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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9701 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2013-03-21 17:36:09 +00:00
parent 5c3e9abce7
commit a289ce92d7
10 changed files with 1998 additions and 121 deletions
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14
src/KSPACE/pair_buck_long_coul_long.cpp
View File

@ -236,7 +236,7 @@ void PairBuckLongCoulLong::init_style()
int irequest;
if (update->whichflag == 0 && strstr(update->integrate_style,"respa")) {
if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) {
int respa = 0;
if (((Respa *) update->integrate)->level_inner >= 0) respa = 1;
if (((Respa *) update->integrate)->level_middle >= 0) respa = 2;
@ -627,14 +627,14 @@ void PairBuckLongCoulLong::compute_inner()
double qri, *cut_bucksqi, *buck1i, *buck2i, *rhoinvi;
vector xi, d;
ineighn = (ineigh = list->ilist) + list->inum;
ineighn = (ineigh = listinner->ilist) + listinner->inum;
for (; ineigh<ineighn; ++ineigh) { // loop over my atoms
i = *ineigh; fi = f0+3*i;
if (order1) qri = qqrd2e*q[i];
memcpy(xi, x0+(i+(i<<1)), sizeof(vector));
cut_bucksqi = cut_bucksq[typei = type[i]];
buck1i = buck1[typei]; buck2i = buck2[typei]; rhoinvi = rhoinv[typei];
jneighn = (jneigh = list->firstneigh[i])+list->numneigh[i];
jneighn = (jneigh = listinner->firstneigh[i])+listinner->numneigh[i];
for (; jneigh<jneighn; ++jneigh) { // loop over neighbors
j = *jneigh;
@ -716,7 +716,7 @@ void PairBuckLongCoulLong::compute_middle()
double qri, *cut_bucksqi, *buck1i, *buck2i, *rhoinvi;
vector xi, d;
ineighn = (ineigh = list->ilist)+list->inum;
ineighn = (ineigh = listmiddle->ilist)+listmiddle->inum;
for (; ineigh<ineighn; ++ineigh) { // loop over my atoms
i = *ineigh; fi = f0+3*i;
@ -724,7 +724,7 @@ void PairBuckLongCoulLong::compute_middle()
memcpy(xi, x0+(i+(i<<1)), sizeof(vector));
cut_bucksqi = cut_bucksq[typei = type[i]];
buck1i = buck1[typei]; buck2i = buck2[typei]; rhoinvi = rhoinv[typei];
jneighn = (jneigh = list->firstneigh[i])+list->numneigh[i];
jneighn = (jneigh = listmiddle->firstneigh[i])+listmiddle->numneigh[i];
for (; jneigh<jneighn; ++jneigh) { // loop over neighbors
j = *jneigh;
@ -815,7 +815,7 @@ void PairBuckLongCoulLong::compute_outer(int eflag, int vflag)
double cut_in_off_sq = cut_in_off*cut_in_off;
double cut_in_on_sq = cut_in_on*cut_in_on;
ineighn = (ineigh = list->ilist)+list->inum;
ineighn = (ineigh = listouter->ilist)+listouter->inum;
for (; ineigh<ineighn; ++ineigh) { // loop over my atoms
i = *ineigh; fi = f0+3*i;
@ -825,7 +825,7 @@ void PairBuckLongCoulLong::compute_outer(int eflag, int vflag)
buckai = buck_a[typei]; buckci = buck_c[typei]; rhoinvi = rhoinv[typei];
cutsqi = cutsq[typei]; cut_bucksqi = cut_bucksq[typei];
memcpy(xi, x0+(i+(i<<1)), sizeof(vector));
jneighn = (jneigh = list->firstneigh[i])+list->numneigh[i];
jneighn = (jneigh = listouter->firstneigh[i])+listouter->numneigh[i];
for (; jneigh<jneighn; ++jneigh) { // loop over neighbors
j = *jneigh;

14
src/KSPACE/pair_lj_long_coul_long.cpp
View File

@ -236,7 +236,7 @@ void PairLJLongCoulLong::init_style()
int irequest;
if (update->whichflag == 0 && strstr(update->integrate_style,"respa")) {
if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) {
int respa = 0;
if (((Respa *) update->integrate)->level_inner >= 0) respa = 1;
if (((Respa *) update->integrate)->level_middle >= 0) respa = 2;
@ -633,13 +633,13 @@ void PairLJLongCoulLong::compute_inner()
double qri, *cut_ljsqi, *lj1i, *lj2i;
vector xi, d;
ineighn = (ineigh = list->ilist)+list->inum;
ineighn = (ineigh = listinner->ilist)+listinner->inum;
for (; ineigh<ineighn; ++ineigh) { // loop over my atoms
i = *ineigh; fi = f0+3*i;
memcpy(xi, x0+(i+(i<<1)), sizeof(vector));
cut_ljsqi = cut_ljsq[typei = type[i]];
lj1i = lj1[typei]; lj2i = lj2[typei];
jneighn = (jneigh = list->firstneigh[i])+list->numneigh[i];
jneighn = (jneigh = listinner->firstneigh[i])+listinner->numneigh[i];
for (; jneigh<jneighn; ++jneigh) { // loop over neighbors
j = *jneigh;
ni = sbmask(j);
@ -720,7 +720,7 @@ void PairLJLongCoulLong::compute_middle()
double qri, *cut_ljsqi, *lj1i, *lj2i;
vector xi, d;
ineighn = (ineigh = list->ilist)+list->inum;
ineighn = (ineigh = listmiddle->ilist)+listmiddle->inum;
for (; ineigh<ineighn; ++ineigh) { // loop over my atoms
i = *ineigh; fi = f0+3*i;
@ -728,7 +728,7 @@ void PairLJLongCoulLong::compute_middle()
memcpy(xi, x0+(i+(i<<1)), sizeof(vector));
cut_ljsqi = cut_ljsq[typei = type[i]];
lj1i = lj1[typei]; lj2i = lj2[typei];
jneighn = (jneigh = list->firstneigh[i])+list->numneigh[i];
jneighn = (jneigh = listmiddle->firstneigh[i])+listmiddle->numneigh[i];
for (; jneigh<jneighn; ++jneigh) {
j = *jneigh;
@ -817,7 +817,7 @@ void PairLJLongCoulLong::compute_outer(int eflag, int vflag)
double cut_in_off_sq = cut_in_off*cut_in_off;
double cut_in_on_sq = cut_in_on*cut_in_on;
ineighn = (ineigh = list->ilist)+list->inum;
ineighn = (ineigh = listouter->ilist)+listouter->inum;
for (; ineigh<ineighn; ++ineigh) { // loop over my atoms
i = *ineigh; fi = f0+3*i;
@ -826,7 +826,7 @@ void PairLJLongCoulLong::compute_outer(int eflag, int vflag)
lj1i = lj1[typei]; lj2i = lj2[typei]; lj3i = lj3[typei]; lj4i = lj4[typei];
cutsqi = cutsq[typei]; cut_ljsqi = cut_ljsq[typei];
memcpy(xi, x0+(i+(i<<1)), sizeof(vector));
jneighn = (jneigh = list->firstneigh[i])+list->numneigh[i];
jneighn = (jneigh = listouter->firstneigh[i])+listouter->numneigh[i];
for (; jneigh<jneighn; ++jneigh) { // loop over neighbors
j = *jneigh;

