From 9bbd1df57b76e2ff540c257afd709b7137b48007 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 9 Mar 2022 17:57:21 -0500 Subject: [PATCH] another chunk of neighbor list request updates --- src/INTERLAYER/pair_ilp_graphene_hbn.cpp | 6 +- .../pair_kolmogorov_crespi_full.cpp | 6 +- src/INTERLAYER/pair_kolmogorov_crespi_z.cpp | 2 +- src/INTERLAYER/pair_lebedeva_z.cpp | 2 +- src/MACHDYN/pair_smd_hertz.cpp | 19 ++- src/MACHDYN/pair_smd_tlsph.cpp | 39 +++-- src/MACHDYN/pair_smd_triangulated_surface.cpp | 29 ++-- src/MACHDYN/pair_smd_ulsph.cpp | 7 +- src/MANYBODY/pair_adp.cpp | 2 +- src/MANYBODY/pair_atm.cpp | 7 +- src/MANYBODY/pair_bop.cpp | 6 +- src/MANYBODY/pair_comb.cpp | 11 +- src/MANYBODY/pair_comb3.cpp | 22 ++- src/MANYBODY/pair_eam.cpp | 2 +- src/MANYBODY/pair_edip.cpp | 5 +- src/MANYBODY/pair_edip_multi.cpp | 5 +- src/MANYBODY/pair_eim.cpp | 2 +- src/MANYBODY/pair_extep.cpp | 16 +-- src/MANYBODY/pair_gw.cpp | 5 +- src/MANYBODY/pair_lcbop.cpp | 6 +- src/MANYBODY/pair_local_density.cpp | 4 +- src/MANYBODY/pair_meam_spline.cpp | 11 +- src/MANYBODY/pair_meam_sw_spline.cpp | 11 +- src/MANYBODY/pair_nb3b_harmonic.cpp | 135 ++++++++---------- src/MANYBODY/pair_polymorphic.cpp | 5 +- src/MANYBODY/pair_sw.cpp | 5 +- src/MANYBODY/pair_tersoff_table.cpp | 5 +- src/MANYBODY/pair_vashishta.cpp | 5 +- src/MC/fix_bond_create.cpp | 28 ++-- src/MC/fix_bond_swap.cpp | 6 +- src/MESONT/pair_mesocnt.cpp | 5 +- src/MESONT/pair_mesont_tpm.cpp | 9 +- src/MGPT/pair_mgpt.cpp | 45 +++--- src/MISC/pair_agni.cpp | 6 +- src/MISC/pair_srp.cpp | 7 +- src/MISC/pair_tracker.cpp | 25 ++-- 36 files changed, 190 insertions(+), 321 deletions(-) diff --git a/src/INTERLAYER/pair_ilp_graphene_hbn.cpp b/src/INTERLAYER/pair_ilp_graphene_hbn.cpp index 85a2d8bfb5..fc1289ff28 100644 --- a/src/INTERLAYER/pair_ilp_graphene_hbn.cpp +++ b/src/INTERLAYER/pair_ilp_graphene_hbn.cpp @@ -31,7 +31,6 @@ #include "memory.h" #include "my_page.h" #include "neigh_list.h" -#include "neigh_request.h" #include "neighbor.h" #include "potential_file_reader.h" @@ -342,10 +341,7 @@ void PairILPGrapheneHBN::init_style() // need a full neighbor list, including neighbors of ghosts - int irequest = neighbor->request(this, instance_me); - neighbor->requests[irequest]->half = 0; - neighbor->requests[irequest]->full = 1; - neighbor->requests[irequest]->ghost = 1; + neighbor->add_request(this, NeighConst::REQ_FULL | NeighConst::REQ_GHOST); // local ILP neighbor list // create pages if first time or if neighbor pgsize/oneatom has changed diff --git a/src/INTERLAYER/pair_kolmogorov_crespi_full.cpp b/src/INTERLAYER/pair_kolmogorov_crespi_full.cpp index a107ed29a0..3076242ee3 100644 --- a/src/INTERLAYER/pair_kolmogorov_crespi_full.cpp +++ b/src/INTERLAYER/pair_kolmogorov_crespi_full.cpp @@ -31,7 +31,6 @@ #include "memory.h" #include "my_page.h" #include "neigh_list.h" -#include "neigh_request.h" #include "neighbor.h" #include "potential_file_reader.h" @@ -313,10 +312,7 @@ void PairKolmogorovCrespiFull::init_style() // need a full neighbor list, including neighbors of ghosts - int irequest = neighbor->request(this, instance_me); - neighbor->requests[irequest]->half = 0; - neighbor->requests[irequest]->full = 1; - neighbor->requests[irequest]->ghost = 1; + neighbor->add_request(this, NeighConst::REQ_FULL | NeighConst::REQ_GHOST); // local KC neighbor list // create pages if first time or if neighbor pgsize/oneatom has changed diff --git a/src/INTERLAYER/pair_kolmogorov_crespi_z.cpp b/src/INTERLAYER/pair_kolmogorov_crespi_z.cpp index bd2ce680d5..144e09cb50 100644 --- a/src/INTERLAYER/pair_kolmogorov_crespi_z.cpp +++ b/src/INTERLAYER/pair_kolmogorov_crespi_z.cpp @@ -248,7 +248,7 @@ void PairKolmogorovCrespiZ::init_style() if (force->newton_pair == 0) error->all(FLERR, "Pair style kolmogorov/crespi/z requires newton pair on"); - neighbor->request(this, instance_me); + neighbor->add_request(this); } /* ---------------------------------------------------------------------- diff --git a/src/INTERLAYER/pair_lebedeva_z.cpp b/src/INTERLAYER/pair_lebedeva_z.cpp index f837934843..95e23d3348 100644 --- a/src/INTERLAYER/pair_lebedeva_z.cpp +++ b/src/INTERLAYER/pair_lebedeva_z.cpp @@ -245,7 +245,7 @@ void PairLebedevaZ::init_style() if (force->newton_pair == 0) error->all(FLERR,"Pair style lebedeva/z requires newton pair on"); - neighbor->request(this,instance_me); + neighbor->add_request(this); } /* ---------------------------------------------------------------------- diff --git a/src/MACHDYN/pair_smd_hertz.cpp b/src/MACHDYN/pair_smd_hertz.cpp index a5355e46e0..d115e71cdf 100644 --- a/src/MACHDYN/pair_smd_hertz.cpp +++ b/src/MACHDYN/pair_smd_hertz.cpp @@ -29,19 +29,17 @@ #include "pair_smd_hertz.h" -#include - -#include #include "atom.h" -#include "domain.h" -#include "force.h" #include "comm.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "memory.h" +#include "domain.h" #include "error.h" +#include "force.h" +#include "memory.h" +#include "neigh_list.h" +#include "neighbor.h" +#include +#include using namespace LAMMPS_NS; @@ -329,8 +327,7 @@ void PairHertz::init_style() { if (!atom->contact_radius_flag) error->all(FLERR, "Pair style smd/hertz requires atom style with contact_radius"); - int irequest = neighbor->request(this); - neighbor->requests[irequest]->size = 1; + neighbor->add_request(this, NeighConst::REQ_SIZE); // set maxrad_dynamic and maxrad_frozen for each type // include future Fix pour particles as dynamic diff --git a/src/MACHDYN/pair_smd_tlsph.cpp b/src/MACHDYN/pair_smd_tlsph.cpp index 748c6b2c0d..5fcc8742de 100644 --- a/src/MACHDYN/pair_smd_tlsph.cpp +++ b/src/MACHDYN/pair_smd_tlsph.cpp @@ -25,27 +25,27 @@ #include "pair_smd_tlsph.h" +#include "fix_smd_tlsph_reference_configuration.h" + +#include "atom.h" +#include "comm.h" +#include "domain.h" +#include "error.h" +#include "fix.h" +#include "force.h" +#include "group.h" +#include "memory.h" +#include "modify.h" +#include "neighbor.h" +#include "smd_kernels.h" +#include "smd_material_models.h" +#include "smd_math.h" +#include "update.h" + #include #include - -#include #include -#include "fix_smd_tlsph_reference_configuration.h" -#include "atom.h" -#include "domain.h" -#include "group.h" -#include "force.h" -#include "update.h" -#include "modify.h" -#include "fix.h" -#include "comm.h" -#include "neighbor.h" -#include "neigh_request.h" -#include "memory.h" -#include "error.h" -#include "smd_material_models.h" -#include "smd_kernels.h" -#include "smd_math.h" +#include using namespace SMD_Kernels; using namespace Eigen; @@ -1725,8 +1725,7 @@ void PairTlsph::init_style() { } // request a granular neighbor list - int irequest = neighbor->request(this); - neighbor->requests[irequest]->size = 1; + neighbor->add_request(this, NeighConst::REQ_SIZE); // set maxrad_dynamic and maxrad_frozen for each type // include future Fix pour particles as dynamic diff --git a/src/MACHDYN/pair_smd_triangulated_surface.cpp b/src/MACHDYN/pair_smd_triangulated_surface.cpp index 0d6abb6dfb..cecdf43ff0 100644 --- a/src/MACHDYN/pair_smd_triangulated_surface.cpp +++ b/src/MACHDYN/pair_smd_triangulated_surface.cpp @@ -29,20 +29,18 @@ #include "pair_smd_triangulated_surface.h" -#include +#include "atom.h" +#include "comm.h" +#include "domain.h" +#include "error.h" +#include "force.h" +#include "memory.h" +#include "neigh_list.h" +#include "neighbor.h" +#include #include #include -#include "atom.h" -#include "domain.h" -#include "force.h" -#include "comm.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "memory.h" -#include "error.h" - using namespace std; using namespace LAMMPS_NS; @@ -411,14 +409,7 @@ void PairTriSurf::init_style() { if (!atom->contact_radius_flag) error->all(FLERR, "Pair style smd/smd/tri_surface requires atom style with contact_radius"); - // old: half list - int irequest = neighbor->request(this); - neighbor->requests[irequest]->size = 1; - - // need a full neighbor list -// int irequest = neighbor->request(this); -// neighbor->requests[irequest]->half = 0; -// neighbor->requests[irequest]->full = 1; + neighbor->add_request(this, NeighConst::REQ_SIZE); // set maxrad_dynamic and maxrad_frozen for each type // include future Fix pour particles as dynamic diff --git a/src/MACHDYN/pair_smd_ulsph.cpp b/src/MACHDYN/pair_smd_ulsph.cpp index 71091a0419..d4e7053446 100644 --- a/src/MACHDYN/pair_smd_ulsph.cpp +++ b/src/MACHDYN/pair_smd_ulsph.cpp @@ -31,7 +31,6 @@ #include "error.h" #include "memory.h" #include "neigh_list.h" -#include "neigh_request.h" #include "neighbor.h" #include "smd_kernels.h" #include "smd_material_models.h" @@ -1434,10 +1433,8 @@ double PairULSPH::init_one(int i, int j) { void PairULSPH::init_style() { int i; -//printf(" in init style\n"); -// request a granular neighbor list - int irequest = neighbor->request(this); - neighbor->requests[irequest]->size = 1; + // request a granular neighbor list + neighbor->add_request(this, NeighConst::REQ_SIZE); // set maxrad_dynamic and maxrad_frozen for each type // include future Fix pour particles as dynamic diff --git a/src/MANYBODY/pair_adp.cpp b/src/MANYBODY/pair_adp.cpp index 0931f9c222..819a57efa2 100644 --- a/src/MANYBODY/pair_adp.cpp +++ b/src/MANYBODY/pair_adp.cpp @@ -512,7 +512,7 @@ void PairADP::init_style() file2array(); array2spline(); - neighbor->request(this,instance_me); + neighbor->add_request(this); } /* ---------------------------------------------------------------------- diff --git a/src/MANYBODY/pair_atm.cpp b/src/MANYBODY/pair_atm.cpp index f7eda909e6..4b61e575a3 100644 --- a/src/MANYBODY/pair_atm.cpp +++ b/src/MANYBODY/pair_atm.cpp @@ -18,7 +18,6 @@ #include "pair_atm.h" -#include #include "atom.h" #include "citeme.h" #include "comm.h" @@ -26,9 +25,9 @@ #include "force.h" #include "memory.h" #include "neigh_list.h" -#include "neigh_request.h" #include "neighbor.h" +#include using namespace LAMMPS_NS; @@ -257,9 +256,7 @@ void PairATM::init_style() // need a full neighbor list - int irequest = neighbor->request(this,instance_me); - neighbor->requests[irequest]->half = 0; - neighbor->requests[irequest]->full = 1; + neighbor->add_request(this, NeighConst::REQ_FULL); } /* ---------------------------------------------------------------------- diff --git a/src/MANYBODY/pair_bop.cpp b/src/MANYBODY/pair_bop.cpp index ebb576dcc9..b3aa470592 100644 --- a/src/MANYBODY/pair_bop.cpp +++ b/src/MANYBODY/pair_bop.cpp @@ -46,7 +46,6 @@ #include "math_special.h" #include "memory.h" #include "neigh_list.h" -#include "neigh_request.h" #include "neighbor.h" #include "potential_file_reader.h" #include "tabular_function.h" @@ -417,10 +416,7 @@ void PairBOP::init_style() // need a full neighbor list and neighbors of ghosts - int irequest = neighbor->request(this,instance_me); - neighbor->requests[irequest]->half = 0; - neighbor->requests[irequest]->full = 1; - neighbor->requests[irequest]->ghost = 1; + neighbor->add_request(this, NeighConst::REQ_FULL | NeighConst::REQ_GHOST); } /* ---------------------------------------------------------------------- */ diff --git a/src/MANYBODY/pair_comb.cpp b/src/MANYBODY/pair_comb.cpp index 82a47b9f6a..90e2d72512 100644 --- a/src/MANYBODY/pair_comb.cpp +++ b/src/MANYBODY/pair_comb.cpp @@ -32,7 +32,6 @@ #include "memory.h" #include "my_page.h" #include "neigh_list.h" -#include "neigh_request.h" #include "neighbor.h" #include "potential_file_reader.h" @@ -108,12 +107,12 @@ PairComb::~PairComb() memory->destroy(sht_num); memory->sfree(sht_first); - delete [] ipage; + delete[] ipage; if (allocated) { memory->destroy(setflag); memory->destroy(cutsq); - delete [] esm; + delete[] esm; } } @@ -483,9 +482,7 @@ void PairComb::init_style() // need a full neighbor list - int irequest = neighbor->request(this,instance_me); - neighbor->requests[irequest]->half = 0; - neighbor->requests[irequest]->full = 1; + neighbor->add_request(this, NeighConst::REQ_FULL); // local Comb neighbor list // create pages if first time or if neighbor pgsize/oneatom has changed @@ -496,7 +493,7 @@ void PairComb::init_style() if (oneatom != neighbor->oneatom) create = 1; if (create) { - delete [] ipage; + delete[] ipage; pgsize = neighbor->pgsize; oneatom = neighbor->oneatom; diff --git a/src/MANYBODY/pair_comb3.cpp b/src/MANYBODY/pair_comb3.cpp index 8f01749358..7c126bf8ab 100644 --- a/src/MANYBODY/pair_comb3.cpp +++ b/src/MANYBODY/pair_comb3.cpp @@ -31,7 +31,6 @@ #include "memory.h" #include "my_page.h" #include "neigh_list.h" -#include "neigh_request.h" #include "neighbor.h" #include "potential_file_reader.h" #include "text_file_reader.h" @@ -126,13 +125,13 @@ PairComb3::~PairComb3() memory->destroy(sht_num); memory->sfree(sht_first); - delete [] ipage; + delete[] ipage; if (allocated) { memory->destroy(setflag); memory->destroy(cutsq); memory->destroy(cutghost); - delete [] esm; + delete[] esm; } } @@ -216,11 +215,8 @@ void PairComb3::init_style() if (!atom->q_flag) error->all(FLERR,"Pair style COMB3 requires atom attribute q"); - // need a full neighbor list - int irequest = neighbor->request(this,instance_me); - neighbor->requests[irequest]->half = 0; - neighbor->requests[irequest]->full = 1; - neighbor->requests[irequest]->ghost = 1; +// need a full neighbor list + neighbor->add_request(this, NeighConst::REQ_FULL | NeighConst::REQ_GHOST); // local Comb neighbor list // create pages if first time or if neighbor pgsize/oneatom has changed @@ -231,7 +227,7 @@ void PairComb3::init_style() if (oneatom != neighbor->oneatom) create = 1; if (create) { - delete [] ipage; + delete[] ipage; pgsize = neighbor->pgsize; oneatom = neighbor->oneatom; @@ -2503,10 +2499,10 @@ void PairComb3::tables() } } - delete [] vrc; - delete [] rrc; - delete [] cc2; - delete [] cc3; + delete[] vrc; + delete[] rrc; + delete[] cc2; + delete[] cc3; memory->destroy(rvdw); } diff --git a/src/MANYBODY/pair_eam.cpp b/src/MANYBODY/pair_eam.cpp index fd8335fca9..77b6d551be 100644 --- a/src/MANYBODY/pair_eam.cpp +++ b/src/MANYBODY/pair_eam.cpp @@ -425,7 +425,7 @@ void PairEAM::init_style() file2array(); array2spline(); - neighbor->request(this,instance_me); + neighbor->add_request(this); embedstep = -1; } diff --git a/src/MANYBODY/pair_edip.cpp b/src/MANYBODY/pair_edip.cpp index 24a7391c92..23361e56cb 100644 --- a/src/MANYBODY/pair_edip.cpp +++ b/src/MANYBODY/pair_edip.cpp @@ -29,7 +29,6 @@ #include "force.h" #include "memory.h" #include "neigh_list.h" -#include "neigh_request.h" #include "neighbor.h" #include "potential_file_reader.h" @@ -747,9 +746,7 @@ void PairEDIP::init_style() // need a full neighbor list - int irequest = neighbor->request(this, instance_me); - neighbor->requests[irequest]->half = 0; - neighbor->requests[irequest]->full = 1; + neighbor->add_request(this, NeighConst::REQ_FULL); } /* ---------------------------------------------------------------------- diff --git a/src/MANYBODY/pair_edip_multi.cpp b/src/MANYBODY/pair_edip_multi.cpp index cdfe120fc4..4710dcce0a 100644 --- a/src/MANYBODY/pair_edip_multi.cpp +++ b/src/MANYBODY/pair_edip_multi.cpp @@ -28,7 +28,6 @@ #include "math_extra.h" #include "memory.h" #include "neigh_list.h" -#include "neigh_request.h" #include "neighbor.h" #include "potential_file_reader.h" @@ -561,9 +560,7 @@ void PairEDIPMulti::init_style() // need a full neighbor list - int irequest = neighbor->request(this,instance_me); - neighbor->requests[irequest]->half = 0; - neighbor->requests[irequest]->full = 1; + neighbor->add_request(this, NeighConst::REQ_FULL); } /* ---------------------------------------------------------------------- diff --git a/src/MANYBODY/pair_eim.cpp b/src/MANYBODY/pair_eim.cpp index badcb28e25..5a97e23b40 100644 --- a/src/MANYBODY/pair_eim.cpp +++ b/src/MANYBODY/pair_eim.cpp @@ -382,7 +382,7 @@ void PairEIM::init_style() file2array(); array2spline(); - neighbor->request(this,instance_me); + neighbor->add_request(this); } /* ---------------------------------------------------------------------- diff --git a/src/MANYBODY/pair_extep.cpp b/src/MANYBODY/pair_extep.cpp index 68db444f31..7c75cfcfc0 100644 --- a/src/MANYBODY/pair_extep.cpp +++ b/src/MANYBODY/pair_extep.cpp @@ -27,7 +27,6 @@ #include "memory.h" #include "my_page.h" #include "neigh_list.h" -#include "neigh_request.h" #include "neighbor.h" #include @@ -76,7 +75,7 @@ PairExTeP::~PairExTeP() memory->destroy(SR_numneigh); memory->sfree(SR_firstneigh); - delete [] ipage; + delete[] ipage; memory->destroy(Nt); memory->destroy(Nd); @@ -473,12 +472,7 @@ void PairExTeP::init_style() // need a full neighbor list - int irequest = neighbor->request(this); - neighbor->requests[irequest]->half = 0; - neighbor->requests[irequest]->full = 1; - - // including neighbors of ghosts - neighbor->requests[irequest]->ghost = 1; + neighbor->add_request(this, NeighConst::REQ_FULL | NeighConst::REQ_GHOST); // create pages if first time or if neighbor pgsize/oneatom has changed @@ -488,7 +482,7 @@ void PairExTeP::init_style() if (oneatom != neighbor->oneatom) create = 1; if (create) { - delete [] ipage; + delete[] ipage; pgsize = neighbor->pgsize; oneatom = neighbor->oneatom; @@ -652,7 +646,7 @@ void PairExTeP::read_file(char *file) } // deallocate words array - delete [] words; + delete[] words; /* F_IJ (3) */ // read the spline coefficients @@ -742,7 +736,7 @@ void PairExTeP::read_file(char *file) } } - delete [] words; + delete[] words; /* END F_IJ (3) */ } diff --git a/src/MANYBODY/pair_gw.cpp b/src/MANYBODY/pair_gw.cpp index 6e76c9ea39..3e948880ca 100644 --- a/src/MANYBODY/pair_gw.cpp +++ b/src/MANYBODY/pair_gw.cpp @@ -27,7 +27,6 @@ #include "math_extra.h" #include "memory.h" #include "neigh_list.h" -#include "neigh_request.h" #include "neighbor.h" #include "potential_file_reader.h" @@ -285,9 +284,7 @@ void PairGW::init_style() // need a full neighbor list - int irequest = neighbor->request(this,instance_me); - neighbor->requests[irequest]->half = 0; - neighbor->requests[irequest]->full = 1; + neighbor->add_request(this, NeighConst::REQ_FULL); } /* ---------------------------------------------------------------------- diff --git a/src/MANYBODY/pair_lcbop.cpp b/src/MANYBODY/pair_lcbop.cpp index 547fc75154..a5e15479e3 100644 --- a/src/MANYBODY/pair_lcbop.cpp +++ b/src/MANYBODY/pair_lcbop.cpp @@ -24,7 +24,6 @@ #include "comm.h" #include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" #include "my_page.h" #include "memory.h" #include "error.h" @@ -153,10 +152,7 @@ void PairLCBOP::init_style() // need a full neighbor list, including neighbors of ghosts - int irequest = neighbor->request(this,instance_me); - neighbor->requests[irequest]->half = 0; - neighbor->requests[irequest]->full = 1; - neighbor->requests[irequest]->ghost = 1; + neighbor->add_request(this, NeighConst::REQ_FULL | NeighConst::REQ_GHOST); // local SR neighbor list // create pages if first time or if neighbor pgsize/oneatom has changed diff --git a/src/MANYBODY/pair_local_density.cpp b/src/MANYBODY/pair_local_density.cpp index a811927ea4..d8bfd9d03a 100644 --- a/src/MANYBODY/pair_local_density.cpp +++ b/src/MANYBODY/pair_local_density.cpp @@ -421,12 +421,12 @@ void PairLocalDensity::coeff(int narg, char **arg) void PairLocalDensity::init_style() { // spline rho and frho arrays - // request half neighbor list array2spline(); // half neighbor request - neighbor->request(this); + + neighbor->add_request(this); } /* ---------------------------------------------------------------------- diff --git a/src/MANYBODY/pair_meam_spline.cpp b/src/MANYBODY/pair_meam_spline.cpp index b09e5b6881..706c4a6013 100644 --- a/src/MANYBODY/pair_meam_spline.cpp +++ b/src/MANYBODY/pair_meam_spline.cpp @@ -579,15 +579,8 @@ void PairMEAMSpline::init_style() error->all(FLERR,"Pair style meam/spline requires newton pair on"); // Need both full and half neighbor list. - int irequest_full = neighbor->request(this,instance_me); - neighbor->requests[irequest_full]->id = 1; - neighbor->requests[irequest_full]->half = 0; - neighbor->requests[irequest_full]->full = 1; - int irequest_half = neighbor->request(this,instance_me); - neighbor->requests[irequest_half]->id = 2; - // neighbor->requests[irequest_half]->half = 1; - // neighbor->requests[irequest_half]->halffull = 1; - // neighbor->requests[irequest_half]->halffulllist = irequest_full; + neighbor->add_request(this, NeighConst::REQ_FULL)->set_id(1); + neighbor->add_request(this)->set_id(2); } /* ---------------------------------------------------------------------- diff --git a/src/MANYBODY/pair_meam_sw_spline.cpp b/src/MANYBODY/pair_meam_sw_spline.cpp index 68f22a28c3..e0225818a2 100644 --- a/src/MANYBODY/pair_meam_sw_spline.cpp +++ b/src/MANYBODY/pair_meam_sw_spline.cpp @@ -381,8 +381,7 @@ void PairMEAMSWSpline::coeff(int narg, char **arg) // for now, only allow single element if (nelements > 1) - error->all(FLERR, - "Pair meam/sw/spline only supports single element potentials"); + error->all(FLERR, "Pair meam/sw/spline only supports single element potentials"); // read potential file @@ -463,12 +462,8 @@ void PairMEAMSWSpline::init_style() error->all(FLERR,"Pair style meam/sw/spline requires newton pair on"); // Need both full and half neighbor list. - int irequest_full = neighbor->request(this,instance_me); - neighbor->requests[irequest_full]->id = 1; - neighbor->requests[irequest_full]->half = 0; - neighbor->requests[irequest_full]->full = 1; - int irequest_half = neighbor->request(this,instance_me); - neighbor->requests[irequest_half]->id = 2; + neighbor->add_request(this, NeighConst::REQ_FULL)->set_id(1); + neighbor->add_request(this)->set_id(2); } /* ---------------------------------------------------------------------- diff --git a/src/MANYBODY/pair_nb3b_harmonic.cpp b/src/MANYBODY/pair_nb3b_harmonic.cpp index 2b86658468..d74c504aea 100644 --- a/src/MANYBODY/pair_nb3b_harmonic.cpp +++ b/src/MANYBODY/pair_nb3b_harmonic.cpp @@ -1,4 +1,3 @@ -// clang-format off /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories @@ -23,9 +22,9 @@ #include "comm.h" #include "error.h" #include "force.h" +#include "math_const.h" #include "memory.h" #include "neigh_list.h" -#include "neigh_request.h" #include "neighbor.h" #include "potential_file_reader.h" @@ -33,10 +32,10 @@ #include using namespace LAMMPS_NS; +using MathConst::MY_PI; #define DELTA 4 #define SMALL 0.001 -#define PI 3.141592653589793238462643383279 /* ---------------------------------------------------------------------- */ @@ -71,15 +70,15 @@ PairNb3bHarmonic::~PairNb3bHarmonic() void PairNb3bHarmonic::compute(int eflag, int vflag) { - int i,j,k,ii,jj,kk,inum,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; + int i, j, k, ii, jj, kk, inum, 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; - ev_init(eflag,vflag); + ev_init(eflag, vflag); double **x = atom->x; double **f = atom->f; @@ -111,10 +110,10 @@ void PairNb3bHarmonic::compute(int eflag, int vflag) delr1[0] = x[j][0] - xtmp; delr1[1] = x[j][1] - ytmp; delr1[2] = x[j][2] - ztmp; - rsq1 = delr1[0]*delr1[0] + delr1[1]*delr1[1] + delr1[2]*delr1[2]; + rsq1 = delr1[0] * delr1[0] + delr1[1] * delr1[1] + delr1[2] * delr1[2]; if (rsq1 > params[ijparam].cutsq) continue; - for (kk = jj+1; kk < jnum; kk++) { + for (kk = jj + 1; kk < jnum; kk++) { k = jlist[kk]; k &= NEIGHMASK; ktype = map[type[k]]; @@ -124,11 +123,11 @@ void PairNb3bHarmonic::compute(int eflag, int vflag) delr2[0] = x[k][0] - xtmp; delr2[1] = x[k][1] - ytmp; delr2[2] = x[k][2] - ztmp; - rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2]; + 