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Merge branch 'master' into core_soft

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This commit is contained in:
Agilio Padua
2019-01-23 12:04:22 +00:00
parent 012d5a55bf bd3b712902
commit bdbb36e570
8 changed files with 215 additions and 154 deletions
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44
src/KOKKOS/pair_snap_kokkos_impl.h
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@ -256,7 +256,6 @@ void PairSNAPKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
if (vflag_fdotr) pair_virial_fdotr_compute(this);
if (eflag_atom) {
k_eatom.template modify<DeviceType>();
k_eatom.template sync<LMPHostType>();
@ -275,8 +274,8 @@ void PairSNAPKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
// free duplicated memory
if (need_dup) {
dup_f = decltype(dup_f)();
dup_vatom = decltype(dup_vatom)();
dup_f = decltype(dup_f)();
dup_vatom = decltype(dup_vatom)();
}
}
@ -453,6 +452,13 @@ void PairSNAPKokkos<DeviceType>::operator() (TagPairSNAP<NEIGHFLAG,EVFLAG>,const
//t4 += timer.seconds(); timer.reset();
team.team_barrier();
if (quadraticflag) {
my_sna.compute_bi(team);
team.team_barrier();
my_sna.copy_bi2bvec(team);
team.team_barrier();
}
// for neighbors of I within cutoff:
// compute dUi/drj and dBi/drj
// Fij = dEi/dRj = -dEi/dRi => add to Fi, subtract from Fj
@ -472,10 +478,6 @@ void PairSNAPKokkos<DeviceType>::operator() (TagPairSNAP<NEIGHFLAG,EVFLAG>,const
my_sna.compute_dbidrj(team);
//t7 += timer2.seconds(); timer2.reset();
my_sna.copy_dbi2dbvec(team);
if (quadraticflag) {
my_sna.compute_bi(team);
my_sna.copy_bi2bvec(team);
}
Kokkos::single(Kokkos::PerThread(team), [&] (){
F_FLOAT fij[3];
@ -536,10 +538,10 @@ void PairSNAPKokkos<DeviceType>::operator() (TagPairSNAP<NEIGHFLAG,EVFLAG>,const
a_f(j,1) -= fij[1];
a_f(j,2) -= fij[2];
// tally per-atom virial contribution
// tally global and per-atom virial contribution
if (EVFLAG) {
if (vflag) {
if (vflag_either) {
v_tally_xyz<NEIGHFLAG>(ev,i,j,
fij[0],fij[1],fij[2],
-my_sna.rij(jj,0),-my_sna.rij(jj,1),
@ -554,11 +556,13 @@ void PairSNAPKokkos<DeviceType>::operator() (TagPairSNAP<NEIGHFLAG,EVFLAG>,const
// tally energy contribution
if (EVFLAG) {
if (eflag) {
if (eflag_either) {
if (!quadraticflag) {
my_sna.compute_bi(team);
team.team_barrier();
my_sna.copy_bi2bvec(team);
team.team_barrier();
}
// E = beta.B + 0.5*B^t.alpha.B
@ -566,14 +570,15 @@ void PairSNAPKokkos<DeviceType>::operator() (TagPairSNAP<NEIGHFLAG,EVFLAG>,const
// coeff[k] = alpha_ii or
// coeff[k] = alpha_ij = alpha_ji, j != i
