 1.2 1.5 2.5 +fix rdf all ave/time 100 10 1000 c_gofr[*] file spce-rdf.dat mode vector +fix adf all ave/time 10 100 1000 c_gofa[*] file spce-adf.dat mode vector + +run 1000 +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) + G vector (1/distance) = 0.279652 + grid = 40 40 40 + stencil order = 5 + estimated absolute RMS force accuracy = 0.000394674 + estimated relative force accuracy = 1.18855e-06 + using double precision FFTs + 3d grid and FFT values/proc = 59643 32000 +Neighbor list info ... + update every 1 steps, delay 2 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 6 6 6 + 3 neighbor lists, perpetual/occasional/extra = 1 2 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + (2) compute rdf, occasional, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (3) compute adf, occasional + attributes: full, newton on + pair build: full/bin + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 26.78 | 26.78 | 26.78 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 298.01615 -16717.015 0 -14052.915 230.81371 + 100 307.1766 -16759.33 0 -14013.341 454.2771 + 200 298.94628 -16674.186 0 -14001.771 114.20846 + 300 293.13091 -16581.542 0 -13961.113 272.85574 + 400 294.47017 -16556.872 0 -13924.471 180.3252 + 500 305.57174 -16647.976 0 -13916.333 -444.14856 + 600 302.53992 -16670.304 0 -13965.764 114.82353 + 700 306.56761 -16616.508 0 -13875.962 534.02537 + 800 299.06297 -16644.133 0 -13970.675 83.643063 + 900 301.15522 -16674.021 0 -13981.859 325.04538 + 1000 298.14963 -16701.663 0 -14036.369 356.0601 +Loop time of 53.3181 on 2 procs for 1000 steps with 4500 atoms + +Performance: 3.241 ns/day, 7.405 hours/ns, 18.755 timesteps/s +97.3% CPU use with 2 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 28.831 | 29.365 | 29.899 | 9.9 | 55.07 +Bond | 0.00097084 | 0.0010794 | 0.001188 | 0.3 | 0.00 +Kspace | 7.3086 | 7.8356 | 8.3626 | 18.8 | 14.70 +Neigh | 3.7241 | 3.7245 | 3.7248 | 0.0 | 6.99 +Comm | 0.32839 | 0.33495 | 0.34151 | 1.1 | 0.63 +Output | 0.00043344 | 0.0015392 | 0.002645 | 2.8 | 0.00 +Modify | 12.013 | 12.014 | 12.015 | 0.0 | 22.53 +Other | | 0.04153 | | | 0.08 + +Nlocal: 2250 ave 2251 max 2249 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Nghost: 16300 ave 16358 max 16242 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Neighs: 1.301e+06 ave 1.31594e+06 max 1.28606e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +FullNghs: 2.602e+06 ave 2.60923e+06 max 2.59476e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 5203998 +Ave neighs/atom = 1156.44 +Ave special neighs/atom = 2 +Neighbor list builds = 93 +Dangerous builds = 0 +Total wall time: 0:01:14 diff --git a/examples/rdf-adf/spce-adf.dat.ref b/examples/rdf-adf/spce-adf.dat.ref new file mode 100644 index 0000000000..1e3f598e16 --- /dev/null +++ b/examples/rdf-adf/spce-adf.dat.ref @@ -0,0 +1,49 @@ +# Time-averaged data for fix adf +# TimeStep Number-of-rows +# Row c_gofa[1] c_gofa[2] c_gofa[3] c_gofa[4] c_gofa[5] +1000 45 +1 2 0 0 0.570997 4.0364e-06 +2 6 0 0 1.34922 1.33246e-05 +3 10 0 0 0.844388 1.94267e-05 +4 14 0 0 0.476996 2.34028e-05 +5 18 0 0 0.161187 2.46115e-05 +6 22 0 0 0.0477465 2.47703e-05 +7 26 0 0 0.00511569 2.48353e-05 +8 30 0 0 0 2.48353e-05 +9 34 0 0 0 2.48353e-05 +10 38 0 0 0.0179049 2.497e-05 +11 42 0.00139303 0.00112 0 2.497e-05 +12 46 0.0970866 0.0791067 0 2.497e-05 +13 50 0.421047 0.417227 0 2.497e-05 +14 54 0.503109 0.821333 0 2.497e-05 +15 58 0.403317 1.14533 0 2.497e-05 +16 62 0.384523 1.45431 0 2.497e-05 +17 66 0.425895 1.79643 0 2.497e-05 +18 70 0.494575 2.1937 0 2.497e-05 +19 74 0.547429 2.63327 0.00716197 2.50218e-05 +20 78 0.584521 3.10253 0.0119366 2.51428e-05 +21 82 0.612285 3.59409 0.0966866 2.56506e-05 +22 86 0.643119 4.1105 0.0868815 2.64003e-05 +23 90 0.669958 4.64829 0.245468 2.77959e-05 +24 94 0.685175 5.19837 0.318537 3.01911e-05 +25 98 0.68985 5.75207 0.608171 3.48379e-05 +26 102 0.681411 6.29909 0.825076 4.16049e-05 +27 106 0.660197 6.82903 1.2987 5.06221e-05 +28 110 0.644879 7.34685 1.58753 6.12867e-05 +29 114 0.613281 7.83923 1.1185 6.98041e-05 +30 118 0.572272 8.29867 0.961282 7.65158e-05 +31 122 0.534702 8.72795 0.546058 8.08946e-05 +32 126 0.496697 9.12669 0.64867 8.51981e-05 +33 130 0.453138 9.49045 0.518561 8.86029e-05 +34 134 0.41004 9.81964 0.561575 9.23251e-05 +35 138 0.36701 10.1143 0.355285 9.51805e-05 +36 142 0.328717 10.3782 0.297648 9.74977e-05 +37 146 0.294236 10.6145 0.0749449 9.81639e-05 +38 150 0.261134 10.8242 0.0856879 9.87562e-05 +39 154 0.223727 11.0039 0.0537574 9.9216e-05 +40 158 0.19037 11.1567 0.0827037 9.95624e-05 +41 162 0.156173 11.2822 0.0149208 9.97358e-05 +42 166 0.119999 11.3785 0.00895247 9.98317e-05 +43 170 0.0853136 11.447 0.00596831 9.98799e-05 +44 174 0.0502058 11.4873 0 9.98799e-05 +45 178 0.0171616 11.5011 0 9.98799e-05 diff --git a/examples/rdf-adf/spce-rdf.dat.ref b/examples/rdf-adf/spce-rdf.dat.ref new file mode 100644 index 0000000000..204e5ffc73 --- /dev/null +++ b/examples/rdf-adf/spce-rdf.dat.ref @@ -0,0 +1,104 @@ +# Time-averaged data for fix rdf +# TimeStep Number-of-rows +# Row c_gofr[1] c_gofr[2] c_gofr[3] c_gofr[4] c_gofr[5] c_gofr[6] c_gofr[7] +1000 100 +1 0.06 0 0 0 0 0 0 +2 0.18 0 0 0 0 0 0 +3 0.3 0 0 0 0 0 0 +4 0.42 0 0 0 0 0 0 +5 0.54 0 0 0 0 0 0 +6 0.66 0 0 0 0 0 0 +7 0.78 0 0 0 0 0 0 +8 0.9 0 0 0 0 0 0 +9 1.02 0 0 0 0 18.9675 2 +10 1.14 0 0 0 0 0 2 +11 1.26 0 0 0 0 0 2 +12 1.38 0 0 0 0 0 2 +13 1.5 0 0 0.00146316 0.000333333 0.0485606 2.01107 +14 1.62 0 0 3.77986 1.00467 0.691259 2.1948 +15 1.74 0 0 0.087001 1.03133 1.5081 2.6572 +16 1.86 0 0 0.261354 1.12287 1.29225 3.10993 +17 1.98 0 0 0.557712 1.3442 0.791284 3.42407 +18 2.1 0 0 0.890071 1.74153 0.441155 3.62107 +19 2.22 0 0 1.18482 2.3326 0.280275 3.76093 +20 2.34 0 0 1.33539 3.07273 0.203573 3.8738 +21 2.46 0.0296137 0.00906667 1.31236 3.8766 0.199433 3.996 +22 2.58 0.910251 0.3156 1.12596 4.6352 0.252635 4.16627 +23 2.7 2.74616 1.3284 0.92755 5.3196 0.399944 4.46147 +24 2.82 2.69277 2.41173 0.776668 5.94473 0.620912 4.9614 +25 2.94 1.69749 3.154 0.715559 6.57073 0.927784 5.77333 +26 3.06 1.12844 3.68853 0.734337 7.26667 1.28373 6.99033 +27 3.18 0.894502 4.14613 0.785685 8.0708 1.53008 8.55687 +28 3.3 0.830879 4.60387 0.853285 9.01127 1.55205 10.2681 +29 3.42 0.837147 5.0992 0.940998 10.1252 1.42789 11.9589 +30 3.54 0.87264 5.6524 1.02352 11.4233 1.30488 13.6145 +31 3.66 0.890146 6.2556 1.10007 12.9147 1.15043 15.1747 +32 3.78 0.923629 6.9232 1.14816 14.5751 1.05067 16.6945 +33 3.9 0.948076 7.65267 1.1789 16.3898 0.995284 18.2271 +34 4.02 1.02003 8.48653 1.14251 18.2584 0.987649 19.843 +35 4.14 1.05003 9.39693 1.09918 20.1651 0.973183 21.5317 +36 4.26 1.0578 10.368 1.05588 22.1043 0.968154 23.3104 +37 4.38 1.08788 11.4237 1.04202 24.1275 0.95294 25.1612 +38 4.5 1.0991 12.5496 1.02603 26.2302 0.948747 27.1062 +39 4.62 1.08758 13.7239 1.0199 28.4333 0.952182 29.1637 +40 4.74 1.08319 14.9549 1.0085 30.7265 0.958425 31.3437 +41 4.86 1.06718 16.23 1.0021 33.1219 0.966773 33.6555 +42 4.98 1.0236 17.5141 0.983127 35.5894 0.975683 36.1051 +43 5.1 0.979245 18.8025 0.968484 38.1387 0.993353 38.7208 +44 5.22 0.967438 20.136 0.960781 40.7882 1.0117 41.5116 +45 5.34 0.9397 21.4915 0.95327 43.5392 1.02048 44.4575 +46 5.46 0.933775 22.8996 0.957903 46.4292 1.02138 47.5401 +47 5.58 0.905728 24.3261 0.96475 49.4692 1.01134 50.7279 +48 5.7 0.908316 25.8189 0.985709 52.7103 1.00699 54.0401 +49 5.82 0.922062 27.3988 0.992001 56.1108 0.993731 57.4477 +50 5.94 0.933444 29.0648 1.00316 59.6929 0.985977 60.9695 +51 6.06 0.967112 30.8613 1.00148 63.4149 0.975667 64.5968 +52 6.18 0.995762 32.7851 1.00378 67.2946 0.966562 68.3339 +53 6.3 1.01856 34.83 1.01103 71.3556 0.980183 72.2723 +54 6.42 1.02375 36.9644 1.00763 75.5586 0.975791 76.3439 +55 6.54 1.02443 39.1808 1.0048 79.9079 0.988272 80.6231 +56 6.66 1.04424 41.5237 0.994556 84.3723 0.992933 85.0817 +57 6.78 1.02624 43.91 0.993082 88.9922 1.00275 89.7481 +58 6.9 1.05342 46.4469 0.995881 93.7905 1.0039 94.5867 +59 7.02 1.04804 49.0595 1.0028 98.7917 1.0061 99.606 +60 7.14 1.03565 51.7301 0.999035 103.946 1.00976 104.817 +61 7.26 1.01185 54.4279 0.999229 109.276 1.01388 110.227 +62 7.38 1.00714 57.2025 0.997563 114.774 1.02243 115.864 +63 7.5 0.997335 60.0403 1.00429 120.491 1.01948 121.67 +64 7.62 0.98964 62.9469 1.00029 126.369 1.01107 127.613 +65 7.74 0.986472 65.9363 1.01014 132.493 1.0127 133.755 +66 7.86 0.976805 68.9888 1.0082 138.797 1.00837 140.061 +67 7.98 0.980184 72.1461 1.00972 145.304 1.00029 146.51 +68 8.1 0.99097 75.4349 1.00403 151.97 0.999714 153.15 +69 8.22 0.988581 78.8137 1.00883 158.869 1.00011 159.991 +70 8.34 1.0046 82.3483 1.00269 165.927 0.994842 166.996 +71 8.46 0.987279 85.9225 0.997968 173.155 0.990283 174.171 +72 8.58 1.00046 89.648 0.999277 180.6 0.990097 181.55 +73 8.7 1.00036 93.478 0.999683 188.257 0.987047 189.113 +74 8.82 1.00138 97.4184 0.995158 196.091 0.991812 196.923 +75 8.94 1.02075 101.545 0.999836 204.178 0.991287 204.944 +76 9.06 1.00201 105.705 0.99005 212.403 0.996973 213.228 +77 9.18 0.990377 109.927 0.994103 220.881 1.00126 221.77 +78 9.3 1.0021 114.311 0.998366 229.619 0.997051 230.5 +79 9.42 1.00911 118.841 0.996714 238.57 1.00147 239.496 +80 9.54 1.00129 123.45 0.997009 247.752 1.00442 248.751 +81 9.66 0.994425 128.144 0.999099 257.187 1.0036 258.231 +82 9.78 0.99875 132.976 1.00089 266.876 1.00798 267.991 +83 9.9 1.00475 137.958 1.00485 276.842 1.00223 277.935 +84 10.02 1.00821 143.078 1.00531 287.057 1.00199 288.119 +85 10.14 1.00146 148.286 1.00396 297.503 1.00607 298.591 +86 10.26 0.987716 153.546 1.00115 308.168 1.00195 309.269 +87 10.38 0.996668 158.978 0.999956 319.072 0.999207 320.167 +88 10.5 1.00737 164.595 1.00266 330.259 0.999525 331.323 +89 10.62 1.00322 170.319 1.00368 341.714 0.991347 342.642 +90 10.74 1.00197 176.165 1.00151 353.405 1.00118 354.333 +91 10.86 1.01265 182.206 0.997669 365.313 1.00021 366.275 +92 10.98 1.00566 188.339 1.00218 377.54 0.998434 378.46 +93 11.1 1.00615 194.61 0.998681 389.992 1.00219 390.96 +94 11.22 0.989815 200.913 0.994781 402.666 0.996803 403.664 +95 11.34 0.995666 207.389 0.998115 415.655 0.99786 416.654 +96 11.46 0.990077 213.966 0.999458 428.938 1.00053 429.956 +97 11.58 0.992053 220.695 0.997809 442.479 0.994388 443.455 +98 11.7 1.00038 227.622 0.999064 456.319 1.00445 457.374 +99 11.82 0.99774 234.673 1.00106 470.473 0.998027 471.49 +100 11.94 1.00539 241.923 0.99896 484.885 1.00035 485.927 From 8aecefe233f9df61c0a10b95a5a746d2fcce19f1 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 20 Oct 2018 08:12:19 -0400 Subject: [PATCH 286/302] fix uninitialized data bug in compute adf --- src/compute_adf.cpp | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/src/compute_adf.cpp b/src/compute_adf.cpp index 5639d073db..bb51a6693f 100644 --- a/src/compute_adf.cpp +++ b/src/compute_adf.cpp @@ -275,20 +275,19 @@ ComputeADF::~ComputeADF() void ComputeADF::init() { - double mycutneigh; - double maxouter; + double mycutneigh = 0.0; + double maxouter = 0.0; if (!cutflag) { if (!force->pair) error->all(FLERR,"Compute adf requires a pair style be defined " - "or outer cutoff specified"); + "or an outer cutoff specified"); rcutinnerj[0] = 0.0; rcutinnerk[0] = 0.0; rcutouterj[0] = force->pair->cutforce; rcutouterk[0] = force->pair->cutforce; maxouter = force->pair->cutforce;; } else { - maxouter = 0.0; for (int m = 0; m < ntriples; m++) { maxouter = MAX(rcutouterj[m],maxouter); maxouter = MAX(rcutouterk[m],maxouter); From 8223f5e0a3c98f9dfea8ede457bd5eb6dc1b6b28 Mon Sep 17 00:00:00 2001 From: Aidan Thompson Date: Sat, 20 Oct 2018 16:46:45 -0600 Subject: [PATCH 287/302] Eliminated another initialization error and tweaked rdf-adf example --- doc/src/compute_adf.txt | 16 ++++-- examples/rdf-adf/in.spce | 6 ++- examples/rdf-adf/spce-adf.dat.ref | 90 +++++++++++++++---------------- src/compute_adf.cpp | 2 +- 4 files changed, 61 insertions(+), 53 deletions(-) diff --git a/doc/src/compute_adf.txt b/doc/src/compute_adf.txt index 5748d93328..3d0646e294 100644 --- a/doc/src/compute_adf.txt +++ b/doc/src/compute_adf.txt @@ -133,7 +133,7 @@ arguments are specified. The first ADF value for a bin is calculated from the histogram count by dividing by the total number of triples satisfying the criteria, -so that the integral of the ADF w.r.t. angle is one i.e. the ADF +so that the integral of the ADF w.r.t. angle is 1, i.e. the ADF is a probability density function. The second ADF value is reported as a cumulative sum of @@ -147,9 +147,15 @@ number radial distribution function. The {ordinate} optional keyword determines whether the bins are of uniform angular size from zero to 180 ({degree}), zero to Pi ({radian}), or the -cosine of the angle uniform in the range \[-1,1\] ({cosine}). -Regardless of which is chosen, the first ADF will be normalized -so that the integral w.r.t. the ordinate is one. +cosine of the angle uniform in the range \[-1,1\] ({cosine}). +{cosine} has the advantage of eliminating the {acos()} function +call, which speeds up the compute by 2-3x, and it is also preferred +on physical grounds, because the for uniformly distributed particles +in 3D, the angular probability density w.r.t dtheta is +sin(theta)/2, while for d(cos(theta)), it is 1/2, +Regardless of which ordinate is chosen, the first column of ADF +values is normalized w.r.t. the range of that ordinate, so that +the integral is 1. The simplest way to output the results of the compute adf calculation to a file is to use the "fix ave/time"_fix_ave_time.html command, for @@ -177,7 +183,7 @@ the angle in degrees or radians, or the cosine of the angle. Each subsequent pair of columns gives the first and second kinds of ADF for a specific set of ({itypeN},{jtypeN},{ktypeN}). The values in the first ADF column are normalized numbers >= 0.0, -whose integral w.r.t. the ordinate is one, +whose integral w.r.t. the ordinate is 1, i.e. the first ADF is a normalized probability distribution. The values in the second ADF column are also numbers >= 0.0. They are the cumulative density distribution of angles per atom. diff --git a/examples/rdf-adf/in.spce b/examples/rdf-adf/in.spce index 265191428e..9a9d99fd42 100644 --- a/examples/rdf-adf/in.spce +++ b/examples/rdf-adf/in.spce @@ -1,3 +1,5 @@ +# Liquid water RDFs and ADFs (~12 O-O-O/atom, ~1 O-H...O/atom) + units real atom_style full @@ -35,8 +37,8 @@ run 500 reset_timestep 0 compute gofr all rdf 100 1 1 2 2 1 2 # O-O, H-H, O-H -compute gofa all adf 45 1 1 1 2.0 3.5 2.0 3.5 & - 1 2 1 0.0 1.2 1.5 2.5 +compute gofa all adf 45 1 1 1 2.0 3.5 2.0 3.5 & + 2 1 1 0.0 1.2 1.5 2.5 # O-O-O, O-H...O fix rdf all ave/time 100 10 1000 c_gofr[*] file spce-rdf.dat mode vector fix adf all ave/time 10 100 1000 c_gofa[*] file spce-adf.dat mode vector diff --git a/examples/rdf-adf/spce-adf.dat.ref b/examples/rdf-adf/spce-adf.dat.ref index 1e3f598e16..31854e9843 100644 --- a/examples/rdf-adf/spce-adf.dat.ref +++ b/examples/rdf-adf/spce-adf.dat.ref @@ -2,48 +2,48 @@ # TimeStep Number-of-rows # Row c_gofa[1] c_gofa[2] c_gofa[3] c_gofa[4] c_gofa[5] 1000 45 -1 2 0 0 0.570997 4.0364e-06 -2 6 0 0 1.34922 1.33246e-05 -3 10 0 0 0.844388 1.94267e-05 -4 14 0 0 0.476996 2.34028e-05 -5 18 0 0 0.161187 2.46115e-05 -6 22 0 0 0.0477465 2.47703e-05 -7 26 0 0 0.00511569 2.48353e-05 -8 30 0 0 0 2.48353e-05 -9 34 0 0 0 2.48353e-05 -10 38 0 0 0.0179049 2.497e-05 -11 42 0.00139303 0.00112 0 2.497e-05 -12 46 0.0970866 0.0791067 0 2.497e-05 -13 50 0.421047 0.417227 0 2.497e-05 -14 54 0.503109 0.821333 0 2.497e-05 -15 58 0.403317 1.14533 0 2.497e-05 -16 62 0.384523 1.45431 0 2.497e-05 -17 66 0.425895 1.79643 0 2.497e-05 -18 70 0.494575 2.1937 0 2.497e-05 -19 74 0.547429 2.63327 0.00716197 2.50218e-05 -20 78 0.584521 3.10253 0.0119366 2.51428e-05 -21 82 0.612285 3.59409 0.0966866 2.56506e-05 -22 86 0.643119 4.1105 0.0868815 2.64003e-05 -23 90 0.669958 4.64829 0.245468 2.77959e-05 -24 94 0.685175 5.19837 0.318537 3.01911e-05 -25 98 0.68985 5.75207 0.608171 3.48379e-05 -26 102 0.681411 6.29909 0.825076 4.16049e-05 -27 106 0.660197 6.82903 1.2987 5.06221e-05 -28 110 0.644879 7.34685 1.58753 6.12867e-05 -29 114 0.613281 7.83923 1.1185 6.98041e-05 -30 118 0.572272 8.29867 0.961282 7.65158e-05 -31 122 0.534702 8.72795 0.546058 8.08946e-05 -32 126 0.496697 9.12669 0.64867 8.51981e-05 -33 130 0.453138 9.49045 0.518561 8.86029e-05 -34 134 0.41004 9.81964 0.561575 9.23251e-05 -35 138 0.36701 10.1143 0.355285 9.51805e-05 -36 142 0.328717 10.3782 0.297648 9.74977e-05 -37 146 0.294236 10.6145 0.0749449 9.81639e-05 -38 150 0.261134 10.8242 0.0856879 9.87562e-05 -39 154 0.223727 11.0039 0.0537574 9.9216e-05 -40 158 0.19037 11.1567 0.0827037 9.95624e-05 -41 162 0.156173 11.2822 0.0149208 9.97358e-05 -42 166 0.119999 11.3785 0.00895247 9.98317e-05 -43 170 0.0853136 11.447 0.00596831 9.98799e-05 -44 174 0.0502058 11.4873 0 9.98799e-05 -45 178 0.0171616 11.5011 0 9.98799e-05 +1 2 0 0 0 0 +2 6 0 0 0 0 +3 10 0 0 0 0 +4 14 0 0 0 0 +5 18 0 0 0 0 +6 22 0 0 0 0 +7 26 0 0 0 0 +8 30 0 0 0 0 +9 34 0 0 0 0 +10 38 0 0 0 0 +11 42 0.00152868 0.00123333 0 0 +12 46 0.096401 0.07888 0 0 +13 50 0.418453 0.41588 0 0 +14 54 0.506477 0.82378 0 0 +15 58 0.408265 1.15264 0 0 +16 62 0.39048 1.46717 0 0 +17 66 0.43199 1.81511 0 0 +18 70 0.495001 2.21377 0 0 +19 74 0.549314 2.65613 0 0 +20 78 0.586929 3.12873 0.000290833 2e-05 +21 82 0.619347 3.62739 0.00150483 0.000123333 +22 86 0.644793 4.14651 0.00573476 0.000516667 +23 90 0.664615 4.68151 0.00996515 0.0012 +24 94 0.680251 5.22921 0.0147164 0.00221 +25 98 0.679622 5.77635 0.0195919 0.00355333 +26 102 0.675331 6.32011 0.0279862 0.00547333 +27 106 0.659266 6.85083 0.0431972 0.00843667 +28 110 0.640721 7.36672 0.0679453 0.0130967 +29 114 0.609075 7.85709 0.0903345 0.0192933 +30 118 0.578386 8.32278 0.12826 0.0280933 +31 122 0.535658 8.75409 0.169594 0.0397267 +32 126 0.494864 9.15256 0.208251 0.05401 +33 130 0.4498 9.51475 0.275366 0.0728967 +34 134 0.40817 9.8434 0.354045 0.09718 +35 138 0.362856 10.1356 0.459385 0.12869 +36 142 0.328968 10.4005 0.606056 0.170257 +37 146 0.291793 10.6354 0.796038 0.224857 +38 150 0.259831 10.8446 1.04618 0.296613 +39 154 0.2281 11.0283 1.34162 0.38863 +40 158 0.191749 11.1827 1.62681 0.500213 +41 162 0.15663 11.3088 1.86309 0.627997 +42 166 0.121865 11.407 1.89445 0.757927 +43 170 0.0881334 11.4779 1.67713 0.872957 +44 174 0.0523029 11.52 1.17909 0.953827 +45 178 0.0169789 11.5337 0.417313 0.98245 diff --git a/src/compute_adf.cpp b/src/compute_adf.cpp index bb51a6693f..7d08682647 100644 --- a/src/compute_adf.cpp +++ b/src/compute_adf.cpp @@ -384,7 +384,7 @@ void ComputeADF::compute_array() // zero the central atom counts for (i = 0; i < ntriples; i++) - iatomcount[m] = 0; + iatomcount[i] = 0; // tally the ADFs // all three atoms i, j, and k must be in fix group From 76a2a9ab0a6ee5e9280b991ce858fb525ec42e30 Mon Sep 17 00:00:00 2001 From: Aidan Thompson Date: Sat, 20 Oct 2018 17:16:47 -0600 Subject: [PATCH 288/302] Fixed normalization error for ordinate degree --- examples/rdf-adf/spce-adf.dat.ref | 70 +++++++++++++++---------------- src/compute_adf.cpp | 38 ++++++++--------- 2 files changed, 54 insertions(+), 54 deletions(-) diff --git a/examples/rdf-adf/spce-adf.dat.ref b/examples/rdf-adf/spce-adf.dat.ref index 31854e9843..2c6b53c291 100644 --- a/examples/rdf-adf/spce-adf.dat.ref +++ b/examples/rdf-adf/spce-adf.dat.ref @@ -12,38 +12,38 @@ 8 30 0 0 0 0 9 34 0 0 0 0 10 38 0 0 0 0 -11 42 0.00152868 0.00123333 0 0 -12 46 0.096401 0.07888 0 0 -13 50 0.418453 0.41588 0 0 -14 54 0.506477 0.82378 0 0 -15 58 0.408265 1.15264 0 0 -16 62 0.39048 1.46717 0 0 -17 66 0.43199 1.81511 0 0 -18 70 0.495001 2.21377 0 0 -19 74 0.549314 2.65613 0 0 -20 78 0.586929 3.12873 0.000290833 2e-05 -21 82 0.619347 3.62739 0.00150483 0.000123333 -22 86 0.644793 4.14651 0.00573476 0.000516667 -23 90 0.664615 4.68151 0.00996515 0.0012 -24 94 0.680251 5.22921 0.0147164 0.00221 -25 98 0.679622 5.77635 0.0195919 0.00355333 -26 102 0.675331 6.32011 0.0279862 0.00547333 -27 106 0.659266 6.85083 0.0431972 0.00843667 -28 110 0.640721 7.36672 0.0679453 0.0130967 -29 114 0.609075 7.85709 0.0903345 0.0192933 -30 118 0.578386 8.32278 0.12826 0.0280933 -31 122 0.535658 8.75409 0.169594 0.0397267 -32 126 0.494864 9.15256 0.208251 0.05401 -33 130 0.4498 9.51475 0.275366 0.0728967 -34 134 0.40817 9.8434 0.354045 0.09718 -35 138 0.362856 10.1356 0.459385 0.12869 -36 142 0.328968 10.4005 0.606056 0.170257 -37 146 0.291793 10.6354 0.796038 0.224857 -38 150 0.259831 10.8446 1.04618 0.296613 -39 154 0.2281 11.0283 1.34162 0.38863 -40 158 0.191749 11.1827 1.62681 0.500213 -41 162 0.15663 11.3088 1.86309 0.627997 -42 166 0.121865 11.407 1.89445 0.757927 -43 170 0.0881334 11.4779 1.67713 0.872957 -44 174 0.0523029 11.52 1.17909 0.953827 -45 178 0.0169789 11.5337 0.417313 0.98245 +11 42 2.66805e-05 0.00123333 0 0 +12 46 0.00168251 0.07888 0 0 +13 50 0.00730338 0.41588 0 0 +14 54 0.00883969 0.82378 0 0 +15 58 0.00712558 1.15264 0 0 +16 62 0.00681516 1.46717 0 0 +17 66 0.00753965 1.81511 0 0 +18 70 0.0086394 2.21377 0 0 +19 74 0.00958735 2.65613 0 0 +20 78 0.0102438 3.12873 5.076e-06 2e-05 +21 82 0.0108097 3.62739 2.62642e-05 0.000123333 +22 86 0.0112538 4.14651 0.000100091 0.000516667 +23 90 0.0115997 4.68151 0.000173925 0.0012 +24 94 0.0118726 5.22921 0.00025685 0.00221 +25 98 0.0118616 5.77635 0.000341943 0.00355333 +26 102 0.0117868 6.32011 0.000488452 0.00547333 +27 106 0.0115064 6.85083 0.000753934 0.00843667 +28 110 0.0111827 7.36672 0.00118587 0.0130967 +29 114 0.0106304 7.85709 0.00157663 0.0192933 +30 118 0.0100947 8.32278 0.00223856 0.0280933 +31 122 0.009349 8.75409 0.00295997 0.0397267 +32 126 0.008637 9.15256 0.00363466 0.05401 +33 130 0.00785049 9.51475 0.00480604 0.0728967 +34 134 0.00712391 9.8434 0.00617924 0.09718 +35 138 0.00633303 10.1356 0.00801778 0.12869 +36 142 0.00574158 10.4005 0.0105777 0.170257 +37 146 0.00509275 10.6354 0.0138935 0.224857 +38 150 0.0045349 10.8446 0.0182593 0.296613 +39 154 0.00398109 11.0283 0.0234156 0.38863 +40 158 0.00334665 11.1827 0.0283932 0.500213 +41 162 0.00273371 11.3088 0.032517 0.627997 +42 166 0.00212695 11.407 0.0330644 0.757927 +43 170 0.00153822 11.4779 0.0292715 0.872957 +44 174 0.000912858 11.52 0.0205789 0.953827 +45 178 0.000296337 11.5337 0.00728348 0.98245 diff --git a/src/compute_adf.cpp b/src/compute_adf.cpp index 7d08682647..6e6239f076 100644 --- a/src/compute_adf.cpp +++ b/src/compute_adf.cpp @@ -133,21 +133,21 @@ ComputeADF::ComputeADF(LAMMPS *lmp, int narg, char **arg) : } else { cutflag = 1; iarg = 4; - for (int itriple = 0; itriple < ntriples; itriple++) { - force->bounds(FLERR,arg[iarg],atom->ntypes,ilo[itriple],ihi[itriple]); - force->bounds(FLERR,arg[iarg+1],atom->ntypes,jlo[itriple],jhi[itriple]); - force->bounds(FLERR,arg[iarg+2],atom->ntypes,klo[itriple],khi[itriple]); - if (ilo[itriple] > ihi[itriple] || - jlo[itriple] > jhi[itriple] || - klo[itriple] > khi[itriple]) + for (int m = 0; m < ntriples; m++) { + force->bounds(FLERR,arg[iarg],atom->ntypes,ilo[m],ihi[m]); + force->bounds(FLERR,arg[iarg+1],atom->ntypes,jlo[m],jhi[m]); + force->bounds(FLERR,arg[iarg+2],atom->ntypes,klo[m],khi[m]); + if (ilo[m] > ihi[m] || + jlo[m] > jhi[m] || + klo[m] > khi[m]) error->all(FLERR,"Illegal compute adf command"); - rcutinnerj[itriple] = force->numeric(FLERR,arg[iarg+3]); - rcutouterj[itriple] = force->numeric(FLERR,arg[iarg+4]); - if (rcutinnerj[itriple] < 0.0 || rcutinnerj[itriple] >= rcutouterj[itriple]) + rcutinnerj[m] = force->numeric(FLERR,arg[iarg+3]); + rcutouterj[m] = force->numeric(FLERR,arg[iarg+4]); + if (rcutinnerj[m] < 0.0 || rcutinnerj[m] >= rcutouterj[m]) error->all(FLERR,"Illegal compute adf command"); - rcutinnerk[itriple] = force->numeric(FLERR,arg[iarg+5]); - rcutouterk[itriple] = force->numeric(FLERR,arg[iarg+6]); - if (rcutinnerk[itriple] < 0.0 || rcutinnerk[itriple] >= rcutouterk[itriple]) + rcutinnerk[m] = force->numeric(FLERR,arg[iarg+5]); + rcutouterk[m] = force->numeric(FLERR,arg[iarg+6]); + if (rcutinnerk[m] < 0.0 || rcutinnerk[m] >= rcutouterk[m]) error->all(FLERR,"Illegal compute adf command"); iarg += nargsperadf; } @@ -377,14 +377,14 @@ void ComputeADF::compute_array() // zero the histogram counts - for (i = 0; i < ntriples; i++) - for (j = 0; j < nbin; j++) - hist[i][j] = 0.0; + for (m = 0; m < ntriples; m++) + for (ibin = 0; ibin < nbin; ibin++) + hist[m][ibin] = 0.0; // zero the central atom counts - for (i = 0; i < ntriples; i++) - iatomcount[i] = 0; + for (m = 0; m < ntriples; m++) + iatomcount[m] = 0; // tally the ADFs // all three atoms i, j, and k must be in fix group @@ -563,7 +563,7 @@ void ComputeADF::compute_array() count += histall[m][ibin]; double normfac1, pdftheta, normfac2, adftheta; - if (count > 0.0) normfac1 = deltaxinv/count; + if (count > 0.0) normfac1 = 1.0/deltax/count; else normfac1 = 0.0; if (iatomcountall[m] > 0.0) normfac2 = 1.0/iatomcountall[m]; else normfac2 = 0.0; From 43f83abe5e0b5120cc4e6d9efdf93b6126798f41 Mon Sep 17 00:00:00 2001 From: "Ronald E. Miller" Date: Tue, 4 Sep 2018 15:28:57 -0400 Subject: [PATCH 289/302] Changes to the NH fix enabling Cauchy stress control (Cauhchystat) due to Miller, Tadmor, Gibson, Bernstein and Pavia, J Chem Phys, 144, 184107 (2016). --- doc/src/fix_nh.txt | 41 + examples/cauchystat/Al_shear_CS/lammps.in | 69 + examples/cauchystat/Al_shear_PR/lammps.in | 69 + .../cauchystat/Mishin-Ni-Al-2009.eam.alloy | 70007 ++++++++++++++++ examples/cauchystat/NiAl_cool/input.dat | 6009 ++ examples/cauchystat/NiAl_cool/lammps.in | 45 + .../cauchystat/NiAl_slow_stretch_CS/input.dat | 6009 ++ .../cauchystat/NiAl_slow_stretch_CS/lammps.in | 45 + .../cauchystat/NiAl_slow_stretch_PR/input.dat | 6009 ++ .../cauchystat/NiAl_slow_stretch_PR/lammps.in | 45 + examples/cauchystat/NiAl_stretch/input.dat | 6009 ++ examples/cauchystat/NiAl_stretch/lammps.in | 48 + examples/cauchystat/README | 42 + src/fix_nh.cpp | 380 +- src/fix_nh.h | 17 + 15 files changed, 94843 insertions(+), 1 deletion(-) create mode 100644 examples/cauchystat/Al_shear_CS/lammps.in create mode 100644 examples/cauchystat/Al_shear_PR/lammps.in create mode 100644 examples/cauchystat/Mishin-Ni-Al-2009.eam.alloy create mode 100644 examples/cauchystat/NiAl_cool/input.dat create mode 100644 examples/cauchystat/NiAl_cool/lammps.in create mode 100644 examples/cauchystat/NiAl_slow_stretch_CS/input.dat create mode 100644 examples/cauchystat/NiAl_slow_stretch_CS/lammps.in create mode 100644 examples/cauchystat/NiAl_slow_stretch_PR/input.dat create mode 100644 examples/cauchystat/NiAl_slow_stretch_PR/lammps.in create mode 100644 examples/cauchystat/NiAl_stretch/input.dat create mode 100644 examples/cauchystat/NiAl_stretch/lammps.in create mode 100644 examples/cauchystat/README diff --git a/doc/src/fix_nh.txt b/doc/src/fix_nh.txt index 644ced4bdc..79e1aa93da 100644 --- a/doc/src/fix_nh.txt +++ b/doc/src/fix_nh.txt @@ -54,6 +54,9 @@ keyword = {temp} or {iso} or {aniso} or {tri} or {x} or {y} or {z} or {xy} or {y {scaleyz} value = {yes} or {no} = scale yz with lz {scalexz} value = {yes} or {no} = scale xz with lz {flip} value = {yes} or {no} = allow or disallow box flips when it becomes highly skewed + {cauchystat} cauchystat values = alpha continue + alpha = strength of Cauchystat control parameter + continue = {yes} or {no} = whether of not to continue from a previous run {fixedpoint} values = x y z x,y,z = perform barostat dilation/contraction around this point (distance units) {update} value = {dipole} or {dipole/dlm} @@ -606,6 +609,39 @@ can only be used if the 2nd dimension in the keyword is periodic, and if the tilt factor is not coupled to the barostat via keywords {tri}, {yz}, {xz}, and {xy}. +Without the {cauchystat} keyword, the barostat algorithm +controls the Second-Piola Kirchhoff stress, which is a stress measure +referred to the undeformed (initial) simulation box. If the box +deforms substantially during the equilibration, the difference between +the set values and the final true (Cauchy) stresses can be +considerable. + +The {cauchystat} keyword modifies the barostat as per Miller et +al. (Miller)_"#nh-Miller" so that the Cauchy stress is controlled. +{alpha} is the non-dimensional parameter, typically set to 0.001 or +0.01 that determines how aggresively the algorithm drives the system +towards the set Cauchy stresses. Larger values of {alpha} will modify +the system more quickly, but can lead to instabilities. Smaller +values will lead to longer convergence time. Since {alpha} also +influences how much the stress fluctuations deviate from the +equilibrium fluctuations, it should be set as small as possible. + +A {continue} value of {yes} indicates that the fix is subsequent to a +previous run with the Cauchystat fix, and the intention is to continue +from the converged stress state at the end of the previous run. This +may be required, for example, when implementing a multi-step loading/unloading +sequence over several fixes. + +Setting {alpha} to zero is not permitted. To "turn off" the +Cauchystat control and thus restore the equilibrium stress +fluctuations, two subsequent fixes should be used. In the first, the +Cauchystat is used and the simulation box equilibrates to the correct +shape for the desired stresses. In the second, the {fix} statement is +identical except that the {cauchystat} keyword is removed (along with +related {alpha} and {continue} values). This restores the original +Parrinello-Rahman algorithm, but now with the correct simulation box +shape from the first fix. + These fixes can be used with dynamic groups as defined by the "group"_group.html command. Likewise they can be used with groups to which atoms are added or deleted over time, e.g. a deposition @@ -623,6 +659,7 @@ over time or the atom count becomes very small. The keyword defaults are tchain = 3, pchain = 3, mtk = yes, tloop = ploop = 1, nreset = 0, drag = 0.0, dilate = all, couple = none, +cauchystat = no, scaleyz = scalexz = scalexy = yes if periodic in 2nd dimension and not coupled to barostat, otherwise no. @@ -644,3 +681,7 @@ Martyna, J Phys A: Math Gen, 39, 5629 (2006). :link(nh-Dullweber) [(Dullweber)] Dullweber, Leimkuhler and McLachlan, J Chem Phys, 107, 5840 (1997). + +:link(nh-Miller) +[(Miller)] Miller, Tadmor, Gibson, Bernstein and Pavia, J Chem Phys, +144, 184107 (2016). diff --git a/examples/cauchystat/Al_shear_CS/lammps.in b/examples/cauchystat/Al_shear_CS/lammps.in new file mode 100644 index 0000000000..0feefeb5b2 --- /dev/null +++ b/examples/cauchystat/Al_shear_CS/lammps.in @@ -0,0 +1,69 @@ +units metal +atom_style atomic +atom_modify map array + +processors 1 1 1 + +# Box and atom positions: +boundary p p p + +# Defining lattice and creating simulation +# box with atoms inside +lattice fcc 4.05 +region simbox prism 0 5 0 5 0 5 0 0 0 units lattice +create_box 2 simbox +create_atoms 2 box + +# Atomic mass: +mass 1 58.69 +mass 2 26.98154 + +# Potential, Al fcc crystal +pair_style eam/alloy +pair_coeff * * ../Mishin-Ni-Al-2009.eam.alloy Ni Al + + +thermo 100 +thermo_style custom step temp pxx pyy pzz pxy pxz pyz +compute cna all cna/atom 2.8 + +fix 1 all npt temp 600.0 600.0 1.0 x 0.0 0.0 0.1 y 0.0 0.0 0.1 z 0.0 0.0 0.1 couple none cauchystat 0.001 no + +dump 1 all cfg 1000 test*.cfg mass type xs ys zs type c_cna + +timestep 0.002 + +variable px equal pxx +variable py equal pyy +variable pz equal pzz +variable sxy equal pxy +variable sxz equal pxz +variable syz equal pyz +variable t equal temp + +fix avg all ave/time 1 100 100 v_t v_px v_py v_pz v_sxy v_sxz v_syz file avg.txt + +variable lx equal lx +variable ly equal ly +variable lz equal ly +variable xy equal xy +variable xz equal xz +variable yz equal yz + +fix box all ave/time 1 100 100 v_lx v_ly v_lz v_xy v_xz v_yz file box.txt + +velocity all create 1200 4928459 rot yes dist gaussian + +run 10000 + +unfix 1 + +fix 1 all npt temp 600.0 600.0 1.0 x 0.0 0.0 0.1 y 0.0 0.0 0.1 z 0.0 0.0 0.1 xy -10000.0 -10000.0 0.1 couple none cauchystat 0.001 yes + +run 10000 + +unfix 1 + +fix 1 all npt temp 600.0 600.0 1.0 x 0.0 0.0 0.1 y 0.0 0.0 0.1 z 0.0 0.0 0.1 xy -10000.0 -10000.0 0.1 couple none + +run 10000 diff --git a/examples/cauchystat/Al_shear_PR/lammps.in b/examples/cauchystat/Al_shear_PR/lammps.in new file mode 100644 index 0000000000..b79d18853b --- /dev/null +++ b/examples/cauchystat/Al_shear_PR/lammps.in @@ -0,0 +1,69 @@ +units metal +atom_style atomic +atom_modify map array + +processors 1 1 1 + +# Box and atom positions: +boundary p p p + +# Defining lattice and creating simulation +# box with atoms inside +lattice fcc 4.05 +region simbox prism 0 5 0 5 0 5 0 0 0 units lattice +create_box 2 simbox +create_atoms 2 box + +# Atomic mass: +mass 1 58.69 +mass 2 26.98154 + +# Potential, Al fcc crystal +pair_style eam/alloy +pair_coeff * * ../Mishin-Ni-Al-2009.eam.alloy Ni Al + + +thermo 100 +thermo_style custom step temp pxx pyy pzz pxy pxz pyz +compute cna all cna/atom 2.8 + +fix 1 all npt temp 600.0 600.0 1.0 x 0.0 0.0 0.1 y 0.0 0.0 0.1 z 0.0 0.0 0.1 couple none + +dump 1 all cfg 1000 test*.cfg mass type xs ys zs type c_cna + +timestep 0.002 + +variable px equal pxx +variable py equal pyy +variable pz equal pzz +variable sxy equal pxy +variable sxz equal pxz +variable syz equal pyz +variable t equal temp + +fix avg all ave/time 1 100 100 v_t v_px v_py v_pz v_sxy v_sxz v_syz file avg.txt + +variable lx equal lx +variable ly equal ly +variable lz equal ly +variable xy equal xy +variable xz equal xz +variable yz equal yz + +fix box all ave/time 1 100 100 v_lx v_ly v_lz v_xy v_xz v_yz file box.txt + +velocity all create 1200 4928459 rot yes dist gaussian + +run 10000 + +unfix 1 + +fix 1 all npt temp 600.0 600.0 1.0 x 0.0 0.0 0.1 y 0.0 0.0 0.1 z 0.0 0.0 0.1 xy -10000.0 -10000.0 0.1 couple none + +run 10000 + +unfix 1 + +fix 1 all npt temp 600.0 600.0 1.0 x 0.0 0.0 0.1 y 0.0 0.0 0.1 z 0.0 0.0 0.1 xy -10000.0 -10000.0 0.1 couple none + +run 10000 diff --git a/examples/cauchystat/Mishin-Ni-Al-2009.eam.alloy b/examples/cauchystat/Mishin-Ni-Al-2009.eam.alloy new file mode 100644 index 0000000000..a4608f5579 --- /dev/null +++ b/examples/cauchystat/Mishin-Ni-Al-2009.eam.alloy @@ -0,0 +1,70007 @@ + G.P. Purja Pun and Y. Mishin, Phil. Mag., in press (2009). + LAMMPS setfl format. Conversion by C. A. Becker from Y. Mishin files. + 13 Aug 2009. http://www.ctcms.nist.gov/potentials + 2 Ni Al +10000 0.5013228884000001E-03 10000 0.6287210000000001E-03 0.6287210000000000E+01 + 28 0.5871000000E+02 0.3520000000E+01 fcc + -2.2546436667E-0002 + -3.9517100033E-0002 + -5.5218483024E-0002 + -6.9748646092E-0002 + -8.3205649690E-0002 + -9.5687071211E-0002 + -1.0728855581E-0001 + -1.1810768086E-0001 + -1.2825168498E-0001 + -1.3783132935E-0001 + -1.4696180428E-0001 + -1.5574426829E-0001 + -1.6421932328E-0001 + -1.7241225154E-0001 + -1.8034761338E-0001 + -1.8804961815E-0001 + -1.9554179349E-0001 + -2.0284611159E-0001 + -2.0997900487E-0001 + -2.1695479964E-0001 + -2.2378493785E-0001 + -2.3047983335E-0001 + -2.3704867186E-0001 + -2.4350010967E-0001 + -2.4984191363E-0001 + -2.5608131864E-0001 + -2.6222432233E-0001 + -2.6827647491E-0001 + -2.7424277333E-0001 + -2.8012796566E-0001 + -2.8593635665E-0001 + -2.9167200423E-0001 + -2.9733842233E-0001 + -3.0293893346E-0001 + -3.0847663943E-0001 + -3.1395450539E-0001 + 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7.068893 +5636 1 32.059505 32.251117 2.629522 +5637 2 31.867763 34.040728 3.960388 +5638 1 31.932973 31.808697 5.917256 +5639 1 30.007373 39.943466 4.51009 +5640 2 39.207186 30.079079 1.703674 +5641 1 32.016417 34.359045 1.391175 +5642 1 32.0796 36.080574 2.990027 +5643 2 32.125016 37.982811 4.244242 +5644 1 32.039867 35.855789 5.754866 +5645 2 30.356301 36.250302 1.436559 +5646 1 32.110296 38.00744 1.426636 +5647 1 33.998604 30.067664 5.743991 +5648 2 33.695324 31.983255 4.383442 +5649 2 30.152086 36.019627 4.245065 +5650 2 34.240197 32.341445 1.32205 +5651 1 33.885438 34.090868 2.902626 +5652 2 34.178132 35.93225 4.482376 +5653 1 33.856287 33.915557 5.543055 +5654 2 34.187255 35.904801 1.570832 +5655 1 34.049489 37.902242 2.794215 +5656 1 34.196846 37.782622 5.597948 +5657 1 32.010141 29.994854 3.963328 +5658 1 30.085473 38.058327 2.970114 +5659 1 37.563886 30.425407 3.132393 +5660 1 35.867335 32.241913 3.116156 +5661 2 35.974255 34.126395 4.519526 +5662 1 36.004069 32.109611 5.814404 +5663 1 34.085538 39.906327 4.293478 +5664 1 36.097439 33.990507 1.502757 +5665 1 36.087679 36.048793 3.035352 +5666 2 36.278328 38.155374 4.063777 +5667 1 36.249913 36.355424 5.927679 +5668 2 31.890573 30.350964 1.619094 +5669 2 31.962807 37.754434 7.179059 +5670 1 35.973947 37.892913 1.48124 +5671 2 35.839322 30.204876 4.375075 +5672 1 37.935879 32.177401 4.195289 +5673 1 38.101493 38.10187 5.953049 +5674 2 37.852909 32.388628 1.664291 +5675 1 37.942171 34.0458 3.006996 +5676 2 38.2641 36.15208 4.530503 +5677 1 38.039433 34.206108 5.79566 +5678 1 33.979517 30.322401 2.668635 +5679 2 38.266202 35.993947 1.484331 +5680 1 38.067048 38.040012 2.752414 +5681 1 37.733806 30.096455 5.970187 +5682 1 39.682213 32.091472 5.993971 +5683 1 39.817487 31.930363 0.000367 +5684 1 36.043395 39.59783 5.676369 +5685 1 31.869558 32.098607 0.138261 +5686 1 39.734652 32.347843 3.042732 +5687 2 40.028718 38.187031 4.420077 +5688 1 35.900797 34.287592 6.911917 +5689 1 34.035098 34.219002 0.088382 +5690 1 35.958161 30.177564 1.36017 +5691 2 34.104037 39.871769 1.666144 +5692 2 31.713648 30.030149 13.126076 +5693 2 38.102561 35.967156 7.519894 +5694 2 31.857312 30.233676 7.601269 +5695 1 34.289545 38.267283 14.401123 +5696 2 35.86683 30.19377 7.315341 +5697 1 30.215661 34.162037 8.437432 +5698 2 32.177106 33.712521 7.258256 +5699 2 36.086337 30.089865 10.102229 +5700 1 31.904414 32.116466 8.706393 +5701 1 31.937094 33.843414 10.07911 +5702 1 31.979885 32.115442 11.535778 +5703 2 31.646163 34.054645 12.923349 +5704 2 34.238187 35.954151 7.232689 +5705 1 32.107596 35.868544 8.568472 +5706 1 31.872832 37.740296 10.246254 +5707 1 32.382757 36.08172 11.390228 +5708 1 31.907287 38.043268 12.759712 +5709 1 33.814113 30.280416 11.361764 +5710 1 30.217972 36.108976 12.75806 +5711 2 33.902634 32.114854 10.131038 +5712 1 33.57231 32.104408 13.09734 +5713 1 31.808268 30.066503 10.372268 +5714 1 34.074533 34.09759 8.82773 +5715 2 34.112978 35.879639 10.008535 +5716 1 33.847258 34.132738 11.781858 +5717 2 33.938795 36.222314 13.025522 +5718 2 29.978741 32.187816 10.235973 +5719 1 34.055911 38.08124 8.660649 +5720 1 33.602601 34.200907 14.256884 +5721 1 34.074479 38.033056 11.548004 +5722 2 36.270647 38.06342 7.227717 +5723 1 35.834976 32.087215 8.752976 +5724 2 36.060859 33.636235 10.421377 +5725 1 35.993855 31.835332 12.022895 +5726 2 35.800428 33.936835 13.252217 +5727 1 36.115212 35.929045 8.653718 +5728 2 36.22813 38.12211 10.18663 +5729 1 36.031176 36.067395 11.711353 +5730 2 36.290793 38.28804 13.110371 +5731 1 38.314803 39.87771 13.628157 +5732 2 37.813718 31.963763 10.266333 +5733 2 38.345306 31.61479 12.746628 +5734 1 37.993817 33.8253 8.828538 +5735 2 37.963385 36.024574 10.310583 +5736 1 37.917131 33.840219 11.529013 +5737 1 38.204273 36.194533 12.982689 +5738 1 38.223785 37.96125 8.694521 +5739 1 38.251957 38.103445 11.574783 +5740 1 32.162162 35.830151 14.368089 +5741 1 38.188088 39.835851 10.200529 +5742 2 37.943506 31.862097 7.486993 +5743 1 34.019779 32.099062 7.382655 +5744 1 37.835648 33.808569 14.272091 +5745 2 30.154664 36.008494 10.278616 +5746 2 34.005569 29.909902 14.221934 +5747 2 39.942399 30.201297 7.221972 +5748 1 31.669489 32.129787 14.202133 +5749 1 33.8553 30.102976 8.785283 +5750 1 36.285019 39.993992 8.473052 +5751 2 34.332311 39.811654 10.053333 +5752 1 32.287985 39.934755 8.544521 +5753 1 32.117424 39.894109 11.328559 +5754 1 34.070494 39.946648 12.675838 +5755 1 33.523905 30.237815 17.092452 +5756 1 37.796875 30.195733 20.074531 +5757 1 36.27689 36.076917 14.383428 +5758 1 31.912415 30.074316 18.962029 +5759 1 31.72877 30.195629 15.548548 +5760 1 39.683801 34.084414 18.996274 +5761 1 31.823255 34.23579 15.916954 +5762 1 32.081111 32.17144 17.423655 +5763 2 32.272671 34.141341 18.923237 +5764 1 31.890319 32.258592 20.174682 +5765 1 32.292252 37.789848 15.657298 +5766 1 31.865994 35.945048 17.430984 +5767 2 32.390605 38.101438 18.756338 +5768 1 32.536255 36.292415 20.33365 +5769 1 30.255802 37.826036 17.398086 +5770 2 30.361913 39.693462 15.767213 +5771 1 33.658364 32.195407 15.713634 +5772 1 37.521125 34.00621 20.179734 +5773 2 34.170474 31.959646 18.774747 +5774 2 30.146126 36.07111 19.193288 +5775 2 34.236512 36.009488 15.705407 +5776 1 33.893052 34.259763 17.152928 +5777 1 34.299465 36.26334 18.583767 +5778 1 34.414431 34.040341 19.801645 +5779 1 38.268782 38.067343 19.882736 +5780 1 38.192119 30.067346 14.65738 +5781 1 34.182659 38.172175 17.379208 +5782 1 34.285582 38.312236 20.114249 +5783 1 35.930101 31.821554 14.523145 +5784 1 38.166996 38.004859 14.725716 +5785 1 35.925271 33.697258 15.741088 +5786 1 35.628801 31.929644 17.21365 +5787 2 36.045808 34.231991 18.304721 +5788 1 36.066783 31.92807 19.890693 +5789 2 30.047091 31.872972 18.511468 +5790 1 38.23536 37.943903 17.225875 +5791 2 36.119549 38.085157 15.846243 +5792 1 36.28338 36.046451 17.021393 +5793 1 36.11202 38.183852 18.648108 +5794 1 36.196383 36.094959 20.14945 +5795 1 39.857714 32.070711 20.545667 +5796 2 38.277117 32.092018 16.056024 +5797 1 30.025257 33.999826 20.265429 +5798 2 37.984137 32.053017 18.664282 +5799 1 32.002215 39.814443 17.350923 +5800 2 38.174586 35.979296 18.941495 +5801 2 38.345772 36.135739 15.897296 +5802 1 38.047733 34.092532 17.193597 +5803 2 30.130578 35.962177 15.540359 +5804 2 36.401926 38.058554 21.346524 +5805 1 30.120957 38.000412 14.522433 +5806 1 30.488998 38.181884 20.233832 +5807 1 30.027329 34.063964 17.498188 +5808 1 37.840062 29.987227 17.565361 +5809 1 32.008478 30.033144 21.485715 +5810 2 39.774533 34.462138 21.415634 +5811 1 30.338184 36.208481 21.405811 +5812 1 29.947563 30.056036 17.165794 +5813 1 39.921352 31.819743 14.64622 +5814 2 34.22915 39.981504 21.655908 +5815 1 30.183329 38.19462 25.743477 +5816 1 35.907762 33.854845 21.824692 +5817 1 38.081846 38.241792 22.993384 +5818 2 34.075816 32.199578 21.47467 +5819 1 32.064265 31.912891 22.91255 +5820 1 31.883139 33.912773 24.608383 +5821 1 31.812805 31.862315 26.174015 +5822 2 32.311833 34.450426 27.53752 +5823 1 32.200878 36.145135 23.147334 +5824 2 32.211767 38.313372 24.442593 +5825 1 32.252693 36.173296 25.56014 +5826 2 32.184178 37.824314 27.059278 +5827 2 35.878916 30.070226 21.715039 +5828 1 37.668689 30.050641 23.045191 +5829 2 31.790668 34.251576 21.855242 +5830 1 30.175916 38.136754 23.248784 +5831 1 33.79328 31.909522 24.576174 +5832 2 33.915875 32.018888 27.178426 +5833 1 33.839278 34.11599 23.063711 +5834 2 34.250078 35.934833 24.487018 +5835 1 33.990054 34.106505 25.930061 +5836 1 34.091025 36.282124 27.332172 +5837 1 39.883217 38.455893 24.705928 +5838 2 38.008034 36.021219 27.398438 +5839 1 34.624327 37.896007 23.016853 +5840 1 34.168936 37.954274 25.436951 +5841 1 39.89339 34.048173 27.027007 +5842 1 38.248268 36.455753 21.536765 +5843 1 35.611768 31.698556 23.347142 +5844 2 36.148802 34.042768 24.34925 +5845 1 35.930043 32.125519 25.878398 +5846 2 35.950538 34.005205 27.219195 +5847 1 37.955393 34.076875 25.799656 +5848 1 37.973062 38.01909 26.230315 +5849 1 36.411999 36.023781 22.980871 +5850 2 36.283519 37.906374 24.521157 +5851 1 36.105429 36.189959 25.968065 +5852 2 35.830991 38.301536 27.267321 +5853 1 30.231426 34.188738 26.125408 +5854 1 30.281973 34.136127 28.552033 +5855 2 37.785563 31.866932 24.278312 +5856 2 31.348335 30.244331 27.485493 +5857 2 37.966809 32.115632 27.589764 +5858 2 35.66017 29.988788 24.878779 +5859 1 38.277476 34.130765 22.79239 +5860 2 37.959129 36.154297 24.437008 +5861 1 33.713618 30.108282 28.642398 +5862 1 39.822964 31.905463 23.110805 +5863 1 37.492689 32.09291 21.995043 +5864 2 30.127031 36.064739 24.638111 +5865 1 35.533243 30.110728 27.243438 +5866 1 36.070605 31.93122 28.695839 +5867 2 34.291131 35.85795 21.75028 +5868 1 31.938061 32.142881 28.504169 +5869 1 33.986813 39.867909 27.012668 +5870 1 30.10822 37.992396 28.395198 +5871 1 39.800701 30.030956 24.347523 +5872 2 39.892552 29.979658 27.134291 +5873 2 32.228297 37.952841 21.875429 +5874 2 39.977135 34.107266 24.499149 +5875 1 39.846344 36.406036 26.033584 +5876 1 32.059083 40.009476 28.464272 +5877 1 35.959269 39.965152 25.93262 +5878 2 30.460566 32.139968 24.447603 +5879 2 39.881804 38.087413 21.696502 +5880 1 30.134489 36.163809 33.336193 +5881 1 37.575878 38.100411 28.849489 +5882 1 37.662104 38.133383 31.571418 +5883 1 32.362045 39.87867 34.884405 +5884 1 39.873173 36.224308 34.920349 +5885 1 31.991424 34.085923 29.999612 +5886 1 31.815171 32.168756 31.641691 +5887 2 31.782096 34.063184 33.062024 +5888 1 31.718037 31.953527 34.554814 +5889 1 39.862898 38.376226 32.906485 +5890 1 37.551931 30.038119 34.432157 +5891 1 31.780802 37.997046 30.254783 +5892 1 31.834761 35.939821 31.604936 +5893 2 32.041736 38.210181 33.326919 +5894 1 32.203699 35.869978 34.596577 +5895 1 34.008946 38.074601 28.827076 +5896 1 37.899592 29.974959 28.916731 +5897 1 38.030007 33.96835 28.91396 +5898 2 33.846774 32.085103 30.081464 +5899 1 29.952597 30.143437 34.499248 +5900 1 33.915497 32.111271 33.150301 +5901 1 31.790321 30.23064 29.991804 +5902 2 37.907438 32.157735 35.935104 +5903 2 33.84716 36.05681 30.26538 +5904 1 34.0432 34.280307 31.67674 +5905 2 34.011752 36.10558 33.143956 +5906 1 33.824017 34.085576 34.552777 +5907 1 34.194027 34.072791 28.967937 +5908 1 33.894909 38.222801 31.657741 +5909 1 33.881652 38.078172 34.899329 +5910 1 38.119296 38.056464 34.569681 +5911 1 34.291634 39.920546 33.178111 +5912 1 33.581454 29.993619 34.681796 +5913 2 36.053229 33.87704 30.318866 +5914 1 35.873901 31.88411 31.537273 +5915 1 35.89848 33.774876 32.823618 +5916 1 35.828028 32.348885 34.478807 +5917 1 35.672787 37.928294 30.518119 +5918 1 35.989671 35.945619 31.826779 +5919 2 35.97259 38.32967 33.142576 +5920 1 35.703331 35.814769 34.580449 +5921 1 33.817908 30.208146 31.599942 +5922 1 35.844503 36.12033 28.831087 +5923 1 38.261976 32.096366 30.088155 +5924 2 37.797891 31.9048 33.114668 +5925 1 39.55682 31.880323 34.531549 +5926 2 37.75043 36.193675 30.248336 +5927 1 38.393997 33.98513 31.905095 +5928 2 37.963057 36.355009 33.181745 +5929 1 37.797425 34.035854 34.376018 +5930 1 30.050396 34.271558 31.538997 +5931 1 39.815357 36.070726 31.654601 +5932 2 39.731271 30.032678 30.327233 +5933 1 39.915975 31.952921 31.714062 +5934 2 31.84562 29.966231 33.068673 +5935 1 31.85693 36.270476 28.934934 +5936 1 31.866016 39.844488 31.814385 +5937 1 30.092134 34.094244 34.755273 +5938 1 39.694807 30.040539 32.997642 +5939 1 36.196648 35.960439 42.925128 +5940 2 32.015598 37.930066 36.230869 +5941 1 37.674069 30.102473 37.130906 +5942 1 39.699003 32.118698 37.217773 +5943 2 29.963786 31.633701 39.162197 +5944 1 32.058675 39.814086 37.607409 +5945 1 35.842471 33.971675 35.989822 +5946 1 34.028551 38.060871 42.983375 +5947 1 31.588672 31.941435 37.383683 +5948 2 31.694069 33.998273 38.693202 +5949 1 31.930294 31.884957 40.381472 +5950 2 32.11349 33.999595 41.798502 +5951 1 31.876844 36.011394 37.307134 +5952 2 31.893158 37.928813 38.973436 +5953 1 31.81531 35.668229 40.479844 +5954 2 31.787646 38.142244 41.698514 +5955 1 31.925559 36.23881 42.924197 +5956 1 36.004443 37.899297 36.000218 +5957 1 38.451312 38.205323 40.038254 +5958 2 33.656378 31.907332 38.819792 +5959 1 33.99011 31.933293 41.627228 +5960 2 37.707146 36.123239 36.332034 +5961 1 33.657247 33.955416 37.665398 +5962 1 33.73943 36.151957 39.054731 +5963 1 33.605884 33.957716 40.193208 +5964 2 34.011058 36.048882 41.690411 +5965 1 38.130598 34.242802 40.052446 +5966 1 34.167865 38.117836 37.628936 +5967 1 34.142536 38.424699 40.41195 +5968 1 40.005739 32.215658 40.003237 +5969 1 39.521882 33.977557 36.015643 +5970 1 38.214368 38.282583 37.333443 +5971 1 31.918418 33.931512 36.157998 +5972 1 35.612055 32.074774 37.387219 +5973 2 35.5831 34.04957 39.047544 +5974 1 35.75246 32.088086 40.149631 +5975 2 35.615657 33.824419 41.713165 +5976 1 35.638569 36.061296 37.614952 +5977 2 36.358444 37.816896 38.884174 +5978 1 35.987046 36.034802 40.28745 +5979 1 36.122176 38.157473 41.827978 +5980 1 37.730089 30.067171 42.889333 +5981 2 39.944726 33.833791 41.642053 +5982 2 37.765477 32.166294 38.745053 +5983 2 38.099767 31.876153 41.350163 +5984 2 38.066621 36.442839 41.48951 +5985 1 37.726393 34.24931 37.606618 +5986 1 38.065514 36.286433 39.031222 +5987 1 37.664687 30.041804 39.941583 +5988 1 36.1403 39.743151 39.963443 +5989 2 34.004128 36.124387 36.139274 +5990 1 38.008343 33.918454 43.060491 +5991 1 36.098653 32.233378 42.976295 +5992 1 30.058867 38.134404 37.476791 +5993 2 35.662195 29.860797 35.905075 +5994 1 33.53205 30.001458 37.176731 +5995 1 38.387155 38.05525 43.009631 +5996 1 36.188595 39.834331 37.505629 +5997 1 39.656895 29.968268 41.372509 +5998 1 39.786156 36.00049 42.804021 +5999 2 33.855117 32.268762 36.090908 +6000 2 31.856527 30.044242 36.001804 diff --git a/examples/cauchystat/NiAl_cool/lammps.in b/examples/cauchystat/NiAl_cool/lammps.in new file mode 100644 index 0000000000..4aa5d327a9 --- /dev/null +++ b/examples/cauchystat/NiAl_cool/lammps.in @@ -0,0 +1,45 @@ +units metal +atom_style atomic +atom_modify map array + +processors 1 1 1 + +# Box and atom positions: +boundary p p p +read_data input.dat + +# Atomic mass: +mass 1 58.69 +mass 2 26.98154 + +# Potential, Al fcc crystal +pair_style eam/alloy +pair_coeff * * ../Mishin-Ni-Al-2009.eam.alloy Ni Al + +thermo 100 +thermo_style custom step temp pxx pyy pzz lx ly lz +compute cna all cna/atom 2.8 + +velocity all create 2400.0 4928459 rot yes dist gaussian + +fix 1 all npt temp 1200.0 1200.0 1.0 x 0.0 0.0 0.1 y 0.0 0.0 0.1 z -2800.0 -2800.0 0.1 couple none cauchystat 0.001 no + +dump 1 all cfg 1000 test*.cfg mass type xs ys zs type c_cna + +timestep 0.002 + +variable l equal lz +variable p equal pzz +variable t equal temp + +fix avg all ave/time 1 1000 1000 v_t v_l v_p file avg.txt + +velocity all create 2400 4928459 rot yes dist gaussian + +run 10000 + +unfix 1 + +fix 1 all npt temp 1200.0 300.0 1.0 x 0.0 0.0 0.1 y 0.0 0.0 0.1 z -2800.0 -2800.0 0.1 couple none cauchystat 0.001 yes + +run 100000 diff --git a/examples/cauchystat/NiAl_slow_stretch_CS/input.dat b/examples/cauchystat/NiAl_slow_stretch_CS/input.dat new file mode 100644 index 0000000000..3b99f3ea8f --- /dev/null +++ b/examples/cauchystat/NiAl_slow_stretch_CS/input.dat @@ -0,0 +1,6009 @@ +Position data for MD simulation + +6000 atoms +2 atom types +0.0000 39.972658977840510 xlo xhi +0.0000 39.970082402467646 ylo yhi +0.0000 43.077168594479417 zlo zhi +Atoms + +1 1 2.265603 1.699233 2.96682 +2 2 2.147625 3.958175 4.336466 +3 1 1.997414 2.08615 5.681268 +4 2 6.222234 0.12344 4.55833 +5 1 4.247865 9.8684 7.188432 +6 2 2.226404 4.008191 1.332846 +7 1 2.558125 5.881235 2.799624 +8 2 2.112892 8.008518 4.084836 +9 1 2.366112 6.194696 5.83623 +10 2 0.308528 9.773154 7.249786 +11 1 1.861699 8.008727 1.634831 +12 2 0.245314 5.864464 4.508327 +13 1 8.139953 -0.02424 5.747139 +14 1 0.178338 3.676069 2.91793 +15 2 0.021903 9.933735 1.645872 +16 1 4.094944 3.990727 2.989711 +17 2 4.25173 6.125247 4.299378 +18 1 4.004975 4.261809 5.650881 +19 2 4.233414 9.883798 4.412874 +20 2 4.158657 5.985987 1.452914 +21 1 3.943003 7.917155 2.809851 +22 1 4.013002 8.032118 5.709128 +23 1 3.913817 0.208102 0.200173 +24 2 4.11186 2.115952 4.39711 +25 1 4.091794 8.080277 0.383691 +26 1 8.239262 4.128528 0.14417 +27 1 4.164942 2.294329 1.435205 +28 1 6.018476 2.048784 2.978318 +29 1 6.189263 4.123374 4.429365 +30 1 5.731913 2.039386 5.760723 +31 2 8.125123 2.396376 4.334063 +32 2 5.956145 3.961461 1.710606 +33 1 6.097732 6.223054 3.105619 +34 2 6.260701 8.269814 4.403081 +35 1 6.135592 6.191014 6.014208 +36 2 6.118481 0.280536 1.660297 +37 2 5.95371 8.134065 1.459117 +38 1 8.112 7.978937 6.025785 +39 1 8.230735 0.317331 0.287501 +40 1 7.984577 0.451106 2.876758 +41 1 8.121358 4.469963 3.000969 +42 2 8.0024 6.398776 4.506808 +43 1 8.265498 4.145515 5.950951 +44 1 8.093687 2.336039 1.599762 +45 2 7.786786 6.082031 1.369435 +46 1 8.051625 8.388788 2.947011 +47 2 1.887169 0.10205 1.232231 +48 1 3.814096 0.184819 2.93152 +49 2 5.999738 4.024912 6.895817 +50 1 0.20906 5.67262 1.62315 +51 1 2.22916 6.007717 0.143509 +52 1 9.864584 8.16224 1.516273 +53 1 0.029687 7.997328 3.090548 +54 1 0.158584 7.813035 5.663186 +55 1 6.149844 9.939956 0.040852 +56 1 1.871208 1.766851 8.960428 +57 2 2.233107 3.807827 10.095989 +58 1 1.960237 1.933156 11.733738 +59 1 2.028536 4.090031 13.399625 +60 2 0.096818 1.982978 13.367683 +61 1 1.962538 5.967991 8.575587 +62 2 1.779869 8.006286 9.997749 +63 1 2.261369 6.075808 11.262585 +64 1 1.878689 7.795749 12.973992 +65 1 8.066595 6.091936 7.32151 +66 2 6.004471 8.10958 7.337536 +67 2 3.807826 9.773306 13.107995 +68 2 3.628292 2.338356 7.627483 +69 1 4.142245 4.127148 8.640624 +70 2 4.430475 5.841591 10.077295 +71 1 3.968136 4.281892 11.552649 +72 2 3.926926 6.059939 13.034315 +73 1 4.163584 8.009554 8.875445 +74 1 3.841536 8.095992 11.564038 +75 1 1.972543 4.098752 7.26509 +76 1 9.833961 8.179066 10.053046 +77 1 3.959427 0.070701 8.628349 +78 1 4.000206 1.99734 10.467815 +79 1 0.175393 5.813256 10.208259 +80 2 3.991668 2.115114 12.987731 +81 2 8.056411 2.098025 12.865242 +82 1 5.64748 2.156225 8.497216 +83 2 6.159432 4.014865 10.196613 +84 1 6.214032 2.165249 11.651601 +85 1 5.856347 3.961477 13.023239 +86 1 7.948437 0.352004 11.304002 +87 2 0.129981 2.04383 7.39824 +88 1 6.181909 5.856377 8.431434 +89 1 5.991539 7.847191 10.091845 +90 1 5.975418 5.816241 11.895283 +91 1 5.86549 8.043369 13.028812 +92 2 4.166236 6.085137 7.231975 +93 1 0.439458 3.829864 11.550798 +94 2 0.21596 5.973334 12.667734 +95 1 10.017517 5.823156 11.545694 +96 1 8.076092 4.274718 8.540188 +97 2 7.924969 6.011881 10.326107 +98 1 8.12022 3.959556 11.608595 +99 1 8.110671 6.08702 13.353502 +100 1 8.135035 2.224763 9.76071 +101 1 8.056404 8.04948 8.608732 +102 1 7.867682 7.986347 11.444105 +103 1 0.057722 3.824193 8.62711 +104 1 9.981584 4.247366 7.362993 +105 2 4.013801 9.873296 9.982524 +106 1 2.329565 8.116478 7.435377 +107 2 5.950495 0.34488 9.79838 +108 1 4.334027 0.076447 11.746114 +109 2 7.945804 9.995075 13.009688 +110 1 2.027284 10.048274 11.752786 +111 2 7.985809 2.177851 7.348854 +112 2 0.227187 9.715111 13.080145 +113 1 4.369771 0.043973 14.298992 +114 1 9.913252 6.303629 8.785055 +115 1 7.984689 3.996322 14.285297 +116 1 6.286022 9.901661 11.434457 +117 2 9.978329 0.129998 10.093528 +118 2 9.898021 7.994926 13.146433 +119 1 2.438629 0.033347 18.603552 +120 2 2.19485 3.927092 15.921048 +121 1 2.266036 2.0106 17.298124 +122 2 2.190625 4.002775 18.808528 +123 1 2.529808 1.858131 19.802924 +124 1 2.121536 8.100548 15.903723 +125 1 1.999174 5.945764 17.409821 +126 2 2.399752 8.317077 18.513998 +127 1 2.085018 6.322971 20.123548 +128 1 0.132331 7.834943 14.417244 +129 2 0.191888 2.055829 18.456008 +130 1 8.035826 8.278124 14.487514 +131 2 3.964165 5.965398 16.034244 +132 1 3.977251 4.106829 17.287135 +133 1 4.083409 6.186923 18.749777 +134 1 4.118697 4.16167 19.924445 +135 2 0.168486 10.031098 15.738364 +136 1 9.834776 5.750065 20.057158 +137 1 4.513739 7.925063 17.284367 +138 1 0.224638 6.311966 18.562 +139 1 4.05173 8.065927 20.327367 +140 1 4.020498 7.877514 14.44079 +141 1 4.143142 1.813412 15.801004 +142 1 2.214548 1.829361 14.565296 +143 2 4.407757 2.318175 18.721975 +144 2 6.016403 3.935276 15.745347 +145 1 6.343375 1.849436 17.205365 +146 2 6.615021 3.988745 18.735217 +147 1 6.455591 1.950789 20.137809 +148 1 6.179932 9.794709 17.21643 +149 2 6.237707 7.849925 15.743301 +150 1 6.151976 5.985244 17.227932 +151 2 6.178229 7.773511 18.829625 +152 1 6.147011 5.845856 20.064817 +153 2 4.124664 9.743815 15.83873 +154 1 8.065185 1.771116 18.726928 +155 1 6.149514 1.938847 14.518073 +156 2 8.136444 6.024316 15.560218 +157 1 8.139342 3.949043 16.901849 +158 1 8.143554 6.219717 18.549219 +159 1 8.181775 3.5232 20.518875 +160 1 1.876074 6.12577 14.691379 +161 2 9.729818 3.920007 18.490075 +162 1 8.23825 8.027751 17.068995 +163 1 4.103417 9.893021 18.750211 +164 1 8.095744 7.73466 20.44646 +165 2 8.348453 1.630886 15.803105 +166 1 0.114526 2.216943 15.877394 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36.278328 38.155374 4.063777 +5667 1 36.249913 36.355424 5.927679 +5668 2 31.890573 30.350964 1.619094 +5669 2 31.962807 37.754434 7.179059 +5670 1 35.973947 37.892913 1.48124 +5671 2 35.839322 30.204876 4.375075 +5672 1 37.935879 32.177401 4.195289 +5673 1 38.101493 38.10187 5.953049 +5674 2 37.852909 32.388628 1.664291 +5675 1 37.942171 34.0458 3.006996 +5676 2 38.2641 36.15208 4.530503 +5677 1 38.039433 34.206108 5.79566 +5678 1 33.979517 30.322401 2.668635 +5679 2 38.266202 35.993947 1.484331 +5680 1 38.067048 38.040012 2.752414 +5681 1 37.733806 30.096455 5.970187 +5682 1 39.682213 32.091472 5.993971 +5683 1 39.817487 31.930363 0.000367 +5684 1 36.043395 39.59783 5.676369 +5685 1 31.869558 32.098607 0.138261 +5686 1 39.734652 32.347843 3.042732 +5687 2 40.028718 38.187031 4.420077 +5688 1 35.900797 34.287592 6.911917 +5689 1 34.035098 34.219002 0.088382 +5690 1 35.958161 30.177564 1.36017 +5691 2 34.104037 39.871769 1.666144 +5692 2 31.713648 30.030149 13.126076 +5693 2 38.102561 35.967156 7.519894 +5694 2 31.857312 30.233676 7.601269 +5695 1 34.289545 38.267283 14.401123 +5696 2 35.86683 30.19377 7.315341 +5697 1 30.215661 34.162037 8.437432 +5698 2 32.177106 33.712521 7.258256 +5699 2 36.086337 30.089865 10.102229 +5700 1 31.904414 32.116466 8.706393 +5701 1 31.937094 33.843414 10.07911 +5702 1 31.979885 32.115442 11.535778 +5703 2 31.646163 34.054645 12.923349 +5704 2 34.238187 35.954151 7.232689 +5705 1 32.107596 35.868544 8.568472 +5706 1 31.872832 37.740296 10.246254 +5707 1 32.382757 36.08172 11.390228 +5708 1 31.907287 38.043268 12.759712 +5709 1 33.814113 30.280416 11.361764 +5710 1 30.217972 36.108976 12.75806 +5711 2 33.902634 32.114854 10.131038 +5712 1 33.57231 32.104408 13.09734 +5713 1 31.808268 30.066503 10.372268 +5714 1 34.074533 34.09759 8.82773 +5715 2 34.112978 35.879639 10.008535 +5716 1 33.847258 34.132738 11.781858 +5717 2 33.938795 36.222314 13.025522 +5718 2 29.978741 32.187816 10.235973 +5719 1 34.055911 38.08124 8.660649 +5720 1 33.602601 34.200907 14.256884 +5721 1 34.074479 38.033056 11.548004 +5722 2 36.270647 38.06342 7.227717 +5723 1 35.834976 32.087215 8.752976 +5724 2 36.060859 33.636235 10.421377 +5725 1 35.993855 31.835332 12.022895 +5726 2 35.800428 33.936835 13.252217 +5727 1 36.115212 35.929045 8.653718 +5728 2 36.22813 38.12211 10.18663 +5729 1 36.031176 36.067395 11.711353 +5730 2 36.290793 38.28804 13.110371 +5731 1 38.314803 39.87771 13.628157 +5732 2 37.813718 31.963763 10.266333 +5733 2 38.345306 31.61479 12.746628 +5734 1 37.993817 33.8253 8.828538 +5735 2 37.963385 36.024574 10.310583 +5736 1 37.917131 33.840219 11.529013 +5737 1 38.204273 36.194533 12.982689 +5738 1 38.223785 37.96125 8.694521 +5739 1 38.251957 38.103445 11.574783 +5740 1 32.162162 35.830151 14.368089 +5741 1 38.188088 39.835851 10.200529 +5742 2 37.943506 31.862097 7.486993 +5743 1 34.019779 32.099062 7.382655 +5744 1 37.835648 33.808569 14.272091 +5745 2 30.154664 36.008494 10.278616 +5746 2 34.005569 29.909902 14.221934 +5747 2 39.942399 30.201297 7.221972 +5748 1 31.669489 32.129787 14.202133 +5749 1 33.8553 30.102976 8.785283 +5750 1 36.285019 39.993992 8.473052 +5751 2 34.332311 39.811654 10.053333 +5752 1 32.287985 39.934755 8.544521 +5753 1 32.117424 39.894109 11.328559 +5754 1 34.070494 39.946648 12.675838 +5755 1 33.523905 30.237815 17.092452 +5756 1 37.796875 30.195733 20.074531 +5757 1 36.27689 36.076917 14.383428 +5758 1 31.912415 30.074316 18.962029 +5759 1 31.72877 30.195629 15.548548 +5760 1 39.683801 34.084414 18.996274 +5761 1 31.823255 34.23579 15.916954 +5762 1 32.081111 32.17144 17.423655 +5763 2 32.272671 34.141341 18.923237 +5764 1 31.890319 32.258592 20.174682 +5765 1 32.292252 37.789848 15.657298 +5766 1 31.865994 35.945048 17.430984 +5767 2 32.390605 38.101438 18.756338 +5768 1 32.536255 36.292415 20.33365 +5769 1 30.255802 37.826036 17.398086 +5770 2 30.361913 39.693462 15.767213 +5771 1 33.658364 32.195407 15.713634 +5772 1 37.521125 34.00621 20.179734 +5773 2 34.170474 31.959646 18.774747 +5774 2 30.146126 36.07111 19.193288 +5775 2 34.236512 36.009488 15.705407 +5776 1 33.893052 34.259763 17.152928 +5777 1 34.299465 36.26334 18.583767 +5778 1 34.414431 34.040341 19.801645 +5779 1 38.268782 38.067343 19.882736 +5780 1 38.192119 30.067346 14.65738 +5781 1 34.182659 38.172175 17.379208 +5782 1 34.285582 38.312236 20.114249 +5783 1 35.930101 31.821554 14.523145 +5784 1 38.166996 38.004859 14.725716 +5785 1 35.925271 33.697258 15.741088 +5786 1 35.628801 31.929644 17.21365 +5787 2 36.045808 34.231991 18.304721 +5788 1 36.066783 31.92807 19.890693 +5789 2 30.047091 31.872972 18.511468 +5790 1 38.23536 37.943903 17.225875 +5791 2 36.119549 38.085157 15.846243 +5792 1 36.28338 36.046451 17.021393 +5793 1 36.11202 38.183852 18.648108 +5794 1 36.196383 36.094959 20.14945 +5795 1 39.857714 32.070711 20.545667 +5796 2 38.277117 32.092018 16.056024 +5797 1 30.025257 33.999826 20.265429 +5798 2 37.984137 32.053017 18.664282 +5799 1 32.002215 39.814443 17.350923 +5800 2 38.174586 35.979296 18.941495 +5801 2 38.345772 36.135739 15.897296 +5802 1 38.047733 34.092532 17.193597 +5803 2 30.130578 35.962177 15.540359 +5804 2 36.401926 38.058554 21.346524 +5805 1 30.120957 38.000412 14.522433 +5806 1 30.488998 38.181884 20.233832 +5807 1 30.027329 34.063964 17.498188 +5808 1 37.840062 29.987227 17.565361 +5809 1 32.008478 30.033144 21.485715 +5810 2 39.774533 34.462138 21.415634 +5811 1 30.338184 36.208481 21.405811 +5812 1 29.947563 30.056036 17.165794 +5813 1 39.921352 31.819743 14.64622 +5814 2 34.22915 39.981504 21.655908 +5815 1 30.183329 38.19462 25.743477 +5816 1 35.907762 33.854845 21.824692 +5817 1 38.081846 38.241792 22.993384 +5818 2 34.075816 32.199578 21.47467 +5819 1 32.064265 31.912891 22.91255 +5820 1 31.883139 33.912773 24.608383 +5821 1 31.812805 31.862315 26.174015 +5822 2 32.311833 34.450426 27.53752 +5823 1 32.200878 36.145135 23.147334 +5824 2 32.211767 38.313372 24.442593 +5825 1 32.252693 36.173296 25.56014 +5826 2 32.184178 37.824314 27.059278 +5827 2 35.878916 30.070226 21.715039 +5828 1 37.668689 30.050641 23.045191 +5829 2 31.790668 34.251576 21.855242 +5830 1 30.175916 38.136754 23.248784 +5831 1 33.79328 31.909522 24.576174 +5832 2 33.915875 32.018888 27.178426 +5833 1 33.839278 34.11599 23.063711 +5834 2 34.250078 35.934833 24.487018 +5835 1 33.990054 34.106505 25.930061 +5836 1 34.091025 36.282124 27.332172 +5837 1 39.883217 38.455893 24.705928 +5838 2 38.008034 36.021219 27.398438 +5839 1 34.624327 37.896007 23.016853 +5840 1 34.168936 37.954274 25.436951 +5841 1 39.89339 34.048173 27.027007 +5842 1 38.248268 36.455753 21.536765 +5843 1 35.611768 31.698556 23.347142 +5844 2 36.148802 34.042768 24.34925 +5845 1 35.930043 32.125519 25.878398 +5846 2 35.950538 34.005205 27.219195 +5847 1 37.955393 34.076875 25.799656 +5848 1 37.973062 38.01909 26.230315 +5849 1 36.411999 36.023781 22.980871 +5850 2 36.283519 37.906374 24.521157 +5851 1 36.105429 36.189959 25.968065 +5852 2 35.830991 38.301536 27.267321 +5853 1 30.231426 34.188738 26.125408 +5854 1 30.281973 34.136127 28.552033 +5855 2 37.785563 31.866932 24.278312 +5856 2 31.348335 30.244331 27.485493 +5857 2 37.966809 32.115632 27.589764 +5858 2 35.66017 29.988788 24.878779 +5859 1 38.277476 34.130765 22.79239 +5860 2 37.959129 36.154297 24.437008 +5861 1 33.713618 30.108282 28.642398 +5862 1 39.822964 31.905463 23.110805 +5863 1 37.492689 32.09291 21.995043 +5864 2 30.127031 36.064739 24.638111 +5865 1 35.533243 30.110728 27.243438 +5866 1 36.070605 31.93122 28.695839 +5867 2 34.291131 35.85795 21.75028 +5868 1 31.938061 32.142881 28.504169 +5869 1 33.986813 39.867909 27.012668 +5870 1 30.10822 37.992396 28.395198 +5871 1 39.800701 30.030956 24.347523 +5872 2 39.892552 29.979658 27.134291 +5873 2 32.228297 37.952841 21.875429 +5874 2 39.977135 34.107266 24.499149 +5875 1 39.846344 36.406036 26.033584 +5876 1 32.059083 40.009476 28.464272 +5877 1 35.959269 39.965152 25.93262 +5878 2 30.460566 32.139968 24.447603 +5879 2 39.881804 38.087413 21.696502 +5880 1 30.134489 36.163809 33.336193 +5881 1 37.575878 38.100411 28.849489 +5882 1 37.662104 38.133383 31.571418 +5883 1 32.362045 39.87867 34.884405 +5884 1 39.873173 36.224308 34.920349 +5885 1 31.991424 34.085923 29.999612 +5886 1 31.815171 32.168756 31.641691 +5887 2 31.782096 34.063184 33.062024 +5888 1 31.718037 31.953527 34.554814 +5889 1 39.862898 38.376226 32.906485 +5890 1 37.551931 30.038119 34.432157 +5891 1 31.780802 37.997046 30.254783 +5892 1 31.834761 35.939821 31.604936 +5893 2 32.041736 38.210181 33.326919 +5894 1 32.203699 35.869978 34.596577 +5895 1 34.008946 38.074601 28.827076 +5896 1 37.899592 29.974959 28.916731 +5897 1 38.030007 33.96835 28.91396 +5898 2 33.846774 32.085103 30.081464 +5899 1 29.952597 30.143437 34.499248 +5900 1 33.915497 32.111271 33.150301 +5901 1 31.790321 30.23064 29.991804 +5902 2 37.907438 32.157735 35.935104 +5903 2 33.84716 36.05681 30.26538 +5904 1 34.0432 34.280307 31.67674 +5905 2 34.011752 36.10558 33.143956 +5906 1 33.824017 34.085576 34.552777 +5907 1 34.194027 34.072791 28.967937 +5908 1 33.894909 38.222801 31.657741 +5909 1 33.881652 38.078172 34.899329 +5910 1 38.119296 38.056464 34.569681 +5911 1 34.291634 39.920546 33.178111 +5912 1 33.581454 29.993619 34.681796 +5913 2 36.053229 33.87704 30.318866 +5914 1 35.873901 31.88411 31.537273 +5915 1 35.89848 33.774876 32.823618 +5916 1 35.828028 32.348885 34.478807 +5917 1 35.672787 37.928294 30.518119 +5918 1 35.989671 35.945619 31.826779 +5919 2 35.97259 38.32967 33.142576 +5920 1 35.703331 35.814769 34.580449 +5921 1 33.817908 30.208146 31.599942 +5922 1 35.844503 36.12033 28.831087 +5923 1 38.261976 32.096366 30.088155 +5924 2 37.797891 31.9048 33.114668 +5925 1 39.55682 31.880323 34.531549 +5926 2 37.75043 36.193675 30.248336 +5927 1 38.393997 33.98513 31.905095 +5928 2 37.963057 36.355009 33.181745 +5929 1 37.797425 34.035854 34.376018 +5930 1 30.050396 34.271558 31.538997 +5931 1 39.815357 36.070726 31.654601 +5932 2 39.731271 30.032678 30.327233 +5933 1 39.915975 31.952921 31.714062 +5934 2 31.84562 29.966231 33.068673 +5935 1 31.85693 36.270476 28.934934 +5936 1 31.866016 39.844488 31.814385 +5937 1 30.092134 34.094244 34.755273 +5938 1 39.694807 30.040539 32.997642 +5939 1 36.196648 35.960439 42.925128 +5940 2 32.015598 37.930066 36.230869 +5941 1 37.674069 30.102473 37.130906 +5942 1 39.699003 32.118698 37.217773 +5943 2 29.963786 31.633701 39.162197 +5944 1 32.058675 39.814086 37.607409 +5945 1 35.842471 33.971675 35.989822 +5946 1 34.028551 38.060871 42.983375 +5947 1 31.588672 31.941435 37.383683 +5948 2 31.694069 33.998273 38.693202 +5949 1 31.930294 31.884957 40.381472 +5950 2 32.11349 33.999595 41.798502 +5951 1 31.876844 36.011394 37.307134 +5952 2 31.893158 37.928813 38.973436 +5953 1 31.81531 35.668229 40.479844 +5954 2 31.787646 38.142244 41.698514 +5955 1 31.925559 36.23881 42.924197 +5956 1 36.004443 37.899297 36.000218 +5957 1 38.451312 38.205323 40.038254 +5958 2 33.656378 31.907332 38.819792 +5959 1 33.99011 31.933293 41.627228 +5960 2 37.707146 36.123239 36.332034 +5961 1 33.657247 33.955416 37.665398 +5962 1 33.73943 36.151957 39.054731 +5963 1 33.605884 33.957716 40.193208 +5964 2 34.011058 36.048882 41.690411 +5965 1 38.130598 34.242802 40.052446 +5966 1 34.167865 38.117836 37.628936 +5967 1 34.142536 38.424699 40.41195 +5968 1 40.005739 32.215658 40.003237 +5969 1 39.521882 33.977557 36.015643 +5970 1 38.214368 38.282583 37.333443 +5971 1 31.918418 33.931512 36.157998 +5972 1 35.612055 32.074774 37.387219 +5973 2 35.5831 34.04957 39.047544 +5974 1 35.75246 32.088086 40.149631 +5975 2 35.615657 33.824419 41.713165 +5976 1 35.638569 36.061296 37.614952 +5977 2 36.358444 37.816896 38.884174 +5978 1 35.987046 36.034802 40.28745 +5979 1 36.122176 38.157473 41.827978 +5980 1 37.730089 30.067171 42.889333 +5981 2 39.944726 33.833791 41.642053 +5982 2 37.765477 32.166294 38.745053 +5983 2 38.099767 31.876153 41.350163 +5984 2 38.066621 36.442839 41.48951 +5985 1 37.726393 34.24931 37.606618 +5986 1 38.065514 36.286433 39.031222 +5987 1 37.664687 30.041804 39.941583 +5988 1 36.1403 39.743151 39.963443 +5989 2 34.004128 36.124387 36.139274 +5990 1 38.008343 33.918454 43.060491 +5991 1 36.098653 32.233378 42.976295 +5992 1 30.058867 38.134404 37.476791 +5993 2 35.662195 29.860797 35.905075 +5994 1 33.53205 30.001458 37.176731 +5995 1 38.387155 38.05525 43.009631 +5996 1 36.188595 39.834331 37.505629 +5997 1 39.656895 29.968268 41.372509 +5998 1 39.786156 36.00049 42.804021 +5999 2 33.855117 32.268762 36.090908 +6000 2 31.856527 30.044242 36.001804 diff --git a/examples/cauchystat/NiAl_slow_stretch_CS/lammps.in b/examples/cauchystat/NiAl_slow_stretch_CS/lammps.in new file mode 100644 index 0000000000..e90bd9f3a9 --- /dev/null +++ b/examples/cauchystat/NiAl_slow_stretch_CS/lammps.in @@ -0,0 +1,45 @@ +units metal +atom_style atomic +atom_modify map array + +processors 1 1 1 + +# Box and atom positions: +boundary p p p +read_data input.dat + +# Atomic mass: +mass 1 58.69 +mass 2 26.98154 + +# Potential, Al fcc crystal +pair_style eam/alloy +pair_coeff * * ../Mishin-Ni-Al-2009.eam.alloy Ni Al + +thermo 100 +thermo_style custom step temp pxx pyy pzz lx ly lz +compute cna all cna/atom 2.8 + +velocity all create 1000.0 4928459 rot yes dist gaussian + +fix 1 all npt temp 500.0 500.0 1.0 x 0.0 0.0 0.1 y 0.0 0.0 0.1 z 0.0 0.0 0.1 couple none cauchystat 0.001 no + +dump 1 all cfg 5000 test*.cfg mass type xs ys zs type c_cna + +timestep 0.002 + +variable l equal lz +variable p equal pzz +variable t equal temp + +fix avg all ave/time 1 1000 1000 v_t v_l v_p file avg.txt + +velocity all create 2400 4928459 rot yes dist gaussian + +run 10000 + +unfix 1 + +fix 1 all npt temp 500.0 500.0 1.0 x 0.0 0.0 0.1 y 0.0 0.0 0.1 z 0.0 -14000.0 0.1 couple none cauchystat 0.001 yes + +run 350000 diff --git a/examples/cauchystat/NiAl_slow_stretch_PR/input.dat b/examples/cauchystat/NiAl_slow_stretch_PR/input.dat new file mode 100644 index 0000000000..3b99f3ea8f --- /dev/null +++ b/examples/cauchystat/NiAl_slow_stretch_PR/input.dat @@ -0,0 +1,6009 @@ +Position data for MD simulation + +6000 atoms +2 atom types +0.0000 39.972658977840510 xlo xhi +0.0000 39.970082402467646 ylo yhi +0.0000 43.077168594479417 zlo zhi +Atoms + +1 1 2.265603 1.699233 2.96682 +2 2 2.147625 3.958175 4.336466 +3 1 1.997414 2.08615 5.681268 +4 2 6.222234 0.12344 4.55833 +5 1 4.247865 9.8684 7.188432 +6 2 2.226404 4.008191 1.332846 +7 1 2.558125 5.881235 2.799624 +8 2 2.112892 8.008518 4.084836 +9 1 2.366112 6.194696 5.83623 +10 2 0.308528 9.773154 7.249786 +11 1 1.861699 8.008727 1.634831 +12 2 0.245314 5.864464 4.508327 +13 1 8.139953 -0.02424 5.747139 +14 1 0.178338 3.676069 2.91793 +15 2 0.021903 9.933735 1.645872 +16 1 4.094944 3.990727 2.989711 +17 2 4.25173 6.125247 4.299378 +18 1 4.004975 4.261809 5.650881 +19 2 4.233414 9.883798 4.412874 +20 2 4.158657 5.985987 1.452914 +21 1 3.943003 7.917155 2.809851 +22 1 4.013002 8.032118 5.709128 +23 1 3.913817 0.208102 0.200173 +24 2 4.11186 2.115952 4.39711 +25 1 4.091794 8.080277 0.383691 +26 1 8.239262 4.128528 0.14417 +27 1 4.164942 2.294329 1.435205 +28 1 6.018476 2.048784 2.978318 +29 1 6.189263 4.123374 4.429365 +30 1 5.731913 2.039386 5.760723 +31 2 8.125123 2.396376 4.334063 +32 2 5.956145 3.961461 1.710606 +33 1 6.097732 6.223054 3.105619 +34 2 6.260701 8.269814 4.403081 +35 1 6.135592 6.191014 6.014208 +36 2 6.118481 0.280536 1.660297 +37 2 5.95371 8.134065 1.459117 +38 1 8.112 7.978937 6.025785 +39 1 8.230735 0.317331 0.287501 +40 1 7.984577 0.451106 2.876758 +41 1 8.121358 4.469963 3.000969 +42 2 8.0024 6.398776 4.506808 +43 1 8.265498 4.145515 5.950951 +44 1 8.093687 2.336039 1.599762 +45 2 7.786786 6.082031 1.369435 +46 1 8.051625 8.388788 2.947011 +47 2 1.887169 0.10205 1.232231 +48 1 3.814096 0.184819 2.93152 +49 2 5.999738 4.024912 6.895817 +50 1 0.20906 5.67262 1.62315 +51 1 2.22916 6.007717 0.143509 +52 1 9.864584 8.16224 1.516273 +53 1 0.029687 7.997328 3.090548 +54 1 0.158584 7.813035 5.663186 +55 1 6.149844 9.939956 0.040852 +56 1 1.871208 1.766851 8.960428 +57 2 2.233107 3.807827 10.095989 +58 1 1.960237 1.933156 11.733738 +59 1 2.028536 4.090031 13.399625 +60 2 0.096818 1.982978 13.367683 +61 1 1.962538 5.967991 8.575587 +62 2 1.779869 8.006286 9.997749 +63 1 2.261369 6.075808 11.262585 +64 1 1.878689 7.795749 12.973992 +65 1 8.066595 6.091936 7.32151 +66 2 6.004471 8.10958 7.337536 +67 2 3.807826 9.773306 13.107995 +68 2 3.628292 2.338356 7.627483 +69 1 4.142245 4.127148 8.640624 +70 2 4.430475 5.841591 10.077295 +71 1 3.968136 4.281892 11.552649 +72 2 3.926926 6.059939 13.034315 +73 1 4.163584 8.009554 8.875445 +74 1 3.841536 8.095992 11.564038 +75 1 1.972543 4.098752 7.26509 +76 1 9.833961 8.179066 10.053046 +77 1 3.959427 0.070701 8.628349 +78 1 4.000206 1.99734 10.467815 +79 1 0.175393 5.813256 10.208259 +80 2 3.991668 2.115114 12.987731 +81 2 8.056411 2.098025 12.865242 +82 1 5.64748 2.156225 8.497216 +83 2 6.159432 4.014865 10.196613 +84 1 6.214032 2.165249 11.651601 +85 1 5.856347 3.961477 13.023239 +86 1 7.948437 0.352004 11.304002 +87 2 0.129981 2.04383 7.39824 +88 1 6.181909 5.856377 8.431434 +89 1 5.991539 7.847191 10.091845 +90 1 5.975418 5.816241 11.895283 +91 1 5.86549 8.043369 13.028812 +92 2 4.166236 6.085137 7.231975 +93 1 0.439458 3.829864 11.550798 +94 2 0.21596 5.973334 12.667734 +95 1 10.017517 5.823156 11.545694 +96 1 8.076092 4.274718 8.540188 +97 2 7.924969 6.011881 10.326107 +98 1 8.12022 3.959556 11.608595 +99 1 8.110671 6.08702 13.353502 +100 1 8.135035 2.224763 9.76071 +101 1 8.056404 8.04948 8.608732 +102 1 7.867682 7.986347 11.444105 +103 1 0.057722 3.824193 8.62711 +104 1 9.981584 4.247366 7.362993 +105 2 4.013801 9.873296 9.982524 +106 1 2.329565 8.116478 7.435377 +107 2 5.950495 0.34488 9.79838 +108 1 4.334027 0.076447 11.746114 +109 2 7.945804 9.995075 13.009688 +110 1 2.027284 10.048274 11.752786 +111 2 7.985809 2.177851 7.348854 +112 2 0.227187 9.715111 13.080145 +113 1 4.369771 0.043973 14.298992 +114 1 9.913252 6.303629 8.785055 +115 1 7.984689 3.996322 14.285297 +116 1 6.286022 9.901661 11.434457 +117 2 9.978329 0.129998 10.093528 +118 2 9.898021 7.994926 13.146433 +119 1 2.438629 0.033347 18.603552 +120 2 2.19485 3.927092 15.921048 +121 1 2.266036 2.0106 17.298124 +122 2 2.190625 4.002775 18.808528 +123 1 2.529808 1.858131 19.802924 +124 1 2.121536 8.100548 15.903723 +125 1 1.999174 5.945764 17.409821 +126 2 2.399752 8.317077 18.513998 +127 1 2.085018 6.322971 20.123548 +128 1 0.132331 7.834943 14.417244 +129 2 0.191888 2.055829 18.456008 +130 1 8.035826 8.278124 14.487514 +131 2 3.964165 5.965398 16.034244 +132 1 3.977251 4.106829 17.287135 +133 1 4.083409 6.186923 18.749777 +134 1 4.118697 4.16167 19.924445 +135 2 0.168486 10.031098 15.738364 +136 1 9.834776 5.750065 20.057158 +137 1 4.513739 7.925063 17.284367 +138 1 0.224638 6.311966 18.562 +139 1 4.05173 8.065927 20.327367 +140 1 4.020498 7.877514 14.44079 +141 1 4.143142 1.813412 15.801004 +142 1 2.214548 1.829361 14.565296 +143 2 4.407757 2.318175 18.721975 +144 2 6.016403 3.935276 15.745347 +145 1 6.343375 1.849436 17.205365 +146 2 6.615021 3.988745 18.735217 +147 1 6.455591 1.950789 20.137809 +148 1 6.179932 9.794709 17.21643 +149 2 6.237707 7.849925 15.743301 +150 1 6.151976 5.985244 17.227932 +151 2 6.178229 7.773511 18.829625 +152 1 6.147011 5.845856 20.064817 +153 2 4.124664 9.743815 15.83873 +154 1 8.065185 1.771116 18.726928 +155 1 6.149514 1.938847 14.518073 +156 2 8.136444 6.024316 15.560218 +157 1 8.139342 3.949043 16.901849 +158 1 8.143554 6.219717 18.549219 +159 1 8.181775 3.5232 20.518875 +160 1 1.876074 6.12577 14.691379 +161 2 9.729818 3.920007 18.490075 +162 1 8.23825 8.027751 17.068995 +163 1 4.103417 9.893021 18.750211 +164 1 8.095744 7.73466 20.44646 +165 2 8.348453 1.630886 15.803105 +166 1 0.114526 2.216943 15.877394 +167 2 4.178332 6.016772 21.363439 +168 1 1.899673 9.855866 20.182773 +169 1 0.06894 8.212942 17.306197 +170 1 5.88851 5.844373 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1 37.935879 32.177401 4.195289 +5673 1 38.101493 38.10187 5.953049 +5674 2 37.852909 32.388628 1.664291 +5675 1 37.942171 34.0458 3.006996 +5676 2 38.2641 36.15208 4.530503 +5677 1 38.039433 34.206108 5.79566 +5678 1 33.979517 30.322401 2.668635 +5679 2 38.266202 35.993947 1.484331 +5680 1 38.067048 38.040012 2.752414 +5681 1 37.733806 30.096455 5.970187 +5682 1 39.682213 32.091472 5.993971 +5683 1 39.817487 31.930363 0.000367 +5684 1 36.043395 39.59783 5.676369 +5685 1 31.869558 32.098607 0.138261 +5686 1 39.734652 32.347843 3.042732 +5687 2 40.028718 38.187031 4.420077 +5688 1 35.900797 34.287592 6.911917 +5689 1 34.035098 34.219002 0.088382 +5690 1 35.958161 30.177564 1.36017 +5691 2 34.104037 39.871769 1.666144 +5692 2 31.713648 30.030149 13.126076 +5693 2 38.102561 35.967156 7.519894 +5694 2 31.857312 30.233676 7.601269 +5695 1 34.289545 38.267283 14.401123 +5696 2 35.86683 30.19377 7.315341 +5697 1 30.215661 34.162037 8.437432 +5698 2 32.177106 33.712521 7.258256 +5699 2 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39.920546 33.178111 +5912 1 33.581454 29.993619 34.681796 +5913 2 36.053229 33.87704 30.318866 +5914 1 35.873901 31.88411 31.537273 +5915 1 35.89848 33.774876 32.823618 +5916 1 35.828028 32.348885 34.478807 +5917 1 35.672787 37.928294 30.518119 +5918 1 35.989671 35.945619 31.826779 +5919 2 35.97259 38.32967 33.142576 +5920 1 35.703331 35.814769 34.580449 +5921 1 33.817908 30.208146 31.599942 +5922 1 35.844503 36.12033 28.831087 +5923 1 38.261976 32.096366 30.088155 +5924 2 37.797891 31.9048 33.114668 +5925 1 39.55682 31.880323 34.531549 +5926 2 37.75043 36.193675 30.248336 +5927 1 38.393997 33.98513 31.905095 +5928 2 37.963057 36.355009 33.181745 +5929 1 37.797425 34.035854 34.376018 +5930 1 30.050396 34.271558 31.538997 +5931 1 39.815357 36.070726 31.654601 +5932 2 39.731271 30.032678 30.327233 +5933 1 39.915975 31.952921 31.714062 +5934 2 31.84562 29.966231 33.068673 +5935 1 31.85693 36.270476 28.934934 +5936 1 31.866016 39.844488 31.814385 +5937 1 30.092134 34.094244 34.755273 +5938 1 39.694807 30.040539 32.997642 +5939 1 36.196648 35.960439 42.925128 +5940 2 32.015598 37.930066 36.230869 +5941 1 37.674069 30.102473 37.130906 +5942 1 39.699003 32.118698 37.217773 +5943 2 29.963786 31.633701 39.162197 +5944 1 32.058675 39.814086 37.607409 +5945 1 35.842471 33.971675 35.989822 +5946 1 34.028551 38.060871 42.983375 +5947 1 31.588672 31.941435 37.383683 +5948 2 31.694069 33.998273 38.693202 +5949 1 31.930294 31.884957 40.381472 +5950 2 32.11349 33.999595 41.798502 +5951 1 31.876844 36.011394 37.307134 +5952 2 31.893158 37.928813 38.973436 +5953 1 31.81531 35.668229 40.479844 +5954 2 31.787646 38.142244 41.698514 +5955 1 31.925559 36.23881 42.924197 +5956 1 36.004443 37.899297 36.000218 +5957 1 38.451312 38.205323 40.038254 +5958 2 33.656378 31.907332 38.819792 +5959 1 33.99011 31.933293 41.627228 +5960 2 37.707146 36.123239 36.332034 +5961 1 33.657247 33.955416 37.665398 +5962 1 33.73943 36.151957 39.054731 +5963 1 33.605884 33.957716 40.193208 +5964 2 34.011058 36.048882 41.690411 +5965 1 38.130598 34.242802 40.052446 +5966 1 34.167865 38.117836 37.628936 +5967 1 34.142536 38.424699 40.41195 +5968 1 40.005739 32.215658 40.003237 +5969 1 39.521882 33.977557 36.015643 +5970 1 38.214368 38.282583 37.333443 +5971 1 31.918418 33.931512 36.157998 +5972 1 35.612055 32.074774 37.387219 +5973 2 35.5831 34.04957 39.047544 +5974 1 35.75246 32.088086 40.149631 +5975 2 35.615657 33.824419 41.713165 +5976 1 35.638569 36.061296 37.614952 +5977 2 36.358444 37.816896 38.884174 +5978 1 35.987046 36.034802 40.28745 +5979 1 36.122176 38.157473 41.827978 +5980 1 37.730089 30.067171 42.889333 +5981 2 39.944726 33.833791 41.642053 +5982 2 37.765477 32.166294 38.745053 +5983 2 38.099767 31.876153 41.350163 +5984 2 38.066621 36.442839 41.48951 +5985 1 37.726393 34.24931 37.606618 +5986 1 38.065514 36.286433 39.031222 +5987 1 37.664687 30.041804 39.941583 +5988 1 36.1403 39.743151 39.963443 +5989 2 34.004128 36.124387 36.139274 +5990 1 38.008343 33.918454 43.060491 +5991 1 36.098653 32.233378 42.976295 +5992 1 30.058867 38.134404 37.476791 +5993 2 35.662195 29.860797 35.905075 +5994 1 33.53205 30.001458 37.176731 +5995 1 38.387155 38.05525 43.009631 +5996 1 36.188595 39.834331 37.505629 +5997 1 39.656895 29.968268 41.372509 +5998 1 39.786156 36.00049 42.804021 +5999 2 33.855117 32.268762 36.090908 +6000 2 31.856527 30.044242 36.001804 diff --git a/examples/cauchystat/NiAl_slow_stretch_PR/lammps.in b/examples/cauchystat/NiAl_slow_stretch_PR/lammps.in new file mode 100644 index 0000000000..93840793b8 --- /dev/null +++ b/examples/cauchystat/NiAl_slow_stretch_PR/lammps.in @@ -0,0 +1,45 @@ +units metal +atom_style atomic +atom_modify map array + +processors 1 1 1 + +# Box and atom positions: +boundary p p p +read_data input.dat + +# Atomic mass: +mass 1 58.69 +mass 2 26.98154 + +# Potential, Al fcc crystal +pair_style eam/alloy +pair_coeff * * ../Mishin-Ni-Al-2009.eam.alloy Ni Al + +thermo 100 +thermo_style custom step temp pxx pyy pzz lx ly lz +compute cna all cna/atom 2.8 + +velocity all create 1000.0 4928459 rot yes dist gaussian + +fix 1 all npt temp 500.0 500.0 1.0 x 0.0 0.0 0.1 y 0.0 0.0 0.1 z 0.0 0.0 0.1 couple none + +dump 1 all cfg 5000 test*.cfg mass type xs ys zs type c_cna + +timestep 0.002 + +variable l equal lz +variable p equal pzz +variable t equal temp + +fix avg all ave/time 1 1000 1000 v_t v_l v_p file avg.txt + +velocity all create 2400 4928459 rot yes dist gaussian + +run 10000 + +unfix 1 + +fix 1 all npt temp 500.0 500.0 1.0 x 0.0 0.0 0.1 y 0.0 0.0 0.1 z 0.0 -14000.0 0.1 couple none + +run 350000 diff --git a/examples/cauchystat/NiAl_stretch/input.dat b/examples/cauchystat/NiAl_stretch/input.dat new file mode 100644 index 0000000000..3b99f3ea8f --- /dev/null +++ b/examples/cauchystat/NiAl_stretch/input.dat @@ -0,0 +1,6009 @@ +Position data for MD simulation + +6000 atoms +2 atom types +0.0000 39.972658977840510 xlo xhi +0.0000 39.970082402467646 ylo yhi +0.0000 43.077168594479417 zlo zhi +Atoms + +1 1 2.265603 1.699233 2.96682 +2 2 2.147625 3.958175 4.336466 +3 1 1.997414 2.08615 5.681268 +4 2 6.222234 0.12344 4.55833 +5 1 4.247865 9.8684 7.188432 +6 2 2.226404 4.008191 1.332846 +7 1 2.558125 5.881235 2.799624 +8 2 2.112892 8.008518 4.084836 +9 1 2.366112 6.194696 5.83623 +10 2 0.308528 9.773154 7.249786 +11 1 1.861699 8.008727 1.634831 +12 2 0.245314 5.864464 4.508327 +13 1 8.139953 -0.02424 5.747139 +14 1 0.178338 3.676069 2.91793 +15 2 0.021903 9.933735 1.645872 +16 1 4.094944 3.990727 2.989711 +17 2 4.25173 6.125247 4.299378 +18 1 4.004975 4.261809 5.650881 +19 2 4.233414 9.883798 4.412874 +20 2 4.158657 5.985987 1.452914 +21 1 3.943003 7.917155 2.809851 +22 1 4.013002 8.032118 5.709128 +23 1 3.913817 0.208102 0.200173 +24 2 4.11186 2.115952 4.39711 +25 1 4.091794 8.080277 0.383691 +26 1 8.239262 4.128528 0.14417 +27 1 4.164942 2.294329 1.435205 +28 1 6.018476 2.048784 2.978318 +29 1 6.189263 4.123374 4.429365 +30 1 5.731913 2.039386 5.760723 +31 2 8.125123 2.396376 4.334063 +32 2 5.956145 3.961461 1.710606 +33 1 6.097732 6.223054 3.105619 +34 2 6.260701 8.269814 4.403081 +35 1 6.135592 6.191014 6.014208 +36 2 6.118481 0.280536 1.660297 +37 2 5.95371 8.134065 1.459117 +38 1 8.112 7.978937 6.025785 +39 1 8.230735 0.317331 0.287501 +40 1 7.984577 0.451106 2.876758 +41 1 8.121358 4.469963 3.000969 +42 2 8.0024 6.398776 4.506808 +43 1 8.265498 4.145515 5.950951 +44 1 8.093687 2.336039 1.599762 +45 2 7.786786 6.082031 1.369435 +46 1 8.051625 8.388788 2.947011 +47 2 1.887169 0.10205 1.232231 +48 1 3.814096 0.184819 2.93152 +49 2 5.999738 4.024912 6.895817 +50 1 0.20906 5.67262 1.62315 +51 1 2.22916 6.007717 0.143509 +52 1 9.864584 8.16224 1.516273 +53 1 0.029687 7.997328 3.090548 +54 1 0.158584 7.813035 5.663186 +55 1 6.149844 9.939956 0.040852 +56 1 1.871208 1.766851 8.960428 +57 2 2.233107 3.807827 10.095989 +58 1 1.960237 1.933156 11.733738 +59 1 2.028536 4.090031 13.399625 +60 2 0.096818 1.982978 13.367683 +61 1 1.962538 5.967991 8.575587 +62 2 1.779869 8.006286 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31.872832 37.740296 10.246254 +5707 1 32.382757 36.08172 11.390228 +5708 1 31.907287 38.043268 12.759712 +5709 1 33.814113 30.280416 11.361764 +5710 1 30.217972 36.108976 12.75806 +5711 2 33.902634 32.114854 10.131038 +5712 1 33.57231 32.104408 13.09734 +5713 1 31.808268 30.066503 10.372268 +5714 1 34.074533 34.09759 8.82773 +5715 2 34.112978 35.879639 10.008535 +5716 1 33.847258 34.132738 11.781858 +5717 2 33.938795 36.222314 13.025522 +5718 2 29.978741 32.187816 10.235973 +5719 1 34.055911 38.08124 8.660649 +5720 1 33.602601 34.200907 14.256884 +5721 1 34.074479 38.033056 11.548004 +5722 2 36.270647 38.06342 7.227717 +5723 1 35.834976 32.087215 8.752976 +5724 2 36.060859 33.636235 10.421377 +5725 1 35.993855 31.835332 12.022895 +5726 2 35.800428 33.936835 13.252217 +5727 1 36.115212 35.929045 8.653718 +5728 2 36.22813 38.12211 10.18663 +5729 1 36.031176 36.067395 11.711353 +5730 2 36.290793 38.28804 13.110371 +5731 1 38.314803 39.87771 13.628157 +5732 2 37.813718 31.963763 10.266333 +5733 2 38.345306 31.61479 12.746628 +5734 1 37.993817 33.8253 8.828538 +5735 2 37.963385 36.024574 10.310583 +5736 1 37.917131 33.840219 11.529013 +5737 1 38.204273 36.194533 12.982689 +5738 1 38.223785 37.96125 8.694521 +5739 1 38.251957 38.103445 11.574783 +5740 1 32.162162 35.830151 14.368089 +5741 1 38.188088 39.835851 10.200529 +5742 2 37.943506 31.862097 7.486993 +5743 1 34.019779 32.099062 7.382655 +5744 1 37.835648 33.808569 14.272091 +5745 2 30.154664 36.008494 10.278616 +5746 2 34.005569 29.909902 14.221934 +5747 2 39.942399 30.201297 7.221972 +5748 1 31.669489 32.129787 14.202133 +5749 1 33.8553 30.102976 8.785283 +5750 1 36.285019 39.993992 8.473052 +5751 2 34.332311 39.811654 10.053333 +5752 1 32.287985 39.934755 8.544521 +5753 1 32.117424 39.894109 11.328559 +5754 1 34.070494 39.946648 12.675838 +5755 1 33.523905 30.237815 17.092452 +5756 1 37.796875 30.195733 20.074531 +5757 1 36.27689 36.076917 14.383428 +5758 1 31.912415 30.074316 18.962029 +5759 1 31.72877 30.195629 15.548548 +5760 1 39.683801 34.084414 18.996274 +5761 1 31.823255 34.23579 15.916954 +5762 1 32.081111 32.17144 17.423655 +5763 2 32.272671 34.141341 18.923237 +5764 1 31.890319 32.258592 20.174682 +5765 1 32.292252 37.789848 15.657298 +5766 1 31.865994 35.945048 17.430984 +5767 2 32.390605 38.101438 18.756338 +5768 1 32.536255 36.292415 20.33365 +5769 1 30.255802 37.826036 17.398086 +5770 2 30.361913 39.693462 15.767213 +5771 1 33.658364 32.195407 15.713634 +5772 1 37.521125 34.00621 20.179734 +5773 2 34.170474 31.959646 18.774747 +5774 2 30.146126 36.07111 19.193288 +5775 2 34.236512 36.009488 15.705407 +5776 1 33.893052 34.259763 17.152928 +5777 1 34.299465 36.26334 18.583767 +5778 1 34.414431 34.040341 19.801645 +5779 1 38.268782 38.067343 19.882736 +5780 1 38.192119 30.067346 14.65738 +5781 1 34.182659 38.172175 17.379208 +5782 1 34.285582 38.312236 20.114249 +5783 1 35.930101 31.821554 14.523145 +5784 1 38.166996 38.004859 14.725716 +5785 1 35.925271 33.697258 15.741088 +5786 1 35.628801 31.929644 17.21365 +5787 2 36.045808 34.231991 18.304721 +5788 1 36.066783 31.92807 19.890693 +5789 2 30.047091 31.872972 18.511468 +5790 1 38.23536 37.943903 17.225875 +5791 2 36.119549 38.085157 15.846243 +5792 1 36.28338 36.046451 17.021393 +5793 1 36.11202 38.183852 18.648108 +5794 1 36.196383 36.094959 20.14945 +5795 1 39.857714 32.070711 20.545667 +5796 2 38.277117 32.092018 16.056024 +5797 1 30.025257 33.999826 20.265429 +5798 2 37.984137 32.053017 18.664282 +5799 1 32.002215 39.814443 17.350923 +5800 2 38.174586 35.979296 18.941495 +5801 2 38.345772 36.135739 15.897296 +5802 1 38.047733 34.092532 17.193597 +5803 2 30.130578 35.962177 15.540359 +5804 2 36.401926 38.058554 21.346524 +5805 1 30.120957 38.000412 14.522433 +5806 1 30.488998 38.181884 20.233832 +5807 1 30.027329 34.063964 17.498188 +5808 1 37.840062 29.987227 17.565361 +5809 1 32.008478 30.033144 21.485715 +5810 2 39.774533 34.462138 21.415634 +5811 1 30.338184 36.208481 21.405811 +5812 1 29.947563 30.056036 17.165794 +5813 1 39.921352 31.819743 14.64622 +5814 2 34.22915 39.981504 21.655908 +5815 1 30.183329 38.19462 25.743477 +5816 1 35.907762 33.854845 21.824692 +5817 1 38.081846 38.241792 22.993384 +5818 2 34.075816 32.199578 21.47467 +5819 1 32.064265 31.912891 22.91255 +5820 1 31.883139 33.912773 24.608383 +5821 1 31.812805 31.862315 26.174015 +5822 2 32.311833 34.450426 27.53752 +5823 1 32.200878 36.145135 23.147334 +5824 2 32.211767 38.313372 24.442593 +5825 1 32.252693 36.173296 25.56014 +5826 2 32.184178 37.824314 27.059278 +5827 2 35.878916 30.070226 21.715039 +5828 1 37.668689 30.050641 23.045191 +5829 2 31.790668 34.251576 21.855242 +5830 1 30.175916 38.136754 23.248784 +5831 1 33.79328 31.909522 24.576174 +5832 2 33.915875 32.018888 27.178426 +5833 1 33.839278 34.11599 23.063711 +5834 2 34.250078 35.934833 24.487018 +5835 1 33.990054 34.106505 25.930061 +5836 1 34.091025 36.282124 27.332172 +5837 1 39.883217 38.455893 24.705928 +5838 2 38.008034 36.021219 27.398438 +5839 1 34.624327 37.896007 23.016853 +5840 1 34.168936 37.954274 25.436951 +5841 1 39.89339 34.048173 27.027007 +5842 1 38.248268 36.455753 21.536765 +5843 1 35.611768 31.698556 23.347142 +5844 2 36.148802 34.042768 24.34925 +5845 1 35.930043 32.125519 25.878398 +5846 2 35.950538 34.005205 27.219195 +5847 1 37.955393 34.076875 25.799656 +5848 1 37.973062 38.01909 26.230315 +5849 1 36.411999 36.023781 22.980871 +5850 2 36.283519 37.906374 24.521157 +5851 1 36.105429 36.189959 25.968065 +5852 2 35.830991 38.301536 27.267321 +5853 1 30.231426 34.188738 26.125408 +5854 1 30.281973 34.136127 28.552033 +5855 2 37.785563 31.866932 24.278312 +5856 2 31.348335 30.244331 27.485493 +5857 2 37.966809 32.115632 27.589764 +5858 2 35.66017 29.988788 24.878779 +5859 1 38.277476 34.130765 22.79239 +5860 2 37.959129 36.154297 24.437008 +5861 1 33.713618 30.108282 28.642398 +5862 1 39.822964 31.905463 23.110805 +5863 1 37.492689 32.09291 21.995043 +5864 2 30.127031 36.064739 24.638111 +5865 1 35.533243 30.110728 27.243438 +5866 1 36.070605 31.93122 28.695839 +5867 2 34.291131 35.85795 21.75028 +5868 1 31.938061 32.142881 28.504169 +5869 1 33.986813 39.867909 27.012668 +5870 1 30.10822 37.992396 28.395198 +5871 1 39.800701 30.030956 24.347523 +5872 2 39.892552 29.979658 27.134291 +5873 2 32.228297 37.952841 21.875429 +5874 2 39.977135 34.107266 24.499149 +5875 1 39.846344 36.406036 26.033584 +5876 1 32.059083 40.009476 28.464272 +5877 1 35.959269 39.965152 25.93262 +5878 2 30.460566 32.139968 24.447603 +5879 2 39.881804 38.087413 21.696502 +5880 1 30.134489 36.163809 33.336193 +5881 1 37.575878 38.100411 28.849489 +5882 1 37.662104 38.133383 31.571418 +5883 1 32.362045 39.87867 34.884405 +5884 1 39.873173 36.224308 34.920349 +5885 1 31.991424 34.085923 29.999612 +5886 1 31.815171 32.168756 31.641691 +5887 2 31.782096 34.063184 33.062024 +5888 1 31.718037 31.953527 34.554814 +5889 1 39.862898 38.376226 32.906485 +5890 1 37.551931 30.038119 34.432157 +5891 1 31.780802 37.997046 30.254783 +5892 1 31.834761 35.939821 31.604936 +5893 2 32.041736 38.210181 33.326919 +5894 1 32.203699 35.869978 34.596577 +5895 1 34.008946 38.074601 28.827076 +5896 1 37.899592 29.974959 28.916731 +5897 1 38.030007 33.96835 28.91396 +5898 2 33.846774 32.085103 30.081464 +5899 1 29.952597 30.143437 34.499248 +5900 1 33.915497 32.111271 33.150301 +5901 1 31.790321 30.23064 29.991804 +5902 2 37.907438 32.157735 35.935104 +5903 2 33.84716 36.05681 30.26538 +5904 1 34.0432 34.280307 31.67674 +5905 2 34.011752 36.10558 33.143956 +5906 1 33.824017 34.085576 34.552777 +5907 1 34.194027 34.072791 28.967937 +5908 1 33.894909 38.222801 31.657741 +5909 1 33.881652 38.078172 34.899329 +5910 1 38.119296 38.056464 34.569681 +5911 1 34.291634 39.920546 33.178111 +5912 1 33.581454 29.993619 34.681796 +5913 2 36.053229 33.87704 30.318866 +5914 1 35.873901 31.88411 31.537273 +5915 1 35.89848 33.774876 32.823618 +5916 1 35.828028 32.348885 34.478807 +5917 1 35.672787 37.928294 30.518119 +5918 1 35.989671 35.945619 31.826779 +5919 2 35.97259 38.32967 33.142576 +5920 1 35.703331 35.814769 34.580449 +5921 1 33.817908 30.208146 31.599942 +5922 1 35.844503 36.12033 28.831087 +5923 1 38.261976 32.096366 30.088155 +5924 2 37.797891 31.9048 33.114668 +5925 1 39.55682 31.880323 34.531549 +5926 2 37.75043 36.193675 30.248336 +5927 1 38.393997 33.98513 31.905095 +5928 2 37.963057 36.355009 33.181745 +5929 1 37.797425 34.035854 34.376018 +5930 1 30.050396 34.271558 31.538997 +5931 1 39.815357 36.070726 31.654601 +5932 2 39.731271 30.032678 30.327233 +5933 1 39.915975 31.952921 31.714062 +5934 2 31.84562 29.966231 33.068673 +5935 1 31.85693 36.270476 28.934934 +5936 1 31.866016 39.844488 31.814385 +5937 1 30.092134 34.094244 34.755273 +5938 1 39.694807 30.040539 32.997642 +5939 1 36.196648 35.960439 42.925128 +5940 2 32.015598 37.930066 36.230869 +5941 1 37.674069 30.102473 37.130906 +5942 1 39.699003 32.118698 37.217773 +5943 2 29.963786 31.633701 39.162197 +5944 1 32.058675 39.814086 37.607409 +5945 1 35.842471 33.971675 35.989822 +5946 1 34.028551 38.060871 42.983375 +5947 1 31.588672 31.941435 37.383683 +5948 2 31.694069 33.998273 38.693202 +5949 1 31.930294 31.884957 40.381472 +5950 2 32.11349 33.999595 41.798502 +5951 1 31.876844 36.011394 37.307134 +5952 2 31.893158 37.928813 38.973436 +5953 1 31.81531 35.668229 40.479844 +5954 2 31.787646 38.142244 41.698514 +5955 1 31.925559 36.23881 42.924197 +5956 1 36.004443 37.899297 36.000218 +5957 1 38.451312 38.205323 40.038254 +5958 2 33.656378 31.907332 38.819792 +5959 1 33.99011 31.933293 41.627228 +5960 2 37.707146 36.123239 36.332034 +5961 1 33.657247 33.955416 37.665398 +5962 1 33.73943 36.151957 39.054731 +5963 1 33.605884 33.957716 40.193208 +5964 2 34.011058 36.048882 41.690411 +5965 1 38.130598 34.242802 40.052446 +5966 1 34.167865 38.117836 37.628936 +5967 1 34.142536 38.424699 40.41195 +5968 1 40.005739 32.215658 40.003237 +5969 1 39.521882 33.977557 36.015643 +5970 1 38.214368 38.282583 37.333443 +5971 1 31.918418 33.931512 36.157998 +5972 1 35.612055 32.074774 37.387219 +5973 2 35.5831 34.04957 39.047544 +5974 1 35.75246 32.088086 40.149631 +5975 2 35.615657 33.824419 41.713165 +5976 1 35.638569 36.061296 37.614952 +5977 2 36.358444 37.816896 38.884174 +5978 1 35.987046 36.034802 40.28745 +5979 1 36.122176 38.157473 41.827978 +5980 1 37.730089 30.067171 42.889333 +5981 2 39.944726 33.833791 41.642053 +5982 2 37.765477 32.166294 38.745053 +5983 2 38.099767 31.876153 41.350163 +5984 2 38.066621 36.442839 41.48951 +5985 1 37.726393 34.24931 37.606618 +5986 1 38.065514 36.286433 39.031222 +5987 1 37.664687 30.041804 39.941583 +5988 1 36.1403 39.743151 39.963443 +5989 2 34.004128 36.124387 36.139274 +5990 1 38.008343 33.918454 43.060491 +5991 1 36.098653 32.233378 42.976295 +5992 1 30.058867 38.134404 37.476791 +5993 2 35.662195 29.860797 35.905075 +5994 1 33.53205 30.001458 37.176731 +5995 1 38.387155 38.05525 43.009631 +5996 1 36.188595 39.834331 37.505629 +5997 1 39.656895 29.968268 41.372509 +5998 1 39.786156 36.00049 42.804021 +5999 2 33.855117 32.268762 36.090908 +6000 2 31.856527 30.044242 36.001804 diff --git a/examples/cauchystat/NiAl_stretch/lammps.in b/examples/cauchystat/NiAl_stretch/lammps.in new file mode 100644 index 0000000000..77ba62e783 --- /dev/null +++ b/examples/cauchystat/NiAl_stretch/lammps.in @@ -0,0 +1,48 @@ +units metal +atom_style atomic +atom_modify map array + +processors 1 1 1 + +# Box and atom positions: +boundary p p p +read_data input.dat + +# Atomic mass: +mass 1 58.69 +mass 2 26.98154 + +# Potential, Al fcc crystal +pair_style eam/alloy +pair_coeff * * ../Mishin-Ni-Al-2009.eam.alloy Ni Al + + +thermo 100 +thermo_style custom step temp pxx pyy pzz lx ly lz +compute cna all cna/atom 2.8 + +velocity all create 2400.0 4928459 rot yes dist gaussian + +fix 1 all npt temp 600.0 600.0 1.0 x 0.0 0.0 0.1 y 0.0 0.0 0.1 z 0.0 0.0 0.1 couple none cauchystat 0.001 no + +dump 1 all cfg 1000 test*.cfg mass type xs ys zs type c_cna + +timestep 0.002 + +variable l equal lz +variable p equal pzz +variable t equal temp + +fix avg all ave/time 1 1000 1000 v_t v_l v_p file avg.txt + +#restart 1000 restart.*.test + +velocity all create 2400 4928459 rot yes dist gaussian + +run 10000 + +unfix 1 + +fix 1 all npt temp 600.0 600.0 1.0 x 0.0 0.0 0.1 y 0.0 0.0 0.1 z 0.0 -6000.0 0.1 couple none cauchystat 0.001 yes + +run 100000 diff --git a/examples/cauchystat/README b/examples/cauchystat/README new file mode 100644 index 0000000000..f42ce0cba1 --- /dev/null +++ b/examples/cauchystat/README @@ -0,0 +1,42 @@ +There are 6 examples in this directory. All are run by executing: + +% lmp_serial < lammps.in + +from the respective home directory. + +Note that these examples use an EAM potential, and therefore must be +run with a LAMMPS executable built with the MANYBODY package. + +Al_shear_PR: Application of a simple shear stress, illustrating that +there is a non-zero direct stress in the equilibrated system due to +the fact that Parinello-Rahman controls the second Piola-Kirchhoff +stress instead of the Cauchy stress. First fix equilibrates the +temperature at zero stress, second fix applies the shear. The third +fix corrects the problem because each new run resets the reference +simulation cell (H0) to the current cell shape. + +Al_shear_CS: Cauchystat example. Same as above, using the Cauchystat +instead of PR control. In this case, the equilibrated stresses are as +prescribed (ie., the set stresses control the Cauchy stress, not Piola +Kirchhoff) + +NiAl_cool: Cauchystat example. First fix equilibrates the system to +uniaxial tension of 2800 bars, 1200K. Second fix cools to 300 K, +causing a phase transformation. Cauchy stress remains at the set +level after the transformation + +NiAl_stretch: Cauchystat example. After a brief equilibration +at 600 K and zero stress, quickly ramp up the applied tensile stress +from 0 to 6000 bars over 100000 time steps. After the phase +transformation, Cauchy stress continues to follow the set value. + +NiAl_slow_stretch_CS: Cauchystat example. After a brief equilibration +at 500 K and zero stress, gradually ramp up the applied tensile stress +from 0 to 14000 bars over 350000 time steps. After the phase +transformation, Cauchy stress continues to follow the set value. + +NiAl_slow_stretch_PR: After a brief equilibration at 500 K and zero +stress, gradually ramp up the applied tensile stress from 0 to 14000 +bars over 350000 time steps. After the phase transformation, Cauchy +stress departs substantially from the set value, because the PR +control is used instead of the Cauchystat. diff --git a/src/fix_nh.cpp b/src/fix_nh.cpp index a1a562f2bb..c91e07eeac 100644 --- a/src/fix_nh.cpp +++ b/src/fix_nh.cpp @@ -46,6 +46,10 @@ enum{NOBIAS,BIAS}; enum{NONE,XYZ,XY,YZ,XZ}; enum{ISO,ANISO,TRICLINIC}; +int FixNH::restartPK; +int FixNH::restart_stored=0; +double FixNH::setPKinit[6]; + /* ---------------------------------------------------------------------- NVT,NPH,NPT integrators for improved Nose-Hoover equations of motion ---------------------------------------------------------------------- */ @@ -59,6 +63,7 @@ FixNH::FixNH(LAMMPS *lmp, int narg, char **arg) : { if (narg < 4) error->all(FLERR,"Illegal fix nvt/npt/nph command"); + usePK = 1; restart_global = 1; dynamic_group_allow = 1; time_integrate = 1; @@ -341,6 +346,78 @@ FixNH::FixNH(LAMMPS *lmp, int narg, char **arg) : dlm_flag = 1; } else error->all(FLERR,"Illegal fix nvt/npt/nph command"); iarg += 2; + } else if (strcmp(arg[iarg],"cauchystat") == 0) { + if (iarg+3 > narg) error->all(FLERR,"Illegal fix npt cauchystat command: wrong number of arguments"); + if (strcmp(arg[iarg+2],"yes") != 0 && strcmp(arg[iarg+2],"no") != 0) error->all(FLERR,"Illegal cauchystat continue value. Must be 'yes' or 'no'"); + alpha = force->numeric(FLERR,arg[iarg+1]); + restartPK = !strcmp(arg[iarg+2],"yes"); + + + if (comm->me == 0) { + if (screen) { + fprintf(screen,"Using the Cauchystat fix with alpha=%f\n",alpha); + if(restartPK==1) { + fprintf(screen," (this is a continuation fix)\n"); + } + else { + fprintf(screen," (this is NOT a continuation fix)\n"); + } + } + if (logfile) { + fprintf(logfile,"Using the Cauchystat with alpha=%f\n",alpha); + if(restartPK==1) { + fprintf(logfile," this is a continuation run\n"); + } + else { + fprintf(logfile," this is NOT a continuation run\n"); + } + } + } + + + if(restartPK==1 && restart_stored==0) { + error->all(FLERR,"Illegal cauchystat command. Continuation run must follow a previously equilibrated Cauchystat run"); + } + + if(alpha<=0.0) { + error->all(FLERR,"Illegal cauchystat command. Alpha cannot be zero or negative"); + } + + initRUN = 0; + initPK = 1; + usePK = 0; + + #define H0(row,col) (H0[(row-1)][(col-1)]) + #define invH0(row,col) (invH0[(row-1)][(col-1)]) + + + // initialize H0 to current box shape + + int triclinic = domain->triclinic; + double *h = domain->h; + double *h_inv = domain->h_inv; + double *boxhi = domain->boxhi; + double *boxlo = domain->boxlo; + double yz = domain->yz; + double xz = domain->xz; + double xy = domain->xy; + + + H0(1,1)=h[0]; H0(1,2)=h[5]; H0(1,3)=h[4]; + H0(2,1)=0.0; H0(2,2)=h[1]; H0(2,3)=h[3]; + H0(3,1)=0.0; H0(3,2)=0.0; H0(3,3)=h[2]; + + invH0(1,1)=h_inv[0]; invH0(1,2)=h_inv[5]; invH0(1,3)=h_inv[4]; + invH0(2,1)=0.0; invH0(2,2)=h_inv[1]; invH0(2,3)=h_inv[3]; + invH0(3,1)=0.0; invH0(3,2)=0.0; invH0(3,3)=h_inv[2]; + + myvol0 = abs(MathExtra::det3(H0)); //find reference volume + + #undef H0 + #undef invH0 + + iarg += 3; + } else if (strcmp(arg[iarg],"fixedpoint") == 0) { if (iarg+4 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command"); fixedpoint[0] = force->numeric(FLERR,arg[iarg+1]); @@ -2230,8 +2307,170 @@ void FixNH::compute_press_target() for (int i = 3; i < 6; i++) p_target[i] = p_start[i] + delta * (p_stop[i]-p_start[i]); - // if deviatoric, recompute sigma each time p_target changes + // CauchyStat: call CauchyStat to modify p_target[i] and p_hydro, they are used in compute_sigma() + // if CauchyStat enabled and pressure->vector computation has been initiated + if( (usePK==0) && (initRUN==1) ) { + double* h = domain->h; // shape matrix in Voigt notation + double* h_rate = domain->h_rate; // rate of box size/shape change in Voigt notation + double H[3][3]; + double Hdot[3][3]; + + #define H(row,col) (H[(row-1)][(col-1)]) + #define Hdot(row,col) (Hdot[(row-1)][(col-1)]) + #define F(row,col) (F[(row-1)][(col-1)]) + #define Fi(row,col) (Fi[(row-1)][(col-1)]) + #define Fdot(row,col) (Fdot[(row-1)][(col-1)]) + #define invH0(row,col) (invH0[(row-1)][(col-1)]) + #define cauchy(row,col) (cauchy[(row-1)][(col-1)]) + #define setcauchy(row,col) (setcauchy[(row-1)][(col-1)]) + #define setPK(row,col) (setPK[(row-1)][(col-1)]) + #define sigmahat(row,col) (sigmahat[(row-1)][(col-1)]) + + H(1,1)=h[0]; H(1,2)=0.0; H(1,3)=0.0; + H(2,1)=0.0; H(2,2)=h[1]; H(2,3)=0.0; + H(3,1)=0.0; H(3,2)=0.0; H(3,3)=h[2]; + + for (int i=0;i<6;i++) { + h_rate[i]=(h[i]-h_old[i])/update->dt; + h_old[i]=h[i]; + } + + Hdot(1,1)=h_rate[0]; Hdot(1,2)=0.0; Hdot(1,3)=0.0; + Hdot(2,1)=0.0; Hdot(2,2)=h_rate[1]; Hdot(2,3)=0.0; + Hdot(3,1)=0.0; Hdot(3,2)=0.0; Hdot(3,3)=h_rate[2]; + + if (domain->triclinic) { + H(1,2)=h[5]; H(1,3)=h[4]; H(2,3)=h[3]; + Hdot(1,2)=h_rate[5]; Hdot(1,3)=h_rate[4]; Hdot(2,3)=h_rate[3]; + } + + double F[3][3]={0.0}; + double FT[3][3]={0.0}; + double Fi[3][3]={0.0}; + double Fdot[3][3]={0.0}; + double J,vol; + + MathExtra::times3(H,invH0,F); //find F + MathExtra::times3(Hdot,invH0,Fdot); //find Fdot + + MathExtra::invert3(F,Fi); + J = MathExtra::det3(F); //find J + vol=myvol0*J; // actual volume + + double deltat; + deltat = update->dt; //increment of time step + + // Current pressure on the cell boundaries: + //tensor: 0 1 2 3 4 5 + // x y z xy xz yz + + double *tensor = pressure->vector; + + double cauchy[3][3]; //stress + cauchy(1,1)=-tensor[0]; cauchy(1,2)=0.0; cauchy(1,3)=0.0; + cauchy(2,1)=0.0; cauchy(2,2)=-tensor[1]; cauchy(2,3)=0.0; + cauchy(3,1)=0.0; cauchy(3,2)=0.0; cauchy(3,3)=-tensor[2]; + + if (domain->triclinic) { + cauchy(1,2)=-tensor[3]; cauchy(1,3)=-tensor[4]; + cauchy(2,1)=-tensor[3]; cauchy(2,3)=-tensor[5]; + cauchy(3,1)=-tensor[4]; cauchy(3,2)=-tensor[5]; + } + + // target pressure on the cell boundaries: + //p_target: 0 1 2 3 4 5 + // x y z yz xz xy + + double setcauchy[3][3]; //stress + setcauchy(1,1)=-p_target[0]; setcauchy(1,2)=0.0; setcauchy(1,3)=0.0; + setcauchy(2,1)=0.0; setcauchy(2,2)=-p_target[1]; setcauchy(2,3)=0.0; + setcauchy(3,1)=0.0; setcauchy(3,2)=0.0; setcauchy(3,3)=-p_target[2]; + + if (domain->triclinic) { + setcauchy(1,2)=-p_target[5]; setcauchy(1,3)=-p_target[4]; + setcauchy(2,1)=-p_target[5]; setcauchy(2,3)=-p_target[3]; + setcauchy(3,1)=-p_target[4]; setcauchy(3,2)=-p_target[3]; + } + + //initialize: + if(initPK==1) { + if(restartPK==1) { + setPK(1,1)=setPKinit[0]; setPK(1,2)=setPKinit[1]; setPK(1,3)=setPKinit[2]; + setPK(2,1)=setPKinit[1]; setPK(2,2)=setPKinit[3]; setPK(2,3)=setPKinit[4]; + setPK(3,1)=setPKinit[2]; setPK(3,2)=setPKinit[4]; setPK(3,3)=setPKinit[5]; + }else { + setPK(1,1)=cauchy(1,1); setPK(1,2)=cauchy(1,2); setPK(1,3)=cauchy(1,3); + setPK(2,1)=cauchy(2,1); setPK(2,2)=cauchy(2,2); setPK(2,3)=cauchy(2,3); + setPK(3,1)=cauchy(3,1); setPK(3,2)=cauchy(3,2); setPK(3,3)=cauchy(3,3); + } + + initPK=0; + } + + //cauchystat: + bigint step = update->ntimestep; + + + + + + CauchyStat(step,F,Fi,Fdot,cauchy,setcauchy,setPK,vol,myvol0,deltat,alpha); + + // use currentPK as new target: + //p_target: 0 1 2 3 4 5 + // x y z yz xz xy + + p_target[0]=-setPK(1,1); + p_target[1]=-setPK(2,2); + p_target[2]=-setPK(3,3); + if (pstyle == TRICLINIC) { + p_target[3]=-setPK(2,3); + p_target[4]=-setPK(1,3); + p_target[5]=-setPK(1,2); + } + + p_hydro = 0.0; + for (int i = 0; i < 3; i++) + if (p_flag[i]) { + p_hydro += p_target[i]; + } + p_hydro /= pdim; + + // save information for Cauchystat restart + setPKinit[0] = setcauchy(1,1); + setPKinit[1] = setcauchy(1,2); + setPKinit[2] = setcauchy(1,3); + setPKinit[3] = setcauchy(2,2); + setPKinit[4] = setcauchy(2,3); + setPKinit[5] = setcauchy(3,3); + restart_stored=1; + + #undef H + #undef Hdot + #undef F + #undef Fi + #undef Fdot + #undef invH0 + #undef cauchy + #undef setcauchy + #undef setPK + #undef sigmahat + + } + + if(initRUN==0){ + double* h = domain->h; // shape matrix in Voigt notation + for (int i=0;i<6;i++) { + h_old[i]=h[i]; + } + } + + + initRUN=1; // when run is initialized tensor[] not available (pressure on cell wall) + + + // if deviatoric, recompute sigma each time p_target changes if (deviatoric_flag) compute_sigma(); } @@ -2381,3 +2620,142 @@ double FixNH::memory_usage() if (irregular) bytes += irregular->memory_usage(); return bytes; } + +/* ---------------------------------------------------------------------- + CauchyStat + + Inputs: + step : current step number + F(3,3) : current deformation gradient + Fi(3,3) : inverse of the deformation gradient + Fdot(3,3) : time derivative of the deformation gradient (velocity) + cauchy(3,3) : current cauchy stress tensor + setcauchy(3,3) : target cauchy stress tensor + alpha : parameter =0.01 + nstat : =1, flag for mod(step,nstat).ne.0 + setPK(3,3) : current PK stress tensor, at initialization (time=0) setPK=cauchy + volume : current volume of the periodic box + volume0 : initial volume of the periodic box + deltat : simulation step increment + alpha : parameter + + Outputs: + setPK(3,3) : PK stress tensor at the next time step +------------------------------------------------------------------------- */ + +void FixNH::CauchyStat(bigint step, double (&F)[3][3], double (&Fi)[3][3], double (&Fdot)[3][3], double (&cauchy)[3][3], double (&setcauchy)[3][3], double (&setPK)[3][3], double volume, double volume0, double deltat, double alpha) +{ + + int nstat=1; + + //macros to go from c to fortran style for arrays: + #define F(row,col) (F[(row-1)][(col-1)]) + #define Fi(row,col) (Fi[(row-1)][(col-1)]) + #define Fdot(row,col) (Fdot[(row-1)][(col-1)]) + #define cauchy(row,col) (cauchy[(row-1)][(col-1)]) + #define setcauchy(row,col) (setcauchy[(row-1)][(col-1)]) + #define setPK(row,col) (setPK[(row-1)][(col-1)]) + + #define uv(row,col) (uv[(row-1)][(col-1)]) + #define deltastress(row) (deltastress[(row-1)]) + #define fdotvec(row) (fdotvec[(row-1)]) + #define dsdf(row,col) (dsdf[(row-1)][(col-1)]) + #define dsds(row,col) (dsds[(row-1)][(col-1)]) + #define deltaF(row) (deltaF[(row-1)]) + #define deltaPK(row) (deltaPK[(row-1)]) + + //initialize local variables: + int i,j,m,n; + + double deltastress[6],fdotvec[6]; + double dsdf[6][6]={0.0}; //zeroed, used in incremental form + double dsds[6][6]={0.0}; //zeroed, used in incremental form + double jac; + double deltaF[6]={0.0}; //zeroed, used in incremental form + double deltaPK[6]={0.0}; //zeroed, used in incremental form + + int uv[6][2]; + uv(1,1)=1; uv(1,2)=1; + uv(2,1)=2; uv(2,2)=2; + uv(3,1)=3; uv(3,2)=3; + uv(4,1)=2; uv(4,2)=3; + uv(5,1)=1; uv(5,2)=3; + uv(6,1)=1; uv(6,2)=2; + + if( (step % nstat) != 0) { + //do nothing! + }else { + for(int ii = 1;ii <= 6;ii++) { + i=uv(ii,1); + j=uv(ii,2); + deltastress(ii)=setcauchy(i,j)-cauchy(i,j); + if(ii>3) deltastress(ii)=deltastress(ii)*2.0; + fdotvec(ii)=Fdot(i,j)*deltat; + } + + for(int ii = 1;ii <= 6;ii++) { + i=uv(ii,1); + j=uv(ii,2); + for(int jj = 1;jj <= 6;jj++) { + m=uv(jj,1); + n=uv(jj,2); + dsds(ii,jj) = Fi(i,m)*Fi(j,n) + Fi(i,n)*Fi(j,m) + Fi(j,m)*Fi(i,n) + Fi(j,n)*Fi(i,m); + for(int l = 1;l <= 3;l++) { + for(int k = 1;k <= 3;k++) { + dsdf(ii,jj) = dsdf(ii,jj) + cauchy(k,l)*( Fi(i,k)*Fi(j,l)*Fi(n,m) - Fi(i,m)*Fi(j,l)*Fi(n,k) - Fi(i,k)*Fi(j,m)*Fi(n,l) ); + }//k + }//l + }//jj + }//ii + + jac=volume/volume0; + for(int ii = 1;ii <= 6;ii++) { + for(int jj = 1;jj <= 6;jj++) { + dsds(ii,jj)=dsds(ii,jj)*jac/4.0; + dsdf(ii,jj)=dsdf(ii,jj)*jac; + }//jj + }//ii + + for(int ii = 1;ii <= 6;ii++) { + for(int jj = 1;jj <= 6;jj++) { + deltaF(ii)=deltaF(ii)+dsdf(ii,jj)*fdotvec(jj); // deltaF=matmul(dsdf,fdotvec) in the fortran implementation + }//jj + }//ii + + for(int ii = 1;ii <= 6;ii++) { + for(int jj = 1;jj <= 6;jj++) { + deltaPK(ii)=deltaPK(ii)+alpha*dsds(ii,jj)*deltastress(jj); // deltaPK=alpha*matmul(dsds,deltastress) + deltaF in the fortran implementation + }//jj + // this line applies alpha to both terms instead of just the delta sigma term. + deltaPK(ii)=deltaPK(ii)+alpha*deltaF(ii); + // this is the old version + //deltaPK(ii)=deltaPK(ii)+deltaF(ii); + }//ii + + setPK(1,1)=setPK(1,1)+deltaPK(1); //equation (4) in SD-notes.pdf + setPK(2,2)=setPK(2,2)+deltaPK(2); + setPK(3,3)=setPK(3,3)+deltaPK(3); + setPK(2,3)=setPK(2,3)+deltaPK(4); + setPK(3,2)=setPK(3,2)+deltaPK(4); + setPK(1,3)=setPK(1,3)+deltaPK(5); + setPK(3,1)=setPK(3,1)+deltaPK(5); + setPK(1,2)=setPK(1,2)+deltaPK(6); + setPK(2,1)=setPK(2,1)+deltaPK(6); + } + + //undefine macros: + #undef F + #undef Fi + #undef Fdot + #undef cauchy + #undef setcauchy + #undef setPK + #undef uv + #undef deltastress + #undef fdotvec + #undef dsdf + #undef dsds + #undef deltaF + #undef deltaPK + +} diff --git a/src/fix_nh.h b/src/fix_nh.h index 807ea2a71f..ba8523f86d 100644 --- a/src/fix_nh.h +++ b/src/fix_nh.h @@ -139,6 +139,23 @@ class FixNH : public Fix { double compute_strain_energy(); void compute_press_target(); void nh_omega_dot(); + + // Implementation of CauchyStat + double H0[3][3]; //shape matrix for the undeformed cell + double h_old[6]; //previous time step shape matrix for the undeformed cell + double invH0[3][3]; //inverse of H0; + double myvol0; + double setPK[3][3]; + static double setPKinit[6]; + double alpha; //integration parameter cauchystat + int initPK; // 1 if setPK needs to be initialized either from cauchy or restart, else 0 + int usePK; // 0 if use CauchyStat else 1 + static int restartPK; // Read PK stress from the previous step + static int restart_stored; // Read PK stress from the previous step + int initRUN; // 0 if run not initialized (pressure->vector not computed yet), else 1 (pressure->vector available) + + virtual void CauchyStat(bigint step, double (&F)[3][3], double (&Fi)[3][3], double (&Fdot)[3][3], double (&cauchy)[3][3], double (&setcauchy)[3][3], double (&setPK)[3][3], double volume, double volume0, double deltat, double alpha); + }; } From 5c686be33d4653cd7dcd4b2ef6b49431fd74f7e2 Mon Sep 17 00:00:00 2001 From: "Ronald E. Miller" Date: Mon, 24 Sep 2018 11:30:06 -0400 Subject: [PATCH 290/302] clean up whitespace, indentation, isolate all cauchystat-related code, remove extraneous examples --- examples/cauchystat/Al_shear_PR/lammps.in | 69 - examples/cauchystat/NiAl_cool/input.dat | 6009 ----------------- examples/cauchystat/NiAl_cool/lammps.in | 45 - .../cauchystat/NiAl_slow_stretch_CS/input.dat | 6009 ----------------- .../cauchystat/NiAl_slow_stretch_CS/lammps.in | 45 - .../cauchystat/NiAl_slow_stretch_PR/input.dat | 6009 ----------------- .../cauchystat/NiAl_slow_stretch_PR/lammps.in | 45 - examples/cauchystat/NiAl_stretch/input.dat | 6009 ----------------- examples/cauchystat/NiAl_stretch/lammps.in | 48 - examples/cauchystat/README | 42 +- .../cauchystat/{Al_shear_CS => }/lammps.in | 8 +- src/fix_nh.cpp | 622 +- src/fix_nh.h | 16 +- 13 files changed, 323 insertions(+), 24653 deletions(-) delete mode 100644 examples/cauchystat/Al_shear_PR/lammps.in delete mode 100644 examples/cauchystat/NiAl_cool/input.dat delete mode 100644 examples/cauchystat/NiAl_cool/lammps.in delete mode 100644 examples/cauchystat/NiAl_slow_stretch_CS/input.dat delete mode 100644 examples/cauchystat/NiAl_slow_stretch_CS/lammps.in delete mode 100644 examples/cauchystat/NiAl_slow_stretch_PR/input.dat delete mode 100644 examples/cauchystat/NiAl_slow_stretch_PR/lammps.in delete mode 100644 examples/cauchystat/NiAl_stretch/input.dat delete mode 100644 examples/cauchystat/NiAl_stretch/lammps.in rename examples/cauchystat/{Al_shear_CS => }/lammps.in (87%) diff --git a/examples/cauchystat/Al_shear_PR/lammps.in b/examples/cauchystat/Al_shear_PR/lammps.in deleted file mode 100644 index b79d18853b..0000000000 --- a/examples/cauchystat/Al_shear_PR/lammps.in +++ /dev/null @@ -1,69 +0,0 @@ -units metal -atom_style atomic -atom_modify map array - -processors 1 1 1 - -# Box and atom positions: -boundary p p p - -# Defining lattice and creating simulation -# box with atoms inside -lattice fcc 4.05 -region simbox prism 0 5 0 5 0 5 0 0 0 units lattice -create_box 2 simbox -create_atoms 2 box - -# Atomic mass: -mass 1 58.69 -mass 2 26.98154 - -# Potential, Al fcc crystal -pair_style eam/alloy -pair_coeff * * ../Mishin-Ni-Al-2009.eam.alloy Ni Al - - -thermo 100 -thermo_style custom step temp pxx pyy pzz pxy pxz pyz -compute cna all cna/atom 2.8 - -fix 1 all npt temp 600.0 600.0 1.0 x 0.0 0.0 0.1 y 0.0 0.0 0.1 z 0.0 0.0 0.1 couple none - -dump 1 all cfg 1000 test*.cfg mass type xs ys zs type c_cna - -timestep 0.002 - -variable px equal pxx -variable py equal pyy -variable pz equal pzz -variable sxy equal pxy -variable sxz equal pxz -variable syz equal pyz -variable t equal temp - -fix avg all ave/time 1 100 100 v_t v_px v_py v_pz v_sxy v_sxz v_syz file avg.txt - -variable lx equal lx -variable ly