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); + threebody(¶ms[ijparam], ¶ms[ikparam], ¶ms[ijkparam], rsq1, rsq2, delr1, delr2, + fj, fk, eflag, evdwl); f[i][0] -= fj[0] + fk[0]; f[i][1] -= fj[1] + fk[1]; @@ -140,7 +139,7 @@ void PairNb3bHarmonic::compute(int eflag, int vflag) f[k][1] += fk[1]; f[k][2] += fk[2]; - if (evflag) ev_tally3(i,j,k,evdwl,0.0,fj,fk,delr1,delr2); + if (evflag) ev_tally3(i, j, k, evdwl, 0.0, fj, fk, delr1, delr2); } } } @@ -153,21 +152,21 @@ void PairNb3bHarmonic::compute(int eflag, int vflag) void PairNb3bHarmonic::allocate() { allocated = 1; - int n = atom->ntypes; + int np1 = atom->ntypes + 1; - memory->create(setflag,n+1,n+1,"pair:setflag"); - memory->create(cutsq,n+1,n+1,"pair:cutsq"); + memory->create(setflag, np1, np1, "pair:setflag"); + memory->create(cutsq, np1, np1, "pair:cutsq"); - map = new int[n+1]; + map = new int[np1]; } /* ---------------------------------------------------------------------- global settings ------------------------------------------------------------------------- */ -void PairNb3bHarmonic::settings(int narg, char **/*arg*/) +void PairNb3bHarmonic::settings(int narg, char ** /*arg*/) { - if (narg != 0) error->all(FLERR,"Illegal pair_style command"); + if (narg != 0) error->all(FLERR, "Illegal pair_style command"); } /* ---------------------------------------------------------------------- @@ -178,7 +177,7 @@ void PairNb3bHarmonic::coeff(int narg, char **arg) { if (!allocated) allocate(); - map_element2type(narg-3,arg+3); + map_element2type(narg - 3, arg + 3); // read potential file and initialize potential parameters @@ -186,23 +185,19 @@ void PairNb3bHarmonic::coeff(int narg, char **arg) setup_params(); } - /* ---------------------------------------------------------------------- init specific to this pair style ------------------------------------------------------------------------- */ void PairNb3bHarmonic::init_style() { - if (atom->tag_enable == 0) - error->all(FLERR,"Pair style nb3b/harmonic requires atom IDs"); + if (atom->tag_enable == 0) error->all(FLERR, "Pair style nb3b/harmonic requires atom IDs"); if (force->newton_pair == 0) - error->all(FLERR,"Pair style nb3b/harmonic requires newton pair on"); + error->all(FLERR, "Pair style nb3b/harmonic requires newton pair on"); // need a full neighbor list - int irequest = neighbor->request(this,instance_me); - neighbor->requests[irequest]->half = 0; - neighbor->requests[irequest]->full = 1; + neighbor->add_request(this, NeighConst::REQ_FULL); } /* ---------------------------------------------------------------------- @@ -211,7 +206,7 @@ void PairNb3bHarmonic::init_style() double PairNb3bHarmonic::init_one(int i, int j) { - if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set"); + if (setflag[i][j] == 0) error->all(FLERR, "All pair coeffs are not set"); return cutmax; } @@ -228,13 +223,12 @@ void PairNb3bHarmonic::read_file(char *file) if (comm->me == 0) { PotentialFileReader reader(lmp, file, "nb3b/harmonic", unit_convert_flag); - char * line; + char *line; // transparently convert units for supported conversions int unit_convert = reader.get_unit_convert(); - double conversion_factor = utils::get_conversion_factor(utils::ENERGY, - unit_convert); + double conversion_factor = utils::get_conversion_factor(utils::ENERGY, unit_convert); while ((line = reader.next_line(NPARAMS_PER_LINE))) { try { ValueTokenizer values(line); @@ -262,21 +256,20 @@ void PairNb3bHarmonic::read_file(char *file) if (nparams == maxparam) { maxparam += DELTA; - params = (Param *) memory->srealloc(params,maxparam*sizeof(Param), - "pair:params"); + params = (Param *) memory->srealloc(params, maxparam * sizeof(Param), "pair:params"); // make certain all addional allocated storage is initialized // to avoid false positives when checking with valgrind - memset(params + nparams, 0, DELTA*sizeof(Param)); + memset(params + nparams, 0, DELTA * sizeof(Param)); } params[nparams].ielement = ielement; params[nparams].jelement = jelement; params[nparams].kelement = kelement; - params[nparams].k_theta = values.next_double(); - params[nparams].theta0 = values.next_double(); - params[nparams].cutoff = values.next_double(); + params[nparams].k_theta = values.next_double(); + params[nparams].theta0 = values.next_double(); + params[nparams].cutoff = values.next_double(); if (unit_convert) params[nparams].k_theta *= conversion_factor; } catch (TokenizerException &e) { @@ -285,7 +278,7 @@ void PairNb3bHarmonic::read_file(char *file) if (params[nparams].k_theta < 0.0 || params[nparams].theta0 < 0.0 || params[nparams].cutoff < 0.0) - error->one(FLERR,"Illegal nb3b/harmonic parameter"); + error->one(FLERR, "Illegal nb3b/harmonic parameter"); nparams++; } @@ -295,17 +288,17 @@ void PairNb3bHarmonic::read_file(char *file) MPI_Bcast(&maxparam, 1, MPI_INT, 0, world); if (comm->me != 0) { - params = (Param *) memory->srealloc(params,maxparam*sizeof(Param), "pair:params"); + params = (Param *) memory->srealloc(params, maxparam * sizeof(Param), "pair:params"); } - MPI_Bcast(params, maxparam*sizeof(Param), MPI_BYTE, 0, world); + MPI_Bcast(params, maxparam * sizeof(Param), MPI_BYTE, 0, world); } /* ---------------------------------------------------------------------- */ void PairNb3bHarmonic::setup_params() { - int i,j,k,m,n; + int i, j, k, m, n; double rtmp; // set elem3param for all triplet combinations @@ -313,20 +306,19 @@ void PairNb3bHarmonic::setup_params() // do not allow for ACB in place of ABC memory->destroy(elem3param); - memory->create(elem3param,nelements,nelements,nelements,"pair:elem3param"); + memory->create(elem3param, nelements, nelements, nelements, "pair:elem3param"); for (i = 0; i < nelements; i++) for (j = 0; j < nelements; j++) for (k = 0; k < nelements; k++) { n = -1; for (m = 0; m < nparams; m++) { - if (i == params[m].ielement && j == params[m].jelement && - k == params[m].kelement) { - if (n >= 0) error->all(FLERR,"Potential