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Small cleanup

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This commit is contained in:
Stan Gerald Moore
2023-01-03 10:09:47 -07:00
parent 295d8a6903
commit a3572b61d8
3 changed files with 64 additions and 71 deletions
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2
src/KOKKOS/Install.sh
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@ -320,6 +320,8 @@ action pair_multi_lucy_rx_kokkos.cpp pair_multi_lucy_rx.cpp
action pair_multi_lucy_rx_kokkos.h pair_multi_lucy_rx.h
action pair_pace_kokkos.cpp pair_pace.cpp
action pair_pace_kokkos.h pair_pace.h
action pair_pace_extrapolation_kokkos.cpp pair_pace_extrapolation.cpp
action pair_pace_extrapolation_kokkos.h pair_pace_extrapolation.h
action pair_reaxff_kokkos.cpp pair_reaxff.cpp
action pair_reaxff_kokkos.h pair_reaxff.h
action pair_snap_kokkos.cpp pair_snap.cpp

129
src/KOKKOS/pair_pace_extrapolation_kokkos.cpp
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@ -38,19 +38,18 @@
#include <cstring>
namespace LAMMPS_NS {
struct ACEALImpl {
ACEALImpl() : basis_set(nullptr), ace(nullptr) {}
struct ACEALImpl {
ACEALImpl() : basis_set(nullptr), ace(nullptr) {}
~ACEALImpl()
{
delete basis_set;
delete ace;
}
~ACEALImpl() {
delete basis_set;
delete ace;
}
ACEBBasisSet *basis_set;
ACEBEvaluator *ace;
};
} // namespace LAMMPS_NS
ACEBBasisSet *basis_set;
ACEBEvaluator *ace;
};
} // namespace LAMMPS_NS
using namespace LAMMPS_NS;
using namespace MathConst;
@ -187,7 +186,7 @@ void PairPACEExtrapolationKokkos<DeviceType>::copy_pertype()
h_rho_core_cutoff[n] = basis_set->map_embedding_specifications.at(n).rho_core_cutoff;
h_drho_core_cutoff[n] = basis_set->map_embedding_specifications.at(n).drho_core_cutoff;
h_E0vals(n)= basis_set->E0vals(n);
h_E0vals(n) = basis_set->E0vals(n);
h_ndensity(n) = basis_set->map_embedding_specifications.at(n).ndensity;
@ -321,8 +320,6 @@ void PairPACEExtrapolationKokkos<DeviceType>::copy_tilde()
t_ace_3d d_ASI_temp;
MemKK::realloc_kokkos(d_ASI_temp, "pace:ASI_temp", nelements, total_num_functions_max, total_num_functions_max);
auto h_rank = Kokkos::create_mirror_view(d_rank);
auto h_num_ms_combs = Kokkos::create_mirror_view(d_num_ms_combs);
auto h_func_inds = Kokkos::create_mirror_view(d_func_inds);
@ -332,7 +329,7 @@ void PairPACEExtrapolationKokkos<DeviceType>::copy_tilde()
auto h_ms_combs = Kokkos::create_mirror_view(d_ms_combs);
auto h_gen_cgs = Kokkos::create_mirror_view(d_gen_cgs);
auto h_coeffs = Kokkos::create_mirror_view(d_coeffs);
// asi
// asi
auto h_ASI = Kokkos::create_mirror_view(d_ASI_temp);
// copy values on host
@ -380,7 +377,7 @@ void PairPACEExtrapolationKokkos<DeviceType>::copy_tilde()
}
for (int p = 0; p < ndensity; ++p)
h_coeffs(mu, func_ind_through, p) = func->coeff[p];
h_coeffs(mu, func_ind_through, p) = func->coeff[p];
// loop over {ms} combinations in sum
@ -400,11 +397,10 @@ void PairPACEExtrapolationKokkos<DeviceType>::copy_tilde()
// ASI
const auto &A_as_inv = b_evaluator->A_active_set_inv.at(mu);
for(int i = 0; i < total_basis_size_rank1 + total_basis_size; i++)
for(int j = 0; j < total_basis_size_rank1 + total_basis_size; j++){
h_ASI(mu,i,j)=A_as_inv(j,i); // transpose back for better performance on GPU
for (int i = 0; i < total_basis_size_rank1 + total_basis_size; i++)
for (int j = 0; j < total_basis_size_rank1 + total_basis_size; j++){
h_ASI(mu,i,j) = A_as_inv(j,i); // transpose back for better performance on GPU
}
}
Kokkos::deep_copy(d_rank, h_rank);
@ -565,6 +561,7 @@ void PairPACEExtrapolationKokkos<DeviceType>::compute(int eflag_in, int vflag_in
ev_init(eflag,vflag,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");
@ -742,7 +739,7 @@ void PairPACEExtrapolationKokkos<DeviceType>::compute(int eflag_in, int vflag_in
ev += ev_tmp;
//if gamma_flag - copy current d_gamma to extrapolation_grade_gamma
if(gamma_flag){
if (gamma_flag){
h_gamma = Kokkos::create_mirror_view(d_gamma);
Kokkos:deep_copy(h_gamma, d_gamma);
memcpy(extrapolation_grade_gamma+chunk_offset, (void *) h_gamma.data(), sizeof(double)*chunk_size);
@ -1001,7 +998,7 @@ void PairPACEExtrapolationKokkos<DeviceType>::operator() (TagPairPACEComputeRho,
//gamma_i
if(gamma_flag)
if (gamma_flag)
Kokkos::atomic_add(&projections(ii, func_ind), d_gen_cgs(mu_i, idx_ms_comb) * A_cur);
} else { // rank > 1
@ -1040,14 +1037,13 @@ void PairPACEExtrapolationKokkos<DeviceType>::operator() (TagPairPACEComputeRho,
Kokkos::atomic_add(&rhos(ii, p), B.real_part_product(d_coeffs(mu_i, func_ind, p) * d_gen_cgs(mu_i, idx_ms_comb)));
