void PairLJCutCoulDSFOMP::compute(int eflag, int vflag)
{
if (eflag || vflag) {
ev_setup(eflag,vflag);
} else evflag = vflag_fdotr = 0;
const int nall = atom->nlocal + atom->nghost;
const int nthreads = comm->nthreads;
const int inum = list->inum;
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(eflag,vflag)
#endif
{
int ifrom, ito, tid;
loop_setup_thr(ifrom, ito, tid, inum, nthreads);
ThrData *thr = fix->get_thr(tid);
thr->timer(Timer::START);
ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
if (evflag) {
if (eflag) {
if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
else eval<1,1,0>(ifrom, ito, thr);
} else {
if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr);
else eval<0,0,0>(ifrom, ito, thr);
}
thr->timer(Timer::PAIR);
reduce_thr(this, eflag, vflag, thr);
} // end of omp parallel region
}
void AngleSDKOMP::compute(int eflag, int vflag)
{
ev_init(eflag,vflag);
const int nall = atom->nlocal + atom->nghost;
const int nthreads = comm->nthreads;
const int inum = neighbor->nanglelist;
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(eflag,vflag)
#endif
{
int ifrom, ito, tid;
loop_setup_thr(ifrom, ito, tid, inum, nthreads);
ThrData *thr = fix->get_thr(tid);
thr->timer(Timer::START);
ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
if (inum > 0) {
if (evflag) {
if (eflag) {
if (force->newton_bond) eval<1,1,1>(ifrom, ito, thr);
else eval<1,1,0>(ifrom, ito, thr);
} else {
if (force->newton_bond) eval<1,0,1>(ifrom, ito, thr);
else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_bond) eval<0,0,1>(ifrom, ito, thr);
else eval<0,0,0>(ifrom, ito, thr);
}
}
thr->timer(Timer::BOND);
reduce_thr(this, eflag, vflag, thr);
} // end of omp parallel region
}
void PPPMCGOMP::compute(int eflag, int vflag)
{
PPPMCG::compute(eflag,vflag);
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(eflag,vflag)
#endif
{
#if defined(_OPENMP)
const int tid = omp_get_thread_num();
#else
const int tid = 0;
#endif
ThrData *thr = fix->get_thr(tid);
thr->timer(Timer::START);
reduce_thr(this, eflag, vflag, thr);
} // end of omp parallel region
}
void PPPMCGOMP::compute_gf_ad()
{
const double * const prd = (triclinic==0) ? domain->prd : domain->prd_lamda;
const double xprd = prd[0];
const double yprd = prd[1];
const double zprd = prd[2];
const double zprd_slab = zprd*slab_volfactor;
const double unitkx = (MY_2PI/xprd);
const double unitky = (MY_2PI/yprd);
const double unitkz = (MY_2PI/zprd_slab);
const int numk = nxhi_fft - nxlo_fft + 1;
const int numl = nyhi_fft - nylo_fft + 1;
const int twoorder = 2*order;
double sf0=0.0,sf1=0.0,sf2=0.0,sf3=0.0,sf4=0.0,sf5=0.0;
#if defined(_OPENMP)
#pragma omp parallel default(none) reduction(+:sf0,sf1,sf2,sf3,sf4,sf5)
#endif
{
double snx,sny,snz,sqk;
double argx,argy,argz,wx,wy,wz,sx,sy,sz,qx,qy,qz;
double numerator,denominator;
int k,l,m,kper,lper,mper,n,nfrom,nto,tid;
loop_setup_thr(nfrom, nto, tid, nfft, comm->nthreads);
ThrData *thr = fix->get_thr(tid);
thr->timer(Timer::START);
for (n = nfrom; n < nto; ++n) {
m = n / (numl*numk);
l = (n - m*numl*numk) / numk;
k = n - m*numl*numk - l*numk;
m += nzlo_fft;
l += nylo_fft;
k += nxlo_fft;
mper = m - nz_pppm*(2*m/nz_pppm);
qz = unitkz*mper;
snz = square(sin(0.5*qz*zprd_slab/nz_pppm));
sz = exp(-0.25*square(qz/g_ewald));
argz = 0.5*qz*zprd_slab/nz_pppm;
wz = powsinxx(argz,twoorder);