968
src/KSPACE/pair_lj_long_tip4p_long.cpp
View File

@ -53,7 +53,7 @@ PairLJLongTIP4PLong::PairLJLongTIP4PLong(LAMMPS *lmp) :
{
dispersionflag = tip4pflag = 1;
single_enable = 0;
respa_enable = 0;
respa_enable = 1;
nmax = 0;
hneigh = NULL;
@ -184,22 +184,40 @@ void PairLJLongTIP4PLong::compute(int eflag, int vflag)
if (rsq < cut_ljsq[itype][jtype]) { // lj
r2inv = 1.0/rsq;
if (order6) { // long-range lj
register double rn = r2inv*r2inv*r2inv;
register double x2 = g2*rsq, a2 = 1.0/x2;
x2 = a2*exp(-x2)*lj4i[jtype];
if (ni == 0) {
forcelj =
(rn*=rn)*lj1i[jtype]-g8*(((6.0*a2+6.0)*a2+3.0)*a2+1.0)*x2*rsq;
if (eflag)
evdwl = rn*lj3i[jtype]-g6*((a2+1.0)*a2+0.5)*x2;
}
else { // special case
register double f = special_lj[ni], t = rn*(1.0-f);
forcelj = f*(rn *= rn)*lj1i[jtype]-
g8*(((6.0*a2+6.0)*a2+3.0)*a2+1.0)*x2*rsq+t*lj2i[jtype];
if (eflag)
evdwl = f*rn*lj3i[jtype]-g6*((a2+1.0)*a2+0.5)*x2+t*lj4i[jtype];
}
if (!ndisptablebits || rsq <= tabinnerdispsq) {
register double rn = r2inv*r2inv*r2inv;
register double x2 = g2*rsq, a2 = 1.0/x2;
x2 = a2*exp(-x2)*lj4i[jtype];
if (ni == 0) {
forcelj =
(rn*=rn)*lj1i[jtype]-g8*(((6.0*a2+6.0)*a2+3.0)*a2+1.0)*x2*rsq;
if (eflag)
evdwl = rn*lj3i[jtype]-g6*((a2+1.0)*a2+0.5)*x2;
}
else { // special case
register double f = special_lj[ni], t = rn*(1.0-f);
forcelj = f*(rn *= rn)*lj1i[jtype]-
g8*(((6.0*a2+6.0)*a2+3.0)*a2+1.0)*x2*rsq+t*lj2i[jtype];
if (eflag)
evdwl = f*rn*lj3i[jtype]-g6*((a2+1.0)*a2+0.5)*x2+t*lj4i[jtype];
}
}
else { // table real space
register union_int_float_t disp_t;
disp_t.f = rsq;
register const int disp_k = (disp_t.i & ndispmask)>>ndispshiftbits;
register double f_disp = (rsq-rdisptable[disp_k])*drdisptable[disp_k];
register double rn = r2inv*r2inv*r2inv;
if (ni == 0) {
forcelj = (rn*=rn)*lj1i[jtype]-(fdisptable[disp_k]+f_disp*dfdisptable[disp_k])*lj4i[jtype];
if (eflag) evdwl = rn*lj3i[jtype]-(edisptable[disp_k]+f_disp*dedisptable[disp_k])*lj4i[jtype];
}
else { // special case
register double f = special_lj[ni], t = rn*(1.0-f);
forcelj = f*(rn *= rn)*lj1i[jtype]-(fdisptable[disp_k]+f_disp*dfdisptable[disp_k])*lj4i[jtype]+t*lj2i[jtype];
if (eflag) evdwl = f*rn*lj3i[jtype]-(edisptable[disp_k]+f_disp*dedisptable[disp_k])*lj4i[jtype]+t*lj4i[jtype];
}
}
}
else { // cut lj
register double rn = r2inv*r2inv*r2inv;
@ -437,6 +455,922 @@ void PairLJLongTIP4PLong::compute(int eflag, int vflag)
}
}
/* --------------------------------------------------------------------- */
void PairLJLongTIP4PLong::compute_inner()
{
int i,j,ii,jj,inum,jnum,itype,jtype,itable;
int iH1,iH2,jH1,jH2;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul;
double r,r2inv,forcecoul,forcelj,cforce;
double factor_coul,factor_lj;
double grij,expm2,prefactor,t,erfc;
double xiM[3],xjM[3],fO[3],fH[3],fd[3],v[6],xH1[3],xH2[3];// f1[3];
double *x1,*x2;
int *ilist,*jlist,*numneigh,**firstneigh;
double rsq, qri;
double cut_out_on = cut_respa[0];
double cut_out_off = cut_respa[1];
double cut_out_diff = cut_out_off - cut_out_on;
double cut_out_on_sq = cut_out_on*cut_out_on;
double cut_out_off_sq = cut_out_off*cut_out_off;
// reallocate hneigh & newsite if necessary
// initialize hneigh[0] to -1 on steps when reneighboring occurred
// initialize hneigh[2] to 0 every step
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
if (atom->nmax > nmax) {
nmax = atom->nmax;
memory->destroy(hneigh);
memory->create(hneigh,nmax,3,"pair:hneigh");
memory->destroy(newsite);
memory->create(newsite,nmax,3,"pair:newsite");
}
if (neighbor->ago == 0)
for (i = 0; i < nall; i++) hneigh[i][0] = -1;
for (i = 0; i < nall; i++) hneigh[i][2] = 0;
double **f = atom->f;
double **x = atom->x;
double *q = atom->q;
int *type = atom->type;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
double qqrd2e = force->qqrd2e;
double cut_coulsqplus = (cut_coul+2.0*qdist)*(cut_coul+2.0*qdist);
int order1 = ewald_order&(1<<1);
int ni;
double *cut_ljsqi, *lj1i, *lj2i, *lj3i, *lj4i, *offseti;
inum = listinner->inum;
ilist = listinner->ilist;
numneigh = listinner->numneigh;
firstneigh = listinner->firstneigh;
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
qtmp = q[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
if (itype == typeO && order1) {
if (hneigh[i][0] < 0) {
hneigh[i][0] = iH1 = atom->map(atom->tag[i] + 1);
hneigh[i][1] = iH2 = atom->map(atom->tag[i] + 2);
hneigh[i][2] = 1;
if (iH1 == -1 || iH2 == -1)
error->one(FLERR,"TIP4P hydrogen is missing");
if (atom->type[iH1] != typeH || atom->type[iH2] != typeH)
error->one(FLERR,"TIP4P hydrogen has incorrect atom type");
compute_newsite(x[i],x[iH1],x[iH2],newsite[i]);
} else {
iH1 = hneigh[i][0];
iH2 = hneigh[i][1];
if (hneigh[i][2] == 0) {
hneigh[i][2] = 1;
compute_newsite(x[i],x[iH1],x[iH2],newsite[i]);
}
}
x1 = newsite[i];
} else x1 = x[i];
jlist = firstneigh[i];
jnum = numneigh[i];
offseti = offset[itype];
lj1i = lj1[itype]; lj2i = lj2[itype]; lj3i = lj3[itype]; lj4i = lj4[itype];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
ni = sbmask(j);
factor_lj = special_lj[sbmask(j)];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
if (rsq < cut_ljsq[itype][jtype] && rsq < cut_out_off_sq ) { // lj
r2inv = 1.0/rsq;