if (team.team_rank() == 0)
Kokkos::single(Kokkos::PerThread(team), [&] () {
Kokkos::single(Kokkos::PerTeam(team), [&] () {
// evdwl = energy of atom I, sum over coeffs_k * Bi_k
// evdwl = energy of atom I, sum over coeffs_k * Bi_k
double evdwl = d_coeffi[0];
double evdwl = d_coeffi[0];
// linear contributions
// could use thread vector range on this loop
// linear contributions
for (int k = 1; k <= ncoeff; k++)
evdwl += d_coeffi[k]*my_sna.bvec[k-1];
@ -589,11 +594,10 @@ void PairSNAPKokkos<DeviceType>::operator() (TagPairSNAP<NEIGHFLAG,EVFLAG>,const
}
}
}
// ev_tally_full(i,2.0*evdwl,0.0,0.0,0.0,0.0,0.0);
if (eflag_either) {
if (eflag_global) ev.evdwl += evdwl;
if (eflag_atom) d_eatom[i] += evdwl;
}
//ev_tally_full(i,2.0*evdwl,0.0,0.0,0.0,0.0,0.0);
if (eflag_global) ev.evdwl += evdwl;
if (eflag_atom) d_eatom[i] += evdwl;
});
}
}

53
src/KOKKOS/sna_kokkos_impl.h
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@ -327,29 +327,40 @@ void SNAKokkos<DeviceType>::compute_bi(const typename Kokkos::TeamPolicy<DeviceT
clock_gettime(CLOCK_REALTIME, &starttime);
#endif
Kokkos::parallel_for(Kokkos::ThreadVectorRange(team,idxj_max),
Kokkos::parallel_for(Kokkos::TeamThreadRange(team,idxj_full_max),
[&] (const int& idx) {
const int j1 = idxj(idx).j1;
const int j2 = idxj(idx).j2;
const int j = idxj(idx).j;
double b_j1_j2_j = 0.0;
const int j1 = idxj_full(idx).j1;
const int j2 = idxj_full(idx).j2;
const int j = idxj_full(idx).j;
for(int mb = 0; 2*mb < j; mb++)
for(int ma = 0; ma <= j; ma++) {
b_j1_j2_j +=
const int bound = (j+2)/2;
double b_j1_j2_j = 0.0;
double b_j1_j2_j_temp = 0.0;
Kokkos::parallel_reduce(Kokkos::ThreadVectorRange(team,(j+1)*bound),
[&] (const int mbma, double& sum) {
//for(int mb = 0; 2*mb <= j; mb++)
//for(int ma = 0; ma <= j; ma++) {
const int ma = mbma%(j+1);
const int mb = mbma/(j+1);
if (2*mb == j) return;
sum +=
uarraytot_r(j,ma,mb) * zarray_r(j1,j2,j,mb,ma) +
uarraytot_i(j,ma,mb) * zarray_i(j1,j2,j,mb,ma);
} // end loop over ma, mb
},b_j1_j2_j_temp); // end loop over ma, mb
b_j1_j2_j += b_j1_j2_j_temp;
// For j even, special treatment for middle column
if (j%2 == 0) {
const int mb = j/2;
for(int ma = 0; ma < mb; ma++) {
b_j1_j2_j +=
Kokkos::parallel_reduce(Kokkos::ThreadVectorRange(team, mb),
[&] (const int ma, double& sum) {
//for(int ma = 0; ma < mb; ma++) {
sum +=
uarraytot_r(j,ma,mb) * zarray_r(j1,j2,j,mb,ma) +
uarraytot_i(j,ma,mb) * zarray_i(j1,j2,j,mb,ma);
}
},b_j1_j2_j_temp); // end loop over ma
b_j1_j2_j += b_j1_j2_j_temp;
const int ma = mb;
b_j1_j2_j +=