equal ly -variable lz equal ly -variable xy equal xy -variable xz equal xz -variable yz equal yz - -fix box all ave/time 1 100 100 v_lx v_ly v_lz v_xy v_xz v_yz file box.txt - -velocity all create 1200 4928459 rot yes dist gaussian - -run 10000 - -unfix 1 - -fix 1 all npt temp 600.0 600.0 1.0 x 0.0 0.0 0.1 y 0.0 0.0 0.1 z 0.0 0.0 0.1 xy -10000.0 -10000.0 0.1 couple none - -run 10000 - -unfix 1 - -fix 1 all npt temp 600.0 600.0 1.0 x 0.0 0.0 0.1 y 0.0 0.0 0.1 z 0.0 0.0 0.1 xy -10000.0 -10000.0 0.1 couple none - -run 10000 diff --git a/examples/cauchystat/NiAl_cool/input.dat b/examples/cauchystat/NiAl_cool/input.dat deleted file mode 100644 index 3b99f3ea8f..0000000000 --- a/examples/cauchystat/NiAl_cool/input.dat +++ /dev/null @@ -1,6009 +0,0 @@ -Position data for MD simulation - -6000 atoms -2 atom types -0.0000 39.972658977840510 xlo xhi -0.0000 39.970082402467646 ylo yhi -0.0000 43.077168594479417 zlo zhi -Atoms - -1 1 2.265603 1.699233 2.96682 -2 2 2.147625 3.958175 4.336466 -3 1 1.997414 2.08615 5.681268 -4 2 6.222234 0.12344 4.55833 -5 1 4.247865 9.8684 7.188432 -6 2 2.226404 4.008191 1.332846 -7 1 2.558125 5.881235 2.799624 -8 2 2.112892 8.008518 4.084836 -9 1 2.366112 6.194696 5.83623 -10 2 0.308528 9.773154 7.249786 -11 1 1.861699 8.008727 1.634831 -12 2 0.245314 5.864464 4.508327 -13 1 8.139953 -0.02424 5.747139 -14 1 0.178338 3.676069 2.91793 -15 2 0.021903 9.933735 1.645872 -16 1 4.094944 3.990727 2.989711 -17 2 4.25173 6.125247 4.299378 -18 1 4.004975 4.261809 5.650881 -19 2 4.233414 9.883798 4.412874 -20 2 4.158657 5.985987 1.452914 -21 1 3.943003 7.917155 2.809851 -22 1 4.013002 8.032118 5.709128 -23 1 3.913817 0.208102 0.200173 -24 2 4.11186 2.115952 4.39711 -25 1 4.091794 8.080277 0.383691 -26 1 8.239262 4.128528 0.14417 -27 1 4.164942 2.294329 1.435205 -28 1 6.018476 2.048784 2.978318 -29 1 6.189263 4.123374 4.429365 -30 1 5.731913 2.039386 5.760723 -31 2 8.125123 2.396376 4.334063 -32 2 5.956145 3.961461 1.710606 -33 1 6.097732 6.223054 3.105619 -34 2 6.260701 8.269814 4.403081 -35 1 6.135592 6.191014 6.014208 -36 2 6.118481 0.280536 1.660297 -37 2 5.95371 8.134065 1.459117 -38 1 8.112 7.978937 6.025785 -39 1 8.230735 0.317331 0.287501 -40 1 7.984577 0.451106 2.876758 -41 1 8.121358 4.469963 3.000969 -42 2 8.0024 6.398776 4.506808 -43 1 8.265498 4.145515 5.950951 -44 1 8.093687 2.336039 1.599762 -45 2 7.786786 6.082031 1.369435 -46 1 8.051625 8.388788 2.947011 -47 2 1.887169 0.10205 1.232231 -48 1 3.814096 0.184819 2.93152 -49 2 5.999738 4.024912 6.895817 -50 1 0.20906 5.67262 1.62315 -51 1 2.22916 6.007717 0.143509 -52 1 9.864584 8.16224 1.516273 -53 1 0.029687 7.997328 3.090548 -54 1 0.158584 7.813035 5.663186 -55 1 6.149844 9.939956 0.040852 -56 1 1.871208 1.766851 8.960428 -57 2 2.233107 3.807827 10.095989 -58 1 1.960237 1.933156 11.733738 -59 1 2.028536 4.090031 13.399625 -60 2 0.096818 1.982978 13.367683 -61 1 1.962538 5.967991 8.575587 -62 2 1.779869 8.006286 9.997749 -63 1 2.261369 6.075808 11.262585 -64 1 1.878689 7.795749 12.973992 -65 1 8.066595 6.091936 7.32151 -66 2 6.004471 8.10958 7.337536 -67 2 3.807826 9.773306 13.107995 -68 2 3.628292 2.338356 7.627483 -69 1 4.142245 4.127148 8.640624 -70 2 4.430475 5.841591 10.077295 -71 1 3.968136 4.281892 11.552649 -72 2 3.926926 6.059939 13.034315 -73 1 4.163584 8.009554 8.875445 -74 1 3.841536 8.095992 11.564038 -75 1 1.972543 4.098752 7.26509 -76 1 9.833961 8.179066 10.053046 -77 1 3.959427 0.070701 8.628349 -78 1 4.000206 1.99734 10.467815 -79 1 0.175393 5.813256 10.208259 -80 2 3.991668 2.115114 12.987731 -81 2 8.056411 2.098025 12.865242 -82 1 5.64748 2.156225 8.497216 -83 2 6.159432 4.014865 10.196613 -84 1 6.214032 2.165249 11.651601 -85 1 5.856347 3.961477 13.023239 -86 1 7.948437 0.352004 11.304002 -87 2 0.129981 2.04383 7.39824 -88 1 6.181909 5.856377 8.431434 -89 1 5.991539 7.847191 10.091845 -90 1 5.975418 5.816241 11.895283 -91 1 5.86549 8.043369 13.028812 -92 2 4.166236 6.085137 7.231975 -93 1 0.439458 3.829864 11.550798 -94 2 0.21596 5.973334 12.667734 -95 1 10.017517 5.823156 11.545694 -96 1 8.076092 4.274718 8.540188 -97 2 7.924969 6.011881 10.326107 -98 1 8.12022 3.959556 11.608595 -99 1 8.110671 6.08702 13.353502 -100 1 8.135035 2.224763 9.76071 -101 1 8.056404 8.04948 8.608732 -102 1 7.867682 7.986347 11.444105 -103 1 0.057722 3.824193 8.62711 -104 1 9.981584 4.247366 7.362993 -105 2 4.013801 9.873296 9.982524 -106 1 2.329565 8.116478 7.435377 -107 2 5.950495 0.34488 9.79838 -108 1 4.334027 0.076447 11.746114 -109 2 7.945804 9.995075 13.009688 -110 1 2.027284 10.048274 11.752786 -111 2 7.985809 2.177851 7.348854 -112 2 0.227187 9.715111 13.080145 -113 1 4.369771 0.043973 14.298992 -114 1 9.913252 6.303629 8.785055 -115 1 7.984689 3.996322 14.285297 -116 1 6.286022 9.901661 11.434457 -117 2 9.978329 0.129998 10.093528 -118 2 9.898021 7.994926 13.146433 -119 1 2.438629 0.033347 18.603552 -120 2 2.19485 3.927092 15.921048 -121 1 2.266036 2.0106 17.298124 -122 2 2.190625 4.002775 18.808528 -123 1 2.529808 1.858131 19.802924 -124 1 2.121536 8.100548 15.903723 -125 1 1.999174 5.945764 17.409821 -126 2 2.399752 8.317077 18.513998 -127 1 2.085018 6.322971 20.123548 -128 1 0.132331 7.834943 14.417244 -129 2 0.191888 2.055829 18.456008 -130 1 8.035826 8.278124 14.487514 -131 2 3.964165 5.965398 16.034244 -132 1 3.977251 4.106829 17.287135 -133 1 4.083409 6.186923 18.749777 -134 1 4.118697 4.16167 19.924445 -135 2 0.168486 10.031098 15.738364 -136 1 9.834776 5.750065 20.057158 -137 1 4.513739 7.925063 17.284367 -138 1 0.224638 6.311966 18.562 -139 1 4.05173 8.065927 20.327367 -140 1 4.020498 7.877514 14.44079 -141 1 4.143142 1.813412 15.801004 -142 1 2.214548 1.829361 14.565296 -143 2 4.407757 2.318175 18.721975 -144 2 6.016403 3.935276 15.745347 -145 1 6.343375 1.849436 17.205365 -146 2 6.615021 3.988745 18.735217 -147 1 6.455591 1.950789 20.137809 -148 1 6.179932 9.794709 17.21643 -149 2 6.237707 7.849925 15.743301 -150 1 6.151976 5.985244 17.227932 -151 2 6.178229 7.773511 18.829625 -152 1 6.147011 5.845856 20.064817 -153 2 4.124664 9.743815 15.83873 -154 1 8.065185 1.771116 18.726928 -155 1 6.149514 1.938847 14.518073 -156 2 8.136444 6.024316 15.560218 -157 1 8.139342 3.949043 16.901849 -158 1 8.143554 6.219717 18.549219 -159 1 8.181775 3.5232 20.518875 -160 1 1.876074 6.12577 14.691379 -161 2 9.729818 3.920007 18.490075 -162 1 8.23825 8.027751 17.068995 -163 1 4.103417 9.893021 18.750211 -164 1 8.095744 7.73466 20.44646 -165 2 8.348453 1.630886 15.803105 -166 1 0.114526 2.216943 15.877394 -167 2 4.178332 6.016772 21.363439 -168 1 1.899673 9.855866 20.182773 -169 1 0.06894 8.212942 17.306197 -170 1 5.88851 5.844373 14.487209 -171 1 0.059742 4.374953 14.646907 -172 1 3.878323 4.145978 14.489788 -173 2 4.294142 2.069501 21.441214 -174 1 8.064234 9.497999 18.769847 -175 1 0.054546 7.976599 20.116681 -176 1 8.525044 0.101361 14.328798 -177 2 9.906967 7.812697 18.799053 -178 1 2.121141 3.832231 21.274441 -179 2 0.246791 1.874452 21.452019 -180 1 0.500726 0.008693 17.033685 -181 1 6.032205 3.972779 21.459867 -182 1 6.228607 9.827219 20.293439 -183 1 1.999764 9.905509 14.422608 -184 2 0.044761 6.18458 27.221929 -185 1 2.164891 1.954699 22.914632 -186 1 2.035794 3.798225 24.476506 -187 1 2.328794 2.047568 26.040855 -188 2 1.965861 4.051758 27.120895 -189 1 0.39788 0.200226 23.107141 -190 1 2.011846 6.031691 22.819617 -191 2 1.784066 7.880599 24.253767 -192 1 1.950682 5.925284 25.629958 -193 1 2.108877 7.833186 26.877206 -194 2 1.9192 8.201599 21.667898 -195 1 1.939171 2.209822 28.547 -196 1 0.09557 5.722002 24.118636 -197 1 0.059192 4.031101 25.673341 -198 1 4.156274 3.971969 23.108429 -199 2 3.825507 5.899235 24.328013 -200 1 3.962602 4.17038 25.711458 -201 2 4.032842 6.194348 27.234817 -202 2 8.150839 1.460228 21.735164 -203 1 3.925207 7.821015 23.037858 -204 1 6.069434 7.849806 21.58918 -205 1 4.081687 8.179044 25.728661 -206 1 2.137517 -0.00179 27.361868 -207 1 8.039753 0.124328 26.068543 -208 2 4.114742 2.131087 24.2305 -209 1 3.99908 4.281021 28.716402 -210 2 4.144388 2.150469 27.49599 -211 1 6.148998 1.905923 22.975359 -212 2 6.074117 3.917472 24.352374 -213 1 6.069578 2.074776 25.719405 -214 1 6.002174 3.93371 27.186956 -215 1 0.192839 0.413941 26.157945 -216 1 6.145721 5.660607 23.004422 -217 2 6.18359 8.088504 24.428869 -218 1 6.000198 5.825479 25.71821 -219 1 6.173333 7.895994 27.094366 -220 1 3.765773 8.320714 28.630547 -221 2 0.032589 9.821813 27.080523 -222 2 4.122723 9.91071 21.592517 -223 2 8.048219 2.189184 27.563754 -224 1 8.05413 3.580001 22.926534 -225 1 8.342736 5.763964 24.213119 -226 1 8.211594 4.017763 25.861054 -227 2 8.184076 5.933488 27.242654 -228 1 8.118291 7.605214 22.802609 -229 1 8.324479 7.783863 25.586707 -230 1 0.016695 3.877657 22.732209 -231 2 8.078514 1.732391 24.510591 -232 1 1.840212 9.799991 28.612751 -233 1 8.133488 9.896767 24.464749 -234 2 0.259027 2.202193 24.255994 -235 1 0.314216 4.172421 28.718513 -236 1 9.938719 0.110931 27.366007 -237 2 7.9826 5.671003 21.68818 -238 2 8.501796 9.719738 21.94795 -239 1 9.867172 1.961233 25.98457 -240 2 0.147317 6.141791 21.547334 -241 1 5.959987 9.88575 28.446264 -242 1 2.08124 9.932871 25.652862 -243 1 6.215991 9.875565 22.814788 -244 2 9.884 7.985376 27.46384 -245 1 2.053337 6.324696 28.651576 -246 1 6.049775 1.929788 28.696521 -247 2 0.06014 2.237289 27.488449 -248 1 3.934882 0.178228 25.967545 -249 1 9.840405 6.042091 28.967975 -250 2 2.173984 4.036239 30.18994 -251 1 2.138694 1.819959 31.295867 -252 1 1.8032 4.150642 32.867061 -253 1 2.047457 2.163034 34.573733 -254 1 9.757157 5.856956 31.585972 -255 2 1.984761 8.057482 30.442659 -256 1 1.902189 6.299208 31.518263 -257 1 2.00465 7.876566 33.246864 -258 1 2.092474 5.940699 34.381242 -259 1 9.849722 7.582239 35.867784 -260 1 5.975592 5.892618 28.820784 -261 1 7.881925 4.231188 28.715136 -262 2 3.96919 6.108456 30.036646 -263 1 4.304991 4.019067 31.58604 -264 2 3.874978 6.090045 33.013177 -265 1 3.883657 4.012262 34.047762 -266 2 7.971177 9.618775 30.35461 -267 1 4.038509 7.895079 31.563612 -268 2 9.882866 8.060992 32.88089 -269 1 3.852553 7.973326 34.658588 -270 2 8.029513 1.689238 30.31777 -271 1 4.163056 1.923283 30.299358 -272 2 0.30731 9.900525 33.238415 -273 2 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0.193149 4.044633 40.128658 -360 1 0.208035 7.768173 42.967627 -361 1 9.743918 7.677695 41.398408 -362 1 4.262636 0.235264 37.428049 -363 1 8.043101 8.089437 43.017835 -364 1 10.040909 5.794271 40.133159 -365 1 4.408416 0.116462 40.438985 -366 1 4.023578 4.299548 42.858497 -367 1 5.738192 6.080328 42.916263 -368 2 0.095082 9.809621 39.101012 -369 2 2.214579 0.240932 36.189444 -370 1 5.84047 3.923468 36.042476 -371 1 0.100734 0.195132 37.583149 -372 1 9.981436 1.84605 40.456977 -373 2 0.100733 6.115963 38.581553 -374 1 6.330599 0.057798 41.9442 -375 1 2.035748 9.928114 40.400686 -376 2 2.028957 12.029791 4.343529 -377 2 1.832717 12.0538 1.526233 -378 1 2.470958 13.791291 2.764359 -379 1 2.300685 15.961461 4.291057 -380 1 2.060136 13.885327 5.519295 -381 1 5.834238 10.070177 2.927694 -382 2 1.886408 16.065865 1.66092 -383 1 2.119671 18.096749 3.047313 -384 1 2.163548 18.168685 5.762644 -385 1 10.050827 19.899402 1.574428 -386 1 9.948295 15.901995 1.529421 -387 1 0.210418 11.651505 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1.962857 26.015373 37.239011 -1819 1 1.855742 27.865871 38.783671 -1820 1 1.946136 26.114415 40.445845 -1821 2 1.342698 28.356759 41.677946 -1822 1 3.866247 20.162337 40.622125 -1823 2 3.812973 22.128926 36.114766 -1824 2 3.760552 22.028975 39.129353 -1825 1 0.120133 23.847195 42.944885 -1826 2 4.069006 22.075437 41.863068 -1827 1 5.907632 20.36903 38.501592 -1828 1 7.614067 27.968649 40.109559 -1829 1 3.897056 23.931653 37.406176 -1830 2 3.67424 25.831572 38.858188 -1831 1 3.697155 23.98423 40.178372 -1832 1 3.958999 25.902285 41.773782 -1833 1 9.702453 23.999789 36.048473 -1834 1 3.862301 28.11303 37.453615 -1835 1 3.835868 28.048802 40.57469 -1836 2 5.854804 27.776995 36.005821 -1837 1 2.018496 25.837414 42.987148 -1838 1 9.960693 25.630934 40.389307 -1839 1 5.93268 22.351558 37.363635 -1840 2 5.893761 24.161725 38.918752 -1841 1 5.808679 22.051292 40.511129 -1842 2 5.792864 24.116392 41.554559 -1843 1 9.64084 21.675057 37.276932 -1844 1 7.878713 27.9153 37.259426 -1845 1 6.175937 25.901323 37.471311 -1846 2 5.668787 27.931006 38.872038 -1847 1 5.833656 25.947867 40.073284 -1848 1 5.883119 28.188772 41.564271 -1849 1 1.968623 29.760132 37.440712 -1850 1 9.720776 21.931094 39.953354 -1851 2 7.71657 22.068573 38.940437 -1852 2 7.898218 26.165005 41.361678 -1853 2 8.069464 22.281116 41.639197 -1854 1 7.671941 23.931719 37.325285 -1855 2 8.224025 25.910081 38.501705 -1856 1 7.708054 24.12057 40.424826 -1857 1 3.73122 28.006194 42.903257 -1858 2 5.75438 20.111404 41.853219 -1859 1 9.831402 27.825768 38.818019 -1860 1 7.702614 27.990192 42.759806 -1861 1 7.820889 20.318748 42.936774 -1862 1 1.696378 24.07867 36.051323 -1863 2 1.929861 28.112364 36.261692 -1864 2 5.747452 20.123867 36.071437 -1865 2 9.856877 23.914266 38.695016 -1866 2 7.756468 29.813429 38.680181 -1867 1 7.682461 20.159018 37.348845 -1868 2 9.776865 19.989829 38.744389 -1869 1 9.815791 23.652977 41.622566 -1870 1 7.858893 24.330568 42.982576 -1871 2 8.002454 29.899258 41.430193 -1872 1 0.077683 20.128085 37.436998 -1873 2 1.626697 20.07364 41.83293 -1874 1 1.777573 31.918884 4.516148 -1875 1 0.224503 39.97377 2.747323 -1876 1 2.112303 39.817069 4.528393 -1877 2 1.981899 32.150865 1.347891 -1878 1 2.322442 33.979858 3.19387 -1879 2 2.096374 36.191635 4.230691 -1880 1 1.999648 34.152278 5.938815 -1881 1 1.73114 30.291033 2.935219 -1882 1 3.665367 29.983954 1.275677 -1883 2 1.943018 36.004664 1.697384 -1884 1 2.019378 38.176143 2.972324 -1885 1 2.19126 37.889176 5.917314 -1886 1 0.019605 35.984478 3.104091 -1887 2 7.787834 30.403461 4.344497 -1888 1 6.050812 33.918162 -0.027918 -1889 1 3.814711 31.691419 2.816277 -1890 2 4.20332 33.715468 4.180703 -1891 1 3.914581 32.066382 5.971622 -1892 2 3.895933 33.805468 1.20281 -1893 1 4.340385 35.802877 2.943593 -1894 1 4.271659 37.949305 4.314292 -1895 1 4.068788 35.686982 5.513423 -1896 2 4.190929 37.662517 7.182865 -1897 2 4.200636 38.226632 1.691189 -1898 1 9.716958 31.962759 4.249426 -1899 1 5.810481 32.019245 4.382481 -1900 1 5.938979 35.885235 7.16864 -1901 1 0.267384 35.760048 6.061532 -1902 2 6.018619 31.95181 1.612974 -1903 1 5.938914 34.057443 2.77635 -1904 2 6.183116 36.065698 4.376274 -1905 1 6.089476 34.019022 5.411901 -1906 1 6.359106 35.990867 1.578601 -1907 1 6.152011 38.058648 2.943561 -1908 1 5.711164 30.034724 2.988084 -1909 1 6.045542 37.798257 5.727308 -1910 1 8.009398 36.153578 0.053676 -1911 1 0.238276 33.896375 4.533811 -1912 1 7.902329 32.340963 2.922426 -1913 2 8.222407 34.13168 4.116176 -1914 1 7.936717 32.22354 5.888103 -1915 2 8.123641 38.41175 1.891536 -1916 2 7.927555 34.06589 1.21075 -1917 1 8.412195 35.913547 2.85742 -1918 1 8.139566 38.142702 4.120627 -1919 1 8.317254 36.194514 5.407003 -1920 1 4.034964 36.04412 0.47011 -1921 2 3.83481 30.240395 4.561724 -1922 2 0.249553 38.107374 7.140438 -1923 1 2.126706 37.874136 0.15149 -1924 1 9.770714 33.872567 5.735309 -1925 1 7.651907 31.89674 -0.001589 -1926 1 6.265497 38.190114 0.387488 -1927 2 0.091323 38.034686 1.579889 -1928 1 6.013525 30.091058 5.903567 -1929 2 9.613745 31.989409 1.558474 -1930 1 9.893134 38.099463 -0.000176 -1931 1 0.012372 34.088485 1.353111 -1932 1 1.957372 34.025261 0.135755 -1933 1 9.930552 30.036571 0.064988 -1934 1 1.356847 30.09059 0.587218 -1935 2 2.165378 39.90345 7.155948 -1936 1 9.928802 38.103943 5.693619 -1937 1 4.231897 39.892291 5.78739 -1938 2 3.93426 34.036259 7.069656 -1939 2 2.074177 32.270109 10.089125 -1940 1 3.932043 30.108354 7.345143 -1941 2 1.820986 31.836134 13.124076 -1942 1 1.929382 34.316614 8.776464 -1943 2 2.083627 36.058658 10.081855 -1944 1 1.997221 33.916084 11.577718 -1945 1 2.267799 35.662279 13.073333 -1946 2 4.209744 30.111608 9.908398 -1947 1 2.104601 38.082098 8.735584 -1948 2 8.24053 38.05696 7.216926 -1949 1 2.109203 38.067126 11.734018 -1950 2 0.042241 38.005125 10.32451 -1951 1 1.957287 39.865839 10.426779 -1952 2 8.203196 30.05132 9.912922 -1953 1 2.246349 30.143579 11.639665 -1954 1 4.199959 32.106503 8.70465 -1955 1 3.976417 34.112906 10.198306 -1956 1 3.884958 31.967651 11.562891 -1957 2 4.063522 34.032621 13.004991 -1958 1 4.232266 36.19468 8.962151 -1959 2 4.097197 38.230412 10.13239 -1960 1 4.118617 35.849094 11.679739 -1961 2 4.350691 37.885411 12.898671 -1962 1 6.201046 32.417633 10.15369 -1963 2 5.816252 31.722772 13.101456 -1964 1 6.157578 39.769939 7.197304 -1965 1 6.184596 34.126547 8.504052 -1966 2 6.346713 35.703957 10.195727 -1967 1 6.288059 33.992499 11.799552 -1968 1 6.483281 35.967443 12.860859 -1969 2 7.835082 34.145462 7.179037 -1970 1 6.256423 37.691882 8.993285 -1971 1 6.2337 37.988064 11.537765 -1972 2 9.772215 31.919829 7.180665 -1973 1 7.981132 32.165581 14.333143 -1974 1 2.309997 36.061233 7.359038 -1975 1 4.433034 36.045633 14.35862 -1976 1 7.955328 32.223129 8.507808 -1977 2 8.286523 34.141907 10.013388 -1978 1 7.939052 31.949186 11.600717 -1979 1 8.104476 34.231193 13.030137 -1980 2 1.884476 31.865234 7.19113 -1981 1 8.333692 36.082489 8.414603 -1982 2 8.168537 38.03579 10.329742 -1983 1 8.420403 35.985684 11.517078 -1984 1 8.327179 38.029547 12.910471 -1985 2 6.20532 31.903657 7.381951 -1986 2 0.085009 37.638839 13.154459 -1987 1 7.552329 30.251663 13.212821 -1988 2 2.355047 39.830169 13.072665 -1989 1 0.148785 31.885164 11.209718 -1990 1 1.848807 30.245173 8.940225 -1991 1 0.166389 36.076965 8.575072 -1992 1 5.894085 30.228735 11.200379 -1993 1 0.232408 36.202468 11.578646 -1994 1 2.4752 37.687884 14.341623 -1995 1 0.334254 39.866494 8.663952 -1996 1 0.04027 39.756099 11.961945 -1997 1 0.083418 34.195005 10.175316 -1998 2 0.043097 34.005541 7.193221 -1999 2 0.052476 33.834131 12.929227 -2000 1 8.114393 39.929142 8.406226 -2001 1 6.281515 37.719535 14.225496 -2002 2 9.768912 32.130689 12.866513 -2003 1 9.864669 32.192496 10.045288 -2004 1 0.028148 32.153045 8.783822 -2005 2 6.417236 39.879341 13.202851 -2006 1 8.005375 39.836615 20.349358 -2007 2 2.017709 31.870952 15.889762 -2008 2 7.716399 30.062983 18.430151 -2009 2 2.119264 32.351346 19.061283 -2010 2 6.658976 39.77428 18.733464 -2011 2 2.321302 35.607604 15.702355 -2012 1 1.966843 34.024507 17.339235 -2013 2 2.33321 35.646813 18.814154 -2014 1 1.794484 34.194282 20.582509 -2015 1 1.984336 29.928657 17.680043 -2016 1 2.238075 37.571948 17.445144 -2017 1 4.466772 39.923317 17.544828 -2018 1 2.072213 37.924398 20.106708 -2019 1 3.990864 31.761546 14.785242 -2020 1 4.020518 33.927189 15.729606 -2021 1 3.897539 31.807357 17.561737 -2022 1 4.265924 33.937397 18.871352 -2023 1 4.376327 32.03663 20.389624 -2024 1 6.400496 39.782735 15.767263 -2025 2 4.461272 37.709843 15.835142 -2026 1 4.42096 35.817684 17.119638 -2027 2 4.054798 37.811976 18.867409 -2028 1 3.994208 35.957797 20.233365 -2029 1 1.972412 30.096734 20.271564 -2030 1 5.988832 31.90054 15.667667 -2031 2 6.100535 31.913125 18.798462 -2032 1 0.28224 35.927235 17.246921 -2033 1 9.878186 30.085685 17.138849 -2034 1 6.416487 35.895999 15.857104 -2035 2 5.962689 34.078738 16.936543 -2036 1 6.325491 35.483857 19.110752 -2037 1 6.245971 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-5629 1 32.168293 24.104265 42.975893 -5630 1 35.411443 29.813844 38.643913 -5631 2 37.976528 20.120682 38.533653 -5632 1 39.779362 30.230874 4.652211 -5633 1 29.983878 33.982126 0.04316 -5634 2 30.086369 31.993647 4.231995 -5635 2 33.932165 39.866251 7.068893 -5636 1 32.059505 32.251117 2.629522 -5637 2 31.867763 34.040728 3.960388 -5638 1 31.932973 31.808697 5.917256 -5639 1 30.007373 39.943466 4.51009 -5640 2 39.207186 30.079079 1.703674 -5641 1 32.016417 34.359045 1.391175 -5642 1 32.0796 36.080574 2.990027 -5643 2 32.125016 37.982811 4.244242 -5644 1 32.039867 35.855789 5.754866 -5645 2 30.356301 36.250302 1.436559 -5646 1 32.110296 38.00744 1.426636 -5647 1 33.998604 30.067664 5.743991 -5648 2 33.695324 31.983255 4.383442 -5649 2 30.152086 36.019627 4.245065 -5650 2 34.240197 32.341445 1.32205 -5651 1 33.885438 34.090868 2.902626 -5652 2 34.178132 35.93225 4.482376 -5653 1 33.856287 33.915557 5.543055 -5654 2 34.187255 35.904801 1.570832 -5655 1 34.049489 37.902242 2.794215 -5656 1 34.196846 37.782622 5.597948 -5657 1 32.010141 29.994854 3.963328 -5658 1 30.085473 38.058327 2.970114 -5659 1 37.563886 30.425407 3.132393 -5660 1 35.867335 32.241913 3.116156 -5661 2 35.974255 34.126395 4.519526 -5662 1 36.004069 32.109611 5.814404 -5663 1 34.085538 39.906327 4.293478 -5664 1 36.097439 33.990507 1.502757 -5665 1 36.087679 36.048793 3.035352 -5666 2 36.278328 38.155374 4.063777 -5667 1 36.249913 36.355424 5.927679 -5668 2 31.890573 30.350964 1.619094 -5669 2 31.962807 37.754434 7.179059 -5670 1 35.973947 37.892913 1.48124 -5671 2 35.839322 30.204876 4.375075 -5672 1 37.935879 32.177401 4.195289 -5673 1 38.101493 38.10187 5.953049 -5674 2 37.852909 32.388628 1.664291 -5675 1 37.942171 34.0458 3.006996 -5676 2 38.2641 36.15208 4.530503 -5677 1 38.039433 34.206108 5.79566 -5678 1 33.979517 30.322401 2.668635 -5679 2 38.266202 35.993947 1.484331 -5680 1 38.067048 38.040012 2.752414 -5681 1 37.733806 30.096455 5.970187 -5682 1 39.682213 32.091472 5.993971 -5683 1 39.817487 31.930363 0.000367 -5684 1 36.043395 39.59783 5.676369 -5685 1 31.869558 32.098607 0.138261 -5686 1 39.734652 32.347843 3.042732 -5687 2 40.028718 38.187031 4.420077 -5688 1 35.900797 34.287592 6.911917 -5689 1 34.035098 34.219002 0.088382 -5690 1 35.958161 30.177564 1.36017 -5691 2 34.104037 39.871769 1.666144 -5692 2 31.713648 30.030149 13.126076 -5693 2 38.102561 35.967156 7.519894 -5694 2 31.857312 30.233676 7.601269 -5695 1 34.289545 38.267283 14.401123 -5696 2 35.86683 30.19377 7.315341 -5697 1 30.215661 34.162037 8.437432 -5698 2 32.177106 33.712521 7.258256 -5699 2 36.086337 30.089865 10.102229 -5700 1 31.904414 32.116466 8.706393 -5701 1 31.937094 33.843414 10.07911 -5702 1 31.979885 32.115442 11.535778 -5703 2 31.646163 34.054645 12.923349 -5704 2 34.238187 35.954151 7.232689 -5705 1 32.107596 35.868544 8.568472 -5706 1 31.872832 37.740296 10.246254 -5707 1 32.382757 36.08172 11.390228 -5708 1 31.907287 38.043268 12.759712 -5709 1 33.814113 30.280416 11.361764 -5710 1 30.217972 36.108976 12.75806 -5711 2 33.902634 32.114854 10.131038 -5712 1 33.57231 32.104408 13.09734 -5713 1 31.808268 30.066503 10.372268 -5714 1 34.074533 34.09759 8.82773 -5715 2 34.112978 35.879639 10.008535 -5716 1 33.847258 34.132738 11.781858 -5717 2 33.938795 36.222314 13.025522 -5718 2 29.978741 32.187816 10.235973 -5719 1 34.055911 38.08124 8.660649 -5720 1 33.602601 34.200907 14.256884 -5721 1 34.074479 38.033056 11.548004 -5722 2 36.270647 38.06342 7.227717 -5723 1 35.834976 32.087215 8.752976 -5724 2 36.060859 33.636235 10.421377 -5725 1 35.993855 31.835332 12.022895 -5726 2 35.800428 33.936835 13.252217 -5727 1 36.115212 35.929045 8.653718 -5728 2 36.22813 38.12211 10.18663 -5729 1 36.031176 36.067395 11.711353 -5730 2 36.290793 38.28804 13.110371 -5731 1 38.314803 39.87771 13.628157 -5732 2 37.813718 31.963763 10.266333 -5733 2 38.345306 31.61479 12.746628 -5734 1 37.993817 33.8253 8.828538 -5735 2 37.963385 36.024574 10.310583 -5736 1 37.917131 33.840219 11.529013 -5737 1 38.204273 36.194533 12.982689 -5738 1 38.223785 37.96125 8.694521 -5739 1 38.251957 38.103445 11.574783 -5740 1 32.162162 35.830151 14.368089 -5741 1 38.188088 39.835851 10.200529 -5742 2 37.943506 31.862097 7.486993 -5743 1 34.019779 32.099062 7.382655 -5744 1 37.835648 33.808569 14.272091 -5745 2 30.154664 36.008494 10.278616 -5746 2 34.005569 29.909902 14.221934 -5747 2 39.942399 30.201297 7.221972 -5748 1 31.669489 32.129787 14.202133 -5749 1 33.8553 30.102976 8.785283 -5750 1 36.285019 39.993992 8.473052 -5751 2 34.332311 39.811654 10.053333 -5752 1 32.287985 39.934755 8.544521 -5753 1 32.117424 39.894109 11.328559 -5754 1 34.070494 39.946648 12.675838 -5755 1 33.523905 30.237815 17.092452 -5756 1 37.796875 30.195733 20.074531 -5757 1 36.27689 36.076917 14.383428 -5758 1 31.912415 30.074316 18.962029 -5759 1 31.72877 30.195629 15.548548 -5760 1 39.683801 34.084414 18.996274 -5761 1 31.823255 34.23579 15.916954 -5762 1 32.081111 32.17144 17.423655 -5763 2 32.272671 34.141341 18.923237 -5764 1 31.890319 32.258592 20.174682 -5765 1 32.292252 37.789848 15.657298 -5766 1 31.865994 35.945048 17.430984 -5767 2 32.390605 38.101438 18.756338 -5768 1 32.536255 36.292415 20.33365 -5769 1 30.255802 37.826036 17.398086 -5770 2 30.361913 39.693462 15.767213 -5771 1 33.658364 32.195407 15.713634 -5772 1 37.521125 34.00621 20.179734 -5773 2 34.170474 31.959646 18.774747 -5774 2 30.146126 36.07111 19.193288 -5775 2 34.236512 36.009488 15.705407 -5776 1 33.893052 34.259763 17.152928 -5777 1 34.299465 36.26334 18.583767 -5778 1 34.414431 34.040341 19.801645 -5779 1 38.268782 38.067343 19.882736 -5780 1 38.192119 30.067346 14.65738 -5781 1 34.182659 38.172175 17.379208 -5782 1 34.285582 38.312236 20.114249 -5783 1 35.930101 31.821554 14.523145 -5784 1 38.166996 38.004859 14.725716 -5785 1 35.925271 33.697258 15.741088 -5786 1 35.628801 31.929644 17.21365 -5787 2 36.045808 34.231991 18.304721 -5788 1 36.066783 31.92807 19.890693 -5789 2 30.047091 31.872972 18.511468 -5790 1 38.23536 37.943903 17.225875 -5791 2 36.119549 38.085157 15.846243 -5792 1 36.28338 36.046451 17.021393 -5793 1 36.11202 38.183852 18.648108 -5794 1 36.196383 36.094959 20.14945 -5795 1 39.857714 32.070711 20.545667 -5796 2 38.277117 32.092018 16.056024 -5797 1 30.025257 33.999826 20.265429 -5798 2 37.984137 32.053017 18.664282 -5799 1 32.002215 39.814443 17.350923 -5800 2 38.174586 35.979296 18.941495 -5801 2 38.345772 36.135739 15.897296 -5802 1 38.047733 34.092532 17.193597 -5803 2 30.130578 35.962177 15.540359 -5804 2 36.401926 38.058554 21.346524 -5805 1 30.120957 38.000412 14.522433 -5806 1 30.488998 38.181884 20.233832 -5807 1 30.027329 34.063964 17.498188 -5808 1 37.840062 29.987227 17.565361 -5809 1 32.008478 30.033144 21.485715 -5810 2 39.774533 34.462138 21.415634 -5811 1 30.338184 36.208481 21.405811 -5812 1 29.947563 30.056036 17.165794 -5813 1 39.921352 31.819743 14.64622 -5814 2 34.22915 39.981504 21.655908 -5815 1 30.183329 38.19462 25.743477 -5816 1 35.907762 33.854845 21.824692 -5817 1 38.081846 38.241792 22.993384 -5818 2 34.075816 32.199578 21.47467 -5819 1 32.064265 31.912891 22.91255 -5820 1 31.883139 33.912773 24.608383 -5821 1 31.812805 31.862315 26.174015 -5822 2 32.311833 34.450426 27.53752 -5823 1 32.200878 36.145135 23.147334 -5824 2 32.211767 38.313372 24.442593 -5825 1 32.252693 36.173296 25.56014 -5826 2 32.184178 37.824314 27.059278 -5827 2 35.878916 30.070226 21.715039 -5828 1 37.668689 30.050641 23.045191 -5829 2 31.790668 34.251576 21.855242 -5830 1 30.175916 38.136754 23.248784 -5831 1 33.79328 31.909522 24.576174 -5832 2 33.915875 32.018888 27.178426 -5833 1 33.839278 34.11599 23.063711 -5834 2 34.250078 35.934833 24.487018 -5835 1 33.990054 34.106505 25.930061 -5836 1 34.091025 36.282124 27.332172 -5837 1 39.883217 38.455893 24.705928 -5838 2 38.008034 36.021219 27.398438 -5839 1 34.624327 37.896007 23.016853 -5840 1 34.168936 37.954274 25.436951 -5841 1 39.89339 34.048173 27.027007 -5842 1 38.248268 36.455753 21.536765 -5843 1 35.611768 31.698556 23.347142 -5844 2 36.148802 34.042768 24.34925 -5845 1 35.930043 32.125519 25.878398 -5846 2 35.950538 34.005205 27.219195 -5847 1 37.955393 34.076875 25.799656 -5848 1 37.973062 38.01909 26.230315 -5849 1 36.411999 36.023781 22.980871 -5850 2 36.283519 37.906374 24.521157 -5851 1 36.105429 36.189959 25.968065 -5852 2 35.830991 38.301536 27.267321 -5853 1 30.231426 34.188738 26.125408 -5854 1 30.281973 34.136127 28.552033 -5855 2 37.785563 31.866932 24.278312 -5856 2 31.348335 30.244331 27.485493 -5857 2 37.966809 32.115632 27.589764 -5858 2 35.66017 29.988788 24.878779 -5859 1 38.277476 34.130765 22.79239 -5860 2 37.959129 36.154297 24.437008 -5861 1 33.713618 30.108282 28.642398 -5862 1 39.822964 31.905463 23.110805 -5863 1 37.492689 32.09291 21.995043 -5864 2 30.127031 36.064739 24.638111 -5865 1 35.533243 30.110728 27.243438 -5866 1 36.070605 31.93122 28.695839 -5867 2 34.291131 35.85795 21.75028 -5868 1 31.938061 32.142881 28.504169 -5869 1 33.986813 39.867909 27.012668 -5870 1 30.10822 37.992396 28.395198 -5871 1 39.800701 30.030956 24.347523 -5872 2 39.892552 29.979658 27.134291 -5873 2 32.228297 37.952841 21.875429 -5874 2 39.977135 34.107266 24.499149 -5875 1 39.846344 36.406036 26.033584 -5876 1 32.059083 40.009476 28.464272 -5877 1 35.959269 39.965152 25.93262 -5878 2 30.460566 32.139968 24.447603 -5879 2 39.881804 38.087413 21.696502 -5880 1 30.134489 36.163809 33.336193 -5881 1 37.575878 38.100411 28.849489 -5882 1 37.662104 38.133383 31.571418 -5883 1 32.362045 39.87867 34.884405 -5884 1 39.873173 36.224308 34.920349 -5885 1 31.991424 34.085923 29.999612 -5886 1 31.815171 32.168756 31.641691 -5887 2 31.782096 34.063184 33.062024 -5888 1 31.718037 31.953527 34.554814 -5889 1 39.862898 38.376226 32.906485 -5890 1 37.551931 30.038119 34.432157 -5891 1 31.780802 37.997046 30.254783 -5892 1 31.834761 35.939821 31.604936 -5893 2 32.041736 38.210181 33.326919 -5894 1 32.203699 35.869978 34.596577 -5895 1 34.008946 38.074601 28.827076 -5896 1 37.899592 29.974959 28.916731 -5897 1 38.030007 33.96835 28.91396 -5898 2 33.846774 32.085103 30.081464 -5899 1 29.952597 30.143437 34.499248 -5900 1 33.915497 32.111271 33.150301 -5901 1 31.790321 30.23064 29.991804 -5902 2 37.907438 32.157735 35.935104 -5903 2 33.84716 36.05681 30.26538 -5904 1 34.0432 34.280307 31.67674 -5905 2 34.011752 36.10558 33.143956 -5906 1 33.824017 34.085576 34.552777 -5907 1 34.194027 34.072791 28.967937 -5908 1 33.894909 38.222801 31.657741 -5909 1 33.881652 38.078172 34.899329 -5910 1 38.119296 38.056464 34.569681 -5911 1 34.291634 39.920546 33.178111 -5912 1 33.581454 29.993619 34.681796 -5913 2 36.053229 33.87704 30.318866 -5914 1 35.873901 31.88411 31.537273 -5915 1 35.89848 33.774876 32.823618 -5916 1 35.828028 32.348885 34.478807 -5917 1 35.672787 37.928294 30.518119 -5918 1 35.989671 35.945619 31.826779 -5919 2 35.97259 38.32967 33.142576 -5920 1 35.703331 35.814769 34.580449 -5921 1 33.817908 30.208146 31.599942 -5922 1 35.844503 36.12033 28.831087 -5923 1 38.261976 32.096366 30.088155 -5924 2 37.797891 31.9048 33.114668 -5925 1 39.55682 31.880323 34.531549 -5926 2 37.75043 36.193675 30.248336 -5927 1 38.393997 33.98513 31.905095 -5928 2 37.963057 36.355009 33.181745 -5929 1 37.797425 34.035854 34.376018 -5930 1 30.050396 34.271558 31.538997 -5931 1 39.815357 36.070726 31.654601 -5932 2 39.731271 30.032678 30.327233 -5933 1 39.915975 31.952921 31.714062 -5934 2 31.84562 29.966231 33.068673 -5935 1 31.85693 36.270476 28.934934 -5936 1 31.866016 39.844488 31.814385 -5937 1 30.092134 34.094244 34.755273 -5938 1 39.694807 30.040539 32.997642 -5939 1 36.196648 35.960439 42.925128 -5940 2 32.015598 37.930066 36.230869 -5941 1 37.674069 30.102473 37.130906 -5942 1 39.699003 32.118698 37.217773 -5943 2 29.963786 31.633701 39.162197 -5944 1 32.058675 39.814086 37.607409 -5945 1 35.842471 33.971675 35.989822 -5946 1 34.028551 38.060871 42.983375 -5947 1 31.588672 31.941435 37.383683 -5948 2 31.694069 33.998273 38.693202 -5949 1 31.930294 31.884957 40.381472 -5950 2 32.11349 33.999595 41.798502 -5951 1 31.876844 36.011394 37.307134 -5952 2 31.893158 37.928813 38.973436 -5953 1 31.81531 35.668229 40.479844 -5954 2 31.787646 38.142244 41.698514 -5955 1 31.925559 36.23881 42.924197 -5956 1 36.004443 37.899297 36.000218 -5957 1 38.451312 38.205323 40.038254 -5958 2 33.656378 31.907332 38.819792 -5959 1 33.99011 31.933293 41.627228 -5960 2 37.707146 36.123239 36.332034 -5961 1 33.657247 33.955416 37.665398 -5962 1 33.73943 36.151957 39.054731 -5963 1 33.605884 33.957716 40.193208 -5964 2 34.011058 36.048882 41.690411 -5965 1 38.130598 34.242802 40.052446 -5966 1 34.167865 38.117836 37.628936 -5967 1 34.142536 38.424699 40.41195 -5968 1 40.005739 32.215658 40.003237 -5969 1 39.521882 33.977557 36.015643 -5970 1 38.214368 38.282583 37.333443 -5971 1 31.918418 33.931512 36.157998 -5972 1 35.612055 32.074774 37.387219 -5973 2 35.5831 34.04957 39.047544 -5974 1 35.75246 32.088086 40.149631 -5975 2 35.615657 33.824419 41.713165 -5976 1 35.638569 36.061296 37.614952 -5977 2 36.358444 37.816896 38.884174 -5978 1 35.987046 36.034802 40.28745 -5979 1 36.122176 38.157473 41.827978 -5980 1 37.730089 30.067171 42.889333 -5981 2 39.944726 33.833791 41.642053 -5982 2 37.765477 32.166294 38.745053 -5983 2 38.099767 31.876153 41.350163 -5984 2 38.066621 36.442839 41.48951 -5985 1 37.726393 34.24931 37.606618 -5986 1 38.065514 36.286433 39.031222 -5987 1 37.664687 30.041804 39.941583 -5988 1 36.1403 39.743151 39.963443 -5989 2 34.004128 36.124387 36.139274 -5990 1 38.008343 33.918454 43.060491 -5991 1 36.098653 32.233378 42.976295 -5992 1 30.058867 38.134404 37.476791 -5993 2 35.662195 29.860797 35.905075 -5994 1 33.53205 30.001458 37.176731 -5995 1 38.387155 38.05525 43.009631 -5996 1 36.188595 39.834331 37.505629 -5997 1 39.656895 29.968268 41.372509 -5998 1 39.786156 36.00049 42.804021 -5999 2 33.855117 32.268762 36.090908 -6000 2 31.856527 30.044242 36.001804 diff --git a/examples/cauchystat/NiAl_cool/lammps.in b/examples/cauchystat/NiAl_cool/lammps.in deleted file mode 100644 index 4aa5d327a9..0000000000 --- a/examples/cauchystat/NiAl_cool/lammps.in +++ /dev/null @@ -1,45 +0,0 @@ -units metal -atom_style atomic -atom_modify map array - -processors 1 1 1 - -# Box and atom positions: -boundary p p p -read_data input.dat - -# Atomic mass: -mass 1 58.69 -mass 2 26.98154 - -# Potential, Al fcc crystal -pair_style eam/alloy -pair_coeff * * ../Mishin-Ni-Al-2009.eam.alloy Ni Al - -thermo 100 -thermo_style custom step temp pxx pyy pzz lx ly lz -compute cna all cna/atom 2.8 - -velocity all create 2400.0 4928459 rot yes dist gaussian - -fix 1 all npt temp 1200.0 1200.0 1.0 x 0.0 0.0 0.1 y 0.0 0.0 0.1 z -2800.0 -2800.0 0.1 couple none cauchystat 0.001 no - -dump 1 all cfg 1000 test*.cfg mass type xs ys zs type c_cna - -timestep 0.002 - -variable l equal lz -variable p equal pzz -variable t equal temp - -fix avg all ave/time 1 1000 1000 v_t v_l v_p file avg.txt - -velocity all create 2400 4928459 rot yes dist gaussian - -run 10000 - -unfix 1 - -fix 1 all npt temp 1200.0 300.0 1.0 x 0.0 0.0 0.1 y 0.0 0.0 0.1 z -2800.0 -2800.0 0.1 couple none cauchystat 0.001 yes - -run 100000 diff --git a/examples/cauchystat/NiAl_slow_stretch_CS/input.dat b/examples/cauchystat/NiAl_slow_stretch_CS/input.dat deleted file mode 100644 index 3b99f3ea8f..0000000000 --- a/examples/cauchystat/NiAl_slow_stretch_CS/input.dat +++ /dev/null @@ -1,6009 +0,0 @@ -Position data for MD simulation - -6000 atoms -2 atom types -0.0000 39.972658977840510 xlo xhi -0.0000 39.970082402467646 ylo yhi -0.0000 43.077168594479417 zlo zhi -Atoms - -1 1 2.265603 1.699233 2.96682 -2 2 2.147625 3.958175 4.336466 -3 1 1.997414 2.08615 5.681268 -4 2 6.222234 0.12344 4.55833 -5 1 4.247865 9.8684 7.188432 -6 2 2.226404 4.008191 1.332846 -7 1 2.558125 5.881235 2.799624 -8 2 2.112892 8.008518 4.084836 -9 1 2.366112 6.194696 5.83623 -10 2 0.308528 9.773154 7.249786 -11 1 1.861699 8.008727 1.634831 -12 2 0.245314 5.864464 4.508327 -13 1 8.139953 -0.02424 5.747139 -14 1 0.178338 3.676069 2.91793 -15 2 0.021903 9.933735 1.645872 -16 1 4.094944 3.990727 2.989711 -17 2 4.25173 6.125247 4.299378 -18 1 4.004975 4.261809 5.650881 -19 2 4.233414 9.883798 4.412874 -20 2 4.158657 5.985987 1.452914 -21 1 3.943003 7.917155 2.809851 -22 1 4.013002 8.032118 5.709128 -23 1 3.913817 0.208102 0.200173 -24 2 4.11186 2.115952 4.39711 -25 1 4.091794 8.080277 0.383691 -26 1 8.239262 4.128528 0.14417 -27 1 4.164942 2.294329 1.435205 -28 1 6.018476 2.048784 2.978318 -29 1 6.189263 4.123374 4.429365 -30 1 5.731913 2.039386 5.760723 -31 2 8.125123 2.396376 4.334063 -32 2 5.956145 3.961461 1.710606 -33 1 6.097732 6.223054 3.105619 -34 2 6.260701 8.269814 4.403081 -35 1 6.135592 6.191014 6.014208 -36 2 6.118481 0.280536 1.660297 -37 2 5.95371 8.134065 1.459117 -38 1 8.112 7.978937 6.025785 -39 1 8.230735 0.317331 0.287501 -40 1 7.984577 0.451106 2.876758 -41 1 8.121358 4.469963 3.000969 -42 2 8.0024 6.398776 4.506808 -43 1 8.265498 4.145515 5.950951 -44 1 8.093687 2.336039 1.599762 -45 2 7.786786 6.082031 1.369435 -46 1 8.051625 8.388788 2.947011 -47 2 1.887169 0.10205 1.232231 -48 1 3.814096 0.184819 2.93152 -49 2 5.999738 4.024912 6.895817 -50 1 0.20906 5.67262 1.62315 -51 1 2.22916 6.007717 0.143509 -52 1 9.864584 8.16224 1.516273 -53 1 0.029687 7.997328 3.090548 -54 1 0.158584 7.813035 5.663186 -55 1 6.149844 9.939956 0.040852 -56 1 1.871208 1.766851 8.960428 -57 2 2.233107 3.807827 10.095989 -58 1 1.960237 1.933156 11.733738 -59 1 2.028536 4.090031 13.399625 -60 2 0.096818 1.982978 13.367683 -61 1 1.962538 5.967991 8.575587 -62 2 1.779869 8.006286 9.997749 -63 1 2.261369 6.075808 11.262585 -64 1 1.878689 7.795749 12.973992 -65 1 8.066595 6.091936 7.32151 -66 2 6.004471 8.10958 7.337536 -67 2 3.807826 9.773306 13.107995 -68 2 3.628292 2.338356 7.627483 -69 1 4.142245 4.127148 8.640624 -70 2 4.430475 5.841591 10.077295 -71 1 3.968136 4.281892 11.552649 -72 2 3.926926 6.059939 13.034315 -73 1 4.163584 8.009554 8.875445 -74 1 3.841536 8.095992 11.564038 -75 1 1.972543 4.098752 7.26509 -76 1 9.833961 8.179066 10.053046 -77 1 3.959427 0.070701 8.628349 -78 1 4.000206 1.99734 10.467815 -79 1 0.175393 5.813256 10.208259 -80 2 3.991668 2.115114 12.987731 -81 2 8.056411 2.098025 12.865242 -82 1 5.64748 2.156225 8.497216 -83 2 6.159432 4.014865 10.196613 -84 1 6.214032 2.165249 11.651601 -85 1 5.856347 3.961477 13.023239 -86 1 7.948437 0.352004 11.304002 -87 2 0.129981 2.04383 7.39824 -88 1 6.181909 5.856377 8.431434 -89 1 5.991539 7.847191 10.091845 -90 1 5.975418 5.816241 11.895283 -91 1 5.86549 8.043369 13.028812 -92 2 4.166236 6.085137 7.231975 -93 1 0.439458 3.829864 11.550798 -94 2 0.21596 5.973334 12.667734 -95 1 10.017517 5.823156 11.545694 -96 1 8.076092 4.274718 8.540188 -97 2 7.924969 6.011881 10.326107 -98 1 8.12022 3.959556 11.608595 -99 1 8.110671 6.08702 13.353502 -100 1 8.135035 2.224763 9.76071 -101 1 8.056404 8.04948 8.608732 -102 1 7.867682 7.986347 11.444105 -103 1 0.057722 3.824193 8.62711 -104 1 9.981584 4.247366 7.362993 -105 2 4.013801 9.873296 9.982524 -106 1 2.329565 8.116478 7.435377 -107 2 5.950495 0.34488 9.79838 -108 1 4.334027 0.076447 11.746114 -109 2 7.945804 9.995075 13.009688 -110 1 2.027284 10.048274 11.752786 -111 2 7.985809 2.177851 7.348854 -112 2 0.227187 9.715111 13.080145 -113 1 4.369771 0.043973 14.298992 -114 1 9.913252 6.303629 8.785055 -115 1 7.984689 3.996322 14.285297 -116 1 6.286022 9.901661 11.434457 -117 2 9.978329 0.129998 10.093528 -118 2 9.898021 7.994926 13.146433 -119 1 2.438629 0.033347 18.603552 -120 2 2.19485 3.927092 15.921048 -121 1 2.266036 2.0106 17.298124 -122 2 2.190625 4.002775 18.808528 -123 1 2.529808 1.858131 19.802924 -124 1 2.121536 8.100548 15.903723 -125 1 1.999174 5.945764 17.409821 -126 2 2.399752 8.317077 18.513998 -127 1 2.085018 6.322971 20.123548 -128 1 0.132331 7.834943 14.417244 -129 2 0.191888 2.055829 18.456008 -130 1 8.035826 8.278124 14.487514 -131 2 3.964165 5.965398 16.034244 -132 1 3.977251 4.106829 17.287135 -133 1 4.083409 6.186923 18.749777 -134 1 4.118697 4.16167 19.924445 -135 2 0.168486 10.031098 15.738364 -136 1 9.834776 5.750065 20.057158 -137 1 4.513739 7.925063 17.284367 -138 1 0.224638 6.311966 18.562 -139 1 4.05173 8.065927 20.327367 -140 1 4.020498 7.877514 14.44079 -141 1 4.143142 1.813412 15.801004 -142 1 2.214548 1.829361 14.565296 -143 2 4.407757 2.318175 18.721975 -144 2 6.016403 3.935276 15.745347 -145 1 6.343375 1.849436 17.205365 -146 2 6.615021 3.988745 18.735217 -147 1 6.455591 1.950789 20.137809 -148 1 6.179932 9.794709 17.21643 -149 2 6.237707 7.849925 15.743301 -150 1 6.151976 5.985244 17.227932 -151 2 6.178229 7.773511 18.829625 -152 1 6.147011 5.845856 20.064817 -153 2 4.124664 9.743815 15.83873 -154 1 8.065185 1.771116 18.726928 -155 1 6.149514 1.938847 14.518073 -156 2 8.136444 6.024316 15.560218 -157 1 8.139342 3.949043 16.901849 -158 1 8.143554 6.219717 18.549219 -159 1 8.181775 3.5232 20.518875 -160 1 1.876074 6.12577 14.691379 -161 2 9.729818 3.920007 18.490075 -162 1 8.23825 8.027751 17.068995 -163 1 4.103417 9.893021 18.750211 -164 1 8.095744 7.73466 20.44646 -165 2 8.348453 1.630886 15.803105 -166 1 0.114526 2.216943 15.877394 -167 2 4.178332 6.016772 21.363439 -168 1 1.899673 9.855866 20.182773 -169 1 0.06894 8.212942 17.306197 -170 1 5.88851 5.844373 14.487209 -171 1 0.059742 4.374953 14.646907 -172 1 3.878323 4.145978 14.489788 -173 2 4.294142 2.069501 21.441214 -174 1 8.064234 9.497999 18.769847 -175 1 0.054546 7.976599 20.116681 -176 1 8.525044 0.101361 14.328798 -177 2 9.906967 7.812697 18.799053 -178 1 2.121141 3.832231 21.274441 -179 2 0.246791 1.874452 21.452019 -180 1 0.500726 0.008693 17.033685 -181 1 6.032205 3.972779 21.459867 -182 1 6.228607 9.827219 20.293439 -183 1 1.999764 9.905509 14.422608 -184 2 0.044761 6.18458 27.221929 -185 1 2.164891 1.954699 22.914632 -186 1 2.035794 3.798225 24.476506 -187 1 2.328794 2.047568 26.040855 -188 2 1.965861 4.051758 27.120895 -189 1 0.39788 0.200226 23.107141 -190 1 2.011846 6.031691 22.819617 -191 2 1.784066 7.880599 24.253767 -192 1 1.950682 5.925284 25.629958 -193 1 2.108877 7.833186 26.877206 -194 2 1.9192 8.201599 21.667898 -195 1 1.939171 2.209822 28.547 -196 1 0.09557 5.722002 24.118636 -197 1 0.059192 4.031101 25.673341 -198 1 4.156274 3.971969 23.108429 -199 2 3.825507 5.899235 24.328013 -200 1 3.962602 4.17038 25.711458 -201 2 4.032842 6.194348 27.234817 -202 2 8.150839 1.460228 21.735164 -203 1 3.925207 7.821015 23.037858 -204 1 6.069434 7.849806 21.58918 -205 1 4.081687 8.179044 25.728661 -206 1 2.137517 -0.00179 27.361868 -207 1 8.039753 0.124328 26.068543 -208 2 4.114742 2.131087 24.2305 -209 1 3.99908 4.281021 28.716402 -210 2 4.144388 2.150469 27.49599 -211 1 6.148998 1.905923 22.975359 -212 2 6.074117 3.917472 24.352374 -213 1 6.069578 2.074776 25.719405 -214 1 6.002174 3.93371 27.186956 -215 1 0.192839 0.413941 26.157945 -216 1 6.145721 5.660607 23.004422 -217 2 6.18359 8.088504 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8.515126 26.113194 32.84505 -1794 1 7.87091 24.018792 34.546662 -1795 1 5.909818 25.850381 28.937903 -1796 1 1.855525 29.676343 34.402837 -1797 2 1.806439 20.090666 33.039472 -1798 1 7.815372 27.873969 28.973443 -1799 1 -0.02518 25.867262 33.08217 -1800 1 3.939606 30.030686 30.487508 -1801 2 9.865144 23.649709 33.392389 -1802 2 5.779526 24.002128 35.664124 -1803 1 4.247465 25.982549 35.80953 -1804 1 0.012022 24.158979 31.494615 -1805 1 5.845287 29.969937 34.69315 -1806 2 8.436976 26.046465 35.817561 -1807 1 7.795622 29.898607 30.128644 -1808 2 7.768617 22.215251 35.856895 -1809 2 7.93569 29.886699 33.196602 -1810 1 9.883607 29.838353 28.975335 -1811 1 1.946835 22.280384 43.066776 -1812 1 1.809398 21.863784 37.34337 -1813 1 1.976036 23.841911 38.755625 -1814 1 1.767727 21.824198 40.56452 -1815 2 2.083742 24.029053 41.450421 -1816 1 7.673731 20.199299 40.455877 -1817 1 3.883739 20.063979 37.43537 -1818 1 1.962857 26.015373 37.239011 -1819 1 1.855742 27.865871 38.783671 -1820 1 1.946136 26.114415 40.445845 -1821 2 1.342698 28.356759 41.677946 -1822 1 3.866247 20.162337 40.622125 -1823 2 3.812973 22.128926 36.114766 -1824 2 3.760552 22.028975 39.129353 -1825 1 0.120133 23.847195 42.944885 -1826 2 4.069006 22.075437 41.863068 -1827 1 5.907632 20.36903 38.501592 -1828 1 7.614067 27.968649 40.109559 -1829 1 3.897056 23.931653 37.406176 -1830 2 3.67424 25.831572 38.858188 -1831 1 3.697155 23.98423 40.178372 -1832 1 3.958999 25.902285 41.773782 -1833 1 9.702453 23.999789 36.048473 -1834 1 3.862301 28.11303 37.453615 -1835 1 3.835868 28.048802 40.57469 -1836 2 5.854804 27.776995 36.005821 -1837 1 2.018496 25.837414 42.987148 -1838 1 9.960693 25.630934 40.389307 -1839 1 5.93268 22.351558 37.363635 -1840 2 5.893761 24.161725 38.918752 -1841 1 5.808679 22.051292 40.511129 -1842 2 5.792864 24.116392 41.554559 -1843 1 9.64084 21.675057 37.276932 -1844 1 7.878713 27.9153 37.259426 -1845 1 6.175937 25.901323 37.471311 -1846 2 5.668787 27.931006 38.872038 -1847 1 5.833656 25.947867 40.073284 -1848 1 5.883119 28.188772 41.564271 -1849 1 1.968623 29.760132 37.440712 -1850 1 9.720776 21.931094 39.953354 -1851 2 7.71657 22.068573 38.940437 -1852 2 7.898218 26.165005 41.361678 -1853 2 8.069464 22.281116 41.639197 -1854 1 7.671941 23.931719 37.325285 -1855 2 8.224025 25.910081 38.501705 -1856 1 7.708054 24.12057 40.424826 -1857 1 3.73122 28.006194 42.903257 -1858 2 5.75438 20.111404 41.853219 -1859 1 9.831402 27.825768 38.818019 -1860 1 7.702614 27.990192 42.759806 -1861 1 7.820889 20.318748 42.936774 -1862 1 1.696378 24.07867 36.051323 -1863 2 1.929861 28.112364 36.261692 -1864 2 5.747452 20.123867 36.071437 -1865 2 9.856877 23.914266 38.695016 -1866 2 7.756468 29.813429 38.680181 -1867 1 7.682461 20.159018 37.348845 -1868 2 9.776865 19.989829 38.744389 -1869 1 9.815791 23.652977 41.622566 -1870 1 7.858893 24.330568 42.982576 -1871 2 8.002454 29.899258 41.430193 -1872 1 0.077683 20.128085 37.436998 -1873 2 1.626697 20.07364 41.83293 -1874 1 1.777573 31.918884 4.516148 -1875 1 0.224503 39.97377 2.747323 -1876 1 2.112303 39.817069 4.528393 -1877 2 1.981899 32.150865 1.347891 -1878 1 2.322442 33.979858 3.19387 -1879 2 2.096374 36.191635 4.230691 -1880 1 1.999648 34.152278 5.938815 -1881 1 1.73114 30.291033 2.935219 -1882 1 3.665367 29.983954 1.275677 -1883 2 1.943018 36.004664 1.697384 -1884 1 2.019378 38.176143 2.972324 -1885 1 2.19126 37.889176 5.917314 -1886 1 0.019605 35.984478 3.104091 -1887 2 7.787834 30.403461 4.344497 -1888 1 6.050812 33.918162 -0.027918 -1889 1 3.814711 31.691419 2.816277 -1890 2 4.20332 33.715468 4.180703 -1891 1 3.914581 32.066382 5.971622 -1892 2 3.895933 33.805468 1.20281 -1893 1 4.340385 35.802877 2.943593 -1894 1 4.271659 37.949305 4.314292 -1895 1 4.068788 35.686982 5.513423 -1896 2 4.190929 37.662517 7.182865 -1897 2 4.200636 38.226632 1.691189 -1898 1 9.716958 31.962759 4.249426 -1899 1 5.810481 32.019245 4.382481 -1900 1 5.938979 35.885235 7.16864 -1901 1 0.267384 35.760048 6.061532 -1902 2 6.018619 31.95181 1.612974 -1903 1 5.938914 34.057443 2.77635 -1904 2 6.183116 36.065698 4.376274 -1905 1 6.089476 34.019022 5.411901 -1906 1 6.359106 35.990867 1.578601 -1907 1 6.152011 38.058648 2.943561 -1908 1 5.711164 30.034724 2.988084 -1909 1 6.045542 37.798257 5.727308 -1910 1 8.009398 36.153578 0.053676 -1911 1 0.238276 33.896375 4.533811 -1912 1 7.902329 32.340963 2.922426 -1913 2 8.222407 34.13168 4.116176 -1914 1 7.936717 32.22354 5.888103 -1915 2 8.123641 38.41175 1.891536 -1916 2 7.927555 34.06589 1.21075 -1917 1 8.412195 35.913547 2.85742 -1918 1 8.139566 38.142702 4.120627 -1919 1 8.317254 36.194514 5.407003 -1920 1 4.034964 36.04412 0.47011 -1921 2 3.83481 30.240395 4.561724 -1922 2 0.249553 38.107374 7.140438 -1923 1 2.126706 37.874136 0.15149 -1924 1 9.770714 33.872567 5.735309 -1925 1 7.651907 31.89674 -0.001589 -1926 1 6.265497 38.190114 0.387488 -1927 2 0.091323 38.034686 1.579889 -1928 1 6.013525 30.091058 5.903567 -1929 2 9.613745 31.989409 1.558474 -1930 1 9.893134 38.099463 -0.000176 -1931 1 0.012372 34.088485 1.353111 -1932 1 1.957372 34.025261 0.135755 -1933 1 9.930552 30.036571 0.064988 -1934 1 1.356847 30.09059 0.587218 -1935 2 2.165378 39.90345 7.155948 -1936 1 9.928802 38.103943 5.693619 -1937 1 4.231897 39.892291 5.78739 -1938 2 3.93426 34.036259 7.069656 -1939 2 2.074177 32.270109 10.089125 -1940 1 3.932043 30.108354 7.345143 -1941 2 1.820986 31.836134 13.124076 -1942 1 1.929382 34.316614 8.776464 -1943 2 2.083627 36.058658 10.081855 -1944 1 1.997221 33.916084 11.577718 -1945 1 2.267799 35.662279 13.073333 -1946 2 4.209744 30.111608 9.908398 -1947 1 2.104601 38.082098 8.735584 -1948 2 8.24053 38.05696 7.216926 -1949 1 2.109203 38.067126 11.734018 -1950 2 0.042241 38.005125 10.32451 -1951 1 1.957287 39.865839 10.426779 -1952 2 8.203196 30.05132 9.912922 -1953 1 2.246349 30.143579 11.639665 -1954 1 4.199959 32.106503 8.70465 -1955 1 3.976417 34.112906 10.198306 -1956 1 3.884958 31.967651 11.562891 -1957 2 4.063522 34.032621 13.004991 -1958 1 4.232266 36.19468 8.962151 -1959 2 4.097197 38.230412 10.13239 -1960 1 4.118617 35.849094 11.679739 -1961 2 4.350691 37.885411 12.898671 -1962 1 6.201046 32.417633 10.15369 -1963 2 5.816252 31.722772 13.101456 -1964 1 6.157578 39.769939 7.197304 -1965 1 6.184596 34.126547 8.504052 -1966 2 6.346713 35.703957 10.195727 -1967 1 6.288059 33.992499 11.799552 -1968 1 6.483281 35.967443 12.860859 -1969 2 7.835082 34.145462 7.179037 -1970 1 6.256423 37.691882 8.993285 -1971 1 6.2337 37.988064 11.537765 -1972 2 9.772215 31.919829 7.180665 -1973 1 7.981132 32.165581 14.333143 -1974 1 2.309997 36.061233 7.359038 -1975 1 4.433034 36.045633 14.35862 -1976 1 7.955328 32.223129 8.507808 -1977 2 8.286523 34.141907 10.013388 -1978 1 7.939052 31.949186 11.600717 -1979 1 8.104476 34.231193 13.030137 -1980 2 1.884476 31.865234 7.19113 -1981 1 8.333692 36.082489 8.414603 -1982 2 8.168537 38.03579 10.329742 -1983 1 8.420403 35.985684 11.517078 -1984 1 8.327179 38.029547 12.910471 -1985 2 6.20532 31.903657 7.381951 -1986 2 0.085009 37.638839 13.154459 -1987 1 7.552329 30.251663 13.212821 -1988 2 2.355047 39.830169 13.072665 -1989 1 0.148785 31.885164 11.209718 -1990 1 1.848807 30.245173 8.940225 -1991 1 0.166389 36.076965 8.575072 -1992 1 5.894085 30.228735 11.200379 -1993 1 0.232408 36.202468 11.578646 -1994 1 2.4752 37.687884 14.341623 -1995 1 0.334254 39.866494 8.663952 -1996 1 0.04027 39.756099 11.961945 -1997 1 0.083418 34.195005 10.175316 -1998 2 0.043097 34.005541 7.193221 -1999 2 0.052476 33.834131 12.929227 -2000 1 8.114393 39.929142 8.406226 -2001 1 6.281515 37.719535 14.225496 -2002 2 9.768912 32.130689 12.866513 -2003 1 9.864669 32.192496 10.045288 -2004 1 0.028148 32.153045 8.783822 -2005 2 6.417236 39.879341 13.202851 -2006 1 8.005375 39.836615 20.349358 -2007 2 2.017709 31.870952 15.889762 -2008 2 7.716399 30.062983 18.430151 -2009 2 2.119264 32.351346 19.061283 -2010 2 6.658976 39.77428 18.733464 -2011 2 2.321302 35.607604 15.702355 -2012 1 1.966843 34.024507 17.339235 -2013 2 2.33321 35.646813 18.814154 -2014 1 1.794484 34.194282 20.582509 -2015 1 1.984336 29.928657 17.680043 -2016 1 2.238075 37.571948 17.445144 -2017 1 4.466772 39.923317 17.544828 -2018 1 2.072213 37.924398 20.106708 -2019 1 3.990864 31.761546 14.785242 -2020 1 4.020518 33.927189 15.729606 -2021 1 3.897539 31.807357 17.561737 -2022 1 4.265924 33.937397 18.871352 -2023 1 4.376327 32.03663 20.389624 -2024 1 6.400496 39.782735 15.767263 -2025 2 4.461272 37.709843 15.835142 -2026 1 4.42096 35.817684 17.119638 -2027 2 4.054798 37.811976 18.867409 -2028 1 3.994208 35.957797 20.233365 -2029 1 1.972412 30.096734 20.271564 -2030 1 5.988832 31.90054 15.667667 -2031 2 6.100535 31.913125 18.798462 -2032 1 0.28224 35.927235 17.246921 -2033 1 9.878186 30.085685 17.138849 -2034 1 6.416487 35.895999 15.857104 -2035 2 5.962689 34.078738 16.936543 -2036 1 6.325491 35.483857 19.110752 -2037 1 6.245971 33.832167 20.618167 -2038 1 6.042072 33.77268 14.335557 -2039 1 6.090957 37.771252 17.365844 -2040 1 9.965189 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29.983878 33.982126 0.04316 -5634 2 30.086369 31.993647 4.231995 -5635 2 33.932165 39.866251 7.068893 -5636 1 32.059505 32.251117 2.629522 -5637 2 31.867763 34.040728 3.960388 -5638 1 31.932973 31.808697 5.917256 -5639 1 30.007373 39.943466 4.51009 -5640 2 39.207186 30.079079 1.703674 -5641 1 32.016417 34.359045 1.391175 -5642 1 32.0796 36.080574 2.990027 -5643 2 32.125016 37.982811 4.244242 -5644 1 32.039867 35.855789 5.754866 -5645 2 30.356301 36.250302 1.436559 -5646 1 32.110296 38.00744 1.426636 -5647 1 33.998604 30.067664 5.743991 -5648 2 33.695324 31.983255 4.383442 -5649 2 30.152086 36.019627 4.245065 -5650 2 34.240197 32.341445 1.32205 -5651 1 33.885438 34.090868 2.902626 -5652 2 34.178132 35.93225 4.482376 -5653 1 33.856287 33.915557 5.543055 -5654 2 34.187255 35.904801 1.570832 -5655 1 34.049489 37.902242 2.794215 -5656 1 34.196846 37.782622 5.597948 -5657 1 32.010141 29.994854 3.963328 -5658 1 30.085473 38.058327 2.970114 -5659 1 37.563886 30.425407 3.132393 -5660 1 35.867335 32.241913 3.116156 -5661 2 35.974255 34.126395 4.519526 -5662 1 36.004069 32.109611 5.814404 -5663 1 34.085538 39.906327 4.293478 -5664 1 36.097439 33.990507 1.502757 -5665 1 36.087679 36.048793 3.035352 -5666 2 36.278328 38.155374 4.063777 -5667 1 36.249913 36.355424 5.927679 -5668 2 31.890573 30.350964 1.619094 -5669 2 31.962807 37.754434 7.179059 -5670 1 35.973947 37.892913 1.48124 -5671 2 35.839322 30.204876 4.375075 -5672 1 37.935879 32.177401 4.195289 -5673 1 38.101493 38.10187 5.953049 -5674 2 37.852909 32.388628 1.664291 -5675 1 37.942171 34.0458 3.006996 -5676 2 38.2641 36.15208 4.530503 -5677 1 38.039433 34.206108 5.79566 -5678 1 33.979517 30.322401 2.668635 -5679 2 38.266202 35.993947 1.484331 -5680 1 38.067048 38.040012 2.752414 -5681 1 37.733806 30.096455 5.970187 -5682 1 39.682213 32.091472 5.993971 -5683 1 39.817487 31.930363 0.000367 -5684 1 36.043395 39.59783 5.676369 -5685 1 31.869558 32.098607 0.138261 -5686 1 39.734652 32.347843 3.042732 -5687 2 40.028718 38.187031 4.420077 -5688 1 35.900797 34.287592 6.911917 -5689 1 34.035098 34.219002 0.088382 -5690 1 35.958161 30.177564 1.36017 -5691 2 34.104037 39.871769 1.666144 -5692 2 31.713648 30.030149 13.126076 -5693 2 38.102561 35.967156 7.519894 -5694 2 31.857312 30.233676 7.601269 -5695 1 34.289545 38.267283 14.401123 -5696 2 35.86683 30.19377 7.315341 -5697 1 30.215661 34.162037 8.437432 -5698 2 32.177106 33.712521 7.258256 -5699 2 36.086337 30.089865 10.102229 -5700 1 31.904414 32.116466 8.706393 -5701 1 31.937094 33.843414 10.07911 -5702 1 31.979885 32.115442 11.535778 -5703 2 31.646163 34.054645 12.923349 -5704 2 34.238187 35.954151 7.232689 -5705 1 32.107596 35.868544 8.568472 -5706 1 31.872832 37.740296 10.246254 -5707 1 32.382757 36.08172 11.390228 -5708 1 31.907287 38.043268 12.759712 -5709 1 33.814113 30.280416 11.361764 -5710 1 30.217972 36.108976 12.75806 -5711 2 33.902634 32.114854 10.131038 -5712 1 33.57231 32.104408 13.09734 -5713 1 31.808268 30.066503 10.372268 -5714 1 34.074533 34.09759 8.82773 -5715 2 34.112978 35.879639 10.008535 -5716 1 33.847258 34.132738 11.781858 -5717 2 33.938795 36.222314 13.025522 -5718 2 29.978741 32.187816 10.235973 -5719 1 34.055911 38.08124 8.660649 -5720 1 33.602601 34.200907 14.256884 -5721 1 34.074479 38.033056 11.548004 -5722 2 36.270647 38.06342 7.227717 -5723 1 35.834976 32.087215 8.752976 -5724 2 36.060859 33.636235 10.421377 -5725 1 35.993855 31.835332 12.022895 -5726 2 35.800428 33.936835 13.252217 -5727 1 36.115212 35.929045 8.653718 -5728 2 36.22813 38.12211 10.18663 -5729 1 36.031176 36.067395 11.711353 -5730 2 36.290793 38.28804 13.110371 -5731 1 38.314803 39.87771 13.628157 -5732 2 37.813718 31.963763 10.266333 -5733 2 38.345306 31.61479 12.746628 -5734 1 37.993817 33.8253 8.828538 -5735 2 37.963385 36.024574 10.310583 -5736 1 37.917131 33.840219 11.529013 -5737 1 38.204273 36.194533 12.982689 -5738 1 38.223785 37.96125 8.694521 -5739 1 38.251957 38.103445 11.574783 -5740 1 32.162162 35.830151 14.368089 -5741 1 38.188088 39.835851 10.200529 -5742 2 37.943506 31.862097 7.486993 -5743 1 34.019779 32.099062 7.382655 -5744 1 37.835648 33.808569 14.272091 -5745 2 30.154664 36.008494 10.278616 -5746 2 34.005569 29.909902 14.221934 -5747 2 39.942399 30.201297 7.221972 -5748 1 31.669489 32.129787 14.202133 -5749 1 33.8553 30.102976 8.785283 -5750 1 36.285019 39.993992 8.473052 -5751 2 34.332311 39.811654 10.053333 -5752 1 32.287985 39.934755 8.544521 -5753 1 32.117424 39.894109 11.328559 -5754 1 34.070494 39.946648 12.675838 -5755 1 33.523905 30.237815 17.092452 -5756 1 37.796875 30.195733 20.074531 -5757 1 36.27689 36.076917 14.383428 -5758 1 31.912415 30.074316 18.962029 -5759 1 31.72877 30.195629 15.548548 -5760 1 39.683801 34.084414 18.996274 -5761 1 31.823255 34.23579 15.916954 -5762 1 32.081111 32.17144 17.423655 -5763 2 32.272671 34.141341 18.923237 -5764 1 31.890319 32.258592 20.174682 -5765 1 32.292252 37.789848 15.657298 -5766 1 31.865994 35.945048 17.430984 -5767 2 32.390605 38.101438 18.756338 -5768 1 32.536255 36.292415 20.33365 -5769 1 30.255802 37.826036 17.398086 -5770 2 30.361913 39.693462 15.767213 -5771 1 33.658364 32.195407 15.713634 -5772 1 37.521125 34.00621 20.179734 -5773 2 34.170474 31.959646 18.774747 -5774 2 30.146126 36.07111 19.193288 -5775 2 34.236512 36.009488 15.705407 -5776 1 33.893052 34.259763 17.152928 -5777 1 34.299465 36.26334 18.583767 -5778 1 34.414431 34.040341 19.801645 -5779 1 38.268782 38.067343 19.882736 -5780 1 38.192119 30.067346 14.65738 -5781 1 34.182659 38.172175 17.379208 -5782 1 34.285582 38.312236 20.114249 -5783 1 35.930101 31.821554 14.523145 -5784 1 38.166996 38.004859 14.725716 -5785 1 35.925271 33.697258 15.741088 -5786 1 35.628801 31.929644 17.21365 -5787 2 36.045808 34.231991 18.304721 -5788 1 36.066783 31.92807 19.890693 -5789 2 30.047091 31.872972 18.511468 -5790 1 38.23536 37.943903 17.225875 -5791 2 36.119549 38.085157 15.846243 -5792 1 36.28338 36.046451 17.021393 -5793 1 36.11202 38.183852 18.648108 -5794 1 36.196383 36.094959 20.14945 -5795 1 39.857714 32.070711 20.545667 -5796 2 38.277117 32.092018 16.056024 -5797 1 30.025257 33.999826 20.265429 -5798 2 37.984137 32.053017 18.664282 -5799 1 32.002215 39.814443 17.350923 -5800 2 38.174586 35.979296 18.941495 -5801 2 38.345772 36.135739 15.897296 -5802 1 38.047733 34.092532 17.193597 -5803 