register double rn = r2inv*r2inv*r2inv;
if (ni == 0) forcelj = rn*(rn*lj1i[jtype]-lj2i[jtype]);
else { // special case
register double f = special_lj[ni];
forcelj = f*rn*(rn*lj1i[jtype]-lj2i[jtype]);
}
if (rsq > cut_out_on_sq) { // switching
register double rsw = (sqrt(rsq) - cut_out_on)/cut_out_diff;
forcelj *= 1.0 + rsw*rsw*(2.0*rsw-3.0);
}
forcelj *= r2inv;
f[i][0] += delx*forcelj;
f[i][1] += dely*forcelj;
f[i][2] += delz*forcelj;
f[j][0] -= delx*forcelj;
f[j][1] -= dely*forcelj;
f[j][2] -= delz*forcelj;
}
// adjust rsq and delxyz for off-site O charge(s)
// ADDITIONAL REQEUST REQUIRED HERE!!!!!
if (rsq < cut_coulsqplus && order1) {
if (itype == typeO || jtype == typeO) {
if (jtype == typeO) {
if (hneigh[j][0] < 0) {
hneigh[j][0] = jH1 = atom->map(atom->tag[j] + 1);
hneigh[j][1] = jH2 = atom->map(atom->tag[j] + 2);
hneigh[j][2] = 1;
if (jH1 == -1 || jH2 == -1)
error->one(FLERR,"TIP4P hydrogen is missing");
if (atom->type[jH1] != typeH || atom->type[jH2] != typeH)
error->one(FLERR,"TIP4P hydrogen has incorrect atom type");
compute_newsite(x[j],x[jH1],x[jH2],newsite[j]);
} else {
jH1 = hneigh[j][0];
jH2 = hneigh[j][1];
if (hneigh[j][2] == 0) {
hneigh[j][2] = 1;
compute_newsite(x[j],x[jH1],x[jH2],newsite[j]);
}
}
x2 = newsite[j];
} else x2 = x[j];
delx = x1[0] - x2[0];
dely = x1[1] - x2[1];
delz = x1[2] - x2[2];
rsq = delx*delx + dely*dely + delz*delz;
}
// test current rsq against cutoff and compute Coulombic force
if (rsq < cut_coulsq && rsq < cut_out_off_sq) {
r2inv = 1.0 / rsq;
qri = qqrd2e*qtmp;
if (ni == 0) forcecoul = qri*q[j]*sqrt(r2inv);
else {
forcecoul = qri*q[j]*sqrt(r2inv)*special_coul[ni];
}
if (rsq > cut_out_on_sq) { // switching
register double rsw = (sqrt(rsq) - cut_out_on)/cut_out_diff;
forcecoul *= 1.0 + rsw*rsw*(2.0*rsw-3.0);
}
cforce = forcecoul * r2inv;
//if (evflag) ev_tally(i,j,nlocal,newton_pair,
// evdwl,0.0,cforce,delx,dely,delz);
// if i,j are not O atoms, force is applied directly
// if i or j are O atoms, force is on fictitious atom & partitioned
// force partitioning due to Feenstra, J Comp Chem, 20, 786 (1999)
// f_f = fictitious force, fO = f_f (1 - 2 alpha), fH = alpha f_f
// preserves total force and torque on water molecule
// virial = sum(r x F) where each water's atoms are near xi and xj
// vlist stores 2,4,6 atoms whose forces contribute to virial
if (itype != typeO) {
f[i][0] += delx * cforce;
f[i][1] += dely * cforce;
f[i][2] += delz * cforce;
} else {
fd[0] = delx*cforce;
fd[1] = dely*cforce;
fd[2] = delz*cforce;
fO[0] = fd[0]*(1 - alpha);
fO[1] = fd[1]*(1 - alpha);
fO[2] = fd[2]*(1 - alpha);
fH[0] = 0.5 * alpha * fd[0];
fH[1] = 0.5 * alpha * fd[1];
fH[2] = 0.5 * alpha * fd[2];
f[i][0] += fO[0];
f[i][1] += fO[1];
f[i][2] += fO[2];
f[iH1][0] += fH[0];
f[iH1][1] += fH[1];
f[iH1][2] += fH[2];
f[iH2][0] += fH[0];
f[iH2][1] += fH[1];
f[iH2][2] += fH[2];
}
if (jtype != typeO) {
f[j][0] -= delx * cforce;
f[j][1] -= dely * cforce;
f[j][2] -= delz * cforce;
} else {
fd[0] = -delx*cforce;
fd[1] = -dely*cforce;
fd[2] = -delz*cforce;
fO[0] = fd[0]*(1 - alpha);
fO[1] = fd[1]*(1 - alpha);
fO[2] = fd[2]*(1 - alpha);
fH[0] = 0.5 * alpha * fd[0];
fH[1] = 0.5 * alpha * fd[1];
fH[2] = 0.5 * alpha * fd[2];
f[j][0] += fO[0];
f[j][1] += fO[1];
f[j][2] += fO[2];
f[jH1][0] += fH[0];
f[jH1][1] += fH[1];
f[jH1][2] += fH[2];
f[jH2][0] += fH[0];
f[jH2][1] += fH[1];
f[jH2][2] += fH[2];
}
}
}
}
}
}
/* --------------------------------------------------------------------- */
void PairLJLongTIP4PLong::compute_middle()
{
int i,j,ii,jj,inum,jnum,itype,jtype,itable;
int iH1,iH2,jH1,jH2;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul;
double r,r2inv,forcecoul,forcelj,cforce;
double factor_coul,factor_lj;
double grij,expm2,prefactor,t,erfc;
double xiM[3],xjM[3],fO[3],fH[3],fd[3],v[6],xH1[3],xH2[3];// f1[3];
double *x1,*x2;
int *ilist,*jlist,*numneigh,**firstneigh;
double rsq,qri;
double cut_in_off = cut_respa[0];
double cut_in_on = cut_respa[1];
double cut_out_on = cut_respa[2];
double cut_out_off = cut_respa[3];
double cut_in_diff = cut_in_on - cut_in_off;
double cut_out_diff = cut_out_off - cut_out_on;
double cut_in_off_sq = cut_in_off*cut_in_off;
double cut_in_on_sq = cut_in_on*cut_in_on;
double cut_out_on_sq = cut_out_on*cut_out_on;
double cut_out_off_sq = cut_out_off*cut_out_off;
// reallocate hneigh & newsite if necessary
// initialize hneigh[0] to -1 on steps when reneighboring occurred
// initialize hneigh[2] to 0 every step
int nlocal = atom->nlocal;
double **f = atom->f;
double **x = atom->x;
double *q = atom->q;
int *type = atom->type;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
double qqrd2e = force->qqrd2e;
double cut_coulsqplus = (cut_coul+2.0*qdist)*(cut_coul+2.0*qdist);
int order1 = ewald_order&(1<<1);
int ni;
double *cut_ljsqi, *lj1i, *lj2i, *lj3i, *lj4i, *offseti;
double g2 = g_ewald_6*g_ewald_6, g6 = g2*g2*g2, g8 = g6*g2;
inum = listmiddle->inum;
ilist = listmiddle->ilist;
numneigh = listmiddle->numneigh;
firstneigh = listmiddle->firstneigh;
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
qtmp = q[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
if (itype == typeO && order1) {
if (hneigh[i][0] < 0) {