}
//gamma_i
if(gamma_flag)
Kokkos::atomic_add(&projections(ii, func_ind), B.real_part_product(d_gen_cgs(mu_i, idx_ms_comb)));
if (gamma_flag)
Kokkos::atomic_add(&projections(ii, func_ind), B.real_part_product(d_gen_cgs(mu_i, idx_ms_comb)));
}
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
void PairPACEExtrapolationKokkos<DeviceType>::operator() (TagPairPACEComputeFS, const int& ii) const
@ -1079,37 +1075,34 @@ void PairPACEExtrapolationKokkos<DeviceType>::operator() (TagPairPACEComputeFS,
}
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
void PairPACEExtrapolationKokkos<DeviceType>::operator() (TagPairPACEComputeGamma, const int& ii) const
{
const int i = d_ilist[ii + chunk_offset];
const int mu_i = d_map(type(i));
const int basis_size = d_total_basis_size(mu_i);
const int i = d_ilist[ii + chunk_offset];
const int mu_i = d_map(type(i));
const int basis_size = d_total_basis_size(mu_i);
double gamma_max = 0;
double current_gamma;
for (int j = 0; j <basis_size; j++) {
current_gamma = 0;
double gamma_max = 0;
double current_gamma;
for (int j = 0; j <basis_size; j++) { //
current_gamma = 0;
// compute row-matrix-multiplication asi_vector * A_as_inv (transposed matrix)
for (int k = 0; k < basis_size; k++)
current_gamma += projections(ii,k) * d_ASI(mu_i, k, j); //correct d_ASI(mu_i, j, k), but it is transposed during initialization
// compute row-matrix-multiplication asi_vector * A_as_inv (transposed matrix)
for (int k = 0; k < basis_size; k++)
current_gamma += projections(ii,k) * d_ASI(mu_i, k, j); //correct d_ASI(mu_i, j, k), but it is transposed during initialization
current_gamma = fabs(current_gamma);
if (current_gamma > gamma_max)
gamma_max = current_gamma;
}
// tally energy contribution
d_gamma(ii) = gamma_max;
current_gamma = fabs(current_gamma);
if (current_gamma > gamma_max)
gamma_max = current_gamma;
}
// tally energy contribution
d_gamma(ii) = gamma_max;
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
@ -1824,29 +1817,20 @@ double PairPACEExtrapolationKokkos<DeviceType>::memory_usage()
return bytes;
}
/* ---------------------------------------------------------------------- */
namespace LAMMPS_NS {
template class PairPACEExtrapolationKokkos<LMPDeviceType>;
#ifdef LMP_KOKKOS_GPU
template class PairPACEExtrapolationKokkos<LMPHostType>;
#endif
}
/* ---------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
extract method for extracting value of scale variable
---------------------------------------------------------------------- */
template<class DeviceType>
void *PairPACEExtrapolationKokkos<DeviceType>::extract(const char *str, int &dim)
{
//check if str=="gamma_flag" then compute extrapolation grades on this iteration
dim = 0;
if (strcmp(str, "gamma_flag") == 0) return (void *) &gamma_flag;
//check if str=="gamma_flag" then compute extrapolation grades on this iteration
dim = 0;
if (strcmp(str, "gamma_flag") == 0) return (void *) &gamma_flag;
dim = 2;
if (strcmp(str, "scale") == 0) return (void *) scale;
return nullptr;
dim = 2;
if (strcmp(str, "scale") == 0) return (void *) scale;
return nullptr;
}
/* ----------------------------------------------------------------------
@ -1857,13 +1841,24 @@ void *PairPACEExtrapolationKokkos<DeviceType>::extract(const char *str, int &dim
1 or more = # of columns in per-atom array
return NULL if str is not recognized
---------------------------------------------------------------------- */
template<class DeviceType>
void *PairPACEExtrapolationKokkos<DeviceType>::extract_peratom(const char *str, int &ncol)
{
if (strcmp(str, "gamma") == 0) {
ncol = 0;
return (void *) extrapolation_grade_gamma;
}
if (strcmp(str, "gamma") == 0) {
ncol = 0;
return (void *) extrapolation_grade_gamma;
}
return nullptr;
}
/* ---------------------------------------------------------------------- */
namespace LAMMPS_NS {
template class PairPACEExtrapolationKokkos<LMPDeviceType>;
#ifdef LMP_KOKKOS_GPU
template class PairPACEExtrapolationKokkos<LMPHostType>;
#endif
}
return nullptr;
}

4
src/ML-PACE/pair_pace_extrapolation.cpp
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@ -135,16 +135,12 @@ void PairPACEExtrapolation::compute(int eflag, int vflag)
double **x = atom->x;
double **f = atom->f;
// tagint *tag = atom->tag;
int *type = atom->type;
// number of atoms in cell
int nlocal = atom->nlocal;
int newton_pair = force->newton_pair;
// number of atoms including ghost atoms
// int nall = nlocal + atom->nghost;
// inum: length of the neighborlists list
inum = list->inum;