2 30.130578 35.962177 15.540359 -5804 2 36.401926 38.058554 21.346524 -5805 1 30.120957 38.000412 14.522433 -5806 1 30.488998 38.181884 20.233832 -5807 1 30.027329 34.063964 17.498188 -5808 1 37.840062 29.987227 17.565361 -5809 1 32.008478 30.033144 21.485715 -5810 2 39.774533 34.462138 21.415634 -5811 1 30.338184 36.208481 21.405811 -5812 1 29.947563 30.056036 17.165794 -5813 1 39.921352 31.819743 14.64622 -5814 2 34.22915 39.981504 21.655908 -5815 1 30.183329 38.19462 25.743477 -5816 1 35.907762 33.854845 21.824692 -5817 1 38.081846 38.241792 22.993384 -5818 2 34.075816 32.199578 21.47467 -5819 1 32.064265 31.912891 22.91255 -5820 1 31.883139 33.912773 24.608383 -5821 1 31.812805 31.862315 26.174015 -5822 2 32.311833 34.450426 27.53752 -5823 1 32.200878 36.145135 23.147334 -5824 2 32.211767 38.313372 24.442593 -5825 1 32.252693 36.173296 25.56014 -5826 2 32.184178 37.824314 27.059278 -5827 2 35.878916 30.070226 21.715039 -5828 1 37.668689 30.050641 23.045191 -5829 2 31.790668 34.251576 21.855242 -5830 1 30.175916 38.136754 23.248784 -5831 1 33.79328 31.909522 24.576174 -5832 2 33.915875 32.018888 27.178426 -5833 1 33.839278 34.11599 23.063711 -5834 2 34.250078 35.934833 24.487018 -5835 1 33.990054 34.106505 25.930061 -5836 1 34.091025 36.282124 27.332172 -5837 1 39.883217 38.455893 24.705928 -5838 2 38.008034 36.021219 27.398438 -5839 1 34.624327 37.896007 23.016853 -5840 1 34.168936 37.954274 25.436951 -5841 1 39.89339 34.048173 27.027007 -5842 1 38.248268 36.455753 21.536765 -5843 1 35.611768 31.698556 23.347142 -5844 2 36.148802 34.042768 24.34925 -5845 1 35.930043 32.125519 25.878398 -5846 2 35.950538 34.005205 27.219195 -5847 1 37.955393 34.076875 25.799656 -5848 1 37.973062 38.01909 26.230315 -5849 1 36.411999 36.023781 22.980871 -5850 2 36.283519 37.906374 24.521157 -5851 1 36.105429 36.189959 25.968065 -5852 2 35.830991 38.301536 27.267321 -5853 1 30.231426 34.188738 26.125408 -5854 1 30.281973 34.136127 28.552033 -5855 2 37.785563 31.866932 24.278312 -5856 2 31.348335 30.244331 27.485493 -5857 2 37.966809 32.115632 27.589764 -5858 2 35.66017 29.988788 24.878779 -5859 1 38.277476 34.130765 22.79239 -5860 2 37.959129 36.154297 24.437008 -5861 1 33.713618 30.108282 28.642398 -5862 1 39.822964 31.905463 23.110805 -5863 1 37.492689 32.09291 21.995043 -5864 2 30.127031 36.064739 24.638111 -5865 1 35.533243 30.110728 27.243438 -5866 1 36.070605 31.93122 28.695839 -5867 2 34.291131 35.85795 21.75028 -5868 1 31.938061 32.142881 28.504169 -5869 1 33.986813 39.867909 27.012668 -5870 1 30.10822 37.992396 28.395198 -5871 1 39.800701 30.030956 24.347523 -5872 2 39.892552 29.979658 27.134291 -5873 2 32.228297 37.952841 21.875429 -5874 2 39.977135 34.107266 24.499149 -5875 1 39.846344 36.406036 26.033584 -5876 1 32.059083 40.009476 28.464272 -5877 1 35.959269 39.965152 25.93262 -5878 2 30.460566 32.139968 24.447603 -5879 2 39.881804 38.087413 21.696502 -5880 1 30.134489 36.163809 33.336193 -5881 1 37.575878 38.100411 28.849489 -5882 1 37.662104 38.133383 31.571418 -5883 1 32.362045 39.87867 34.884405 -5884 1 39.873173 36.224308 34.920349 -5885 1 31.991424 34.085923 29.999612 -5886 1 31.815171 32.168756 31.641691 -5887 2 31.782096 34.063184 33.062024 -5888 1 31.718037 31.953527 34.554814 -5889 1 39.862898 38.376226 32.906485 -5890 1 37.551931 30.038119 34.432157 -5891 1 31.780802 37.997046 30.254783 -5892 1 31.834761 35.939821 31.604936 -5893 2 32.041736 38.210181 33.326919 -5894 1 32.203699 35.869978 34.596577 -5895 1 34.008946 38.074601 28.827076 -5896 1 37.899592 29.974959 28.916731 -5897 1 38.030007 33.96835 28.91396 -5898 2 33.846774 32.085103 30.081464 -5899 1 29.952597 30.143437 34.499248 -5900 1 33.915497 32.111271 33.150301 -5901 1 31.790321 30.23064 29.991804 -5902 2 37.907438 32.157735 35.935104 -5903 2 33.84716 36.05681 30.26538 -5904 1 34.0432 34.280307 31.67674 -5905 2 34.011752 36.10558 33.143956 -5906 1 33.824017 34.085576 34.552777 -5907 1 34.194027 34.072791 28.967937 -5908 1 33.894909 38.222801 31.657741 -5909 1 33.881652 38.078172 34.899329 -5910 1 38.119296 38.056464 34.569681 -5911 1 34.291634 39.920546 33.178111 -5912 1 33.581454 29.993619 34.681796 -5913 2 36.053229 33.87704 30.318866 -5914 1 35.873901 31.88411 31.537273 -5915 1 35.89848 33.774876 32.823618 -5916 1 35.828028 32.348885 34.478807 -5917 1 35.672787 37.928294 30.518119 -5918 1 35.989671 35.945619 31.826779 -5919 2 35.97259 38.32967 33.142576 -5920 1 35.703331 35.814769 34.580449 -5921 1 33.817908 30.208146 31.599942 -5922 1 35.844503 36.12033 28.831087 -5923 1 38.261976 32.096366 30.088155 -5924 2 37.797891 31.9048 33.114668 -5925 1 39.55682 31.880323 34.531549 -5926 2 37.75043 36.193675 30.248336 -5927 1 38.393997 33.98513 31.905095 -5928 2 37.963057 36.355009 33.181745 -5929 1 37.797425 34.035854 34.376018 -5930 1 30.050396 34.271558 31.538997 -5931 1 39.815357 36.070726 31.654601 -5932 2 39.731271 30.032678 30.327233 -5933 1 39.915975 31.952921 31.714062 -5934 2 31.84562 29.966231 33.068673 -5935 1 31.85693 36.270476 28.934934 -5936 1 31.866016 39.844488 31.814385 -5937 1 30.092134 34.094244 34.755273 -5938 1 39.694807 30.040539 32.997642 -5939 1 36.196648 35.960439 42.925128 -5940 2 32.015598 37.930066 36.230869 -5941 1 37.674069 30.102473 37.130906 -5942 1 39.699003 32.118698 37.217773 -5943 2 29.963786 31.633701 39.162197 -5944 1 32.058675 39.814086 37.607409 -5945 1 35.842471 33.971675 35.989822 -5946 1 34.028551 38.060871 42.983375 -5947 1 31.588672 31.941435 37.383683 -5948 2 31.694069 33.998273 38.693202 -5949 1 31.930294 31.884957 40.381472 -5950 2 32.11349 33.999595 41.798502 -5951 1 31.876844 36.011394 37.307134 -5952 2 31.893158 37.928813 38.973436 -5953 1 31.81531 35.668229 40.479844 -5954 2 31.787646 38.142244 41.698514 -5955 1 31.925559 36.23881 42.924197 -5956 1 36.004443 37.899297 36.000218 -5957 1 38.451312 38.205323 40.038254 -5958 2 33.656378 31.907332 38.819792 -5959 1 33.99011 31.933293 41.627228 -5960 2 37.707146 36.123239 36.332034 -5961 1 33.657247 33.955416 37.665398 -5962 1 33.73943 36.151957 39.054731 -5963 1 33.605884 33.957716 40.193208 -5964 2 34.011058 36.048882 41.690411 -5965 1 38.130598 34.242802 40.052446 -5966 1 34.167865 38.117836 37.628936 -5967 1 34.142536 38.424699 40.41195 -5968 1 40.005739 32.215658 40.003237 -5969 1 39.521882 33.977557 36.015643 -5970 1 38.214368 38.282583 37.333443 -5971 1 31.918418 33.931512 36.157998 -5972 1 35.612055 32.074774 37.387219 -5973 2 35.5831 34.04957 39.047544 -5974 1 35.75246 32.088086 40.149631 -5975 2 35.615657 33.824419 41.713165 -5976 1 35.638569 36.061296 37.614952 -5977 2 36.358444 37.816896 38.884174 -5978 1 35.987046 36.034802 40.28745 -5979 1 36.122176 38.157473 41.827978 -5980 1 37.730089 30.067171 42.889333 -5981 2 39.944726 33.833791 41.642053 -5982 2 37.765477 32.166294 38.745053 -5983 2 38.099767 31.876153 41.350163 -5984 2 38.066621 36.442839 41.48951 -5985 1 37.726393 34.24931 37.606618 -5986 1 38.065514 36.286433 39.031222 -5987 1 37.664687 30.041804 39.941583 -5988 1 36.1403 39.743151 39.963443 -5989 2 34.004128 36.124387 36.139274 -5990 1 38.008343 33.918454 43.060491 -5991 1 36.098653 32.233378 42.976295 -5992 1 30.058867 38.134404 37.476791 -5993 2 35.662195 29.860797 35.905075 -5994 1 33.53205 30.001458 37.176731 -5995 1 38.387155 38.05525 43.009631 -5996 1 36.188595 39.834331 37.505629 -5997 1 39.656895 29.968268 41.372509 -5998 1 39.786156 36.00049 42.804021 -5999 2 33.855117 32.268762 36.090908 -6000 2 31.856527 30.044242 36.001804 diff --git a/examples/cauchystat/NiAl_slow_stretch_CS/lammps.in b/examples/cauchystat/NiAl_slow_stretch_CS/lammps.in deleted file mode 100644 index e90bd9f3a9..0000000000 --- a/examples/cauchystat/NiAl_slow_stretch_CS/lammps.in +++ /dev/null @@ -1,45 +0,0 @@ -units metal -atom_style atomic -atom_modify map array - -processors 1 1 1 - -# Box and atom positions: -boundary p p p -read_data input.dat - -# Atomic mass: -mass 1 58.69 -mass 2 26.98154 - -# Potential, Al fcc crystal -pair_style eam/alloy -pair_coeff * * ../Mishin-Ni-Al-2009.eam.alloy Ni Al - -thermo 100 -thermo_style custom step temp pxx pyy pzz lx ly lz -compute cna all cna/atom 2.8 - -velocity all create 1000.0 4928459 rot yes dist gaussian - -fix 1 all npt temp 500.0 500.0 1.0 x 0.0 0.0 0.1 y 0.0 0.0 0.1 z 0.0 0.0 0.1 couple none cauchystat 0.001 no - -dump 1 all cfg 5000 test*.cfg mass type xs ys zs type c_cna - -timestep 0.002 - -variable l equal lz -variable p equal pzz -variable t equal temp - -fix avg all ave/time 1 1000 1000 v_t v_l v_p file avg.txt - -velocity all create 2400 4928459 rot yes dist gaussian - -run 10000 - -unfix 1 - -fix 1 all npt temp 500.0 500.0 1.0 x 0.0 0.0 0.1 y 0.0 0.0 0.1 z 0.0 -14000.0 0.1 couple none cauchystat 0.001 yes - -run 350000 diff --git a/examples/cauchystat/NiAl_slow_stretch_PR/input.dat b/examples/cauchystat/NiAl_slow_stretch_PR/input.dat deleted file mode 100644 index 3b99f3ea8f..0000000000 --- a/examples/cauchystat/NiAl_slow_stretch_PR/input.dat +++ /dev/null @@ -1,6009 +0,0 @@ -Position data for MD simulation - -6000 atoms -2 atom types -0.0000 39.972658977840510 xlo xhi -0.0000 39.970082402467646 ylo yhi -0.0000 43.077168594479417 zlo zhi -Atoms - -1 1 2.265603 1.699233 2.96682 -2 2 2.147625 3.958175 4.336466 -3 1 1.997414 2.08615 5.681268 -4 2 6.222234 0.12344 4.55833 -5 1 4.247865 9.8684 7.188432 -6 2 2.226404 4.008191 1.332846 -7 1 2.558125 5.881235 2.799624 -8 2 2.112892 8.008518 4.084836 -9 1 2.366112 6.194696 5.83623 -10 2 0.308528 9.773154 7.249786 -11 1 1.861699 8.008727 1.634831 -12 2 0.245314 5.864464 4.508327 -13 1 8.139953 -0.02424 5.747139 -14 1 0.178338 3.676069 2.91793 -15 2 0.021903 9.933735 1.645872 -16 1 4.094944 3.990727 2.989711 -17 2 4.25173 6.125247 4.299378 -18 1 4.004975 4.261809 5.650881 -19 2 4.233414 9.883798 4.412874 -20 2 4.158657 5.985987 1.452914 -21 1 3.943003 7.917155 2.809851 -22 1 4.013002 8.032118 5.709128 -23 1 3.913817 0.208102 0.200173 -24 2 4.11186 2.115952 4.39711 -25 1 4.091794 8.080277 0.383691 -26 1 8.239262 4.128528 0.14417 -27 1 4.164942 2.294329 1.435205 -28 1 6.018476 2.048784 2.978318 -29 1 6.189263 4.123374 4.429365 -30 1 5.731913 2.039386 5.760723 -31 2 8.125123 2.396376 4.334063 -32 2 5.956145 3.961461 1.710606 -33 1 6.097732 6.223054 3.105619 -34 2 6.260701 8.269814 4.403081 -35 1 6.135592 6.191014 6.014208 -36 2 6.118481 0.280536 1.660297 -37 2 5.95371 8.134065 1.459117 -38 1 8.112 7.978937 6.025785 -39 1 8.230735 0.317331 0.287501 -40 1 7.984577 0.451106 2.876758 -41 1 8.121358 4.469963 3.000969 -42 2 8.0024 6.398776 4.506808 -43 1 8.265498 4.145515 5.950951 -44 1 8.093687 2.336039 1.599762 -45 2 7.786786 6.082031 1.369435 -46 1 8.051625 8.388788 2.947011 -47 2 1.887169 0.10205 1.232231 -48 1 3.814096 0.184819 2.93152 -49 2 5.999738 4.024912 6.895817 -50 1 0.20906 5.67262 1.62315 -51 1 2.22916 6.007717 0.143509 -52 1 9.864584 8.16224 1.516273 -53 1 0.029687 7.997328 3.090548 -54 1 0.158584 7.813035 5.663186 -55 1 6.149844 9.939956 0.040852 -56 1 1.871208 1.766851 8.960428 -57 2 2.233107 3.807827 10.095989 -58 1 1.960237 1.933156 11.733738 -59 1 2.028536 4.090031 13.399625 -60 2 0.096818 1.982978 13.367683 -61 1 1.962538 5.967991 8.575587 -62 2 1.779869 8.006286 9.997749 -63 1 2.261369 6.075808 11.262585 -64 1 1.878689 7.795749 12.973992 -65 1 8.066595 6.091936 7.32151 -66 2 6.004471 8.10958 7.337536 -67 2 3.807826 9.773306 13.107995 -68 2 3.628292 2.338356 7.627483 -69 1 4.142245 4.127148 8.640624 -70 2 4.430475 5.841591 10.077295 -71 1 3.968136 4.281892 11.552649 -72 2 3.926926 6.059939 13.034315 -73 1 4.163584 8.009554 8.875445 -74 1 3.841536 8.095992 11.564038 -75 1 1.972543 4.098752 7.26509 -76 1 9.833961 8.179066 10.053046 -77 1 3.959427 0.070701 8.628349 -78 1 4.000206 1.99734 10.467815 -79 1 0.175393 5.813256 10.208259 -80 2 3.991668 2.115114 12.987731 -81 2 8.056411 2.098025 12.865242 -82 1 5.64748 2.156225 8.497216 -83 2 6.159432 4.014865 10.196613 -84 1 6.214032 2.165249 11.651601 -85 1 5.856347 3.961477 13.023239 -86 1 7.948437 0.352004 11.304002 -87 2 0.129981 2.04383 7.39824 -88 1 6.181909 5.856377 8.431434 -89 1 5.991539 7.847191 10.091845 -90 1 5.975418 5.816241 11.895283 -91 1 5.86549 8.043369 13.028812 -92 2 4.166236 6.085137 7.231975 -93 1 0.439458 3.829864 11.550798 -94 2 0.21596 5.973334 12.667734 -95 1 10.017517 5.823156 11.545694 -96 1 8.076092 4.274718 8.540188 -97 2 7.924969 6.011881 10.326107 -98 1 8.12022 3.959556 11.608595 -99 1 8.110671 6.08702 13.353502 -100 1 8.135035 2.224763 9.76071 -101 1 8.056404 8.04948 8.608732 -102 1 7.867682 7.986347 11.444105 -103 1 0.057722 3.824193 8.62711 -104 1 9.981584 4.247366 7.362993 -105 2 4.013801 9.873296 9.982524 -106 1 2.329565 8.116478 7.435377 -107 2 5.950495 0.34488 9.79838 -108 1 4.334027 0.076447 11.746114 -109 2 7.945804 9.995075 13.009688 -110 1 2.027284 10.048274 11.752786 -111 2 7.985809 2.177851 7.348854 -112 2 0.227187 9.715111 13.080145 -113 1 4.369771 0.043973 14.298992 -114 1 9.913252 6.303629 8.785055 -115 1 7.984689 3.996322 14.285297 -116 1 6.286022 9.901661 11.434457 -117 2 9.978329 0.129998 10.093528 -118 2 9.898021 7.994926 13.146433 -119 1 2.438629 0.033347 18.603552 -120 2 2.19485 3.927092 15.921048 -121 1 2.266036 2.0106 17.298124 -122 2 2.190625 4.002775 18.808528 -123 1 2.529808 1.858131 19.802924 -124 1 2.121536 8.100548 15.903723 -125 1 1.999174 5.945764 17.409821 -126 2 2.399752 8.317077 18.513998 -127 1 2.085018 6.322971 20.123548 -128 1 0.132331 7.834943 14.417244 -129 2 0.191888 2.055829 18.456008 -130 1 8.035826 8.278124 14.487514 -131 2 3.964165 5.965398 16.034244 -132 1 3.977251 4.106829 17.287135 -133 1 4.083409 6.186923 18.749777 -134 1 4.118697 4.16167 19.924445 -135 2 0.168486 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9.972938 20.0169 27.489172 -1716 1 5.703997 25.711756 23.09432 -1717 2 6.280153 27.688392 24.474129 -1718 1 5.849202 25.758661 25.982363 -1719 2 5.933837 27.749401 27.395382 -1720 1 3.845896 20.13447 26.326059 -1721 1 1.926669 29.939905 28.626722 -1722 1 7.922929 22.1633 24.335514 -1723 2 8.344669 22.25109 27.215609 -1724 2 8.071558 26.117467 21.751054 -1725 1 7.968057 24.030988 22.727487 -1726 1 7.880729 25.822015 24.453191 -1727 1 7.761149 24.101212 25.874457 -1728 2 8.001074 25.678691 27.331612 -1729 1 8.199395 27.998508 23.147257 -1730 1 7.958944 27.762717 25.92964 -1731 2 6.105711 19.923887 27.319612 -1732 2 8.311788 29.835697 27.460372 -1733 1 0.010508 25.892668 24.309353 -1734 1 8.223805 20.060932 22.851601 -1735 1 8.056356 20.284564 28.761815 -1736 1 9.690116 27.803495 27.615456 -1737 1 9.827582 22.075609 22.638185 -1738 1 0.04681 27.870388 25.583825 -1739 2 1.854514 20.151336 27.561133 -1740 1 8.263011 20.002518 25.592661 -1741 1 4.010108 28.120308 28.682348 -1742 1 4.038857 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31.838347 -1770 2 9.854146 28.058626 30.296512 -1771 1 3.779252 28.116412 34.495303 -1772 1 9.896008 23.604726 30.76787 -1773 1 5.834675 29.939037 28.667512 -1774 2 5.776089 24.020213 30.371621 -1775 1 5.904354 22.03533 31.674341 -1776 2 5.555846 24.041033 33.033625 -1777 1 5.320865 21.956109 34.328935 -1778 1 4.014827 24.047016 29.023606 -1779 1 8.135704 24.045338 28.967134 -1780 2 5.838501 28.161605 30.300142 -1781 1 6.028928 25.762962 31.778482 -1782 2 5.949245 27.840682 33.103347 -1783 1 6.362363 25.902461 34.39925 -1784 1 7.81058 20.070316 34.587706 -1785 2 9.903459 27.99613 33.001775 -1786 1 0.232461 28.190603 28.813738 -1787 2 8.234656 21.917561 30.419501 -1788 2 7.904954 21.779034 32.964622 -1789 1 7.852524 27.919044 34.569765 -1790 1 7.595396 28.048353 31.625959 -1791 2 7.925112 25.887627 30.394049 -1792 1 7.728644 23.97055 31.916084 -1793 1 8.515126 26.113194 32.84505 -1794 1 7.87091 24.018792 34.546662 -1795 1 5.909818 25.850381 28.937903 -1796 1 1.855525 29.676343 34.402837 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3.760552 22.028975 39.129353 -1825 1 0.120133 23.847195 42.944885 -1826 2 4.069006 22.075437 41.863068 -1827 1 5.907632 20.36903 38.501592 -1828 1 7.614067 27.968649 40.109559 -1829 1 3.897056 23.931653 37.406176 -1830 2 3.67424 25.831572 38.858188 -1831 1 3.697155 23.98423 40.178372 -1832 1 3.958999 25.902285 41.773782 -1833 1 9.702453 23.999789 36.048473 -1834 1 3.862301 28.11303 37.453615 -1835 1 3.835868 28.048802 40.57469 -1836 2 5.854804 27.776995 36.005821 -1837 1 2.018496 25.837414 42.987148 -1838 1 9.960693 25.630934 40.389307 -1839 1 5.93268 22.351558 37.363635 -1840 2 5.893761 24.161725 38.918752 -1841 1 5.808679 22.051292 40.511129 -1842 2 5.792864 24.116392 41.554559 -1843 1 9.64084 21.675057 37.276932 -1844 1 7.878713 27.9153 37.259426 -1845 1 6.175937 25.901323 37.471311 -1846 2 5.668787 27.931006 38.872038 -1847 1 5.833656 25.947867 40.073284 -1848 1 5.883119 28.188772 41.564271 -1849 1 1.968623 29.760132 37.440712 -1850 1 9.720776 21.931094 39.953354 -1851 2 7.71657 22.068573 38.940437 -1852 2 7.898218 26.165005 41.361678 -1853 2 8.069464 22.281116 41.639197 -1854 1 7.671941 23.931719 37.325285 -1855 2 8.224025 25.910081 38.501705 -1856 1 7.708054 24.12057 40.424826 -1857 1 3.73122 28.006194 42.903257 -1858 2 5.75438 20.111404 41.853219 -1859 1 9.831402 27.825768 38.818019 -1860 1 7.702614 27.990192 42.759806 -1861 1 7.820889 20.318748 42.936774 -1862 1 1.696378 24.07867 36.051323 -1863 2 1.929861 28.112364 36.261692 -1864 2 5.747452 20.123867 36.071437 -1865 2 9.856877 23.914266 38.695016 -1866 2 7.756468 29.813429 38.680181 -1867 1 7.682461 20.159018 37.348845 -1868 2 9.776865 19.989829 38.744389 -1869 1 9.815791 23.652977 41.622566 -1870 1 7.858893 24.330568 42.982576 -1871 2 8.002454 29.899258 41.430193 -1872 1 0.077683 20.128085 37.436998 -1873 2 1.626697 20.07364 41.83293 -1874 1 1.777573 31.918884 4.516148 -1875 1 0.224503 39.97377 2.747323 -1876 1 2.112303 39.817069 4.528393 -1877 2 1.981899 32.150865 1.347891 -1878 1 2.322442 33.979858 3.19387 -1879 2 2.096374 36.191635 4.230691 -1880 1 1.999648 34.152278 5.938815 -1881 1 1.73114 30.291033 2.935219 -1882 1 3.665367 29.983954 1.275677 -1883 2 1.943018 36.004664 1.697384 -1884 1 2.019378 38.176143 2.972324 -1885 1 2.19126 37.889176 5.917314 -1886 1 0.019605 35.984478 3.104091 -1887 2 7.787834 30.403461 4.344497 -1888 1 6.050812 33.918162 -0.027918 -1889 1 3.814711 31.691419 2.816277 -1890 2 4.20332 33.715468 4.180703 -1891 1 3.914581 32.066382 5.971622 -1892 2 3.895933 33.805468 1.20281 -1893 1 4.340385 35.802877 2.943593 -1894 1 4.271659 37.949305 4.314292 -1895 1 4.068788 35.686982 5.513423 -1896 2 4.190929 37.662517 7.182865 -1897 2 4.200636 38.226632 1.691189 -1898 1 9.716958 31.962759 4.249426 -1899 1 5.810481 32.019245 4.382481 -1900 1 5.938979 35.885235 7.16864 -1901 1 0.267384 35.760048 6.061532 -1902 2 6.018619 31.95181 1.612974 -1903 1 5.938914 34.057443 2.77635 -1904 2 6.183116 36.065698 4.376274 -1905 1 6.089476 34.019022 5.411901 -1906 1 6.359106 35.990867 1.578601 -1907 1 6.152011 38.058648 2.943561 -1908 1 5.711164 30.034724 2.988084 -1909 1 6.045542 37.798257 5.727308 -1910 1 8.009398 36.153578 0.053676 -1911 1 0.238276 33.896375 4.533811 -1912 1 7.902329 32.340963 2.922426 -1913 2 8.222407 34.13168 4.116176 -1914 1 7.936717 32.22354 5.888103 -1915 2 8.123641 38.41175 1.891536 -1916 2 7.927555 34.06589 1.21075 -1917 1 8.412195 35.913547 2.85742 -1918 1 8.139566 38.142702 4.120627 -1919 1 8.317254 36.194514 5.407003 -1920 1 4.034964 36.04412 0.47011 -1921 2 3.83481 30.240395 4.561724 -1922 2 0.249553 38.107374 7.140438 -1923 1 2.126706 37.874136 0.15149 -1924 1 9.770714 33.872567 5.735309 -1925 1 7.651907 31.89674 -0.001589 -1926 1 6.265497 38.190114 0.387488 -1927 2 0.091323 38.034686 1.579889 -1928 1 6.013525 30.091058 5.903567 -1929 2 9.613745 31.989409 1.558474 -1930 1 9.893134 38.099463 -0.000176 -1931 1 0.012372 34.088485 1.353111 -1932 1 1.957372 34.025261 0.135755 -1933 1 9.930552 30.036571 0.064988 -1934 1 1.356847 30.09059 0.587218 -1935 2 2.165378 39.90345 7.155948 -1936 1 9.928802 38.103943 5.693619 -1937 1 4.231897 39.892291 5.78739 -1938 2 3.93426 34.036259 7.069656 -1939 2 2.074177 32.270109 10.089125 -1940 1 3.932043 30.108354 7.345143 -1941 2 1.820986 31.836134 13.124076 -1942 1 1.929382 34.316614 8.776464 -1943 2 2.083627 36.058658 10.081855 -1944 1 1.997221 33.916084 11.577718 -1945 1 2.267799 35.662279 13.073333 -1946 2 4.209744 30.111608 9.908398 -1947 1 2.104601 38.082098 8.735584 -1948 2 8.24053 38.05696 7.216926 -1949 1 2.109203 38.067126 11.734018 -1950 2 0.042241 38.005125 10.32451 -1951 1 1.957287 39.865839 10.426779 -1952 2 8.203196 30.05132 9.912922 -1953 1 2.246349 30.143579 11.639665 -1954 1 4.199959 32.106503 8.70465 -1955 1 3.976417 34.112906 10.198306 -1956 1 3.884958 31.967651 11.562891 -1957 2 4.063522 34.032621 13.004991 -1958 1 4.232266 36.19468 8.962151 -1959 2 4.097197 38.230412 10.13239 -1960 1 4.118617 35.849094 11.679739 -1961 2 4.350691 37.885411 12.898671 -1962 1 6.201046 32.417633 10.15369 -1963 2 5.816252 31.722772 13.101456 -1964 1 6.157578 39.769939 7.197304 -1965 1 6.184596 34.126547 8.504052 -1966 2 6.346713 35.703957 10.195727 -1967 1 6.288059 33.992499 11.799552 -1968 1 6.483281 35.967443 12.860859 -1969 2 7.835082 34.145462 7.179037 -1970 1 6.256423 37.691882 8.993285 -1971 1 6.2337 37.988064 11.537765 -1972 2 9.772215 31.919829 7.180665 -1973 1 7.981132 32.165581 14.333143 -1974 1 2.309997 36.061233 7.359038 -1975 1 4.433034 36.045633 14.35862 -1976 1 7.955328 32.223129 8.507808 -1977 2 8.286523 34.141907 10.013388 -1978 1 7.939052 31.949186 11.600717 -1979 1 8.104476 34.231193 13.030137 -1980 2 1.884476 31.865234 7.19113 -1981 1 8.333692 36.082489 8.414603 -1982 2 8.168537 38.03579 10.329742 -1983 1 8.420403 35.985684 11.517078 -1984 1 8.327179 38.029547 12.910471 -1985 2 6.20532 31.903657 7.381951 -1986 2 0.085009 37.638839 13.154459 -1987 1 7.552329 30.251663 13.212821 -1988 2 2.355047 39.830169 13.072665 -1989 1 0.148785 31.885164 11.209718 -1990 1 1.848807 30.245173 8.940225 -1991 1 0.166389 36.076965 8.575072 -1992 1 5.894085 30.228735 11.200379 -1993 1 0.232408 36.202468 11.578646 -1994 1 2.4752 37.687884 14.341623 -1995 1 0.334254 39.866494 8.663952 -1996 1 0.04027 39.756099 11.961945 -1997 1 0.083418 34.195005 10.175316 -1998 2 0.043097 34.005541 7.193221 -1999 2 0.052476 33.834131 12.929227 -2000 1 8.114393 39.929142 8.406226 -2001 1 6.281515 37.719535 14.225496 -2002 2 9.768912 32.130689 12.866513 -2003 1 9.864669 32.192496 10.045288 -2004 1 0.028148 32.153045 8.783822 -2005 2 6.417236 39.879341 13.202851 -2006 1 8.005375 39.836615 20.349358 -2007 2 2.017709 31.870952 15.889762 -2008 2 7.716399 30.062983 18.430151 -2009 2 2.119264 32.351346 19.061283 -2010 2 6.658976 39.77428 18.733464 -2011 2 2.321302 35.607604 15.702355 -2012 1 1.966843 34.024507 17.339235 -2013 2 2.33321 35.646813 18.814154 -2014 1 1.794484 34.194282 20.582509 -2015 1 1.984336 29.928657 17.680043 -2016 1 2.238075 37.571948 17.445144 -2017 1 4.466772 39.923317 17.544828 -2018 1 2.072213 37.924398 20.106708 -2019 1 3.990864 31.761546 14.785242 -2020 1 4.020518 33.927189 15.729606 -2021 1 3.897539 31.807357 17.561737 -2022 1 4.265924 33.937397 18.871352 -2023 1 4.376327 32.03663 20.389624 -2024 1 6.400496 39.782735 15.767263 -2025 2 4.461272 37.709843 15.835142 -2026 1 4.42096 35.817684 17.119638 -2027 2 4.054798 37.811976 18.867409 -2028 1 3.994208 35.957797 20.233365 -2029 1 1.972412 30.096734 20.271564 -2030 1 5.988832 31.90054 15.667667 -2031 2 6.100535 31.913125 18.798462 -2032 1 0.28224 35.927235 17.246921 -2033 1 9.878186 30.085685 17.138849 -2034 1 6.416487 35.895999 15.857104 -2035 2 5.962689 34.078738 16.936543 -2036 1 6.325491 35.483857 19.110752 -2037 1 6.245971 33.832167 20.618167 -2038 1 6.042072 33.77268 14.335557 -2039 1 6.090957 37.771252 17.365844 -2040 1 9.965189 29.988789 20.309186 -2041 1 6.076905 37.611337 20.045471 -2042 1 5.896032 30.00014 17.243068 -2043 1 8.07936 33.904732 15.859046 -2044 1 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31.7757 20.059463 34.518741 -5504 2 31.689207 21.887308 32.975541 -5505 2 39.805981 25.795509 35.838343 -5506 1 37.74723 21.903725 28.960526 -5507 1 31.979939 26.07293 30.17699 -5508 1 32.004898 23.95945 31.44988 -5509 2 31.974772 25.933622 32.803723 -5510 1 32.040506 24.042768 34.357335 -5511 1 37.739832 27.907443 30.245666 -5512 1 32.044626 28.118447 31.454017 -5513 1 31.654444 28.014414 34.509235 -5514 1 34.138301 27.997212 35.896313 -5515 1 31.889366 20.004044 28.761331 -5516 1 39.835262 22.07408 33.089516 -5517 2 34.007603 23.908774 30.342078 -5518 1 33.740263 21.868589 31.78797 -5519 1 33.991626 24.018147 32.935314 -5520 1 33.671435 22.23316 34.4639 -5521 1 37.963203 26.127816 33.948218 -5522 2 35.671548 29.887379 30.006429 -5523 1 33.829651 28.102906 29.943869 -5524 1 33.787523 26.067977 31.577331 -5525 2 33.715682 28.130095 33.162643 -5526 1 33.802101 26.210103 34.202265 -5527 1 37.730482 22.197376 34.403749 -5528 1 35.831101 21.95767 30.135533 -5529 2 37.999963 23.981171 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37.808939 25.88862 28.786806 -5557 2 37.605151 20.062234 30.298688 -5558 1 39.683146 24.074149 28.774708 -5559 2 39.707573 22.163726 35.729637 -5560 2 35.837795 29.959675 33.198016 -5561 1 37.531197 29.956826 31.453986 -5562 2 39.738624 29.728913 38.753431 -5563 1 30.041991 21.54866 43.088993 -5564 1 30.04925 20.092756 36.030677 -5565 1 30.104198 22.099525 40.482417 -5566 2 32.166095 22.126699 39.089437 -5567 1 31.30678 29.835939 38.614314 -5568 2 32.154498 22.033941 41.947583 -5569 2 31.750661 22.180652 36.030577 -5570 1 32.223184 23.946743 37.571147 -5571 2 31.857028 25.930615 38.61725 -5572 1 31.807569 24.008036 40.432686 -5573 1 31.912421 25.941854 41.820678 -5574 1 31.963997 27.922257 37.038409 -5575 1 31.654875 27.878145 40.187242 -5576 1 35.955999 28.067776 42.957294 -5577 2 34.231791 20.028899 42.029044 -5578 1 33.922224 22.241081 37.17316 -5579 2 34.125087 24.143446 39.010304 -5580 1 33.997499 22.06184 40.374786 -5581 1 34.225665 24.069461 41.736873 -5582 1 33.932104 25.893531 37.519827 -5583 2 33.77329 27.943689 38.48262 -5584 1 33.713028 25.960392 40.09306 -5585 2 33.759151 27.899985 41.583325 -5586 2 33.689627 20.140057 36.219908 -5587 2 36.007824 22.144071 36.071922 -5588 2 37.620658 27.864602 38.755932 -5589 1 39.738066 23.868111 40.35193 -5590 1 36.044603 22.198895 38.939329 -5591 1 33.554331 29.877621 40.218971 -5592 2 36.210984 22.124513 41.901686 -5593 2 38.321777 20.14745 42.021594 -5594 1 35.891168 24.174352 37.042395 -5595 1 35.94011 25.975562 38.850673 -5596 1 36.086096 23.949456 40.287057 -5597 2 35.791035 25.814753 41.294699 -5598 1 38.121169 25.85346 40.303076 -5599 1 39.766821 22.077842 41.533013 -5600 1 35.898072 27.608031 37.346086 -5601 1 35.536703 27.971258 40.062924 -5602 1 37.725397 25.89497 37.190171 -5603 2 37.79448 28.357372 41.583156 -5604 1 32.130663 20.179465 40.490265 -5605 1 37.805212 22.189132 37.454434 -5606 2 37.845302 23.980917 38.951707 -5607 1 38.018734 22.01441 40.25018 -5608 1 37.998999 23.83693 41.969539 -5609 1 32.000064 20.176196 37.541736 -5610 2 37.944544 27.863124 35.858277 -5611 1 39.781907 29.831429 35.898085 -5612 2 35.490384 29.962999 41.453455 -5613 1 39.758098 24.039153 37.528235 -5614 2 39.892583 25.906438 41.854944 -5615 1 36.285268 19.999603 40.745261 -5616 2 30.09655 24.022449 41.945798 -5617 2 39.993697 25.996395 38.728838 -5618 1 37.81422 26.290042 42.848087 -5619 2 30.055901 19.935486 38.573149 -5620 1 37.973864 20.290243 36.046389 -5621 1 39.678251 27.704428 37.302745 -5622 2 39.966918 21.895199 38.767152 -5623 1 39.609699 27.894456 40.148854 -5624 1 35.857722 20.273774 37.567161 -5625 2 31.876516 29.975478 41.679184 -5626 2 29.990823 24.134634 38.782012 -5627 1 30.110123 28.422528 35.957979 -5628 1 30.166791 21.94758 37.4415 -5629 1 32.168293 24.104265 42.975893 -5630 1 35.411443 29.813844 38.643913 -5631 2 37.976528 20.120682 38.533653 -5632 1 39.779362 30.230874 4.652211 -5633 1 29.983878 33.982126 0.04316 -5634 2 30.086369 31.993647 4.231995 -5635 2 33.932165 39.866251 7.068893 -5636 1 32.059505 32.251117 2.629522 -5637 2 31.867763 34.040728 3.960388 -5638 1 31.932973 31.808697 5.917256 -5639 1 30.007373 39.943466 4.51009 -5640 2 39.207186 30.079079 1.703674 -5641 1 32.016417 34.359045 1.391175 -5642 1 32.0796 36.080574 2.990027 -5643 2 32.125016 37.982811 4.244242 -5644 1 32.039867 35.855789 5.754866 -5645 2 30.356301 36.250302 1.436559 -5646 1 32.110296 38.00744 1.426636 -5647 1 33.998604 30.067664 5.743991 -5648 2 33.695324 31.983255 4.383442 -5649 2 30.152086 36.019627 4.245065 -5650 2 34.240197 32.341445 1.32205 -5651 1 33.885438 34.090868 2.902626 -5652 2 34.178132 35.93225 4.482376 -5653 1 33.856287 33.915557 5.543055 -5654 2 34.187255 35.904801 1.570832 -5655 1 34.049489 37.902242 2.794215 -5656 1 34.196846 37.782622 5.597948 -5657 1 32.010141 29.994854 3.963328 -5658 1 30.085473 38.058327 2.970114 -5659 1 37.563886 30.425407 3.132393 -5660 1 35.867335 32.241913 3.116156 -5661 2 35.974255 34.126395 4.519526 -5662 1 36.004069 32.109611 5.814404 -5663 1 34.085538 39.906327 4.293478 -5664 1 36.097439 33.990507 1.502757 -5665 1 36.087679 36.048793 3.035352 -5666 2 36.278328 38.155374 4.063777 -5667 1 36.249913 36.355424 5.927679 -5668 2 31.890573 30.350964 1.619094 -5669 2 31.962807 37.754434 7.179059 -5670 1 35.973947 37.892913 1.48124 -5671 2 35.839322 30.204876 4.375075 -5672 1 37.935879 32.177401 4.195289 -5673 1 38.101493 38.10187 5.953049 -5674 2 37.852909 32.388628 1.664291 -5675 1 37.942171 34.0458 3.006996 -5676 2 38.2641 36.15208 4.530503 -5677 1 38.039433 34.206108 5.79566 -5678 1 33.979517 30.322401 2.668635 -5679 2 38.266202 35.993947 1.484331 -5680 1 38.067048 38.040012 2.752414 -5681 1 37.733806 30.096455 5.970187 -5682 1 39.682213 32.091472 5.993971 -5683 1 39.817487 31.930363 0.000367 -5684 1 36.043395 39.59783 5.676369 -5685 1 31.869558 32.098607 0.138261 -5686 1 39.734652 32.347843 3.042732 -5687 2 40.028718 38.187031 4.420077 -5688 1 35.900797 34.287592 6.911917 -5689 1 34.035098 34.219002 0.088382 -5690 1 35.958161 30.177564 1.36017 -5691 2 34.104037 39.871769 1.666144 -5692 2 31.713648 30.030149 13.126076 -5693 2 38.102561 35.967156 7.519894 -5694 2 31.857312 30.233676 7.601269 -5695 1 34.289545 38.267283 14.401123 -5696 2 35.86683 30.19377 7.315341 -5697 1 30.215661 34.162037 8.437432 -5698 2 32.177106 33.712521 7.258256 -5699 2 36.086337 30.089865 10.102229 -5700 1 31.904414 32.116466 8.706393 -5701 1 31.937094 33.843414 10.07911 -5702 1 31.979885 32.115442 11.535778 -5703 2 31.646163 34.054645 12.923349 -5704 2 34.238187 35.954151 7.232689 -5705 1 32.107596 35.868544 8.568472 -5706 1 31.872832 37.740296 10.246254 -5707 1 32.382757 36.08172 11.390228 -5708 1 31.907287 38.043268 12.759712 -5709 1 33.814113 30.280416 11.361764 -5710 1 30.217972 36.108976 12.75806 -5711 2 33.902634 32.114854 10.131038 -5712 1 33.57231 32.104408 13.09734 -5713 1 31.808268 30.066503 10.372268 -5714 1 34.074533 34.09759 8.82773 -5715 2 34.112978 35.879639 10.008535 -5716 1 33.847258 34.132738 11.781858 -5717 2 33.938795 36.222314 13.025522 -5718 2 29.978741 32.187816 10.235973 -5719 1 34.055911 38.08124 8.660649 -5720 1 33.602601 34.200907 14.256884 -5721 1 34.074479 38.033056 11.548004 -5722 2 36.270647 38.06342 7.227717 -5723 1 35.834976 32.087215 8.752976 -5724 2 36.060859 33.636235 10.421377 -5725 1 35.993855 31.835332 12.022895 -5726 2 35.800428 33.936835 13.252217 -5727 1 36.115212 35.929045 8.653718 -5728 2 36.22813 38.12211 10.18663 -5729 1 36.031176 36.067395 11.711353 -5730 2 36.290793 38.28804 13.110371 -5731 1 38.314803 39.87771 13.628157 -5732 2 37.813718 31.963763 10.266333 -5733 2 38.345306 31.61479 12.746628 -5734 1 37.993817 33.8253 8.828538 -5735 2 37.963385 36.024574 10.310583 -5736 1 37.917131 33.840219 11.529013 -5737 1 38.204273 36.194533 12.982689 -5738 1 38.223785 37.96125 8.694521 -5739 1 38.251957 38.103445 11.574783 -5740 1 32.162162 35.830151 14.368089 -5741 1 38.188088 39.835851 10.200529 -5742 2 37.943506 31.862097 7.486993 -5743 1 34.019779 32.099062 7.382655 -5744 1 37.835648 33.808569 14.272091 -5745 2 30.154664 36.008494 10.278616 -5746 2 34.005569 29.909902 14.221934 -5747 2 39.942399 30.201297 7.221972 -5748 1 31.669489 32.129787 14.202133 -5749 1 33.8553 30.102976 8.785283 -5750 1 36.285019 39.993992 8.473052 -5751 2 34.332311 39.811654 10.053333 -5752 1 32.287985 39.934755 8.544521 -5753 1 32.117424 39.894109 11.328559 -5754 1 34.070494 39.946648 12.675838 -5755 1 33.523905 30.237815 17.092452 -5756 1 37.796875 30.195733 20.074531 -5757 1 36.27689 36.076917 14.383428 -5758 1 31.912415 30.074316 18.962029 -5759 1 31.72877 30.195629 15.548548 -5760 1 39.683801 34.084414 18.996274 -5761 1 31.823255 34.23579 15.916954 -5762 1 32.081111 32.17144 17.423655 -5763 2 32.272671 34.141341 18.923237 -5764 1 31.890319 32.258592 20.174682 -5765 1 32.292252 37.789848 15.657298 -5766 1 31.865994 35.945048 17.430984 -5767 2 32.390605 38.101438 18.756338 -5768 1 32.536255 36.292415 20.33365 -5769 1 30.255802 37.826036 17.398086 -5770 2 30.361913 39.693462 15.767213 -5771 1 33.658364 32.195407 15.713634 -5772 1 37.521125 34.00621 20.179734 -5773 2 34.170474 31.959646 18.774747 -5774 2 30.146126 36.07111 19.193288 -5775 2 34.236512 36.009488 15.705407 -5776 1 33.893052 34.259763 17.152928 -5777 1 34.299465 36.26334 18.583767 -5778 1 34.414431 34.040341 19.801645 -5779 1 38.268782 38.067343 19.882736 -5780 1 38.192119 30.067346 14.65738 -5781 1 34.182659 38.172175 17.379208 -5782 1 34.285582 38.312236 20.114249 -5783 1 35.930101 31.821554 14.523145 -5784 1 38.166996 38.004859 14.725716 -5785 1 35.925271 33.697258 15.741088 -5786 1 35.628801 31.929644 17.21365 -5787 2 36.045808 34.231991 18.304721 -5788 1 36.066783 31.92807 19.890693 -5789 2 30.047091 31.872972 18.511468 -5790 1 38.23536 37.943903 17.225875 -5791 2 36.119549 38.085157 15.846243 -5792 1 36.28338 36.046451 17.021393 -5793 1 36.11202 38.183852 18.648108 -5794 1 36.196383 36.094959 20.14945 -5795 1 39.857714 32.070711 20.545667 -5796 2 38.277117 32.092018 16.056024 -5797 1 30.025257 33.999826 20.265429 -5798 2 37.984137 32.053017 18.664282 -5799 1 32.002215 39.814443 17.350923 -5800 2 38.174586 35.979296 18.941495 -5801 2 38.345772 36.135739 15.897296 -5802 1 38.047733 34.092532 17.193597 -5803 2 30.130578 35.962177 15.540359 -5804 2 36.401926 38.058554 21.346524 -5805 1 30.120957 38.000412 14.522433 -5806 1 30.488998 38.181884 20.233832 -5807 1 30.027329 34.063964 17.498188 -5808 1 37.840062 29.987227 17.565361 -5809 1 32.008478 30.033144 21.485715 -5810 2 39.774533 34.462138 21.415634 -5811 1 30.338184 36.208481 21.405811 -5812 1 29.947563 30.056036 17.165794 -5813 1 39.921352 31.819743 14.64622 -5814 2 34.22915 39.981504 21.655908 -5815 1 30.183329 38.19462 25.743477 -5816 1 35.907762 33.854845 21.824692 -5817 1 38.081846 38.241792 22.993384 -5818 2 34.075816 32.199578 21.47467 -5819 1 32.064265 31.912891 22.91255 -5820 1 31.883139 33.912773 24.608383 -5821 1 31.812805 31.862315 26.174015 -5822 2 32.311833 34.450426 27.53752 -5823 1 32.200878 36.145135 23.147334 -5824 2 32.211767 38.313372 24.442593 -5825 1 32.252693 36.173296 25.56014 -5826 2 32.184178 37.824314 27.059278 -5827 2 35.878916 30.070226 21.715039 -5828 1 37.668689 30.050641 23.045191 -5829 2 31.790668 34.251576 21.855242 -5830 1 30.175916 38.136754 23.248784 -5831 1 33.79328 31.909522 24.576174 -5832 2 33.915875 32.018888 27.178426 -5833 1 33.839278 34.11599 23.063711 -5834 2 34.250078 35.934833 24.487018 -5835 1 33.990054 34.106505 25.930061 -5836 1 34.091025 36.282124 27.332172 -5837 1 39.883217 38.455893 24.705928 -5838 2 38.008034 36.021219 27.398438 -5839 1 34.624327 37.896007 23.016853 -5840 1 34.168936 37.954274 25.436951 -5841 1 39.89339 34.048173 27.027007 -5842 1 38.248268 36.455753 21.536765 -5843 1 35.611768 31.698556 23.347142 -5844 2 36.148802 34.042768 24.34925 -5845 1 35.930043 32.125519 25.878398 -5846 2 35.950538 34.005205 27.219195 -5847 1 37.955393 34.076875 25.799656 -5848 1 37.973062 38.01909 26.230315 -5849 1 36.411999 36.023781 22.980871 -5850 2 36.283519 37.906374 24.521157 -5851 1 36.105429 36.189959 25.968065 -5852 2 35.830991 38.301536 27.267321 -5853 1 30.231426 34.188738 26.125408 -5854 1 30.281973 34.136127 28.552033 -5855 2 37.785563 31.866932 24.278312 -5856 2 31.348335 30.244331 27.485493 -5857 2 37.966809 32.115632 27.589764 -5858 2 35.66017 29.988788 24.878779 -5859 1 38.277476 34.130765 22.79239 -5860 2 37.959129 36.154297 24.437008 -5861 1 33.713618 30.108282 28.642398 -5862 1 39.822964 31.905463 23.110805 -5863 1 37.492689 32.09291 21.995043 -5864 2 30.127031 36.064739 24.638111 -5865 1 35.533243 30.110728 27.243438 -5866 1 36.070605 31.93122 28.695839 -5867 2 34.291131 35.85795 21.75028 -5868 1 31.938061 32.142881 28.504169 -5869 1 33.986813 39.867909 27.012668 -5870 1 30.10822 37.992396 28.395198 -5871 1 39.800701 30.030956 24.347523 -5872 2 39.892552 29.979658 27.134291 -5873 2 32.228297 37.952841 21.875429 -5874 2 39.977135 34.107266 24.499149 -5875 1 39.846344 36.406036 26.033584 -5876 1 32.059083 40.009476 28.464272 -5877 1 35.959269 39.965152 25.93262 -5878 2 30.460566 32.139968 24.447603 -5879 2 39.881804 38.087413 21.696502 -5880 1 30.134489 36.163809 33.336193 -5881 1 37.575878 38.100411 28.849489 -5882 1 37.662104 38.133383 31.571418 -5883 1 32.362045 39.87867 34.884405 -5884 1 39.873173 36.224308 34.920349 -5885 1 31.991424 34.085923 29.999612 -5886 1 31.815171 32.168756 31.641691 -5887 2 31.782096 34.063184 33.062024 -5888 1 31.718037 31.953527 34.554814 -5889 1 39.862898 38.376226 32.906485 -5890 1 37.551931 30.038119 34.432157 -5891 1 31.780802 37.997046 30.254783 -5892 1 31.834761 35.939821 31.604936 -5893 2 32.041736 38.210181 33.326919 -5894 1 32.203699 35.869978 34.596577 -5895 1 34.008946 38.074601 28.827076 -5896 1 37.899592 29.974959 28.916731 -5897 1 38.030007 33.96835 28.91396 -5898 2 33.846774 32.085103 30.081464 -5899 1 29.952597 30.143437 34.499248 -5900 1 33.915497 32.111271 33.150301 -5901 1 31.790321 30.23064 29.991804 -5902 2 37.907438 32.157735 35.935104 -5903 2 33.84716 36.05681 30.26538 -5904 1 34.0432 34.280307 31.67674 -5905 2 34.011752 36.10558 33.143956 -5906 1 33.824017 34.085576 34.552777 -5907 1 34.194027 34.072791 28.967937 -5908 1 33.894909 38.222801 31.657741 -5909 1 33.881652 38.078172 34.899329 -5910 1 38.119296 38.056464 34.569681 -5911 1 34.291634 39.920546 33.178111 -5912 1 33.581454 29.993619 34.681796 -5913 2 36.053229 33.87704 30.318866 -5914 1 35.873901 31.88411 31.537273 -5915 1 35.89848 33.774876 32.823618 -5916 1 35.828028 32.348885 34.478807 -5917 1 35.672787 37.928294 30.518119 -5918 1 35.989671 35.945619 31.826779 -5919 2 35.97259 38.32967 33.142576 -5920 1 35.703331 35.814769 34.580449 -5921 1 33.817908 30.208146 31.599942 -5922 1 35.844503 36.12033 28.831087 -5923 1 38.261976 32.096366 30.088155 -5924 2 37.797891 31.9048 33.114668 -5925 1 39.55682 31.880323 34.531549 -5926 2 37.75043 36.193675 30.248336 -5927 1 38.393997 33.98513 31.905095 -5928 2 37.963057 36.355009 33.181745 -5929 1 37.797425 34.035854 34.376018 -5930 1 30.050396 34.271558 31.538997 -5931 1 39.815357 36.070726 31.654601 -5932 2 39.731271 30.032678 30.327233 -5933 1 39.915975 31.952921 31.714062 -5934 2 31.84562 29.966231 33.068673 -5935 1 31.85693 36.270476 28.934934 -5936 1 31.866016 39.844488 31.814385 -5937 1 30.092134 34.094244 34.755273 -5938 1 39.694807 30.040539 32.997642 -5939 1 36.196648 35.960439 42.925128 -5940 2 32.015598 37.930066 36.230869 -5941 1 37.674069 30.102473 37.130906 -5942 1 39.699003 32.118698 37.217773 -5943 2 29.963786 31.633701 39.162197 -5944 1 32.058675 39.814086 37.607409 -5945 1 35.842471 33.971675 35.989822 -5946 1 34.028551 38.060871 42.983375 -5947 1 31.588672 31.941435 37.383683 -5948 2 31.694069 33.998273 38.693202 -5949 1 31.930294 31.884957 40.381472 -5950 2 32.11349 33.999595 41.798502 -5951 1 31.876844 36.011394 37.307134 -5952 2 31.893158 37.928813 38.973436 -5953 1 31.81531 35.668229 40.479844 -5954 2 31.787646 38.142244 41.698514 -5955 1 31.925559 36.23881 42.924197 -5956 1 36.004443 37.899297 36.000218 -5957 1 38.451312 38.205323 40.038254 -5958 2 33.656378 31.907332 38.819792 -5959 1 33.99011 31.933293 41.627228 -5960 2 37.707146 36.123239 36.332034 -5961 1 33.657247 33.955416 37.665398 -5962 1 33.73943 36.151957 39.054731 -5963 1 33.605884 33.957716 40.193208 -5964 2 34.011058 36.048882 41.690411 -5965 1 38.130598 34.242802 40.052446 -5966 1 34.167865 38.117836 37.628936 -5967 1 34.142536 38.424699 40.41195 -5968 1 40.005739 32.215658 40.003237 -5969 1 39.521882 33.977557 36.015643 -5970 1 38.214368 38.282583 37.333443 -5971 1 31.918418 33.931512 36.157998 -5972 1 35.612055 32.074774 37.387219 -5973 2 35.5831 34.04957 39.047544 -5974 1 35.75246 32.088086 40.149631 -5975 2 35.615657 33.824419 41.713165 -5976 1 35.638569 36.061296 37.614952 -5977 2 36.358444 37.816896 38.884174 -5978 1 35.987046 36.034802 40.28745 -5979 1 36.122176 38.157473 41.827978 -5980 1 37.730089 30.067171 42.889333 -5981 2 39.944726 33.833791 41.642053 -5982 2 37.765477 32.166294 38.745053 -5983 2 38.099767 31.876153 41.350163 -5984 2 38.066621 36.442839 41.48951 -5985 1 37.726393 34.24931 37.606618 -5986 1 38.065514 36.286433 39.031222 -5987 1 37.664687 30.041804 39.941583 -5988 1 36.1403 39.743151 39.963443 -5989 2 34.004128 36.124387 36.139274 -5990 1 38.008343 33.918454 43.060491 -5991 1 36.098653 32.233378 42.976295 -5992 1 30.058867 38.134404 37.476791 -5993 2 35.662195 29.860797 35.905075 -5994 1 33.53205 30.001458 37.176731 -5995 1 38.387155 38.05525 43.009631 -5996 1 36.188595 39.834331 37.505629 -5997 1 39.656895 29.968268 41.372509 -5998 1 39.786156 36.00049 42.804021 -5999 2 33.855117 32.268762 36.090908 -6000 2 31.856527 30.044242 36.001804 diff --git a/examples/cauchystat/NiAl_slow_stretch_PR/lammps.in b/examples/cauchystat/NiAl_slow_stretch_PR/lammps.in deleted file mode 100644 index 93840793b8..0000000000 --- a/examples/cauchystat/NiAl_slow_stretch_PR/lammps.in +++ /dev/null @@ -1,45 +0,0 @@ -units metal -atom_style atomic -atom_modify map array - -processors 1 1 1 - -# Box and atom positions: -boundary p p p -read_data input.dat - -# Atomic mass: -mass 1 58.69 -mass 2 26.98154 - -# Potential, Al fcc crystal -pair_style eam/alloy -pair_coeff * * ../Mishin-Ni-Al-2009.eam.alloy Ni Al - -thermo 100 -thermo_style custom step temp pxx pyy pzz lx ly lz -compute cna all cna/atom 2.8 - -velocity all create 1000.0 4928459 rot yes dist gaussian - -fix 1 all npt temp 500.0 500.0 1.0 x 0.0 0.0 0.1 y 0.0 0.0 0.1 z 0.0 0.0 0.1 couple none - -dump 1 all cfg 5000 test*.cfg mass type xs ys zs type c_cna - -timestep 0.002 - -variable l equal lz -variable p equal pzz -variable t equal temp - -fix avg all ave/time 1 1000 1000 v_t v_l v_p file avg.txt - -velocity all create 2400 4928459 rot yes dist gaussian - -run 10000 - -unfix 1 - -fix 1 all npt temp 500.0 500.0 1.0 x 0.0 0.0 0.1 y 0.0 0.0 0.1 z 0.0 -14000.0 0.1 couple none - -run 350000 diff --git a/examples/cauchystat/NiAl_stretch/input.dat b/examples/cauchystat/NiAl_stretch/input.dat deleted file mode 100644 index 3b99f3ea8f..0000000000 --- a/examples/cauchystat/NiAl_stretch/input.dat +++ /dev/null @@ -1,6009 +0,0 @@ -Position data for MD simulation - -6000 atoms -2 atom types -0.0000 39.972658977840510 xlo xhi -0.0000 39.970082402467646 ylo yhi -0.0000 43.077168594479417 zlo zhi -Atoms - -1 1 2.265603 1.699233 2.96682 -2 2 2.147625 3.958175 4.336466 -3 1 1.997414 2.08615 5.681268 -4 2 6.222234 0.12344 4.55833 -5 1 4.247865 9.8684 7.188432 -6 2 2.226404 4.008191 1.332846 -7 1 2.558125 5.881235 2.799624 -8 2 2.112892 8.008518 4.084836 -9 1 2.366112 6.194696 5.83623 -10 2 0.308528 9.773154 7.249786 -11 1 1.861699 8.008727 1.634831 -12 2 0.245314 5.864464 4.508327 -13 1 8.139953 -0.02424 5.747139 -14 1 0.178338 3.676069 2.91793 -15 2 0.021903 9.933735 1.645872 -16 1 4.094944 3.990727 2.989711 -17 2 4.25173 6.125247 4.299378 -18 1 4.004975 4.261809 5.650881 -19 2 4.233414 9.883798 4.412874 -20 2 4.158657 5.985987 1.452914 -21 1 3.943003 7.917155 2.809851 -22 1 4.013002 8.032118 5.709128 -23 1 3.913817 0.208102 0.200173 -24 2 4.11186 2.115952 4.39711 -25 1 4.091794 8.080277 0.383691 -26 1 8.239262 4.128528 0.14417 -27 1 4.164942 2.294329 1.435205 -28 1 6.018476 2.048784 2.978318 -29 1 6.189263 4.123374 4.429365 -30 1 5.731913 2.039386 5.760723 -31 2 8.125123 2.396376 4.334063 -32 2 5.956145 3.961461 1.710606 -33 1 6.097732 6.223054 3.105619 -34 2 6.260701 8.269814 4.403081 -35 1 6.135592 6.191014 6.014208 -36 2 6.118481 0.280536 1.660297 -37 2 5.95371 8.134065 1.459117 -38 1 8.112 7.978937 6.025785 -39 1 8.230735 0.317331 0.287501 -40 1 7.984577 0.451106 2.876758 -41 1 8.121358 4.469963 3.000969 -42 2 8.0024 6.398776 4.506808 -43 1 8.265498 4.145515 5.950951 -44 1 8.093687 2.336039 1.599762 -45 2 7.786786 6.082031 1.369435 -46 1 8.051625 8.388788 2.947011 -47 2 1.887169 0.10205 1.232231 -48 1 3.814096 0.184819 2.93152 -49 2 5.999738 4.024912 6.895817 -50 1 0.20906 5.67262 1.62315 -51 1 2.22916 6.007717 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35.664124 -1803 1 4.247465 25.982549 35.80953 -1804 1 0.012022 24.158979 31.494615 -1805 1 5.845287 29.969937 34.69315 -1806 2 8.436976 26.046465 35.817561 -1807 1 7.795622 29.898607 30.128644 -1808 2 7.768617 22.215251 35.856895 -1809 2 7.93569 29.886699 33.196602 -1810 1 9.883607 29.838353 28.975335 -1811 1 1.946835 22.280384 43.066776 -1812 1 1.809398 21.863784 37.34337 -1813 1 1.976036 23.841911 38.755625 -1814 1 1.767727 21.824198 40.56452 -1815 2 2.083742 24.029053 41.450421 -1816 1 7.673731 20.199299 40.455877 -1817 1 3.883739 20.063979 37.43537 -1818 1 1.962857 26.015373 37.239011 -1819 1 1.855742 27.865871 38.783671 -1820 1 1.946136 26.114415 40.445845 -1821 2 1.342698 28.356759 41.677946 -1822 1 3.866247 20.162337 40.622125 -1823 2 3.812973 22.128926 36.114766 -1824 2 3.760552 22.028975 39.129353 -1825 1 0.120133 23.847195 42.944885 -1826 2 4.069006 22.075437 41.863068 -1827 1 5.907632 20.36903 38.501592 -1828 1 7.614067 27.968649 40.109559 -1829 1 3.897056 23.931653 37.406176 -1830 2 3.67424 25.831572 38.858188 -1831 1 3.697155 23.98423 40.178372 -1832 1 3.958999 25.902285 41.773782 -1833 1 9.702453 23.999789 36.048473 -1834 1 3.862301 28.11303 37.453615 -1835 1 3.835868 28.048802 40.57469 -1836 2 5.854804 27.776995 36.005821 -1837 1 2.018496 25.837414 42.987148 -1838 1 9.960693 25.630934 40.389307 -1839 1 5.93268 22.351558 37.363635 -1840 2 5.893761 24.161725 38.918752 -1841 1 5.808679 22.051292 40.511129 -1842 2 5.792864 24.116392 41.554559 -1843 1 9.64084 21.675057 37.276932 -1844 1 7.878713 27.9153 37.259426 -1845 1 6.175937 25.901323 37.471311 -1846 2 5.668787 27.931006 38.872038 -1847 1 5.833656 25.947867 40.073284 -1848 1 5.883119 28.188772 41.564271 -1849 1 1.968623 29.760132 37.440712 -1850 1 9.720776 21.931094 39.953354 -1851 2 7.71657 22.068573 38.940437 -1852 2 7.898218 26.165005 41.361678 -1853 2 8.069464 22.281116 41.639197 -1854 1 7.671941 23.931719 37.325285 -1855 2 8.224025 25.910081 38.501705 -1856 1 7.708054 24.12057 40.424826 -1857 1 3.73122 28.006194 42.903257 -1858 2 5.75438 20.111404 41.853219 -1859 1 9.831402 27.825768 38.818019 -1860 1 7.702614 27.990192 42.759806 -1861 1 7.820889 20.318748 42.936774 -1862 1 1.696378 24.07867 36.051323 -1863 2 1.929861 28.112364 36.261692 -1864 2 5.747452 20.123867 36.071437 -1865 2 9.856877 23.914266 38.695016 -1866 2 7.756468 29.813429 38.680181 -1867 1 7.682461 20.159018 37.348845 -1868 2 9.776865 19.989829 38.744389 -1869 1 9.815791 23.652977 41.622566 -1870 1 7.858893 24.330568 42.982576 -1871 2 8.002454 29.899258 41.430193 -1872 1 0.077683 20.128085 37.436998 -1873 2 1.626697 20.07364 41.83293 -1874 1 1.777573 31.918884 4.516148 -1875 1 0.224503 39.97377 2.747323 -1876 1 2.112303 39.817069 4.528393 -1877 2 1.981899 32.150865 1.347891 -1878 1 2.322442 33.979858 3.19387 -1879 2 2.096374 36.191635 4.230691 -1880 1 1.999648 34.152278 5.938815 -1881 1 1.73114 30.291033 2.935219 -1882 1 3.665367 29.983954 1.275677 -1883 2 1.943018 36.004664 1.697384 -1884 1 2.019378 38.176143 2.972324 -1885 1 2.19126 37.889176 5.917314 -1886 1 0.019605 35.984478 3.104091 -1887 2 7.787834 30.403461 4.344497 -1888 1 6.050812 33.918162 -0.027918 -1889 1 3.814711 31.691419 2.816277 -1890 2 4.20332 33.715468 4.180703 -1891 1 3.914581 32.066382 5.971622 -1892 2 3.895933 33.805468 1.20281 -1893 1 4.340385 35.802877 2.943593 -1894 1 4.271659 37.949305 4.314292 -1895 1 4.068788 35.686982 5.513423 -1896 2 4.190929 37.662517 7.182865 -1897 2 4.200636 38.226632 1.691189 -1898 1 9.716958 31.962759 4.249426 -1899 1 5.810481 32.019245 4.382481 -1900 1 5.938979 35.885235 7.16864 -1901 1 0.267384 35.760048 6.061532 -1902 2 6.018619 31.95181 1.612974 -1903 1 5.938914 34.057443 2.77635 -1904 2 6.183116 36.065698 4.376274 -1905 1 6.089476 34.019022 5.411901 -1906 1 6.359106 35.990867 1.578601 -1907 1 6.152011 38.058648 2.943561 -1908 1 5.711164 30.034724 2.988084 -1909 1 6.045542 37.798257 5.727308 -1910 1 8.009398 36.153578 0.053676 -1911 1 0.238276 33.896375 4.533811 -1912 1 7.902329 32.340963 2.922426 -1913 2 8.222407 34.13168 4.116176 -1914 1 7.936717 32.22354 5.888103 -1915 2 8.123641 38.41175 1.891536 -1916 2 7.927555 34.06589 1.21075 -1917 1 8.412195 35.913547 2.85742 -1918 1 8.139566 38.142702 4.120627 -1919 1 8.317254 36.194514 5.407003 -1920 1 4.034964 36.04412 0.47011 -1921 2 3.83481 30.240395 4.561724 -1922 2 0.249553 38.107374 7.140438 -1923 1 2.126706 37.874136 0.15149 -1924 1 9.770714 33.872567 5.735309 -1925 1 7.651907 31.89674 -0.001589 -1926 1 6.265497 38.190114 0.387488 -1927 2 0.091323 38.034686 1.579889 -1928 1 6.013525 30.091058 5.903567 -1929 2 9.613745 31.989409 1.558474 -1930 1 9.893134 38.099463 -0.000176 -1931 1 0.012372 34.088485 1.353111 -1932 1 1.957372 34.025261 0.135755 -1933 1 9.930552 30.036571 0.064988 -1934 1 1.356847 30.09059 0.587218 -1935 2 2.165378 39.90345 7.155948 -1936 1 9.928802 38.103943 5.693619 -1937 1 4.231897 39.892291 5.78739 -1938 2 3.93426 34.036259 7.069656 -1939 2 2.074177 32.270109 10.089125 -1940 1 3.932043 30.108354 7.345143 -1941 2 1.820986 31.836134 13.124076 -1942 1 1.929382 34.316614 8.776464 -1943 2 2.083627 36.058658 10.081855 -1944 1 1.997221 33.916084 11.577718 -1945 1 2.267799 35.662279 13.073333 -1946 2 4.209744 30.111608 9.908398 -1947 1 2.104601 38.082098 8.735584 -1948 2 8.24053 38.05696 7.216926 -1949 1 2.109203 38.067126 11.734018 -1950 2 0.042241 38.005125 10.32451 -1951 1 1.957287 39.865839 10.426779 -1952 2 8.203196 30.05132 9.912922 -1953 1 2.246349 30.143579 11.639665 -1954 1 4.199959 32.106503 8.70465 -1955 1 3.976417 34.112906 10.198306 -1956 1 3.884958 31.967651 11.562891 -1957 2 4.063522 34.032621 13.004991 -1958 1 4.232266 36.19468 8.962151 -1959 2 4.097197 38.230412 10.13239 -1960 1 4.118617 35.849094 11.679739 -1961 2 4.350691 37.885411 12.898671 -1962 1 6.201046 32.417633 10.15369 -1963 2 5.816252 31.722772 13.101456 -1964 1 6.157578 39.769939 7.197304 -1965 1 6.184596 34.126547 8.504052 -1966 2 6.346713 35.703957 10.195727 -1967 1 6.288059 33.992499 11.799552 -1968 1 6.483281 35.967443 12.860859 -1969 2 7.835082 34.145462 7.179037 -1970 1 6.256423 37.691882 8.993285 -1971 1 6.2337 37.988064 11.537765 -1972 2 9.772215 31.919829 7.180665 -1973 1 7.981132 32.165581 14.333143 -1974 1 2.309997 36.061233 7.359038 -1975 1 4.433034 36.045633 14.35862 -1976 1 7.955328 32.223129 8.507808 -1977 2 8.286523 34.141907 10.013388 -1978 1 7.939052 31.949186 11.600717 -1979 1 8.104476 34.231193 13.030137 -1980 2 1.884476 31.865234 7.19113 -1981 1 8.333692 36.082489 8.414603 -1982 2 8.168537 38.03579 10.329742 -1983 1 8.420403 35.985684 11.517078 -1984 1 8.327179 38.029547 12.910471 -1985 2 6.20532 31.903657 7.381951 -1986 2 0.085009 37.638839 13.154459 -1987 1 7.552329 30.251663 13.212821 -1988 2 2.355047 39.830169 13.072665 -1989 1 0.148785 31.885164 11.209718 -1990 1 1.848807 30.245173 8.940225 -1991 1 0.166389 36.076965 8.575072 -1992 1 5.894085 30.228735 11.200379 -1993 1 0.232408 36.202468 11.578646 -1994 1 2.4752 37.687884 14.341623 -1995 1 0.334254 39.866494 8.663952 -1996 1 0.04027 39.756099 11.961945 -1997 1 0.083418 34.195005 10.175316 -1998 2 0.043097 34.005541 7.193221 -1999 2 0.052476 33.834131 12.929227 -2000 1 8.114393 39.929142 8.406226 -2001 1 6.281515 37.719535 14.225496 -2002 2 9.768912 32.130689 12.866513 -2003 1 9.864669 32.192496 10.045288 -2004 1 0.028148 32.153045 8.783822 -2005 2 6.417236 39.879341 13.202851 -2006 1 8.005375 39.836615 20.349358 -2007 2 2.017709 31.870952 15.889762 -2008 2 7.716399 30.062983 18.430151 -2009 2 2.119264 32.351346 19.061283 -2010 2 6.658976 39.77428 18.733464 -2011 2 2.321302 35.607604 15.702355 -2012 1 1.966843 34.024507 17.339235 -2013 2 2.33321 35.646813 18.814154 -2014 1 1.794484 34.194282 20.582509 -2015 1 1.984336 29.928657 17.680043 -2016 1 2.238075 37.571948 17.445144 -2017 1 4.466772 39.923317 17.544828 -2018 1 2.072213 37.924398 20.106708 -2019 1 3.990864 31.761546 14.785242 -2020 1 4.020518 33.927189 15.729606 -2021 1 3.897539 31.807357 17.561737 -2022 1 4.265924 33.937397 18.871352 -2023 1 4.376327 32.03663 20.389624 -2024 1 6.400496 39.782735 15.767263 -2025 2 4.461272 37.709843 15.835142 -2026 1 4.42096 35.817684 17.119638 -2027 2 4.054798 37.811976 18.867409 -2028 1 3.994208 35.957797 20.233365 -2029 1 1.972412 30.096734 20.271564 -2030 1 5.988832 31.90054 15.667667 -2031 2 6.100535 31.913125 18.798462 -2032 1 0.28224 35.927235 17.246921 -2033 1 9.878186 30.085685 17.138849 -2034 1 6.416487 35.895999 15.857104 -2035 2 5.962689 34.078738 16.936543 -2036 1 6.325491 35.483857 19.110752 -2037 1 6.245971 33.832167 20.618167 -2038 1 6.042072 33.77268 14.335557 -2039 1 6.090957 37.771252 17.365844 -2040 1 9.965189 29.988789 20.309186 -2041 1 6.076905 37.611337 20.045471 -2042 1 5.896032 30.00014 17.243068 -2043 1 8.07936 33.904732 15.859046 -2044 1 8.054869 32.064974 17.179067 -2045 1 8.005802 33.797373 18.711026 -2046 1 8.057981 31.963545 20.146211 -2047 2 0.309963 38.150861 18.320971 -2048 1 4.115614 39.67221 20.110889 -2049 2 8.081998 38.170352 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30.09655 24.022449 41.945798 -5617 2 39.993697 25.996395 38.728838 -5618 1 37.81422 26.290042 42.848087 -5619 2 30.055901 19.935486 38.573149 -5620 1 37.973864 20.290243 36.046389 -5621 1 39.678251 27.704428 37.302745 -5622 2 39.966918 21.895199 38.767152 -5623 1 39.609699 27.894456 40.148854 -5624 1 35.857722 20.273774 37.567161 -5625 2 31.876516 29.975478 41.679184 -5626 2 29.990823 24.134634 38.782012 -5627 1 30.110123 28.422528 35.957979 -5628 1 30.166791 21.94758 37.4415 -5629 1 32.168293 24.104265 42.975893 -5630 1 35.411443 29.813844 38.643913 -5631 2 37.976528 20.120682 38.533653 -5632 1 39.779362 30.230874 4.652211 -5633 1 29.983878 33.982126 0.04316 -5634 2 30.086369 31.993647 4.231995 -5635 2 33.932165 39.866251 7.068893 -5636 1 32.059505 32.251117 2.629522 -5637 2 31.867763 34.040728 3.960388 -5638 1 31.932973 31.808697 5.917256 -5639 1 30.007373 39.943466 4.51009 -5640 2 39.207186 30.079079 1.703674 -5641 1 32.016417 34.359045 1.391175 -5642 1 32.0796 36.080574 2.990027 -5643 2 32.125016 37.982811 4.244242 -5644 1 32.039867 35.855789 5.754866 -5645 2 30.356301 36.250302 1.436559 -5646 1 32.110296 38.00744 1.426636 -5647 1 33.998604 30.067664 5.743991 -5648 2 33.695324 31.983255 4.383442 -5649 2 30.152086 36.019627 4.245065 -5650 2 34.240197 32.341445 1.32205 -5651 1 33.885438 34.090868 2.902626 -5652 2 34.178132 35.93225 4.482376 -5653 1 33.856287 33.915557 5.543055 -5654 2 34.187255 35.904801 1.570832 -5655 1 34.049489 37.902242 2.794215 -5656 1 34.196846 37.782622 5.597948 -5657 1 32.010141 29.994854 3.963328 -5658 1 30.085473 38.058327 2.970114 -5659 1 37.563886 30.425407 3.132393 -5660 1 35.867335 32.241913 3.116156 -5661 2 35.974255 34.126395 4.519526 -5662 1 36.004069 32.109611 5.814404 -5663 1 34.085538 39.906327 4.293478 -5664 1 36.097439 33.990507 1.502757 -5665 1 36.087679 36.048793 3.035352 -5666 2 36.278328 38.155374 4.063777 -5667 1 36.249913 36.355424 5.927679 -5668 2 31.890573 30.350964 1.619094 -5669 2 31.962807 37.754434 7.179059 -5670 1 35.973947 37.892913 1.48124 -5671 2 35.839322 30.204876 4.375075 -5672 1 37.935879 32.177401 4.195289 -5673 1 38.101493 38.10187 5.953049 -5674 2 37.852909 32.388628 1.664291 -5675 1 37.942171 34.0458 3.006996 -5676 2 38.2641 36.15208 4.530503 -5677 1 38.039433 34.206108 5.79566 -5678 1 33.979517 30.322401 2.668635 -5679 2 38.266202 35.993947 1.484331 -5680 1 38.067048 38.040012 2.752414 -5681 1 37.733806 30.096455 5.970187 -5682 1 39.682213 32.091472 5.993971 -5683 1 39.817487 31.930363 0.000367 -5684 1 36.043395 39.59783 5.676369 -5685 1 31.869558 32.098607 0.138261 -5686 1 39.734652 32.347843 3.042732 -5687 2 40.028718 38.187031 4.420077 -5688 1 35.900797 34.287592 6.911917 -5689 1 34.035098 34.219002 0.088382 -5690 1 35.958161 30.177564 1.36017 -5691 2 34.104037 39.871769 1.666144 -5692 2 31.713648 30.030149 13.126076 -5693 2 38.102561 35.967156 7.519894 -5694 2 31.857312 30.233676 7.601269 -5695 1 34.289545 38.267283 14.401123 -5696 2 35.86683 30.19377 7.315341 -5697 1 30.215661 34.162037 8.437432 -5698 2 32.177106 33.712521 7.258256 -5699 2 36.086337 30.089865 10.102229 -5700 1 31.904414 32.116466 8.706393 -5701 1 31.937094 33.843414 10.07911 -5702 1 31.979885 32.115442 11.535778 -5703 2 31.646163 34.054645 12.923349 -5704 2 34.238187 35.954151 7.232689 -5705 1 32.107596 35.868544 8.568472 -5706 1 31.872832 37.740296 10.246254 -5707 1 32.382757 36.08172 11.390228 -5708 1 31.907287 38.043268 12.759712 -5709 1 33.814113 30.280416 11.361764 -5710 1 30.217972 36.108976 12.75806 -5711 2 33.902634 32.114854 10.131038 -5712 1 33.57231 32.104408 13.09734 -5713 1 31.808268 30.066503 10.372268 -5714 1 34.074533 34.09759 8.82773 -5715 2 34.112978 35.879639 10.008535 -5716 1 33.847258 34.132738 11.781858 -5717 2 