file has duplicate entry"); + if (i == params[m].ielement && j == params[m].jelement && k == params[m].kelement) { + if (n >= 0) error->all(FLERR, "Potential file has duplicate entry"); n = m; } } - if (n < 0) error->all(FLERR,"Potential file is missing an entry"); + if (n < 0) error->all(FLERR, "Potential file is missing an entry"); elem3param[i][j][k] = n; } @@ -341,8 +333,7 @@ void PairNb3bHarmonic::setup_params() params[m].cut = params[m].cutoff; params[m].cutsq = params[m].cut * params[m].cut; - params[m].theta0 = params[m].theta0 / 180.0 * PI; - + params[m].theta0 = params[m].theta0 / 180.0 * MY_PI; } // set cutmax to max of all params @@ -356,48 +347,44 @@ void PairNb3bHarmonic::setup_params() /* ---------------------------------------------------------------------- */ - -void PairNb3bHarmonic::threebody(Param * /*paramij*/, Param * /*paramik*/, - Param *paramijk, - double rsq1, double rsq2, - double *delr1, double *delr2, - double *fj, double *fk, int eflag, double &eng) +void PairNb3bHarmonic::threebody(Param * /*paramij*/, Param * /*paramik*/, Param *paramijk, + double rsq1, double rsq2, double *delr1, double *delr2, double *fj, + double *fk, int eflag, double &eng) { - double dtheta,tk; - double r1,r2,c,s,a,a11,a12,a22; + double dtheta, tk; + double r1, r2, c, s, a, a11, a12, a22; // angle (cos and sin) r1 = sqrt(rsq1); r2 = sqrt(rsq2); - c = delr1[0]*delr2[0] + delr1[1]*delr2[1] + delr1[2]*delr2[2]; - c /= r1*r2; + c = delr1[0] * delr2[0] + delr1[1] * delr2[1] + delr1[2] * delr2[2]; + c /= r1 * r2; if (c > 1.0) c = 1.0; if (c < -1.0) c = -1.0; - s = sqrt(1.0 - c*c); + s = sqrt(1.0 - c * c); if (s < SMALL) s = SMALL; - s = 1.0/s; + s = 1.0 / s; // force & energy dtheta = acos(c) - paramijk->theta0; tk = paramijk->k_theta * dtheta; - if (eflag) eng = tk*dtheta; + if (eflag) eng = tk * dtheta; a = -2.0 * tk * s; - a11 = a*c / rsq1; - a12 = -a / (r1*r2); - a22 = a*c / rsq2; + a11 = a * c / rsq1; + a12 = -a / (r1 * r2); + a22 = a * c / rsq2; - fj[0] = a11*delr1[0] + a12*delr2[0]; - fj[1] = a11*delr1[1] + a12*delr2[1]; - fj[2] = a11*delr1[2] + a12*delr2[2]; - fk[0] = a22*delr2[0] + a12*delr1[0]; - fk[1] = a22*delr2[1] + a12*delr1[1]; - fk[2] = a22*delr2[2] + a12*delr1[2]; + fj[0] = a11 * delr1[0] + a12 * delr2[0]; + fj[1] = a11 * delr1[1] + a12 * delr2[1]; + fj[2] = a11 * delr1[2] + a12 * delr2[2]; + fk[0] = a22 * delr2[0] + a12 * delr1[0]; + fk[1] = a22 * delr2[1] + a12 * delr1[1]; + fk[2] = a22 * delr2[2] + a12 * delr1[2]; } - diff --git a/src/MANYBODY/pair_polymorphic.cpp b/src/MANYBODY/pair_polymorphic.cpp index 3d2bf9497e..21aba6d6df 100644 --- a/src/MANYBODY/pair_polymorphic.cpp +++ b/src/MANYBODY/pair_polymorphic.cpp @@ -29,7 +29,6 @@ #include "math_extra.h" #include "memory.h" #include "neigh_list.h" -#include "neigh_request.h" #include "neighbor.h" #include "potential_file_reader.h" #include "tabular_function.h" @@ -525,9 +524,7 @@ void PairPolymorphic::init_style() // need a full neighbor list - int irequest = neighbor->request(this); - neighbor->requests[irequest]->half = 0; - neighbor->requests[irequest]->full = 1; + neighbor->add_request(this, NeighConst::REQ_FULL); } /* ---------------------------------------------------------------------- diff --git a/src/MANYBODY/pair_sw.cpp b/src/MANYBODY/pair_sw.cpp index bac65a2464..2bef1cb11c 100644 --- a/src/MANYBODY/pair_sw.cpp +++ b/src/MANYBODY/pair_sw.cpp @@ -24,7 +24,6 @@ #include "force.h" #include "memory.h" #include "neigh_list.h" -#include "neigh_request.h" #include "neighbor.h" #include "potential_file_reader.h" @@ -264,9 +263,7 @@ void PairSW::init_style() // need a full neighbor list - int irequest = neighbor->request(this,instance_me); - neighbor->requests[irequest]->half = 0; - neighbor->requests[irequest]->full = 1; + neighbor->add_request(this, NeighConst::REQ_FULL); } /* ---------------------------------------------------------------------- diff --git a/src/MANYBODY/pair_tersoff_table.cpp b/src/MANYBODY/pair_tersoff_table.cpp index 0c11760737..5a04cc60ca 100644 --- a/src/MANYBODY/pair_tersoff_table.cpp +++ b/src/MANYBODY/pair_tersoff_table.cpp @@ -29,7 +29,6 @@ #include "force.h" #include "memory.h" #include "neigh_list.h" -#include "neigh_request.h" #include "neighbor.h" #include "potential_file_reader.h" @@ -743,9 +742,7 @@ void PairTersoffTable::init_style() // need a full neighbor list - int irequest = neighbor->request(this,instance_me); - neighbor->requests[irequest]->half = 0; - neighbor->requests[irequest]->full = 1; + neighbor->add_request(this, NeighConst::REQ_FULL); } /* ---------------------------------------------------------------------- diff --git a/src/MANYBODY/pair_vashishta.cpp b/src/MANYBODY/pair_vashishta.cpp index 40a42cd44b..6ce6c6f59a 100644 --- a/src/MANYBODY/pair_vashishta.cpp +++ b/src/MANYBODY/pair_vashishta.cpp @@ -26,7 +26,6 @@ #include "memory.h" #include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" #include "potential_file_reader.h" #include @@ -270,9 +269,7 @@ void PairVashishta::init_style() // need a full neighbor list - int irequest = neighbor->request(this); - neighbor->requests[irequest]->half = 0; - neighbor->requests[irequest]->full = 1; + neighbor->add_request(this, NeighConst::REQ_FULL); } /* ---------------------------------------------------------------------- diff --git a/src/MC/fix_bond_create.cpp b/src/MC/fix_bond_create.cpp index eecf8763b7..c05a37cb38 100644 --- a/src/MC/fix_bond_create.cpp +++ b/src/MC/fix_bond_create.cpp @@ -14,21 +14,21 @@ #include "fix_bond_create.h" -#include -#include "update.h" -#include "respa.h" #include "atom.h" -#include "force.h" -#include "modify.h" -#include "pair.h" #include "comm.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "random_mars.h" -#include "memory.h" #include "error.h" +#include "force.h" #include "math_const.h" +#include "memory.h" +#include "modify.h" +#include "neigh_list.h" +#include "neighbor.h" +#include "pair.h" +#include "random_mars.h" +#include "respa.h" +#include "update.