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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8434 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2012-06-29 18:01:14 +00:00
parent fee52f2fac
commit 945fc5a36a
11 changed files with 415 additions and 66 deletions
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4
src/USER-CG-CMM/Package.sh
View File

@ -15,10 +15,10 @@ for file in *.cpp *.h; do
if (test $file = pair_cg_cmm_coul_long.h -a ! -e ../pair_lj_cut_coul_long.h) then
continue
fi
if (test $file = angle_sdk.cpp -a ! -e ../pair_angle_harmonic.cpp) then
if (test $file = angle_sdk.cpp -a ! -e ../angle_harmonic.cpp) then
continue
fi
if (test $file = angle_sdk.h -a ! -e ../pair_angle_harmonic.h) then
if (test $file = angle_sdk.h -a ! -e ../angle_harmonic.h) then
continue
fi
if (test $file = pair_lj_sdk_coul_long.cpp -a ! -e ../pair_lj_cut_coul_long.cpp) then

54
src/USER-OMP/fix_qeq_comb_omp.cpp
View File

@ -19,11 +19,17 @@
#include "mpi.h"
#include "math.h"
#include "fix_qeq_comb_omp.h"
#include "fix_omp.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "group.h"
#include "memory.h"
#include "modify.h"
#include "error.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "respa.h"
#include "update.h"
#include "pair_comb_omp.h"
@ -58,13 +64,28 @@ void FixQEQCombOMP::init()
ngroup = group->count(igroup);
if (ngroup == 0) error->all(FLERR,"Fix qeq/comb group has no atoms");
// determine status of neighbor flag of the omp package command
int ifix = modify->find_fix("package_omp");
int use_omp = 0;
if (ifix >=0) {
FixOMP * fix = static_cast<FixOMP *>(lmp->modify->fix[ifix]);
if (fix->get_neighbor()) use_omp = 1;
}
int irequest = neighbor->request(this);
neighbor->requests[irequest]->pair = 0;
neighbor->requests[irequest]->fix = 1;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
neighbor->requests[irequest]->omp = use_omp;
}
/* ---------------------------------------------------------------------- */
void FixQEQCombOMP::post_force(int vflag)
{
int i,iloop,loopmax;
int i,ii,iloop,loopmax,inum,*ilist;
double heatpq,qmass,dtq,dtq2;
double enegchkall,enegmaxall;
@ -89,8 +110,8 @@ void FixQEQCombOMP::post_force(int vflag)
// more loops for first-time charge equilibrium
iloop = 0;
if (firstflag) loopmax = 5000;
else loopmax = 2000;
if (firstflag) loopmax = 500;
else loopmax = 200;
// charge-equilibration loop
@ -99,8 +120,8 @@ void FixQEQCombOMP::post_force(int vflag)
update->ntimestep);
heatpq = 0.05;
qmass = 0.000548580;
dtq = 0.0006;
qmass = 0.016;
dtq = 0.01;
dtq2 = 0.5*dtq*dtq/qmass;
double enegchk = 0.0;
@ -109,29 +130,38 @@ void FixQEQCombOMP::post_force(int vflag)
double *q = atom->q;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++)
inum = comb->list->inum;
ilist = comb->list->ilist;
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
q1[i] = q2[i] = qf[i] = 0.0;
}
for (iloop = 0; iloop < loopmax; iloop ++ ) {
for (i = 0; i < nlocal; i++)
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
if (mask[i] & groupbit) {
q1[i] += qf[i]*dtq2 - heatpq*q1[i];
q[i] += q1[i];
}
}
comm->forward_comm_fix(this);
enegtot = comb->yasu_char(qf,igroup);
if(comb) enegtot = comb->yasu_char(qf,igroup);
enegtot /= ngroup;
enegchk = enegmax = 0.0;
for (i = 0; i < nlocal ; i++)
for (ii = 0; ii < inum ; ii++) {
i = ilist[ii];
if (mask[i] & groupbit) {
q2[i] = enegtot-qf[i];
enegmax = MAX(enegmax,fabs(q2[i]));
enegchk += fabs(q2[i]);
qf[i] = q2[i];
}
}
MPI_Allreduce(&enegchk,&enegchkall,1,MPI_DOUBLE,MPI_SUM,world);
enegchk = enegchkall/ngroup;
@ -145,10 +175,12 @@ void FixQEQCombOMP::post_force(int vflag)
"enegmax %.6g, fq deviation: %.6g\n",
iloop,enegtot,enegmax,enegchk);
for (i = 0; i < nlocal; i++)
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
if (mask[i] & groupbit)
q1[i] += qf[i]*dtq2 - heatpq*q1[i];
}
}
if (me == 0 && fp) {
if (iloop == loopmax)