lper = l - ny_pppm*(2*l/ny_pppm);
qy = unitky*lper;
sny = square(sin(0.5*qy*yprd/ny_pppm));
sy = exp(-0.25*square(qy/g_ewald));
argy = 0.5*qy*yprd/ny_pppm;
wy = powsinxx(argy,twoorder);
kper = k - nx_pppm*(2*k/nx_pppm);
qx = unitkx*kper;
snx = square(sin(0.5*qx*xprd/nx_pppm));
sx = exp(-0.25*square(qx/g_ewald));
argx = 0.5*qx*xprd/nx_pppm;
wx = powsinxx(argx,twoorder);
sqk = qx*qx + qy*qy + qz*qz;
if (sqk != 0.0) {
numerator = MY_4PI/sqk;
denominator = gf_denom(snx,sny,snz);
greensfn[n] = numerator*sx*sy*sz*wx*wy*wz/denominator;
sf0 += sf_precoeff1[n]*greensfn[n];
sf1 += sf_precoeff2[n]*greensfn[n];
sf2 += sf_precoeff3[n]*greensfn[n];
sf3 += sf_precoeff4[n]*greensfn[n];
sf4 += sf_precoeff5[n]*greensfn[n];
sf5 += sf_precoeff6[n]*greensfn[n];
} else {
greensfn[n] = 0.0;
sf0 += sf_precoeff1[n]*greensfn[n];
sf1 += sf_precoeff2[n]*greensfn[n];
sf2 += sf_precoeff3[n]*greensfn[n];
sf3 += sf_precoeff4[n]*greensfn[n];
sf4 += sf_precoeff5[n]*greensfn[n];
sf5 += sf_precoeff6[n]*greensfn[n];
}
}
thr->timer(Timer::KSPACE);
} // end of paralle region
// compute the coefficients for the self-force correction
double prex, prey, prez, tmp[6];
prex = prey = prez = MY_PI/volume;
prex *= nx_pppm/xprd;
prey *= ny_pppm/yprd;
prez *= nz_pppm/zprd_slab;
tmp[0] = sf0 * prex;
tmp[1] = sf1 * prex*2;
tmp[2] = sf2 * prey;
tmp[3] = sf3 * prey*2;
tmp[4] = sf4 * prez;
tmp[5] = sf5 * prez*2;
// communicate values with other procs
MPI_Allreduce(tmp,sf_coeff,6,MPI_DOUBLE,MPI_SUM,world);
}
void PPPMCGOMP::compute_gf_ik()
{
const double * const prd = (triclinic==0) ? domain->prd : domain->prd_lamda;
const double xprd = prd[0];
const double yprd = prd[1];
const double zprd = prd[2];
const double zprd_slab = zprd*slab_volfactor;
const double unitkx = (MY_2PI/xprd);
const double unitky = (MY_2PI/yprd);
const double unitkz = (MY_2PI/zprd_slab);
const int nbx = static_cast<int> ((g_ewald*xprd/(MY_PI*nx_pppm)) *
pow(-log(EPS_HOC),0.25));
const int nby = static_cast<int> ((g_ewald*yprd/(MY_PI*ny_pppm)) *
pow(-log(EPS_HOC),0.25));
const int nbz = static_cast<int> ((g_ewald*zprd_slab/(MY_PI*nz_pppm)) *
pow(-log(EPS_HOC),0.25));
const int numk = nxhi_fft - nxlo_fft + 1;
const int numl = nyhi_fft - nylo_fft + 1;
const int twoorder = 2*order;
#if defined(_OPENMP)
#pragma omp parallel default(none)
#endif
{
double snx,sny,snz;
double argx,argy,argz,wx,wy,wz,sx,sy,sz,qx,qy,qz;
double sum1,dot1,dot2;
double numerator,denominator;
double sqk;
int k,l,m,nx,ny,nz,kper,lper,mper,n,nfrom,nto,tid;
loop_setup_thr(nfrom, nto, tid, nfft, comm->nthreads);
ThrData *thr = fix->get_thr(tid);
thr->timer(Timer::START);
for (n = nfrom; n < nto; ++n) {
m = n / (numl*numk);
l = (n - m*numl*numk) / numk;
k = n - m*numl*numk - l*numk;
m += nzlo_fft;
l += nylo_fft;
k += nxlo_fft;
mper = m - nz_pppm*(2*m/nz_pppm);
snz = square(sin(0.5*unitkz*mper*zprd_slab/nz_pppm));
lper = l - ny_pppm*(2*l/ny_pppm);
sny = square(sin(0.5*unitky*lper*yprd/ny_pppm));
kper = k - nx_pppm*(2*k/nx_pppm);
snx = square(sin(0.5*unitkx*kper*xprd/nx_pppm));
sqk = square(unitkx*kper) + square(unitky*lper) + square(unitkz*mper);
if (sqk != 0.0) {
numerator = 12.5663706/sqk;
denominator = gf_denom(snx,sny,snz);
sum1 = 0.0;
for (nx = -nbx; nx <= nbx; nx++) {
qx = unitkx*(kper+nx_pppm*nx);
sx = exp(-0.25*square(qx/g_ewald));
argx = 0.5*qx*xprd/nx_pppm;
wx = powsinxx(argx,twoorder);