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; @@ -283,11 +283,7 @@ void FixBondCreate::init() } // need a half neighbor list, built every Nevery steps - - int irequest = neighbor->request(this,instance_me); - neighbor->requests[irequest]->pair = 0; - neighbor->requests[irequest]->fix = 1; - neighbor->requests[irequest]->occasional = 1; + neighbor->add_request(this, NeighConst::REQ_OCCASIONAL); lastcheck = -1; } diff --git a/src/MC/fix_bond_swap.cpp b/src/MC/fix_bond_swap.cpp index c0978f51cb..c4abf31f16 100644 --- a/src/MC/fix_bond_swap.cpp +++ b/src/MC/fix_bond_swap.cpp @@ -26,7 +26,6 @@ #include "memory.h" #include "modify.h" #include "neigh_list.h" -#include "neigh_request.h" #include "neighbor.h" #include "pair.h" #include "random_mars.h" @@ -160,10 +159,7 @@ void FixBondSwap::init() // need a half neighbor list, built every Nevery steps - int irequest = neighbor->request(this,instance_me); - neighbor->requests[irequest]->pair = 0; - neighbor->requests[irequest]->fix = 1; - neighbor->requests[irequest]->occasional = 1; + neighbor->add_request(this, NeighConst::REQ_OCCASIONAL); // zero out stats diff --git a/src/MESONT/pair_mesocnt.cpp b/src/MESONT/pair_mesocnt.cpp index 4d6e30c191..728296d274 100644 --- a/src/MESONT/pair_mesocnt.cpp +++ b/src/MESONT/pair_mesocnt.cpp @@ -26,7 +26,6 @@ #include "math_extra.h" #include "memory.h" #include "neigh_list.h" -#include "neigh_request.h" #include "neighbor.h" #include "potential_file_reader.h" #include "update.h" @@ -503,9 +502,7 @@ void PairMesoCNT::init_style() // need a full neighbor list - int irequest = neighbor->request(this, instance_me); - neighbor->requests[irequest]->half = 0; - neighbor->requests[irequest]->full = 1; + neighbor->add_request(this, NeighConst::REQ_FULL); } /* ---------------------------------------------------------------------- diff --git a/src/MESONT/pair_mesont_tpm.cpp b/src/MESONT/pair_mesont_tpm.cpp index b52adafe89..0c1ef1939a 100644 --- a/src/MESONT/pair_mesont_tpm.cpp +++ b/src/MESONT/pair_mesont_tpm.cpp @@ -16,7 +16,6 @@ #include "pair_mesont_tpm.h" #include "export_mesont.h" - #include "atom.h" #include "comm.h" #include "force.h" @@ -24,12 +23,11 @@ #include "error.h" #include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" #include #include -#include +#include #include #include @@ -765,10 +763,7 @@ void PairMESONTTPM::write_data_all(FILE *fp) { void PairMESONTTPM::init_style() { //make sure that a full list is created (including ghost nodes) - int r = neighbor->request(this,instance_me); - neighbor->requests[r]->half = false; - neighbor->requests[r]->full = true; - neighbor->requests[r]->ghost = true; + neighbor->add_request(this, NeighConst::REQ_FULL | NeighConst::REQ_GHOST); } void* PairMESONTTPM::extract(const char *str, int &) { diff --git a/src/MGPT/pair_mgpt.cpp b/src/MGPT/pair_mgpt.cpp index 4744693b0f..98c02732a1 100644 --- a/src/MGPT/pair_mgpt.cpp +++ b/src/MGPT/pair_mgpt.cpp @@ -769,7 +769,7 @@ void PairMGPT::compute_x(const int *nnei,const int * const *nlist, if (domain->triclinic) { if (comm->me == 0) printf("Can not handle triclinic box yet\n"); - error->all(__FILE__,__LINE__,"Can not handle triclinic cell with mgpt yet."); + error->all(FLERR,"Can not handle triclinic cell with mgpt yet."); } /* @@ -876,7 +876,7 @@ void PairMGPT::compute_x(const int *nnei,const int * const *nlist, if (first[i+1] > nneitot) { printf("nneitot = %d, short list full. i=%d\n", nneitot,i); - error->one(__FILE__,__LINE__,"Shit! Short list full\n"); + error->one(FLERR,"Shit! Short list full\n"); } } @@ -1272,7 +1272,7 @@ void PairMGPT::compute_x(const int *nnei,const int * const *nlist, " k=%d first[k]=%d first[k+1]=%d mk=%d\n", j,first[j],first[j+1],mj, k,first[k],first[k+1],mk); - error->one(__FILE__,__LINE__,"Shit, brkoen quad loop"); + error->one(FLERR,"Shit, brkoen quad loop"); } if (nlist_short[mj] == nlist_short[mk]) { @@ -1804,7 +1804,7 @@ void PairMGPT::allocate() ------------------------------------------------------------------------- */ void PairMGPT::settings(int narg, char **/*arg*/) { - if (narg != 0) error->all(__FILE__,__LINE__,"Illegal pair_style command"); + if (narg != 0) error->all(FLERR,"Illegal pair_style command"); } /* ---------------------------------------------------------------------- @@ -1816,18 +1816,18 @@ void PairMGPT::coeff(int narg, char **arg) int single_precision = 0; if (narg < 5) - error->all(__FILE__,__LINE__, + error->all(FLERR, "Not enough arguments for mgpt (MGPT) pair coefficients."); if (!allocated) allocate(); // Make sure I,J args are * * if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0) - error->all(__FILE__,__LINE__,"Incorrect args for pair coefficients"); + error->all(FLERR,"Incorrect args for pair coefficients"); double vol; if (sscanf(arg[4], "%lg", &vol) != 1 || vol <= 0.0) - error->all(__FILE__,__LINE__,"Invalid volume in mgpt (MGPT) pair coefficients."); + error->all(FLERR,"Invalid volume in mgpt (MGPT) pair coefficients."); volpres_flag = 1; single_precision = 0; @@ -1846,8 +1846,8 @@ void PairMGPT::coeff(int narg, char **arg) char line[1024]; sprintf(line,"(In %s:%d) Invalid value for volumetric pressure argument.\n" "It should be \"volpress yes\" or \"volpress no\".\n" - "The value is \"%s\".\n",__FILE__,__LINE__,arg[iarg+1]); - error->all(__FILE__,__LINE__,line); + "The value is \"%s\".\n",FLERR,arg[iarg+1]); + error->all(FLERR,line); } volpres_tag = 1; iarg += 2; @@ -1868,8 +1868,8 @@ void PairMGPT::coeff(int narg, char **arg) "It should be e.g. \"nbody=1234\" (for single, pair, triple, and quad forces/energiers)\n" "For e.g. only pair and triple forces/energies, use \"nbody=23\".\n" "The default is \"nbody=1234\".\n" - "The current value is \"%s\".