8
src/USER-OMP/neigh_full_omp.cpp
View File

@ -178,6 +178,7 @@ void Neighbor::full_nsq_ghost_omp(NeighList *list)
// loop over all atoms, owned and ghost
// skip i = j
// no molecular test when i = ghost atom
if (i < nlocal) {
for (j = 0; j < nall; j++) {
@ -210,8 +211,7 @@ void Neighbor::full_nsq_ghost_omp(NeighList *list)
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighghostsq[itype][jtype])
neighptr[n++] = j;
if (rsq <= cutneighghostsq[itype][jtype]) neighptr[n++] = j;
}
}
@ -401,6 +401,7 @@ void Neighbor::full_bin_ghost_omp(NeighList *list)
// loop over all atoms in surrounding bins in stencil including self
// when i is a ghost atom, must check if stencil bin is out of bounds
// skip i = j
// no molecular test when i = ghost atom
if (i < nlocal) {
ibin = coord2bin(x[i]);
@ -448,8 +449,7 @@ void Neighbor::full_bin_ghost_omp(NeighList *list)
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighghostsq[itype][jtype])
neighptr[n++] = j;
if (rsq <= cutneighghostsq[itype][jtype]) neighptr[n++] = j;
}
}
}

143
src/USER-OMP/neigh_half_bin_omp.cpp
View File

@ -129,6 +129,149 @@ void Neighbor::half_bin_no_newton_omp(NeighList *list)
list->inum = nlocal;
}
/* ----------------------------------------------------------------------
binned neighbor list construction with partial Newton's 3rd law
include neighbors of ghost atoms, but no "special neighbors" for ghosts
owned and ghost atoms check own bin and other bins in stencil
pair stored once if i,j are both owned and i < j
pair stored by me if i owned and j ghost (also stored by proc owning j)
pair stored once if i,j are both ghost and i < j
------------------------------------------------------------------------- */
void Neighbor::half_bin_no_newton_ghost_omp(NeighList *list)
{
const int nlocal = atom->nlocal;
const int nall = nlocal + atom->nghost;
NEIGH_OMP_INIT;
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(list)
#endif
NEIGH_OMP_SETUP(nall);
int i,j,k,n,itype,jtype,ibin,which;
int xbin,ybin,zbin,xbin2,ybin2,zbin2;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *neighptr;
// bin local & ghost atoms
bin_atoms();
// loop over each atom, storing neighbors
int **special = atom->special;
int **nspecial = atom->nspecial;
int *tag = atom->tag;
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int *molecule = atom->molecule;
int molecular = atom->molecular;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
int nstencil = list->nstencil;
int *stencil = list->stencil;
int **stencilxyz = list->stencilxyz;
// each thread works on its own page
int npage = tid;
int npnt = 0;
for (i = ifrom; i < ito; i++) {
#if defined(_OPENMP)
#pragma omp critical
#endif
if (pgsize - npnt < oneatom) {
npnt = 0;
npage += nthreads;
if (npage >= list->maxpage) list->add_pages(nthreads);
}
neighptr = &(list->pages[npage][npnt]);
n = 0;
itype = type[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
// loop over all atoms in other bins in stencil including self
// when i is a ghost atom, must check if stencil bin is out of bounds
// only store pair if i < j
// stores own/own pairs only once
// stores own/ghost pairs with owned atom only, on both procs
// stores ghost/ghost pairs only once
// no molecular test when i = ghost atom
if (i < nlocal) {
ibin = coord2bin(x[i]);
for (k = 0; k < nstencil; k++) {
for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
if (j <= i) continue;
jtype = type[j];
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighsq[itype][jtype]) {
if (molecular) {
which = find_special(special[i],nspecial[i],tag[j]);
if (which == 0) neighptr[n++] = j;
else if (domain->minimum_image_check(delx,dely,delz))
neighptr[n++] = j;
else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
} else neighptr[n++] = j;
}
}
}
} else {
ibin = coord2bin(x[i],xbin,ybin,zbin);
for (k = 0; k < nstencil; k++) {
xbin2 = xbin + stencilxyz[k][0];
ybin2 = ybin + stencilxyz[k][1];
zbin2 = zbin + stencilxyz[k][2];
if (xbin2 < 0 || xbin2 >= mbinx ||
ybin2 < 0 || ybin2 >= mbiny ||
zbin2 < 0 || zbin2 >= mbinz) continue;
for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
if (j <= i) continue;
jtype = type[j];
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighghostsq[itype][jtype]) neighptr[n++] = j;
}
}
}
ilist[i] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
npnt += n;
if (n > oneatom)
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
NEIGH_OMP_CLOSE;
list->inum = nlocal;
list->gnum = nall - atom->nlocal;
}
/* ----------------------------------------------------------------------
binned neighbor list construction with full Newton's 3rd law
each owned atom i checks its own bin and other bins in Newton stencil