@ -357,11 +368,13 @@ void SNAKokkos<DeviceType>::compute_bi(const typename Kokkos::TeamPolicy<DeviceT
uarraytot_i(j,ma,mb) * zarray_i(j1,j2,j,mb,ma))*0.5;
}
b_j1_j2_j *= 2.0;
if (bzero_flag)
b_j1_j2_j -= bzero[j];
Kokkos::single(Kokkos::PerThread(team), [&] () {
b_j1_j2_j *= 2.0;
if (bzero_flag)
b_j1_j2_j -= bzero[j];
barray(j1,j2,j) = b_j1_j2_j;
barray(j1,j2,j) = b_j1_j2_j;
});
});
//} // end loop over j
//} // end loop over j1, j2
@ -1028,6 +1041,8 @@ void SNAKokkos<DeviceType>::create_team_scratch_arrays(const typename Kokkos::Te
uarraytot_i_a = uarraytot_i = t_sna_3d(team.team_scratch(1),jdim,jdim,jdim);
zarray_r = t_sna_5d(team.team_scratch(1),jdim,jdim,jdim,jdim,jdim);
zarray_i = t_sna_5d(team.team_scratch(1),jdim,jdim,jdim,jdim,jdim);
bvec = Kokkos::View<double*, Kokkos::LayoutRight, DeviceType>(team.team_scratch(1),ncoeff);
barray = t_sna_3d(team.team_scratch(1),jdim,jdim,jdim);
rij = t_sna_2d(team.team_scratch(1),nmax,3);
rcutij = t_sna_1d(team.team_scratch(1),nmax);
@ -1046,6 +1061,8 @@ T_INT SNAKokkos<DeviceType>::size_team_scratch_arrays() {
size += t_sna_3d::shmem_size(jdim,jdim,jdim); // uarraytot_i_a
size += t_sna_5d::shmem_size(jdim,jdim,jdim,jdim,jdim); // zarray_r
size += t_sna_5d::shmem_size(jdim,jdim,jdim,jdim,jdim); // zarray_i
size += Kokkos::View<double*, Kokkos::LayoutRight, DeviceType>::shmem_size(ncoeff); // bvec
size += t_sna_3d::shmem_size(jdim,jdim,jdim); // barray
size += t_sna_2d::shmem_size(nmax,3); // rij
size += t_sna_1d::shmem_size(nmax); // rcutij
@ -1062,8 +1079,6 @@ KOKKOS_INLINE_FUNCTION
void SNAKokkos<DeviceType>::create_thread_scratch_arrays(const typename Kokkos::TeamPolicy<DeviceType>::member_type& team)
{
int jdim = twojmax + 1;
bvec = Kokkos::View<double*, Kokkos::LayoutRight, DeviceType>(team.thread_scratch(1),ncoeff);
barray = t_sna_3d(team.thread_scratch(1),jdim,jdim,jdim);
dbvec = Kokkos::View<double*[3], Kokkos::LayoutRight, DeviceType>(team.thread_scratch(1),ncoeff);
dbarray = t_sna_4d(team.thread_scratch(1),jdim,jdim,jdim);
@ -1079,8 +1094,6 @@ inline
T_INT SNAKokkos<DeviceType>::size_thread_scratch_arrays() {
T_INT size = 0;
int jdim = twojmax + 1;
size += Kokkos::View<double*, Kokkos::LayoutRight, DeviceType>::shmem_size(ncoeff); // bvec
size += t_sna_3d::shmem_size(jdim,jdim,jdim); // barray
size += Kokkos::View<double*[3], Kokkos::LayoutRight, DeviceType>::shmem_size(ncoeff); // dbvec
size += t_sna_4d::shmem_size(jdim,jdim,jdim); // dbarray

44
src/MOLECULE/improper_umbrella.cpp
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@ -189,17 +189,17 @@ void ImproperUmbrella::compute(int eflag, int vflag)
