ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Fix issue with Kokkos ReaxFF and pair hybrid

Browse Source
This commit is contained in:
Stan Moore
2020-07-14 09:02:57 -06:00
parent 9068d17afc
commit 001dcb6bb1
6 changed files with 37 additions and 46 deletions
Download Patch File Download Diff File Expand all files Collapse all files

11
src/KOKKOS/fix_qeq_reax_kokkos.cpp
View File

@ -195,7 +195,6 @@ void FixQEqReaxKokkos<DeviceType>::pre_force(int vflag)
type = atomKK->k_type.view<DeviceType>();
mask = atomKK->k_mask.view<DeviceType>();
nlocal = atomKK->nlocal;
nall = atom->nlocal + atom->nghost;
newton_pair = force->newton_pair;
k_params.template sync<DeviceType>();
@ -207,6 +206,7 @@ void FixQEqReaxKokkos<DeviceType>::pre_force(int vflag)
d_neighbors = k_list->d_neighbors;
d_ilist = k_list->d_ilist;
inum = list->inum;
ignum = inum + list->gnum;
copymode = 1;
@ -373,7 +373,6 @@ void FixQEqReaxKokkos<DeviceType>::allocate_array()
}
// init_storage
const int ignum = atom->nlocal + atom->nghost;
FixQEqReaxKokkosZeroFunctor<DeviceType> zero_functor(this);
Kokkos::parallel_for(ignum,zero_functor);
@ -732,7 +731,7 @@ void FixQEqReaxKokkos<DeviceType>::cg_solve1()
FixQEqReaxKokkosSparse12Functor<DeviceType> sparse12_functor(this);
Kokkos::parallel_for(inum,sparse12_functor);
if (neighflag != FULL) {
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType,TagZeroQGhosts>(nlocal,nlocal+atom->nghost),*this);
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType,TagZeroQGhosts>(inum,ignum),*this);
if (neighflag == HALF) {
FixQEqReaxKokkosSparse13Functor<DeviceType,HALF> sparse13_functor(this);
Kokkos::parallel_for(inum,sparse13_functor);
@ -788,7 +787,7 @@ void FixQEqReaxKokkos<DeviceType>::cg_solve1()
FixQEqReaxKokkosSparse22Functor<DeviceType> sparse22_functor(this);
Kokkos::parallel_for(inum,sparse22_functor);
if (neighflag != FULL) {
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType,TagZeroQGhosts>(nlocal,nlocal+atom->nghost),*this);
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType,TagZeroQGhosts>(inum,ignum),*this);
if (need_dup)
dup_o.reset_except(d_o);
if (neighflag == HALF) {
@ -869,7 +868,7 @@ void FixQEqReaxKokkos<DeviceType>::cg_solve2()
FixQEqReaxKokkosSparse32Functor<DeviceType> sparse32_functor(this);
Kokkos::parallel_for(inum,sparse32_functor);
if (neighflag != FULL) {
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType,TagZeroQGhosts>(nlocal,nlocal+atom->nghost),*this);
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType,TagZeroQGhosts>(inum,ignum),*this);
if (need_dup)
dup_o.reset_except(d_o);
if (neighflag == HALF) {
@ -927,7 +926,7 @@ void FixQEqReaxKokkos<DeviceType>::cg_solve2()
FixQEqReaxKokkosSparse22Functor<DeviceType> sparse22_functor(this);
Kokkos::parallel_for(inum,sparse22_functor);
if (neighflag != FULL) {
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType,TagZeroQGhosts>(nlocal,nlocal+atom->nghost),*this);
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType,TagZeroQGhosts>(inum,ignum),*this);
if (need_dup)
dup_o.reset_except(d_o);
if (neighflag == HALF) {

2
src/KOKKOS/fix_qeq_reax_kokkos.h
View File

@ -151,7 +151,7 @@ class FixQEqReaxKokkos : public FixQEqReax {
double memory_usage();
private:
int inum;
int inum,ignum;
int allocated_flag;
int need_dup;

