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Merge pull request #3954 from bnebgen-LANL/mliap_null_fix

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Mliap null fix
This commit is contained in:
Axel Kohlmeyer
2023-10-26 20:18:32 -04:00
committed by GitHub
parent 7051852f8f eea3b1a757
commit ed6c603488
11 changed files with 38 additions and 14 deletions
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1
src/KOKKOS/mliap_data_kokkos.cpp
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@ -85,6 +85,7 @@ void MLIAPDataKokkos<DeviceType>::generate_neighdata(class NeighList *list_in, i
// clear gradforce and elems arrays
int nall = atom->nlocal + atom->nghost;
nlocal = atom->nlocal;
ntotal = nall;
if (gradgradflag > -1){
auto d_gradforce = k_gradforce.template view<DeviceType>();

4
src/KOKKOS/mliap_data_kokkos.h
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@ -118,6 +118,7 @@ public:
egradient(nullptr),
ntotal(base.ntotal),
nlistatoms(base.nlistatoms),
nlocal(base.nlocal),
natomneigh(base.natomneigh),
numneighs(base.numneighs),
iatoms(base.k_iatoms.d_view.data()),
@ -171,6 +172,7 @@ public:
// Neighborlist stuff
const int ntotal;
const int nlistatoms;
const int nlocal;
const int natomneigh;
int *numneighs;
int *iatoms;
@ -191,7 +193,7 @@ public:
int dev;
#ifdef LMP_KOKKOS_GPU
MLIAPDataKokkosDevice(MLIAPDataKokkos<LMPHostType> &base) : ndescriptors(-1),nparams(-1),nelements(-1),ntotal(-1),nlistatoms(-1),natomneigh(-1),
MLIAPDataKokkosDevice(MLIAPDataKokkos<LMPHostType> &base) : ndescriptors(-1),nparams(-1),nelements(-1),ntotal(-1),nlistatoms(-1),nlocal(-1),natomneigh(-1),
nneigh_max(-1),npairs(-1)
{
// It cannot get here, but needed for compilation

1
src/KOKKOS/mliap_model_python_couple_kokkos.pyx
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@ -25,6 +25,7 @@ cdef extern from "mliap_data_kokkos.h" namespace "LAMMPS_NS":
cdef cppclass MLIAPDataKokkosDevice:
# Array shapes
int nlistatoms
int nlocal
int ndescriptors
# Input data

5
src/KOKKOS/mliap_unified_couple_kokkos.pyx
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@ -59,6 +59,7 @@ cdef extern from "mliap_data_kokkos.h" namespace "LAMMPS_NS":
int ntotal # total number of owned and ghost atoms on this proc
int nlistatoms # current number of atoms in local atom lists
int nlocal
int natomneigh # current number of atoms and ghosts in atom neighbor arrays
int * numneighs # neighbors count for each atom
int * iatoms # index of each atom
@ -290,6 +291,10 @@ cdef class MLIAPDataPy:
@property
def nlistatoms(self):
return self.data.nlistatoms
@property
def nlocal(self):
return self.data.nlocal
@property
def natomneigh(self):

16
src/KOKKOS/mliap_unified_kokkos.cpp
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@ -271,8 +271,8 @@ void LAMMPS_NS::update_pair_energy(MLIAPDataKokkosDevice *data, double *eij)
{
auto d_eatoms = data->eatoms;
auto d_pair_i= data->pair_i;
const auto nlistatoms = data->nlistatoms;
Kokkos::parallel_for(nlistatoms, KOKKOS_LAMBDA(int ii){
const auto nlocal = data->nlocal;
Kokkos::parallel_for(nlocal, KOKKOS_LAMBDA(int ii){
d_eatoms[ii] = 0;
});
@ -281,7 +281,7 @@ void LAMMPS_NS::update_pair_energy(MLIAPDataKokkosDevice *data, double *eij)
double e = 0.5 * eij[ii];
// must not count any contribution where i is not a local atom
if (i < nlistatoms) {
if (i < nlocal) {
Kokkos::atomic_add(&d_eatoms[i], e);
local_sum += e;
}
@ -294,7 +294,7 @@ void LAMMPS_NS::update_pair_energy(MLIAPDataKokkosDevice *data, double *eij)
void LAMMPS_NS::update_pair_forces(MLIAPDataKokkosDevice *data, double *fij)
{
const auto nlistatoms = data->nlistatoms;
const auto nlocal = data->nlocal;
auto *f = data->f;
auto pair_i = data->pair_i;
auto j_atoms = data->jatoms;
@ -315,7 +315,7 @@ void LAMMPS_NS::update_pair_forces(MLIAPDataKokkosDevice *data, double *fij)
int i = pair_i[ii];
int j = j_atoms[ii];
// must not count any contribution where i is not a local atom
if (i < nlistatoms) {
if (i < nlocal) {
Kokkos::atomic_add(&f[i*3+0], fij[ii3+0]);
Kokkos::atomic_add(&f[i*3+1], fij[ii3+1]);
Kokkos::atomic_add(&f[i*3+2], fij[ii3+2]);
@ -378,12 +378,12 @@ void LAMMPS_NS::update_pair_forces(MLIAPDataKokkosDevice *data, double *fij)
void LAMMPS_NS::update_atom_energy(MLIAPDataKokkosDevice *data, double *ei)
{
auto d_eatoms = data->eatoms;
const auto nlistatoms = data->nlistatoms;
const auto nlocal = data->nlocal;
Kokkos::parallel_reduce(nlistatoms, KOKKOS_LAMBDA(int i, double &local_sum){
Kokkos::parallel_reduce(nlocal, KOKKOS_LAMBDA(int i, double &local_sum){
double e = ei[i];
// must not count any contribution where i is not a local atom
if (i < nlistatoms) {
if (i < nlocal) {
d_eatoms[i] = e;
local_sum += e;
}