for (ny = -nby; ny <= nby; ny++) {
qy = unitky*(lper+ny_pppm*ny);
sy = exp(-0.25*square(qy/g_ewald));
argy = 0.5*qy*yprd/ny_pppm;
wy = powsinxx(argy,twoorder);
for (nz = -nbz; nz <= nbz; nz++) {
qz = unitkz*(mper+nz_pppm*nz);
sz = exp(-0.25*square(qz/g_ewald));
argz = 0.5*qz*zprd_slab/nz_pppm;
wz = powsinxx(argz,twoorder);
dot1 = unitkx*kper*qx + unitky*lper*qy + unitkz*mper*qz;
dot2 = qx*qx+qy*qy+qz*qz;
sum1 += (dot1/dot2) * sx*sy*sz * wx*wy*wz;
}
}
}
greensfn[n] = numerator*sum1/denominator;
} else greensfn[n] = 0.0;
}
thr->timer(Timer::KSPACE);
} // end of parallel region
}
void PairCDEAMOMP::compute(int eflag, int vflag)
{
if (eflag || vflag) {
ev_setup(eflag,vflag);
} else evflag = vflag_fdotr = eflag_global = eflag_atom = 0;
const int nall = atom->nlocal + atom->nghost;
const int nthreads = comm->nthreads;
const int inum = list->inum;
// grow energy and fp arrays if necessary
// need to be atom->nmax in length
if (atom->nmax > nmax) {
memory->destroy(rho);
memory->destroy(rhoB);
memory->destroy(D_values);
memory->destroy(fp);
nmax = atom->nmax;
memory->create(rho,nthreads*nmax,"pair:rho");
memory->create(rhoB,nthreads*nmax,"pair:mu");
memory->create(D_values,nthreads*nmax,"pair:D_values");
memory->create(fp,nmax,"pair:fp");
}
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(eflag,vflag)
#endif
{
int ifrom, ito, tid;
loop_setup_thr(ifrom, ito, tid, inum, nthreads);
ThrData *thr = fix->get_thr(tid);
thr->timer(Timer::START);
ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
if (force->newton_pair)
thr->init_cdeam(nall, rho, rhoB, D_values);
else
thr->init_cdeam(atom->nlocal, rho, rhoB, D_values);
switch (cdeamVersion) {
case 1:
if (evflag) {
if (eflag) {
if (force->newton_pair) eval<1,1,1,1>(ifrom, ito, thr);
else eval<1,1,0,1>(ifrom, ito, thr);
} else {
if (force->newton_pair) eval<1,0,1,1>(ifrom, ito, thr);
else eval<1,0,0,1>(ifrom, ito, thr);
}
} else {
if (force->newton_pair) eval<0,0,1,1>(ifrom, ito, thr);
else eval<0,0,0,1>(ifrom, ito, thr);
}
break;
case 2:
if (evflag) {
if (eflag) {
if (force->newton_pair) eval<1,1,1,2>(ifrom, ito, thr);
else eval<1,1,0,2>(ifrom, ito, thr);
} else {
if (force->newton_pair) eval<1,0,1,2>(ifrom, ito, thr);
else eval<1,0,0,2>(ifrom, ito, thr);
}
} else {
if (force->newton_pair) eval<0,0,1,2>(ifrom, ito, thr);
else eval<0,0,0,2>(ifrom, ito, thr);
}
break;
default:
{
#if defined(_OPENMP)
#pragma omp master
#endif
error->all(FLERR,"unsupported eam/cd pair style variant");
}
}
thr->timer(Timer::PAIR);
reduce_thr(this, eflag, vflag, thr);
} // end of omp parallel region
}
void PairGranHertzHistoryOMP::compute(int eflag, int vflag)
{
if (eflag || vflag) {
ev_setup(eflag,vflag);
} else evflag = vflag_fdotr = 0;
const int nall = atom->nlocal + atom->nghost;
const int nthreads = comm->nthreads;
const int inum = list->inum;
const int shearupdate = (update->setupflag) ? 0 : 1;
// update rigid body info for owned & ghost atoms if using FixRigid masses
// body[i] = which body atom I is in, -1 if none
// mass_body = mass of each rigid body
if (fix_rigid && neighbor->ago == 0) {
int tmp;
int *body = (int *) fix_rigid->extract("body",tmp);
double *mass_body = (double *) fix_rigid->extract("masstotal",tmp);
if (atom->nmax > nmax) {
memory->destroy(mass_rigid);
nmax = atom->nmax;
memory->create(mass_rigid,nmax,"pair:mass_rigid");
}
