virial bugfix
This commit is contained in:
alphataubio
@ -28,8 +28,6 @@
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#include "variable.h"
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#include "update.h"
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#include <iostream>
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using namespace LAMMPS_NS;
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using MathSpecial::powint;
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@ -44,7 +42,6 @@ FixWallLJ93Kokkos<DeviceType>::FixWallLJ93Kokkos(LAMMPS *lmp, int narg, char **a
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execution_space = ExecutionSpaceFromDevice<DeviceType>::space;
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datamask_read = X_MASK | V_MASK | MASK_MASK;
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datamask_modify = F_MASK;
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virial_global_flag = virial_peratom_flag = 0;
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memoryKK->create_kokkos(k_epsilon,6,"wall_lj93:epsilon");
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memoryKK->create_kokkos(k_sigma,6,"wall_lj93:sigma");
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@ -94,7 +91,7 @@ FixWallLJ93Kokkos<DeviceType>::~FixWallLJ93Kokkos()
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memoryKK->destroy_kokkos(d_coeff4);
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memoryKK->destroy_kokkos(d_offset);
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//std::cerr << "ok 2\n";
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memoryKK->destroy_kokkos(k_vatom,vatom);
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}
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@ -120,9 +117,6 @@ void FixWallLJ93Kokkos<DeviceType>::precompute(int m)
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template <class DeviceType>
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void FixWallLJ93Kokkos<DeviceType>::post_force(int vflag)
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{
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//std::cerr << "post_force DeviceType=" << DeviceType << "\n";
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atomKK->sync(execution_space,datamask_read);
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atomKK->modified(execution_space,datamask_modify);
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@ -130,12 +124,19 @@ void FixWallLJ93Kokkos<DeviceType>::post_force(int vflag)
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v_init(vflag);
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// reallocate per-atom arrays if necessary
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if (vflag_atom) {
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memoryKK->destroy_kokkos(k_vatom,vatom);
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memoryKK->create_kokkos(k_vatom,vatom,maxvatom,"wall_lj93:vatom");
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d_vatom = k_vatom.template view<DeviceType>();
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}
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// energy intialize.
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// eflag is used to track whether wall energies have been communicated.
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eflag = 0;
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//for (int m = 0; m <= nwall; m++) d_ewall(m) = 0.0;
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for (int m = 0; m <= nwall; m++) k_ewall.d_view(m) = 0.0;
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for (int m = 0; m <= nwall; m++) d_ewall(m) = 0.0;
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// coord = current position of wall
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// evaluate variables if necessary, wrap with clear/add
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@ -144,6 +145,7 @@ void FixWallLJ93Kokkos<DeviceType>::post_force(int vflag)
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if (varflag) modify->clearstep_compute();
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double coord;
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for (int m = 0; m < nwall; m++) {
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if (xstyle[m] == VARIABLE) {
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coord = input->variable->compute_equal(xindex[m]);
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@ -168,12 +170,22 @@ void FixWallLJ93Kokkos<DeviceType>::post_force(int vflag)
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}
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wall_particle(m, wallwhich[m], coord);
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}
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k_ewall.template modify<DeviceType>();
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k_ewall.template sync<LMPHostType>();