33.938795 36.222314 13.025522 -5718 2 29.978741 32.187816 10.235973 -5719 1 34.055911 38.08124 8.660649 -5720 1 33.602601 34.200907 14.256884 -5721 1 34.074479 38.033056 11.548004 -5722 2 36.270647 38.06342 7.227717 -5723 1 35.834976 32.087215 8.752976 -5724 2 36.060859 33.636235 10.421377 -5725 1 35.993855 31.835332 12.022895 -5726 2 35.800428 33.936835 13.252217 -5727 1 36.115212 35.929045 8.653718 -5728 2 36.22813 38.12211 10.18663 -5729 1 36.031176 36.067395 11.711353 -5730 2 36.290793 38.28804 13.110371 -5731 1 38.314803 39.87771 13.628157 -5732 2 37.813718 31.963763 10.266333 -5733 2 38.345306 31.61479 12.746628 -5734 1 37.993817 33.8253 8.828538 -5735 2 37.963385 36.024574 10.310583 -5736 1 37.917131 33.840219 11.529013 -5737 1 38.204273 36.194533 12.982689 -5738 1 38.223785 37.96125 8.694521 -5739 1 38.251957 38.103445 11.574783 -5740 1 32.162162 35.830151 14.368089 -5741 1 38.188088 39.835851 10.200529 -5742 2 37.943506 31.862097 7.486993 -5743 1 34.019779 32.099062 7.382655 -5744 1 37.835648 33.808569 14.272091 -5745 2 30.154664 36.008494 10.278616 -5746 2 34.005569 29.909902 14.221934 -5747 2 39.942399 30.201297 7.221972 -5748 1 31.669489 32.129787 14.202133 -5749 1 33.8553 30.102976 8.785283 -5750 1 36.285019 39.993992 8.473052 -5751 2 34.332311 39.811654 10.053333 -5752 1 32.287985 39.934755 8.544521 -5753 1 32.117424 39.894109 11.328559 -5754 1 34.070494 39.946648 12.675838 -5755 1 33.523905 30.237815 17.092452 -5756 1 37.796875 30.195733 20.074531 -5757 1 36.27689 36.076917 14.383428 -5758 1 31.912415 30.074316 18.962029 -5759 1 31.72877 30.195629 15.548548 -5760 1 39.683801 34.084414 18.996274 -5761 1 31.823255 34.23579 15.916954 -5762 1 32.081111 32.17144 17.423655 -5763 2 32.272671 34.141341 18.923237 -5764 1 31.890319 32.258592 20.174682 -5765 1 32.292252 37.789848 15.657298 -5766 1 31.865994 35.945048 17.430984 -5767 2 32.390605 38.101438 18.756338 -5768 1 32.536255 36.292415 20.33365 -5769 1 30.255802 37.826036 17.398086 -5770 2 30.361913 39.693462 15.767213 -5771 1 33.658364 32.195407 15.713634 -5772 1 37.521125 34.00621 20.179734 -5773 2 34.170474 31.959646 18.774747 -5774 2 30.146126 36.07111 19.193288 -5775 2 34.236512 36.009488 15.705407 -5776 1 33.893052 34.259763 17.152928 -5777 1 34.299465 36.26334 18.583767 -5778 1 34.414431 34.040341 19.801645 -5779 1 38.268782 38.067343 19.882736 -5780 1 38.192119 30.067346 14.65738 -5781 1 34.182659 38.172175 17.379208 -5782 1 34.285582 38.312236 20.114249 -5783 1 35.930101 31.821554 14.523145 -5784 1 38.166996 38.004859 14.725716 -5785 1 35.925271 33.697258 15.741088 -5786 1 35.628801 31.929644 17.21365 -5787 2 36.045808 34.231991 18.304721 -5788 1 36.066783 31.92807 19.890693 -5789 2 30.047091 31.872972 18.511468 -5790 1 38.23536 37.943903 17.225875 -5791 2 36.119549 38.085157 15.846243 -5792 1 36.28338 36.046451 17.021393 -5793 1 36.11202 38.183852 18.648108 -5794 1 36.196383 36.094959 20.14945 -5795 1 39.857714 32.070711 20.545667 -5796 2 38.277117 32.092018 16.056024 -5797 1 30.025257 33.999826 20.265429 -5798 2 37.984137 32.053017 18.664282 -5799 1 32.002215 39.814443 17.350923 -5800 2 38.174586 35.979296 18.941495 -5801 2 38.345772 36.135739 15.897296 -5802 1 38.047733 34.092532 17.193597 -5803 2 30.130578 35.962177 15.540359 -5804 2 36.401926 38.058554 21.346524 -5805 1 30.120957 38.000412 14.522433 -5806 1 30.488998 38.181884 20.233832 -5807 1 30.027329 34.063964 17.498188 -5808 1 37.840062 29.987227 17.565361 -5809 1 32.008478 30.033144 21.485715 -5810 2 39.774533 34.462138 21.415634 -5811 1 30.338184 36.208481 21.405811 -5812 1 29.947563 30.056036 17.165794 -5813 1 39.921352 31.819743 14.64622 -5814 2 34.22915 39.981504 21.655908 -5815 1 30.183329 38.19462 25.743477 -5816 1 35.907762 33.854845 21.824692 -5817 1 38.081846 38.241792 22.993384 -5818 2 34.075816 32.199578 21.47467 -5819 1 32.064265 31.912891 22.91255 -5820 1 31.883139 33.912773 24.608383 -5821 1 31.812805 31.862315 26.174015 -5822 2 32.311833 34.450426 27.53752 -5823 1 32.200878 36.145135 23.147334 -5824 2 32.211767 38.313372 24.442593 -5825 1 32.252693 36.173296 25.56014 -5826 2 32.184178 37.824314 27.059278 -5827 2 35.878916 30.070226 21.715039 -5828 1 37.668689 30.050641 23.045191 -5829 2 31.790668 34.251576 21.855242 -5830 1 30.175916 38.136754 23.248784 -5831 1 33.79328 31.909522 24.576174 -5832 2 33.915875 32.018888 27.178426 -5833 1 33.839278 34.11599 23.063711 -5834 2 34.250078 35.934833 24.487018 -5835 1 33.990054 34.106505 25.930061 -5836 1 34.091025 36.282124 27.332172 -5837 1 39.883217 38.455893 24.705928 -5838 2 38.008034 36.021219 27.398438 -5839 1 34.624327 37.896007 23.016853 -5840 1 34.168936 37.954274 25.436951 -5841 1 39.89339 34.048173 27.027007 -5842 1 38.248268 36.455753 21.536765 -5843 1 35.611768 31.698556 23.347142 -5844 2 36.148802 34.042768 24.34925 -5845 1 35.930043 32.125519 25.878398 -5846 2 35.950538 34.005205 27.219195 -5847 1 37.955393 34.076875 25.799656 -5848 1 37.973062 38.01909 26.230315 -5849 1 36.411999 36.023781 22.980871 -5850 2 36.283519 37.906374 24.521157 -5851 1 36.105429 36.189959 25.968065 -5852 2 35.830991 38.301536 27.267321 -5853 1 30.231426 34.188738 26.125408 -5854 1 30.281973 34.136127 28.552033 -5855 2 37.785563 31.866932 24.278312 -5856 2 31.348335 30.244331 27.485493 -5857 2 37.966809 32.115632 27.589764 -5858 2 35.66017 29.988788 24.878779 -5859 1 38.277476 34.130765 22.79239 -5860 2 37.959129 36.154297 24.437008 -5861 1 33.713618 30.108282 28.642398 -5862 1 39.822964 31.905463 23.110805 -5863 1 37.492689 32.09291 21.995043 -5864 2 30.127031 36.064739 24.638111 -5865 1 35.533243 30.110728 27.243438 -5866 1 36.070605 31.93122 28.695839 -5867 2 34.291131 35.85795 21.75028 -5868 1 31.938061 32.142881 28.504169 -5869 1 33.986813 39.867909 27.012668 -5870 1 30.10822 37.992396 28.395198 -5871 1 39.800701 30.030956 24.347523 -5872 2 39.892552 29.979658 27.134291 -5873 2 32.228297 37.952841 21.875429 -5874 2 39.977135 34.107266 24.499149 -5875 1 39.846344 36.406036 26.033584 -5876 1 32.059083 40.009476 28.464272 -5877 1 35.959269 39.965152 25.93262 -5878 2 30.460566 32.139968 24.447603 -5879 2 39.881804 38.087413 21.696502 -5880 1 30.134489 36.163809 33.336193 -5881 1 37.575878 38.100411 28.849489 -5882 1 37.662104 38.133383 31.571418 -5883 1 32.362045 39.87867 34.884405 -5884 1 39.873173 36.224308 34.920349 -5885 1 31.991424 34.085923 29.999612 -5886 1 31.815171 32.168756 31.641691 -5887 2 31.782096 34.063184 33.062024 -5888 1 31.718037 31.953527 34.554814 -5889 1 39.862898 38.376226 32.906485 -5890 1 37.551931 30.038119 34.432157 -5891 1 31.780802 37.997046 30.254783 -5892 1 31.834761 35.939821 31.604936 -5893 2 32.041736 38.210181 33.326919 -5894 1 32.203699 35.869978 34.596577 -5895 1 34.008946 38.074601 28.827076 -5896 1 37.899592 29.974959 28.916731 -5897 1 38.030007 33.96835 28.91396 -5898 2 33.846774 32.085103 30.081464 -5899 1 29.952597 30.143437 34.499248 -5900 1 33.915497 32.111271 33.150301 -5901 1 31.790321 30.23064 29.991804 -5902 2 37.907438 32.157735 35.935104 -5903 2 33.84716 36.05681 30.26538 -5904 1 34.0432 34.280307 31.67674 -5905 2 34.011752 36.10558 33.143956 -5906 1 33.824017 34.085576 34.552777 -5907 1 34.194027 34.072791 28.967937 -5908 1 33.894909 38.222801 31.657741 -5909 1 33.881652 38.078172 34.899329 -5910 1 38.119296 38.056464 34.569681 -5911 1 34.291634 39.920546 33.178111 -5912 1 33.581454 29.993619 34.681796 -5913 2 36.053229 33.87704 30.318866 -5914 1 35.873901 31.88411 31.537273 -5915 1 35.89848 33.774876 32.823618 -5916 1 35.828028 32.348885 34.478807 -5917 1 35.672787 37.928294 30.518119 -5918 1 35.989671 35.945619 31.826779 -5919 2 35.97259 38.32967 33.142576 -5920 1 35.703331 35.814769 34.580449 -5921 1 33.817908 30.208146 31.599942 -5922 1 35.844503 36.12033 28.831087 -5923 1 38.261976 32.096366 30.088155 -5924 2 37.797891 31.9048 33.114668 -5925 1 39.55682 31.880323 34.531549 -5926 2 37.75043 36.193675 30.248336 -5927 1 38.393997 33.98513 31.905095 -5928 2 37.963057 36.355009 33.181745 -5929 1 37.797425 34.035854 34.376018 -5930 1 30.050396 34.271558 31.538997 -5931 1 39.815357 36.070726 31.654601 -5932 2 39.731271 30.032678 30.327233 -5933 1 39.915975 31.952921 31.714062 -5934 2 31.84562 29.966231 33.068673 -5935 1 31.85693 36.270476 28.934934 -5936 1 31.866016 39.844488 31.814385 -5937 1 30.092134 34.094244 34.755273 -5938 1 39.694807 30.040539 32.997642 -5939 1 36.196648 35.960439 42.925128 -5940 2 32.015598 37.930066 36.230869 -5941 1 37.674069 30.102473 37.130906 -5942 1 39.699003 32.118698 37.217773 -5943 2 29.963786 31.633701 39.162197 -5944 1 32.058675 39.814086 37.607409 -5945 1 35.842471 33.971675 35.989822 -5946 1 34.028551 38.060871 42.983375 -5947 1 31.588672 31.941435 37.383683 -5948 2 31.694069 33.998273 38.693202 -5949 1 31.930294 31.884957 40.381472 -5950 2 32.11349 33.999595 41.798502 -5951 1 31.876844 36.011394 37.307134 -5952 2 31.893158 37.928813 38.973436 -5953 1 31.81531 35.668229 40.479844 -5954 2 31.787646 38.142244 41.698514 -5955 1 31.925559 36.23881 42.924197 -5956 1 36.004443 37.899297 36.000218 -5957 1 38.451312 38.205323 40.038254 -5958 2 33.656378 31.907332 38.819792 -5959 1 33.99011 31.933293 41.627228 -5960 2 37.707146 36.123239 36.332034 -5961 1 33.657247 33.955416 37.665398 -5962 1 33.73943 36.151957 39.054731 -5963 1 33.605884 33.957716 40.193208 -5964 2 34.011058 36.048882 41.690411 -5965 1 38.130598 34.242802 40.052446 -5966 1 34.167865 38.117836 37.628936 -5967 1 34.142536 38.424699 40.41195 -5968 1 40.005739 32.215658 40.003237 -5969 1 39.521882 33.977557 36.015643 -5970 1 38.214368 38.282583 37.333443 -5971 1 31.918418 33.931512 36.157998 -5972 1 35.612055 32.074774 37.387219 -5973 2 35.5831 34.04957 39.047544 -5974 1 35.75246 32.088086 40.149631 -5975 2 35.615657 33.824419 41.713165 -5976 1 35.638569 36.061296 37.614952 -5977 2 36.358444 37.816896 38.884174 -5978 1 35.987046 36.034802 40.28745 -5979 1 36.122176 38.157473 41.827978 -5980 1 37.730089 30.067171 42.889333 -5981 2 39.944726 33.833791 41.642053 -5982 2 37.765477 32.166294 38.745053 -5983 2 38.099767 31.876153 41.350163 -5984 2 38.066621 36.442839 41.48951 -5985 1 37.726393 34.24931 37.606618 -5986 1 38.065514 36.286433 39.031222 -5987 1 37.664687 30.041804 39.941583 -5988 1 36.1403 39.743151 39.963443 -5989 2 34.004128 36.124387 36.139274 -5990 1 38.008343 33.918454 43.060491 -5991 1 36.098653 32.233378 42.976295 -5992 1 30.058867 38.134404 37.476791 -5993 2 35.662195 29.860797 35.905075 -5994 1 33.53205 30.001458 37.176731 -5995 1 38.387155 38.05525 43.009631 -5996 1 36.188595 39.834331 37.505629 -5997 1 39.656895 29.968268 41.372509 -5998 1 39.786156 36.00049 42.804021 -5999 2 33.855117 32.268762 36.090908 -6000 2 31.856527 30.044242 36.001804 diff --git a/examples/cauchystat/NiAl_stretch/lammps.in b/examples/cauchystat/NiAl_stretch/lammps.in deleted file mode 100644 index 77ba62e783..0000000000 --- a/examples/cauchystat/NiAl_stretch/lammps.in +++ /dev/null @@ -1,48 +0,0 @@ -units metal -atom_style atomic -atom_modify map array - -processors 1 1 1 - -# Box and atom positions: -boundary p p p -read_data input.dat - -# Atomic mass: -mass 1 58.69 -mass 2 26.98154 - -# Potential, Al fcc crystal -pair_style eam/alloy -pair_coeff * * ../Mishin-Ni-Al-2009.eam.alloy Ni Al - - -thermo 100 -thermo_style custom step temp pxx pyy pzz lx ly lz -compute cna all cna/atom 2.8 - -velocity all create 2400.0 4928459 rot yes dist gaussian - -fix 1 all npt temp 600.0 600.0 1.0 x 0.0 0.0 0.1 y 0.0 0.0 0.1 z 0.0 0.0 0.1 couple none cauchystat 0.001 no - -dump 1 all cfg 1000 test*.cfg mass type xs ys zs type c_cna - -timestep 0.002 - -variable l equal lz -variable p equal pzz -variable t equal temp - -fix avg all ave/time 1 1000 1000 v_t v_l v_p file avg.txt - -#restart 1000 restart.*.test - -velocity all create 2400 4928459 rot yes dist gaussian - -run 10000 - -unfix 1 - -fix 1 all npt temp 600.0 600.0 1.0 x 0.0 0.0 0.1 y 0.0 0.0 0.1 z 0.0 -6000.0 0.1 couple none cauchystat 0.001 yes - -run 100000 diff --git a/examples/cauchystat/README b/examples/cauchystat/README index f42ce0cba1..fb6c63bff6 100644 --- a/examples/cauchystat/README +++ b/examples/cauchystat/README @@ -1,42 +1,10 @@ -There are 6 examples in this directory. All are run by executing: +Run this example by executing: % lmp_serial < lammps.in -from the respective home directory. - -Note that these examples use an EAM potential, and therefore must be +Note that this example use an EAM potential, and therefore must be run with a LAMMPS executable built with the MANYBODY package. -Al_shear_PR: Application of a simple shear stress, illustrating that -there is a non-zero direct stress in the equilibrated system due to -the fact that Parinello-Rahman controls the second Piola-Kirchhoff -stress instead of the Cauchy stress. First fix equilibrates the -temperature at zero stress, second fix applies the shear. The third -fix corrects the problem because each new run resets the reference -simulation cell (H0) to the current cell shape. - -Al_shear_CS: Cauchystat example. Same as above, using the Cauchystat -instead of PR control. In this case, the equilibrated stresses are as -prescribed (ie., the set stresses control the Cauchy stress, not Piola -Kirchhoff) - -NiAl_cool: Cauchystat example. First fix equilibrates the system to -uniaxial tension of 2800 bars, 1200K. Second fix cools to 300 K, -causing a phase transformation. Cauchy stress remains at the set -level after the transformation - -NiAl_stretch: Cauchystat example. After a brief equilibration -at 600 K and zero stress, quickly ramp up the applied tensile stress -from 0 to 6000 bars over 100000 time steps. After the phase -transformation, Cauchy stress continues to follow the set value. - -NiAl_slow_stretch_CS: Cauchystat example. After a brief equilibration -at 500 K and zero stress, gradually ramp up the applied tensile stress -from 0 to 14000 bars over 350000 time steps. After the phase -transformation, Cauchy stress continues to follow the set value. - -NiAl_slow_stretch_PR: After a brief equilibration at 500 K and zero -stress, gradually ramp up the applied tensile stress from 0 to 14000 -bars over 350000 time steps. After the phase transformation, Cauchy -stress departs substantially from the set value, because the PR -control is used instead of the Cauchystat. +The first cauchystat fix equilibrates the temperature at zero stress, +the second fix applies a shear stress. Output in avg.txt shows +convergence to correct values. diff --git a/examples/cauchystat/Al_shear_CS/lammps.in b/examples/cauchystat/lammps.in similarity index 87% rename from examples/cauchystat/Al_shear_CS/lammps.in rename to examples/cauchystat/lammps.in index 0feefeb5b2..218bef3308 100644 --- a/examples/cauchystat/Al_shear_CS/lammps.in +++ b/examples/cauchystat/lammps.in @@ -20,7 +20,7 @@ mass 2 26.98154 # Potential, Al fcc crystal pair_style eam/alloy -pair_coeff * * ../Mishin-Ni-Al-2009.eam.alloy Ni Al +pair_coeff * * Mishin-Ni-Al-2009.eam.alloy Ni Al thermo 100 @@ -61,9 +61,3 @@ unfix 1 fix 1 all npt temp 600.0 600.0 1.0 x 0.0 0.0 0.1 y 0.0 0.0 0.1 z 0.0 0.0 0.1 xy -10000.0 -10000.0 0.1 couple none cauchystat 0.001 yes run 10000 - -unfix 1 - -fix 1 all npt temp 600.0 600.0 1.0 x 0.0 0.0 0.1 y 0.0 0.0 0.1 z 0.0 0.0 0.1 xy -10000.0 -10000.0 0.1 couple none - -run 10000 diff --git a/src/fix_nh.cpp b/src/fix_nh.cpp index c91e07eeac..9cd0987a54 100644 --- a/src/fix_nh.cpp +++ b/src/fix_nh.cpp @@ -347,77 +347,15 @@ FixNH::FixNH(LAMMPS *lmp, int narg, char **arg) : } else error->all(FLERR,"Illegal fix nvt/npt/nph command"); iarg += 2; } else if (strcmp(arg[iarg],"cauchystat") == 0) { - if (iarg+3 > narg) error->all(FLERR,"Illegal fix npt cauchystat command: wrong number of arguments"); - if (strcmp(arg[iarg+2],"yes") != 0 && strcmp(arg[iarg+2],"no") != 0) error->all(FLERR,"Illegal cauchystat continue value. Must be 'yes' or 'no'"); + if (iarg+3 > narg) error->all(FLERR, + "Illegal fix npt cauchystat command:" + " wrong number of arguments"); + if (strcmp(arg[iarg+2],"yes") != 0 && strcmp(arg[iarg+2],"no") != 0) + error->all(FLERR,"Illegal cauchystat continue value. Must be 'yes' or 'no'"); alpha = force->numeric(FLERR,arg[iarg+1]); restartPK = !strcmp(arg[iarg+2],"yes"); - - - if (comm->me == 0) { - if (screen) { - fprintf(screen,"Using the Cauchystat fix with alpha=%f\n",alpha); - if(restartPK==1) { - fprintf(screen," (this is a continuation fix)\n"); - } - else { - fprintf(screen," (this is NOT a continuation fix)\n"); - } - } - if (logfile) { - fprintf(logfile,"Using the Cauchystat with alpha=%f\n",alpha); - if(restartPK==1) { - fprintf(logfile," this is a continuation run\n"); - } - else { - fprintf(logfile," this is NOT a continuation run\n"); - } - } - } - - - if(restartPK==1 && restart_stored==0) { - error->all(FLERR,"Illegal cauchystat command. Continuation run must follow a previously equilibrated Cauchystat run"); - } - - if(alpha<=0.0) { - error->all(FLERR,"Illegal cauchystat command. Alpha cannot be zero or negative"); - } - - initRUN = 0; - initPK = 1; - usePK = 0; - - #define H0(row,col) (H0[(row-1)][(col-1)]) - #define invH0(row,col) (invH0[(row-1)][(col-1)]) - - - // initialize H0 to current box shape - - int triclinic = domain->triclinic; - double *h = domain->h; - double *h_inv = domain->h_inv; - double *boxhi = domain->boxhi; - double *boxlo = domain->boxlo; - double yz = domain->yz; - double xz = domain->xz; - double xy = domain->xy; - - - H0(1,1)=h[0]; H0(1,2)=h[5]; H0(1,3)=h[4]; - H0(2,1)=0.0; H0(2,2)=h[1]; H0(2,3)=h[3]; - H0(3,1)=0.0; H0(3,2)=0.0; H0(3,3)=h[2]; - - invH0(1,1)=h_inv[0]; invH0(1,2)=h_inv[5]; invH0(1,3)=h_inv[4]; - invH0(2,1)=0.0; invH0(2,2)=h_inv[1]; invH0(2,3)=h_inv[3]; - invH0(3,1)=0.0; invH0(3,2)=0.0; invH0(3,3)=h_inv[2]; - - myvol0 = abs(MathExtra::det3(H0)); //find reference volume - - #undef H0 - #undef invH0 - + CauchyStat_init(); iarg += 3; - } else if (strcmp(arg[iarg],"fixedpoint") == 0) { if (iarg+4 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command"); fixedpoint[0] = force->numeric(FLERR,arg[iarg+1]); @@ -2307,170 +2245,19 @@ void FixNH::compute_press_target() for (int i = 3; i < 6; i++) p_target[i] = p_start[i] + delta * (p_stop[i]-p_start[i]); - // CauchyStat: call CauchyStat to modify p_target[i] and p_hydro, they are used in compute_sigma() + // CauchyStat: call CauchyStat to modify p_target[i] and p_hydro, // if CauchyStat enabled and pressure->vector computation has been initiated - if( (usePK==0) && (initRUN==1) ) { - - double* h = domain->h; // shape matrix in Voigt notation - double* h_rate = domain->h_rate; // rate of box size/shape change in Voigt notation - double H[3][3]; - double Hdot[3][3]; - - #define H(row,col) (H[(row-1)][(col-1)]) - #define Hdot(row,col) (Hdot[(row-1)][(col-1)]) - #define F(row,col) (F[(row-1)][(col-1)]) - #define Fi(row,col) (Fi[(row-1)][(col-1)]) - #define Fdot(row,col) (Fdot[(row-1)][(col-1)]) - #define invH0(row,col) (invH0[(row-1)][(col-1)]) - #define cauchy(row,col) (cauchy[(row-1)][(col-1)]) - #define setcauchy(row,col) (setcauchy[(row-1)][(col-1)]) - #define setPK(row,col) (setPK[(row-1)][(col-1)]) - #define sigmahat(row,col) (sigmahat[(row-1)][(col-1)]) - - H(1,1)=h[0]; H(1,2)=0.0; H(1,3)=0.0; - H(2,1)=0.0; H(2,2)=h[1]; H(2,3)=0.0; - H(3,1)=0.0; H(3,2)=0.0; H(3,3)=h[2]; - - for (int i=0;i<6;i++) { - h_rate[i]=(h[i]-h_old[i])/update->dt; - h_old[i]=h[i]; - } - - Hdot(1,1)=h_rate[0]; Hdot(1,2)=0.0; Hdot(1,3)=0.0; - Hdot(2,1)=0.0; Hdot(2,2)=h_rate[1]; Hdot(2,3)=0.0; - Hdot(3,1)=0.0; Hdot(3,2)=0.0; Hdot(3,3)=h_rate[2]; - - if (domain->triclinic) { - H(1,2)=h[5]; H(1,3)=h[4]; H(2,3)=h[3]; - Hdot(1,2)=h_rate[5]; Hdot(1,3)=h_rate[4]; Hdot(2,3)=h_rate[3]; - } - - double F[3][3]={0.0}; - double FT[3][3]={0.0}; - double Fi[3][3]={0.0}; - double Fdot[3][3]={0.0}; - double J,vol; - - MathExtra::times3(H,invH0,F); //find F - MathExtra::times3(Hdot,invH0,Fdot); //find Fdot - - MathExtra::invert3(F,Fi); - J = MathExtra::det3(F); //find J - vol=myvol0*J; // actual volume - - double deltat; - deltat = update->dt; //increment of time step - - // Current pressure on the cell boundaries: - //tensor: 0 1 2 3 4 5 - // x y z xy xz yz - - double *tensor = pressure->vector; - - double cauchy[3][3]; //stress - cauchy(1,1)=-tensor[0]; cauchy(1,2)=0.0; cauchy(1,3)=0.0; - cauchy(2,1)=0.0; cauchy(2,2)=-tensor[1]; cauchy(2,3)=0.0; - cauchy(3,1)=0.0; cauchy(3,2)=0.0; cauchy(3,3)=-tensor[2]; - - if (domain->triclinic) { - cauchy(1,2)=-tensor[3]; cauchy(1,3)=-tensor[4]; - cauchy(2,1)=-tensor[3]; cauchy(2,3)=-tensor[5]; - cauchy(3,1)=-tensor[4]; cauchy(3,2)=-tensor[5]; - } - - // target pressure on the cell boundaries: - //p_target: 0 1 2 3 4 5 - // x y z yz xz xy - - double setcauchy[3][3]; //stress - setcauchy(1,1)=-p_target[0]; setcauchy(1,2)=0.0; setcauchy(1,3)=0.0; - setcauchy(2,1)=0.0; setcauchy(2,2)=-p_target[1]; setcauchy(2,3)=0.0; - setcauchy(3,1)=0.0; setcauchy(3,2)=0.0; setcauchy(3,3)=-p_target[2]; - - if (domain->triclinic) { - setcauchy(1,2)=-p_target[5]; setcauchy(1,3)=-p_target[4]; - setcauchy(2,1)=-p_target[5]; setcauchy(2,3)=-p_target[3]; - setcauchy(3,1)=-p_target[4]; setcauchy(3,2)=-p_target[3]; - } - - //initialize: - if(initPK==1) { - if(restartPK==1) { - setPK(1,1)=setPKinit[0]; setPK(1,2)=setPKinit[1]; setPK(1,3)=setPKinit[2]; - setPK(2,1)=setPKinit[1]; setPK(2,2)=setPKinit[3]; setPK(2,3)=setPKinit[4]; - setPK(3,1)=setPKinit[2]; setPK(3,2)=setPKinit[4]; setPK(3,3)=setPKinit[5]; - }else { - setPK(1,1)=cauchy(1,1); setPK(1,2)=cauchy(1,2); setPK(1,3)=cauchy(1,3); - setPK(2,1)=cauchy(2,1); setPK(2,2)=cauchy(2,2); setPK(2,3)=cauchy(2,3); - setPK(3,1)=cauchy(3,1); setPK(3,2)=cauchy(3,2); setPK(3,3)=cauchy(3,3); - } - - initPK=0; - } - - //cauchystat: - bigint step = update->ntimestep; - - - - - - CauchyStat(step,F,Fi,Fdot,cauchy,setcauchy,setPK,vol,myvol0,deltat,alpha); - - // use currentPK as new target: - //p_target: 0 1 2 3 4 5 - // x y z yz xz xy - - p_target[0]=-setPK(1,1); - p_target[1]=-setPK(2,2); - p_target[2]=-setPK(3,3); - if (pstyle == TRICLINIC) { - p_target[3]=-setPK(2,3); - p_target[4]=-setPK(1,3); - p_target[5]=-setPK(1,2); - } - - p_hydro = 0.0; - for (int i = 0; i < 3; i++) - if (p_flag[i]) { - p_hydro += p_target[i]; - } - p_hydro /= pdim; - - // save information for Cauchystat restart - setPKinit[0] = setcauchy(1,1); - setPKinit[1] = setcauchy(1,2); - setPKinit[2] = setcauchy(1,3); - setPKinit[3] = setcauchy(2,2); - setPKinit[4] = setcauchy(2,3); - setPKinit[5] = setcauchy(3,3); - restart_stored=1; - - #undef H - #undef Hdot - #undef F - #undef Fi - #undef Fdot - #undef invH0 - #undef cauchy - #undef setcauchy - #undef setPK - #undef sigmahat - - } - + if((usePK==0) && (initRUN==1)) CauchyStat(); if(initRUN==0){ - double* h = domain->h; // shape matrix in Voigt notation for (int i=0;i<6;i++) { - h_old[i]=h[i]; + h_old[i]=domain->h[i]; } } - initRUN=1; // when run is initialized tensor[] not available (pressure on cell wall) - // if deviatoric, recompute sigma each time p_target changes + if (deviatoric_flag) compute_sigma(); } @@ -2622,7 +2409,222 @@ double FixNH::memory_usage() } /* ---------------------------------------------------------------------- - CauchyStat + initialize Cauchystat +------------------------------------------------------------------------- */ + +void FixNH::CauchyStat_init() +{ + if (comm->me == 0) { + if (screen) { + fprintf(screen,"Using the Cauchystat fix with alpha=%f\n",alpha); + if(restartPK==1) { + fprintf(screen," (this is a continuation fix)\n"); + } + else { + fprintf(screen," (this is NOT a continuation fix)\n"); + } + } + if (logfile) { + fprintf(logfile,"Using the Cauchystat with alpha=%f\n",alpha); + if(restartPK==1) { + fprintf(logfile," this is a continuation run\n"); + } + else { + fprintf(logfile," this is NOT a continuation run\n"); + } + } + } + if(restartPK==1 && restart_stored==0) { + error->all(FLERR,"Illegal cauchystat command. Continuation run" + " must follow a previously equilibrated Cauchystat run"); + } + if(alpha<=0.0) { + error->all(FLERR,"Illegal cauchystat command. Alpha cannot be zero or negative"); + } + + initRUN = 0; + initPK = 1; + usePK = 0; + +#define H0(row,col) (H0[(row-1)][(col-1)]) +#define invH0(row,col) (invH0[(row-1)][(col-1)]) + + // initialize H0 to current box shape + + int triclinic = domain->triclinic; + double *h = domain->h; + double *h_inv = domain->h_inv; + double *boxhi = domain->boxhi; + double *boxlo = domain->boxlo; + double yz = domain->yz; + double xz = domain->xz; + double xy = domain->xy; + + H0(1,1)=h[0]; H0(1,2)=h[5]; H0(1,3)=h[4]; + H0(2,1)=0.0; H0(2,2)=h[1]; H0(2,3)=h[3]; + H0(3,1)=0.0; H0(3,2)=0.0; H0(3,3)=h[2]; + + invH0(1,1)=h_inv[0]; invH0(1,2)=h_inv[5]; invH0(1,3)=h_inv[4]; + invH0(2,1)=0.0; invH0(2,2)=h_inv[1]; invH0(2,3)=h_inv[3]; + invH0(3,1)=0.0; invH0(3,2)=0.0; invH0(3,3)=h_inv[2]; + + CSvol0 = abs(MathExtra::det3(H0)); //find reference volume + +#undef H0 +#undef invH0 +} + + + +/* ---------------------------------------------------------------------- + Cauchystat +------------------------------------------------------------------------- */ + +void FixNH::CauchyStat() +{ + double* h = domain->h; // shape matrix in Voigt notation + double* h_rate = domain->h_rate; // rate of box size/shape change in Voigt notation + double H[3][3]; + double Hdot[3][3]; + +#define H(row,col) (H[(row-1)][(col-1)]) +#define Hdot(row,col) (Hdot[(row-1)][(col-1)]) +#define F(row,col) (F[(row-1)][(col-1)]) +#define Fi(row,col) (Fi[(row-1)][(col-1)]) +#define Fdot(row,col) (Fdot[(row-1)][(col-1)]) +#define invH0(row,col) (invH0[(row-1)][(col-1)]) +#define cauchy(row,col) (cauchy[(row-1)][(col-1)]) +#define setcauchy(row,col) (setcauchy[(row-1)][(col-1)]) +#define setPK(row,col) (setPK[(row-1)][(col-1)]) +#define sigmahat(row,col) (sigmahat[(row-1)][(col-1)]) + + H(1,1)=h[0]; H(1,2)=0.0; H(1,3)=0.0; + H(2,1)=0.0; H(2,2)=h[1]; H(2,3)=0.0; + H(3,1)=0.0; H(3,2)=0.0; H(3,3)=h[2]; + + for (int i=0;i<6;i++) { + h_rate[i]=(h[i]-h_old[i])/update->dt; + h_old[i]=h[i]; + } + + Hdot(1,1)=h_rate[0]; Hdot(1,2)=0.0; Hdot(1,3)=0.0; + Hdot(2,1)=0.0; Hdot(2,2)=h_rate[1]; Hdot(2,3)=0.0; + Hdot(3,1)=0.0; Hdot(3,2)=0.0; Hdot(3,3)=h_rate[2]; + + if (domain->triclinic) { + H(1,2)=h[5]; H(1,3)=h[4]; H(2,3)=h[3]; + Hdot(1,2)=h_rate[5]; Hdot(1,3)=h_rate[4]; Hdot(2,3)=h_rate[3]; + } + + double F[3][3]={0.0}; + double FT[3][3]={0.0}; + double Fi[3][3]={0.0}; + double Fdot[3][3]={0.0}; + double J,vol; + + MathExtra::times3(H,invH0,F); + MathExtra::times3(Hdot,invH0,Fdot); + MathExtra::invert3(F,Fi); + J = MathExtra::det3(F); + vol=CSvol0*J; + + double deltat; + deltat = update->dt; //increment of time step + + // Current pressure on the cell boundaries: + //tensor: 0 1 2 3 4 5 + // x y z xy xz yz + + double *tensor = pressure->vector; + + double cauchy[3][3]; + cauchy(1,1)=-tensor[0]; cauchy(1,2)=0.0; cauchy(1,3)=0.0; + cauchy(2,1)=0.0; cauchy(2,2)=-tensor[1]; cauchy(2,3)=0.0; + cauchy(3,1)=0.0; cauchy(3,2)=0.0; cauchy(3,3)=-tensor[2]; + + if (domain->triclinic) { + cauchy(1,2)=-tensor[3]; cauchy(1,3)=-tensor[4]; + cauchy(2,1)=-tensor[3]; cauchy(2,3)=-tensor[5]; + cauchy(3,1)=-tensor[4]; cauchy(3,2)=-tensor[5]; + } + + // target pressure on the cell boundaries: + // p_target: 0 1 2 3 4 5 + // x y z yz xz xy + + double setcauchy[3][3]; + setcauchy(1,1)=-p_target[0]; setcauchy(1,2)=0.0; setcauchy(1,3)=0.0; + setcauchy(2,1)=0.0; setcauchy(2,2)=-p_target[1]; setcauchy(2,3)=0.0; + setcauchy(3,1)=0.0; setcauchy(3,2)=0.0; setcauchy(3,3)=-p_target[2]; + + if (domain->triclinic) { + setcauchy(1,2)=-p_target[5]; setcauchy(1,3)=-p_target[4]; + setcauchy(2,1)=-p_target[5]; setcauchy(2,3)=-p_target[3]; + setcauchy(3,1)=-p_target[4]; setcauchy(3,2)=-p_target[3]; + } + + //initialize: + if(initPK==1) { + if(restartPK==1) { + setPK(1,1)=setPKinit[0]; setPK(1,2)=setPKinit[1]; setPK(1,3)=setPKinit[2]; + setPK(2,1)=setPKinit[1]; setPK(2,2)=setPKinit[3]; setPK(2,3)=setPKinit[4]; + setPK(3,1)=setPKinit[2]; setPK(3,2)=setPKinit[4]; setPK(3,3)=setPKinit[5]; + }else { + setPK(1,1)=cauchy(1,1); setPK(1,2)=cauchy(1,2); setPK(1,3)=cauchy(1,3); + setPK(2,1)=cauchy(2,1); setPK(2,2)=cauchy(2,2); setPK(2,3)=cauchy(2,3); + setPK(3,1)=cauchy(3,1); setPK(3,2)=cauchy(3,2); setPK(3,3)=cauchy(3,3); + } + initPK=0; + } + + CauchyStat_Step(update->ntimestep,F,Fi,Fdot,cauchy,setcauchy,setPK,vol,CSvol0,deltat,alpha); + + // use currentPK as new target: + //p_target: 0 1 2 3 4 5 + // x y z yz xz xy + + p_target[0]=-setPK(1,1); + p_target[1]=-setPK(2,2); + p_target[2]=-setPK(3,3); + if (pstyle == TRICLINIC) { + p_target[3]=-setPK(2,3); + p_target[4]=-setPK(1,3); + p_target[5]=-setPK(1,2); + } + + p_hydro = 0.0; + for (int i = 0; i < 3; i++) + if (p_flag[i]) { + p_hydro += p_target[i]; + } + p_hydro /= pdim; + + // save information for Cauchystat restart + setPKinit[0] = setcauchy(1,1); + setPKinit[1] = setcauchy(1,2); + setPKinit[2] = setcauchy(1,3); + setPKinit[3] = setcauchy(2,2); + setPKinit[4] = setcauchy(2,3); + setPKinit[5] = setcauchy(3,3); + restart_stored=1; + +#undef H +#undef Hdot +#undef F +#undef Fi +#undef Fdot +#undef invH0 +#undef cauchy +#undef setcauchy +#undef setPK +#undef sigmahat + +} + + + +/* ---------------------------------------------------------------------- + CauchyStat_Step Inputs: step : current step number @@ -2632,7 +2634,6 @@ double FixNH::memory_usage() cauchy(3,3) : current cauchy stress tensor setcauchy(3,3) : target cauchy stress tensor alpha : parameter =0.01 - nstat : =1, flag for mod(step,nstat).ne.0 setPK(3,3) : current PK stress tensor, at initialization (time=0) setPK=cauchy volume : current volume of the periodic box volume0 : initial volume of the periodic box @@ -2641,28 +2642,26 @@ double FixNH::memory_usage() Outputs: setPK(3,3) : PK stress tensor at the next time step -------------------------------------------------------------------------- */ + ------------------------------------------------------------------------- */ -void FixNH::CauchyStat(bigint step, double (&F)[3][3], double (&Fi)[3][3], double (&Fdot)[3][3], double (&cauchy)[3][3], double (&setcauchy)[3][3], double (&setPK)[3][3], double volume, double volume0, double deltat, double alpha) +void FixNH::CauchyStat_Step(bigint step, double (&F)[3][3], double (&Fi)[3][3], double (&Fdot)[3][3], double (&cauchy)[3][3], double (&setcauchy)[3][3], double (&setPK)[3][3], double volume, double volume0, double deltat, double alpha) { - int nstat=1; //macros to go from c to fortran style for arrays: - #define F(row,col) (F[(row-1)][(col-1)]) - #define Fi(row,col) (Fi[(row-1)][(col-1)]) - #define Fdot(row,col) (Fdot[(row-1)][(col-1)]) - #define cauchy(row,col) (cauchy[(row-1)][(col-1)]) - #define setcauchy(row,col) (setcauchy[(row-1)][(col-1)]) - #define setPK(row,col) (setPK[(row-1)][(col-1)]) - - #define uv(row,col) (uv[(row-1)][(col-1)]) - #define deltastress(row) (deltastress[(row-1)]) - #define fdotvec(row) (fdotvec[(row-1)]) - #define dsdf(row,col) (dsdf[(row-1)][(col-1)]) - #define dsds(row,col) (dsds[(row-1)][(col-1)]) - #define deltaF(row) (deltaF[(row-1)]) - #define deltaPK(row) (deltaPK[(row-1)]) +#define F(row,col) (F[(row-1)][(col-1)]) +#define Fi(row,col) (Fi[(row-1)][(col-1)]) +#define Fdot(row,col) (Fdot[(row-1)][(col-1)]) +#define cauchy(row,col) (cauchy[(row-1)][(col-1)]) +#define setcauchy(row,col) (setcauchy[(row-1)][(col-1)]) +#define setPK(row,col) (setPK[(row-1)][(col-1)]) +#define uv(row,col) (uv[(row-1)][(col-1)]) +#define deltastress(row) (deltastress[(row-1)]) +#define fdotvec(row) (fdotvec[(row-1)]) +#define dsdf(row,col) (dsdf[(row-1)][(col-1)]) +#define dsds(row,col) (dsds[(row-1)][(col-1)]) +#define deltaF(row) (deltaF[(row-1)]) +#define deltaPK(row) (deltaPK[(row-1)]) //initialize local variables: int i,j,m,n; @@ -2682,80 +2681,73 @@ void FixNH::CauchyStat(bigint step, double (&F)[3][3], double (&Fi)[3][3], doubl uv(5,1)=1; uv(5,2)=3; uv(6,1)=1; uv(6,2)=2; - if( (step % nstat) != 0) { - //do nothing! - }else { - for(int ii = 1;ii <= 6;ii++) { - i=uv(ii,1); - j=uv(ii,2); - deltastress(ii)=setcauchy(i,j)-cauchy(i,j); - if(ii>3) deltastress(ii)=deltastress(ii)*2.0; - fdotvec(ii)=Fdot(i,j)*deltat; - } - - for(int ii = 1;ii <= 6;ii++) { - i=uv(ii,1); - j=uv(ii,2); - for(int jj = 1;jj <= 6;jj++) { - m=uv(jj,1); - n=uv(jj,2); - dsds(ii,jj) = Fi(i,m)*Fi(j,n) + Fi(i,n)*Fi(j,m) + Fi(j,m)*Fi(i,n) + Fi(j,n)*Fi(i,m); - for(int l = 1;l <= 3;l++) { - for(int k = 1;k <= 3;k++) { - dsdf(ii,jj) = dsdf(ii,jj) + cauchy(k,l)*( Fi(i,k)*Fi(j,l)*Fi(n,m) - Fi(i,m)*Fi(j,l)*Fi(n,k) - Fi(i,k)*Fi(j,m)*Fi(n,l) ); - }//k - }//l - }//jj - }//ii - - jac=volume/volume0; - for(int ii = 1;ii <= 6;ii++) { - for(int jj = 1;jj <= 6;jj++) { - dsds(ii,jj)=dsds(ii,jj)*jac/4.0; - dsdf(ii,jj)=dsdf(ii,jj)*jac; - }//jj - }//ii - - for(int ii = 1;ii <= 6;ii++) { - for(int jj = 1;jj <= 6;jj++) { - deltaF(ii)=deltaF(ii)+dsdf(ii,jj)*fdotvec(jj); // deltaF=matmul(dsdf,fdotvec) in the fortran implementation - }//jj - }//ii - - for(int ii = 1;ii <= 6;ii++) { - for(int jj = 1;jj <= 6;jj++) { - deltaPK(ii)=deltaPK(ii)+alpha*dsds(ii,jj)*deltastress(jj); // deltaPK=alpha*matmul(dsds,deltastress) + deltaF in the fortran implementation - }//jj - // this line applies alpha to both terms instead of just the delta sigma term. - deltaPK(ii)=deltaPK(ii)+alpha*deltaF(ii); - // this is the old version - //deltaPK(ii)=deltaPK(ii)+deltaF(ii); - }//ii - - setPK(1,1)=setPK(1,1)+deltaPK(1); //equation (4) in SD-notes.pdf - setPK(2,2)=setPK(2,2)+deltaPK(2); - setPK(3,3)=setPK(3,3)+deltaPK(3); - setPK(2,3)=setPK(2,3)+deltaPK(4); - setPK(3,2)=setPK(3,2)+deltaPK(4); - setPK(1,3)=setPK(1,3)+deltaPK(5); - setPK(3,1)=setPK(3,1)+deltaPK(5); - setPK(1,2)=setPK(1,2)+deltaPK(6); - setPK(2,1)=setPK(2,1)+deltaPK(6); + for(int ii = 1;ii <= 6;ii++) { + i=uv(ii,1); + j=uv(ii,2); + deltastress(ii)=setcauchy(i,j)-cauchy(i,j); + if(ii>3) deltastress(ii)=deltastress(ii)*2.0; + fdotvec(ii)=Fdot(i,j)*deltat; } - //undefine macros: - #undef F - #undef Fi - #undef Fdot - #undef cauchy - #undef setcauchy - #undef setPK - #undef uv - #undef deltastress - #undef fdotvec - #undef dsdf - #undef dsds - #undef deltaF - #undef deltaPK + for(int ii = 1;ii <= 6;ii++) { + i=uv(ii,1); + j=uv(ii,2); + for(int jj = 1;jj <= 6;jj++) { + m=uv(jj,1); + n=uv(jj,2); + dsds(ii,jj) = Fi(i,m)*Fi(j,n) + Fi(i,n)*Fi(j,m) + Fi(j,m)*Fi(i,n) + Fi(j,n)*Fi(i,m); + for(int l = 1;l <= 3;l++) { + for(int k = 1;k <= 3;k++) { + dsdf(ii,jj) = dsdf(ii,jj) + cauchy(k,l)* + ( Fi(i,k)*Fi(j,l)*Fi(n,m) - Fi(i,m)*Fi(j,l)*Fi(n,k) - Fi(i,k)*Fi(j,m)*Fi(n,l) ); + } + } + } + } + + jac=volume/volume0; + for(int ii = 1;ii <= 6;ii++) { + for(int jj = 1;jj <= 6;jj++) { + dsds(ii,jj)=dsds(ii,jj)*jac/4.0; + dsdf(ii,jj)=dsdf(ii,jj)*jac; + } + } + + for(int ii = 1;ii <= 6;ii++) { + for(int jj = 1;jj <= 6;jj++) { + deltaF(ii)=deltaF(ii)+dsdf(ii,jj)*fdotvec(jj); + } + } + + for(int ii = 1;ii <= 6;ii++) { + for(int jj = 1;jj <= 6;jj++) { + deltaPK(ii)=deltaPK(ii)+alpha*dsds(ii,jj)*deltastress(jj); + } + deltaPK(ii)=deltaPK(ii)+alpha*deltaF(ii); + } + + setPK(1,1)=setPK(1,1)+deltaPK(1); + setPK(2,2)=setPK(2,2)+deltaPK(2); + setPK(3,3)=setPK(3,3)+deltaPK(3); + setPK(2,3)=setPK(2,3)+deltaPK(4); + setPK(3,2)=setPK(3,2)+deltaPK(4); + setPK(1,3)=setPK(1,3)+deltaPK(5); + setPK(3,1)=setPK(3,1)+deltaPK(5); + setPK(1,2)=setPK(1,2)+deltaPK(6); + setPK(2,1)=setPK(2,1)+deltaPK(6); + +#undef F +#undef Fi +#undef Fdot +#undef cauchy +#undef setcauchy +#undef setPK +#undef uv +#undef deltastress +#undef fdotvec +#undef dsdf +#undef dsds +#undef deltaF +#undef deltaPK } diff --git a/src/fix_nh.h b/src/fix_nh.h index ba8523f86d..e54780a4b1 100644 --- a/src/fix_nh.h +++ b/src/fix_nh.h @@ -144,17 +144,21 @@ class FixNH : public Fix { double H0[3][3]; //shape matrix for the undeformed cell double h_old[6]; //previous time step shape matrix for the undeformed cell double invH0[3][3]; //inverse of H0; - double myvol0; - double setPK[3][3]; - static double setPKinit[6]; - double alpha; //integration parameter cauchystat + double CSvol0; //volume of undeformed cell + double setPK[3][3]; //current set values of the PK stress (this is modified until the cauchy stress converges) + static double setPKinit[6]; // initialization value of setPK for continuation runs + double alpha; //integration parameter for the cauchystat int initPK; // 1 if setPK needs to be initialized either from cauchy or restart, else 0 int usePK; // 0 if use CauchyStat else 1 static int restartPK; // Read PK stress from the previous step - static int restart_stored; // Read PK stress from the previous step + static int restart_stored; // Read PK stress from the previous step int initRUN; // 0 if run not initialized (pressure->vector not computed yet), else 1 (pressure->vector available) - virtual void CauchyStat(bigint step, double (&F)[3][3], double (&Fi)[3][3], double (&Fdot)[3][3], double (&cauchy)[3][3], double (&setcauchy)[3][3], double (&setPK)[3][3], double volume, double volume0, double deltat, double alpha); + virtual void CauchyStat_init(); + virtual void CauchyStat(); + virtual void CauchyStat_Step(bigint step, double (&F)[3][3], double (&Fi)[3][3], double (&Fdot)[3][3], + double (&cauchy)[3][3], double (&setcauchy)[3][3], double (&setPK)[3][3], + double volume, double volume0, double deltat, double alpha); }; From 864958216a0f4b77f00cb4a18f2dcb0944cdc3bc Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 2 Oct 2018 16:24:10 -0400 Subject: [PATCH 291/302] remove static class members. some cosmetic changes --- src/fix_nh.cpp | 72 ++++++++++++++++++++++++++------------------------ src/fix_nh.h | 40 +++++++++++++++++----------- 2 files changed, 62 insertions(+), 50 deletions(-) diff --git a/src/fix_nh.cpp b/src/fix_nh.cpp index 9cd0987a54..e3fe70a733 100644 --- a/src/fix_nh.cpp +++ b/src/fix_nh.cpp @@ -46,10 +46,6 @@ enum{NOBIAS,BIAS}; enum{NONE,XYZ,XY,YZ,XZ}; enum{ISO,ANISO,TRICLINIC}; -int FixNH::restartPK; -int FixNH::restart_stored=0; -double FixNH::setPKinit[6]; - /* ---------------------------------------------------------------------- NVT,NPH,NPT integrators for improved Nose-Hoover equations of motion ---------------------------------------------------------------------- */ @@ -63,8 +59,6 @@ FixNH::FixNH(LAMMPS *lmp, int narg, char **arg) : { if (narg < 4) error->all(FLERR,"Illegal fix nvt/npt/nph command"); - usePK = 1; - restart_global = 1; dynamic_group_allow = 1; time_integrate = 1; scalar_flag = 1; @@ -73,6 +67,12 @@ FixNH::FixNH(LAMMPS *lmp, int narg, char **arg) : extscalar = 1; extvector = 0; + // for CauchyStat + + usePK = 1; + restart_global = 1; + restart_stored = 0; + // default values pcouple = NONE; @@ -2246,15 +2246,18 @@ void FixNH::compute_press_target() p_target[i] = p_start[i] + delta * (p_stop[i]-p_start[i]); // CauchyStat: call CauchyStat to modify p_target[i] and p_hydro, - // if CauchyStat enabled and pressure->vector computation has been initiated - if((usePK==0) && (initRUN==1)) CauchyStat(); - if(initRUN==0){ - for (int i=0;i<6;i++) { + // if CauchyStat enabled and pressure->vector computation has been initiated + + if ((usePK == 0) && (initRUN == 1)) CauchyStat(); + if (initRUN == 0) { + for (int i=0; i < 6; i++) { h_old[i]=domain->h[i]; } } - initRUN=1; // when run is initialized tensor[] not available (pressure on cell wall) + // when run is initialized tensor[] not available (pressure on cell wall) + + initRUN=1; // if deviatoric, recompute sigma each time p_target changes @@ -2417,30 +2420,29 @@ void FixNH::CauchyStat_init() if (comm->me == 0) { if (screen) { fprintf(screen,"Using the Cauchystat fix with alpha=%f\n",alpha); - if(restartPK==1) { - fprintf(screen," (this is a continuation fix)\n"); - } - else { - fprintf(screen," (this is NOT a continuation fix)\n"); + if (restartPK==1) { + fprintf(screen," (this is a continuation fix)\n"); + } else { + fprintf(screen," (this is NOT a continuation fix)\n"); } } if (logfile) { fprintf(logfile,"Using the Cauchystat with alpha=%f\n",alpha); - if(restartPK==1) { - fprintf(logfile," this is a continuation run\n"); - } - else { - fprintf(logfile," this is NOT a continuation run\n"); + if (restartPK==1) { + fprintf(logfile," this is a continuation run\n"); + } else { + fprintf(logfile," this is NOT a continuation run\n"); } } } - if(restartPK==1 && restart_stored==0) { + + if (restartPK==1 && restart_stored==0) error->all(FLERR,"Illegal cauchystat command. Continuation run" - " must follow a previously equilibrated Cauchystat run"); - } - if(alpha<=0.0) { - error->all(FLERR,"Illegal cauchystat command. Alpha cannot be zero or negative"); - } + " must follow a previously equilibrated Cauchystat run"); + + if (alpha<=0.0) + error->all(FLERR,"Illegal cauchystat command: " + " Alpha cannot be zero or negative."); initRUN = 0; initPK = 1; @@ -2564,8 +2566,8 @@ void FixNH::CauchyStat() } //initialize: - if(initPK==1) { - if(restartPK==1) { + if (initPK==1) { + if (restartPK==1) { setPK(1,1)=setPKinit[0]; setPK(1,2)=setPKinit[1]; setPK(1,3)=setPKinit[2]; setPK(2,1)=setPKinit[1]; setPK(2,2)=setPKinit[3]; setPK(2,3)=setPKinit[4]; setPK(3,1)=setPKinit[2]; setPK(3,2)=setPKinit[4]; setPK(3,3)=setPKinit[5]; @@ -2580,7 +2582,7 @@ void FixNH::CauchyStat() CauchyStat_Step(update->ntimestep,F,Fi,Fdot,cauchy,setcauchy,setPK,vol,CSvol0,deltat,alpha); // use currentPK as new target: - //p_target: 0 1 2 3 4 5 + // p_target: 0 1 2 3 4 5 // x y z yz xz xy p_target[0]=-setPK(1,1); @@ -2600,6 +2602,7 @@ void FixNH::CauchyStat() p_hydro /= pdim; // save information for Cauchystat restart + setPKinit[0] = setcauchy(1,1); setPKinit[1] = setcauchy(1,2); setPKinit[2] = setcauchy(1,3); @@ -2621,8 +2624,6 @@ void FixNH::CauchyStat() } - - /* ---------------------------------------------------------------------- CauchyStat_Step @@ -2644,10 +2645,13 @@ void FixNH::CauchyStat() setPK(3,3) : PK stress tensor at the next time step ------------------------------------------------------------------------- */ -void FixNH::CauchyStat_Step(bigint step, double (&F)[3][3], double (&Fi)[3][3], double (&Fdot)[3][3], double (&cauchy)[3][3], double (&setcauchy)[3][3], double (&setPK)[3][3], double volume, double volume0, double deltat, double alpha) +void FixNH::CauchyStat_Step(bigint step, double (&F)[3][3], + double (&Fi)[3][3], double (&Fdot)[3][3], + double (&cauchy)[3][3], double (&setcauchy)[3][3], + double (&setPK)[3][3], double volume, + double volume0, double deltat, double alpha) { - //macros to go from c to fortran style for arrays: #define F(row,col) (F[(row-1)][(col-1)]) #define Fi(row,col) (Fi[(row-1)][(col-1)]) diff --git a/src/fix_nh.h b/src/fix_nh.h index e54780a4b1..b39eda447f 100644 --- a/src/fix_nh.h +++ b/src/fix_nh.h @@ -141,23 +141,31 @@ class FixNH : public Fix { void nh_omega_dot(); // Implementation of CauchyStat - double H0[3][3]; //shape matrix for the undeformed cell - double h_old[6]; //previous time step shape matrix for the undeformed cell - double invH0[3][3]; //inverse of H0; - double CSvol0; //volume of undeformed cell - double setPK[3][3]; //current set values of the PK stress (this is modified until the cauchy stress converges) - static double setPKinit[6]; // initialization value of setPK for continuation runs - double alpha; //integration parameter for the cauchystat - int initPK; // 1 if setPK needs to be initialized either from cauchy or restart, else 0 - int usePK; // 0 if use CauchyStat else 1 - static int restartPK; // Read PK stress from the previous step - static int restart_stored; // Read PK stress from the previous step - int initRUN; // 0 if run not initialized (pressure->vector not computed yet), else 1 (pressure->vector available) + double H0[3][3]; // shape matrix for the undeformed cell + double h_old[6]; // previous time step shape matrix for + // the undeformed cell + double invH0[3][3]; // inverse of H0; + double CSvol0; // volume of undeformed cell + double setPK[3][3]; // current set values of the PK stress + // (this is modified until the cauchy + // stress converges) + double setPKinit[6]; // initialization value of setPK for + // continuation runs + double alpha; // integration parameter for the cauchystat + int initPK; // 1 if setPK needs to be initialized either + // from cauchy or restart, else 0 + int usePK; // 0 if use CauchyStat else 1 + int restartPK; // Read PK stress from the previous run + int restart_stored; // values of PK stress from the previous step stored + int initRUN; // 0 if run not initialized + // (pressure->vector not computed yet), + // else 1 (pressure->vector available) - virtual void CauchyStat_init(); - virtual void CauchyStat(); - virtual void CauchyStat_Step(bigint step, double (&F)[3][3], double (&Fi)[3][3], double (&Fdot)[3][3], - double (&cauchy)[3][3], double (&setcauchy)[3][3], double (&setPK)[3][3], + void CauchyStat_init(); + void CauchyStat(); + void CauchyStat_Step(bigint step, double (&F)[3][3], double (&Fi)[3][3], + double (&Fdot)[3][3], double (&cauchy)[3][3], + double (&setcauchy)[3][3], double (&setPK)[3][3], double volume, double volume0, double deltat, double alpha); }; From 13d7514ea01555b5d7293ace079789b85a91421d Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 2 Oct 2018 16:33:15 -0400 Subject: [PATCH 292/302] remove dead code and reduce compiler warnings because of it --- src/fix_nh.cpp | 20 +++++--------------- src/fix_nh.h | 8 ++++---- 2 files changed, 9 insertions(+), 19 deletions(-) diff --git a/src/fix_nh.cpp b/src/fix_nh.cpp index e3fe70a733..6ad38194f0 100644 --- a/src/fix_nh.cpp +++ b/src/fix_nh.cpp @@ -2453,14 +2453,8 @@ void FixNH::CauchyStat_init() // initialize H0 to current box shape - int triclinic = domain->triclinic; double *h = domain->h; double *h_inv = domain->h_inv; - double *boxhi = domain->boxhi; - double *boxlo = domain->boxlo; - double yz = domain->yz; - double xz = domain->xz; - double xy = domain->xy; H0(1,1)=h[0]; H0(1,2)=h[5]; H0(1,3)=h[4]; H0(2,1)=0.0; H0(2,2)=h[1]; H0(2,3)=h[3]; @@ -2518,10 +2512,9 @@ void FixNH::CauchyStat() Hdot(1,2)=h_rate[5]; Hdot(1,3)=h_rate[4]; Hdot(2,3)=h_rate[3]; } - double F[3][3]={0.0}; - double FT[3][3]={0.0}; - double Fi[3][3]={0.0}; - double Fdot[3][3]={0.0}; + double F[3][3]={{0.0,0.0,0.0},{0.0,0.0,0.0},{0.0,0.0,0.0}}; + double Fi[3][3]={{0.0,0.0,0.0},{0.0,0.0,0.0},{0.0,0.0,0.0}}; + double Fdot[3][3]={{0.0,0.0,0.0},{0.0,0.0,0.0},{0.0,0.0,0.0}}; double J,vol; MathExtra::times3(H,invH0,F); @@ -2579,7 +2572,7 @@ void FixNH::CauchyStat() initPK=0; } - CauchyStat_Step(update->ntimestep,F,Fi,Fdot,cauchy,setcauchy,setPK,vol,CSvol0,deltat,alpha); + CauchyStat_Step(Fi,Fdot,cauchy,setcauchy,setPK,vol,CSvol0,deltat,alpha); // use currentPK as new target: // p_target: 0 1 2 3 4 5 @@ -2628,8 +2621,6 @@ void FixNH::CauchyStat() CauchyStat_Step Inputs: - step : current step number - F(3,3) : current deformation gradient Fi(3,3) : inverse of the deformation gradient Fdot(3,3) : time derivative of the deformation gradient (velocity) cauchy(3,3) : current cauchy stress tensor @@ -2645,8 +2636,7 @@ void FixNH::CauchyStat() setPK(3,3) : PK stress tensor at the next time step ------------------------------------------------------------------------- */ -void FixNH::CauchyStat_Step(bigint step, double (&F)[3][3], - double (&Fi)[3][3], double (&Fdot)[3][3], +void FixNH::CauchyStat_Step(double (&Fi)[3][3], double (&Fdot)[3][3], double (&cauchy)[3][3], double (&setcauchy)[3][3], double (&setPK)[3][3], double volume, double volume0, double deltat, double alpha) diff --git a/src/fix_nh.h b/src/fix_nh.h index b39eda447f..904271ec11 100644 --- a/src/fix_nh.h +++ b/src/fix_nh.h @@ -163,10 +163,10 @@ class FixNH : public Fix { void CauchyStat_init(); void CauchyStat(); - void CauchyStat_Step(bigint step, double (&F)[3][3], double (&Fi)[3][3], - double (&Fdot)[3][3], double (&cauchy)[3][3], - double (&setcauchy)[3][3], double (&setPK)[3][3], - double volume, double volume0, double deltat, double alpha); + void CauchyStat_Step(double (&Fi)[3][3], double (&Fdot)[3][3], + double (&cauchy)[3][3], double (&setcauchy)[3][3], + double (&setPK)[3][3], double volume, double volume0, + double deltat, double alpha); }; From c094831617016a3903ac84ddb09762d0d1b6d7cf Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 4 Oct 2018 14:50:10 -0400 Subject: [PATCH 293/302] tweak example input and readme --- examples/cauchystat/README | 2 +- examples/cauchystat/lammps.in | 19 ++++++++++++------- 2 files changed, 13 insertions(+), 8 deletions(-) diff --git a/examples/cauchystat/README b/examples/cauchystat/README index fb6c63bff6..78435c96c5 100644 --- a/examples/cauchystat/README +++ b/examples/cauchystat/README @@ -1,6 +1,6 @@ Run this example by executing: -% lmp_serial < lammps.in +% lmp -in lammps.in Note that this example use an EAM potential, and therefore must be run with a LAMMPS executable built with the MANYBODY package. diff --git a/examples/cauchystat/lammps.in b/examples/cauchystat/lammps.in index 218bef3308..2190957c8f 100644 --- a/examples/cauchystat/lammps.in +++ b/examples/cauchystat/lammps.in @@ -2,8 +2,6 @@ units metal atom_style atomic atom_modify map array -processors 1 1 1 - # Box and atom positions: boundary p p p @@ -21,13 +19,17 @@ mass 2 26.98154 # Potential, Al fcc crystal pair_style eam/alloy pair_coeff * * Mishin-Ni-Al-2009.eam.alloy Ni Al - +neigh_modify delay 5 thermo 100 thermo_style custom step temp pxx pyy pzz pxy pxz pyz compute cna all cna/atom 2.8 -fix 1 all npt temp 600.0 600.0 1.0 x 0.0 0.0 0.1 y 0.0 0.0 0.1 z 0.0 0.0 0.1 couple none cauchystat 0.001 no +fix 1 all npt temp 600.0 600.0 1.0 & + x 0.0 0.0 0.1 & + y 0.0 0.0 0.1 & + z 0.0 0.0 0.1 & + couple none cauchystat 0.001 no dump 1 all cfg 1000 test*.cfg mass type xs ys zs type c_cna @@ -56,8 +58,11 @@ velocity all create 1200 4928459 rot yes dist gaussian run 10000 -unfix 1 - -fix 1 all npt temp 600.0 600.0 1.0 x 0.0 0.0 0.1 y 0.0 0.0 0.1 z 0.0 0.0 0.1 xy -10000.0 -10000.0 0.1 couple none cauchystat 0.001 yes +fix 1 all npt temp 600.0 600.0 1.0 & + x 0.0 0.0 0.1 & + y 0.0 0.0 0.1 & + z 0.0 0.0 0.1 & + xy -10000.0 -10000.0 0.1 & + couple none cauchystat 0.001 yes run 10000 From 8f6f7eb4cdb9df475ff54b5efd7f3e6d0b8a1b06 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 4 Oct 2018 14:50:49 -0400 Subject: [PATCH 294/302] add infratructure to add an instance of fix STORE for persistent storage --- src/fix_nh.cpp | 36 ++++++++++++++++++++++++++++++++---- src/fix_nh.h | 2 ++ 2 files changed, 34 insertions(+), 4 deletions(-) diff --git a/src/fix_nh.cpp b/src/fix_nh.cpp index 6ad38194f0..cbd1f34152 100644 --- a/src/fix_nh.cpp +++ b/src/fix_nh.cpp @@ -28,6 +28,7 @@ #include "irregular.h" #include "modify.h" #include "fix_deform.h" +#include "fix_store.h" #include "compute.h" #include "kspace.h" #include "update.h" @@ -55,7 +56,7 @@ FixNH::FixNH(LAMMPS *lmp, int narg, char **arg) : rfix(NULL), id_dilate(NULL), irregular(NULL), id_temp(NULL), id_press(NULL), eta(NULL), eta_dot(NULL), eta_dotdot(NULL), eta_mass(NULL), etap(NULL), etap_dot(NULL), etap_dotdot(NULL), - etap_mass(NULL) + etap_mass(NULL), id_store(NULL),init_store(NULL) { if (narg < 4) error->all(FLERR,"Illegal fix nvt/npt/nph command"); @@ -600,6 +601,7 @@ FixNH::~FixNH() delete [] id_dilate; delete [] rfix; + delete [] id_store; delete irregular; // delete temperature and pressure if fix created them @@ -2421,9 +2423,9 @@ void FixNH::CauchyStat_init() if (screen) { fprintf(screen,"Using the Cauchystat fix with alpha=%f\n",alpha); if (restartPK==1) { - fprintf(screen," (this is a continuation fix)\n"); + fprintf(screen," (this is a continuation run)\n"); } else { - fprintf(screen," (this is NOT a continuation fix)\n"); + fprintf(screen," (this is NOT a continuation run)\n"); } } if (logfile) { @@ -2436,7 +2438,16 @@ void FixNH::CauchyStat_init() } } - if (restartPK==1 && restart_stored==0) + if (!id_store) { + int n = strlen(id) + 11; + id_store = new char[n]; + strcpy(id_store,id); + strcat(id_store,"_FIX_STORE"); + } + + restart_stored = modify->find_fix(id_store); + + if (restartPK==1 && restart_stored < 0) error->all(FLERR,"Illegal cauchystat command. Continuation run" " must follow a previously equilibrated Cauchystat run"); @@ -2444,6 +2455,23 @@ void FixNH::CauchyStat_init() error->all(FLERR,"Illegal cauchystat command: " " Alpha cannot be zero or negative."); + + if (restartPK == 0) { + if (restart_stored < 0) { + char **newarg = new char *[6]; + newarg[0] = id_store; + newarg[1] = (char *) "all"; + newarg[2] = (char *) "STORE"; + newarg[3] = (char *) "global"; + newarg[4] = (char *) "1"; + newarg[5] = (char *) "6"; + modify->add_fix(6,newarg); + delete[] newarg; + } + int n = modify->find_fix(id_store); + init_store = (FixStore *)modify->fix[n]; + } + initRUN = 0; initPK = 1; usePK = 0; diff --git a/src/fix_nh.h b/src/fix_nh.h index 904271ec11..50dc8210ab 100644 --- a/src/fix_nh.h +++ b/src/fix_nh.h @@ -141,6 +141,8 @@ class FixNH : public Fix { void nh_omega_dot(); // Implementation of CauchyStat + char *id_store; // fix id of the STORE fix for retaining data + class FixStore *init_store; // fix pointer to STORE fix double H0[3][3]; // shape matrix for the undeformed cell double h_old[6]; // previous time step shape matrix for // the undeformed cell From baea04b913f3815713822334f9efa42d937cf32d Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 22 Oct 2018 15:56:41 -0400 Subject: [PATCH 295/302] update cauchystat example to conform more with standard LAMMPS examples --- .../cauchystat/Mishin-Ni-Al-2009.eam.alloy | 140014 +++++++-------- examples/cauchystat/README | 2 +- .../cauchystat/{lammps.in => in.cauchystat} | 10 + 3 files changed, 70018 insertions(+), 70008 deletions(-) rename examples/cauchystat/{lammps.in => in.cauchystat} (85%) diff --git a/examples/cauchystat/Mishin-Ni-Al-2009.eam.alloy b/examples/cauchystat/Mishin-Ni-Al-2009.eam.alloy index a4608f5579..92c06fd794 100644 --- a/examples/cauchystat/Mishin-Ni-Al-2009.eam.alloy +++ b/examples/cauchystat/Mishin-Ni-Al-2009.eam.alloy @@ -1,70007 +1,70007 @@ - G.P. Purja Pun and Y. Mishin, Phil. Mag., in press (2009). - LAMMPS setfl format. Conversion by C. A. Becker from Y. Mishin files. - 13 Aug 2009. http://www.ctcms.nist.gov/potentials - 2 Ni Al -10000 0.5013228884000001E-03 10000 0.6287210000000001E-03 0.6287210000000000E+01 - 28 0.5871000000E+02 0.3520000000E+01 fcc - -2.2546436667E-0002 - -3.9517100033E-0002 - -5.5218483024E-0002 - -6.9748646092E-0002 - -8.3205649690E-0002 - -9.5687071211E-0002 - -1.0728855581E-0001 - -1.1810768086E-0001 - -1.2825168498E-0001 - -1.3783132935E-0001 - -1.4696180428E-0001 - -1.5574426829E-0001 - -1.6421932328E-0001 - -1.7241225154E-0001 - -1.8034761338E-0001 - -1.8804961815E-0001 - -1.9554179349E-0001 - -2.0284611159E-0001 - -2.0997900487E-0001 - -2.1695479964E-0001 - -2.2378493785E-0001 - -2.3047983335E-0001 - -2.3704867186E-0001 - -2.4350010967E-0001 - -2.4984191363E-0001 - -2.5608131864E-0001 - -2.6222432233E-0001 - -2.6827647491E-0001 - -2.7424277333E-0001 - -2.8012796566E-0001 - -2.8593635665E-0001 - -2.9167200423E-0001 - -2.9733842233E-0001 - -3.0293893346E-0001 - -3.0847663943E-0001 - -3.1395450539E-0001 - -3.1937516974E-0001 - 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Purja Pun and Y. Mishin, Phil. Mag., in press (2009). + LAMMPS setfl format. Conversion by C. A. Becker from Y. 