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (body[i] >= 0) mass_rigid[i] = mass_body[body[i]];
else mass_rigid[i] = 0.0;
comm->forward_comm_pair(this);
}
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(eflag,vflag)
#endif
{
int ifrom, ito, tid;
loop_setup_thr(ifrom, ito, tid, inum, nthreads);
ThrData *thr = fix->get_thr(tid);
thr->timer(Timer::START);
ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
if (evflag) {
if (shearupdate) {
if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
else eval<1,1,0>(ifrom, ito, thr);
} else {
if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (shearupdate) {
if (force->newton_pair) eval<0,1,1>(ifrom, ito, thr);
else eval<0,1,0>(ifrom, ito, thr);
} else {
if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr);
else eval<0,0,0>(ifrom, ito, thr);
}
}
thr->timer(Timer::PAIR);
reduce_thr(this, eflag, vflag, thr);
} // end of omp parallel region
}
void PairBrownianPolyOMP::compute(int eflag, int vflag)
{
if (eflag || vflag) {
ev_setup(eflag,vflag);
} else evflag = vflag_fdotr = 0;
const int nall = atom->nlocal + atom->nghost;
const int inum = list->inum;
// This section of code adjusts R0/RT0/RS0 if necessary due to changes
// in the volume fraction as a result of fix deform or moving walls
double dims[3], wallcoord;
if (flagVF) // Flag for volume fraction corrections
if (flagdeform || flagwall == 2){ // Possible changes in volume fraction
if (flagdeform && !flagwall)
for (int j = 0; j < 3; j++)
dims[j] = domain->prd[j];
else if (flagwall == 2 || (flagdeform && flagwall == 1)){
double wallhi[3], walllo[3];
for (int j = 0; j < 3; j++){
wallhi[j] = domain->prd[j];
walllo[j] = 0;
}
for (int m = 0; m < wallfix->nwall; m++){
int dim = wallfix->wallwhich[m] / 2;
int side = wallfix->wallwhich[m] % 2;
if (wallfix->xstyle[m] == VARIABLE){
wallcoord = input->variable->compute_equal(wallfix->xindex[m]);
}
else wallcoord = wallfix->coord0[m];
if (side == 0) walllo[dim] = wallcoord;
else wallhi[dim] = wallcoord;
}
for (int j = 0; j < 3; j++)
dims[j] = wallhi[j] - walllo[j];
}
double vol_T = dims[0]*dims[1]*dims[2];
double vol_f = vol_P/vol_T;
if (flaglog == 0) {
R0 = 6*MY_PI*mu*rad*(1.0 + 2.16*vol_f);
RT0 = 8*MY_PI*mu*cube(rad);
//RS0 = 20.0/3.0*MY_PI*mu*pow(rad,3)*(1.0 + 3.33*vol_f + 2.80*vol_f*vol_f);
} else {
R0 = 6*MY_PI*mu*rad*(1.0 + 2.725*vol_f - 6.583*vol_f*vol_f);
RT0 = 8*MY_PI*mu*cube(rad)*(1.0 + 0.749*vol_f - 2.469*vol_f*vol_f);
//RS0 = 20.0/3.0*MY_PI*mu*pow(rad,3)*(1.0 + 3.64*vol_f - 6.95*vol_f*vol_f);
}
}
// number of threads has changed. reallocate pool of pRNGs
if (nthreads != comm->nthreads) {
if (random_thr) {
for (int i=1; i < nthreads; ++i)
delete random_thr[i];
delete[] random_thr;
}
nthreads = comm->nthreads;
random_thr = new RanMars*[nthreads];
for (int i=1; i < nthreads; ++i)
random_thr[i] = NULL;
// to ensure full compatibility with the serial BrownianPoly style
// we use is random number generator instance for thread 0
random_thr[0] = random;
}
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(eflag,vflag)
#endif
{
int ifrom, ito, tid;
loop_setup_thr(ifrom, ito, tid, inum, nthreads);
ThrData *thr = fix->get_thr(tid);
thr->timer(Timer::START);
ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
// generate a random number generator instance for
// all threads != 0. make sure we use unique seeds.