127
src/USER-OMP/neigh_half_nsq_omp.cpp
View File

@ -32,6 +32,7 @@ void Neighbor::half_nsq_no_newton_omp(NeighList *list)
{
const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
const int bitmask = (includegroup) ? group->bitmask[includegroup] : 0;
const int nall = atom->nlocal + atom->nghost;
NEIGH_OMP_INIT;
#if defined(_OPENMP)
@ -43,8 +44,6 @@ void Neighbor::half_nsq_no_newton_omp(NeighList *list)
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *neighptr;
// loop over each atom, storing neighbors
int **special = atom->special;
int **nspecial = atom->nspecial;
int *tag = atom->tag;
@ -53,16 +52,18 @@ void Neighbor::half_nsq_no_newton_omp(NeighList *list)
int *type = atom->type;
int *mask = atom->mask;
int *molecule = atom->molecule;
int nall = atom->nlocal + atom->nghost;
int molecular = atom->molecular;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
// each thread works on its own page
int npage = tid;
int npnt = 0;
// loop over owned atoms, storing neighbors
for (i = ifrom; i < ito; i++) {
#if defined(_OPENMP)
@ -83,6 +84,7 @@ void Neighbor::half_nsq_no_newton_omp(NeighList *list)
ztmp = x[i][2];
// loop over remaining atoms, owned and ghost
// only store pair if i < j
for (j = i+1; j < nall; j++) {
if (includegroup && !(mask[j] & bitmask)) continue;
@ -116,6 +118,125 @@ void Neighbor::half_nsq_no_newton_omp(NeighList *list)
list->inum = nlocal;
}
/* ----------------------------------------------------------------------
N^2 / 2 search for neighbor pairs with partial Newton's 3rd law
include neighbors of ghost atoms, but no "special neighbors" for ghosts
pair stored once if i,j are both owned and i < j
pair stored by me if i owned and j ghost (also stored by proc owning j)
pair stored once if i,j are both ghost and i < j
------------------------------------------------------------------------- */
void Neighbor::half_nsq_no_newton_ghost_omp(NeighList *list)
{
const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
const int bitmask = (includegroup) ? group->bitmask[includegroup] : 0;
const int nall = nlocal + atom->nghost;
NEIGH_OMP_INIT;
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(list)
#endif
NEIGH_OMP_SETUP(nall);
int i,j,n,itype,jtype,which;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *neighptr;
int **special = atom->special;
int **nspecial = atom->nspecial;
int *tag = atom->tag;
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int *molecule = atom->molecule;
int molecular = atom->molecular;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
// each thread works on its own page
int npage = tid;
int npnt = 0;
// loop over owned & ghost atoms, storing neighbors
for (i = ifrom; i < ito; i++) {
#if defined(_OPENMP)
#pragma omp critical
#endif
if (pgsize - npnt < oneatom) {
npnt = 0;
npage += nthreads;
if (npage >= list->maxpage) list->add_pages(nthreads);
}
neighptr = &(list->pages[npage][npnt]);
n = 0;
itype = type[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
// loop over remaining atoms, owned and ghost
// only store pair if i < j
// stores own/own pairs only once
// stores own/ghost pairs with owned atom only, on both procs
// stores ghost/ghost pairs only once
// no molecular test when i = ghost atom
if (i < nlocal) {
for (j = i+1; j < nall; j++) {
if (includegroup && !(mask[j] & bitmask)) continue;
jtype = type[j];
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighsq[itype][jtype]) {
if (molecular) {
which = find_special(special[i],nspecial[i],tag[j]);
if (which == 0) neighptr[n++] = j;
else if (domain->minimum_image_check(delx,dely,delz))
neighptr[n++] = j;
else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
} else neighptr[n++] = j;
}
}
} else {
for (j = i+1; j < nall; j++) {
if (includegroup && !(mask[j] & bitmask)) continue;
jtype = type[j];
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighsq[itype][jtype]) neighptr[n++] = j;
}
}
ilist[i] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
npnt += n;
if (n > oneatom)
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
NEIGH_OMP_CLOSE;
list->inum = atom->nlocal;
list->gnum = nall - atom->nlocal;
}
/* ----------------------------------------------------------------------
N^2 / 2 search for neighbor pairs with full Newton's 3rd law
every pair stored exactly once by some processor