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if (varflag) modify->addstep_compute(update->ntimestep + 1);
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atomKK->modified(execution_space,F_MASK);
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if (vflag_atom) {
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k_vatom.template modify<DeviceType>();
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k_vatom.template sync<LMPHostType>();
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}
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}
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@ -194,31 +206,35 @@ void FixWallLJ93Kokkos<DeviceType>::wall_particle(int m_in, int which, double co
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d_f = atomKK->k_f.template view<DeviceType>();
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d_mask = atomKK->k_mask.template view<DeviceType>();
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int nlocal = atomKK->nlocal;
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double tmp[7];
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dim = which / 2;
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side = which % 2;
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if (side == 0) side = -1;
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double result[13];
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copymode = 1;
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FixWallLJ93KokkosFunctor<DeviceType> wp_functor(this);
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Kokkos::parallel_reduce(nlocal,wp_functor,tmp);
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FixWallLJ93KokkosFunctor<DeviceType> functor(this);
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Kokkos::parallel_reduce(nlocal,functor,result);
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copymode = 0;
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//std::cerr << fmt::format("tmp[0]={} tmp[{}]={} \n",tmp[0],m+1,tmp[m+1]);
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Kokkos::atomic_add(&(d_ewall[0]),tmp[0]);
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Kokkos::atomic_add(&(d_ewall[m+1]),tmp[m+1]);
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//std::cerr << fmt::format("k_ewall.d_view[0]={} k_ewall.d_view[{}]={} \n",k_ewall.d_view[0],m+1,k_ewall.d_view[m+1]);
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Kokkos::atomic_add(&(d_ewall[0]),result[0]);
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Kokkos::atomic_add(&(d_ewall[m+1]),result[m+1]);
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if (vflag_global) {
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virial[0] += result[7];
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virial[1] += result[8];
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virial[2] += result[9];
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virial[3] += result[10];
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virial[4] += result[11];
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virial[5] += result[12];
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}
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}
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template <class DeviceType>
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KOKKOS_INLINE_FUNCTION
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void FixWallLJ93Kokkos<DeviceType>::wall_particle_item(int i, value_type ewall) const {
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void FixWallLJ93Kokkos<DeviceType>::wall_particle_item(int i, value_type result) const {
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if (d_mask(i) & groupbit) {
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double delta;
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if (side < 0) delta = d_x(i,dim) - coord;
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@ -232,37 +248,46 @@ void FixWallLJ93Kokkos<DeviceType>::wall_particle_item(int i, value_type ewall)
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double r10inv = r4inv*r4inv*r2inv;
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double fwall = side * (d_coeff1(m)*r10inv - d_coeff2(m)*r4inv);
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d_f(i,dim) -= fwall;
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ewall[0] += d_coeff3(m)*r4inv*r4inv*rinv - d_coeff4(m)*r2inv*rinv - d_offset(m);
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ewall[m+1] += fwall;
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result[0] += d_coeff3(m)*r4inv*r4inv*rinv - d_coeff4(m)*r2inv*rinv - d_offset(m);
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result[m+1] += fwall;
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if (evflag) {
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double vn;