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-7.2599650704E-0009 + -4.2021195608E-0009 + -2.1518858600E-0009 + -9.0795206777E-0010 + -2.6892859495E-0010 + -3.3435472661E-0011 diff --git a/examples/cauchystat/README b/examples/cauchystat/README index 78435c96c5..73b94ec153 100644 --- a/examples/cauchystat/README +++ b/examples/cauchystat/README @@ -1,6 +1,6 @@ Run this example by executing: -% lmp -in lammps.in +% lmp -in in.cauchystat Note that this example use an EAM potential, and therefore must be run with a LAMMPS executable built with the MANYBODY package. diff --git a/examples/cauchystat/lammps.in b/examples/cauchystat/in.cauchystat similarity index 85% rename from examples/cauchystat/lammps.in rename to examples/cauchystat/in.cauchystat index 2190957c8f..dbcfa2ad07 100644 --- a/examples/cauchystat/lammps.in +++ b/examples/cauchystat/in.cauchystat @@ -33,6 +33,8 @@ fix 1 all npt temp 600.0 600.0 1.0 & dump 1 all cfg 1000 test*.cfg mass type xs ys zs type c_cna +info fixes + timestep 0.002 variable px equal pxx @@ -66,3 +68,11 @@ fix 1 all npt temp 600.0 600.0 1.0 & couple none cauchystat 0.001 yes run 10000 + +fix 1 all npt temp 600.0 600.0 1.0 & + x 0.0 0.0 0.1 & + y 0.0 0.0 0.1 & + z 0.0 0.0 0.1 & + xy -10000.0 -10000.0 0.1 & + couple none cauchystat 0.001 no +run 10000 From cf91a93876f9a8afc4b295659a543adc833baf9a Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 22 Oct 2018 16:13:00 -0400 Subject: [PATCH 296/302] update example to check if the store fix is removed properly --- examples/cauchystat/in.cauchystat | 9 +- .../cauchystat/log.10Oct2018.cauchystat.g++.4 | 423 ++++++++++++++++++ 2 files changed, 430 insertions(+), 2 deletions(-) create mode 100644 examples/cauchystat/log.10Oct2018.cauchystat.g++.4 diff --git a/examples/cauchystat/in.cauchystat b/examples/cauchystat/in.cauchystat index dbcfa2ad07..0505cf29c9 100644 --- a/examples/cauchystat/in.cauchystat +++ b/examples/cauchystat/in.cauchystat @@ -31,7 +31,7 @@ fix 1 all npt temp 600.0 600.0 1.0 & z 0.0 0.0 0.1 & couple none cauchystat 0.001 no -dump 1 all cfg 1000 test*.cfg mass type xs ys zs type c_cna +# dump 1 all cfg 1000 test*.cfg mass type xs ys zs type c_cna info fixes @@ -60,6 +60,8 @@ velocity all create 1200 4928459 rot yes dist gaussian run 10000 +info fixes + fix 1 all npt temp 600.0 600.0 1.0 & x 0.0 0.0 0.1 & y 0.0 0.0 0.1 & @@ -67,6 +69,8 @@ fix 1 all npt temp 600.0 600.0 1.0 & xy -10000.0 -10000.0 0.1 & couple none cauchystat 0.001 yes +info fixes + run 10000 fix 1 all npt temp 600.0 600.0 1.0 & @@ -74,5 +78,6 @@ fix 1 all npt temp 600.0 600.0 1.0 & y 0.0 0.0 0.1 & z 0.0 0.0 0.1 & xy -10000.0 -10000.0 0.1 & - couple none cauchystat 0.001 no + couple none +info fixes run 10000 diff --git a/examples/cauchystat/log.10Oct2018.cauchystat.g++.4 b/examples/cauchystat/log.10Oct2018.cauchystat.g++.4 new file mode 100644 index 0000000000..b14a92fcc2 --- /dev/null +++ b/examples/cauchystat/log.10Oct2018.cauchystat.g++.4 @@ -0,0 +1,423 @@ +LAMMPS (10 Oct 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +Lattice spacing in x,y,z = 4.05 4.05 4.05 +Created triclinic box = (0 0 0) to (20.25 20.25 20.25) with tilt (0 0 0) + 1 by 2 by 2 MPI processor grid +Created 500 atoms + Time spent = 0.000171185 secs +Using the Cauchystat with alpha=0.001000 + this is NOT a continuation run +Neighbor list info ... + update every 1 steps, delay 5 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 8.28721 + ghost atom cutoff = 8.28721 + binsize = 4.1436, bins = 5 5 5 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) pair eam/alloy, perpetual + attributes: half, newton on + pair build: half/bin/newton/tri + stencil: half/bin/3d/newton/tri + bin: standard + (2) compute cna/atom, occasional + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.042 | 4.042 | 4.042 Mbytes +Step Temp Pxx Pyy Pzz Pxy Pxz 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-5345.0328 -2418.5524 -4906.7514 -320.6323 1180.1709 1152.8276 + 7700 606.86368 -4826.2775 -3328.5693 -4272.3286 959.70305 -327.2001 -607.4565 + 7800 625.87208 1659.3584 155.68312 -1822.7299 -519.02245 1484.5732 1325.8291 + 7900 625.84193 5139.1663 5233.1046 5932.3522 -645.14021 -579.14501 456.01972 + 8000 617.62116 1257.0064 3534.353 5411.9973 -110.20968 403.36986 -442.30967 + 8100 584.82213 3539.4934 3879.524 -1539.2611 1506.3505 434.92291 -1079.4487 + 8200 645.50439 -845.6885 -504.51024 -672.44557 -808.28448 93.617584 638.11821 + 8300 623.20703 -5510.4318 -5269.6793 826.962 112.37676 178.61653 264.39931 + 8400 603.70254 355.71267 -1510.4568 -3023.9202 -1644.264 415.96411 118.17403 + 8500 611.2171 2401.084 -504.71697 -6200.2246 -153.93927 -1184.4069 -907.28708 + 8600 583.23473 -504.22147 4271.8103 -836.74227 -177.68126 -908.49219 -751.95423 + 8700 612.17523 5540.8126 -61.50399 8736.9335 595.27885 718.60872 -716.77887 + 8800 580.71181 3101.2207 327.20061 1280.8378 -1411.6131 -1568.1159 -369.21789 + 8900 614.13105 1270.4205 -421.91098 -1851.1426 -250.35147 147.06752 -116.31683 + 9000 589.26682 -3204.2367 -1642.7912 -2502.5794 -465.30063 -530.48473 -837.30864 + 9100 601.73809 -5202.3289 -3887.5772 -7031.2003 -320.41357 -606.03079 -382.09785 + 9200 600.82114 -3093.0858 -1766.956 281.45612 501.03069 703.58009 -578.26493 + 9300 593.55953 4881.2795 2399.6543 1148.5403 1278.6064 -945.12016 -203.66816 + 9400 577.31005 5417.3641 3450.4658 972.47557 -1617.687 337.19403 187.60063 + 9500 605.36885 -66.561031 0.83958684 2104.1391 -471.964 -806.89807 -365.8591 + 9600 577.7181 -2079.0845 -3599.5686 -1128.3815 539.9303 -343.96327 -255.39579 + 9700 568.85405 -2665.7477 667.24262 -2720.4027 -372.57451 -485.52334 556.25739 + 9800 589.68454 -2611.5675 769.65422 740.94187 1077.5563 673.55855 652.27667 + 9900 606.04668 2452.272 -238.77203 1205.743 -309.3651 -1198.4251 230.77461 + 10000 612.87958 1630.6542 1442.713 863.07105 776.93604 584.60976 -582.35343 +Loop time of 3.61569 on 4 procs for 10000 steps with 500 atoms + +Performance: 477.916 ns/day, 0.050 hours/ns, 2765.720 timesteps/s +96.3% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.7694 | 2.7951 | 2.8194 | 1.2 | 77.31 +Neigh | 0.074689 | 0.075052 | 0.075583 | 0.1 | 2.08 +Comm | 0.32281 | 0.38608 | 0.4383 | 7.0 | 10.68 +Output | 0.0042112 | 0.0051484 | 0.0078425 | 2.2 | 0.14 +Modify | 0.28548 | 0.32571 | 0.366 | 6.9 | 9.01 +Other | | 0.02859 | | | 0.79 + +Nlocal: 125 ave 130 max 115 min +Histogram: 1 0 0 0 0 0 0 1 0 2 +Nghost: 1594.25 ave 1619 max 1582 min +Histogram: 2 0 1 0 0 0 0 0 0 1 +Neighs: 8712.75 ave 9092 max 8057 min +Histogram: 1 0 0 0 0 0 1 0 1 1 +FullNghs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 34851 +Ave neighs/atom = 69.702 +Neighbor list builds = 192 +Dangerous builds = 0 +Using the Cauchystat with alpha=0.001000 + this is a continuation run +Per MPI rank memory allocation (min/avg/max) = 4.058 | 4.058 | 4.058 Mbytes +Step Temp Pxx Pyy Pzz Pxy Pxz Pyz + 10000 612.87958 1630.6542 1442.713 863.07105 776.93604 584.60976 -582.35343 + 10100 590.63792 2105.7397 407.18889 3615.707 -778.34352 64.902608 -1131.4185 + 10200 599.82015 1477.345 -3256.0438 -1928.8393 -2721.9994 -603.25784 450.65393 + 10300 570.44775 -2709.2309 -2856.7016 -7706.7245 -3761.6014 751.19248 538.50642 + 10400 614.94213 -3938.0877 100.4614 -3338.0966 -2559.8736 456.77459 -89.650996 + 10500 608.71969 1876.3667 -924.83652 -99.759016 -2532.2039 -755.84621 -1226.4238 + 10600 618.21973 7785.4058 3612.8417 2879.0094 -6941.2416 432.60772 -386.32096 + 10700 577.46358 1515.7214 4227.3941 2270.8419 -2957.6042 -132.48468 -422.86445 + 10800 608.5477 -1488.208 2635.6047 1271.8951 -3300.4694 -871.55104 -428.03854 + 10900 597.96902 -1894.5241 -218.00252 -5042.2076 -5651.5821 -1478.2615 -414.52115 + 11000 603.91795 -5902.0171 -7394.4965 -5101.8069 -9222.473 947.56596 -180.04863 + 11100 588.7392 -875.31615 -3093.7427 -2080.798 -3880.569 63.245218 -190.15752 + 11200 642.21711 524.76616 -203.20989 -139.32701 -7850.4207 9.6225634 -731.69651 + 11300 612.37523 6060.5954 3349.8568 -1492.7174 -8961.9479 -1357.9766 86.099912 + 11400 652.53769 4419.9008 3863.4466 1030.8547 -6310.672 -622.21535 -1358.4633 + 11500 636.55598 180.55995 -408.29151 2870.4414 -6849.2881 891.75965 -1012.5305 + 11600 616.11863 -4718.155 1807.2585 -51.526425 -8488.9133 -589.3792 -267.67114 + 11700 633.54357 -3780.5733 -847.50973 -1528.4906 -5335.2818 801.11434 -1001.3841 + 11800 610.90433 2835.6395 -3878.3782 -3561.3055 -8520.973 -326.82184 -623.64233 + 11900 631.03273 1882.3782 -1279.8364 -1890.4651 -6779.1159 -489.30728 -711.42013 + 12000 614.97894 -1646.5811 1996.4295 1841.9011 -8751.4747 201.61813 1455.0798 + 12100 626.07467 1378.3718 2388.5812 5886.7808 -7869.2564 323.4468 128.83163 + 12200 615.18237 -447.07467 1133.7171 4511.7674 -9867.3527 -1602.6464 -64.036908 + 12300 617.45485 1776.7587 212.41579 -1213.7199 -8591.5025 -66.877767 -478.75683 + 12400 601.08762 -1447.3022 2044.6269 -1154.1319 -7463.9369 -1483.0648 -184.76187 + 12500 586.09846 -1089.4098 1649.9242 -3847.1296 -5202.5976 -132.86066 -275.84212 + 12600 593.05705 -2978.4626 -328.34295 549.36613 -10021.85 1012.1258 656.59113 + 12700 622.17655 -2596.4696 1539.3849 1885.9268 -9369.6472 111.74843 -106.23352 + 12800 576.09217 6719.3262 -469.03945 1586.9119 -11572.224 -413.52774 192.34415 + 12900 561.46261 3234.297 838.83683 20.245498 -10234.358 -1321.5013 -117.95163 + 13000 582.16457 1049.3546 3748.2172 -2814.9675 -8242.6504 -47.974851 -1.0464312 + 13100 575.64543 -1686.7798 -2924.0432 670.57916 -8283.7314 -336.61707 148.21068 + 13200 623.64628 -5089.4664 -5533.4331 482.73263 -8104.1361 -51.635232 941.86419 + 13300 618.06183 -4279.8807 -6035.0244 -7317.482 -13517.007 1209.6409 -790.76808 + 13400 582.27011 -202.86647 2394.7414 -832.06461 -10750.988 1104.8648 -814.74346 + 13500 590.83019 9493.3577 756.0307 7854.358 -9300.2455 578.55349 536.17298 + 13600 614.59848 2584.3475 2984.9318 3277.9091 -9452.5454 143.61019 -403.72334 + 13700 619.82757 -932.19961 2412.9186 -1260.3773 -11245.796 489.9455 -165.6918 + 13800 574.9001 -3488.0886 -4107.8474 -6181.7225 -6059.1787 1243.8554 -660.73241 + 13900 564.8109 -3503.5363 -8566.2493 -4248.3219 -8150.3499 916.16484 667.48874 + 14000 599.18774 -2254.3181 -1518.4061 -1323.6182 -9932.0018 1945.9013 -363.07726 + 14100 629.54058 4149.2744 6444.8456 3122.7675 -9774.9087 70.257412 -983.32357 + 14200 630.64148 5636.3595 5417.1488 3451.4304 -11251.944 732.63001 1698.3517 + 14300 636.88054 6490.1485 1139.4007 1854.2365 -9329.3564 -955.22579 326.65417 + 14400 608.95937 679.53975 -1505.1824 -1360.3363 -9304.1935 978.12975 -59.169424 + 14500 601.23153 -8726.9266 -8328.2526 -5451.5865 -9932.2473 -134.71397 -85.634134 + 14600 605.48952 -3495.0302 -4973.9138 -7344.2898 -8647.3621 -1683.4037 144.07088 + 14700 618.5206 -3718.3486 -1424.544 -2937.9027 -11590.465 -466.24143 -2052.2054 + 14800 616.59782 1573.1062 4233.0615 395.74859 -11489.134 -219.51579 433.70467 + 14900 659.26114 5021.2518 5225.6412 6167.347 -8150.4749 -538.45633 680.72634 + 15000 659.25733 3609.8095 6458.2228 7989.8189 -11192.671 100.52458 1013.6743 + 15100 631.84165 97.725952 211.89405 -255.96383 -10647.53 -1501.9936 757.81726 + 15200 652.80392 -4495.9435 -4888.0664 -2569.0601 -7406.2023 257.16208 -932.41288 + 15300 675.35073 -4116.5275 -3778.8935 -7290.7357 -11400.851 293.65728 -1107.7338 + 15400 647.57172 -1764.3426 -5117.6233 -3121.0357 -8998.0471 -1350.4874 948.95114 + 15500 617.07484 -1493.4646 2515.4476 2552.9605 -9128.6045 -389.22106 -1166.351 + 15600 636.50861 3200.8813 5598.2178 3776.9504 -12654.357 -472.67282 -535.11673 + 15700 594.0731 4139.2978 5869.1939 4608.5816 -8660.8825 -793.3936 159.00429 + 15800 609.3601 2084.9274 621.32879 1500.7841 -11679.222 1274.4954 527.27307 + 15900 608.23613 -1467.2674 -5781.237 -4508.5759 -5709.0493 -118.43532 1088.8165 + 16000 583.35692 -4314.4395 -1277.4884 -4541.7272 -11476.052 -180.94491 -1488.5668 + 16100 602.80528 -7503.2244 -1077.6597 -2019.0774 -8079.0197 979.96691 337.49128 + 16200 575.17523 48.064858 20.90471 3956.6362 -11226.444 105.64103 562.77638 + 16300 562.93544 5635.2302 3983.9899 6298.8042 -8059.286 422.09141 -137.96608 + 16400 625.78949 3422.1465 1941.975 1059.6869 -11356.134 -113.71934 1224.354 + 16500 600.99485 484.64163 1522.1817 -1768.7325 -5258.1434 828.78727 -1289.069 + 16600 586.36732 -1286.312 -2153.5895 -1279.5514 -10425.35 -1560.6553 475.39553 + 16700 617.02201 -2422.3058 -1537.573 -6349.8192 -11548.985 1274.3353 -528.74896 + 16800 602.2294 -911.26767 -914.33459 -2646.7866 -10589.36 -190.4123 -958.10146 + 16900 567.51537 1522.7727 824.21663 545.02062 -9966.4721 -1495.5384 35.112304 + 17000 608.43577 6992.611 7966.003 6093.2675 -10797.159 -54.653364 -214.77759 + 17100 594.7589 4585.0662 6860.3557 4334.7767 -9592.0026 -806.53225 -691.65886 + 17200 609.03174 -103.49013 -830.99725 -89.697769 -9841.7978 783.85057 -42.059977 + 17300 577.5032 -6535.1979 -6894.7487 -579.13339 -11399.067 232.09278 1063.1021 + 17400 592.79841 -3737.7485 -2488.0052 -4241.5011 -8586.8323 -193.46611 -945.24642 + 17500 593.36065 -2114.1132 387.55666 -956.59598 -7419.1434 475.81586 98.523189 + 17600 605.97259 2354.7709 -1121.2395 4589.4855 -6978.2443 -378.77761 -1142.1378 + 17700 608.13402 4158.9712 -217.24423 1216.2658 -12272.663 -1382.6361 -727.71601 + 17800 627.40665 765.97111 5724.3737 4232.5439 -13312.495 -420.77837 411.64338 + 17900 620.26403 810.35844 2514.3486 -291.35461 -8024.9098 -668.70499 277.93765 + 18000 658.06643 77.46526 -2625.1401 -4259.0104 -9696.9346 -1252.5503 1133.9307 + 18100 610.8745 -5840.2706 -6322.1457 -3882.9747 -11867.74 -296.91835 276.50503 + 18200 618.60469 -2283.045 -2039.3552 -2886.5205 -8313.8411 47.663907 617.70349 + 18300 620.93157 -1202.7586 1588.237 2408.8614 -10518.273 152.89283 677.03984 + 18400 627.13957 3048.3835 5556.1661 5811.2475 -10576.032 1215.6153 -148.99795 + 18500 625.94801 4264.7309 3477.8588 2628.4906 -9153.1186 1181.1776 -1635.7628 + 18600 622.64636 5262.4892 2103.5974 1428.0094 -9249.7315 -638.64365 2013.8476 + 18700 584.00743 -3081.1288 -1092.8084 -614.87191 -12072.206 -3.3860818 -209.18698 + 18800 603.89026 -2837.256 -2464.2004 -4104.9191 -11274.988 213.25667 -685.40543 + 18900 599.75836 -6401.1562 -4614.1815 -3609.0863 -8681.2526 580.10047 -977.74629 + 19000 600.59881 -2921.3236 -453.25893 1507.1078 -7325.4299 721.97437 182.06052 + 19100 560.42263 4232.8755 2637.4725 3111.9129 -9542.1688 -180.76512 -305.22348 + 19200 575.90822 4901.4471 2455.9989 1993.591 -11375.02 -617.85238 -987.29497 + 19300 573.64172 6150.9357 3684.9187 -232.96408 -13870.829 -890.49885 479.57109 + 19400 584.49511 -2878.7716 -2618.1079 -677.61644 -11600.343 3083.8754 299.48283 + 19500 580.01102 -1853.4665 -1883.8079 -2506.6295 -11165.73 1213.4406 1518.2189 + 19600 586.54376 -3241.0725 -1159.1065 -2602.6725 -6755.1336 65.248733 -126.39133 + 19700 563.76829 -953.66522 -1719.2586 2068.0954 -10009.3 -332.63018 588.21915 + 19800 587.28806 2253.6347 8423.5514 1338.6781 -10854.794 -271.90578 -728.28536 + 19900 586.67958 2119.8007 4238.086 1739.8343 -10881.606 197.58163 625.01521 + 20000 577.1146 -481.42825 -1046.3708 2417.5108 -9370.1295 674.87445 -713.46447 +Loop time of 3.76444 on 4 procs for 10000 steps with 500 atoms + +Performance: 459.033 ns/day, 0.052 hours/ns, 2656.440 timesteps/s +95.9% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.7631 | 2.8184 | 2.91 | 3.3 | 74.87 +Neigh | 0.1452 | 0.14825 | 0.15475 | 1.0 | 3.94 +Comm | 0.35653 | 0.42847 | 0.49527 | 8.1 | 11.38 +Output | 0.0088019 | 0.010534 | 0.015527 | 2.8 | 0.28 +Modify | 0.30177 | 0.33373 | 0.36411 | 5.2 | 8.87 +Other | | 0.02503 | | | 0.66 + +Nlocal: 125 ave 126 max 124 min +Histogram: 1 0 0 0 0 2 0 0 0 1 +Nghost: 1598.75 ave 1625 max 1579 min +Histogram: 1 1 0 0 0 0 1 0 0 1 +Neighs: 8709.5 ave 8762 max 8675 min +Histogram: 1 0 2 0 0 0 0 0 0 1 +FullNghs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 34838 +Ave neighs/atom = 69.676 +Neighbor list builds = 397 +Dangerous builds = 0 +Per MPI rank memory allocation (min/avg/max) = 4.058 | 4.058 | 4.058 Mbytes +Step Temp Pxx Pyy Pzz Pxy Pxz Pyz + 20000 577.1146 -481.42825 -1046.3708 2417.5108 -9370.1295 674.87445 -713.46447 + 20100 604.36803 1484.7186 1504.7689 -121.48152 -6916.3299 -615.21083 556.80824 + 20200 577.20725 -25.006669 3191.534 -3672.9543 -12638.944 380.8416 -542.12811 + 20300 613.17918 1107.4719 -190.86445 -1293.3667 -9811.1278 -598.86019 822.35762 + 20400 598.69607 -1007.4206 -3662.2853 -1389.7984 -8338.0617 215.67759 -749.14919 + 20500 607.15479 -5448.4873 1230.9711 -1038.1257 -12021.182 663.13641 198.64156 + 20600 591.00739 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-9878.6629 -198.4277 171.41107 + 29300 603.09104 1881.9871 1416.9869 2627.4771 -10543.607 498.40251 -959.29802 + 29400 594.06496 -3607.9477 2206.0916 -1098.6891 -9526.962 -922.31493 -973.89099 + 29500 619.48524 -4857.6889 -7940.507 -4873.3084 -6485.5716 -160.11061 312.41138 + 29600 608.63306 -1169.0524 -4396.0797 -1026.4404 -11793.823 -83.275861 -118.56396 + 29700 573.59042 3904.4281 1498.8247 -5219.5372 -10641.609 -433.91653 -264.38751 + 29800 578.81508 3574.6571 493.38829 2266.9973 -6449.0462 -283.35829 592.84622 + 29900 570.60306 2235.6317 49.337576 2544.2358 -9104.3485 -519.08388 166.07569 + 30000 560.20016 -3277.214 2789.5183 -90.218855 -12643.324 350.34246 1247.5469 +Loop time of 3.75476 on 4 procs for 10000 steps with 500 atoms + +Performance: 460.216 ns/day, 0.052 hours/ns, 2663.285 timesteps/s +96.3% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.786 | 2.8439 | 2.9806 | 4.7 | 75.74 +Neigh | 0.14653 | 0.15108 | 0.16297 | 1.8 | 4.02 +Comm | 0.28847 | 0.43147 | 0.49811 | 12.8 | 11.49 +Output | 0.0033712 | 0.0048664 | 0.0091705 | 3.6 | 0.13 +Modify | 0.28143 | 0.29057 | 0.29483 | 1.0 | 7.74 +Other | | 0.03292 | | | 0.88 + +Nlocal: 125 ave 127 max 123 min +Histogram: 1 0 0 0 0 2 0 0 0 1 +Nghost: 1548 ave 1560 max 1536 min +Histogram: 1 0 0 1 0 0 1 0 0 1 +Neighs: 8686.5 ave 8913 max 8531 min +Histogram: 1 0 1 0 1 0 0 0 0 1 +FullNghs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 34746 +Ave neighs/atom = 69.492 +Neighbor list builds = 403 +Dangerous builds = 0 +Total wall time: 0:00:11 From a20c38af80390c2856a5e031d281383e66f0abfe Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 22 Oct 2018 16:14:18 -0400 Subject: [PATCH 297/302] complete implementation of using an instance of fix STORE for persistent storage --- src/fix_nh.cpp | 73 ++++++++++++++++++++++++++++++++------------------ src/fix_nh.h | 4 +-- 2 files changed, 49 insertions(+), 28 deletions(-) diff --git a/src/fix_nh.cpp b/src/fix_nh.cpp index cbd1f34152..b7f4390b4e 100644 --- a/src/fix_nh.cpp +++ b/src/fix_nh.cpp @@ -71,6 +71,7 @@ FixNH::FixNH(LAMMPS *lmp, int narg, char **arg) : // for CauchyStat usePK = 1; + restartPK = 0; restart_global = 1; restart_stored = 0; @@ -79,7 +80,6 @@ FixNH::FixNH(LAMMPS *lmp, int narg, char **arg) : pcouple = NONE; drag = 0.0; allremap = 1; - id_dilate = NULL; mtchain = mpchain = 3; nc_tchain = nc_pchain = 1; mtk_flag = 1; @@ -94,8 +94,6 @@ FixNH::FixNH(LAMMPS *lmp, int narg, char **arg) : tcomputeflag = 0; pcomputeflag = 0; - id_temp = NULL; - id_press = NULL; // turn on tilt factor scaling, whenever applicable @@ -348,14 +346,15 @@ FixNH::FixNH(LAMMPS *lmp, int narg, char **arg) : } else error->all(FLERR,"Illegal fix nvt/npt/nph command"); iarg += 2; } else if (strcmp(arg[iarg],"cauchystat") == 0) { + usePK = 0; if (iarg+3 > narg) error->all(FLERR, "Illegal fix npt cauchystat command:" " wrong number of arguments"); if (strcmp(arg[iarg+2],"yes") != 0 && strcmp(arg[iarg+2],"no") != 0) - error->all(FLERR,"Illegal cauchystat continue value. Must be 'yes' or 'no'"); + error->all(FLERR,"Illegal cauchystat continue value. " + "Must be 'yes' or 'no'"); alpha = force->numeric(FLERR,arg[iarg+1]); restartPK = !strcmp(arg[iarg+2],"yes"); - CauchyStat_init(); iarg += 3; } else if (strcmp(arg[iarg],"fixedpoint") == 0) { if (iarg+4 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command"); @@ -594,6 +593,14 @@ FixNH::FixNH(LAMMPS *lmp, int narg, char **arg) : /* ---------------------------------------------------------------------- */ +void FixNH::post_constructor() +{ + if (!usePK) CauchyStat_init(); + else CauchyStat_cleanup(); +} + +/* ---------------------------------------------------------------------- */ + FixNH::~FixNH() { if (copymode) return; @@ -2439,12 +2446,11 @@ void FixNH::CauchyStat_init() } if (!id_store) { - int n = strlen(id) + 11; + int n = strlen(id) + 14; id_store = new char[n]; strcpy(id_store,id); - strcat(id_store,"_FIX_STORE"); + strcat(id_store,"_FIX_NH_STORE"); } - restart_stored = modify->find_fix(id_store); if (restartPK==1 && restart_stored < 0) @@ -2455,26 +2461,22 @@ void FixNH::CauchyStat_init() error->all(FLERR,"Illegal cauchystat command: " " Alpha cannot be zero or negative."); - - if (restartPK == 0) { - if (restart_stored < 0) { - char **newarg = new char *[6]; - newarg[0] = id_store; - newarg[1] = (char *) "all"; - newarg[2] = (char *) "STORE"; - newarg[3] = (char *) "global"; - newarg[4] = (char *) "1"; - newarg[5] = (char *) "6"; - modify->add_fix(6,newarg); - delete[] newarg; - } - int n = modify->find_fix(id_store); - init_store = (FixStore *)modify->fix[n]; + if (restart_stored < 0) { + char **newarg = new char *[6]; + newarg[0] = id_store; + newarg[1] = (char *) "all"; + newarg[2] = (char *) "STORE"; + newarg[3] = (char *) "global"; + newarg[4] = (char *) "1"; + newarg[5] = (char *) "6"; + modify->add_fix(6,newarg); + delete[] newarg; + restart_stored = modify->find_fix(id_store); } + init_store = (FixStore *)modify->fix[restart_stored]; initRUN = 0; initPK = 1; - usePK = 0; #define H0(row,col) (H0[(row-1)][(col-1)]) #define invH0(row,col) (invH0[(row-1)][(col-1)]) @@ -2498,7 +2500,26 @@ void FixNH::CauchyStat_init() #undef invH0 } +/* ---------------------------------------------------------------------- + cleanup when not using Cauchystat +------------------------------------------------------------------------- */ +void FixNH::CauchyStat_cleanup() +{ + if (id_store) { + modify->delete_fix(id_store); + delete[] id_store; + } else { + int n = strlen(id) + 14; + id_store = new char[n]; + strcpy(id_store,id); + strcat(id_store,"_FIX_NH_STORE"); + modify->delete_fix(id_store); + delete[] id_store; + } + id_store = NULL; + restart_stored = -1; +} /* ---------------------------------------------------------------------- Cauchystat @@ -2589,6 +2610,7 @@ void FixNH::CauchyStat() //initialize: if (initPK==1) { if (restartPK==1) { + double *setPKinit = init_store->astore[0]; setPK(1,1)=setPKinit[0]; setPK(1,2)=setPKinit[1]; setPK(1,3)=setPKinit[2]; setPK(2,1)=setPKinit[1]; setPK(2,2)=setPKinit[3]; setPK(2,3)=setPKinit[4]; setPK(3,1)=setPKinit[2]; setPK(3,2)=setPKinit[4]; setPK(3,3)=setPKinit[5]; @@ -2623,14 +2645,13 @@ void FixNH::CauchyStat() p_hydro /= pdim; // save information for Cauchystat restart - + double *setPKinit = init_store->astore[0]; setPKinit[0] = setcauchy(1,1); setPKinit[1] = setcauchy(1,2); setPKinit[2] = setcauchy(1,3); setPKinit[3] = setcauchy(2,2); setPKinit[4] = setcauchy(2,3); setPKinit[5] = setcauchy(3,3); - restart_stored=1; #undef H #undef Hdot diff --git a/src/fix_nh.h b/src/fix_nh.h index 50dc8210ab..2bc64281ff 100644 --- a/src/fix_nh.h +++ b/src/fix_nh.h @@ -21,6 +21,7 @@ namespace LAMMPS_NS { class FixNH : public Fix { public: FixNH(class LAMMPS *, int, char **); + virtual void post_constructor(); virtual ~FixNH(); int setmask(); virtual void init(); @@ -151,8 +152,6 @@ class FixNH : public Fix { double setPK[3][3]; // current set values of the PK stress // (this is modified until the cauchy // stress converges) - double setPKinit[6]; // initialization value of setPK for - // continuation runs double alpha; // integration parameter for the cauchystat int initPK; // 1 if setPK needs to be initialized either // from cauchy or restart, else 0 @@ -164,6 +163,7 @@ class FixNH : public Fix { // else 1 (pressure->vector available) void CauchyStat_init(); + void CauchyStat_cleanup(); void CauchyStat(); void CauchyStat_Step(double (&Fi)[3][3], double (&Fdot)[3][3], double (&cauchy)[3][3], double (&setcauchy)[3][3], From a726cb50e170c0b68dbec8736052acbb06989bf4 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 22 Oct 2018 16:35:55 -0400 Subject: [PATCH 298/302] fix uninitialized data issue detected by valgrind --- src/fix_nh.cpp | 1 + 1 file changed, 1 insertion(+) diff --git a/src/fix_nh.cpp b/src/fix_nh.cpp index b7f4390b4e..bcae8b23dd 100644 --- a/src/fix_nh.cpp +++ b/src/fix_nh.cpp @@ -71,6 +71,7 @@ FixNH::FixNH(LAMMPS *lmp, int narg, char **arg) : // for CauchyStat usePK = 1; + initRUN = 0; restartPK = 0; restart_global = 1; restart_stored = 0; From d1ff90eacfdf5f0c794b2452057b88a1d6bdda20 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 13 Nov 2018 17:18:37 -0500 Subject: [PATCH 299/302] copy and rename fix_nh.cpp/.h to USER-CAUCHY/fix_cauchy.cpp/.h related changes this moves the code into the corresponding folders, renames the classes, adds copies of the doc files, moves the examples, integrates the USER-CAUCHY package into the build system. --- cmake/CMakeLists.txt | 3 +- doc/src/Commands_fix.txt | 1 + doc/src/fixes.txt | 1 + doc/src/lammps.book | 1 + .../cauchy}/Mishin-Ni-Al-2009.eam.alloy | 0 examples/{cauchystat => USER/cauchy}/README | 0 .../{cauchystat => USER/cauchy}/in.cauchystat | 6 +- .../cauchy}/log.10Oct2018.cauchystat.g++.4 | 0 src/.gitignore | 3 + src/Makefile | 5 +- src/USER-CAUCHY/fix_cauchy.cpp | 2797 +++++++++++++++++ src/USER-CAUCHY/fix_cauchy.h | 310 ++ src/USER-CAUCHY/fix_npt_cauchy.cpp | 68 + src/USER-CAUCHY/fix_npt_cauchy.h | 48 + 14 files changed, 3237 insertions(+), 6 deletions(-) rename examples/{cauchystat => USER/cauchy}/Mishin-Ni-Al-2009.eam.alloy (100%) rename examples/{cauchystat => USER/cauchy}/README (100%) rename examples/{cauchystat => USER/cauchy}/in.cauchystat (93%) rename examples/{cauchystat => USER/cauchy}/log.10Oct2018.cauchystat.g++.4 (100%) create mode 100644 src/USER-CAUCHY/fix_cauchy.cpp create mode 100644 src/USER-CAUCHY/fix_cauchy.h create mode 100644 src/USER-CAUCHY/fix_npt_cauchy.cpp create mode 100644 src/USER-CAUCHY/fix_npt_cauchy.h diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index b3c0a70e4a..3806b5bf0c 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -168,7 +168,8 @@ set(LAMMPS_API_DEFINES) set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE GRANULAR KSPACE MANYBODY MC MEAM MESSAGE MISC MOLECULE PERI REAX REPLICA RIGID SHOCK SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE USER-ATC USER-AWPMD - USER-BOCS USER-CGDNA USER-MESO USER-CGSDK USER-COLVARS USER-DIFFRACTION + USER-BOCS USER-CAUCHY USER-CGDNA USER-MESO USER-CGSDK USER-COLVARS + USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD USER-LB USER-MANIFOLD USER-MEAMC USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-PHONON USER-PTM USER-QTB USER-REAXC USER-SCAFACOS USER-SMD USER-SMTBQ diff --git a/doc/src/Commands_fix.txt b/doc/src/Commands_fix.txt index 58828d5c9e..1d12f84298 100644 --- a/doc/src/Commands_fix.txt +++ b/doc/src/Commands_fix.txt @@ -110,6 +110,7 @@ OPT. "npt (kio)"_fix_nh.html, "npt/asphere (o)"_fix_npt_asphere.html, "npt/body"_fix_npt_body.html, +"npt/cauchy"_fix_cauchy.html, "npt/eff"_fix_nh_eff.html, "npt/sphere (o)"_fix_npt_sphere.html, "npt/uef"_fix_nh_uef.html, diff --git a/doc/src/fixes.txt b/doc/src/fixes.txt index 66f6633124..b91e68a7f8 100644 --- a/doc/src/fixes.txt +++ b/doc/src/fixes.txt @@ -89,6 +89,7 @@ Fixes :h1 fix_nphug fix_npt_asphere fix_npt_body + fix_cauchy fix_npt_sphere fix_nve fix_nve_asphere diff --git a/doc/src/lammps.book b/doc/src/lammps.book index f739712f08..b1973cd036 100644 --- a/doc/src/lammps.book +++ b/doc/src/lammps.book @@ -308,6 +308,7 @@ fix_nph_sphere.html fix_nphug.html fix_npt_asphere.html fix_npt_body.html +fix_npt_cauchy.html fix_npt_sphere.html fix_nve.html fix_nve_asphere.html diff --git a/examples/cauchystat/Mishin-Ni-Al-2009.eam.alloy b/examples/USER/cauchy/Mishin-Ni-Al-2009.eam.alloy similarity index 100% rename from examples/cauchystat/Mishin-Ni-Al-2009.eam.alloy rename to examples/USER/cauchy/Mishin-Ni-Al-2009.eam.alloy diff --git a/examples/cauchystat/README b/examples/USER/cauchy/README similarity index 100% rename from examples/cauchystat/README rename to examples/USER/cauchy/README diff --git a/examples/cauchystat/in.cauchystat b/examples/USER/cauchy/in.cauchystat similarity index 93% rename from examples/cauchystat/in.cauchystat rename to examples/USER/cauchy/in.cauchystat index 0505cf29c9..8a95f48f1a 100644 --- a/examples/cauchystat/in.cauchystat +++ b/examples/USER/cauchy/in.cauchystat @@ -25,7 +25,7 @@ thermo 100 thermo_style custom step temp pxx pyy pzz pxy pxz pyz compute cna all cna/atom 2.8 -fix 1 all npt temp 600.0 600.0 1.0 & +fix 1 all npt/cauchy temp 600.0 600.0 1.0 & x 0.0 0.0 0.1 & y 0.0 0.0 0.1 & z 0.0 0.0 0.1 & @@ -62,7 +62,7 @@ run 10000 info fixes -fix 1 all npt temp 600.0 600.0 1.0 & +fix 1 all npt/cauchy temp 600.0 600.0 1.0 & x 0.0 0.0 0.1 & y 0.0 0.0 0.1 & z 0.0 0.0 0.1 & @@ -73,7 +73,7 @@ info fixes run 10000 -fix 1 all npt temp 600.0 600.0 1.0 & +fix 1 all npt/cauchy temp 600.0 600.0 1.0 & x 0.0 0.0 0.1 & y 0.0 0.0 0.1 & z 0.0 0.0 0.1 & diff --git a/examples/cauchystat/log.10Oct2018.cauchystat.g++.4 b/examples/USER/cauchy/log.10Oct2018.cauchystat.g++.4 similarity index 100% rename from examples/cauchystat/log.10Oct2018.cauchystat.g++.4 rename to examples/USER/cauchy/log.10Oct2018.cauchystat.g++.4 diff --git a/src/.gitignore b/src/.gitignore index 4f517af3af..cb52b14cd4 100644 --- a/src/.gitignore +++ b/src/.gitignore @@ -49,6 +49,9 @@ /fix_qeq*.cpp /fix_qeq*.h +/fix_*cauchy.cpp +/fix_*cauchy.h + /compute_test_nbl.cpp /compute_test_nbl.h /pair_multi_lucy.cpp diff --git a/src/Makefile b/src/Makefile index 7d31c81c75..4e0e49b3f5 100644 --- a/src/Makefile +++ b/src/Makefile @@ -57,8 +57,9 @@ PACKAGE = asphere body class2 colloid compress coreshell dipole gpu \ molecule mpiio mscg opt peri poems \ python qeq reax replica rigid shock snap spin srd voronoi -PACKUSER = user-atc user-awpmd user-bocs user-cgdna user-cgsdk user-colvars \ - user-diffraction user-dpd user-drude user-eff user-fep user-h5md \ +PACKUSER = user-atc user-awpmd user-bocs user-cauchy user-cgdna user-cgsdk \ + user-colvars user-diffraction user-dpd user-drude user-eff \ + user-fep user-h5md \ user-intel user-lb user-manifold user-meamc user-meso \ user-mgpt user-misc user-mofff user-molfile \ user-netcdf user-omp user-phonon user-ptm user-qmmm user-qtb \ diff --git a/src/USER-CAUCHY/fix_cauchy.cpp b/src/USER-CAUCHY/fix_cauchy.cpp new file mode 100644 index 0000000000..d2cd6c3a59 --- /dev/null +++ b/src/USER-CAUCHY/fix_cauchy.cpp @@ -0,0 +1,2797 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing authors: +------------------------------------------------------------------------- */ + +#include +#include +#include +#include "fix_cauchy.h" +#include "math_extra.h" +#include "atom.h" +#include "force.h" +#include "group.h" +#include "comm.h" +#include "neighbor.h" +#include "irregular.h" +#include "modify.h" +#include "fix_deform.h" +#include "fix_store.h" +#include "compute.h" +#include "kspace.h" +#include "update.h" +#include "respa.h" +#include "domain.h" +#include "memory.h" +#include "error.h" + +using namespace LAMMPS_NS; +using namespace FixConst; + +#define DELTAFLIP 0.1 +#define TILTMAX 1.5 + +enum{NOBIAS,BIAS}; +enum{NONE,XYZ,XY,YZ,XZ}; +enum{ISO,ANISO,TRICLINIC}; + +/* ---------------------------------------------------------------------- + NVT,NPH,NPT integrators for improved Nose-Hoover equations of motion + ---------------------------------------------------------------------- */ + +FixCauchy::FixCauchy(LAMMPS *lmp, int narg, char **arg) : + Fix(lmp, narg, arg), + rfix(NULL), id_dilate(NULL), irregular(NULL), id_temp(NULL), id_press(NULL), + eta(NULL), eta_dot(NULL), eta_dotdot(NULL), + eta_mass(NULL), etap(NULL), etap_dot(NULL), etap_dotdot(NULL), + etap_mass(NULL), id_store(NULL),init_store(NULL) +{ + if (narg < 4) error->all(FLERR,"Illegal fix nvt/npt/nph command"); + + dynamic_group_allow = 1; + time_integrate = 1; + scalar_flag = 1; + vector_flag = 1; + global_freq = 1; + extscalar = 1; + extvector = 0; + + // for CauchyStat + + usePK = 1; + initRUN = 0; + restartPK = 0; + restart_global = 1; + restart_stored = 0; + + // default values + + pcouple = NONE; + drag = 0.0; + allremap = 1; + mtchain = mpchain = 3; + nc_tchain = nc_pchain = 1; + mtk_flag = 1; + deviatoric_flag = 0; + nreset_h0 = 0; + eta_mass_flag = 1; + omega_mass_flag = 0; + etap_mass_flag = 0; + flipflag = 1; + dipole_flag = 0; + dlm_flag = 0; + + tcomputeflag = 0; + pcomputeflag = 0; + + // turn on tilt factor scaling, whenever applicable + + dimension = domain->dimension; + + scaleyz = scalexz = scalexy = 0; + if (domain->yperiodic && domain->xy != 0.0) scalexy = 1; + if (domain->zperiodic && dimension == 3) { + if (domain->yz != 0.0) scaleyz = 1; + if (domain->xz != 0.0) scalexz = 1; + } + + // set fixed-point to default = center of cell + + fixedpoint[0] = 0.5*(domain->boxlo[0]+domain->boxhi[0]); + fixedpoint[1] = 0.5*(domain->boxlo[1]+domain->boxhi[1]); + fixedpoint[2] = 0.5*(domain->boxlo[2]+domain->boxhi[2]); + + // used by FixNVTSllod to preserve non-default value + + mtchain_default_flag = 1; + + tstat_flag = 0; + double t_period = 0.0; + + double p_period[6]; + for (int i = 0; i < 6; i++) { + p_start[i] = p_stop[i] = p_period[i] = p_target[i] = 0.0; + p_flag[i] = 0; + } + + // process keywords + + int iarg = 3; + + while (iarg < narg) { + if (strcmp(arg[iarg],"temp") == 0) { + if (iarg+4 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command"); + tstat_flag = 1; + t_start = force->numeric(FLERR,arg[iarg+1]); + t_target = t_start; + t_stop = force->numeric(FLERR,arg[iarg+2]); + t_period = force->numeric(FLERR,arg[iarg+3]); + if (t_start <= 0.0 || t_stop <= 0.0) + error->all(FLERR, + "Target temperature for fix nvt/npt/nph cannot be 0.0"); + iarg += 4; + + } else if (strcmp(arg[iarg],"iso") == 0) { + if (iarg+4 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command"); + pcouple = XYZ; + p_start[0] = p_start[1] = p_start[2] = force->numeric(FLERR,arg[iarg+1]); + p_stop[0] = p_stop[1] = p_stop[2] = force->numeric(FLERR,arg[iarg+2]); + p_period[0] = p_period[1] = p_period[2] = + force->numeric(FLERR,arg[iarg+3]); + p_flag[0] = p_flag[1] = p_flag[2] = 1; + if (dimension == 2) { + p_start[2] = p_stop[2] = p_period[2] = 0.0; + p_flag[2] = 0; + } + iarg += 4; + } else if (strcmp(arg[iarg],"aniso") == 0) { + if (iarg+4 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command"); + pcouple = NONE; + p_start[0] = p_start[1] = p_start[2] = force->numeric(FLERR,arg[iarg+1]); + p_stop[0] = p_stop[1] = p_stop[2] = force->numeric(FLERR,arg[iarg+2]); + p_period[0] = p_period[1] = p_period[2] = + force->numeric(FLERR,arg[iarg+3]); + p_flag[0] = p_flag[1] = p_flag[2] = 1; + if (dimension == 2) { + p_start[2] = p_stop[2] = p_period[2] = 0.0; + p_flag[2] = 0; + } + iarg += 4; + } else if (strcmp(arg[iarg],"tri") == 0) { + if (iarg+4 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command"); + pcouple = NONE; + scalexy = scalexz = scaleyz = 0; + p_start[0] = p_start[1] = p_start[2] = force->numeric(FLERR,arg[iarg+1]); + p_stop[0] = p_stop[1] = p_stop[2] = force->numeric(FLERR,arg[iarg+2]); + p_period[0] = p_period[1] = p_period[2] = + force->numeric(FLERR,arg[iarg+3]); + p_flag[0] = p_flag[1] = p_flag[2] = 1; + p_start[3] = p_start[4] = p_start[5] = 0.0; + p_stop[3] = p_stop[4] = p_stop[5] = 0.0; + p_period[3] = p_period[4] = p_period[5] = + force->numeric(FLERR,arg[iarg+3]); + p_flag[3] = p_flag[4] = p_flag[5] = 1; + if (dimension == 2) { + p_start[2] = p_stop[2] = p_period[2] = 0.0; + p_flag[2] = 0; + p_start[3] = p_stop[3] = p_period[3] = 0.0; + p_flag[3] = 0; + p_start[4] = p_stop[4] = p_period[4] = 0.0; + p_flag[4] = 0; + } + iarg += 4; + } else if (strcmp(arg[iarg],"x") == 0) { + if (iarg+4 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command"); + p_start[0] = force->numeric(FLERR,arg[iarg+1]); + p_stop[0] = force->numeric(FLERR,arg[iarg+2]); + p_period[0] = force->numeric(FLERR,arg[iarg+3]); + p_flag[0] = 1; + deviatoric_flag = 1; + iarg += 4; + } else if (strcmp(arg[iarg],"y") == 0) { + if (iarg+4 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command"); + p_start[1] = force->numeric(FLERR,arg[iarg+1]); + p_stop[1] = force->numeric(FLERR,arg[iarg+2]); + p_period[1] = force->numeric(FLERR,arg[iarg+3]); + p_flag[1] = 1; + deviatoric_flag = 1; + iarg += 4; + } else if (strcmp(arg[iarg],"z") == 0) { + if (iarg+4 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command"); + p_start[2] = force->numeric(FLERR,arg[iarg+1]); + p_stop[2] = force->numeric(FLERR,arg[iarg+2]); + p_period[2] = force->numeric(FLERR,arg[iarg+3]); + p_flag[2] = 1; + deviatoric_flag = 1; + iarg += 4; + if (dimension == 2) + error->all(FLERR,"Invalid fix nvt/npt/nph command for a 2d simulation"); + + } else if (strcmp(arg[iarg],"yz") == 0) { + if (iarg+4 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command"); + p_start[3] = force->numeric(FLERR,arg[iarg+1]); + p_stop[3] = force->numeric(FLERR,arg[iarg+2]); + p_period[3] = force->numeric(FLERR,arg[iarg+3]); + p_flag[3] = 1; + deviatoric_flag = 1; + scaleyz = 0; + iarg += 4; + if (dimension == 2) + error->all(FLERR,"Invalid fix nvt/npt/nph command for a 2d simulation"); + } else if (strcmp(arg[iarg],"xz") == 0) { + if (iarg+4 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command"); + p_start[4] = force->numeric(FLERR,arg[iarg+1]); + p_stop[4] = force->numeric(FLERR,arg[iarg+2]); + p_period[4] = force->numeric(FLERR,arg[iarg+3]); + p_flag[4] = 1; + deviatoric_flag = 1; + scalexz = 0; + iarg += 4; + if (dimension == 2) + error->all(FLERR,"Invalid fix nvt/npt/nph command for a 2d simulation"); + } else if (strcmp(arg[iarg],"xy") == 0) { + if (iarg+4 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command"); + p_start[5] = force->numeric(FLERR,arg[iarg+1]); + p_stop[5] = force->numeric(FLERR,arg[iarg+2]); + p_period[5] = force->numeric(FLERR,arg[iarg+3]); + p_flag[5] = 1; + deviatoric_flag = 1; + scalexy = 0; + iarg += 4; + + } else if (strcmp(arg[iarg],"couple") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command"); + if (strcmp(arg[iarg+1],"xyz") == 0) pcouple = XYZ; + else if (strcmp(arg[iarg+1],"xy") == 0) pcouple = XY; + else if (strcmp(arg[iarg+1],"yz") == 0) pcouple = YZ; + else if (strcmp(arg[iarg+1],"xz") == 0) pcouple = XZ; + else if (strcmp(arg[iarg+1],"none") == 0) pcouple = NONE; + else error->all(FLERR,"Illegal fix nvt/npt/nph command"); + iarg += 2; + + } else if (strcmp(arg[iarg],"drag") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command"); + drag = force->numeric(FLERR,arg[iarg+1]); + if (drag < 0.0) error->all(FLERR,"Illegal fix nvt/npt/nph command"); + iarg += 2; + } else if (strcmp(arg[iarg],"dilate") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command"); + if (strcmp(arg[iarg+1],"all") == 0) allremap = 1; + else { + allremap = 0; + delete [] id_dilate; + int n = strlen(arg[iarg+1]) + 1; + id_dilate = new char[n]; + strcpy(id_dilate,arg[iarg+1]); + int idilate = group->find(id_dilate); + if (idilate == -1) + error->all(FLERR,"Fix nvt/npt/nph dilate group ID does not exist"); + } + iarg += 2; + + } else if (strcmp(arg[iarg],"tchain") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command"); + mtchain = force->inumeric(FLERR,arg[iarg+1]); + // used by FixNVTSllod to preserve non-default value + mtchain_default_flag = 0; + if (mtchain < 1) error->all(FLERR,"Illegal fix nvt/npt/nph command"); + iarg += 2; + } else if (strcmp(arg[iarg],"pchain") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command"); + mpchain = force->inumeric(FLERR,arg[iarg+1]); + if (mpchain < 0) error->all(FLERR,"Illegal fix nvt/npt/nph command"); + iarg += 2; + } else if (strcmp(arg[iarg],"mtk") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command"); + if (strcmp(arg[iarg+1],"yes") == 0) mtk_flag = 1; + else if (strcmp(arg[iarg+1],"no") == 0) mtk_flag = 0; + else error->all(FLERR,"Illegal fix nvt/npt/nph command"); + iarg += 2; + } else if (strcmp(arg[iarg],"tloop") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command"); + nc_tchain = force->inumeric(FLERR,arg[iarg+1]); + if (nc_tchain < 0) error->all(FLERR,"Illegal fix nvt/npt/nph command"); + iarg += 2; + } else if (strcmp(arg[iarg],"ploop") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command"); + nc_pchain = force->inumeric(FLERR,arg[iarg+1]); + if (nc_pchain < 0) error->all(FLERR,"Illegal fix nvt/npt/nph command"); + iarg += 2; + } else if (strcmp(arg[iarg],"nreset") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command"); + nreset_h0 = force->inumeric(FLERR,arg[iarg+1]); + if (nreset_h0 < 0) error->all(FLERR,"Illegal fix nvt/npt/nph command"); + iarg += 2; + } else if (strcmp(arg[iarg],"scalexy") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command"); + if (strcmp(arg[iarg+1],"yes") == 0) scalexy = 1; + else if (strcmp(arg[iarg+1],"no") == 0) scalexy = 0; + else error->all(FLERR,"Illegal fix nvt/npt/nph command"); + iarg += 2; + } else if (strcmp(arg[iarg],"scalexz") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command"); + if (strcmp(arg[iarg+1],"yes") == 0) scalexz = 1; + else if (strcmp(arg[iarg+1],"no") == 0) scalexz = 0; + else error->all(FLERR,"Illegal fix nvt/npt/nph command"); + iarg += 2; + } else if (strcmp(arg[iarg],"scaleyz") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command"); + if (strcmp(arg[iarg+1],"yes") == 0) scaleyz = 1; + else if (strcmp(arg[iarg+1],"no") == 0) scaleyz = 0; + else error->all(FLERR,"Illegal fix nvt/npt/nph command"); + iarg += 2; + } else if (strcmp(arg[iarg],"flip") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command"); + if (strcmp(arg[iarg+1],"yes") == 0) flipflag = 1; + else if (strcmp(arg[iarg+1],"no") == 0) flipflag = 0; + else error->all(FLERR,"Illegal fix nvt/npt/nph command"); + iarg += 2; + } else if (strcmp(arg[iarg],"update") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command"); + if (strcmp(arg[iarg+1],"dipole") == 0) dipole_flag = 1; + else if (strcmp(arg[iarg+1],"dipole/dlm") == 0) { + dipole_flag = 1; + dlm_flag = 1; + } else error->all(FLERR,"Illegal fix nvt/npt/nph command"); + iarg += 2; + } else if (strcmp(arg[iarg],"cauchystat") == 0) { + usePK = 0; + if (iarg+3 > narg) error->all(FLERR, + "Illegal fix npt cauchystat command:" + " wrong number of arguments"); + if (strcmp(arg[iarg+2],"yes") != 0 && strcmp(arg[iarg+2],"no") != 0) + error->all(FLERR,"Illegal cauchystat continue value. " + "Must be 'yes' or 'no'"); + alpha = force->numeric(FLERR,arg[iarg+1]); + restartPK = !strcmp(arg[iarg+2],"yes"); + iarg += 3; + } else if (strcmp(arg[iarg],"fixedpoint") == 0) { + if (iarg+4 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command"); + fixedpoint[0] = force->numeric(FLERR,arg[iarg+1]); + fixedpoint[1] = force->numeric(FLERR,arg[iarg+2]); + fixedpoint[2] = force->numeric(FLERR,arg[iarg+3]); + iarg += 4; + + // disc keyword is also parsed in fix/nh/sphere + + } else if (strcmp(arg[iarg],"disc") == 0) { + iarg++; + + // keywords erate, strain, and ext are also parsed in fix/nh/uef + + } else if (strcmp(arg[iarg],"erate") == 0) { + iarg += 3; + } else if (strcmp(arg[iarg],"strain") == 0) { + iarg += 3; + } else if (strcmp(arg[iarg],"ext") == 0) { + iarg += 2; + + } else error->all(FLERR,"Illegal fix nvt/npt/nph command"); + } + + // error checks + + if (dimension == 2 && (p_flag[2] || p_flag[3] || p_flag[4])) + error->all(FLERR,"Invalid fix nvt/npt/nph command for a 2d simulation"); + if (dimension == 2 && (pcouple == YZ || pcouple == XZ)) + error->all(FLERR,"Invalid fix nvt/npt/nph command for a 2d simulation"); + if (dimension == 2 && (scalexz == 1 || scaleyz == 1 )) + error->all(FLERR,"Invalid fix nvt/npt/nph command for a 2d simulation"); + + if (pcouple == XYZ && (p_flag[0] == 0 || p_flag[1] == 0)) + error->all(FLERR,"Invalid fix nvt/npt/nph command pressure settings"); + if (pcouple == XYZ && dimension == 3 && p_flag[2] == 0) + error->all(FLERR,"Invalid fix nvt/npt/nph command pressure settings"); + if (pcouple == XY && (p_flag[0] == 0 || p_flag[1] == 0)) + error->all(FLERR,"Invalid fix nvt/npt/nph command pressure settings"); + if (pcouple == YZ && (p_flag[1] == 0 || p_flag[2] == 0)) + error->all(FLERR,"Invalid fix nvt/npt/nph command pressure settings"); + if (pcouple == XZ && (p_flag[0] == 0 || p_flag[2] == 0)) + error->all(FLERR,"Invalid fix nvt/npt/nph command pressure settings"); + + // require periodicity in tensile dimension + + if (p_flag[0] && domain->xperiodic == 0) + error->all(FLERR,"Cannot use fix nvt/npt/nph on a non-periodic dimension"); + if (p_flag[1] && domain->yperiodic == 0) + error->all(FLERR,"Cannot use fix nvt/npt/nph on a non-periodic dimension"); + if (p_flag[2] && domain->zperiodic == 0) + error->all(FLERR,"Cannot use fix nvt/npt/nph on a non-periodic dimension"); + + // require periodicity in 2nd dim of off-diagonal tilt component + + if (p_flag[3] && domain->zperiodic == 0) + error->all(FLERR, + "Cannot use fix nvt/npt/nph on a 2nd non-periodic dimension"); + if (p_flag[4] && domain->zperiodic == 0) + error->all(FLERR, + "Cannot use fix nvt/npt/nph on a 2nd non-periodic dimension"); + if (p_flag[5] && domain->yperiodic == 0) + error->all(FLERR, + "Cannot use fix nvt/npt/nph on a 2nd non-periodic dimension"); + + if (scaleyz == 1 && domain->zperiodic == 0) + error->all(FLERR,"Cannot use fix nvt/npt/nph " + "with yz scaling when z is non-periodic dimension"); + if (scalexz == 1 && domain->zperiodic == 0) + error->all(FLERR,"Cannot use fix nvt/npt/nph " + "with xz scaling when z is non-periodic dimension"); + if (scalexy == 1 && domain->yperiodic == 0) + error->all(FLERR,"Cannot use fix nvt/npt/nph " + "with xy scaling when y is non-periodic dimension"); + + if (p_flag[3] && scaleyz == 1) + error->all(FLERR,"Cannot use fix nvt/npt/nph with " + "both yz dynamics and yz scaling"); + if (p_flag[4] && scalexz == 1) + error->all(FLERR,"Cannot use fix nvt/npt/nph with " + "both xz dynamics and xz scaling"); + if (p_flag[5] && scalexy == 1) + error->all(FLERR,"Cannot use fix nvt/npt/nph with " + "both xy dynamics and xy scaling"); + + if (!domain->triclinic && (p_flag[3] || p_flag[4] || p_flag[5])) + error->all(FLERR,"Can not specify Pxy/Pxz/Pyz in " + "fix nvt/npt/nph with non-triclinic box"); + + if (pcouple == XYZ && dimension == 3 && + (p_start[0] != p_start[1] || p_start[0] != p_start[2] || + p_stop[0] != p_stop[1] || p_stop[0] != p_stop[2] || + p_period[0] != p_period[1] || p_period[0] != p_period[2])) + error->all(FLERR,"Invalid fix nvt/npt/nph pressure settings"); + if (pcouple == XYZ && dimension == 2 && + (p_start[0] != p_start[1] || p_stop[0] != p_stop[1] || + p_period[0] != p_period[1])) + error->all(FLERR,"Invalid fix nvt/npt/nph pressure settings"); + if (pcouple == XY && + (p_start[0] != p_start[1] || p_stop[0] != p_stop[1] || + p_period[0] != p_period[1])) + error->all(FLERR,"Invalid fix nvt/npt/nph pressure settings"); + if (pcouple == YZ && + (p_start[1] != p_start[2] || p_stop[1] != p_stop[2] || + p_period[1] != p_period[2])) + error->all(FLERR,"Invalid fix nvt/npt/nph pressure settings"); + if (pcouple == XZ && + (p_start[0] != p_start[2] || p_stop[0] != p_stop[2] || + p_period[0] != p_period[2])) + error->all(FLERR,"Invalid fix nvt/npt/nph pressure settings"); + + if (dipole_flag) { + if (!atom->sphere_flag) + error->all(FLERR,"Using update dipole flag requires atom style sphere"); + if (!atom->mu_flag) + error->all(FLERR,"Using update dipole flag requires atom attribute mu"); + } + + if ((tstat_flag && t_period <= 0.0) || + (p_flag[0] && p_period[0] <= 0.0) || + (p_flag[1] && p_period[1] <= 0.0) || + (p_flag[2] && p_period[2] <= 0.0) || + (p_flag[3] && p_period[3] <= 0.0) || + (p_flag[4] && p_period[4] <= 0.0) || + (p_flag[5] && p_period[5] <= 0.0)) + error->all(FLERR,"Fix nvt/npt/nph damping parameters must be > 0.0"); + + // set pstat_flag and box change and restart_pbc variables + + pre_exchange_flag = 0; + pstat_flag = 0; + pstyle = ISO; + + for (int i = 0; i < 6; i++) + if (p_flag[i]) pstat_flag = 1; + + if (pstat_flag) { + if (p_flag[0] || p_flag[1] || p_flag[2]) box_change_size = 1; + if (p_flag[3] || p_flag[4] || p_flag[5]) box_change_shape = 1; + no_change_box = 1; + if (allremap == 0) restart_pbc = 1; + + // pstyle = TRICLINIC if any off-diagonal term is controlled -> 6 dof + // else pstyle = ISO if XYZ coupling or XY coupling in 2d -> 1 dof + // else pstyle = ANISO -> 3 dof + + if (p_flag[3] || p_flag[4] || p_flag[5]) pstyle = TRICLINIC; + else if (pcouple == XYZ || (dimension == 2 && pcouple == XY)) pstyle = ISO; + else pstyle = ANISO; + + // pre_exchange only required if flips can occur due to shape changes + + if (flipflag && (p_flag[3] || p_flag[4] || p_flag[5])) + pre_exchange_flag = 1; + if (flipflag && (domain->yz != 0.0 || domain->xz != 0.0 || + domain->xy != 0.0)) + pre_exchange_flag = 1; + } + + // convert input periods to frequencies + + t_freq = 0.0; + p_freq[0] = p_freq[1] = p_freq[2] = p_freq[3] = p_freq[4] = p_freq[5] = 0.0; + + if (tstat_flag) t_freq = 1.0 / t_period; + if (p_flag[0]) p_freq[0] = 1.0 / p_period[0]; + if (p_flag[1]) p_freq[1] = 1.0 / p_period[1]; + if (p_flag[2]) p_freq[2] = 1.0 / p_period[2]; + if (p_flag[3]) p_freq[3] = 1.0 / p_period[3]; + if (p_flag[4]) p_freq[4] = 1.0 / p_period[4]; + if (p_flag[5]) p_freq[5] = 1.0 / p_period[5]; + + // Nose/Hoover temp and pressure init + + size_vector = 0; + + if (tstat_flag) { + int ich; + eta = new double[mtchain]; + + // add one extra dummy thermostat, set to zero + + eta_dot = new double[mtchain+1]; + eta_dot[mtchain] = 0.0; + eta_dotdot = new double[mtchain]; + for (ich = 0; ich < mtchain; ich++) { + eta[ich] = eta_dot[ich] = eta_dotdot[ich] = 0.0; + } + eta_mass = new double[mtchain]; + size_vector += 2*2*mtchain; + } + + if (pstat_flag) { + omega[0] = omega[1] = omega[2] = 0.0; + omega_dot[0] = omega_dot[1] = omega_dot[2] = 0.0; + omega_mass[0] = omega_mass[1] = omega_mass[2] = 0.0; + omega[3] = omega[4] = omega[5] = 0.0; + omega_dot[3] = omega_dot[4] = omega_dot[5] = 0.0; + omega_mass[3] = omega_mass[4] = omega_mass[5] = 0.0; + if (pstyle == ISO) size_vector += 2*2*1; + else if (pstyle == ANISO) size_vector += 2*2*3; + else if (pstyle == TRICLINIC) size_vector += 2*2*6; + + if (mpchain) { + int ich; + etap = new double[mpchain]; + + // add one extra dummy thermostat, set to zero + + etap_dot = new double[mpchain+1]; + etap_dot[mpchain] = 0.0; + etap_dotdot = new double[mpchain]; + for (ich = 0; ich < mpchain; ich++) { + etap[ich] = etap_dot[ich] = + etap_dotdot[ich] = 0.0; + } + etap_mass = new double[mpchain]; + size_vector += 2*2*mpchain; + } + + if (deviatoric_flag) size_vector += 1; + } + + nrigid = 0; + rfix = NULL; + + if (pre_exchange_flag) irregular = new Irregular(lmp); + else irregular = NULL; + + // initialize vol0,t0 to zero to signal uninitialized + // values then assigned in init(), if necessary + + vol0 = t0 = 0.0; +} + +/* ---------------------------------------------------------------------- */ + +void FixCauchy::post_constructor() +{ + if (!usePK) CauchyStat_init(); + else CauchyStat_cleanup(); +} + +/* ---------------------------------------------------------------------- */ + +FixCauchy::~FixCauchy() +{ + if (copymode) return; + + delete [] id_dilate; + delete [] rfix; + + delete [] id_store; + delete irregular; + + // delete temperature and pressure if fix created them + + if (tcomputeflag) modify->delete_compute(id_temp); + delete [] id_temp; + + if (tstat_flag) { + delete [] eta; + delete [] eta_dot; + delete [] eta_dotdot; + delete [] eta_mass; + } + + if (pstat_flag) { + if (pcomputeflag) modify->delete_compute(id_press); + delete [] id_press; + if (mpchain) { + delete [] etap; + delete [] etap_dot; + delete [] etap_dotdot; + delete [] etap_mass; + } + } +} + +/* ---------------------------------------------------------------------- */ + +int FixCauchy::setmask() +{ + int mask = 0; + mask |= INITIAL_INTEGRATE; + mask |= FINAL_INTEGRATE; + mask |= THERMO_ENERGY; + mask |= INITIAL_INTEGRATE_RESPA; + mask |= FINAL_INTEGRATE_RESPA; + if (pre_exchange_flag) mask |= PRE_EXCHANGE; + return mask; +} + +/* ---------------------------------------------------------------------- */ + +void FixCauchy::init() +{ + // recheck that dilate group has not been deleted + + if (allremap == 0) { + int idilate = group->find(id_dilate); + if (idilate == -1) + error->all(FLERR,"Fix nvt/npt/nph dilate group ID does not exist"); + dilate_group_bit = group->bitmask[idilate]; + } + + // ensure no conflict with fix deform + + if (pstat_flag) + for (int i = 0; i < modify->nfix; i++) + if (strcmp(modify->fix[i]->style,"deform") == 0) { + int *dimflag = ((FixDeform *) modify->fix[i])->dimflag; + if ((p_flag[0] && dimflag[0]) || (p_flag[1] && dimflag[1]) || + (p_flag[2] && dimflag[2]) || (p_flag[3] && dimflag[3]) || + (p_flag[4] && dimflag[4]) || (p_flag[5] && dimflag[5])) + error->all(FLERR,"Cannot use fix npt and fix deform on " + "same component of stress tensor"); + } + + // set temperature and pressure ptrs + + int icompute = modify->find_compute(id_temp); + if (icompute < 0) + error->all(FLERR,"Temperature ID for fix nvt/npt does not exist"); + temperature = modify->compute[icompute]; + + if (temperature->tempbias) which = BIAS; + else which = NOBIAS; + + if (pstat_flag) { + icompute = modify->find_compute(id_press); + if (icompute < 0) + error->all(FLERR,"Pressure ID for fix npt/nph does not exist"); + pressure = modify->compute[icompute]; + } + + // set timesteps and frequencies + + dtv = update->dt; + dtf = 0.5 * update->dt * force->ftm2v; + dthalf = 0.5 * update->dt; + dt4 = 0.25 * update->dt; + dt8 = 0.125 * update->dt; + dto = dthalf; + + p_freq_max = 0.0; + if (pstat_flag) { + p_freq_max = MAX(p_freq[0],p_freq[1]); + p_freq_max = MAX(p_freq_max,p_freq[2]); + if (pstyle == TRICLINIC) { + p_freq_max = MAX(p_freq_max,p_freq[3]); + p_freq_max = MAX(p_freq_max,p_freq[4]); + p_freq_max = MAX(p_freq_max,p_freq[5]); + } + pdrag_factor = 1.0 - (update->dt * p_freq_max * drag / nc_pchain); + } + + if (tstat_flag) + tdrag_factor = 1.0 - (update->dt * t_freq * drag / nc_tchain); + + // tally the number of dimensions that are barostatted + // set initial volume and reference cell, if not already done + + if (pstat_flag) { + pdim = p_flag[0] + p_flag[1] + p_flag[2]; + if (vol0 == 0.0) { + if (dimension == 3) vol0 = domain->xprd * domain->yprd * domain->zprd; + else vol0 = domain->xprd * domain->yprd; + h0_inv[0] = domain->h_inv[0]; + h0_inv[1] = domain->h_inv[1]; + h0_inv[2] = domain->h_inv[2]; + h0_inv[3] = domain->h_inv[3]; + h0_inv[4] = domain->h_inv[4]; + h0_inv[5] = domain->h_inv[5]; + } + } + + boltz = force->boltz; + nktv2p = force->nktv2p; + + if (force->kspace) kspace_flag = 1; + else kspace_flag = 0; + + if (strstr(update->integrate_style,"respa")) { + nlevels_respa = ((Respa *) update->integrate)->nlevels; + step_respa = ((Respa *) update->integrate)->step; + dto = 0.5*step_respa[0]; + } + + // detect if any rigid fixes exist so rigid bodies move when box is remapped + // rfix[] = indices to each fix rigid + + delete [] rfix; + nrigid = 0; + rfix = NULL; + + for (int i = 0; i < modify->nfix; i++) + if (modify->fix[i]->rigid_flag) nrigid++; + if (nrigid) { + rfix = new int[nrigid]; + nrigid = 0; + for (int i = 0; i < modify->nfix; i++) + if (modify->fix[i]->rigid_flag) rfix[nrigid++] = i; + } +} + +/* ---------------------------------------------------------------------- + compute T,P before integrator starts +------------------------------------------------------------------------- */ + +void FixCauchy::setup(int /*vflag*/) +{ + // tdof needed by compute_temp_target() + + t_current = temperature->compute_scalar(); + tdof = temperature->dof; + + // t_target is needed by NVT and NPT in compute_scalar() + // If no thermostat or using fix nphug, + // t_target must be defined by other means. + + if (tstat_flag && strstr(style,"nphug") == NULL) { + compute_temp_target(); + } else if (pstat_flag) { + + // t0 = reference temperature for masses + // cannot be done in init() b/c temperature cannot be called there + // is b/c Modify::init() inits computes after fixes due to dof dependence + // guesstimate a unit-dependent t0 if actual T = 0.0 + // if it was read in from a restart file, leave it be + + if (t0 == 0.0) { + t0 = temperature->compute_scalar(); + if (t0 == 0.0) { + if (strcmp(update->unit_style,"lj") == 0) t0 = 1.0; + else t0 = 300.0; + } + } + t_target = t0; + } + + if (pstat_flag) compute_press_target(); + + if (pstat_flag) { + if (pstyle == ISO) pressure->compute_scalar(); + else pressure->compute_vector(); + couple(); + pressure->addstep(update->ntimestep+1); + } + + // masses and initial forces on thermostat variables + + if (tstat_flag) { + eta_mass[0] = tdof * boltz * t_target / (t_freq*t_freq); + for (int ich = 1; ich < mtchain; ich++) + eta_mass[ich] = boltz * t_target / (t_freq*t_freq); + for (int ich = 1; ich < mtchain; ich++) { + eta_dotdot[ich] = (eta_mass[ich-1]*eta_dot[ich-1]*eta_dot[ich-1] - + boltz * t_target) / eta_mass[ich]; + } + } + + // masses and initial forces on barostat variables + + if (pstat_flag) { + double kt = boltz * t_target; + double nkt = (atom->natoms + 1) * kt; + + for (int i = 0; i < 3; i++) + if (p_flag[i]) + omega_mass[i] = nkt/(p_freq[i]*p_freq[i]); + + if (pstyle == TRICLINIC) { + for (int i = 3; i < 6; i++) + if (p_flag[i]) omega_mass[i] = nkt/(p_freq[i]*p_freq[i]); + } + + // masses and initial forces on barostat thermostat variables + + if (mpchain) { + etap_mass[0] = boltz * t_target / (p_freq_max*p_freq_max); + for (int ich = 1; ich < mpchain; ich++) + etap_mass[ich] = boltz * t_target / (p_freq_max*p_freq_max); + for (int ich = 1; ich < mpchain; ich++) + etap_dotdot[ich] = + (etap_mass[ich-1]*etap_dot[ich-1]*etap_dot[ich-1] - + boltz * t_target) / etap_mass[ich]; + } + } +} + +/* ---------------------------------------------------------------------- + 1st half of Verlet update +------------------------------------------------------------------------- */ + +void FixCauchy::initial_integrate(int /*vflag*/) +{ + // update eta_press_dot + + if (pstat_flag && mpchain) nhc_press_integrate(); + + // update eta_dot + + if (tstat_flag) { + compute_temp_target(); + nhc_temp_integrate(); + } + + // need to recompute pressure to account for change in KE + // t_current is up-to-date, but compute_temperature is not + // compute appropriately coupled elements of mvv_current + + if (pstat_flag) { + if (pstyle == ISO) { + temperature->compute_scalar(); + pressure->compute_scalar(); + } else { + temperature->compute_vector(); + pressure->compute_vector(); + } + couple(); + pressure->addstep(update->ntimestep+1); + } + + if (pstat_flag) { + compute_press_target(); + nh_omega_dot(); + nh_v_press(); + } + + nve_v(); + + // remap simulation box by 1/2 step + + if (pstat_flag) remap(); + + nve_x(); + + // remap simulation box by 1/2 step + // redo KSpace coeffs since volume has changed + + if (pstat_flag) { + remap(); + if (kspace_flag) force->kspace->setup(); + } +} + +/* ---------------------------------------------------------------------- + 2nd half of Verlet update +------------------------------------------------------------------------- */ + +void FixCauchy::final_integrate() +{ + nve_v(); + + // re-compute temp before nh_v_press() + // only needed for temperature computes with BIAS on reneighboring steps: + // b/c some biases store per-atom values (e.g. temp/profile) + // per-atom values are invalid if reneigh/comm occurred + // since temp->compute() in initial_integrate() + + if (which == BIAS && neighbor->ago == 0) + t_current = temperature->compute_scalar(); + + if (pstat_flag) nh_v_press(); + + // compute new T,P after velocities rescaled by nh_v_press() + // compute appropriately coupled elements of mvv_current + + t_current = temperature->compute_scalar(); + tdof = temperature->dof; + + if (pstat_flag) { + if (pstyle == ISO) pressure->compute_scalar(); + else pressure->compute_vector(); + couple(); + pressure->addstep(update->ntimestep+1); + } + + if (pstat_flag) nh_omega_dot(); + + // update