42
src/KOKKOS/pair_reaxc_kokkos.cpp
View File

@ -199,6 +199,8 @@ void PairReaxCKokkos<DeviceType>::setup()
hbond_parameters *hbp;
for (i = 1; i <= n; i++) {
if (map[i] == -1) continue;
// general
k_params_sing.h_view(i).mass = system->reax_param.sbp[map[i]].mass;
@ -229,6 +231,8 @@ void PairReaxCKokkos<DeviceType>::setup()
k_params_sing.h_view(i).p_hbond = system->reax_param.sbp[map[i]].p_hbond;
for (j = 1; j <= n; j++) {
if (map[j] == -1) continue;
twbp = &(system->reax_param.tbp[map[i]][map[j]]);
// vdW
@ -270,6 +274,8 @@ void PairReaxCKokkos<DeviceType>::setup()
k_params_twbp.h_view(i,j).p_ovun1 = twbp->p_ovun1;
for (k = 1; k <= n; k++) {
if (map[k] == -1) continue;
// Angular
thbh = &(system->reax_param.thbp[map[i]][map[j]][map[k]]);
thbp = &(thbh->prm[0]);
@ -290,6 +296,8 @@ void PairReaxCKokkos<DeviceType>::setup()
k_params_hbp.h_view(i,j,k).r0_hb = hbp->r0_hb;
for (m = 1; m <= n; m++) {
if (map[m] == -1) continue;
// Torsion
fbh = &(system->reax_param.fbp[map[i]][map[j]][map[k]][map[m]]);
fbp = &(fbh->prm[0]);
@ -377,7 +385,9 @@ void PairReaxCKokkos<DeviceType>::init_md()
d_LR = k_LR.template view<DeviceType>();
for (int i = 1; i <= ntypes; ++i) {
if (map[i] == -1) continue;
for (int j = i; j <= ntypes; ++j) {
if (map[j] == -1) continue;
int n = LR[i][j].n;
if (n == 0) continue;
k_LR.h_view(i,j).dx = LR[i][j].dx;
@ -539,7 +549,9 @@ void PairReaxCKokkos<DeviceType>::Deallocate_Lookup_Tables()
ntypes = atom->ntypes;
for( i = 0; i <= ntypes; ++i ) {
for( j = i; j <= ntypes; ++j )
if (map[i] == -1) continue;
for( j = i; j <= ntypes; ++j ) {
if (map[i] == -1) continue;
if (LR[i][j].n) {
sfree( control->error_ptr, LR[i][j].y, "LR[i,j].y" );
sfree( control->error_ptr, LR[i][j].H, "LR[i,j].H" );
@ -548,6 +560,7 @@ void PairReaxCKokkos<DeviceType>::Deallocate_Lookup_Tables()
sfree( control->error_ptr, LR[i][j].ele, "LR[i,j].ele" );
sfree( control->error_ptr, LR[i][j].CEclmb, "LR[i,j].CEclmb" );
}
}
sfree( control->error_ptr, LR[i], "LR[i]" );
}
sfree( control->error_ptr, LR, "LR" );
@ -3659,33 +3672,6 @@ void PairReaxCKokkos<DeviceType>::v_tally3_atom(EV_FLOAT_REAX &ev, const int &i,
}
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
void *PairReaxCKokkos<DeviceType>::extract(const char *str, int &dim)
{
dim = 1;
if (strcmp(str,"chi") == 0 && chi) {
for (int i = 1; i <= atom->ntypes; i++)
if (map[i] >= 0) chi[i] = system->reax_param.sbp[map[i]].chi;
else chi[i] = 0.0;
return (void *) chi;
}
if (strcmp(str,"eta") == 0 && eta) {
for (int i = 1; i <= atom->ntypes; i++)
if (map[i] >= 0) eta[i] = system->reax_param.sbp[map[i]].eta;
else eta[i] = 0.0;
return (void *) eta;
}
if (strcmp(str,"gamma") == 0 && gamma) {
for (int i = 1; i <= atom->ntypes; i++)
if (map[i] >= 0) gamma[i] = system->reax_param.sbp[map[i]].gamma;
else gamma[i] = 0.0;
return (void *) gamma;
}
return NULL;
}
/* ----------------------------------------------------------------------
setup for energy, virial computation
see integrate::ev_set() for values of eflag (0-3) and vflag (0-6)

1
src/KOKKOS/pair_reaxc_kokkos.h
View File

@ -121,7 +121,6 @@ class PairReaxCKokkos : public PairReaxC {
void ev_setup(int, int, int alloc = 1);
void compute(int, int);
void *extract(const char *, int &);
void init_style();
double memory_usage();
void FindBond(int &);

25
src/USER-REAXC/fix_qeq_reax.cpp
View File

@ -463,19 +463,26 @@ void FixQEqReax::min_setup_pre_force(int vflag)
void FixQEqReax::init_storage()
{
int NN;
int *ilist;
if (reaxc)
if (reaxc) {
NN = reaxc->list->inum + reaxc->list->gnum;
else
ilist = reaxc->list->ilist;
} else {
NN = list->inum + list->gnum;
ilist = list->ilist;
}
for (int i = 0; i < NN; i++) {
Hdia_inv[i] = 1. / eta[atom->type[i]];
b_s[i] = -chi[atom->type[i]];
b_t[i] = -1.0;
b_prc[i] = 0;
b_prm[i] = 0;
s[i] = t[i] = 0;
for (int ii = 0; ii < NN; ii++) {
int i = ilist[ii];
if (atom->mask[i] & groupbit) {
Hdia_inv[i] = 1. / eta[atom->type[i]];
b_s[i] = -chi[atom->type[i]];
b_t[i] = -1.0;
b_prc[i] = 0;
b_prm[i] = 0;
s[i] = t[i] = 0;
}
}
}

2
src/USER-REAXC/pair_reaxc.h
View File

@ -44,7 +44,7 @@ class PairReaxC : public Pair {
void coeff(int, char **);
virtual void init_style();
double init_one(int, int);
void *extract(const char *, int &);
virtual void *extract(const char *, int &);
int fixbond_flag, fixspecies_flag;
int **tmpid;
double **tmpbo,**tmpr;