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if (side < 0)
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vn = -fwall * delta;
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else
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vn = fwall * delta;
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v_tally(result, dim, i, vn);
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}
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}
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}
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/* ----------------------------------------------------------------------
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energy of wall interaction
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tally virial component into global and per-atom accumulators
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n = index of virial component (0-5)
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i = local index of atom
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vn = nth component of virial for the interaction
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increment nth component of global virial by vn
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increment nth component of per-atom virial by vn
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this method can be used when fix computes forces in post_force()
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and the force depends on a distance to some external object
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e.g. fix wall/lj93: compute virial only on owned atoms
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------------------------------------------------------------------------- */
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/*
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template <class DeviceType>
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double FixWallLJ93Kokkos<DeviceType>::compute_scalar()
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KOKKOS_INLINE_FUNCTION
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void FixWallLJ93Kokkos<DeviceType>::v_tally(value_type result, int n, int i, double vn) const
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{
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// only sum across procs one time
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//std::cerr << fmt::format("k_ewall[0] = {} d_ewall[0] = {}\n", k_ewall.h_view[0], k_ewall.d_view[0] );
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if (vflag_global)
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result[n+7] += vn;
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k_ewall.template sync<DeviceType>();
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if (eflag == 0) {
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MPI_Allreduce(k_ewall.h_view.data(), ewall_all, 7, MPI_DOUBLE, MPI_SUM, world);
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eflag = 1;
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}
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std::cerr << fmt::format("compute_scalar() = {}\n", ewall_all[0]);
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return ewall_all[0];
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if (vflag_atom)
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Kokkos::atomic_add(&(d_vatom(i,n)),vn);
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}
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*/
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namespace LAMMPS_NS {
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template class FixWallLJ93Kokkos<LMPDeviceType>;
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@ -28,6 +28,7 @@ FixStyle(wall/lj93/kk/host,FixWallLJ93Kokkos<LMPHostType>);
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namespace LAMMPS_NS {
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template <class DeviceType>
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class FixWallLJ93Kokkos : public FixWallLJ93 {
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public:
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@ -54,6 +55,9 @@ class FixWallLJ93Kokkos : public FixWallLJ93 {
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typename AT::t_f_array d_f;
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typename AT::t_int_1d d_mask;
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DAT::tdual_virial_array k_vatom;
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typename AT::t_virial_array d_vatom;
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typename AT::tdual_ffloat_1d k_epsilon,k_sigma,k_cutoff;
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typename AT::t_ffloat_1d d_epsilon,d_sigma,d_cutoff;
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@ -62,25 +66,34 @@ class FixWallLJ93Kokkos : public FixWallLJ93 {