dahy = ary-c*hry;
dahz = arz-c*hrz;
f2[0] = (dhay*vb1z - dhaz*vb1y)*rar;
f2[1] = (dhaz*vb1x - dhax*vb1z)*rar;
f2[2] = (dhax*vb1y - dhay*vb1x)*rar;
f2[0] = (dhay*vb1z - dhaz*vb1y)*rar*a;
f2[1] = (dhaz*vb1x - dhax*vb1z)*rar*a;
f2[2] = (dhax*vb1y - dhay*vb1x)*rar*a;
f3[0] = (-dhay*vb2z + dhaz*vb2y)*rar;
f3[1] = (-dhaz*vb2x + dhax*vb2z)*rar;
f3[2] = (-dhax*vb2y + dhay*vb2x)*rar;
f3[0] = (-dhay*vb2z + dhaz*vb2y)*rar*a;
f3[1] = (-dhaz*vb2x + dhax*vb2z)*rar*a;
f3[2] = (-dhax*vb2y + dhay*vb2x)*rar*a;
f4[0] = dahx*rhr;
f4[1] = dahy*rhr;
f4[2] = dahz*rhr;
f4[0] = dahx*rhr*a;
f4[1] = dahy*rhr*a;
f4[2] = dahz*rhr*a;
f1[0] = -(f2[0] + f3[0] + f4[0]);
f1[1] = -(f2[1] + f3[1] + f4[1]);
@ -208,27 +208,27 @@ void ImproperUmbrella::compute(int eflag, int vflag)
// apply force to each of 4 atoms
if (newton_bond || i1 < nlocal) {
f[i1][0] += f1[0]*a;
f[i1][1] += f1[1]*a;
f[i1][2] += f1[2]*a;
f[i1][0] += f1[0];
f[i1][1] += f1[1];
f[i1][2] += f1[2];
}
if (newton_bond || i2 < nlocal) {
f[i2][0] += f3[0]*a;
f[i2][1] += f3[1]*a;
f[i2][2] += f3[2]*a;
f[i2][0] += f3[0];
f[i2][1] += f3[1];
f[i2][2] += f3[2];
}
if (newton_bond || i3 < nlocal) {
f[i3][0] += f2[0]*a;
f[i3][1] += f2[1]*a;
f[i3][2] += f2[2]*a;
f[i3][0] += f2[0];
f[i3][1] += f2[1];
f[i3][2] += f2[2];
}
if (newton_bond || i4 < nlocal) {
f[i4][0] += f4[0]*a;
f[i4][1] += f4[1]*a;
f[i4][2] += f4[2]*a;
f[i4][0] += f4[0];
f[i4][1] += f4[1];
f[i4][2] += f4[2];
}
if (evflag) {
@ -247,7 +247,7 @@ void ImproperUmbrella::compute(int eflag, int vflag)
vb3y = x[i4][1] - x[i3][1];
vb3z = x[i4][2] - x[i3][2];
ev_tally(i1,i2,i3,i4,nlocal,newton_bond,eimproper,f1,f3,f4,
ev_tally(i1,i2,i3,i4,nlocal,newton_bond,eimproper,f1,f2,f4,
vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z);
}
}

88
src/USER-MISC/fix_bond_react.cpp
View File

@ -162,6 +162,8 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
memory->create(reacted_mol,nreacts,"bond/react:reacted_mol");
memory->create(fraction,nreacts,"bond/react:fraction");
memory->create(max_rxn,nreacts,"bond/react:max_rxn");
memory->create(nlocalskips,nreacts,"bond/react:nlocalskips");
memory->create(nghostlyskips,nreacts,"bond/react:nghostlyskips");
memory->create(seed,nreacts,"bond/react:seed");
memory->create(limit_duration,nreacts,"bond/react:limit_duration");
memory->create(stabilize_steps_flag,nreacts,"bond/react:stabilize_steps_flag");
@ -180,7 +182,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
for (int i = 0; i < nreacts; i++) {
fraction[i] = 1;
seed[i] = 12345;
max_rxn[i] = BIG;