hneigh[i][0] = iH1 = atom->map(atom->tag[i] + 1);
hneigh[i][1] = iH2 = atom->map(atom->tag[i] + 2);
hneigh[i][2] = 1;
if (iH1 == -1 || iH2 == -1)
error->one(FLERR,"TIP4P hydrogen is missing");
if (atom->type[iH1] != typeH || atom->type[iH2] != typeH)
error->one(FLERR,"TIP4P hydrogen has incorrect atom type");
compute_newsite(x[i],x[iH1],x[iH2],newsite[i]);
} else {
iH1 = hneigh[i][0];
iH2 = hneigh[i][1];
if (hneigh[i][2] == 0) {
hneigh[i][2] = 1;
compute_newsite(x[i],x[iH1],x[iH2],newsite[i]);
}
}
x1 = newsite[i];
} else x1 = x[i];
jlist = firstneigh[i];
jnum = numneigh[i];
offseti = offset[itype];
lj1i = lj1[itype]; lj2i = lj2[itype]; lj3i = lj3[itype]; lj4i = lj4[itype];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
ni = sbmask(j);
factor_lj = special_lj[sbmask(j)];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
if (rsq < cut_ljsq[itype][jtype] && rsq >= cut_in_off_sq && rsq <= cut_out_off_sq ) { // lj
r2inv = 1.0/rsq;
register double rn = r2inv*r2inv*r2inv;
if (ni == 0) forcelj = rn*(rn*lj1i[jtype]-lj2i[jtype]);
else { // special case
register double f = special_lj[ni];
forcelj = f*rn*(rn*lj1i[jtype]-lj2i[jtype]);
}
if (rsq < cut_in_on_sq) { // switching
register double rsw = (sqrt(rsq) - cut_in_off)/cut_in_diff;
forcelj *= rsw*rsw*(3.0 - 2.0*rsw);
}
if (rsq > cut_out_on_sq) {
register double rsw = (sqrt(rsq) - cut_out_on)/cut_out_diff;
forcelj *= 1.0 + rsw*rsw*(2.0*rsw-3.0);
}
forcelj *= r2inv;
f[i][0] += delx*forcelj;
f[i][1] += dely*forcelj;
f[i][2] += delz*forcelj;
f[j][0] -= delx*forcelj;
f[j][1] -= dely*forcelj;
f[j][2] -= delz*forcelj;
}
// adjust rsq and delxyz for off-site O charge(s)
// ADDITIONAL REQEUST REQUIRED HERE!!!!!
if (rsq < cut_coulsqplus && order1) {
if (itype == typeO || jtype == typeO) {
if (jtype == typeO) {
if (hneigh[j][0] < 0) {
hneigh[j][0] = jH1 = atom->map(atom->tag[j] + 1);
hneigh[j][1] = jH2 = atom->map(atom->tag[j] + 2);
hneigh[j][2] = 1;
if (jH1 == -1 || jH2 == -1)
error->one(FLERR,"TIP4P hydrogen is missing");
if (atom->type[jH1] != typeH || atom->type[jH2] != typeH)
error->one(FLERR,"TIP4P hydrogen has incorrect atom type");
compute_newsite(x[j],x[jH1],x[jH2],newsite[j]);
} else {
jH1 = hneigh[j][0];
jH2 = hneigh[j][1];
if (hneigh[j][2] == 0) {
hneigh[j][2] = 1;
compute_newsite(x[j],x[jH1],x[jH2],newsite[j]);
}
}
x2 = newsite[j];
} else x2 = x[j];
delx = x1[0] - x2[0];
dely = x1[1] - x2[1];
delz = x1[2] - x2[2];
rsq = delx*delx + dely*dely + delz*delz;
}
// test current rsq against cutoff and compute Coulombic force
if (rsq < cut_coulsq && rsq >= cut_in_off_sq && rsq <= cut_out_off_sq) {
r2inv = 1.0 / rsq;
qri = qqrd2e*qtmp;
if (ni == 0) forcecoul = qri*q[j]*sqrt(r2inv);
else {
forcecoul = qri*q[j]*sqrt(r2inv)*special_coul[ni];
}
if (rsq < cut_in_on_sq) { // switching
register double rsw = (sqrt(rsq) - cut_in_off)/cut_in_diff;
forcecoul *= rsw*rsw*(3.0 - 2.0*rsw);
}
if (rsq > cut_out_on_sq) {
register double rsw = (sqrt(rsq) - cut_out_on)/cut_out_diff;
forcecoul *= 1.0 + rsw*rsw*(2.0*rsw-3.0);
}
cforce = forcecoul * r2inv;
//if (evflag) ev_tally(i,j,nlocal,newton_pair,
// evdwl,0.0,cforce,delx,dely,delz);
// if i,j are not O atoms, force is applied directly
// if i or j are O atoms, force is on fictitious atom & partitioned
// force partitioning due to Feenstra, J Comp Chem, 20, 786 (1999)
// f_f = fictitious force, fO = f_f (1 - 2 alpha), fH = alpha f_f
// preserves total force and torque on water molecule
// virial = sum(r x F) where each water's atoms are near xi and xj
// vlist stores 2,4,6 atoms whose forces contribute to virial
if (itype != typeO) {
f[i][0] += delx * cforce;
f[i][1] += dely * cforce;
f[i][2] += delz * cforce;
} else {
fd[0] = delx*cforce;
fd[1] = dely*cforce;
fd[2] = delz*cforce;
fO[0] = fd[0]*(1 - alpha);
fO[1] = fd[1]*(1 - alpha);
fO[2] = fd[2]*(1 - alpha);
fH[0] = 0.5 * alpha * fd[0];
fH[1] = 0.5 * alpha * fd[1];
fH[2] = 0.5 * alpha * fd[2];
f[i][0] += fO[0];
f[i][1] += fO[1];
f[i][2] += fO[2];
f[iH1][0] += fH[0];
f[iH1][1] += fH[1];
f[iH1][2] += fH[2];
f[iH2][0] += fH[0];
f[iH2][1] += fH[1];
f[iH2][2] += fH[2];
}
if (jtype != typeO) {
f[j][0] -= delx * cforce;
f[j][1] -= dely * cforce;
f[j][2] -= delz * cforce;
} else {
fd[0] = -delx*cforce;
fd[1] = -dely*cforce;
fd[2] = -delz*cforce;
fO[0] = fd[0]*(1 - alpha);
fO[1] = fd[1]*(1 - alpha);
fO[2] = fd[2]*(1 - alpha);
fH[0] = 0.5 * alpha * fd[0];
fH[1] = 0.5 * alpha * fd[1];
fH[2] = 0.5 * alpha * fd[2];
f[j][0] += fO[0];
f[j][1] += fO[1];
f[j][2] += fO[2];
f[jH1][0] += fH[0];
f[jH1][1] += fH[1];
f[jH1][2] += fH[2];
f[jH2][0] += fH[0];
f[jH2][1] += fH[1];
f[jH2][2] += fH[2];
}
}
}
}
}
}
/* --------------------------------------------------------------------- */
void PairLJLongTIP4PLong::compute_outer(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype,itable;
int n,vlist[6];
int key;
int iH1,iH2,jH1,jH2;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul;
double fraction,table;
double r,r2inv,forcecoul,forcelj,cforce, respa_coul, respa_lj, frespa,fvirial;
double factor_coul,factor_lj;
double grij,expm2,prefactor,t,erfc;
double xiM[3],xjM[3],fO[3],fH[3],fd[3],v[6],xH1[3],xH2[3];// f1[3];
double *x1,*x2;