6
src/KOKKOS/pair_mliap_kokkos.cpp
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@ -138,6 +138,7 @@ template<class DeviceType>
void PairMLIAPKokkos<DeviceType>::allocate()
{
int n = atom->ntypes;
memoryKK->destroy_kokkos(k_map, map);
memoryKK->destroy_kokkos(k_cutsq, cutsq);
memoryKK->destroy_kokkos(k_setflag, setflag);
@ -275,7 +276,10 @@ void PairMLIAPKokkos<DeviceType>::coeff(int narg, char **arg) {
auto h_cutsq=k_cutsq.template view<LMPHostType>();
for (int itype=1; itype <= atom->ntypes; ++itype)
for (int jtype=1; jtype <= atom->ntypes; ++jtype)
h_cutsq(itype,jtype) = descriptor->cutsq[map[itype]][map[jtype]];
// do not set cuts for NULL atoms
if (map[itype] >= 0 && map[jtype] >= 0) {
h_cutsq(itype,jtype) = descriptor->cutsq[map[itype]][map[jtype]];
}
k_cutsq.modify<LMPHostType>();
k_cutsq.sync<DeviceType>();
constexpr int gradgradflag = -1;

1
src/ML-IAP/mliap_data.cpp
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@ -115,6 +115,7 @@ void MLIAPData::generate_neighdata(NeighList *list_in, int eflag_in, int vflag_i
int **firstneigh = list->firstneigh;
int nall = atom->nlocal + atom->nghost;
nlocal = atom->nlocal;
ntotal = nall;
// grow nmax gradforce, elems arrays if necessary

1
src/ML-IAP/mliap_data.h
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@ -60,6 +60,7 @@ class MLIAPData : protected Pointers {
int ntotal; // total number of owned and ghost atoms on this proc
int nlistatoms; // current number of atoms in local atom lists
int nlocal;
int nlistatoms_max; // allocated size of descriptor array
int natomneigh; // current number of atoms and ghosts in atom neighbor arrays
int natomneigh_max; // allocated size of atom neighbor arrays

1
src/ML-IAP/mliap_model_python_couple.pyx
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@ -18,6 +18,7 @@ cdef extern from "mliap_data.h" namespace "LAMMPS_NS":
cdef cppclass MLIAPData:
# Array shapes
int nlistatoms
int nlocal
int ndescriptors
# Input data

9
src/ML-IAP/mliap_unified.cpp
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@ -246,6 +246,7 @@ void LAMMPS_NS::update_pair_energy(MLIAPData *data, double *eij)
{
double e_total = 0.0;
const auto nlistatoms = data->nlistatoms;
const auto nlocal = data->nlocal;
for (int ii = 0; ii < nlistatoms; ii++) data->eatoms[ii] = 0;
for (int ii = 0; ii < data->npairs; ii++) {
@ -253,7 +254,7 @@ void LAMMPS_NS::update_pair_energy(MLIAPData *data, double *eij)
double e = 0.5 * eij[ii];
// must not count any contribution where i is not a local atom
if (i < nlistatoms) {
if (i < nlocal) {
data->eatoms[i] += e;
e_total += e;
}
@ -267,7 +268,9 @@ void LAMMPS_NS::update_pair_energy(MLIAPData *data, double *eij)
void LAMMPS_NS::update_pair_forces(MLIAPData *data, double *fij)
{
const auto nlistatoms = data->nlistatoms;
//Bugfix: need to account for Null atoms in local atoms
//const auto nlistatoms = data->nlistatoms;
const auto nlocal = data->nlocal;
double **f = data->f;
for (int ii = 0; ii < data->npairs; ii++) {
int ii3 = ii * 3;
@ -275,7 +278,7 @@ void LAMMPS_NS::update_pair_forces(MLIAPData *data, double *fij)
int j = data->jatoms[ii];
// must not count any contribution where i is not a local atom
if (i < nlistatoms) {
if (i < nlocal) {
f[i][0] += fij[ii3];
f[i][1] += fij[ii3 + 1];
f[i][2] += fij[ii3 + 2];

7
src/ML-IAP/mliap_unified_couple.pyx
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@ -53,7 +53,8 @@ cdef extern from "mliap_data.h" namespace "LAMMPS_NS":
# only neighbors strictly inside descriptor cutoff
int ntotal # total number of owned and ghost atoms on this proc
int nlistatoms # current number of atoms in local atom lists
int nlistatoms # current number of non-NULL atoms in local atom lists
int nlocal # current number of NULL and normal atoms in local atom lists
int natomneigh # current number of atoms and ghosts in atom neighbor arrays
int * numneighs # neighbors count for each atom
int * iatoms # index of each atom
@ -226,6 +227,10 @@ cdef class MLIAPDataPy:
@property
def nlistatoms(self):
return self.data.nlistatoms
@property
def nlocal(self):
return self.data.nlocal
@property
def natomneigh(self):