max_rxn[i] = INT_MAX;
stabilize_steps_flag[i] = 0;
update_edges_flag[i] = 0;
// set default limit duration to 60 timesteps
@ -413,6 +415,8 @@ FixBondReact::~FixBondReact()
memory->destroy(fraction);
memory->destroy(seed);
memory->destroy(max_rxn);
memory->destroy(nlocalskips);
memory->destroy(nghostlyskips);
memory->destroy(limit_duration);
memory->destroy(stabilize_steps_flag);
memory->destroy(update_edges_flag);
@ -684,6 +688,8 @@ void FixBondReact::post_integrate()
reaction_count[i] = 0;
local_rxn_count[i] = 0;
ghostly_rxn_count[i] = 0;
nlocalskips[i] = 0;
nghostlyskips[i] = 0;
}
if (nevery_check) {
@ -1153,16 +1159,44 @@ void FixBondReact::superimpose_algorithm()
MPI_Allreduce(&local_rxn_count[0],&reaction_count[0],nreacts,MPI_INT,MPI_SUM,world);
for (int i = 0; i < nreacts; i++)
reaction_count_total[i] += reaction_count[i];
if (me == 0)
for (int i = 0; i < nreacts; i++)
reaction_count_total[i] += ghostly_rxn_count[i];
reaction_count_total[i] += reaction_count[i] + ghostly_rxn_count[i];
// bcast ghostly_rxn_count
MPI_Bcast(&reaction_count_total[0], nreacts, MPI_INT, 0, world);
// check if we overstepped our reaction limit
for (int i = 0; i < nreacts; i++) {
if (reaction_count_total[i] > max_rxn[i]) {
// let's randomly choose rxns to skip, unbiasedly from local and ghostly
int local_rxncounts[nprocs];
int all_localskips[nprocs];
MPI_Gather(&local_rxn_count[i],1,MPI_INT,local_rxncounts,1,MPI_INT,0,world);
if (me == 0) {
int overstep = reaction_count_total[i] - max_rxn[i];
int delta_rxn = reaction_count[i] + ghostly_rxn_count[i];
int rxn_by_proc[delta_rxn];
for (int j = 0; j < delta_rxn; j++)
rxn_by_proc[j] = -1; // corresponds to ghostly
int itemp = 0;
for (int j = 0; j < nprocs; j++)
for (int k = 0; k < local_rxn_count[j]; k++)
rxn_by_proc[itemp++] = j;
std::random_shuffle(&rxn_by_proc[0],&rxn_by_proc[delta_rxn]);
for (int j = 0; j < nprocs; j++)
all_localskips[j] = 0;
nghostlyskips[i] = 0;
for (int j = 0; j < overstep; j++) {
if (rxn_by_proc[j] == -1) nghostlyskips[i]++;
else all_localskips[rxn_by_proc[j]]++;
}
}
reaction_count_total[i] = max_rxn[i];
MPI_Scatter(&all_localskips[0],1,MPI_INT,&nlocalskips[i],1,MPI_INT,0,world);
MPI_Bcast(&nghostlyskips[i],1,MPI_INT,0,world);
}
}
// this updates topology next step
next_reneighbor = update->ntimestep;
@ -1957,19 +1991,19 @@ void FixBondReact::glove_ghostcheck()
// 'ghosts of another' indication taken from comm->sendlist
int ghostly = 0;
if (comm->style == 0) {
for (int i = 0; i < onemol->natoms; i++) {
int ilocal = atom->map(glove[i][1]);