int *ilist,*jlist,*numneigh,**firstneigh;
double rsq,qri;
int respa_flag;
evdwl = ecoul = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
// reallocate hneigh & newsite if necessary
// initialize hneigh[0] to -1 on steps when reneighboring occurred
// initialize hneigh[2] to 0 every step
int nlocal = atom->nlocal;
double **f = atom->f;
double **x = atom->x;
double *q = atom->q;
int *type = atom->type;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
double qqrd2e = force->qqrd2e;
double cut_coulsqplus = (cut_coul+2.0*qdist)*(cut_coul+2.0*qdist);
int order1 = ewald_order&(1<<1), order6 = ewald_order&(1<<6);
int ni;
double *cut_ljsqi, *lj1i, *lj2i, *lj3i, *lj4i, *offseti;
double g2 = g_ewald_6*g_ewald_6, g6 = g2*g2*g2, g8 = g6*g2;
double cut_in_off = cut_respa[2];
double cut_in_on = cut_respa[3];
double cut_in_diff = cut_in_on - cut_in_off;
double cut_in_off_sq = cut_in_off*cut_in_off;
double cut_in_on_sq = cut_in_on*cut_in_on;
inum = listouter->inum;
ilist = listouter->ilist;
numneigh = listouter->numneigh;
firstneigh = listouter->firstneigh;
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
qtmp = q[i];
qri = qtmp*qqrd2e;
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
if (itype == typeO) {
if (hneigh[i][0] < 0) {
hneigh[i][0] = iH1 = atom->map(atom->tag[i] + 1);
hneigh[i][1] = iH2 = atom->map(atom->tag[i] + 2);
hneigh[i][2] = 1;
if (iH1 == -1 || iH2 == -1)
error->one(FLERR,"TIP4P hydrogen is missing");
if (atom->type[iH1] != typeH || atom->type[iH2] != typeH)
error->one(FLERR,"TIP4P hydrogen has incorrect atom type");
compute_newsite(x[i],x[iH1],x[iH2],newsite[i]);
} else {
iH1 = hneigh[i][0];
iH2 = hneigh[i][1];
if (hneigh[i][2] == 0) {
hneigh[i][2] = 1;
compute_newsite(x[i],x[iH1],x[iH2],newsite[i]);
}
}
x1 = newsite[i];
} else x1 = x[i];
jlist = firstneigh[i];
jnum = numneigh[i];
offseti = offset[itype];
lj1i = lj1[itype]; lj2i = lj2[itype]; lj3i = lj3[itype]; lj4i = lj4[itype];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
ni = sbmask(j);
factor_lj = special_lj[sbmask(j)];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
respa_coul = 0;
respa_lj = 0;
if (rsq < cut_ljsq[itype][jtype]) { // lj
frespa = 1.0; // check whether and how to compute respa corrections
respa_flag = rsq < cut_in_on_sq ? 1 : 0;
if (respa_flag && (rsq > cut_in_off_sq)) {
register double rsw = (sqrt(rsq)-cut_in_off)/cut_in_diff;
frespa = 1-rsw*rsw*(3.0-2.0*rsw);
}
r2inv = 1.0/rsq;
register double rn = r2inv*r2inv*r2inv;
if (respa_flag) respa_lj = ni == 0 ? // correct for respa
frespa*rn*(rn*lj1i[jtype]-lj2i[jtype]) :
frespa*rn*(rn*lj1i[jtype]-lj2i[jtype])*special_lj[ni];
if (order6) { // long-range form
if (!ndisptablebits || rsq <= tabinnerdispsq) {
register double x2 = g2*rsq, a2 = 1.0/x2;
x2 = a2*exp(-x2)*lj4i[jtype];
if (ni == 0) {
forcelj =
(rn*=rn)*lj1i[jtype]-g8*(((6.0*a2+6.0)*a2+3.0)*a2+1.0)*x2*rsq-respa_lj;
if (eflag) evdwl = rn*lj3i[jtype]-g6*((a2+1.0)*a2+0.5)*x2;
}
else { // correct for special
register double f = special_lj[ni], t = rn*(1.0-f);
forcelj = f*(rn *= rn)*lj1i[jtype]-
g8*(((6.0*a2+6.0)*a2+3.0)*a2+1.0)*x2*rsq+t*lj2i[jtype]-respa_lj;
if (eflag)
evdwl = f*rn*lj3i[jtype]-g6*((a2+1.0)*a2+0.5)*x2+t*lj4i[jtype];
}
}
else { // table real space
register union_int_float_t disp_t;
disp_t.f = rsq;
register const int disp_k = (disp_t.i & ndispmask)>>ndispshiftbits;
register double f_disp = (rsq-rdisptable[disp_k])*drdisptable[disp_k];
if (ni == 0) {
forcelj = (rn*=rn)*lj1i[jtype]-(fdisptable[disp_k]+f_disp*dfdisptable[disp_k])*lj4i[jtype]-respa_lj;
if (eflag) evdwl = rn*lj3i[jtype]-(edisptable[disp_k]+f_disp*dedisptable[disp_k])*lj4i[jtype];
}
else { // special case
register double f = special_lj[ni], t = rn*(1.0-f);
forcelj = f*(rn *= rn)*lj1i[jtype]-(fdisptable[disp_k]+f_disp*dfdisptable[disp_k])*lj4i[jtype]+t*lj2i[jtype]-respa_lj;
if (eflag) evdwl = f*rn*lj3i[jtype]-(edisptable[disp_k]+f_disp*dedisptable[disp_k])*lj4i[jtype]+t*lj4i[jtype];
}
}
}
else { // cut form
if (ni == 0) {
forcelj = rn*(rn*lj1i[jtype]-lj2i[jtype])-respa_lj;
if (eflag) evdwl = rn*(rn*lj3i[jtype]-lj4i[jtype])-offseti[jtype];
}
else { // correct for special
register double f = special_lj[ni];
forcelj = f*rn*(rn*lj1i[jtype]-lj2i[jtype])-respa_lj;
if (eflag)
evdwl = f*(rn*(rn*lj3i[jtype]-lj4i[jtype])-offseti[jtype]);
}
}
forcelj *= r2inv;
f[i][0] += delx*forcelj;
f[i][1] += dely*forcelj;
f[i][2] += delz*forcelj;
f[j][0] -= delx*forcelj;
f[j][1] -= dely*forcelj;
f[j][2] -= delz*forcelj;
if (evflag) {
fvirial = forcelj + respa_lj*r2inv;
ev_tally(i,j,nlocal,newton_pair,
evdwl,0.0,fvirial,delx,dely,delz);
}
}
// adjust rsq and delxyz for off-site O charge(s)
// ADDITIONAL REQEUST REQUIRED HERE!!!!!
if (rsq < cut_coulsqplus) {
if (itype == typeO || jtype == typeO) {
if (jtype == typeO) {
if (hneigh[j][0] < 0) {
hneigh[j][0] = jH1 = atom->map(atom->tag[j] + 1);
hneigh[j][1] = jH2 = atom->map(atom->tag[j] + 2);
hneigh[j][2] = 1;
if (jH1 == -1 || jH2 == -1)
error->one(FLERR,"TIP4P hydrogen is missing");
if (atom->type[jH1] != typeH || atom->type[jH2] != typeH)
error->one(FLERR,"TIP4P hydrogen has incorrect atom type");
compute_newsite(x[j],x[jH1],x[jH2],newsite[j]);