36
src/USER-OMP/pair_gran_hertz_history_omp.cpp
View File

@ -16,6 +16,7 @@
#include "pair_gran_hertz_history_omp.h"
#include "atom.h"
#include "comm.h"
#include "fix_rigid.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"
@ -48,6 +49,13 @@ void PairGranHertzHistoryOMP::compute(int eflag, int vflag)
computeflag = 1;
const int shearupdate = (update->setupflag) ? 0 : 1;
// update body ptr and values for ghost atoms if using FixRigid masses
if (fix_rigid && neighbor->ago == 0) {
body = fix_rigid->body;
comm->forward_comm_pair(this);
}
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(eflag,vflag)
#endif
@ -78,7 +86,7 @@ void PairGranHertzHistoryOMP::eval(int iifrom, int iito, ThrData * const thr)
double vr1,vr2,vr3,vnnr,vn1,vn2,vn3,vt1,vt2,vt3;
double wr1,wr2,wr3;
double vtr1,vtr2,vtr3,vrel;
double meff,damp,ccel,tor1,tor2,tor3;
double mi,mj,meff,damp,ccel,tor1,tor2,tor3;
double fn,fs,fs1,fs2,fs3;
double shrmag,rsht,polyhertz;
int *ilist,*jlist,*numneigh,**firstneigh;
@ -171,19 +179,27 @@ void PairGranHertzHistoryOMP::eval(int iifrom, int iito, ThrData * const thr)
wr2 = (radi*omega[i][1] + radj*omega[j][1]) * rinv;
wr3 = (radi*omega[i][2] + radj*omega[j][2]) * rinv;
// normal force = Hertzian contact + normal velocity damping
// meff = effective mass of pair of particles
// if I or J part of rigid body, use body mass
// if I or J is frozen, meff is other particle
if (rmass) {
meff = rmass[i]*rmass[j] / (rmass[i]+rmass[j]);
if (mask[i] & freeze_group_bit) meff = rmass[j];
if (mask[j] & freeze_group_bit) meff = rmass[i];
mi = rmass[i];
mj = rmass[j];
} else {
itype = type[i];
jtype = type[j];
meff = mass[itype]*mass[jtype] / (mass[itype]+mass[jtype]);
if (mask[i] & freeze_group_bit) meff = mass[jtype];
if (mask[j] & freeze_group_bit) meff = mass[itype];
mi = mass[type[i]];
mj = mass[type[j]];
}
if (fix_rigid) {
if (body[i] >= 0) mi = fix_rigid->masstotal[body[i]];
if (body[j] >= 0) mj = fix_rigid->masstotal[body[j]];
}
meff = mi*mj / (mi+mj);
if (mask[i] & freeze_group_bit) meff = mj;
if (mask[j] & freeze_group_bit) meff = mi;
// normal force = Hertzian contact + normal velocity damping
damp = meff*gamman*vnnr*rsqinv;
ccel = kn*(radsum-r)*rinv - damp;