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typename AT::tdual_ffloat_1d k_ewall;
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typename AT::t_ffloat_1d d_ewall;
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KOKKOS_INLINE_FUNCTION
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void v_tally(value_type, int, int, double) const;
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};
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template <class DeviceType>
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struct FixWallLJ93KokkosFunctor {
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typedef DeviceType device_type ;
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typedef DeviceType device_type;
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typedef double value_type[];
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const int value_count;
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FixWallLJ93Kokkos<DeviceType> c;
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FixWallLJ93KokkosFunctor(FixWallLJ93Kokkos<DeviceType>* c_ptr):
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//value_count(c_ptr->m+1), c(*c_ptr) {}
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value_count(7), c(*c_ptr) {}
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value_count(13), c(*c_ptr) {}
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KOKKOS_INLINE_FUNCTION
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void operator()(const int i, value_type ewall) const {
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c.wall_particle_item(i,ewall);
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void init(value_type result) const {
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for (int i=0 ; i<13 ; i++ ) result[i] = 0.0;
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}
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};
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KOKKOS_INLINE_FUNCTION
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void operator()(const int i, value_type result) const {
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c.wall_particle_item(i,result);
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}
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};
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}
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@ -1,82 +1,83 @@
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---
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lammps_version: 17 Feb 2022
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date_generated: Fri Mar 18 22:18:01 2022
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lammps_version: 27 Jun 2024
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tags: generated
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date_generated: Fri Aug 2 23:56:34 2024
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epsilon: 2e-14
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skip_tests:
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prerequisites: ! |
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atom full
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fix wall/lj93
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pre_commands: ! |
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boundary p f p
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boundary f f f
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post_commands: ! |
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fix move all nve
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fix test solute wall/lj93 ylo EDGE 100.0 2.0 5.0 yhi EDGE 100.0 2.0 5.0
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# fix_modify test virial yes
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fix test solute wall/lj93 xlo EDGE 10 1 9 xhi EDGE 20 2 8 ylo EDGE 30 3 7 yhi EDGE 40 4 6 zlo EDGE 50 9 1 zhi EDGE 60 8 2
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fix_modify test virial yes
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input_file: in.fourmol
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natoms: 29
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run_stress: ! |2-
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0.0000000000000000e+00 -5.0602303343219951e+01 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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global_scalar: -4.108987997282236
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run_stress: ! |-
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-2.0397146716028331e+01 -2.2856621254611628e+02 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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global_scalar: -40.30685365068726
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global_vector: ! |-
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2 0 -11.164431050504302