if (ilocal >= atom->nlocal || localsendlist[ilocal] == 1) {
ghostly = 1;
break;
#if !defined(MPI_STUBS)
if (comm->style == 0) {
for (int i = 0; i < onemol->natoms; i++) {
int ilocal = atom->map(glove[i][1]);
if (ilocal >= atom->nlocal || localsendlist[ilocal] == 1) {
ghostly = 1;
break;
}
}
}
} else {
#if !defined(MPI_STUBS)
} else {
ghostly = 1;
#endif
}
}
#endif
if (ghostly == 1) {
ghostly_mega_glove[0][ghostly_num_mega] = rxnID;
@ -2104,18 +2138,26 @@ void FixBondReact::update_everything()
memory->create(update_mega_glove,max_natoms+1,MAX(local_num_mega,global_megasize),"bond/react:update_mega_glove");
for (int pass = 0; pass < 2; pass++) {
update_num_mega = 0;
int iskip[nreacts];
for (int i = 0; i < nreacts; i++) iskip[i] = 0;
if (pass == 0) {
update_num_mega = local_num_mega;
for (int i = 0; i < update_num_mega; i++) {
for (int i = 0; i < local_num_mega; i++) {
rxnID = local_mega_glove[0][i];
// reactions already shuffled from dedup procedure, so can skip first N
if (iskip[rxnID]++ < nlocalskips[rxnID]) continue;
for (int j = 0; j < max_natoms+1; j++)
update_mega_glove[j][i] = local_mega_glove[j][i];
update_mega_glove[j][update_num_mega] = local_mega_glove[j][i];
update_num_mega++;
}
} else if (pass == 1) {
update_num_mega = global_megasize;
for (int i = 0; i < global_megasize; i++) {
rxnID = global_mega_glove[0][i];
// reactions already shuffled from dedup procedure, so can skip first N
if (iskip[rxnID]++ < nghostlyskips[rxnID]) continue;
for (int j = 0; j < max_natoms+1; j++)
update_mega_glove[j][i] = global_mega_glove[j][i];
update_mega_glove[j][update_num_mega] = global_mega_glove[j][i];
update_num_mega++;
}
}

3
src/USER-MISC/fix_bond_react.h
View File

@ -54,7 +54,8 @@ class FixBondReact : public Fix {
FILE *fp;
int *iatomtype,*jatomtype;
int *seed;
double **cutsq,*fraction,*max_rxn;
double **cutsq,*fraction;
int *max_rxn,*nlocalskips,*nghostlyskips;
tagint lastcheck;
int stabilization_flag;
int custom_exclude_flag;

46
src/USER-MISC/improper_fourier.cpp
View File

@ -206,17 +206,17 @@ void ImproperFourier::addone(const int &i1,const int &i2,const int &i3,const int
dahy = ary-c*hry;
dahz = arz-c*hrz;
f2[0] = (dhay*vb1z - dhaz*vb1y)*rar;
f2[1] = (dhaz*vb1x - dhax*vb1z)*rar;
f2[2] = (dhax*vb1y - dhay*vb1x)*rar;
f2[0] = (dhay*vb1z - dhaz*vb1y)*rar*a;
f2[1] = (dhaz*vb1x - dhax*vb1z)*rar*a;
f2[2] = (dhax*vb1y - dhay*vb1x)*rar*a;
f3[0] = (-dhay*vb2z + dhaz*vb2y)*rar;
f3[1] = (-dhaz*vb2x + dhax*vb2z)*rar;
f3[2] = (-dhax*vb2y + dhay*vb2x)*rar;
f3[0] = (-dhay*vb2z + dhaz*vb2y)*rar*a;
f3[1] = (-dhaz*vb2x + dhax*vb2z)*rar*a;