35
src/USER-OMP/pair_gran_hooke_history_omp.cpp
View File

@ -16,6 +16,7 @@
#include "pair_gran_hooke_history_omp.h"
#include "atom.h"
#include "comm.h"
#include "fix_rigid.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"
@ -49,6 +50,13 @@ void PairGranHookeHistoryOMP::compute(int eflag, int vflag)
computeflag = 1;
const int shearupdate = (update->setupflag) ? 0 : 1;
// update body ptr and values for ghost atoms if using FixRigid masses
if (fix_rigid && neighbor->ago == 0) {
body = fix_rigid->body;
comm->forward_comm_pair(this);
}
const int nall = atom->nlocal + atom->nghost;
const int nthreads = comm->nthreads;
const int inum = list->inum;
@ -84,7 +92,7 @@ void PairGranHookeHistoryOMP::eval(int iifrom, int iito, ThrData * const thr)
double vr1,vr2,vr3,vnnr,vn1,vn2,vn3,vt1,vt2,vt3;
double wr1,wr2,wr3;
double vtr1,vtr2,vtr3,vrel;
double meff,damp,ccel,tor1,tor2,tor3;
double mi,mj,meff,damp,ccel,tor1,tor2,tor3;
double fn,fs,fs1,fs2,fs3;
double shrmag,rsht;
int *ilist,*jlist,*numneigh,**firstneigh;
@ -176,18 +184,27 @@ void PairGranHookeHistoryOMP::eval(int iifrom, int iito, ThrData * const thr)
wr2 = (radi*omega[i][1] + radj*omega[j][1]) * rinv;
wr3 = (radi*omega[i][2] + radj*omega[j][2]) * rinv;
// normal forces = Hookian contact + normal velocity damping
// meff = effective mass of pair of particles
// if I or J part of rigid body, use body mass
// if I or J is frozen, meff is other particle
if (rmass) {
meff = rmass[i]*rmass[j] / (rmass[i]+rmass[j]);
if (mask[i] & freeze_group_bit) meff = rmass[j];
if (mask[j] & freeze_group_bit) meff = rmass[i];
mi = rmass[i];
mj = rmass[j];
} else {
jtype = type[j];
meff = mass[itype]*mass[jtype] / (mass[itype]+mass[jtype]);
if (mask[i] & freeze_group_bit) meff = mass[jtype];
if (mask[j] & freeze_group_bit) meff = mass[itype];
mi = mass[type[i]];
mj = mass[type[j]];
}
if (fix_rigid) {
if (body[i] >= 0) mi = fix_rigid->masstotal[body[i]];
if (body[j] >= 0) mj = fix_rigid->masstotal[body[j]];
}
meff = mi*mj / (mi+mj);
if (mask[i] & freeze_group_bit) meff = mj;
if (mask[j] & freeze_group_bit) meff = mi;
// normal forces = Hookian contact + normal velocity damping
damp = meff*gamman*vnnr*rsqinv;
ccel = kn*(radsum-r)*rinv - damp;

36
src/USER-OMP/pair_gran_hooke_omp.cpp
View File

@ -16,6 +16,7 @@
#include "pair_gran_hooke_omp.h"
#include "atom.h"
#include "comm.h"
#include "fix_rigid.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"
@ -44,6 +45,13 @@ void PairGranHookeOMP::compute(int eflag, int vflag)
const int nthreads = comm->nthreads;
const int inum = list->inum;
// update body ptr and values for ghost atoms if using FixRigid masses
if (fix_rigid && neighbor->ago == 0) {
body = fix_rigid->body;
comm->forward_comm_pair(this);
}
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(eflag,vflag)
#endif
@ -74,7 +82,7 @@ void PairGranHookeOMP::eval(int iifrom, int iito, ThrData * const thr)
double vr1,vr2,vr3,vnnr,vn1,vn2,vn3,vt1,vt2,vt3;
double wr1,wr2,wr3;
double vtr1,vtr2,vtr3,vrel;
double meff,damp,ccel,tor1,tor2,tor3;
double mi,mj,meff,damp,ccel,tor1,tor2,tor3;
double fn,fs,ft,fs1,fs2,fs3;
int *ilist,*jlist,*numneigh,**firstneigh;
@ -150,19 +158,27 @@ void PairGranHookeOMP::eval(int iifrom, int iito, ThrData * const thr)
wr2 = (radi*omega[i][1] + radj*omega[j][1]) * rinv;
wr3 = (radi*omega[i][2] + radj*omega[j][2]) * rinv;
// normal forces = Hookian contact + normal velocity damping
// meff = effective mass of pair of particles
// if I or J part of rigid body, use body mass
// if I or J is frozen, meff is other particle
if (rmass) {
meff = rmass[i]*rmass[j] / (rmass[i]+rmass[j]);
if (mask[i] & freeze_group_bit) meff = rmass[j];
if (mask[j] & freeze_group_bit) meff = rmass[i];
mi = rmass[i];
mj = rmass[j];
} else {
itype = type[i];
jtype = type[j];
meff = mass[itype]*mass[jtype] / (mass[itype]+mass[jtype]);
if (mask[i] & freeze_group_bit) meff = mass[jtype];
if (mask[j] & freeze_group_bit) meff = mass[itype];
mi = mass[type[i]];
mj = mass[type[j]];
}
if (fix_rigid) {
if (body[i] >= 0) mi = fix_rigid->masstotal[body[i]];
if (body[j] >= 0) mj = fix_rigid->masstotal[body[j]];
}
meff = mi*mj / (mi+mj);
if (mask[i] & freeze_group_bit) meff = mj;
if (mask[j] & freeze_group_bit) meff = mi;
// normal forces = Hookian contact + normal velocity damping
damp = meff*gamman*vnnr*rsqinv;
ccel = kn*(radsum-r)*rinv - damp;