eta_dot + // update eta_press_dot + + if (tstat_flag) nhc_temp_integrate(); + if (pstat_flag && mpchain) nhc_press_integrate(); +} + +/* ---------------------------------------------------------------------- */ + +void FixCauchy::initial_integrate_respa(int /*vflag*/, int ilevel, int /*iloop*/) +{ + // set timesteps by level + + dtv = step_respa[ilevel]; + dtf = 0.5 * step_respa[ilevel] * force->ftm2v; + dthalf = 0.5 * step_respa[ilevel]; + + // outermost level - update eta_dot and omega_dot, apply to v + // all other levels - NVE update of v + // x,v updates only performed for atoms in group + + if (ilevel == nlevels_respa-1) { + + // update eta_press_dot + + if (pstat_flag && mpchain) nhc_press_integrate(); + + // update eta_dot + + if (tstat_flag) { + compute_temp_target(); + nhc_temp_integrate(); + } + + // recompute pressure to account for change in KE + // t_current is up-to-date, but compute_temperature is not + // compute appropriately coupled elements of mvv_current + + if (pstat_flag) { + if (pstyle == ISO) { + temperature->compute_scalar(); + pressure->compute_scalar(); + } else { + temperature->compute_vector(); + pressure->compute_vector(); + } + couple(); + pressure->addstep(update->ntimestep+1); + } + + if (pstat_flag) { + compute_press_target(); + nh_omega_dot(); + nh_v_press(); + } + + nve_v(); + + } else nve_v(); + + // innermost level - also update x only for atoms in group + // if barostat, perform 1/2 step remap before and after + + if (ilevel == 0) { + if (pstat_flag) remap(); + nve_x(); + if (pstat_flag) remap(); + } + + // if barostat, redo KSpace coeffs at outermost level, + // since volume has changed + + if (ilevel == nlevels_respa-1 && kspace_flag && pstat_flag) + force->kspace->setup(); +} + +/* ---------------------------------------------------------------------- */ + +void FixCauchy::final_integrate_respa(int ilevel, int /*iloop*/) +{ + // set timesteps by level + + dtf = 0.5 * step_respa[ilevel] * force->ftm2v; + dthalf = 0.5 * step_respa[ilevel]; + + // outermost level - update eta_dot and omega_dot, apply via final_integrate + // all other levels - NVE update of v + + if (ilevel == nlevels_respa-1) final_integrate(); + else nve_v(); +} + +/* ---------------------------------------------------------------------- */ + +void FixCauchy::couple() +{ + double *tensor = pressure->vector; + + if (pstyle == ISO) + p_current[0] = p_current[1] = p_current[2] = pressure->scalar; + else if (pcouple == XYZ) { + double ave = 1.0/3.0 * (tensor[0] + tensor[1] + tensor[2]); + p_current[0] = p_current[1] = p_current[2] = ave; + } else if (pcouple == XY) { + double ave = 0.5 * (tensor[0] + tensor[1]); + p_current[0] = p_current[1] = ave; + p_current[2] = tensor[2]; + } else if (pcouple == YZ) { + double ave = 0.5 * (tensor[1] + tensor[2]); + p_current[1] = p_current[2] = ave; + p_current[0] = tensor[0]; + } else if (pcouple == XZ) { + double ave = 0.5 * (tensor[0] + tensor[2]); + p_current[0] = p_current[2] = ave; + p_current[1] = tensor[1]; + } else { + p_current[0] = tensor[0]; + p_current[1] = tensor[1]; + p_current[2] = tensor[2]; + } + + if (!std::isfinite(p_current[0]) || !std::isfinite(p_current[1]) || !std::isfinite(p_current[2])) + error->all(FLERR,"Non-numeric pressure - simulation unstable"); + + // switch order from xy-xz-yz to Voigt + + if (pstyle == TRICLINIC) { + p_current[3] = tensor[5]; + p_current[4] = tensor[4]; + p_current[5] = tensor[3]; + + if (!std::isfinite(p_current[3]) || !std::isfinite(p_current[4]) || !std::isfinite(p_current[5])) + error->all(FLERR,"Non-numeric pressure - simulation unstable"); + } +} + +/* ---------------------------------------------------------------------- + change box size + remap all atoms or dilate group atoms depending on allremap flag + if rigid bodies exist, scale rigid body centers-of-mass +------------------------------------------------------------------------- */ + +void FixCauchy::remap() +{ + int i; + double oldlo,oldhi; + double expfac; + + double **x = atom->x; + int *mask = atom->mask; + int nlocal = atom->nlocal; + double *h = domain->h; + + // omega is not used, except for book-keeping + + for (int i = 0; i < 6; i++) omega[i] += dto*omega_dot[i]; + + // convert pertinent atoms and rigid bodies to lamda coords + + if (allremap) domain->x2lamda(nlocal); + else { + for (i = 0; i < nlocal; i++) + if (mask[i] & dilate_group_bit) + domain->x2lamda(x[i],x[i]); + } + + if (nrigid) + for (i = 0; i < nrigid; i++) + modify->fix[rfix[i]]->deform(0); + + // reset global and local box to new size/shape + + // this operation corresponds to applying the + // translate and scale operations + // corresponding to the solution of the following ODE: + // + // h_dot = omega_dot * h + // + // where h_dot, omega_dot and h are all upper-triangular + // 3x3 tensors. In Voigt notation, the elements of the + // RHS product tensor are: + // h_dot = [0*0, 1*1, 2*2, 1*3+3*2, 0*4+5*3+4*2, 0*5+5*1] + // + // Ordering of operations preserves time symmetry. + + double dto2 = dto/2.0; + double dto4 = dto/4.0; + double dto8 = dto/8.0; + + // off-diagonal components, first half + + if (pstyle == TRICLINIC) { + + if (p_flag[4]) { + expfac = exp(dto8*omega_dot[0]); + h[4] *= expfac; + h[4] += dto4*(omega_dot[5]*h[3]+omega_dot[4]*h[2]); + h[4] *= expfac; + } + + if (p_flag[3]) { + expfac = exp(dto4*omega_dot[1]); + h[3] *= expfac; + h[3] += dto2*(omega_dot[3]*h[2]); + h[3] *= expfac; + } + + if (p_flag[5]) { + expfac = exp(dto4*omega_dot[0]); + h[5] *= expfac; + h[5] += dto2*(omega_dot[5]*h[1]); + h[5] *= expfac; + } + + if (p_flag[4]) { + expfac = exp(dto8*omega_dot[0]); + h[4] *= expfac; + h[4] += dto4*(omega_dot[5]*h[3]+omega_dot[4]*h[2]); + h[4] *= expfac; + } + } + + // scale diagonal components + // scale tilt factors with cell, if set + + if (p_flag[0]) { + oldlo = domain->boxlo[0]; + oldhi = domain->boxhi[0]; + expfac = exp(dto*omega_dot[0]); + domain->boxlo[0] = (oldlo-fixedpoint[0])*expfac + fixedpoint[0]; + domain->boxhi[0] = (oldhi-fixedpoint[0])*expfac + fixedpoint[0]; + } + + if (p_flag[1]) { + oldlo = domain->boxlo[1]; + oldhi = domain->boxhi[1]; + expfac = exp(dto*omega_dot[1]); + domain->boxlo[1] = (oldlo-fixedpoint[1])*expfac + fixedpoint[1]; + domain->boxhi[1] = (oldhi-fixedpoint[1])*expfac + fixedpoint[1]; + if (scalexy) h[5] *= expfac; + } + + if (p_flag[2]) { + oldlo = domain->boxlo[2]; + oldhi = domain->boxhi[2]; + expfac = exp(dto*omega_dot[2]); + domain->boxlo[2] = (oldlo-fixedpoint[2])*expfac + fixedpoint[2]; + domain->boxhi[2] = (oldhi-fixedpoint[2])*expfac + fixedpoint[2]; + if (scalexz) h[4] *= expfac; + if (scaleyz) h[3] *= expfac; + } + + // off-diagonal components, second half + + if (pstyle == TRICLINIC) { + + if (p_flag[4]) { + expfac = exp(dto8*omega_dot[0]); + h[4] *= expfac; + h[4] += dto4*(omega_dot[5]*h[3]+omega_dot[4]*h[2]); + h[4] *= expfac; + } + + if (p_flag[3]) { + expfac = exp(dto4*omega_dot[1]); + h[3] *= expfac; + h[3] += dto2*(omega_dot[3]*h[2]); + h[3] *= expfac; + } + + if (p_flag[5]) { + expfac = exp(dto4*omega_dot[0]); + h[5] *= expfac; + h[5] += dto2*(omega_dot[5]*h[1]); + h[5] *= expfac; + } + + if (p_flag[4]) { + expfac = exp(dto8*omega_dot[0]); + h[4] *= expfac; + h[4] += dto4*(omega_dot[5]*h[3]+omega_dot[4]*h[2]); + h[4] *= expfac; + } + + } + + domain->yz = h[3]; + domain->xz = h[4]; + domain->xy = h[5]; + + // tilt factor to cell length ratio can not exceed TILTMAX in one step + + if (domain->yz < -TILTMAX*domain->yprd || + domain->yz > TILTMAX*domain->yprd || + domain->xz < -TILTMAX*domain->xprd || + domain->xz > TILTMAX*domain->xprd || + domain->xy < -TILTMAX*domain->xprd || + domain->xy > TILTMAX*domain->xprd) + error->all(FLERR,"Fix npt/nph has tilted box too far in one step - " + "periodic cell is too far from equilibrium state"); + + domain->set_global_box(); + domain->set_local_box(); + + // convert pertinent atoms and rigid bodies back to box coords + + if (allremap) domain->lamda2x(nlocal); + else { + for (i = 0; i < nlocal; i++) + if (mask[i] & dilate_group_bit) + domain->lamda2x(x[i],x[i]); + } + + if (nrigid) + for (i = 0; i < nrigid; i++) + modify->fix[rfix[i]]->deform(1); +} + +/* ---------------------------------------------------------------------- + pack entire state of Fix into one write +------------------------------------------------------------------------- */ + +void FixCauchy::write_restart(FILE *fp) +{ + int nsize = size_restart_global(); + + double *list; + memory->create(list,nsize,"nh:list"); + + pack_restart_data(list); + + if (comm->me == 0) { + int size = nsize * sizeof(double); + fwrite(&size,sizeof(int),1,fp); + fwrite(list,sizeof(double),nsize,fp); + } + + memory->destroy(list); +} + +/* ---------------------------------------------------------------------- + calculate the number of data to be packed +------------------------------------------------------------------------- */ + +int FixCauchy::size_restart_global() +{ + int nsize = 2; + if (tstat_flag) nsize += 1 + 2*mtchain; + if (pstat_flag) { + nsize += 16 + 2*mpchain; + if (deviatoric_flag) nsize += 6; + } + + return nsize; +} + +/* ---------------------------------------------------------------------- + pack restart data +------------------------------------------------------------------------- */ + +int FixCauchy::pack_restart_data(double *list) +{ + int n = 0; + + list[n++] = tstat_flag; + if (tstat_flag) { + list[n++] = mtchain; + for (int ich = 0; ich < mtchain; ich++) + list[n++] = eta[ich]; + for (int ich = 0; ich < mtchain; ich++) + list[n++] = eta_dot[ich]; + } + + list[n++] = pstat_flag; + if (pstat_flag) { + list[n++] = omega[0]; + list[n++] = omega[1]; + list[n++] = omega[2]; + list[n++] = omega[3]; + list[n++] = omega[4]; + list[n++] = omega[5]; + list[n++] = omega_dot[0]; + list[n++] = omega_dot[1]; + list[n++] = omega_dot[2]; + list[n++] = omega_dot[3]; + list[n++] = omega_dot[4]; + list[n++] = omega_dot[5]; + list[n++] = vol0; + list[n++] = t0; + list[n++] = mpchain; + if (mpchain) { + for (int ich = 0; ich < mpchain; ich++) + list[n++] = etap[ich]; + for (int ich = 0; ich < mpchain; ich++) + list[n++] = etap_dot[ich]; + } + + list[n++] = deviatoric_flag; + if (deviatoric_flag) { + list[n++] = h0_inv[0]; + list[n++] = h0_inv[1]; + list[n++] = h0_inv[2]; + list[n++] = h0_inv[3]; + list[n++] = h0_inv[4]; + list[n++] = h0_inv[5]; + } + } + + return n; +} + +/* ---------------------------------------------------------------------- + use state info from restart file to restart the Fix +------------------------------------------------------------------------- */ + +void FixCauchy::restart(char *buf) +{ + int n = 0; + double *list = (double *) buf; + int flag = static_cast (list[n++]); + if (flag) { + int m = static_cast (list[n++]); + if (tstat_flag && m == mtchain) { + for (int ich = 0; ich < mtchain; ich++) + eta[ich] = list[n++]; + for (int ich = 0; ich < mtchain; ich++) + eta_dot[ich] = list[n++]; + } else n += 2*m; + } + flag = static_cast (list[n++]); + if (flag) { + omega[0] = list[n++]; + omega[1] = list[n++]; + omega[2] = list[n++]; + omega[3] = list[n++]; + omega[4] = list[n++]; + omega[5] = list[n++]; + omega_dot[0] = list[n++]; + omega_dot[1] = list[n++]; + omega_dot[2] = list[n++]; + omega_dot[3] = list[n++]; + omega_dot[4] = list[n++]; + omega_dot[5] = list[n++]; + vol0 = list[n++]; + t0 = list[n++]; + int m = static_cast (list[n++]); + if (pstat_flag && m == mpchain) { + for (int ich = 0; ich < mpchain; ich++) + etap[ich] = list[n++]; + for (int ich = 0; ich < mpchain; ich++) + etap_dot[ich] = list[n++]; + } else n+=2*m; + flag = static_cast (list[n++]); + if (flag) { + h0_inv[0] = list[n++]; + h0_inv[1] = list[n++]; + h0_inv[2] = list[n++]; + h0_inv[3] = list[n++]; + h0_inv[4] = list[n++]; + h0_inv[5] = list[n++]; + } + } +} + +/* ---------------------------------------------------------------------- */ + +int FixCauchy::modify_param(int narg, char **arg) +{ + if (strcmp(arg[0],"temp") == 0) { + if (narg < 2) error->all(FLERR,"Illegal fix_modify command"); + if (tcomputeflag) { + modify->delete_compute(id_temp); + tcomputeflag = 0; + } + delete [] id_temp; + int n = strlen(arg[1]) + 1; + id_temp = new char[n]; + strcpy(id_temp,arg[1]); + + int icompute = modify->find_compute(arg[1]); + if (icompute < 0) + error->all(FLERR,"Could not find fix_modify temperature ID"); + temperature = modify->compute[icompute]; + + if (temperature->tempflag == 0) + error->all(FLERR, + "Fix_modify temperature ID does not compute temperature"); + if (temperature->igroup != 0 && comm->me == 0) + error->warning(FLERR,"Temperature for fix modify is not for group all"); + + // reset id_temp of pressure to new temperature ID + + if (pstat_flag) { + icompute = modify->find_compute(id_press); + if (icompute < 0) + error->all(FLERR,"Pressure ID for fix modify does not exist"); + modify->compute[icompute]->reset_extra_compute_fix(id_temp); + } + + return 2; + + } else if (strcmp(arg[0],"press") == 0) { + if (narg < 2) error->all(FLERR,"Illegal fix_modify command"); + if (!pstat_flag) error->all(FLERR,"Illegal fix_modify command"); + if (pcomputeflag) { + modify->delete_compute(id_press); + pcomputeflag = 0; + } + delete [] id_press; + int n = strlen(arg[1]) + 1; + id_press = new char[n]; + strcpy(id_press,arg[1]); + + int icompute = modify->find_compute(arg[1]); + if (icompute < 0) error->all(FLERR,"Could not find fix_modify pressure ID"); + pressure = modify->compute[icompute]; + + if (pressure->pressflag == 0) + error->all(FLERR,"Fix_modify pressure ID does not compute pressure"); + return 2; + } + + return 0; +} + +/* ---------------------------------------------------------------------- */ + +double FixCauchy::compute_scalar() +{ + int i; + double volume; + double energy; + double kt = boltz * t_target; + double lkt_press = 0.0; + int ich; + if (dimension == 3) volume = domain->xprd * domain->yprd * domain->zprd; + else volume = domain->xprd * domain->yprd; + + energy = 0.0; + + // thermostat chain energy is equivalent to Eq. (2) in + // Martyna, Tuckerman, Tobias, Klein, Mol Phys, 87, 1117 + // Sum(0.5*p_eta_k^2/Q_k,k=1,M) + L*k*T*eta_1 + Sum(k*T*eta_k,k=2,M), + // where L = tdof + // M = mtchain + // p_eta_k = Q_k*eta_dot[k-1] + // Q_1 = L*k*T/t_freq^2 + // Q_k = k*T/t_freq^2, k > 1 + + if (tstat_flag) { + energy += ke_target * eta[0] + 0.5*eta_mass[0]*eta_dot[0]*eta_dot[0]; + for (ich = 1; ich < mtchain; ich++) + energy += kt * eta[ich] + 0.5*eta_mass[ich]*eta_dot[ich]*eta_dot[ich]; + } + + // barostat energy is equivalent to Eq. (8) in + // Martyna, Tuckerman, Tobias, Klein, Mol Phys, 87, 1117 + // Sum(0.5*p_omega^2/W + P*V), + // where N = natoms + // p_omega = W*omega_dot + // W = N*k*T/p_freq^2 + // sum is over barostatted dimensions + + if (pstat_flag) { + for (i = 0; i < 3; i++) { + if (p_flag[i]) { + energy += 0.5*omega_dot[i]*omega_dot[i]*omega_mass[i] + + p_hydro*(volume-vol0) / (pdim*nktv2p); + lkt_press += kt; + } + } + + if (pstyle == TRICLINIC) { + for (i = 3; i < 6; i++) { + if (p_flag[i]) { + energy += 0.5*omega_dot[i]*omega_dot[i]*omega_mass[i]; + lkt_press += kt; + } + } + } + + // extra contributions from thermostat chain for barostat + + if (mpchain) { + energy += lkt_press * etap[0] + 0.5*etap_mass[0]*etap_dot[0]*etap_dot[0]; + for (ich = 1; ich < mpchain; ich++) + energy += kt * etap[ich] + + 0.5*etap_mass[ich]*etap_dot[ich]*etap_dot[ich]; + } + + // extra contribution from strain energy + + if (deviatoric_flag) energy += compute_strain_energy(); + } + + return energy; +} + +/* ---------------------------------------------------------------------- + return a single element of the following vectors, in this order: + eta[tchain], eta_dot[tchain], omega[ndof], omega_dot[ndof] + etap[pchain], etap_dot[pchain], PE_eta[tchain], KE_eta_dot[tchain] + PE_omega[ndof], KE_omega_dot[ndof], PE_etap[pchain], KE_etap_dot[pchain] + PE_strain[1] + if no thermostat exists, related quantities are omitted from the list + if no barostat exists, related quantities are omitted from the list + ndof = 1,3,6 degrees of freedom for pstyle = ISO,ANISO,TRI +------------------------------------------------------------------------- */ + +double FixCauchy::compute_vector(int n) +{ + int ilen; + + if (tstat_flag) { + ilen = mtchain; + if (n < ilen) return eta[n]; + n -= ilen; + ilen = mtchain; + if (n < ilen) return eta_dot[n]; + n -= ilen; + } + + if (pstat_flag) { + if (pstyle == ISO) { + ilen = 1; + if (n < ilen) return omega[n]; + n -= ilen; + } else if (pstyle == ANISO) { + ilen = 3; + if (n < ilen) return omega[n]; + n -= ilen; + } else { + ilen = 6; + if (n < ilen) return omega[n]; + n -= ilen; + } + + if (pstyle == ISO) { + ilen = 1; + if (n < ilen) return omega_dot[n]; + n -= ilen; + } else if (pstyle == ANISO) { + ilen = 3; + if (n < ilen) return omega_dot[n]; + n -= ilen; + } else { + ilen = 6; + if (n < ilen) return omega_dot[n]; + n -= ilen; + } + + if (mpchain) { + ilen = mpchain; + if (n < ilen) return etap[n]; + n -= ilen; + ilen = mpchain; + if (n < ilen) return etap_dot[n]; + n -= ilen; + } + } + + double volume; + double kt = boltz * t_target; + double lkt_press = kt; + int ich; + if (dimension == 3) volume = domain->xprd * domain->yprd * domain->zprd; + else volume = domain->xprd * domain->yprd; + + if (tstat_flag) { + ilen = mtchain; + if (n < ilen) { + ich = n; + if (ich == 0) + return ke_target * eta[0]; + else + return kt * eta[ich]; + } + n -= ilen; + ilen = mtchain; + if (n < ilen) { + ich = n; + if (ich == 0) + return 0.5*eta_mass[0]*eta_dot[0]*eta_dot[0]; + else + return 0.5*eta_mass[ich]*eta_dot[ich]*eta_dot[ich]; + } + n -= ilen; + } + + if (pstat_flag) { + if (pstyle == ISO) { + ilen = 1; + if (n < ilen) + return p_hydro*(volume-vol0) / nktv2p; + n -= ilen; + } else if (pstyle == ANISO) { + ilen = 3; + if (n < ilen) { + if (p_flag[n]) + return p_hydro*(volume-vol0) / (pdim*nktv2p); + else + return 0.0; + } + n -= ilen; + } else { + ilen = 6; + if (n < ilen) { + if (n > 2) return 0.0; + else if (p_flag[n]) + return p_hydro*(volume-vol0) / (pdim*nktv2p); + else + return 0.0; + } + n -= ilen; + } + + if (pstyle == ISO) { + ilen = 1; + if (n < ilen) + return pdim*0.5*omega_dot[n]*omega_dot[n]*omega_mass[n]; + n -= ilen; + } else if (pstyle == ANISO) { + ilen = 3; + if (n < ilen) { + if (p_flag[n]) + return 0.5*omega_dot[n]*omega_dot[n]*omega_mass[n]; + else return 0.0; + } + n -= ilen; + } else { + ilen = 6; + if (n < ilen) { + if (p_flag[n]) + return 0.5*omega_dot[n]*omega_dot[n]*omega_mass[n]; + else return 0.0; + } + n -= ilen; + } + + if (mpchain) { + ilen = mpchain; + if (n < ilen) { + ich = n; + if (ich == 0) return lkt_press * etap[0]; + else return kt * etap[ich]; + } + n -= ilen; + ilen = mpchain; + if (n < ilen) { + ich = n; + if (ich == 0) + return 0.5*etap_mass[0]*etap_dot[0]*etap_dot[0]; + else + return 0.5*etap_mass[ich]*etap_dot[ich]*etap_dot[ich]; + } + n -= ilen; + } + + if (deviatoric_flag) { + ilen = 1; + if (n < ilen) + return compute_strain_energy(); + n -= ilen; + } + } + + return 0.0; +} + +/* ---------------------------------------------------------------------- */ + +void FixCauchy::reset_target(double t_new) +{ + t_target = t_start = t_stop = t_new; +} + +/* ---------------------------------------------------------------------- */ + +void FixCauchy::reset_dt() +{ + dtv = update->dt; + dtf = 0.5 * update->dt * force->ftm2v; + dthalf = 0.5 * update->dt; + dt4 = 0.25 * update->dt; + dt8 = 0.125 * update->dt; + dto = dthalf; + + // If using respa, then remap is performed in innermost level + + if (strstr(update->integrate_style,"respa")) + dto = 0.5*step_respa[0]; + + if (pstat_flag) + pdrag_factor = 1.0 - (update->dt * p_freq_max * drag / nc_pchain); + + if (tstat_flag) + tdrag_factor = 1.0 - (update->dt * t_freq * drag / nc_tchain); +} + +/* ---------------------------------------------------------------------- + extract thermostat properties +------------------------------------------------------------------------- */ + +void *FixCauchy::extract(const char *str, int &dim) +{ + dim=0; + if (tstat_flag && strcmp(str,"t_target") == 0) { + return &t_target; + } else if (tstat_flag && strcmp(str,"t_start") == 0) { + return &t_start; + } else if (tstat_flag && strcmp(str,"t_stop") == 0) { + return &t_stop; + } else if (tstat_flag && strcmp(str,"mtchain") == 0) { + return &mtchain; + } else if (pstat_flag && strcmp(str,"mpchain") == 0) { + return &mtchain; + } + dim=1; + if (tstat_flag && strcmp(str,"eta") == 0) { + return η + } else if (pstat_flag && strcmp(str,"etap") == 0) { + return η + } else if (pstat_flag && strcmp(str,"p_flag") == 0) { + return &p_flag; + } else if (pstat_flag && strcmp(str,"p_start") == 0) { + return &p_start; + } else if (pstat_flag && strcmp(str,"p_stop") == 0) { + return &p_stop; + } else if (pstat_flag && strcmp(str,"p_target") == 0) { + return &p_target; + } + return NULL; +} + +/* ---------------------------------------------------------------------- + perform half-step update of chain thermostat variables +------------------------------------------------------------------------- */ + +void FixCauchy::nhc_temp_integrate() +{ + int ich; + double expfac; + double kecurrent = tdof * boltz * t_current; + + // Update masses, to preserve initial freq, if flag set + + if (eta_mass_flag) { + eta_mass[0] = tdof * boltz * t_target / (t_freq*t_freq); + for (int ich = 1; ich < mtchain; ich++) + eta_mass[ich] = boltz * t_target / (t_freq*t_freq); + } + + if (eta_mass[0] > 0.0) + eta_dotdot[0] = (kecurrent - ke_target)/eta_mass[0]; + else eta_dotdot[0] = 0.0; + + double ncfac = 1.0/nc_tchain; + for (int iloop = 0; iloop < nc_tchain; iloop++) { + + for (ich = mtchain-1; ich > 0; ich--) { + expfac = exp(-ncfac*dt8*eta_dot[ich+1]); + eta_dot[ich] *= expfac; + eta_dot[ich] += eta_dotdot[ich] * ncfac*dt4; + eta_dot[ich] *= tdrag_factor; + eta_dot[ich] *= expfac; + } + + expfac = exp(-ncfac*dt8*eta_dot[1]); + eta_dot[0] *= expfac; + eta_dot[0] += eta_dotdot[0] * ncfac*dt4; + eta_dot[0] *= tdrag_factor; + eta_dot[0] *= expfac; + + factor_eta = exp(-ncfac*dthalf*eta_dot[0]); + nh_v_temp(); + + // rescale temperature due to velocity scaling + // should not be necessary to explicitly recompute the temperature + + t_current *= factor_eta*factor_eta; + kecurrent = tdof * boltz * t_current; + + if (eta_mass[0] > 0.0) + eta_dotdot[0] = (kecurrent - ke_target)/eta_mass[0]; + else eta_dotdot[0] = 0.0; + + for (ich = 0; ich < mtchain; ich++) + eta[ich] += ncfac*dthalf*eta_dot[ich]; + + eta_dot[0] *= expfac; + eta_dot[0] += eta_dotdot[0] * ncfac*dt4; + eta_dot[0] *= expfac; + + for (ich = 1; ich < mtchain; ich++) { + expfac = exp(-ncfac*dt8*eta_dot[ich+1]); + eta_dot[ich] *= expfac; + eta_dotdot[ich] = (eta_mass[ich-1]*eta_dot[ich-1]*eta_dot[ich-1] + - boltz * t_target)/eta_mass[ich]; + eta_dot[ich] += eta_dotdot[ich] * ncfac*dt4; + eta_dot[ich] *= expfac; + } + } +} + +/* ---------------------------------------------------------------------- + perform half-step update of chain thermostat variables for barostat + scale barostat velocities +------------------------------------------------------------------------- */ + +void FixCauchy::nhc_press_integrate() +{ + int ich,i,pdof; + double expfac,factor_etap,kecurrent; + double kt = boltz * t_target; + double lkt_press; + + // Update masses, to preserve initial freq, if flag set + + if (omega_mass_flag) { + double nkt = (atom->natoms + 1) * kt; + for (int i = 0; i < 3; i++) + if (p_flag[i]) + omega_mass[i] = nkt/(p_freq[i]*p_freq[i]); + + if (pstyle == TRICLINIC) { + for (int i = 3; i < 6; i++) + if (p_flag[i]) omega_mass[i] = nkt/(p_freq[i]*p_freq[i]); + } + } + + if (etap_mass_flag) { + if (mpchain) { + etap_mass[0] = boltz * t_target / (p_freq_max*p_freq_max); + for (int ich = 1; ich < mpchain; ich++) + etap_mass[ich] = boltz * t_target / (p_freq_max*p_freq_max); + for (int ich = 1; ich < mpchain; ich++) + etap_dotdot[ich] = + (etap_mass[ich-1]*etap_dot[ich-1]*etap_dot[ich-1] - + boltz * t_target) / etap_mass[ich]; + } + } + + kecurrent = 0.0; + pdof = 0; + for (i = 0; i < 3; i++) + if (p_flag[i]) { + kecurrent += omega_mass[i]*omega_dot[i]*omega_dot[i]; + pdof++; + } + + if (pstyle == TRICLINIC) { + for (i = 3; i < 6; i++) + if (p_flag[i]) { + kecurrent += omega_mass[i]*omega_dot[i]*omega_dot[i]; + pdof++; + } + } + + lkt_press = pdof * kt; + etap_dotdot[0] = (kecurrent - lkt_press)/etap_mass[0]; + + double ncfac = 1.0/nc_pchain; + for (int iloop = 0; iloop < nc_pchain; iloop++) { + + for (ich = mpchain-1; ich > 0; ich--) { + expfac = exp(-ncfac*dt8*etap_dot[ich+1]); + etap_dot[ich] *= expfac; + etap_dot[ich] += etap_dotdot[ich] * ncfac*dt4; + etap_dot[ich] *= pdrag_factor; + etap_dot[ich] *= expfac; + } + + expfac = exp(-ncfac*dt8*etap_dot[1]); + etap_dot[0] *= expfac; + etap_dot[0] += etap_dotdot[0] * ncfac*dt4; + etap_dot[0] *= pdrag_factor; + etap_dot[0] *= expfac; + + for (ich = 0; ich < mpchain; ich++) + etap[ich] += ncfac*dthalf*etap_dot[ich]; + + factor_etap = exp(-ncfac*dthalf*etap_dot[0]); + for (i = 0; i < 3; i++) + if (p_flag[i]) omega_dot[i] *= factor_etap; + + if (pstyle == TRICLINIC) { + for (i = 3; i < 6; i++) + if (p_flag[i]) omega_dot[i] *= factor_etap; + } + + kecurrent = 0.0; + for (i = 0; i < 3; i++) + if (p_flag[i]) kecurrent += omega_mass[i]*omega_dot[i]*omega_dot[i]; + + if (pstyle == TRICLINIC) { + for (i = 3; i < 6; i++) + if (p_flag[i]) kecurrent += omega_mass[i]*omega_dot[i]*omega_dot[i]; + } + + etap_dotdot[0] = (kecurrent - lkt_press)/etap_mass[0]; + + etap_dot[0] *= expfac; + etap_dot[0] += etap_dotdot[0] * ncfac*dt4; + etap_dot[0] *= expfac; + + for (ich = 1; ich < mpchain; ich++) { + expfac = exp(-ncfac*dt8*etap_dot[ich+1]); + etap_dot[ich] *= expfac; + etap_dotdot[ich] = + (etap_mass[ich-1]*etap_dot[ich-1]*etap_dot[ich-1] - boltz*t_target) / + etap_mass[ich]; + etap_dot[ich] += etap_dotdot[ich] * ncfac*dt4; + etap_dot[ich] *= expfac; + } + } +} + +/* ---------------------------------------------------------------------- + perform half-step barostat scaling of velocities +-----------------------------------------------------------------------*/ + +void FixCauchy::nh_v_press() +{ + double factor[3]; + double **v = atom->v; + int *mask = atom->mask; + int nlocal = atom->nlocal; + if (igroup == atom->firstgroup) nlocal = atom->nfirst; + + factor[0] = exp(-dt4*(omega_dot[0]+mtk_term2)); + factor[1] = exp(-dt4*(omega_dot[1]+mtk_term2)); + factor[2] = exp(-dt4*(omega_dot[2]+mtk_term2)); + + if (which == NOBIAS) { + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + v[i][0] *= factor[0]; + v[i][1] *= factor[1]; + v[i][2] *= factor[2]; + if (pstyle == TRICLINIC) { + v[i][0] += -dthalf*(v[i][1]*omega_dot[5] + v[i][2]*omega_dot[4]); + v[i][1] += -dthalf*v[i][2]*omega_dot[3]; + } + v[i][0] *= factor[0]; + v[i][1] *= factor[1]; + v[i][2] *= factor[2]; + } + } + } else if (which == BIAS) { + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + temperature->remove_bias(i,v[i]); + v[i][0] *= factor[0]; + v[i][1] *= factor[1]; + v[i][2] *= factor[2]; + if (pstyle == TRICLINIC) { + v[i][0] += -dthalf*(v[i][1]*omega_dot[5] + v[i][2]*omega_dot[4]); + v[i][1] += -dthalf*v[i][2]*omega_dot[3]; + } + v[i][0] *= factor[0]; + v[i][1] *= factor[1]; + v[i][2] *= factor[2]; + temperature->restore_bias(i,v[i]); + } + } + } +} + +/* ---------------------------------------------------------------------- + perform half-step update of velocities +-----------------------------------------------------------------------*/ + +void FixCauchy::nve_v() +{ + double dtfm; + double **v = atom->v; + double **f = atom->f; + double *rmass = atom->rmass; + double *mass = atom->mass; + int *type = atom->type; + int *mask = atom->mask; + int nlocal = atom->nlocal; + if (igroup == atom->firstgroup) nlocal = atom->nfirst; + + if (rmass) { + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + dtfm = dtf / rmass[i]; + v[i][0] += dtfm*f[i][0]; + v[i][1] += dtfm*f[i][1]; + v[i][2] += dtfm*f[i][2]; + } + } + } else { + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + dtfm = dtf / mass[type[i]]; + v[i][0] += dtfm*f[i][0]; + v[i][1] += dtfm*f[i][1]; + v[i][2] += dtfm*f[i][2]; + } + } + } +} + +/* ---------------------------------------------------------------------- + perform full-step update of positions +-----------------------------------------------------------------------*/ + +void FixCauchy::nve_x() +{ + double **x = atom->x; + double **v = atom->v; + int *mask = atom->mask; + int nlocal = atom->nlocal; + if (igroup == atom->firstgroup) nlocal = atom->nfirst; + + // x update by full step only for atoms in group + + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + x[i][0] += dtv * v[i][0]; + x[i][1] += dtv * v[i][1]; + x[i][2] += dtv * v[i][2]; + } + } +} + +/* ---------------------------------------------------------------------- + perform half-step thermostat scaling of velocities +-----------------------------------------------------------------------*/ + +void FixCauchy::nh_v_temp() +{ + double **v = atom->v; + int *mask = atom->mask; + int nlocal = atom->nlocal; + if (igroup == atom->firstgroup) nlocal = atom->nfirst; + + if (which == NOBIAS) { + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + v[i][0] *= factor_eta; + v[i][1] *= factor_eta; + v[i][2] *= factor_eta; + } + } + } else if (which == BIAS) { + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + temperature->remove_bias(i,v[i]); + v[i][0] *= factor_eta; + v[i][1] *= factor_eta; + v[i][2] *= factor_eta; + temperature->restore_bias(i,v[i]); + } + } + } +} + +/* ---------------------------------------------------------------------- + compute sigma tensor + needed whenever p_target or h0_inv changes +-----------------------------------------------------------------------*/ + +void FixCauchy::compute_sigma() +{ + // if nreset_h0 > 0, reset vol0 and h0_inv + // every nreset_h0 timesteps + + if (nreset_h0 > 0) { + int delta = update->ntimestep - update->beginstep; + if (delta % nreset_h0 == 0) { + if (dimension == 3) vol0 = domain->xprd * domain->yprd * domain->zprd; + else vol0 = domain->xprd * domain->yprd; + h0_inv[0] = domain->h_inv[0]; + h0_inv[1] = domain->h_inv[1]; + h0_inv[2] = domain->h_inv[2]; + h0_inv[3] = domain->h_inv[3]; + h0_inv[4] = domain->h_inv[4]; + h0_inv[5] = domain->h_inv[5]; + } + } + + // generate upper-triangular half of + // sigma = vol0*h0inv*(p_target-p_hydro)*h0inv^t + // units of sigma are are PV/L^2 e.g. atm.A + // + // [ 0 5 4 ] [ 0 5 4 ] [ 0 5 4 ] [ 0 - - ] + // [ 5 1 3 ] = [ - 1 3 ] [ 5 1 3 ] [ 5 1 - ] + // [ 4 3 2 ] [ - - 2 ] [ 4 3 2 ] [ 4 3 2 ] + + sigma[0] = + vol0*(h0_inv[0]*((p_target[0]-p_hydro)*h0_inv[0] + + p_target[5]*h0_inv[5]+p_target[4]*h0_inv[4]) + + h0_inv[5]*(p_target[5]*h0_inv[0] + + (p_target[1]-p_hydro)*h0_inv[5]+p_target[3]*h0_inv[4]) + + h0_inv[4]*(p_target[4]*h0_inv[0]+p_target[3]*h0_inv[5] + + (p_target[2]-p_hydro)*h0_inv[4])); + sigma[1] = + vol0*(h0_inv[1]*((p_target[1]-p_hydro)*h0_inv[1] + + p_target[3]*h0_inv[3]) + + h0_inv[3]*(p_target[3]*h0_inv[1] + + (p_target[2]-p_hydro)*h0_inv[3])); + sigma[2] = + vol0*(h0_inv[2]*((p_target[2]-p_hydro)*h0_inv[2])); + sigma[3] = + vol0*(h0_inv[1]*(p_target[3]*h0_inv[2]) + + h0_inv[3]*((p_target[2]-p_hydro)*h0_inv[2])); + sigma[4] = + vol0*(h0_inv[0]*(p_target[4]*h0_inv[2]) + + h0_inv[5]*(p_target[3]*h0_inv[2]) + + h0_inv[4]*((p_target[2]-p_hydro)*h0_inv[2])); + sigma[5] = + vol0*(h0_inv[0]*(p_target[5]*h0_inv[1]+p_target[4]*h0_inv[3]) + + h0_inv[5]*((p_target[1]-p_hydro)*h0_inv[1]+p_target[3]*h0_inv[3]) + + h0_inv[4]*(p_target[3]*h0_inv[1]+(p_target[2]-p_hydro)*h0_inv[3])); +} + +/* ---------------------------------------------------------------------- + compute strain energy +-----------------------------------------------------------------------*/ + +double FixCauchy::compute_strain_energy() +{ + // compute strain energy = 0.5*Tr(sigma*h*h^t) in energy units + + double* h = domain->h; + double d0,d1,d2; + + d0 = + sigma[0]*(h[0]*h[0]+h[5]*h[5]+h[4]*h[4]) + + sigma[5]*( h[1]*h[5]+h[3]*h[4]) + + sigma[4]*( h[2]*h[4]); + d1 = + sigma[5]*( h[5]*h[1]+h[4]*h[3]) + + sigma[1]*( h[1]*h[1]+h[3]*h[3]) + + sigma[3]*( h[2]*h[3]); + d2 = + sigma[4]*( h[4]*h[2]) + + sigma[3]*( h[3]*h[2]) + + sigma[2]*( h[2]*h[2]); + + double energy = 0.5*(d0+d1+d2)/nktv2p; + return energy; +} + +/* ---------------------------------------------------------------------- + compute deviatoric barostat force = h*sigma*h^t +-----------------------------------------------------------------------*/ + +void FixCauchy::compute_deviatoric() +{ + // generate upper-triangular part of h*sigma*h^t + // units of fdev are are PV, e.g. atm*A^3 + // [ 0 5 4 ] [ 0 5 4 ] [ 0 5 4 ] [ 0 - - ] + // [ 5 1 3 ] = [ - 1 3 ] [ 5 1 3 ] [ 5 1 - ] + // [ 4 3 2 ] [ - - 2 ] [ 4 3 2 ] [ 4 3 2 ] + + double* h = domain->h; + + fdev[0] = + h[0]*(sigma[0]*h[0]+sigma[5]*h[5]+sigma[4]*h[4]) + + h[5]*(sigma[5]*h[0]+sigma[1]*h[5]+sigma[3]*h[4]) + + h[4]*(sigma[4]*h[0]+sigma[3]*h[5]+sigma[2]*h[4]); + fdev[1] = + h[1]*( sigma[1]*h[1]+sigma[3]*h[3]) + + h[3]*( sigma[3]*h[1]+sigma[2]*h[3]); + fdev[2] = + h[2]*( sigma[2]*h[2]); + fdev[3] = + h[1]*( sigma[3]*h[2]) + + h[3]*( sigma[2]*h[2]); + fdev[4] = + h[0]*( sigma[4]*h[2]) + + h[5]*( sigma[3]*h[2]) + + h[4]*( sigma[2]*h[2]); + fdev[5] = + h[0]*( sigma[5]*h[1]+sigma[4]*h[3]) + + h[5]*( sigma[1]*h[1]+sigma[3]*h[3]) + + h[4]*( sigma[3]*h[1]+sigma[2]*h[3]); +} + +/* ---------------------------------------------------------------------- + compute target temperature and kinetic energy +-----------------------------------------------------------------------*/ + +void FixCauchy::compute_temp_target() +{ + double delta = update->ntimestep - update->beginstep; + if (delta != 0.0) delta /= update->endstep - update->beginstep; + + t_target = t_start + delta * (t_stop-t_start); + ke_target = tdof * boltz * t_target; +} + +/* ---------------------------------------------------------------------- + compute hydrostatic target pressure +-----------------------------------------------------------------------*/ + +void FixCauchy::compute_press_target() +{ + double delta = update->ntimestep - update->beginstep; + if (delta != 0.0) delta /= update->endstep - update->beginstep; + + p_hydro = 0.0; + for (int i = 0; i < 3; i++) + if (p_flag[i]) { + p_target[i] = p_start[i] + delta * (p_stop[i]-p_start[i]); + p_hydro += p_target[i]; + } + if (pdim > 0) p_hydro /= pdim; + + if (pstyle == TRICLINIC) + for (int i = 3; i < 6; i++) + p_target[i] = p_start[i] + delta * (p_stop[i]-p_start[i]); + + // CauchyStat: call CauchyStat to modify p_target[i] and p_hydro, + // if CauchyStat enabled and pressure->vector computation has been initiated + + if ((usePK == 0) && (initRUN == 1)) CauchyStat(); + if (initRUN == 0) { + for (int i=0; i < 6; i++) { + h_old[i]=domain->h[i]; + } + } + + // when run is initialized tensor[] not available (pressure on cell wall) + + initRUN=1; + + // if deviatoric, recompute sigma each time p_target changes + + if (deviatoric_flag) compute_sigma(); +} + +/* ---------------------------------------------------------------------- + update omega_dot, omega +-----------------------------------------------------------------------*/ + +void FixCauchy::nh_omega_dot() +{ + double f_omega,volume; + + if (dimension == 3) volume = domain->xprd*domain->yprd*domain->zprd; + else volume = domain->xprd*domain->yprd; + + if (deviatoric_flag) compute_deviatoric(); + + mtk_term1 = 0.0; + if (mtk_flag) { + if (pstyle == ISO) { + mtk_term1 = tdof * boltz * t_current; + mtk_term1 /= pdim * atom->natoms; + } else { + double *mvv_current = temperature->vector; + for (int i = 0; i < 3; i++) + if (p_flag[i]) + mtk_term1 += mvv_current[i]; + mtk_term1 /= pdim * atom->natoms; + } + } + + for (int i = 0; i < 3; i++) + if (p_flag[i]) { + f_omega = (p_current[i]-p_hydro)*volume / + (omega_mass[i] * nktv2p) + mtk_term1 / omega_mass[i]; + if (deviatoric_flag) f_omega -= fdev[i]/(omega_mass[i] * nktv2p); + omega_dot[i] += f_omega*dthalf; + omega_dot[i] *= pdrag_factor; + } + + mtk_term2 = 0.0; + if (mtk_flag) { + for (int i = 0; i < 3; i++) + if (p_flag[i]) + mtk_term2 += omega_dot[i]; + if (pdim > 0) mtk_term2 /= pdim * atom->natoms; + } + + if (pstyle == TRICLINIC) { + for (int i = 3; i < 6; i++) { + if (p_flag[i]) { + f_omega = p_current[i]*volume/(omega_mass[i] * nktv2p); + if (deviatoric_flag) + f_omega -= fdev[i]/(omega_mass[i] * nktv2p); + omega_dot[i] += f_omega*dthalf; + omega_dot[i] *= pdrag_factor; + } + } + } +} + +/* ---------------------------------------------------------------------- + if any tilt ratios exceed limits, set flip = 1 and compute new tilt values + do not flip in x or y if non-periodic (can tilt but not flip) + this is b/c the box length would be changed (dramatically) by flip + if yz tilt exceeded, adjust C vector by one B vector + if xz tilt exceeded, adjust C vector by one A vector + if xy tilt exceeded, adjust B vector by one A vector + check yz first since it may change xz, then xz check comes after + if any flip occurs, create new box in domain + image_flip() adjusts image flags due to box shape change induced by flip + remap() puts atoms outside the new box back into the new box + perform irregular on atoms in lamda coords to migrate atoms to new procs + important that image_flip comes before remap, since remap may change + image flags to new values, making eqs in doc of Domain:image_flip incorrect +------------------------------------------------------------------------- */ + +void FixCauchy::pre_exchange() +{ + double xprd = domain->xprd; + double yprd = domain->yprd; + + // flip is only triggered when tilt exceeds 0.5 by DELTAFLIP + // this avoids immediate re-flipping due to tilt oscillations + + double xtiltmax = (0.5+DELTAFLIP)*xprd; + double ytiltmax = (0.5+DELTAFLIP)*yprd; + + int flipxy,flipxz,flipyz; + flipxy = flipxz = flipyz = 0; + + if (domain->yperiodic) { + if (domain->yz < -ytiltmax) { + domain->yz += yprd; + domain->xz += domain->xy; + flipyz = 1; + } else if (domain->yz >= ytiltmax) { + domain->yz -= yprd; + domain->xz -= domain->xy; + flipyz = -1; + } + } + + if (domain->xperiodic) { + if (domain->xz < -xtiltmax) { + domain->xz += xprd; + flipxz = 1; + } else if (domain->xz >= xtiltmax) { + domain->xz -= xprd; + flipxz = -1; + } + if (domain->xy < -xtiltmax) { + domain->xy += xprd; + flipxy = 1; + } else if (domain->xy >= xtiltmax) { + domain->xy -= xprd; + flipxy = -1; + } + } + + int flip = 0; + if (flipxy || flipxz || flipyz) flip = 1; + + if (flip) { + domain->set_global_box(); + domain->set_local_box(); + + domain->image_flip(flipxy,flipxz,flipyz); + + double **x = atom->x; + imageint *image = atom->image; + int nlocal = atom->nlocal; + for (int i = 0; i < nlocal; i++) domain->remap(x[i],image[i]); + + domain->x2lamda(atom->nlocal); + irregular->migrate_atoms(); + domain->lamda2x(atom->nlocal); + } +} + +/* ---------------------------------------------------------------------- + memory usage of Irregular +------------------------------------------------------------------------- */ + +double FixCauchy::memory_usage() +{ + double bytes = 0.0; + if (irregular) bytes += irregular->memory_usage(); + return bytes; +} + +/* ---------------------------------------------------------------------- + initialize Cauchystat +------------------------------------------------------------------------- */ + +void FixCauchy::CauchyStat_init() +{ + if (comm->me == 0) { + if (screen) { + fprintf(screen,"Using the Cauchystat fix with alpha=%f\n",alpha); + if (restartPK==1) { + fprintf(screen," (this is a continuation run)\n"); + } else { + fprintf(screen," (this is NOT a continuation run)\n"); + } + } + if (logfile) { + fprintf(logfile,"Using the Cauchystat with alpha=%f\n",alpha); + if (restartPK==1) { + fprintf(logfile," this is a continuation run\n"); + } else { + fprintf(logfile," this is NOT a continuation run\n"); + } + } + } + + if (!id_store) { + int n = strlen(id) + 14; + id_store = new char[n]; + strcpy(id_store,id); + strcat(id_store,"_FIX_NH_STORE"); + } + restart_stored = modify->find_fix(id_store); + + if (restartPK==1 && restart_stored < 0) + error->all(FLERR,"Illegal cauchystat command. Continuation run" + " must follow a previously equilibrated Cauchystat run"); + + if (alpha<=0.0) + error->all(FLERR,"Illegal cauchystat command: " + " Alpha cannot be zero or negative."); + + if (restart_stored < 0) { + char **newarg = new char *[6]; + newarg[0] = id_store; + newarg[1] = (char *) "all"; + newarg[2] = (char *) "STORE"; + newarg[3] = (char *) "global"; + newarg[4] = (char *) "1"; + newarg[5] = (char *) "6"; + modify->add_fix(6,newarg); + delete[] newarg; + restart_stored = modify->find_fix(id_store); + } + init_store = (FixStore *)modify->fix[restart_stored]; + + initRUN = 0; + initPK = 1; + +#define H0(row,col) (H0[(row-1)][(col-1)]) +#define invH0(row,col) (invH0[(row-1)][(col-1)]) + + // initialize H0 to current box shape + + double *h = domain->h; + double *h_inv = domain->h_inv; + + H0(1,1)=h[0]; H0(1,2)=h[5]; H0(1,3)=h[4]; + H0(2,1)=0.0; H0(2,2)=h[1]; H0(2,3)=h[3]; + H0(3,1)=0.0; H0(3,2)=0.0; H0(3,3)=h[2]; + + invH0(1,1)=h_inv[0]; invH0(1,2)=h_inv[5]; invH0(1,3)=h_inv[4]; + invH0(2,1)=0.0; invH0(2,2)=h_inv[1]; invH0(2,3)=h_inv[3]; + invH0(3,1)=0.0; invH0(3,2)=0.0; invH0(3,3)=h_inv[2]; + + CSvol0 = abs(MathExtra::det3(H0)); //find reference volume + +#undef H0 +#undef invH0 +} + +/* ---------------------------------------------------------------------- + cleanup when not using Cauchystat +------------------------------------------------------------------------- */ + +void FixCauchy::CauchyStat_cleanup() +{ + if (id_store) { + modify->delete_fix(id_store); + delete[] id_store; + } else { + int n = strlen(id) + 14; + id_store = new char[n]; + strcpy(id_store,id); + strcat(id_store,"_FIX_NH_STORE"); + modify->delete_fix(id_store); + delete[] id_store; + } + id_store = NULL; + restart_stored = -1; +} + +/* ---------------------------------------------------------------------- + Cauchystat +------------------------------------------------------------------------- */ + +void FixCauchy::CauchyStat() +{ + double* h = domain->h; // shape matrix in Voigt notation + double* h_rate = domain->h_rate; // rate of box size/shape change in Voigt notation + double H[3][3]; + double Hdot[3][3]; + +#define H(row,col) (H[(row-1)][(col-1)]) +#define Hdot(row,col) (Hdot[(row-1)][(col-1)]) +#define F(row,col) (F[(row-1)][(col-1)]) +#define Fi(row,col) (Fi[(row-1)][(col-1)]) +#define Fdot(row,col) (Fdot[(row-1)][(col-1)]) +#define invH0(row,col) (invH0[(row-1)][(col-1)]) +#define cauchy(row,col) (cauchy[(row-1)][(col-1)]) +#define setcauchy(row,col) (setcauchy[(row-1)][(col-1)]) +#define setPK(row,col) (setPK[(row-1)][(col-1)]) +#define sigmahat(row,col) (sigmahat[(row-1)][(col-1)]) + + H(1,1)=h[0]; H(1,2)=0.0; H(1,3)=0.0; + H(2,1)=0.0; H(2,2)=h[1]; H(2,3)=0.0; + H(3,1)=0.0; H(3,2)=0.0; H(3,3)=h[2]; + + for (int i=0;i<6;i++) { + h_rate[i]=(h[i]-h_old[i])/update->dt; + h_old[i]=h[i]; + } + + Hdot(1,1)=h_rate[0]; Hdot(1,2)=0.0; Hdot(1,3)=0.0; + Hdot(2,1)=0.0; Hdot(2,2)=h_rate[1]; Hdot(2,3)=0.0; + Hdot(3,1)=0.0; Hdot(3,2)=0.0; Hdot(3,3)=h_rate[2]; + + if (domain->triclinic) { + H(1,2)=h[5]; H(1,3)=h[4]; H(2,3)=h[3]; + Hdot(1,2)=h_rate[5]; Hdot(1,3)=h_rate[4]; Hdot(2,3)=h_rate[3]; + } + + double F[3][3]={{0.0,0.0,0.0},{0.0,0.0,0.0},{0.0,0.0,0.0}}; + double Fi[3][3]={{0.0,0.0,0.0},{0.0,0.0,0.0},{0.0,0.0,0.0}}; + double Fdot[3][3]={{0.0,0.0,0.0},{0.0,0.0,0.0},{0.0,0.0,0.0}}; + double J,vol; + + MathExtra::times3(H,invH0,F); + MathExtra::times3(Hdot,invH0,Fdot); + MathExtra::invert3(F,Fi); + J = MathExtra::det3(F); + vol=CSvol0*J; + + double deltat; + deltat = update->dt; //increment of time step + + // Current pressure on the cell boundaries: + //tensor: 0 1 2 3 4 5 + // x y z xy xz yz + + double *tensor = pressure->vector; + + double cauchy[3][3]; + cauchy(1,1)=-tensor[0]; cauchy(1,2)=0.0; cauchy(1,3)=0.0; + cauchy(2,1)=0.0; cauchy(2,2)=-tensor[1]; cauchy(2,3)=0.0; + cauchy(3,1)=0.0; cauchy(3,2)=0.0; cauchy(3,3)=-tensor[2]; + + if (domain->triclinic) { + cauchy(1,2)=-tensor[3]; cauchy(1,3)=-tensor[4]; + cauchy(2,1)=-tensor[3]; cauchy(2,3)=-tensor[5]; + cauchy(3,1)=-tensor[4]; cauchy(3,2)=-tensor[5]; + } + + // target pressure on the cell boundaries: + // p_target: 0 1 2 3 4 5 + // x y z yz xz xy + + double setcauchy[3][3]; + setcauchy(1,1)=-p_target[0]; setcauchy(1,2)=0.0; setcauchy(1,3)=0.0; + setcauchy(2,1)=0.0; setcauchy(2,2)=-p_target[1]; setcauchy(2,3)=0.0; + setcauchy(3,1)=0.0; setcauchy(3,2)=0.0; setcauchy(3,3)=-p_target[2]; + + if (domain->triclinic) { + setcauchy(1,2)=-p_target[5]; setcauchy(1,3)=-p_target[4]; + setcauchy(2,1)=-p_target[5]; setcauchy(2,3)=-p_target[3]; + setcauchy(3,1)=-p_target[4]; setcauchy(3,2)=-p_target[3]; + } + + //initialize: + if (initPK==1) { + if (restartPK==1) { + double *setPKinit = init_store->astore[0]; + setPK(1,1)=setPKinit[0]; setPK(1,2)=setPKinit[1]; setPK(1,3)=setPKinit[2]; + setPK(2,1)=setPKinit[1]; setPK(2,2)=setPKinit[3]; setPK(2,3)=setPKinit[4]; + setPK(3,1)=setPKinit[2]; setPK(3,2)=setPKinit[4]; setPK(3,3)=setPKinit[5]; + }else { + setPK(1,1)=cauchy(1,1); setPK(1,2)=cauchy(1,2); setPK(1,3)=cauchy(1,3); + setPK(2,1)=cauchy(2,1); setPK(2,2)=cauchy(2,2); setPK(2,3)=cauchy(2,3); + setPK(3,1)=cauchy(3,1); setPK(3,2)=cauchy(3,2); setPK(3,3)=cauchy(3,3); + } + initPK=0; + } + + CauchyStat_Step(Fi,Fdot,cauchy,setcauchy,setPK,vol,CSvol0,deltat,alpha); + + // use currentPK as new target: + // p_target: 0 1 2 3 4 5 + // x y z yz xz xy + + p_target[0]=-setPK(1,1); + p_target[1]=-setPK(2,2); + p_target[2]=-setPK(3,3); + if (pstyle == TRICLINIC) { + p_target[3]=-setPK(2,3); + p_target[4]=-setPK(1,3); + p_target[5]=-setPK(1,2); + } + + p_hydro = 0.0; + for (int i = 0; i < 3; i++) + if (p_flag[i]) { + p_hydro += p_target[i]; + } + p_hydro /= pdim; + + // save information for Cauchystat restart + double *setPKinit = init_store->astore[0]; + setPKinit[0] = setcauchy(1,1); + setPKinit[1] = setcauchy(1,2); + setPKinit[2] = setcauchy(1,3); + setPKinit[3] = setcauchy(2,2); + setPKinit[4] = setcauchy(2,3); + setPKinit[5] = setcauchy(3,3); + +#undef H +#undef Hdot +#undef F +#undef Fi +#undef Fdot +#undef invH0 +#undef cauchy +#undef setcauchy +#undef setPK +#undef sigmahat + +} + +/* ---------------------------------------------------------------------- + CauchyStat_Step + + Inputs: + Fi(3,3) : inverse of the deformation gradient + Fdot(3,3) : time derivative of the deformation gradient (velocity) + cauchy(3,3) : current cauchy stress tensor + setcauchy(3,3) : target cauchy stress tensor + alpha : parameter =0.01 + setPK(3,3) : current PK stress tensor, at initialization (time=0) setPK=cauchy + volume : current volume of the periodic box + volume0 : initial volume of the periodic box + deltat : simulation step increment + alpha : parameter + + Outputs: + setPK(3,3) : PK stress tensor at the next time step + ------------------------------------------------------------------------- */ + +void FixCauchy::CauchyStat_Step(double (&Fi)[3][3], double (&Fdot)[3][3], + double (&cauchy)[3][3], double (&setcauchy)[3][3], + double (&setPK)[3][3], double volume, + double volume0, double deltat, double alpha) +{ + + //macros to go from c to fortran style for arrays: +#define F(row,col) (F[(row-1)][(col-1)]) +#define Fi(row,col) (Fi[(row-1)][(col-1)]) +#define Fdot(row,col) (Fdot[(row-1)][(col-1)]) +#define cauchy(row,col) (cauchy[(row-1)][(col-1)]) +#define setcauchy(row,col) (setcauchy[(row-1)][(col-1)]) +#define setPK(row,col) (setPK[(row-1)][(col-1)]) +#define uv(row,col) (uv[(row-1)][(col-1)]) +#define deltastress(row) (deltastress[(row-1)]) +#define fdotvec(row) (fdotvec[(row-1)]) +#define dsdf(row,col) (dsdf[(row-1)][(col-1)]) +#define dsds(row,col) (dsds[(row-1)][(col-1)]) +#define deltaF(row) (deltaF[(row-1)]) +#define deltaPK(row) (deltaPK[(row-1)]) + + //initialize local variables: + int i,j,m,n; + + double deltastress[6],fdotvec[6]; + double dsdf[6][6]={0.0}; //zeroed, used in incremental form + double dsds[6][6]={0.0}; //zeroed, used in incremental form + double jac; + double deltaF[6]={0.0}; //zeroed, used in incremental form + double deltaPK[6]={0.0}; //zeroed, used in incremental form + + int uv[6][2]; + uv(1,1)=1; uv(1,2)=1; + uv(2,1)=2; uv(2,2)=2; + uv(3,1)=3; uv(3,2)=3; + uv(4,1)=2; uv(4,2)=3; + uv(5,1)=1; uv(5,2)=3; + uv(6,1)=1; uv(6,2)=2; + + for(int ii = 1;ii <= 6;ii++) { + i=uv(ii,1); + j=uv(ii,2); + deltastress(ii)=setcauchy(i,j)-cauchy(i,j); + if(ii>3) deltastress(ii)=deltastress(ii)*2.0; + fdotvec(ii)=Fdot(i,j)*deltat; + } + + for(int ii = 1;ii <= 6;ii++) { + i=uv(ii,1); + j=uv(ii,2); + for(int jj = 1;jj <= 6;jj++) { + m=uv(jj,1); + n=uv(jj,2); + dsds(ii,jj) = Fi(i,m)*Fi(j,n) + Fi(i,n)*Fi(j,m) + Fi(j,m)*Fi(i,n) + Fi(j,n)*Fi(i,m); + for(int l = 1;l <= 3;l++) { + for(int k = 1;k <= 3;k++) { + dsdf(ii,jj) = dsdf(ii,jj) + cauchy(k,l)* + ( Fi(i,k)*Fi(j,l)*Fi(n,m) - Fi(i,m)*Fi(j,l)*Fi(n,k) - Fi(i,k)*Fi(j,m)*Fi(n,l) ); + } + } + } + } + + jac=volume/volume0; + for(int ii = 1;ii <= 6;ii++) { + for(int jj = 1;jj <= 6;jj++) { + dsds(ii,jj)=dsds(ii,jj)*jac/4.0; + dsdf(ii,jj)=dsdf(ii,jj)*jac; + } + } + + for(int ii = 1;ii <= 6;ii++) { + for(int jj = 1;jj <= 6;jj++) { + deltaF(ii)=deltaF(ii)+dsdf(ii,jj)*fdotvec(jj); + } + } + + for(int ii = 1;ii <= 6;ii++) { + for(int jj = 1;jj <= 6;jj++) { + deltaPK(ii)=deltaPK(ii)+alpha*dsds(ii,jj)*deltastress(jj); + } + deltaPK(ii)=deltaPK(ii)+alpha*deltaF(ii); + } + + setPK(1,1)=setPK(1,1)+deltaPK(1); + setPK(2,2)=setPK(2,2)+deltaPK(2); + setPK(3,3)=setPK(3,3)+deltaPK(3); + setPK(2,3)=setPK(2,3)+deltaPK(4); + setPK(3,2)=setPK(3,2)+deltaPK(4); + setPK(1,3)=setPK(1,3)+deltaPK(5); + setPK(3,1)=setPK(3,1)+deltaPK(5); + setPK(1,2)=setPK(1,2)+deltaPK(6); + setPK(2,1)=setPK(2,1)+deltaPK(6); + +#undef F +#undef Fi +#undef Fdot +#undef cauchy +#undef setcauchy +#undef setPK +#undef uv +#undef deltastress +#undef fdotvec +#undef dsdf +#undef dsds +#undef deltaF +#undef deltaPK + +} diff --git a/src/USER-CAUCHY/fix_cauchy.h b/src/USER-CAUCHY/fix_cauchy.h new file mode 100644 index 0000000000..5f255dd459 --- /dev/null +++ b/src/USER-CAUCHY/fix_cauchy.h @@ -0,0 +1,310 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifndef LMP_FIX_CAUCHY_H +#define LMP_FIX_CAUCHY_H + +#include "fix.h" + +namespace LAMMPS_NS { + +class FixCauchy : public Fix { + public: + FixCauchy(class LAMMPS *, int, char **); + virtual void post_constructor(); + virtual ~FixCauchy(); + int setmask(); + virtual void init(); + virtual void setup(int); + virtual void initial_integrate(int); + virtual void final_integrate(); + void initial_integrate_respa(int, int, int); + void final_integrate_respa(int, int); + virtual void pre_exchange(); + double compute_scalar(); + virtual double compute_vector(int); + void write_restart(FILE *); + virtual int pack_restart_data(double *); // pack restart data + virtual void restart(char *); + int modify_param(int, char **); + void reset_target(double); + void reset_dt(); + virtual void *extract(const char*,int &); + double memory_usage(); + + protected: + int dimension,which; + double dtv,dtf,dthalf,dt4,dt8,dto; + double boltz,nktv2p,tdof; + double vol0; // reference volume + double t0; // reference temperature + // used for barostat mass + double t_start,t_stop; + double t_current,t_target,ke_target; + double t_freq; + + int tstat_flag; // 1 if control T + int pstat_flag; // 1 if control P + + int pstyle,pcouple,allremap; + int p_flag[6]; // 1 if control P on this dim, 0 if not + double p_start[6],p_stop[6]; + double p_freq[6],p_target[6]; + double omega[6],omega_dot[6]; + double omega_mass[6]; + double p_current[6]; + double drag,tdrag_factor; // drag factor on particle thermostat + double pdrag_factor; // drag factor on barostat + int kspace_flag; // 1 if KSpace invoked, 0 if not + int nrigid; // number of rigid fixes + int dilate_group_bit; // mask for dilation group + int *rfix; // indices of rigid fixes + char *id_dilate; // group name to dilate + class Irregular *irregular; // for migrating atoms after box flips + + int nlevels_respa; + double *step_respa; + + char *id_temp,*id_press; + class Compute *temperature,*pressure; + int tcomputeflag,pcomputeflag; // 1 = compute was created by fix + // 0 = created externally + + double *eta,*eta_dot; // chain thermostat for particles + double *eta_dotdot; + double *eta_mass; + int mtchain; // length of chain + int mtchain_default_flag; // 1 = mtchain is default + + double *etap; // chain thermostat for barostat + double *etap_dot; + double *etap_dotdot; + double *etap_mass; + int mpchain; // length of chain + + int mtk_flag; // 0 if using Hoover barostat + int pdim; // number of barostatted dims + double p_freq_max; // maximum barostat frequency + + double p_hydro; // hydrostatic target pressure + + int nc_tchain,nc_pchain; + double factor_eta; + double sigma[6]; // scaled target stress + double fdev[6]; // deviatoric force on barostat + int deviatoric_flag; // 0 if target stress tensor is hydrostatic + double h0_inv[6]; // h_inv of reference (zero strain) box + int nreset_h0; // interval for resetting h0 + + double mtk_term1,mtk_term2; // Martyna-Tobias-Klein corrections + + int eta_mass_flag; // 1 if eta_mass updated, 0 if not. + int omega_mass_flag; // 1 if omega_mass updated, 0 if not. + int etap_mass_flag; // 1 if etap_mass updated, 0 if not. + int dipole_flag; // 1 if dipole is updated, 0 if not. + int dlm_flag; // 1 if using the DLM rotational integrator, 0 if not + + int scaleyz; // 1 if yz scaled with lz + int scalexz; // 1 if xz scaled with lz + int scalexy; // 1 if xy scaled with ly + int flipflag; // 1 if box flips are invoked as needed + + int pre_exchange_flag; // set if pre_exchange needed for box flips + + double fixedpoint[3]; // location of dilation fixed-point + + void couple(); + virtual void remap(); + void nhc_temp_integrate(); + void nhc_press_integrate(); + + virtual void nve_x(); // may be overwritten by child classes + virtual void nve_v(); + virtual void nh_v_press(); + virtual void nh_v_temp(); + virtual void compute_temp_target(); + virtual int size_restart_global(); + + void compute_sigma(); + void compute_deviatoric(); + double compute_strain_energy(); + void compute_press_target(); + void nh_omega_dot(); + + // Implementation of CauchyStat + char *id_store; // fix id of the STORE fix for retaining data + class FixStore *init_store; // fix pointer to STORE fix + double H0[3][3]; // shape matrix for the undeformed cell + double h_old[6]; // previous time step shape matrix for + // the undeformed cell + double invH0[3][3]; // inverse of H0; + double CSvol0; // volume of undeformed cell + double setPK[3][3]; // current set values of the PK stress + // (this is modified until the cauchy + // stress converges) + double alpha; // integration parameter for the cauchystat + int initPK; // 1 if setPK needs to be initialized either + // from cauchy or restart, else 0 + int usePK; // 0 if use CauchyStat else 1 + int restartPK; // Read PK stress from the previous run + int restart_stored; // values of PK stress from the previous step stored + int initRUN; // 0 if run not initialized + // (pressure->vector not computed yet), + // else 1 (pressure->vector available) + + void CauchyStat_init(); + void CauchyStat_cleanup(); + void CauchyStat(); + void CauchyStat_Step(double (&Fi)[3][3], double (&Fdot)[3][3], + double (&cauchy)[3][3], double (&setcauchy)[3][3], + double (&setPK)[3][3], double volume, double volume0, + double deltat, double alpha); + +}; + +} + +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: Target temperature for fix nvt/npt/nph cannot be 0.0 + +Self-explanatory. + +E: Invalid fix nvt/npt/nph command for a 2d simulation + +Cannot control z dimension in a 2d model. + +E: Fix nvt/npt/nph dilate group ID does not exist + +Self-explanatory. + +E: Invalid fix nvt/npt/nph command pressure settings + +If multiple dimensions are coupled, those dimensions must be +specified. + +E: Cannot use fix nvt/npt/nph on a non-periodic dimension + +When specifying a diagonal pressure component, the dimension must be +periodic. + +E: Cannot use fix nvt/npt/nph on a 2nd non-periodic dimension + +When specifying an off-diagonal pressure component, the 2nd of the two +dimensions must be periodic. E.g. if the xy component is specified, +then the y dimension must be periodic. + +E: Cannot use fix nvt/npt/nph with yz scaling when z is non-periodic dimension + +The 2nd dimension in the barostatted tilt factor must be periodic. + +E: Cannot use fix nvt/npt/nph with xz scaling when z is non-periodic dimension + +The 2nd dimension in the barostatted tilt factor must be periodic. + +E: Cannot use fix nvt/npt/nph with xy scaling when y is non-periodic dimension + +The 2nd dimension in the barostatted tilt factor must be periodic. + +E: Cannot use fix nvt/npt/nph with both yz dynamics and yz scaling + +Self-explanatory. + +E: Cannot use fix nvt/npt/nph with both xz dynamics and xz scaling + +Self-explanatory. + +E: Cannot use fix nvt/npt/nph with both xy dynamics and xy scaling + +Self-explanatory. + +E: Can not specify Pxy/Pxz/Pyz in fix nvt/npt/nph with non-triclinic box + +Only triclinic boxes can be used with off-diagonal pressure components. +See the region prism command for details. + +E: Invalid fix nvt/npt/nph pressure settings + +Settings for coupled dimensions must be the same. + +E: Using update dipole flag requires atom style sphere + +Self-explanatory. + +E: Using update dipole flag requires atom attribute mu + +Self-explanatory. + +E: Fix nvt/npt/nph damping parameters must be > 0.0 + +Self-explanatory. + +E: Cannot use fix npt and fix deform on same component of stress tensor + +This