} else {
jH1 = hneigh[j][0];
jH2 = hneigh[j][1];
if (hneigh[j][2] == 0) {
hneigh[j][2] = 1;
compute_newsite(x[j],x[jH1],x[jH2],newsite[j]);
}
}
x2 = newsite[j];
} else x2 = x[j];
delx = x1[0] - x2[0];
dely = x1[1] - x2[1];
delz = x1[2] - x2[2];
rsq = delx*delx + dely*dely + delz*delz;
}
// test current rsq against cutoff and compute Coulombic force
if ((rsq < cut_coulsq) && order1) {
frespa = 1.0; // check whether and how to compute respa corrections
respa_flag = rsq < cut_in_on_sq ? 1 : 0;
if (respa_flag && (rsq > cut_in_off_sq)) {
register double rsw = (sqrt(rsq)-cut_in_off)/cut_in_diff;
frespa = 1-rsw*rsw*(3.0-2.0*rsw);
}
r2inv = 1.0 / rsq;
if (!ncoultablebits || rsq <= tabinnersq) { // series real space
register double r = sqrt(rsq), s = qri*q[j];
if (respa_flag) // correct for respa
respa_coul = ni == 0 ? frespa*s/r : frespa*s/r*special_coul[ni];
register double x = g_ewald*r, t = 1.0/(1.0+EWALD_P*x);
if (ni == 0) {
s *= g_ewald*exp(-x*x);
forcecoul = (t *= ((((t*A5+A4)*t+A3)*t+A2)*t+A1)*s/x)+EWALD_F*s-respa_coul;
if (eflag) ecoul = t;
}
else { // correct for special
r = s*(1.0-special_coul[ni])/r; s *= g_ewald*exp(-x*x);
forcecoul = (t *= ((((t*A5+A4)*t+A3)*t+A2)*t+A1)*s/x)+EWALD_F*s-r-respa_coul;
if (eflag) ecoul = t-r;
}
} // table real space
else {
if (respa_flag) {
register double r = sqrt(rsq), s = qri*q[j];
respa_coul = ni == 0 ? frespa*s/r : frespa*s/r*special_coul[ni];
}
register union_int_float_t t;
t.f = rsq;
register const int k = (t.i & ncoulmask) >> ncoulshiftbits;
register double f = (t.f-rtable[k])*drtable[k], qiqj = qtmp*q[j];
if (ni == 0) {
forcecoul = qiqj*(ftable[k]+f*dftable[k]);
if (eflag) ecoul = qiqj*(etable[k]+f*detable[k]);
}
else { // correct for special
t.f = (1.0-special_coul[ni])*(ctable[k]+f*dctable[k]);
forcecoul = qiqj*(ftable[k]+f*dftable[k]-t.f);
if (eflag) {
t.f = (1.0-special_coul[ni])*(ptable[k]+f*dptable[k]);
ecoul = qiqj*(etable[k]+f*detable[k]-t.f);
}
}
}
cforce = forcecoul * r2inv;
fvirial = (forcecoul + respa_coul) * r2inv;
double fvcf = fvirial/cforce;
// if i,j are not O atoms, force is applied directly
// if i or j are O atoms, force is on fictitious atom & partitioned
// force partitioning due to Feenstra, J Comp Chem, 20, 786 (1999)
// f_f = fictitious force, fO = f_f (1 - 2 alpha), fH = alpha f_f
// preserves total force and torque on water molecule
// virial = sum(r x F) where each water's atoms are near xi and xj
// vlist stores 2,4,6 atoms whose forces contribute to virial
n = 0;
key = 0;
if (itype != typeO) {
f[i][0] += delx * cforce;
f[i][1] += dely * cforce;
f[i][2] += delz * cforce;
if (vflag) {
v[0] = x[i][0] * delx * fvirial;
v[1] = x[i][1] * dely * fvirial;
v[2] = x[i][2] * delz * fvirial;
v[3] = x[i][0] * dely * fvirial;
v[4] = x[i][0] * delz * fvirial;
v[5] = x[i][1] * delz * fvirial;
}
vlist[n++] = i;
} else {
key += 1;
fd[0] = delx*cforce;
fd[1] = dely*cforce;
fd[2] = delz*cforce;
fO[0] = fd[0]*(1 - alpha);
fO[1] = fd[1]*(1 - alpha);
fO[2] = fd[2]*(1 - alpha);
fH[0] = 0.5 * alpha * fd[0];
fH[1] = 0.5 * alpha * fd[1];
fH[2] = 0.5 * alpha * fd[2];
f[i][0] += fO[0];
f[i][1] += fO[1];
f[i][2] += fO[2];
f[iH1][0] += fH[0];
f[iH1][1] += fH[1];
f[iH1][2] += fH[2];
f[iH2][0] += fH[0];
f[iH2][1] += fH[1];
f[iH2][2] += fH[2];
if (vflag) {
domain->closest_image(x[i],x[iH1],xH1);
domain->closest_image(x[i],x[iH2],xH2);
v[0] = (x[i][0]*fO[0] + xH1[0]*fH[0] + xH2[0]*fH[0])*fvcf;
v[1] = (x[i][1]*fO[1] + xH1[1]*fH[1] + xH2[1]*fH[1])*fvcf;
v[2] = (x[i][2]*fO[2] + xH1[2]*fH[2] + xH2[2]*fH[2])*fvcf;
v[3] = (x[i][0]*fO[1] + xH1[0]*fH[1] + xH2[0]*fH[1])*fvcf;
v[4] = (x[i][0]*fO[2] + xH1[0]*fH[2] + xH2[0]*fH[2])*fvcf;
v[5] = (x[i][1]*fO[2] + xH1[1]*fH[2] + xH2[1]*fH[2])*fvcf;
}
vlist[n++] = i;
vlist[n++] = iH1;
vlist[n++] = iH2;
}
if (jtype != typeO) {
f[j][0] -= delx * cforce;
f[j][1] -= dely * cforce;
f[j][2] -= delz * cforce;
if (vflag) {
v[0] -= x[j][0] * delx * fvirial;
v[1] -= x[j][1] * dely * fvirial;
v[2] -= x[j][2] * delz * fvirial;
v[3] -= x[j][0] * dely * fvirial;
v[4] -= x[j][0] * delz * fvirial;
v[5] -= x[j][1] * delz * fvirial;
}
vlist[n++] = j;
} else {
key += 2;
fd[0] = -delx*cforce;
fd[1] = -dely*cforce;
fd[2] = -delz*cforce;
fO[0] = fd[0]*(1 - alpha);
fO[1] = fd[1]*(1 - alpha);
fO[2] = fd[2]*(1 - alpha);
fH[0] = 0.5 * alpha * fd[0];
fH[1] = 0.5 * alpha * fd[1];
fH[2] = 0.5 * alpha * fd[2];
f[j][0] += fO[0];
f[j][1] += fO[1];
f[j][2] += fO[2];
f[jH1][0] += fH[0];
f[jH1][1] += fH[1];
f[jH1][2] += fH[2];
f[jH2][0] += fH[0];
f[jH2][1] += fH[1];
f[jH2][2] += fH[2];
if (vflag) {
domain->closest_image(x[j],x[jH1],xH1);
domain->closest_image(x[j],x[jH2],xH2);
v[0] += (x[j][0]*fO[0] + xH1[0]*fH[0] + xH2[0]*fH[0])*fvcf;
v[1] += (x[j][1]*fO[1] + xH1[1]*fH[1] + xH2[1]*fH[1])*fvcf;
v[2] += (x[j][2]*fO[2] + xH1[2]*fH[2] + xH2[2]*fH[2])*fvcf;
v[3] += (x[j][0]*fO[1] + xH1[0]*fH[1] + xH2[0]*fH[1])*fvcf;
v[4] += (x[j][0]*fO[2] + xH1[0]*fH[2] + xH2[0]*fH[2])*fvcf;
v[5] += (x[j][1]*fO[2] + xH1[1]*fH[2] + xH2[1]*fH[2])*fvcf;
}
vlist[n++] = j;
vlist[n++] = jH1;
vlist[n++] = jH2;
}
if (evflag) ev_tally_tip4p(key,vlist,v,ecoul,alpha);
}
}
}
}
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */

3
src/KSPACE/pair_lj_long_tip4p_long.h
View File

@ -29,6 +29,9 @@ class PairLJLongTIP4PLong : public PairLJLongCoulLong {
PairLJLongTIP4PLong(class LAMMPS *);
~PairLJLongTIP4PLong();
virtual void compute(int, int);
virtual void compute_inner();
virtual void compute_middle();
virtual void compute_outer(int, int);
void settings(int, char **);
void init_style();
double init_one(int, int);

2
src/KSPACE/pppm_disp.cpp
View File

@ -168,6 +168,8 @@ PPPMDisp::PPPMDisp(LAMMPS *lmp, int narg, char **arg) : KSpace(lmp, narg, arg)
cg_peratom = NULL;
cg_6 = NULL;
cg_peratom_6 = NULL;
memset(function, 0, EWALD_FUNCS*sizeof(int));
}
/* ----------------------------------------------------------------------

4
src/OPT/pair_lj_long_coul_long_opt.cpp
View File

@ -726,7 +726,7 @@ void PairLJLongCoulLongOpt::eval_outer()
double cut_in_off_sq = cut_in_off*cut_in_off;
double cut_in_on_sq = cut_in_on*cut_in_on;
ineighn = (ineigh = list->ilist)+list->inum;
ineighn = (ineigh = listouter->ilist)+listouter->inum;
for (; ineigh<ineighn; ++ineigh) { // loop over my atoms
i = *ineigh; fi = f0+3*i;
@ -735,7 +735,7 @@ void PairLJLongCoulLongOpt::eval_outer()
lj1i = lj1[typei]; lj2i = lj2[typei]; lj3i = lj3[typei]; lj4i = lj4[typei];
cutsqi = cutsq[typei]; cut_ljsqi = cut_ljsq[typei];
memcpy(xi, x0+(i+(i<<1)), sizeof(vector));
jneighn = (jneigh = list->firstneigh[i])+list->numneigh[i];
jneighn = (jneigh = listouter->firstneigh[i])+listouter->numneigh[i];
for (; jneigh<jneighn; ++jneigh) { // loop over neighbors
j = *jneigh;

70
src/USER-OMP/neigh_respa_omp.cpp
View File

@ -100,37 +100,33 @@ void Neighbor::respa_nsq_no_newton_omp(NeighList *list)
#if defined(_OPENMP)
#pragma omp critical
#endif
{
if (pgsize - npnt < oneatom) {
npnt = 0;
npage += nthreads;
if (npage == list->maxpage) list->add_pages(nthreads);
if (npage >= list->maxpage) list->add_pages(nthreads);
}
neighptr = &(list->pages[npage][npnt]);
n = 0;
#if defined(_OPENMP)
#pragma omp critical
#endif
if (pgsize - npnt_inner < oneatom) {
npnt_inner = 0;
npage_inner += nthreads;
if (npage_inner == listinner->maxpage) listinner->add_pages(nthreads);
if (npage_inner >= listinner->maxpage) listinner->add_pages(nthreads);
}
neighptr_inner = &(listinner->pages[npage_inner][npnt_inner]);
n_inner = 0;
#if defined(_OPENMP)
#pragma omp critical
#endif
if (respamiddle) {
if (pgsize - npnt_middle < oneatom) {
npnt_middle = 0;
npage_middle += nthreads;
if (npage_middle == listmiddle->maxpage) listmiddle->add_pages(nthreads);
if (npage_middle >= listmiddle->maxpage) listmiddle->add_pages(nthreads);
}
neighptr_middle = &(listmiddle->pages[npage_middle][npnt_middle]);
n_middle = 0;
}
}
itype = type[i];
xtmp = x[i][0];
@ -281,37 +277,33 @@ void Neighbor::respa_nsq_newton_omp(NeighList *list)
#if defined(_OPENMP)
#pragma omp critical
#endif
{
if (pgsize - npnt < oneatom) {
npnt = 0;
npage += nthreads;
if (npage == list->maxpage) list->add_pages(nthreads);
if (npage >= list->maxpage) list->add_pages(nthreads);
}
neighptr = &(list->pages[npage][npnt]);
n = 0;
#if defined(_OPENMP)
#pragma omp critical
#endif
if (pgsize - npnt_inner < oneatom) {
npnt_inner = 0;
npage_inner += nthreads;
if (npage_inner == listinner->maxpage) listinner->add_pages(nthreads);
if (npage_inner >= listinner->maxpage) listinner->add_pages(nthreads);
}
neighptr_inner = &(listinner->pages[npage_inner][npnt_inner]);
n_inner = 0;
#if defined(_OPENMP)
#pragma omp critical
#endif
if (respamiddle) {
if (pgsize - npnt_middle < oneatom) {
npnt_middle = 0;
npage_middle += nthreads;
if (npage_middle == listmiddle->maxpage) listmiddle->add_pages(nthreads);
if (npage_middle >= listmiddle->maxpage) listmiddle->add_pages(nthreads);
}
neighptr_middle = &(listmiddle->pages[npage_middle][npnt_middle]);
n_middle = 0;
}
}
itag = tag[i];
itype = type[i];
@ -484,37 +476,33 @@ void Neighbor::respa_bin_no_newton_omp(NeighList *list)
#if defined(_OPENMP)
#pragma omp critical
#endif
{
if (pgsize - npnt < oneatom) {
npnt = 0;
npage += nthreads;
if (npage == list->maxpage) list->add_pages(nthreads);
if (npage >= list->maxpage) list->add_pages(nthreads);
}
neighptr = &(list->pages[npage][npnt]);
n = 0;
#if defined(_OPENMP)
#pragma omp critical
#endif
if (pgsize - npnt_inner < oneatom) {
npnt_inner = 0;
npage_inner += nthreads;
if (npage_inner == listinner->maxpage) listinner->add_pages(nthreads);
if (npage_inner >= listinner->maxpage) listinner->add_pages(nthreads);
}
neighptr_inner = &(listinner->pages[npage_inner][npnt_inner]);
n_inner = 0;
#if defined(_OPENMP)
#pragma omp critical
#endif
if (respamiddle) {
if (pgsize - npnt_middle < oneatom) {
npnt_middle = 0;
npage_middle += nthreads;
if (npage_middle == listmiddle->maxpage) listmiddle->add_pages(nthreads);
if (npage_middle >= listmiddle->maxpage) listmiddle->add_pages(nthreads);
}
neighptr_middle = &(listmiddle->pages[npage_middle][npnt_middle]);
n_middle = 0;
}
}
itype = type[i];
xtmp = x[i][0];
@ -677,37 +665,33 @@ void Neighbor::respa_bin_newton_omp(NeighList *list)
#if defined(_OPENMP)
#pragma omp critical
#endif
{
if (pgsize - npnt < oneatom) {
npnt = 0;
npage += nthreads;
if (npage == list->maxpage) list->add_pages(nthreads);
if (npage >= list->maxpage) list->add_pages(nthreads);
}
neighptr = &(list->pages[npage][npnt]);
n = 0;
#if defined(_OPENMP)
#pragma omp critical
#endif
if (pgsize - npnt_inner < oneatom) {
npnt_inner = 0;
npage_inner += nthreads;
if (npage_inner == listinner->maxpage) listinner->add_pages(nthreads);
if (npage_inner >= listinner->maxpage) listinner->add_pages(nthreads);
}
neighptr_inner = &(listinner->pages[npage_inner][npnt_inner]);
n_inner = 0;
#if defined(_OPENMP)
#pragma omp critical
#endif
if (respamiddle) {
if (pgsize - npnt_middle < oneatom) {
npnt_middle = 0;
npage_middle += nthreads;
if (npage_middle == listmiddle->maxpage) listmiddle->add_pages(nthreads);
if (npage_middle >= listmiddle->maxpage) listmiddle->add_pages(nthreads);
}
neighptr_middle = &(listmiddle->pages[npage_middle][npnt_middle]);
n_middle = 0;
}
}
itype = type[i];
xtmp = x[i][0];
@ -911,37 +895,33 @@ void Neighbor::respa_bin_newton_tri_omp(NeighList *list)
#if defined(_OPENMP)
#pragma omp critical
#endif
{
if (pgsize - npnt < oneatom) {
npnt = 0;
npage += nthreads;
if (npage == list->maxpage) list->add_pages(nthreads);
if (npage >= list->maxpage) list->add_pages(nthreads);
}
neighptr = &(list->pages[npage][npnt]);
n = 0;
#if defined(_OPENMP)
#pragma omp critical
#endif
if (pgsize - npnt_inner < oneatom) {
npnt_inner = 0;
npage_inner += nthreads;
if (npage_inner == listinner->maxpage) listinner->add_pages(nthreads);
if (npage_inner >= listinner->maxpage) listinner->add_pages(nthreads);
}
neighptr_inner = &(listinner->pages[npage_inner][npnt_inner]);
n_inner = 0;
#if defined(_OPENMP)
#pragma omp critical
#endif
if (respamiddle) {
if (pgsize - npnt_middle < oneatom) {
npnt_middle = 0;
npage_middle += nthreads;
if (npage_middle == listmiddle->maxpage) listmiddle->add_pages(nthreads);
if (npage_middle >= listmiddle->maxpage) listmiddle->add_pages(nthreads);
}
neighptr_middle = &(listmiddle->pages[npage_middle][npnt_middle]);
n_middle = 0;
}
}
itype = type[i];
xtmp = x[i][0];