6
src/accelerator_omp.h
View File

@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
@ -20,9 +20,11 @@
#ifdef LMP_USER_OMP
void half_nsq_no_newton_omp(class NeighList *);
void half_nsq_no_newton_ghost_omp(class NeighList *);
void half_nsq_newton_omp(class NeighList *);
void half_bin_no_newton_omp(class NeighList *);
void half_bin_no_newton_ghost_omp(class NeighList *);
void half_bin_newton_omp(class NeighList *);
void half_bin_newton_tri_omp(class NeighList *);
@ -57,9 +59,11 @@
// needed for compiling Neighbor class when USER-OMP is not installed
void half_nsq_no_newton_omp(class NeighList *) {}
void half_nsq_no_newton_ghost_omp(class NeighList *) {}
void half_nsq_newton_omp(class NeighList *) {}
void half_bin_no_newton_omp(class NeighList *) {}
void half_bin_no_newton_ghost_omp(class NeighList *) {}
void half_bin_newton_omp(class NeighList *) {}
void half_bin_newton_tri_omp(class NeighList *) {}

12
src/neighbor.cpp
View File

@ -945,8 +945,7 @@ void Neighbor::choose_build(int index, NeighRequest *rq)
else if (includegroup)
error->all(FLERR,"Neighbor include group not allowed "
"with ghost neighbors");
// NOTE: missing OMP version of this one
else pb = &Neighbor::half_nsq_no_newton_ghost;
else pb = &Neighbor::half_nsq_no_newton_ghost_omp;
} else if (newton_pair == 1) pb = &Neighbor::half_nsq_newton_omp;
} else if (rq->newton == 1) {
pb = &Neighbor::half_nsq_newton_omp;
@ -955,8 +954,7 @@ void Neighbor::choose_build(int index, NeighRequest *rq)
else if (includegroup)
error->all(FLERR,"Neighbor include group not allowed "
"with ghost neighbors");
// NOTE: missing OMP version of this one
else pb = &Neighbor::half_nsq_no_newton_ghost;
else pb = &Neighbor::half_nsq_no_newton_ghost_omp;
}
} else if (style == BIN) {
if (rq->newton == 0) {
@ -965,8 +963,7 @@ void Neighbor::choose_build(int index, NeighRequest *rq)
else if (includegroup)
error->all(FLERR,"Neighbor include group not allowed "
"with ghost neighbors");
// NOTE: missing OMP version of this one
else pb = &Neighbor::half_bin_no_newton_ghost;
else pb = &Neighbor::half_bin_no_newton_ghost_omp;
} else if (triclinic == 0) {
pb = &Neighbor::half_bin_newton_omp;
} else if (triclinic == 1)
@ -979,8 +976,7 @@ void Neighbor::choose_build(int index, NeighRequest *rq)
else if (includegroup)
error->all(FLERR,"Neighbor include group not allowed "
"with ghost neighbors");
// NOTE: missing OMP version of this one
else pb = &Neighbor::half_bin_no_newton_ghost;
else pb = &Neighbor::half_bin_no_newton_ghost_omp;
}
} else if (style == MULTI) {
if (rq->ghost == 1)

4
src/region.cpp
View File

@ -379,4 +379,8 @@ void Region::options(int narg, char **arg)
if (moveflag || rotateflag) dynamic = 1;
else dynamic = 0;
// initialize option variables in case region is used between runs
init();
}