if ((tid > 0) && (random_thr[tid] == NULL))
random_thr[tid] = new RanMars(Pair::lmp, seed + comm->me
+ comm->nprocs*tid);
if (flaglog) {
if (evflag)
eval<1,1>(ifrom, ito, thr);
else
eval<1,0>(ifrom, ito, thr);
} else {
if (evflag)
eval<0,1>(ifrom, ito, thr);
else eval<0,0>(ifrom, ito, thr);
}
thr->timer(Timer::PAIR);
reduce_thr(this, eflag, vflag, thr);
} // end of omp parallel region
}
void MSMCGOMP::compute(int eflag, int vflag)
{
if (scalar_pressure_flag)
error->all(FLERR,"Must use 'kspace_modify pressure/scalar no' "
"with kspace_style msm/cg/omp");
const double * const q = atom->q;
const int nlocal = atom->nlocal;
int i,j,n;
// set energy/virial flags
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = evflag_atom = eflag_global = vflag_global =
eflag_atom = vflag_atom = eflag_either = vflag_either = 0;
// invoke allocate_peratom() if needed for first time
if (vflag_atom && !peratom_allocate_flag) {
allocate_peratom();
cg_peratom_all->ghost_notify();
cg_peratom_all->setup();
for (int n=0; n<levels; n++) {
if (!active_flag[n]) continue;
cg_peratom[n]->ghost_notify();
cg_peratom[n]->setup();
}
peratom_allocate_flag = 1;
}
// extend size of per-atom arrays if necessary
if (atom->nmax > nmax) {
memory->destroy(part2grid);
memory->destroy(is_charged);
nmax = atom->nmax;
memory->create(part2grid,nmax,3,"msm:part2grid");
memory->create(is_charged,nmax,"msm/cg:is_charged");
}
// one time setup message
if (num_charged < 0) {
bigint charged_all, charged_num;
double charged_frac, charged_fmax, charged_fmin;
num_charged=0;
for (i=0; i < nlocal; ++i)
if (fabs(q[i]) > smallq)
++num_charged;
// get fraction of charged particles per domain
if (nlocal > 0)
charged_frac = static_cast<double>(num_charged) * 100.0
/ static_cast<double>(nlocal);
else
charged_frac = 0.0;
MPI_Reduce(&charged_frac,&charged_fmax,1,MPI_DOUBLE,MPI_MAX,0,world);
MPI_Reduce(&charged_frac,&charged_fmin,1,MPI_DOUBLE,MPI_MIN,0,world);
// get fraction of charged particles overall
charged_num = num_charged;
MPI_Reduce(&charged_num,&charged_all,1,MPI_LMP_BIGINT,MPI_SUM,0,world);
charged_frac = static_cast<double>(charged_all) * 100.0
/ static_cast<double>(atom->natoms);
if (me == 0) {
if (screen)
fprintf(screen,
" MSM/cg optimization cutoff: %g\n"
" Total charged atoms: %.1f%%\n"
" Min/max charged atoms/proc: %.1f%% %.1f%%\n",
smallq,charged_frac,charged_fmin,charged_fmax);
if (logfile)
fprintf(logfile,
" MSM/cg optimization cutoff: %g\n"
" Total charged atoms: %.1f%%\n"
" Min/max charged atoms/proc: %.1f%% %.1f%%\n",
smallq,charged_frac,charged_fmin,charged_fmax);
}
}
// only need to rebuild this list after a neighbor list update
if (neighbor->ago == 0) {
num_charged = 0;
for (i = 0; i < nlocal; ++i) {
if (fabs(q[i]) > smallq) {
is_charged[num_charged] = i;
++num_charged;
}
}
}
// find grid points for all my particles
// map my particle charge onto my local 3d density grid (aninterpolation)
particle_map();
make_rho();
// all procs reverse communicate charge density values from their ghost grid points
// to fully sum contribution in their 3d grid
current_level = 0;
cg_all->reverse_comm(this,REVERSE_RHO);