18
src/USER-OMP/pair_buck_long_coul_long_omp.cpp
View File

@ -317,7 +317,7 @@ void PairBuckLongCoulLongOMP::compute_inner()
const int nall = atom->nlocal + atom->nghost;
const int nthreads = comm->nthreads;
const int inum = list->inum;
const int inum = listinner->inum;
#if defined(_OPENMP)
#pragma omp parallel default(none)
#endif
@ -339,7 +339,7 @@ void PairBuckLongCoulLongOMP::compute_middle()
const int nall = atom->nlocal + atom->nghost;
const int nthreads = comm->nthreads;
const int inum = list->inum;
const int inum = listmiddle->inum;
#if defined(_OPENMP)
#pragma omp parallel default(none)
@ -367,7 +367,7 @@ void PairBuckLongCoulLongOMP::compute_outer(int eflag, int vflag)
const int nall = atom->nlocal + atom->nghost;
const int nthreads = comm->nthreads;
const int inum = list->inum;
const int inum = listouter->inum;
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(eflag,vflag)
@ -803,7 +803,7 @@ void PairBuckLongCoulLongOMP::eval_inner(int iifrom, int iito, ThrData * const t
const double *x0 = x[0];
double *f0 = f[0], *fi = 0;
int *ilist = list->ilist;
int *ilist = listinner->ilist;
const int newton_pair = force->newton_pair;
@ -827,7 +827,7 @@ void PairBuckLongCoulLongOMP::eval_inner(int iifrom, int iito, ThrData * const t
memcpy(xi, x0+(i+(i<<1)), sizeof(vector));
cut_bucksqi = cut_bucksq[typei = type[i]];
buck1i = buck1[typei]; buck2i = buck2[typei]; rhoinvi = rhoinv[typei];
jneighn = (jneigh = list->firstneigh[i])+list->numneigh[i];
jneighn = (jneigh = listinner->firstneigh[i])+listinner->numneigh[i];
for (; jneigh<jneighn; ++jneigh) { // loop over neighbors
j = *jneigh;
@ -896,7 +896,7 @@ void PairBuckLongCoulLongOMP::eval_middle(int iifrom, int iito, ThrData * const
const double *x0 = x[0];
double *f0 = f[0], *fi = 0;
int *ilist = list->ilist;
int *ilist = listmiddle->ilist;
const int newton_pair = force->newton_pair;
@ -924,7 +924,7 @@ void PairBuckLongCoulLongOMP::eval_middle(int iifrom, int iito, ThrData * const
memcpy(xi, x0+(i+(i<<1)), sizeof(vector));
cut_bucksqi = cut_bucksq[typei = type[i]];
buck1i = buck1[typei]; buck2i = buck2[typei]; rhoinvi = rhoinv[typei];
jneighn = (jneigh = list->firstneigh[i])+list->numneigh[i];
jneighn = (jneigh = listmiddle->firstneigh[i])+listmiddle->numneigh[i];
for (; jneigh<jneighn; ++jneigh) { // loop over neighbors
j = *jneigh;
@ -1001,7 +1001,7 @@ void PairBuckLongCoulLongOMP::eval_outer(int iiform, int iito, ThrData * const t
const double *x0 = x[0];
double *f0 = f[0], *fi = f0;
int *ilist = list->ilist;
int *ilist = listouter->ilist;
int i, j, ii;
int *jneigh, *jneighn, typei, typej, ni, respa_flag;
@ -1027,7 +1027,7 @@ void PairBuckLongCoulLongOMP::eval_outer(int iiform, int iito, ThrData * const t
buckai = buck_a[typei]; buckci = buck_c[typei]; rhoinvi = rhoinv[typei];
cutsqi = cutsq[typei]; cut_bucksqi = cut_bucksq[typei];
memcpy(xi, x0+(i+(i<<1)), sizeof(vector));
jneighn = (jneigh = list->firstneigh[i])+list->numneigh[i];
jneighn = (jneigh = listouter->firstneigh[i])+listouter->numneigh[i];
for (; jneigh<jneighn; ++jneigh) { // loop over neighbors
j = *jneigh;

1005
src/USER-OMP/pair_lj_long_coul_long_omp.cpp
View File

File diff suppressed because it is too large Load Diff

21
src/USER-OMP/pair_lj_long_coul_long_omp.h
View File

@ -35,11 +35,28 @@ class PairLJLongCoulLongOMP : public PairLJLongCoulLong, public ThrOMP {
PairLJLongCoulLongOMP(class LAMMPS *);
virtual void compute(int, int);
virtual void compute_inner();
virtual void compute_middle();
virtual void compute_outer(int, int);
virtual double memory_usage();
private:
template <int EVFLAG, int EFLAG, int NEWTON_PAIR>
void eval(int ifrom, int ito, ThrData * const thr);
template <const int EVFLAG, const int EFLAG,
const int NEWTON_PAIR, const int CTABLE, const int LJTABLE,
const int ORDER1, const int ORDER6 >
void eval(int, int, ThrData * const);
template <const int EVFLAG, const int EFLAG,
const int NEWTON_PAIR, const int CTABLE, const int LJTABLE,
const int ORDER1, const int ORDER6 >
void eval_outer(int, int, ThrData * const);
void eval_inner(int, int, ThrData *const);
void eval_middle(int, int, ThrData *const);
};
}