\n",__FILE__,__LINE__,arg[iarg+1]); - error->all(__FILE__,__LINE__,line); + "The current value is \"%s\".\n",FLERR,arg[iarg+1]); + error->all(FLERR,line); } nbody_tag = 1; iarg += 2; @@ -1882,8 +1882,8 @@ void PairMGPT::coeff(int narg, char **arg) char line[1024]; sprintf(line,"(In %s:%d) Invalid value for precision argument.\n" "It should be \"precision single\" or \"precision double\".\n" - "The value is \"%s\".\n",__FILE__,__LINE__,arg[iarg+1]); - error->all(__FILE__,__LINE__,line); + "The value is \"%s\".\n",FLERR,arg[iarg+1]); + error->all(FLERR,line); } precision_tag = 1; iarg += 2; @@ -1894,8 +1894,8 @@ void PairMGPT::coeff(int narg, char **arg) " volpress {yes|no} , default = yes\n" " precision {single|double} , default = double\n" " nbody {[1234,]*} , default = whichever terms potential require\n" - "The invalid argument is \"%s\".\n",__FILE__,__LINE__,arg[iarg]); - error->all(__FILE__,__LINE__,line); + "The invalid argument is \"%s\".\n",FLERR,arg[iarg]); + error->all(FLERR,line); } } @@ -1995,18 +1995,11 @@ void PairMGPT::coeff(int narg, char **arg) void PairMGPT::init_style() { if (force->newton_pair == 0) - error->all(__FILE__,__LINE__,"Pair style mgpt requires newton pair on."); + error->all(FLERR,"Pair style mgpt requires newton pair on."); - // Need full neighbor list. - int irequest_full = neighbor->request(this); - neighbor->requests[irequest_full]->id = 1; - neighbor->requests[irequest_full]->half = 0; - neighbor->requests[irequest_full]->full = 1; - neighbor->requests[irequest_full]->ghost = 1; - - // Also need half neighbor list. - int irequest_half = neighbor->request(this); - neighbor->requests[irequest_half]->id = 2; + // Need a half list and a full neighbor list with neighbors of ghosts + neighbor->add_request(this, NeighConst::REQ_FULL | NeighConst::REQ_GHOST)->set_id(1); + neighbor->add_request(this)->set_id(2); } /* ---------------------------------------------------------------------- diff --git a/src/MISC/pair_agni.cpp b/src/MISC/pair_agni.cpp index f614dd9c36..46cc630f2d 100644 --- a/src/MISC/pair_agni.cpp +++ b/src/MISC/pair_agni.cpp @@ -27,7 +27,6 @@ #include "math_special.h" #include "memory.h" #include "neigh_list.h" -#include "neigh_request.h" #include "neighbor.h" #include "potential_file_reader.h" @@ -249,10 +248,7 @@ void PairAGNI::coeff(int narg, char **arg) void PairAGNI::init_style() { // need a full neighbor list - - int irequest = neighbor->request(this,instance_me); - neighbor->requests[irequest]->half = 0; - neighbor->requests[irequest]->full = 1; + neighbor->add_request(this, NeighConst::REQ_FULL); } /* ---------------------------------------------------------------------- diff --git a/src/MISC/pair_srp.cpp b/src/MISC/pair_srp.cpp index 77a8eb4c2d..84f7c330a8 100644 --- a/src/MISC/pair_srp.cpp +++ b/src/MISC/pair_srp.cpp @@ -471,16 +471,13 @@ void PairSRP::init_style() // bond particles do not belong to group all // but thermo normalization is by nall // therefore should turn off normalization - int me; - MPI_Comm_rank(world,&me); char *arg1[2]; arg1[0] = (char *) "norm"; arg1[1] = (char *) "no"; output->thermo->modify_params(2, arg1); - if (me == 0) - error->message(FLERR,"Thermo normalization turned off by pair srp"); + if (comm->me == 0) error->message(FLERR,"Thermo normalization turned off by pair srp"); - neighbor->request(this,instance_me); + neighbor->add_request(this); } /* ---------------------------------------------------------------------- diff --git a/src/MISC/pair_tracker.cpp b/src/MISC/pair_tracker.cpp index 43e65d6af7..502b04c49d 100644 --- a/src/MISC/pair_tracker.cpp +++ b/src/MISC/pair_tracker.cpp @@ -24,7 +24,6 @@ #include "memory.h" #include "modify.h" #include "neigh_list.h" -#include "neigh_request.h" #include "neighbor.h" #include "update.h" @@ -271,15 +270,11 @@ void PairTracker::init_style() if (!atom->radius_flag && finitecutflag) error->all(FLERR, "Pair tracker requires atom attribute radius for finite cutoffs"); - // need a history neigh list - - int irequest = neighbor->request(this, instance_me); - if (finitecutflag) { - neighbor->requests[irequest]->size = 1; - neighbor->requests[irequest]->history = 1; - // history flag won't affect results, but match granular pairstyles - // so neighborlist can be copied to reduce overhead - } + int neigh_flags = NeighConst::REQ_DEFAULT; + // history flag won't affect results, but match granular pairstyles + // so neighborlist can be copied to reduce overhead + if (finitecutflag) neigh_flags |= NeighConst::REQ_SIZE | NeighConst::REQ_HISTORY; + neighbor->add_request(this, neigh_flags); // if history is stored and first init, create Fix to store history // it replaces FixDummy, created in the constructor @@ -288,10 +283,12 @@ void PairTracker::init_style() if (fix_history == nullptr) { modify->replace_fix("NEIGH_HISTORY_TRACK_DUMMY", fmt::format("NEIGH_HISTORY_TRACK all NEIGH_HISTORY {}", size_history), 1); - int ifix = modify->find_fix("NEIGH_HISTORY_TRACK"); - fix_history = (FixNeighHistory *) modify->fix[ifix]; + fix_history = (FixNeighHistory *) modify->get_fix_by_id("NEIGH_HISTORY_TRACK"); fix_history->pair = this; fix_history->use_bit_flag = 0; + } else { + fix_history = (FixNeighHistory *) modify->get_fix_by_id("NEIGH_HISTORY_TRACK"); + if (!fix_history) error->all(FLERR, "Could not find pair fix neigh history ID"); } if (finitecutflag) { @@ -342,10 +339,6 @@ void PairTracker::init_style() MPI_Allreduce(&onerad_frozen[1], &maxrad_frozen[1], atom->ntypes, MPI_DOUBLE, MPI_MAX, world); } - int ifix = modify->find_fix("NEIGH_HISTORY_TRACK"); - if (ifix < 0) error->all(FLERR, "Could not find pair fix neigh history ID"); - fix_history = (FixNeighHistory *) modify->fix[ifix]; - auto trackfixes = modify->get_fix_by_style("pair/tracker"); if (trackfixes.size() != 1) error->all(FLERR, "Must use exactly one fix pair/tracker command with pair style tracker");