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6 0.29980999393772645 -3.0501185308112175 10.543906177602482 -35.13125907303744 0 0
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run_pos: ! |2
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1 -2.7045470054680359e-01 2.4914748797509958e+00 -1.6696421170224640e-01
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2 3.1002519717316468e-01 2.9626113274873114e+00 -8.5465020014164161e-01
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3 -7.0398162067377834e-01 1.2305605729036173e+00 -6.2777311164097793e-01
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4 -1.5818159800097509e+00 1.4837403071563420e+00 -1.2538711657744748e+00
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5 -9.0719738875553246e-01 9.2652132637432294e-01 3.9954221603268608e-01
|
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6 2.4831723728788374e-01 2.8313028009631025e-01 -1.2314233417272680e+00
|
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7 3.4143527622588610e-01 -2.2646550717066182e-02 -2.5292291415442443e+00
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8 1.1743552225802836e+00 -4.8863228494885080e-01 -6.3783432950414043e-01
|
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9 1.3800524229825968e+00 -2.5274721033806635e-01 2.8353985887329919e-01
|
||||
10 2.0510765220590312e+00 -1.4604063740279585e+00 -9.8323745081970004e-01
|
||||
11 1.7878031944447623e+00 -1.9921863272956677e+00 -1.8890602447628950e+00
|
||||
12 3.0063007039452563e+00 -4.9013350497696184e-01 -1.6231898107433360e+00
|
||||
13 4.0515402959196631e+00 -8.9202011606671716e-01 -1.6400005529926165e+00
|
||||
14 2.6066963345552767e+00 -4.1789253965578244e-01 -2.6634003608801833e+00
|
||||
15 2.9695287185759982e+00 5.5422613165070589e-01 -1.2342022021804264e+00
|
||||
16 2.6747029695251561e+00 -2.4124119054596429e+00 -2.3435746150366733e-02
|
||||
17 2.2153577785319198e+00 -2.0897985186960004e+00 1.1963150794498112e+00
|
||||
18 2.1369701704057920e+00 3.0158507413651594e+00 -3.5179348337167076e+00
|
||||
19 1.5355837136080241e+00 2.6255292355373734e+00 -4.2353987779868740e+00
|
||||
20 2.7727573003167976e+00 3.6923910440726924e+00 -3.9330842459576383e+00
|
||||
21 4.9040128073837339e+00 -4.0752348170758461e+00 -3.6210314709795299e+00
|
||||
22 4.3582355554510048e+00 -4.2126119427061379e+00 -4.4612844196307497e+00
|
||||
23 5.7439382849366911e+00 -3.5821957939240279e+00 -3.8766361295959513e+00
|
||||
24 2.0689243582397667e+00 3.1513346907334592e+00 3.1550389754792341e+00
|
||||
25 1.3045351331439887e+00 3.2665125705877287e+00 2.5111855257342670e+00
|
||||
26 2.5809237402706717e+00 4.0117602605484128e+00 3.2212060529083963e+00
|
||||
27 -1.9611343130358911e+00 -4.3563411931365605e+00 2.1098293115526028e+00
|
||||
28 -2.7473562684515085e+00 -4.0200819932383203e+00 1.5830052163435302e+00
|
||||
29 -1.3126000191360121e+00 -3.5962518039484110e+00 2.2746342468738372e+00
|
||||
1 -2.7045514660423325e-01 2.4919366600449733e+00 -1.6697231639531507e-01
|
||||
2 3.1000084135335193e-01 2.9645912303343991e+00 -8.5463206395936475e-01
|
||||
3 -7.0397943335818880e-01 1.2305810523260226e+00 -6.2776977494480968e-01
|
||||
4 -1.5818284818588833e+00 1.4850714726761622e+00 -1.2538699508869366e+00
|
||||
5 -9.0720735536750730e-01 9.2652311870881010e-01 3.9954248474779297e-01
|
||||
6 2.4831612077180826e-01 2.8312998598620581e-01 -1.2314234208099035e+00
|
||||
7 3.4143432145485658e-01 -2.2646550480708717e-02 -2.5292291412289485e+00
|
||||
8 1.1743655769886039e+00 -4.8863573859247217e-01 -6.3783597964106820e-01
|
||||
9 1.3800803748715951e+00 -2.5274721986531667e-01 2.8353956705790218e-01
|
||||
10 2.0510864147345527e+00 -1.4605128263713651e+00 -9.8323665039331498e-01
|
||||
11 1.7878396739201072e+00 -1.9926579680652934e+00 -1.8890577068286438e+00
|
||||
12 3.0063280485262682e+00 -4.9013506205958607e-01 -1.6231897745485795e+00
|
||||
13 4.0517059148826196e+00 -8.9225492586105981e-01 -1.6400002853466527e+00
|
||||
14 2.6067556451864973e+00 -4.1789236780812949e-01 -2.6634004714578920e+00
|
||||
15 2.9696053942689340e+00 5.5422609386529809e-01 -1.2342020619448599e+00
|
||||
16 2.6747224655532205e+00 -2.4126238070421215e+00 -2.3433759666701557e-02
|
||||
17 2.2153701802770058e+00 -2.0899272946638008e+00 1.1963135022288505e+00
|
||||
18 2.1369701704036461e+00 3.0158507413784363e+00 -3.5179348337072978e+00
|
||||
19 1.5355837135394632e+00 2.6255292354749651e+00 -4.2353987771402171e+00
|
||||
20 2.7727573003740993e+00 3.6923910441184606e+00 -3.9330842453158126e+00
|
||||
21 4.9040128073779838e+00 -4.0752348170721300e+00 -3.6210314709713383e+00
|
||||
22 4.3582355554508565e+00 -4.2126119427059994e+00 -4.4612844196303154e+00
|
||||
23 5.7439382849363732e+00 -3.5821957939239444e+00 -3.8766361295956120e+00
|
||||
24 2.0689243582383923e+00 3.1513346907508031e+00 3.1550389751044130e+00
|
||||
25 1.3045351331268087e+00 3.2665125705965665e+00 2.5111855257113618e+00
|
||||
26 2.5809237402701828e+00 4.0117602605517018e+00 3.2212060528784647e+00