// forward communicate charge density values to fill ghost grid points
// compute direct sum interaction and then restrict to coarser grid
for (int n=0; n<=levels-2; n++) {
if (!active_flag[n]) continue;
current_level = n;
cg[n]->forward_comm(this,FORWARD_RHO);
direct(n);
restriction(n);
}
// compute direct interation for top grid level for nonperiodic
// and for second from top grid level for periodic
if (active_flag[levels-1]) {
if (domain->nonperiodic) {
current_level = levels-1;
cg[levels-1]->forward_comm(this,FORWARD_RHO);
direct_top(levels-1);
cg[levels-1]->reverse_comm(this,REVERSE_AD);
if (vflag_atom)
cg_peratom[levels-1]->reverse_comm(this,REVERSE_AD_PERATOM);
} else {
// Here using MPI_Allreduce is cheaper than using commgrid
grid_swap_forward(levels-1,qgrid[levels-1]);
direct(levels-1);
grid_swap_reverse(levels-1,egrid[levels-1]);
current_level = levels-1;
if (vflag_atom)
cg_peratom[levels-1]->reverse_comm(this,REVERSE_AD_PERATOM);
}
}
// prolongate energy/virial from coarser grid to finer grid
// reverse communicate from ghost grid points to get full sum
for (int n=levels-2; n>=0; n--) {
if (!active_flag[n]) continue;
prolongation(n);
current_level = n;
cg[n]->reverse_comm(this,REVERSE_AD);
// extra per-atom virial communication
if (vflag_atom)
cg_peratom[n]->reverse_comm(this,REVERSE_AD_PERATOM);
}
// all procs communicate E-field values
// to fill ghost cells surrounding their 3d bricks
current_level = 0;
cg_all->forward_comm(this,FORWARD_AD);
// extra per-atom energy/virial communication
if (vflag_atom)
cg_peratom_all->forward_comm(this,FORWARD_AD_PERATOM);
// calculate the force on my particles (interpolation)
fieldforce();
// calculate the per-atom energy/virial for my particles
if (evflag_atom) fieldforce_peratom();
// update qsum and qsqsum, if atom count has changed and energy needed
if ((eflag_global || eflag_atom) && atom->natoms != natoms_original) {
qsum_qsq();
natoms_original = atom->natoms;
}
// sum global energy across procs and add in self-energy term
const double qscale = force->qqrd2e * scale;
if (eflag_global) {
double energy_all;
MPI_Allreduce(&energy,&energy_all,1,MPI_DOUBLE,MPI_SUM,world);
energy = energy_all;
double e_self = qsqsum*gamma(0.0)/cutoff;
energy -= e_self;
energy *= 0.5*qscale;
}
// total long-range virial
if (vflag_global) {
double virial_all[6];
MPI_Allreduce(virial,virial_all,6,MPI_DOUBLE,MPI_SUM,world);
for (i = 0; i < 6; i++) virial[i] = 0.5*qscale*virial_all[i];
}
// per-atom energy/virial
// energy includes self-energy correction
if (evflag_atom) {
const double qs = 0.5*qscale;
if (eflag_atom) {
const double sf = gamma(0.0)/cutoff;
for (j = 0; j < num_charged; j++) {
i = is_charged[j];
eatom[i] -= q[i]*q[i]*sf;
eatom[i] *= qs;
}
}
if (vflag_atom) {
for (n = 0; n < num_charged; n++) {
i = is_charged[n];
for (j = 0; j < 6; j++)
vatom[i][j] *= qs;
}
}
}
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(eflag,vflag)
#endif
{
#if defined(_OPENMP)
const int tid = omp_get_thread_num();
#else
const int tid = 0;
#endif
ThrData *thr = fix->get_thr(tid);
thr->timer(Timer::START);
reduce_thr(this, eflag, vflag, thr);
} // end of omp parallel region
}