would be changing the same box dimension twice. + +E: Temperature ID for fix nvt/npt does not exist + +Self-explanatory. + +E: Pressure ID for fix npt/nph does not exist + +Self-explanatory. + +E: Non-numeric pressure - simulation unstable + +UNDOCUMENTED + +E: Fix npt/nph has tilted box too far in one step - periodic cell is too far from equilibrium state + +Self-explanatory. The change in the box tilt is too extreme +on a short timescale. + +E: Could not find fix_modify temperature ID + +The compute ID for computing temperature does not exist. + +E: Fix_modify temperature ID does not compute temperature + +The compute ID assigned to the fix must compute temperature. + +W: Temperature for fix modify is not for group all + +The temperature compute is being used with a pressure calculation +which does operate on group all, so this may be inconsistent. + +E: Pressure ID for fix modify does not exist + +Self-explanatory. + +E: Could not find fix_modify pressure ID + +The compute ID for computing pressure does not exist. + +E: Fix_modify pressure ID does not compute pressure + +The compute ID assigned to the fix must compute pressure. + +U: The dlm flag must be used with update dipole + +Self-explanatory. + +*/ diff --git a/src/USER-CAUCHY/fix_npt_cauchy.cpp b/src/USER-CAUCHY/fix_npt_cauchy.cpp new file mode 100644 index 0000000000..76e787befb --- /dev/null +++ b/src/USER-CAUCHY/fix_npt_cauchy.cpp @@ -0,0 +1,68 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include +#include "fix_npt_cauchy.h" +#include "modify.h" +#include "error.h" + +using namespace LAMMPS_NS; +using namespace FixConst; + +/* ---------------------------------------------------------------------- */ + +FixNPTCauchy::FixNPTCauchy(LAMMPS *lmp, int narg, char **arg) : + FixCauchy(lmp, narg, arg) +{ + if (!tstat_flag) + error->all(FLERR,"Temperature control must be used with fix npt/cauchy"); + if (!pstat_flag) + error->all(FLERR,"Pressure control must be used with fix npt/cauchy"); + + // create a new compute temp style + // id = fix-ID + temp + // compute group = all since pressure is always global (group all) + // and thus its KE/temperature contribution should use group all + + int n = strlen(id) + 6; + id_temp = new char[n]; + strcpy(id_temp,id); + strcat(id_temp,"_temp"); + + char **newarg = new char*[3]; + newarg[0] = id_temp; + newarg[1] = (char *) "all"; + newarg[2] = (char *) "temp"; + + modify->add_compute(3,newarg); + delete [] newarg; + tcomputeflag = 1; + + // create a new compute pressure style + // id = fix-ID + press, compute group = all + // pass id_temp as 4th arg to pressure constructor + + n = strlen(id) + 7; + id_press = new char[n]; + strcpy(id_press,id); + strcat(id_press,"_press"); + + newarg = new char*[4]; + newarg[0] = id_press; + newarg[1] = (char *) "all"; + newarg[2] = (char *) "pressure"; + newarg[3] = id_temp; + modify->add_compute(4,newarg); + delete [] newarg; + pcomputeflag = 1; +} diff --git a/src/USER-CAUCHY/fix_npt_cauchy.h b/src/USER-CAUCHY/fix_npt_cauchy.h new file mode 100644 index 0000000000..fbf1f4afbd --- /dev/null +++ b/src/USER-CAUCHY/fix_npt_cauchy.h @@ -0,0 +1,48 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef FIX_CLASS + +FixStyle(npt/cauchy,FixNPTCauchy) + +#else + +#ifndef LMP_FIX_NPT_CAUCHY_H +#define LMP_FIX_NPT_CAUCHY_H + +#include "fix_cauchy.h" + +namespace LAMMPS_NS { + +class FixNPTCauchy : public FixCauchy { + public: + FixNPTCauchy(class LAMMPS *, int, char **); + ~FixNPTCauchy() {} +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Temperature control must be used with fix npt + +Self-explanatory. + +E: Pressure control must be used with fix npt + +Self-explanatory. + +*/ From ad764dbdfb128c9b9a3d4834b6f5ae7aee949fff Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 13 Nov 2018 17:23:39 -0500 Subject: [PATCH 300/302] remove cauchystat changes from fix_nh.cpp/.h and fix_nh.txt --- doc/src/fix_nh.txt | 41 ----- src/fix_nh.cpp | 424 +-------------------------------------------- src/fix_nh.h | 31 ---- 3 files changed, 5 insertions(+), 491 deletions(-) diff --git a/doc/src/fix_nh.txt b/doc/src/fix_nh.txt index 79e1aa93da..644ced4bdc 100644 --- a/doc/src/fix_nh.txt +++ b/doc/src/fix_nh.txt @@ -54,9 +54,6 @@ keyword = {temp} or {iso} or {aniso} or {tri} or {x} or {y} or {z} or {xy} or {y {scaleyz} value = {yes} or {no} = scale yz with lz {scalexz} value = {yes} or {no} = scale xz with lz {flip} value = {yes} or {no} = allow or disallow box flips when it becomes highly skewed - {cauchystat} cauchystat values = alpha continue - alpha = strength of Cauchystat control parameter - continue = {yes} or {no} = whether of not to continue from a previous run {fixedpoint} values = x y z x,y,z = perform barostat dilation/contraction around this point (distance units) {update} value = {dipole} or {dipole/dlm} @@ -609,39 +606,6 @@ can only be used if the 2nd dimension in the keyword is periodic, and if the tilt factor is not coupled to the barostat via keywords {tri}, {yz}, {xz}, and {xy}. -Without the {cauchystat} keyword, the barostat algorithm -controls the Second-Piola Kirchhoff stress, which is a stress measure -referred to the undeformed (initial) simulation box. If the box -deforms substantially during the equilibration, the difference between -the set values and the final true (Cauchy) stresses can be -considerable. - -The {cauchystat} keyword modifies the barostat as per Miller et -al. (Miller)_"#nh-Miller" so that the Cauchy stress is controlled. -{alpha} is the non-dimensional parameter, typically set to 0.001 or -0.01 that determines how aggresively the algorithm drives the system -towards the set Cauchy stresses. Larger values of {alpha} will modify -the system more quickly, but can lead to instabilities. Smaller -values will lead to longer convergence time. Since {alpha} also -influences how much the stress fluctuations deviate from the -equilibrium fluctuations, it should be set as small as possible. - -A {continue} value of {yes} indicates that the fix is subsequent to a -previous run with the Cauchystat fix, and the intention is to continue -from the converged stress state at the end of the previous run. This -may be required, for example, when implementing a multi-step loading/unloading -sequence over several fixes. - -Setting {alpha} to zero is not permitted. To "turn off" the -Cauchystat control and thus restore the equilibrium stress -fluctuations, two subsequent fixes should be used. In the first, the -Cauchystat is used and the simulation box equilibrates to the correct -shape for the desired stresses. In the second, the {fix} statement is -identical except that the {cauchystat} keyword is removed (along with -related {alpha} and {continue} values). This restores the original -Parrinello-Rahman algorithm, but now with the correct simulation box -shape from the first fix. - These fixes can be used with dynamic groups as defined by the "group"_group.html command. Likewise they can be used with groups to which atoms are added or deleted over time, e.g. a deposition @@ -659,7 +623,6 @@ over time or the atom count becomes very small. The keyword defaults are tchain = 3, pchain = 3, mtk = yes, tloop = ploop = 1, nreset = 0, drag = 0.0, dilate = all, couple = none, -cauchystat = no, scaleyz = scalexz = scalexy = yes if periodic in 2nd dimension and not coupled to barostat, otherwise no. @@ -681,7 +644,3 @@ Martyna, J Phys A: Math Gen, 39, 5629 (2006). :link(nh-Dullweber) [(Dullweber)] Dullweber, Leimkuhler and McLachlan, J Chem Phys, 107, 5840 (1997). - -:link(nh-Miller) -[(Miller)] Miller, Tadmor, Gibson, Bernstein and Pavia, J Chem Phys, -144, 184107 (2016). diff --git a/src/fix_nh.cpp b/src/fix_nh.cpp index bcae8b23dd..a1a562f2bb 100644 --- a/src/fix_nh.cpp +++ b/src/fix_nh.cpp @@ -28,7 +28,6 @@ #include "irregular.h" #include "modify.h" #include "fix_deform.h" -#include "fix_store.h" #include "compute.h" #include "kspace.h" #include "update.h" @@ -56,10 +55,11 @@ FixNH::FixNH(LAMMPS *lmp, int narg, char **arg) : rfix(NULL), id_dilate(NULL), irregular(NULL), id_temp(NULL), id_press(NULL), eta(NULL), eta_dot(NULL), eta_dotdot(NULL), eta_mass(NULL), etap(NULL), etap_dot(NULL), etap_dotdot(NULL), - etap_mass(NULL), id_store(NULL),init_store(NULL) + etap_mass(NULL) { if (narg < 4) error->all(FLERR,"Illegal fix nvt/npt/nph command"); + restart_global = 1; dynamic_group_allow = 1; time_integrate = 1; scalar_flag = 1; @@ -68,19 +68,12 @@ FixNH::FixNH(LAMMPS *lmp, int narg, char **arg) : extscalar = 1; extvector = 0; - // for CauchyStat - - usePK = 1; - initRUN = 0; - restartPK = 0; - restart_global = 1; - restart_stored = 0; - // default values pcouple = NONE; drag = 0.0; allremap = 1; + id_dilate = NULL; mtchain = mpchain = 3; nc_tchain = nc_pchain = 1; mtk_flag = 1; @@ -95,6 +88,8 @@ FixNH::FixNH(LAMMPS *lmp, int narg, char **arg) : tcomputeflag = 0; pcomputeflag = 0; + id_temp = NULL; + id_press = NULL; // turn on tilt factor scaling, whenever applicable @@ -346,17 +341,6 @@ FixNH::FixNH(LAMMPS *lmp, int narg, char **arg) : dlm_flag = 1; } else error->all(FLERR,"Illegal fix nvt/npt/nph command"); iarg += 2; - } else if (strcmp(arg[iarg],"cauchystat") == 0) { - usePK = 0; - if (iarg+3 > narg) error->all(FLERR, - "Illegal fix npt cauchystat command:" - " wrong number of arguments"); - if (strcmp(arg[iarg+2],"yes") != 0 && strcmp(arg[iarg+2],"no") != 0) - error->all(FLERR,"Illegal cauchystat continue value. " - "Must be 'yes' or 'no'"); - alpha = force->numeric(FLERR,arg[iarg+1]); - restartPK = !strcmp(arg[iarg+2],"yes"); - iarg += 3; } else if (strcmp(arg[iarg],"fixedpoint") == 0) { if (iarg+4 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command"); fixedpoint[0] = force->numeric(FLERR,arg[iarg+1]); @@ -594,14 +578,6 @@ FixNH::FixNH(LAMMPS *lmp, int narg, char **arg) : /* ---------------------------------------------------------------------- */ -void FixNH::post_constructor() -{ - if (!usePK) CauchyStat_init(); - else CauchyStat_cleanup(); -} - -/* ---------------------------------------------------------------------- */ - FixNH::~FixNH() { if (copymode) return; @@ -609,7 +585,6 @@ FixNH::~FixNH() delete [] id_dilate; delete [] rfix; - delete [] id_store; delete irregular; // delete temperature and pressure if fix created them @@ -2255,20 +2230,6 @@ void FixNH::compute_press_target() for (int i = 3; i < 6; i++) p_target[i] = p_start[i] + delta * (p_stop[i]-p_start[i]); - // CauchyStat: call CauchyStat to modify p_target[i] and p_hydro, - // if CauchyStat enabled and pressure->vector computation has been initiated - - if ((usePK == 0) && (initRUN == 1)) CauchyStat(); - if (initRUN == 0) { - for (int i=0; i < 6; i++) { - h_old[i]=domain->h[i]; - } - } - - // when run is initialized tensor[] not available (pressure on cell wall) - - initRUN=1; - // if deviatoric, recompute sigma each time p_target changes if (deviatoric_flag) compute_sigma(); @@ -2420,378 +2381,3 @@ double FixNH::memory_usage() if (irregular) bytes += irregular->memory_usage(); return bytes; } - -/* ---------------------------------------------------------------------- - initialize Cauchystat -------------------------------------------------------------------------- */ - -void FixNH::CauchyStat_init() -{ - if (comm->me == 0) { - if (screen) { - fprintf(screen,"Using the Cauchystat fix with alpha=%f\n",alpha); - if (restartPK==1) { - fprintf(screen," (this is a continuation run)\n"); - } else { - fprintf(screen," (this is NOT a continuation run)\n"); - } - } - if (logfile) { - fprintf(logfile,"Using the Cauchystat with alpha=%f\n",alpha); - if (restartPK==1) { - fprintf(logfile," this is a continuation run\n"); - } else { - fprintf(logfile," this is NOT a continuation run\n"); - } - } - } - - if (!id_store) { - int n = strlen(id) + 14; - id_store = new char[n]; - strcpy(id_store,id); - strcat(id_store,"_FIX_NH_STORE"); - } - restart_stored = modify->find_fix(id_store); - - if (restartPK==1 && restart_stored < 0) - error->all(FLERR,"Illegal cauchystat command. Continuation run" - " must follow a previously equilibrated Cauchystat run"); - - if (alpha<=0.0) - error->all(FLERR,"Illegal cauchystat command: " - " Alpha cannot be zero or negative."); - - if (restart_stored < 0) { - char **newarg = new char *[6]; - newarg[0] = id_store; - newarg[1] = (char *) "all"; - newarg[2] = (char *) "STORE"; - newarg[3] = (char *) "global"; - newarg[4] = (char *) "1"; - newarg[5] = (char *) "6"; - modify->add_fix(6,newarg); - delete[] newarg; - restart_stored = modify->find_fix(id_store); - } - init_store = (FixStore *)modify->fix[restart_stored]; - - initRUN = 0; - initPK = 1; - -#define H0(row,col) (H0[(row-1)][(col-1)]) -#define invH0(row,col) (invH0[(row-1)][(col-1)]) - - // initialize H0 to current box shape - - double *h = domain->h; - double *h_inv = domain->h_inv; - - H0(1,1)=h[0]; H0(1,2)=h[5]; H0(1,3)=h[4]; - H0(2,1)=0.0; H0(2,2)=h[1]; H0(2,3)=h[3]; - H0(3,1)=0.0; H0(3,2)=0.0; H0(3,3)=h[2]; - - invH0(1,1)=h_inv[0]; invH0(1,2)=h_inv[5]; invH0(1,3)=h_inv[4]; - invH0(2,1)=0.0; invH0(2,2)=h_inv[1]; invH0(2,3)=h_inv[3]; - invH0(3,1)=0.0; invH0(3,2)=0.0; invH0(3,3)=h_inv[2]; - - CSvol0 = abs(MathExtra::det3(H0)); //find reference volume - -#undef H0 -#undef invH0 -} - -/* ---------------------------------------------------------------------- - cleanup when not using Cauchystat -------------------------------------------------------------------------- */ - -void FixNH::CauchyStat_cleanup() -{ - if (id_store) { - modify->delete_fix(id_store); - delete[] id_store; - } else { - int n = strlen(id) + 14; - id_store = new char[n]; - strcpy(id_store,id); - strcat(id_store,"_FIX_NH_STORE"); - modify->delete_fix(id_store); - delete[] id_store; - } - id_store = NULL; - restart_stored = -1; -} - -/* ---------------------------------------------------------------------- - Cauchystat -------------------------------------------------------------------------- */ - -void FixNH::CauchyStat() -{ - double* h = domain->h; // shape matrix in Voigt notation - double* h_rate = domain->h_rate; // rate of box size/shape change in Voigt notation - double H[3][3]; - double Hdot[3][3]; - -#define H(row,col) (H[(row-1)][(col-1)]) -#define Hdot(row,col) (Hdot[(row-1)][(col-1)]) -#define F(row,col) (F[(row-1)][(col-1)]) -#define Fi(row,col) (Fi[(row-1)][(col-1)]) -#define Fdot(row,col) (Fdot[(row-1)][(col-1)]) -#define invH0(row,col) (invH0[(row-1)][(col-1)]) -#define cauchy(row,col) (cauchy[(row-1)][(col-1)]) -#define setcauchy(row,col) (setcauchy[(row-1)][(col-1)]) -#define setPK(row,col) (setPK[(row-1)][(col-1)]) -#define sigmahat(row,col) (sigmahat[(row-1)][(col-1)]) - - H(1,1)=h[0]; H(1,2)=0.0; H(1,3)=0.0; - H(2,1)=0.0; H(2,2)=h[1]; H(2,3)=0.0; - H(3,1)=0.0; H(3,2)=0.0; H(3,3)=h[2]; - - for (int i=0;i<6;i++) { - h_rate[i]=(h[i]-h_old[i])/update->dt; - h_old[i]=h[i]; - } - - Hdot(1,1)=h_rate[0]; Hdot(1,2)=0.0; Hdot(1,3)=0.0; - Hdot(2,1)=0.0; Hdot(2,2)=h_rate[1]; Hdot(2,3)=0.0; - Hdot(3,1)=0.0; Hdot(3,2)=0.0; Hdot(3,3)=h_rate[2]; - - if (domain->triclinic) { - H(1,2)=h[5]; H(1,3)=h[4]; H(2,3)=h[3]; - Hdot(1,2)=h_rate[5]; Hdot(1,3)=h_rate[4]; Hdot(2,3)=h_rate[3]; - } - - double F[3][3]={{0.0,0.0,0.0},{0.0,0.0,0.0},{0.0,0.0,0.0}}; - double Fi[3][3]={{0.0,0.0,0.0},{0.0,0.0,0.0},{0.0,0.0,0.0}}; - double Fdot[3][3]={{0.0,0.0,0.0},{0.0,0.0,0.0},{0.0,0.0,0.0}}; - double J,vol; - - MathExtra::times3(H,invH0,F); - MathExtra::times3(Hdot,invH0,Fdot); - MathExtra::invert3(F,Fi); - J = MathExtra::det3(F); - vol=CSvol0*J; - - double deltat; - deltat = update->dt; //increment of time step - - // Current pressure on the cell boundaries: - //tensor: 0 1 2 3 4 5 - // x y z xy xz yz - - double *tensor = pressure->vector; - - double cauchy[3][3]; - cauchy(1,1)=-tensor[0]; cauchy(1,2)=0.0; cauchy(1,3)=0.0; - cauchy(2,1)=0.0; cauchy(2,2)=-tensor[1]; cauchy(2,3)=0.0; - cauchy(3,1)=0.0; cauchy(3,2)=0.0; cauchy(3,3)=-tensor[2]; - - if (domain->triclinic) { - cauchy(1,2)=-tensor[3]; cauchy(1,3)=-tensor[4]; - cauchy(2,1)=-tensor[3]; cauchy(2,3)=-tensor[5]; - cauchy(3,1)=-tensor[4]; cauchy(3,2)=-tensor[5]; - } - - // target pressure on the cell boundaries: - // p_target: 0 1 2 3 4 5 - // x y z yz xz xy - - double setcauchy[3][3]; - setcauchy(1,1)=-p_target[0]; setcauchy(1,2)=0.0; setcauchy(1,3)=0.0; - setcauchy(2,1)=0.0; setcauchy(2,2)=-p_target[1]; setcauchy(2,3)=0.0; - setcauchy(3,1)=0.0; setcauchy(3,2)=0.0; setcauchy(3,3)=-p_target[2]; - - if (domain->triclinic) { - setcauchy(1,2)=-p_target[5]; setcauchy(1,3)=-p_target[4]; - setcauchy(2,1)=-p_target[5]; setcauchy(2,3)=-p_target[3]; - setcauchy(3,1)=-p_target[4]; setcauchy(3,2)=-p_target[3]; - } - - //initialize: - if (initPK==1) { - if (restartPK==1) { - double *setPKinit = init_store->astore[0]; - setPK(1,1)=setPKinit[0]; setPK(1,2)=setPKinit[1]; setPK(1,3)=setPKinit[2]; - setPK(2,1)=setPKinit[1]; setPK(2,2)=setPKinit[3]; setPK(2,3)=setPKinit[4]; - setPK(3,1)=setPKinit[2]; setPK(3,2)=setPKinit[4]; setPK(3,3)=setPKinit[5]; - }else { - setPK(1,1)=cauchy(1,1); setPK(1,2)=cauchy(1,2); setPK(1,3)=cauchy(1,3); - setPK(2,1)=cauchy(2,1); setPK(2,2)=cauchy(2,2); setPK(2,3)=cauchy(2,3); - setPK(3,1)=cauchy(3,1); setPK(3,2)=cauchy(3,2); setPK(3,3)=cauchy(3,3); - } - initPK=0; - } - - CauchyStat_Step(Fi,Fdot,cauchy,setcauchy,setPK,vol,CSvol0,deltat,alpha); - - // use currentPK as new target: - // p_target: 0 1 2 3 4 5 - // x y z yz xz xy - - p_target[0]=-setPK(1,1); - p_target[1]=-setPK(2,2); - p_target[2]=-setPK(3,3); - if (pstyle == TRICLINIC) { - p_target[3]=-setPK(2,3); - p_target[4]=-setPK(1,3); - p_target[5]=-setPK(1,2); - } - - p_hydro = 0.0; - for (int i = 0; i < 3; i++) - if (p_flag[i]) { - p_hydro += p_target[i]; - } - p_hydro /= pdim; - - // save information for Cauchystat restart - double *setPKinit = init_store->astore[0]; - setPKinit[0] = setcauchy(1,1); - setPKinit[1] = setcauchy(1,2); - setPKinit[2] = setcauchy(1,3); - setPKinit[3] = setcauchy(2,2); - setPKinit[4] = setcauchy(2,3); - setPKinit[5] = setcauchy(3,3); - -#undef H -#undef Hdot -#undef F -#undef Fi -#undef Fdot -#undef invH0 -#undef cauchy -#undef setcauchy -#undef setPK -#undef sigmahat - -} - -/* ---------------------------------------------------------------------- - CauchyStat_Step - - Inputs: - Fi(3,3) : inverse of the deformation gradient - Fdot(3,3) : time derivative of the deformation gradient (velocity) - cauchy(3,3) : current cauchy stress tensor - setcauchy(3,3) : target cauchy stress tensor - alpha : parameter =0.01 - setPK(3,3) : current PK stress tensor, at initialization (time=0) setPK=cauchy - volume : current volume of the periodic box - volume0 : initial volume of the periodic box - deltat : simulation step increment - alpha : parameter - - Outputs: - setPK(3,3) : PK stress tensor at the next time step - ------------------------------------------------------------------------- */ - -void FixNH::CauchyStat_Step(double (&Fi)[3][3], double (&Fdot)[3][3], - double (&cauchy)[3][3], double (&setcauchy)[3][3], - double (&setPK)[3][3], double volume, - double volume0, double deltat, double alpha) -{ - - //macros to go from c to fortran style for arrays: -#define F(row,col) (F[(row-1)][(col-1)]) -#define Fi(row,col) (Fi[(row-1)][(col-1)]) -#define Fdot(row,col) (Fdot[(row-1)][(col-1)]) -#define cauchy(row,col) (cauchy[(row-1)][(col-1)]) -#define setcauchy(row,col) (setcauchy[(row-1)][(col-1)]) -#define setPK(row,col) (setPK[(row-1)][(col-1)]) -#define uv(row,col) (uv[(row-1)][(col-1)]) -#define deltastress(row) (deltastress[(row-1)]) -#define fdotvec(row) (fdotvec[(row-1)]) -#define dsdf(row,col) (dsdf[(row-1)][(col-1)]) -#define dsds(row,col) (dsds[(row-1)][(col-1)]) -#define deltaF(row) (deltaF[(row-1)]) -#define deltaPK(row) (deltaPK[(row-1)]) - - //initialize local variables: - int i,j,m,n; - - double deltastress[6],fdotvec[6]; - double dsdf[6][6]={0.0}; //zeroed, used in incremental form - double dsds[6][6]={0.0}; //zeroed, used in incremental form - double jac; - double deltaF[6]={0.0}; //zeroed, used in incremental form - double deltaPK[6]={0.0}; //zeroed, used in incremental form - - int uv[6][2]; - uv(1,1)=1; uv(1,2)=1; - uv(2,1)=2; uv(2,2)=2; - uv(3,1)=3; uv(3,2)=3; - uv(4,1)=2; uv(4,2)=3; - uv(5,1)=1; uv(5,2)=3; - uv(6,1)=1; uv(6,2)=2; - - for(int ii = 1;ii <= 6;ii++) { - i=uv(ii,1); - j=uv(ii,2); - deltastress(ii)=setcauchy(i,j)-cauchy(i,j); - if(ii>3) deltastress(ii)=deltastress(ii)*2.0; - fdotvec(ii)=Fdot(i,j)*deltat; - } - - for(int ii = 1;ii <= 6;ii++) { - i=uv(ii,1); - j=uv(ii,2); - for(int jj = 1;jj <= 6;jj++) { - m=uv(jj,1); - n=uv(jj,2); - dsds(ii,jj) = Fi(i,m)*Fi(j,n) + Fi(i,n)*Fi(j,m) + Fi(j,m)*Fi(i,n) + Fi(j,n)*Fi(i,m); - for(int l = 1;l <= 3;l++) { - for(int k = 1;k <= 3;k++) { - dsdf(ii,jj) = dsdf(ii,jj) + cauchy(k,l)* - ( Fi(i,k)*Fi(j,l)*Fi(n,m) - Fi(i,m)*Fi(j,l)*Fi(n,k) - Fi(i,k)*Fi(j,m)*Fi(n,l) ); - } - } - } - } - - jac=volume/volume0; - for(int ii = 1;ii <= 6;ii++) { - for(int jj = 1;jj <= 6;jj++) { - dsds(ii,jj)=dsds(ii,jj)*jac/4.0; - dsdf(ii,jj)=dsdf(ii,jj)*jac; - } - } - - for(int ii = 1;ii <= 6;ii++) { - for(int jj = 1;jj <= 6;jj++) { - deltaF(ii)=deltaF(ii)+dsdf(ii,jj)*fdotvec(jj); - } - } - - for(int ii = 1;ii <= 6;ii++) { - for(int jj = 1;jj <= 6;jj++) { - deltaPK(ii)=deltaPK(ii)+alpha*dsds(ii,jj)*deltastress(jj); - } - deltaPK(ii)=deltaPK(ii)+alpha*deltaF(ii); - } - - setPK(1,1)=setPK(1,1)+deltaPK(1); - setPK(2,2)=setPK(2,2)+deltaPK(2); - setPK(3,3)=setPK(3,3)+deltaPK(3); - setPK(2,3)=setPK(2,3)+deltaPK(4); - setPK(3,2)=setPK(3,2)+deltaPK(4); - setPK(1,3)=setPK(1,3)+deltaPK(5); - setPK(3,1)=setPK(3,1)+deltaPK(5); - setPK(1,2)=setPK(1,2)+deltaPK(6); - setPK(2,1)=setPK(2,1)+deltaPK(6); - -#undef F -#undef Fi -#undef Fdot -#undef cauchy -#undef setcauchy -#undef setPK -#undef uv -#undef deltastress -#undef fdotvec -#undef dsdf -#undef dsds -#undef deltaF -#undef deltaPK - -} diff --git a/src/fix_nh.h b/src/fix_nh.h index 2bc64281ff..807ea2a71f 100644 --- a/src/fix_nh.h +++ b/src/fix_nh.h @@ -21,7 +21,6 @@ namespace LAMMPS_NS { class FixNH : public Fix { public: FixNH(class LAMMPS *, int, char **); - virtual void post_constructor(); virtual ~FixNH(); int setmask(); virtual void init(); @@ -140,36 +139,6 @@ class FixNH : public Fix { double compute_strain_energy(); void compute_press_target(); void nh_omega_dot(); - - // Implementation of CauchyStat - char *id_store; // fix id of the STORE fix for retaining data - class FixStore *init_store; // fix pointer to STORE fix - double H0[3][3]; // shape matrix for the undeformed cell - double h_old[6]; // previous time step shape matrix for - // the undeformed cell - double invH0[3][3]; // inverse of H0; - double CSvol0; // volume of undeformed cell - double setPK[3][3]; // current set values of the PK stress - // (this is modified until the cauchy - // stress converges) - double alpha; // integration parameter for the cauchystat - int initPK; // 1 if setPK needs to be initialized either - // from cauchy or restart, else 0 - int usePK; // 0 if use CauchyStat else 1 - int restartPK; // Read PK stress from the previous run - int restart_stored; // values of PK stress from the previous step stored - int initRUN; // 0 if run not initialized - // (pressure->vector not computed yet), - // else 1 (pressure->vector available) - - void CauchyStat_init(); - void CauchyStat_cleanup(); - void CauchyStat(); - void CauchyStat_Step(double (&Fi)[3][3], double (&Fdot)[3][3], - double (&cauchy)[3][3], double (&setcauchy)[3][3], - double (&setPK)[3][3], double volume, double volume0, - double deltat, double alpha); - }; } From 32be742144fb3f370bfcd817873a87af4d75286f Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 13 Nov 2018 17:32:48 -0500 Subject: [PATCH 301/302] fix typo --- doc/src/lammps.book | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/src/lammps.book b/doc/src/lammps.book index b1973cd036..a7dd860fd5 100644 --- a/doc/src/lammps.book +++ b/doc/src/lammps.book @@ -301,6 +301,7 @@ fix_msst.html fix_mvv_dpd.html fix_neb.html fix_nh.html +fix_cauchy.html fix_nh_eff.html fix_nph_asphere.html fix_nph_body.html @@ -308,7 +309,6 @@ fix_nph_sphere.html fix_nphug.html fix_npt_asphere.html fix_npt_body.html -fix_npt_cauchy.html fix_npt_sphere.html fix_nve.html fix_nve_asphere.html From f46478e5ad3a43e992f3ee201d391563c45c3fe0 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 13 Nov 2018 17:40:05 -0500 Subject: [PATCH 302/302] add missing file --- doc/src/fix_cauchy.txt | 674 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 674 insertions(+) create mode 100644 doc/src/fix_cauchy.txt diff --git a/doc/src/fix_cauchy.txt b/doc/src/fix_cauchy.txt new file mode 100644 index 0000000000..7a8fe2f149 --- /dev/null +++ b/doc/src/fix_cauchy.txt @@ -0,0 +1,674 @@ +<"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +fix npt/cauchy command :h3 + +[Syntax:] + +fix ID group-ID style_name keyword value ... :pre + +ID, group-ID are documented in "fix"_fix.html command :ulb,l +style_name = {npt/cauchy} :l +one or more keyword/value pairs may be appended :l +keyword = {temp} or {iso} or {aniso} or {tri} or {x} or {y} or {z} or {xy} or {yz} or {xz} or {couple} or {tchain} or {pchain} or {mtk} or {tloop} or {ploop} or {nreset} or {drag} or {dilate} or {scalexy} or {scaleyz} or {scalexz} or {flip} or {fixedpoint} or {update} + {temp} values = Tstart Tstop Tdamp + Tstart,Tstop = external temperature at start/end of run + Tdamp = temperature damping parameter (time units) + {iso} or {aniso} or {tri} values = Pstart Pstop Pdamp + Pstart,Pstop = scalar external pressure at start/end of run (pressure units) + Pdamp = pressure damping parameter (time units) + {x} or {y} or {z} or {xy} or {yz} or {xz} values = Pstart Pstop Pdamp + Pstart,Pstop = external stress tensor component at start/end of run (pressure units) + Pdamp = stress damping parameter (time units) + {couple} = {none} or {xyz} or {xy} or {yz} or {xz} + {tchain} value = N + N = length of thermostat chain (1 = single thermostat) + {pchain} values = N + N length of thermostat chain on barostat (0 = no thermostat) + {mtk} value = {yes} or {no} = add in MTK adjustment term or not + {tloop} value = M + M = number of sub-cycles to perform on thermostat + {ploop} value = M + M = number of sub-cycles to perform on barostat thermostat + {nreset} value = reset reference cell every this many timesteps + {drag} value = Df + Df = drag factor added to barostat/thermostat (0.0 = no drag) + {dilate} value = dilate-group-ID + dilate-group-ID = only dilate atoms in this group due to barostat volume changes + {scalexy} value = {yes} or {no} = scale xy with ly + {scaleyz} value = {yes} or {no} = scale yz with lz + {scalexz} value = {yes} or {no} = scale xz with lz + {flip} value = {yes} or {no} = allow or disallow box flips when it becomes highly skewed + {cauchystat} cauchystat values = alpha continue + alpha = strength of Cauchystat control parameter + continue = {yes} or {no} = whether of not to continue from a previous run + {fixedpoint} values = x y z + x,y,z = perform barostat dilation/contraction around this point (distance units) + {update} value = {dipole} or {dipole/dlm} + dipole = update dipole orientation (only for sphere variants) + dipole/dlm = use DLM integrator to update dipole orientation (only for sphere variants) :pre +:ule + +[Examples:] + +fix 1 water npt/cauchy temp 300.0 300.0 100.0 iso 0.0 0.0 1000.0 + +[Description:] + +These commands perform time integration on Nose-Hoover style +non-Hamiltonian equations of motion which are designed to generate +positions and velocities sampled from the canonical (nvt), +isothermal-isobaric (npt), and isenthalpic (nph) ensembles. This +updates the position and velocity for atoms in the group each +timestep. + +The thermostatting and barostatting is achieved by adding some dynamic +variables which are coupled to the particle velocities +(thermostatting) and simulation domain dimensions (barostatting). In +addition to basic thermostatting and barostatting, these fixes can +also create a chain of thermostats coupled to the particle thermostat, +and another chain of thermostats coupled to the barostat +variables. The barostat can be coupled to the overall box volume, or +to individual dimensions, including the {xy}, {xz} and {yz} tilt +dimensions. The external pressure of the barostat can be specified as +either a scalar pressure (isobaric ensemble) or as components of a +symmetric stress tensor (constant stress ensemble). When used +correctly, the time-averaged temperature and stress tensor of the +particles will match the target values specified by Tstart/Tstop and +Pstart/Pstop. + +The equations of motion used are those of Shinoda et al in +"(Shinoda)"_#nh-Shinoda, which combine the hydrostatic equations of +Martyna, Tobias and Klein in "(Martyna)"_#nh-Martyna with the strain +energy proposed by Parrinello and Rahman in +"(Parrinello)"_#nh-Parrinello. The time integration schemes closely +follow the time-reversible measure-preserving Verlet and rRESPA +integrators derived by Tuckerman et al in "(Tuckerman)"_#nh-Tuckerman. + +:line + +The thermostat parameters for fix styles {nvt} and {npt} is specified +using the {temp} keyword. Other thermostat-related keywords are +{tchain}, {tloop} and {drag}, which are discussed below. + +The thermostat is applied to only the translational degrees of freedom +for the particles. The translational degrees of freedom can also have +a bias velocity removed before thermostatting takes place; see the +description below. The desired temperature at each timestep is a +ramped value during the run from {Tstart} to {Tstop}. The {Tdamp} +parameter is specified in time units and determines how rapidly the +temperature is relaxed. For example, a value of 10.0 means to relax +the temperature in a timespan of (roughly) 10 time units (e.g. tau or +fmsec or psec - see the "units"_units.html command). The atoms in the +fix group are the only ones whose velocities and positions are updated +by the velocity/position update portion of the integration. + +NOTE: A Nose-Hoover thermostat will not work well for arbitrary values +of {Tdamp}. If {Tdamp} is too small, the temperature can fluctuate +wildly; if it is too large, the temperature will take a very long time +to equilibrate. A good choice for many models is a {Tdamp} of around +100 timesteps. Note that this is NOT the same as 100 time units for +most "units"_units.html settings. + +:line + +The barostat parameters for fix styles {npt} and {nph} is specified +using one or more of the {iso}, {aniso}, {tri}, {x}, {y}, {z}, {xy}, +{xz}, {yz}, and {couple} keywords. These keywords give you the +ability to specify all 6 components of an external stress tensor, and +to couple various of these components together so that the dimensions +they represent are varied together during a constant-pressure +simulation. + +Other barostat-related keywords are {pchain}, {mtk}, {ploop}, +{nreset}, {drag}, and {dilate}, which are discussed below. + +Orthogonal simulation boxes have 3 adjustable dimensions (x,y,z). +Triclinic (non-orthogonal) simulation boxes have 6 adjustable +dimensions (x,y,z,xy,xz,yz). The "create_box"_create_box.html, "read +data"_read_data.html, and "read_restart"_read_restart.html commands +specify whether the simulation box is orthogonal or non-orthogonal +(triclinic) and explain the meaning of the xy,xz,yz tilt factors. + +The target pressures for each of the 6 components of the stress tensor +can be specified independently via the {x}, {y}, {z}, {xy}, {xz}, {yz} +keywords, which correspond to the 6 simulation box dimensions. For +each component, the external pressure or tensor component at each +timestep is a ramped value during the run from {Pstart} to {Pstop}. +If a target pressure is specified for a component, then the +corresponding box dimension will change during a simulation. For +example, if the {y} keyword is used, the y-box length will change. If +the {xy} keyword is used, the xy tilt factor will change. A box +dimension will not change if that component is not specified, although +you have the option to change that dimension via the "fix +deform"_fix_deform.html command. + +Note that in order to use the {xy}, {xz}, or {yz} keywords, the +simulation box must be triclinic, even if its initial tilt factors are +0.0. + +For all barostat keywords, the {Pdamp} parameter operates like the +{Tdamp} parameter, determining the time scale on which pressure is +relaxed. For example, a value of 10.0 means to relax the pressure in +a timespan of (roughly) 10 time units (e.g. tau or fmsec or psec - see +the "units"_units.html command). + +NOTE: A Nose-Hoover barostat will not work well for arbitrary values +of {Pdamp}. If {Pdamp} is too small, the pressure and volume can +fluctuate wildly; if it is too large, the pressure will take a very +long time to equilibrate. A good choice for many models is a {Pdamp} +of around 1000 timesteps. However, note that {Pdamp} is specified in +time units, and that timesteps are NOT the same as time units for most +"units"_units.html settings. + +Regardless of what atoms are in the fix group (the only atoms which +are time integrated), a global pressure or stress tensor is computed +for all atoms. Similarly, when the size of the simulation box is +changed, all atoms are re-scaled to new positions, unless the keyword +{dilate} is specified with a {dilate-group-ID} for a group that +represents a subset of the atoms. This can be useful, for example, to +leave the coordinates of atoms in a solid substrate unchanged and +controlling the pressure of a surrounding fluid. This option should +be used with care, since it can be unphysical to dilate some atoms and +not others, because it can introduce large, instantaneous +displacements between a pair of atoms (one dilated, one not) that are +far from the dilation origin. Also note that for atoms not in the fix +group, a separate time integration fix like "fix nve"_fix_nve.html or +"fix nvt"_fix_nh.html can be used on them, independent of whether they +are dilated or not. + +:line + +The {couple} keyword allows two or three of the diagonal components of +the pressure tensor to be "coupled" together. The value specified +with the keyword determines which are coupled. For example, {xz} +means the {Pxx} and {Pzz} components of the stress tensor are coupled. +{Xyz} means all 3 diagonal components are coupled. Coupling means two +things: the instantaneous stress will be computed as an average of the +corresponding diagonal components, and the coupled box dimensions will +be changed together in lockstep, meaning coupled dimensions will be +dilated or contracted by the same percentage every timestep. The +{Pstart}, {Pstop}, {Pdamp} parameters for any coupled dimensions must +be identical. {Couple xyz} can be used for a 2d simulation; the {z} +dimension is simply ignored. + +:line + +The {iso}, {aniso}, and {tri} keywords are simply shortcuts that are +equivalent to specifying several other keywords together. + +The keyword {iso} means couple all 3 diagonal components together when +pressure is computed (hydrostatic pressure), and dilate/contract the +dimensions together. Using "iso Pstart Pstop Pdamp" is the same as +specifying these 4 keywords: + +x Pstart Pstop Pdamp +y Pstart Pstop Pdamp +z Pstart Pstop Pdamp +couple xyz :pre + +The keyword {aniso} means {x}, {y}, and {z} dimensions are controlled +independently using the {Pxx}, {Pyy}, and {Pzz} components of the +stress tensor as the driving forces, and the specified scalar external +pressure. Using "aniso Pstart Pstop Pdamp" is the same as specifying +these 4 keywords: + +x Pstart Pstop Pdamp +y Pstart Pstop Pdamp +z Pstart Pstop Pdamp +couple none :pre + +The keyword {tri} means {x}, {y}, {z}, {xy}, {xz}, and {yz} dimensions +are controlled independently using their individual stress components +as the driving forces, and the specified scalar pressure as the +external normal stress. Using "tri Pstart Pstop Pdamp" is the same as +specifying these 7 keywords: + +x Pstart Pstop Pdamp +y Pstart Pstop Pdamp +z Pstart Pstop Pdamp +xy 0.0 0.0 Pdamp +yz 0.0 0.0 Pdamp +xz 0.0 0.0 Pdamp +couple none :pre + +:line + +In some cases (e.g. for solids) the pressure (volume) and/or +temperature of the system can oscillate undesirably when a Nose/Hoover +barostat and thermostat is applied. The optional {drag} keyword will +damp these oscillations, although it alters the Nose/Hoover equations. +A value of 0.0 (no drag) leaves the Nose/Hoover formalism unchanged. +A non-zero value adds a drag term; the larger the value specified, the +greater the damping effect. Performing a short run and monitoring the +pressure and temperature is the best way to determine if the drag term +is working. Typically a value between 0.2 to 2.0 is sufficient to +damp oscillations after a few periods. Note that use of the drag +keyword will interfere with energy conservation and will also change +the distribution of positions and velocities so that they do not +correspond to the nominal NVT, NPT, or NPH ensembles. + +An alternative way to control initial oscillations is to use chain +thermostats. The keyword {tchain} determines the number of thermostats +in the particle thermostat. A value of 1 corresponds to the original +Nose-Hoover thermostat. The keyword {pchain} specifies the number of +thermostats in the chain thermostatting the barostat degrees of +freedom. A value of 0 corresponds to no thermostatting of the +barostat variables. + +The {mtk} keyword controls whether or not the correction terms due to +Martyna, Tuckerman, and Klein are included in the equations of motion +"(Martyna)"_#nh-Martyna. Specifying {no} reproduces the original +Hoover barostat, whose volume probability distribution function +differs from the true NPT and NPH ensembles by a factor of 1/V. Hence +using {yes} is more correct, but in many cases the difference is +negligible. + +The keyword {tloop} can be used to improve the accuracy of integration +scheme at little extra cost. The initial and final updates of the +thermostat variables are broken up into {tloop} substeps, each of +length {dt}/{tloop}. This corresponds to using a first-order +Suzuki-Yoshida scheme "(Tuckerman)"_#nh-Tuckerman. The keyword {ploop} +does the same thing for the barostat thermostat. + +The keyword {nreset} controls how often the reference dimensions used +to define the strain energy are reset. If this keyword is not used, +or is given a value of zero, then the reference dimensions are set to +those of the initial simulation domain and are never changed. If the +simulation domain changes significantly during the simulation, then +the final average pressure tensor will differ significantly from the +specified values of the external stress tensor. A value of {nstep} +means that every {nstep} timesteps, the reference dimensions are set +to those of the current simulation domain. + +The {scaleyz}, {scalexz}, and {scalexy} keywords control whether or +not the corresponding tilt factors are scaled with the associated box +dimensions when barostatting triclinic periodic cells. The default +values {yes} will turn on scaling, which corresponds to adjusting the +linear dimensions of the cell while preserving its shape. Choosing +{no} ensures that the tilt factors are not scaled with the box +dimensions. See below for restrictions and default values in different +situations. In older versions of LAMMPS, scaling of tilt factors was +not performed. The old behavior can be recovered by setting all three +scale keywords to {no}. + +The {flip} keyword allows the tilt factors for a triclinic box to +exceed half the distance of the parallel box length, as discussed +below. If the {flip} value is set to {yes}, the bound is enforced by +flipping the box when it is exceeded. If the {flip} value is set to +{no}, the tilt will continue to change without flipping. Note that if +applied stress induces large deformations (e.g. in a liquid), this +means the box shape can tilt dramatically and LAMMPS will run less +efficiently, due to the large volume of communication needed to +acquire ghost atoms around a processor's irregular-shaped sub-domain. +For extreme values of tilt, LAMMPS may also lose atoms and generate an +error. + +The {fixedpoint} keyword specifies the fixed point for barostat volume +changes. By default, it is the center of the box. Whatever point is +chosen will not move during the simulation. For example, if the lower +periodic boundaries pass through (0,0,0), and this point is provided +to {fixedpoint}, then the lower periodic boundaries will remain at +(0,0,0), while the upper periodic boundaries will move twice as +far. In all cases, the particle trajectories are unaffected by the +chosen value, except for a time-dependent constant translation of +positions. + +If the {update} keyword is used with the {dipole} value, then the +orientation of the dipole moment of each particle is also updated +during the time integration. This option should be used for models +where a dipole moment is assigned to finite-size particles, +e.g. spheroids via use of the "atom_style hybrid sphere +dipole"_atom_style.html command. + +The default dipole orientation integrator can be changed to the +Dullweber-Leimkuhler-McLachlan integration scheme +"(Dullweber)"_#nh-Dullweber when using {update} with the value +{dipole/dlm}. This integrator is symplectic and time-reversible, +giving better energy conservation and allows slightly longer timesteps +at only a small additional computational cost. + +:line + +NOTE: Using a barostat coupled to tilt dimensions {xy}, {xz}, {yz} can +sometimes result in arbitrarily large values of the tilt dimensions, +i.e. a dramatically deformed simulation box. LAMMPS allows the tilt +factors to grow a small amount beyond the normal limit of half the box +length (0.6 times the box length), and then performs a box "flip" to +an equivalent periodic cell. See the discussion of the {flip} keyword +above, to allow this bound to be exceeded, if desired. + +The flip operation is described in more detail in the doc page for +"fix deform"_fix_deform.html. Both the barostat dynamics and the atom +trajectories are unaffected by this operation. However, if a tilt +factor is incremented by a large amount (1.5 times the box length) on +a single timestep, LAMMPS can not accomodate this event and will +terminate the simulation with an error. This error typically indicates +that there is something badly wrong with how the simulation was +constructed, such as specifying values of {Pstart} that are too far +from the current stress value, or specifying a timestep that is too +large. Triclinic barostatting should be used with care. This also is +true for other barostat styles, although they tend to be more +forgiving of insults. In particular, it is important to recognize that +equilibrium liquids can not support a shear stress and that +equilibrium solids can not support shear stresses that exceed the +yield stress. + +One exception to this rule is if the 1st dimension in the tilt factor +(x for xy) is non-periodic. In that case, the limits on the tilt +factor are not enforced, since flipping the box in that dimension does +not change the atom positions due to non-periodicity. In this mode, +if you tilt the system to extreme angles, the simulation will simply +become inefficient due to the highly skewed simulation box. + +NOTE: Unlike the "fix temp/berendsen"_fix_temp_berendsen.html command +which performs thermostatting but NO time integration, these fixes +perform thermostatting/barostatting AND time integration. Thus you +should not use any other time integration fix, such as "fix +nve"_fix_nve.html on atoms to which this fix is applied. Likewise, +fix nvt and fix npt should not normally be used on atoms that also +have their temperature controlled by another fix - e.g. by "fix +langevin"_fix_nh.html or "fix temp/rescale"_fix_temp_rescale.html +commands. + +See the "Howto thermostat"_Howto_thermostat.html and "Howto +barostat"_Howto_barostat.html doc pages for a discussion of different +ways to compute temperature and perform thermostatting and +barostatting. + +:line + +These fixes compute a temperature and pressure each timestep. To do +this, the thermostat and barostat fixes create their own computes of +style "temp" and "pressure", as if one of these sets of commands had +been issued: + +For fix nvt: +compute fix-ID_temp group-ID temp + +For fix npt and fix nph: +compute fix-ID_temp all temp +compute fix-ID_press all pressure fix-ID_temp :pre + +For fix nvt, the group for the new temperature compute is the same as +the fix group. For fix npt and fix nph, the group for both the new +temperature and pressure compute is "all" since pressure is computed +for the entire system. In the case of fix nph, the temperature +compute is not used for thermostatting, but just for a kinetic-energy +contribution to the pressure. See the "compute +temp"_compute_temp.html and "compute pressure"_compute_pressure.html +commands for details. Note that the IDs of the new computes are the +fix-ID + underscore + "temp" or fix_ID + underscore + "press". + +Note that these are NOT the computes used by thermodynamic output (see +the "thermo_style"_thermo_style.html command) with ID = {thermo_temp} +and {thermo_press}. This means you can change the attributes of these +fix's temperature or pressure via the +"compute_modify"_compute_modify.html command. Or you can print this +temperature or pressure during thermodynamic output via the +"thermo_style custom"_thermo_style.html command using the appropriate +compute-ID. It also means that changing attributes of {thermo_temp} +or {thermo_press} will have no effect on this fix. + +Like other fixes that perform thermostatting, fix nvt and fix npt can +be used with "compute commands"_compute.html that calculate a +temperature after removing a "bias" from the atom velocities. +E.g. removing the center-of-mass velocity from a group of atoms or +only calculating temperature on the x-component of velocity or only +calculating temperature for atoms in a geometric region. This is not +done by default, but only if the "fix_modify"_fix_modify.html command +is used to assign a temperature compute to this fix that includes such +a bias term. See the doc pages for individual "compute +commands"_compute.html to determine which ones include a bias. In +this case, the thermostat works in the following manner: the current +temperature is calculated taking the bias into account, bias is +removed from each atom, thermostatting is performed on the remaining +thermal degrees of freedom, and the bias is added back in. + +:line + +These fixes can be used with either the {verlet} or {respa} +"integrators"_run_style.html. When using one of the barostat fixes +with {respa}, LAMMPS uses an integrator constructed +according to the following factorization of the Liouville propagator +(for two rRESPA levels): + +:c,image(Eqs/fix_nh1.jpg) + +This factorization differs somewhat from that of Tuckerman et al, in +that the barostat is only updated at the outermost rRESPA level, +whereas Tuckerman's factorization requires splitting the pressure into +pieces corresponding to the forces computed at each rRESPA level. In +theory, the latter method will exhibit better numerical stability. In +practice, because Pdamp is normally chosen to be a large multiple of +the outermost rRESPA timestep, the barostat dynamics are not the +limiting factor for numerical stability. Both factorizations are +time-reversible and can be shown to preserve the phase space measure +of the underlying non-Hamiltonian equations of motion. + +NOTE: This implementation has been shown to conserve linear momentum +up to machine precision under NVT dynamics. Under NPT dynamics, +for a system with zero initial total linear momentum, the total +momentum fluctuates close to zero. It may occasionally undergo brief +excursions to non-negligible values, before returning close to zero. +Over long simulations, this has the effect of causing the center-of-mass +to undergo a slow random walk. This can be mitigated by resetting +the momentum at infrequent intervals using the +"fix momentum"_fix_momentum.html command. + +:line + +The fix npt and fix nph commands can be used with rigid bodies or +mixtures of rigid bodies and non-rigid particles (e.g. solvent). But +there are also "fix rigid/npt"_fix_rigid.html and "fix +rigid/nph"_fix_rigid.html commands, which are typically a more natural +choice. See the doc page for those commands for more discussion of +the various ways to do this. + +:line + +Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. + +These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, +USER-OMP and OPT packages, respectively. They are only enabled if +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the "-suffix command-line +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. + +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. + +:line + +[Restart, fix_modify, output, run start/stop, minimize info:] + +These fixes writes the state of all the thermostat and barostat +variables to "binary restart files"_restart.html. See the +"read_restart"_read_restart.html command for info on how to re-specify +a fix in an input script that reads a restart file, so that the +operation of the fix continues in an uninterrupted fashion. + +The "fix_modify"_fix_modify.html {temp} and {press} options are +supported by these fixes. You can use them to assign a +"compute"_compute.html you have defined to this fix which will be used +in its thermostatting or barostatting procedure, as described above. +If you do this, note that the kinetic energy derived from the compute +temperature should be consistent with the virial term computed using +all atoms for the pressure. LAMMPS will warn you if you choose to +compute temperature on a subset of atoms. + +NOTE: If both the {temp} and {press} keywords are used in a single +thermo_modify command (or in two separate commands), then the order in +which the keywords are specified is important. Note that a "pressure +compute"_compute_pressure.html defines its own temperature compute as +an argument when it is specified. The {temp} keyword will override +this (for the pressure compute being used by fix npt), but only if the +{temp} keyword comes after the {press} keyword. If the {temp} keyword +comes before the {press} keyword, then the new pressure compute +specified by the {press} keyword will be unaffected by the {temp} +setting. + +The "fix_modify"_fix_modify.html {energy} option is supported by these +fixes to add the energy change induced by Nose/Hoover thermostatting +and barostatting to the system's potential energy as part of +"thermodynamic output"_thermo_style.html. + +These fixes compute a global scalar and a global vector of quantities, +which can be accessed by various "output commands"_Howto_output.html. +The scalar value calculated by these fixes is "extensive"; the vector +values are "intensive". + +The scalar is the cumulative energy change due to the fix. + +The vector stores internal Nose/Hoover thermostat and barostat +variables. The number and meaning of the vector values depends on +which fix is used and the settings for keywords {tchain} and {pchain}, +which specify the number of Nose/Hoover chains for the thermostat and +barostat. If no thermostatting is done, then {tchain} is 0. If no +barostatting is done, then {pchain} is 0. In the following list, +"ndof" is 0, 1, 3, or 6, and is the number of degrees of freedom in +the barostat. Its value is 0 if no barostat is used, else its value +is 6 if any off-diagonal stress tensor component is barostatted, else +its value is 1 if {couple xyz} is used or {couple xy} for a 2d +simulation, otherwise its value is 3. + +The order of values in the global vector and their meaning is as +follows. The notation means there are tchain values for eta, followed +by tchain for eta_dot, followed by ndof for omega, etc: + +eta\[tchain\] = particle thermostat displacements (unitless) +eta_dot\[tchain\] = particle thermostat velocities (1/time units) +omega\[ndof\] = barostat displacements (unitless) +omega_dot\[ndof\] = barostat velocities (1/time units) +etap\[pchain\] = barostat thermostat displacements (unitless) +etap_dot\[pchain\] = barostat thermostat velocities (1/time units) +PE_eta\[tchain\] = potential energy of each particle thermostat displacement (energy units) +KE_eta_dot\[tchain\] = kinetic energy of each particle thermostat velocity (energy units) +PE_omega\[ndof\] = potential energy of each barostat displacement (energy units) +KE_omega_dot\[ndof\] = kinetic energy of each barostat velocity (energy units) +PE_etap\[pchain\] = potential energy of each barostat thermostat displacement (energy units) +KE_etap_dot\[pchain\] = kinetic energy of each barostat thermostat velocity (energy units) +PE_strain\[1\] = scalar strain energy (energy units) :ul + +These fixes can ramp their external temperature and pressure over +multiple runs, using the {start} and {stop} keywords of the +"run"_run.html command. See the "run"_run.html command for details of +how to do this. + +These fixes are not invoked during "energy +minimization"_minimize.html. + +:line + +[Restrictions:] + +{X}, {y}, {z} cannot be barostatted if the associated dimension is not +periodic. {Xy}, {xz}, and {yz} can only be barostatted if the +simulation domain is triclinic and the 2nd dimension in the keyword +({y} dimension in {xy}) is periodic. {Z}, {xz}, and {yz}, cannot be +barostatted for 2D simulations. The "create_box"_create_box.html, +"read data"_read_data.html, and "read_restart"_read_restart.html +commands specify whether the simulation box is orthogonal or +non-orthogonal (triclinic) and explain the meaning of the xy,xz,yz +tilt factors. + +For the {temp} keyword, the final Tstop cannot be 0.0 since it would +make the external T = 0.0 at some timestep during the simulation which +is not allowed in the Nose/Hoover formulation. + +The {scaleyz yes} and {scalexz yes} keyword/value pairs can not be used +for 2D simulations. {scaleyz yes}, {scalexz yes}, and {scalexy yes} options +can only be used if the 2nd dimension in the keyword is periodic, +and if the tilt factor is not coupled to the barostat via keywords +{tri}, {yz}, {xz}, and {xy}. + +Without the {cauchystat} keyword, the barostat algorithm +controls the Second-Piola Kirchhoff stress, which is a stress measure +referred to the undeformed (initial) simulation box. If the box +deforms substantially during the equilibration, the difference between +the set values and the final true (Cauchy) stresses can be +considerable. + +The {cauchystat} keyword modifies the barostat as per Miller et +al. (Miller)_"#nh-Miller" so that the Cauchy stress is controlled. +{alpha} is the non-dimensional parameter, typically set to 0.001 or +0.01 that determines how aggresively the algorithm drives the system +towards the set Cauchy stresses. Larger values of {alpha} will modify +the system more quickly, but can lead to instabilities. Smaller +values will lead to longer convergence time. Since {alpha} also +influences how much the stress fluctuations deviate from the +equilibrium fluctuations, it should be set as small as possible. + +A {continue} value of {yes} indicates that the fix is subsequent to a +previous run with the Cauchystat fix, and the intention is to continue +from the converged stress state at the end of the previous run. This +may be required, for example, when implementing a multi-step loading/unloading +sequence over several fixes. + +Setting {alpha} to zero is not permitted. To "turn off" the +Cauchystat control and thus restore the equilibrium stress +fluctuations, two subsequent fixes should be used. In the first, the +Cauchystat is used and the simulation box equilibrates to the correct +shape for the desired stresses. In the second, the {fix} statement is +identical except that the {cauchystat} keyword is removed (along with +related {alpha} and {continue} values). This restores the original +Parrinello-Rahman algorithm, but now with the correct simulation box +shape from the first fix. + +These fixes can be used with dynamic groups as defined by the +"group"_group.html command. Likewise they can be used with groups to +which atoms are added or deleted over time, e.g. a deposition +simulation. However, the conservation properties of the thermostat +and barostat are defined for systems with a static set of atoms. You +may observe odd behavior if the atoms in a group vary dramatically +over time or the atom count becomes very small. + +[Related commands:] + +"fix nve"_fix_nve.html, "fix_modify"_fix_modify.html, +"run_style"_run_style.html + +[Default:] + +The keyword defaults are tchain = 3, pchain = 3, mtk = yes, tloop = +ploop = 1, nreset = 0, drag = 0.0, dilate = all, couple = none, +cauchystat = no, +scaleyz = scalexz = scalexy = yes if periodic in 2nd dimension and +not coupled to barostat, otherwise no. + +:line + +:link(nh-Martyna) +[(Martyna)] Martyna, Tobias and Klein, J Chem Phys, 101, 4177 (1994). + +:link(nh-Parrinello) +[(Parrinello)] Parrinello and Rahman, J Appl Phys, 52, 7182 (1981). + +:link(nh-Tuckerman) +[(Tuckerman)] Tuckerman, Alejandre, Lopez-Rendon, Jochim, and +Martyna, J Phys A: Math Gen, 39, 5629 (2006). + +:link(nh-Shinoda) +[(Shinoda)] Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004). + +:link(nh-Dullweber) +[(Dullweber)] Dullweber, Leimkuhler and McLachlan, J Chem Phys, 107, +5840 (1997). + +:link(nh-Miller) +[(Miller)] Miller, Tadmor, Gibson, Bernstein and Pavia, J Chem Phys, +144, 184107 (2016).