|
||||
27 -1.9611343130326251e+00 -4.3563411931375260e+00 2.1098293115519637e+00
|
||||
28 -2.7473562684514818e+00 -4.0200819932384704e+00 1.5830052163435808e+00
|
||||
29 -1.3126000191358462e+00 -3.5962518039486921e+00 2.2746342468738376e+00
|
||||
run_vel: ! |2
|
||||
1 8.1727799799441551e-03 1.6773171346479498e-02 4.7791658662457619e-03
|
||||
2 5.4195488166242462e-03 6.5417253116750503e-03 -1.4101336509904706e-03
|
||||
3 -8.2223992085164246e-03 -1.2908451784809975e-02 -4.0945960825392183e-03
|
||||
4 -3.7699737621353186e-03 -6.5732339099368641e-03 -1.1186165990462573e-03
|
||||
5 -1.1021432529769989e-02 -9.8900600342308066e-03 -2.8408577395243402e-03
|
||||
6 -3.9676605755577875e-02 4.6817208693894503e-02 3.7148485968758402e-02
|
||||
7 9.1033903828574569e-04 -1.0128523335196111e-02 -5.1568251845436980e-02
|
||||
8 7.9064705135345748e-03 -3.3507235864772382e-03 3.4557097186682206e-02
|
||||
9 1.5644176974450778e-03 3.7365545213281916e-03 1.5047408817898655e-02
|
||||
10 2.9201446823370270e-02 -2.9249578721348601e-02 -1.5018077430999392e-02
|
||||
11 -4.7835961499775063e-03 -3.7481385151954837e-03 -2.3464104148495902e-03
|
||||
12 2.2696452071679614e-03 -3.4774155893559008e-04 -3.0640770423525257e-03
|
||||
13 2.7531740460470166e-03 5.8171061608719103e-03 -7.9467454050767680e-04
|
||||
14 3.5246182390652257e-03 -5.7939995598917460e-03 -3.9478431188056783e-03
|
||||
15 -1.8547943544027830e-03 -5.8554729976774897e-03 6.2938485111532208e-03
|
||||
16 1.8681499978038456e-02 -1.3262466211006751e-02 -4.5638651456391420e-02
|
||||
17 -1.2896269973838886e-02 9.7527665158999004e-03 3.7296535364672513e-02
|
||||
18 -8.0065796043573602e-04 -8.6270472784857216e-04 -1.4483040597982864e-03
|
||||
19 1.2452390821689194e-03 -2.5061097122815435e-03 7.2998631031035615e-03
|
||||
20 3.5930057864791303e-03 3.6938851570931927e-03 3.2322732168550625e-03
|
||||
21 -1.4689219756961087e-03 -2.7352107824530806e-04 7.0581625180889649e-04
|
||||
22 -7.0694199165145062e-03 -4.2577148692717554e-03 2.8079117911323321e-04
|
||||
23 6.0446963236685256e-03 -1.4000131545098763e-03 2.5819754799379711e-03
|
||||
24 3.1926367400896563e-04 -9.9445663445895099e-04 1.4999996220927227e-04
|
||||
25 1.3789753472275083e-04 -4.4335894812290054e-03 -8.1808138555694750e-04
|
||||
26 2.0485904026313513e-03 2.7813358637372391e-03 4.3245727137078242e-03
|
||||
27 4.5604120258846295e-04 -1.0305523038990200e-03 2.1188058429346654e-04
|
||||
28 -6.2544520868040715e-03 1.4127711161841167e-03 -1.8429821879802923e-03
|
||||
29 6.4110631528576680e-04 3.1273432717073592e-03 3.7253671106756733e-03
|
||||
1 8.1742887450585739e-03 1.7228249520172705e-02 4.7636200154285678e-03
|
||||
2 5.3742131209134954e-03 8.5014084989938534e-03 -1.3734731162460402e-03
|
||||
3 -8.2161778164033632e-03 -1.2869362708201489e-02 -4.0888375199228388e-03
|
||||
4 -3.7787634477676642e-03 -5.2533470458882917e-03 -1.1161118587284771e-03
|
||||
5 -1.1032293389383448e-02 -9.8863340104885598e-03 -2.8403367946737107e-03
|
||||
6 -3.9677570612003256e-02 4.6816683666629423e-02 3.7148298982540365e-02
|
||||
7 9.0938409416312202e-04 -1.0128522535253528e-02 -5.1568254916651068e-02
|
||||
8 7.9194167018994642e-03 -3.3569176675024141e-03 3.4554033379153554e-02
|
||||
9 1.5923285603331428e-03 3.7365113011970019e-03 1.5046752270197748e-02
|
||||
10 2.9208357286776593e-02 -2.9353993769823783e-02 -1.5016704917306721e-02
|
||||
11 -4.7465540645016645e-03 -4.2165276646841865e-03 -2.3412478153019894e-03
|
||||
12 2.2980757077101510e-03 -3.5091405216452847e-04 -3.0640046931904290e-03
|
||||
13 2.9148511000306786e-03 5.5851722208680194e-03 -7.9412268026523897e-04
|
||||
14 3.5836019249020573e-03 -5.7936540681715965e-03 -3.9480663628116922e-03
|
||||
15 -1.7778657432845671e-03 -5.8555598171606280e-03 6.2941335584716009e-03
|
||||
16 1.8700222665862708e-02 -1.3473926436394508e-02 -4.5635589324539552e-02
|
||||
17 -1.2883485803873765e-02 9.6240189248986089e-03 3.7294040194137568e-02
|
||||
18 -8.0065796511591945e-04 -8.6270470075116407e-04 -1.4483040404113881e-03
|
||||
19 1.2452390066448272e-03 -2.5061097760180838e-03 7.2998639311393438e-03
|
||||
20 3.5930058446123790e-03 3.6938852063833996e-03 3.2322738498526673e-03
|
||||
21 -1.4689219875639078e-03 -2.7352107061007723e-04 7.0581626870114592e-04
|
||||
22 -7.0694199167938608e-03 -4.2577148689919644e-03 2.8079118009157448e-04
|
||||
23 6.0446963229432490e-03 -1.4000131543898697e-03 2.5819754806854374e-03
|
||||
24 3.1926367036916678e-04 -9.9445660295952466e-04 1.4999958504844645e-04
|
||||
25 1.3789750016399599e-04 -4.4335894629157517e-03 -8.1808143179135507e-04
|
||||
26 2.0485903999350758e-03 2.7813358672621209e-03 4.3245726820250576e-03
|
||||
27 4.5604120926159787e-04 -1.0305523058923018e-03 2.1188058299333266e-04
|
||||
28 -6.2544520867115292e-03 1.4127711158545754e-03 -1.8429821878482673e-03
|
||||
29 6.4110631563933543e-04 3.1273432711488012e-03 3.7253671106878979e-03
|
||||
...
|
||||
|
||||
Reference in New Issue
Block a user