f3[2] = (-dhax*vb2y + dhay*vb2x)*rar*a;
f4[0] = dahx*rhr;
f4[1] = dahy*rhr;
f4[2] = dahz*rhr;
f4[0] = dahx*rhr*a;
f4[1] = dahy*rhr*a;
f4[2] = dahz*rhr*a;
f1[0] = -(f2[0] + f3[0] + f4[0]);
f1[1] = -(f2[1] + f3[1] + f4[1]);
@ -225,32 +225,32 @@ void ImproperFourier::addone(const int &i1,const int &i2,const int &i3,const int
// apply force to each of 4 atoms
if (newton_bond || i1 < nlocal) {
f[i1][0] += f1[0]*a;
f[i1][1] += f1[1]*a;
f[i1][2] += f1[2]*a;
f[i1][0] += f1[0];
f[i1][1] += f1[1];
f[i1][2] += f1[2];
}
if (newton_bond || i2 < nlocal) {
f[i2][0] += f3[0]*a;
f[i2][1] += f3[1]*a;
f[i2][2] += f3[2]*a;
f[i2][0] += f3[0];
f[i2][1] += f3[1];
f[i2][2] += f3[2];
}
if (newton_bond || i3 < nlocal) {
f[i3][0] += f2[0]*a;
f[i3][1] += f2[1]*a;
f[i3][2] += f2[2]*a;
f[i3][0] += f2[0];
f[i3][1] += f2[1];
f[i3][2] += f2[2];
}
if (newton_bond || i4 < nlocal) {
f[i4][0] += f4[0]*a;
f[i4][1] += f4[1]*a;
f[i4][2] += f4[2]*a;
f[i4][0] += f4[0];
f[i4][1] += f4[1];
f[i4][2] += f4[2];
}
if (evflag)
ev_tally(i1,i2,i3,i4,nlocal,newton_bond,eimproper,f1,f3,f4,
vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z);
ev_tally(i1,i2,i3,i4,nlocal,newton_bond,eimproper,f1,f2,f4,
-vb1x,-vb1y,-vb1z,vb2x-vb1x,vb2y-vb1y,vb2z-vb1z,vb3x-vb2x,vb3y-vb2y,vb3z-vb2z);
}
/* ---------------------------------------------------------------------- */

47
src/USER-OMP/improper_fourier_omp.cpp
View File

@ -239,17 +239,17 @@ void ImproperFourierOMP::add1_thr(const int i1,const int i2,
dahy = ary-c*hry;
dahz = arz-c*hrz;
f2[0] = (dhay*vb1z - dhaz*vb1y)*rar;
f2[1] = (dhaz*vb1x - dhax*vb1z)*rar;
f2[2] = (dhax*vb1y - dhay*vb1x)*rar;
f2[0] = (dhay*vb1z - dhaz*vb1y)*rar*a;
f2[1] = (dhaz*vb1x - dhax*vb1z)*rar*a;
f2[2] = (dhax*vb1y - dhay*vb1x)*rar*a;
f3[0] = (-dhay*vb2z + dhaz*vb2y)*rar;
f3[1] = (-dhaz*vb2x + dhax*vb2z)*rar;
f3[2] = (-dhax*vb2y + dhay*vb2x)*rar;
f3[0] = (-dhay*vb2z + dhaz*vb2y)*rar*a;
f3[1] = (-dhaz*vb2x + dhax*vb2z)*rar*a;
f3[2] = (-dhax*vb2y + dhay*vb2x)*rar*a;
f4[0] = dahx*rhr;
f4[1] = dahy*rhr;
f4[2] = dahz*rhr;
f4[0] = dahx*rhr*a;
f4[1] = dahy*rhr*a;
f4[2] = dahz*rhr*a;
f1[0] = -(f2[0] + f3[0] + f4[0]);
f1[1] = -(f2[1] + f3[1] + f4[1]);
@ -258,30 +258,31 @@ void ImproperFourierOMP::add1_thr(const int i1,const int i2,
// apply force to each of 4 atoms
if (NEWTON_BOND || i1 < nlocal) {
f[i1][0] += f1[0]*a;
f[i1][1] += f1[1]*a;
f[i1][2] += f1[2]*a;
f[i1][0] += f1[0];
f[i1][1] += f1[1];
f[i1][2] += f1[2];
}
if (NEWTON_BOND || i2 < nlocal) {
f[i2][0] += f3[0]*a;
f[i2][1] += f3[1]*a;
f[i2][2] += f3[2]*a;
f[i2][0] += f3[0];
f[i2][1] += f3[1];