void PairTriLJOMP::compute(int eflag, int vflag)
{
if (eflag || vflag) {
ev_setup(eflag,vflag);
} else evflag = vflag_fdotr = 0;
const int nall = atom->nlocal + atom->nghost;
const int nthreads = comm->nthreads;
const int inum = list->inum;
const int * const tri = atom->tri;
const int * const type = atom->type;
AtomVecTri::Bonus * const bonus = avec->bonus;
// grow discrete list if necessary and initialize
if (nall > nmax) {
nmax = nall;
memory->destroy(dnum);
memory->destroy(dfirst);
memory->create(dnum,nall,"pair:dnum");
memory->create(dfirst,nall,"pair:dfirst");
}
memset(dnum,0,nall*sizeof(int));
ndiscrete = 0;
// need to discretize the system ahead of time
// until we find a good way to multi-thread it.
for (int i = 0; i < nall; ++i) {
double dc1[3],dc2[3],dc3[3],p[3][3];
if (tri[i] >= 0) {
if (dnum[i] == 0) {
MathExtra::quat_to_mat(bonus[tri[i]].quat,p);
MathExtra::matvec(p,bonus[tri[i]].c1,dc1);
MathExtra::matvec(p,bonus[tri[i]].c2,dc2);
MathExtra::matvec(p,bonus[tri[i]].c3,dc3);
dfirst[i] = ndiscrete;
discretize(i,sigma[type[i]][type[i]],dc1,dc2,dc3);
dnum[i] = ndiscrete - dfirst[i];
}
}
}
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(eflag,vflag)
#endif
{
int ifrom, ito, tid;
loop_setup_thr(ifrom, ito, tid, inum, nthreads);
ThrData *thr = fix->get_thr(tid);
thr->timer(Timer::START);
ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
if (evflag) {
if (eflag) {
if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
else eval<1,1,0>(ifrom, ito, thr);
} else {
if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr);
else eval<0,0,0>(ifrom, ito, thr);
}
thr->timer(Timer::PAIR);
reduce_thr(this, eflag, vflag, thr);
} // end of omp parallel region
}
void PairDPDOMP::compute(int eflag, int vflag)
{
if (eflag || vflag) {
ev_setup(eflag,vflag);
} else evflag = vflag_fdotr = 0;
const int nall = atom->nlocal + atom->nghost;
const int inum = list->inum;
// number of threads has changed. reallocate pool of pRNGs
if (nthreads != comm->nthreads) {
if (random_thr) {
for (int i=1; i < nthreads; ++i)
delete random_thr[i];
delete[] random_thr;
}
nthreads = comm->nthreads;
random_thr = new RanMars*[nthreads];
for (int i=1; i < nthreads; ++i)
random_thr[i] = NULL;
// to ensure full compatibility with the serial DPD style
// we use the serial random number generator instance for thread 0
random_thr[0] = random;
}
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(eflag,vflag)
#endif
{
int ifrom, ito, tid;
loop_setup_thr(ifrom, ito, tid, inum, nthreads);
ThrData *thr = fix->get_thr(tid);
thr->timer(Timer::START);
ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
// generate a random number generator instance for
// all threads != 0. make sure we use unique seeds.
if ((tid > 0) && (random_thr[tid] == NULL))
random_thr[tid] = new RanMars(Pair::lmp, seed + comm->me
+ comm->nprocs*tid);
if (evflag) {
if (eflag) {
if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
else eval<1,1,0>(ifrom, ito, thr);
} else {
if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr);
else eval<0,0,0>(ifrom, ito, thr);
}
thr->timer(Timer::PAIR);
reduce_thr(this, eflag, vflag, thr);
} // end of omp parallel region
}