f[i2][2] += f3[2];
}
if (NEWTON_BOND || i3 < nlocal) {
f[i3][0] += f2[0]*a;
f[i3][1] += f2[1]*a;
f[i3][2] += f2[2]*a;
f[i3][0] += f2[0];
f[i3][1] += f2[1];
f[i3][2] += f2[2];
}
if (NEWTON_BOND || i4 < nlocal) {
f[i4][0] += f4[0]*a;
f[i4][1] += f4[1]*a;
f[i4][2] += f4[2]*a;
f[i4][0] += f4[0];
f[i4][1] += f4[1];
f[i4][2] += f4[2];
}
if (EVFLAG)
ev_tally_thr(this,i1,i2,i3,i4,nlocal,NEWTON_BOND,eimproper,f1,f3,f4,
vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,thr);
ev_tally_thr(this,i1,i2,i3,i4,nlocal,NEWTON_BOND,eimproper,f1,f2,f4,
-vb1x,-vb1y,-vb1z,vb2x-vb1x,vb2y-vb1y,vb2z-vb1z,vb3x-vb2x,vb3y-vb2y,vb3z-vb2z,thr);
}

44
src/USER-OMP/improper_umbrella_omp.cpp
View File

@ -212,17 +212,17 @@ void ImproperUmbrellaOMP::eval(int nfrom, int nto, ThrData * const thr)
dahy = ary-c*hry;
dahz = arz-c*hrz;
f2[0] = (dhay*vb1z - dhaz*vb1y)*rar;
f2[1] = (dhaz*vb1x - dhax*vb1z)*rar;
f2[2] = (dhax*vb1y - dhay*vb1x)*rar;
f2[0] = (dhay*vb1z - dhaz*vb1y)*rar*a;
f2[1] = (dhaz*vb1x - dhax*vb1z)*rar*a;
f2[2] = (dhax*vb1y - dhay*vb1x)*rar*a;
f3[0] = (-dhay*vb2z + dhaz*vb2y)*rar;
f3[1] = (-dhaz*vb2x + dhax*vb2z)*rar;
f3[2] = (-dhax*vb2y + dhay*vb2x)*rar;
f3[0] = (-dhay*vb2z + dhaz*vb2y)*rar*a;
f3[1] = (-dhaz*vb2x + dhax*vb2z)*rar*a;
f3[2] = (-dhax*vb2y + dhay*vb2x)*rar*a;
f4[0] = dahx*rhr;
f4[1] = dahy*rhr;
f4[2] = dahz*rhr;
f4[0] = dahx*rhr*a;
f4[1] = dahy*rhr*a;
f4[2] = dahz*rhr*a;
f1[0] = -(f2[0] + f3[0] + f4[0]);
f1[1] = -(f2[1] + f3[1] + f4[1]);
@ -231,27 +231,27 @@ void ImproperUmbrellaOMP::eval(int nfrom, int nto, ThrData * const thr)
// apply force to each of 4 atoms
if (NEWTON_BOND || i1 < nlocal) {
f[i1].x += f1[0]*a;
f[i1].y += f1[1]*a;
f[i1].z += f1[2]*a;
f[i1].x += f1[0];
f[i1].y += f1[1];
f[i1].z += f1[2];
}
if (NEWTON_BOND || i2 < nlocal) {
f[i2].x += f3[0]*a;
f[i2].y += f3[1]*a;
f[i2].z += f3[2]*a;
f[i2].x += f3[0];
f[i2].y += f3[1];
f[i2].z += f3[2];
}
if (NEWTON_BOND || i3 < nlocal) {
f[i3].x += f2[0]*a;
f[i3].y += f2[1]*a;
f[i3].z += f2[2]*a;
f[i3].x += f2[0];
f[i3].y += f2[1];
f[i3].z += f2[2];
}
if (NEWTON_BOND || i4 < nlocal) {
f[i4].x += f4[0]*a;
f[i4].y += f4[1]*a;
f[i4].z += f4[2]*a;
f[i4].x += f4[0];
f[i4].y += f4[1];
f[i4].z += f4[2];
}
if (EVFLAG) {
@ -270,7 +270,7 @@ void ImproperUmbrellaOMP::eval(int nfrom, int nto, ThrData * const thr)
vb3y = x[i4].y - x[i3].y;
vb3z = x[i4].z - x[i3].z;
ev_tally_thr(this,i1,i2,i3,i4,nlocal,NEWTON_BOND,eimproper,f1,f3,f4,
ev_tally_thr(this,i1,i2,i3,i4,nlocal,NEWTON_BOND,eimproper,f1,f2,f4,
vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,thr);
}
}