git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9701 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
@ -236,7 +236,7 @@ void PairBuckLongCoulLong::init_style()
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int irequest;
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int irequest;
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if (update->whichflag == 0 && strstr(update->integrate_style,"respa")) {
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if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) {
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int respa = 0;
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int respa = 0;
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if (((Respa *) update->integrate)->level_inner >= 0) respa = 1;
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if (((Respa *) update->integrate)->level_inner >= 0) respa = 1;
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if (((Respa *) update->integrate)->level_middle >= 0) respa = 2;
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if (((Respa *) update->integrate)->level_middle >= 0) respa = 2;
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@ -627,14 +627,14 @@ void PairBuckLongCoulLong::compute_inner()
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double qri, *cut_bucksqi, *buck1i, *buck2i, *rhoinvi;
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double qri, *cut_bucksqi, *buck1i, *buck2i, *rhoinvi;
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vector xi, d;
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vector xi, d;
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ineighn = (ineigh = list->ilist) + list->inum;
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ineighn = (ineigh = listinner->ilist) + listinner->inum;
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for (; ineigh<ineighn; ++ineigh) { // loop over my atoms
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for (; ineigh<ineighn; ++ineigh) { // loop over my atoms
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i = *ineigh; fi = f0+3*i;
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i = *ineigh; fi = f0+3*i;
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if (order1) qri = qqrd2e*q[i];
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if (order1) qri = qqrd2e*q[i];
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memcpy(xi, x0+(i+(i<<1)), sizeof(vector));
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memcpy(xi, x0+(i+(i<<1)), sizeof(vector));
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cut_bucksqi = cut_bucksq[typei = type[i]];
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cut_bucksqi = cut_bucksq[typei = type[i]];
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buck1i = buck1[typei]; buck2i = buck2[typei]; rhoinvi = rhoinv[typei];
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buck1i = buck1[typei]; buck2i = buck2[typei]; rhoinvi = rhoinv[typei];
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jneighn = (jneigh = list->firstneigh[i])+list->numneigh[i];
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jneighn = (jneigh = listinner->firstneigh[i])+listinner->numneigh[i];
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for (; jneigh<jneighn; ++jneigh) { // loop over neighbors
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for (; jneigh<jneighn; ++jneigh) { // loop over neighbors
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j = *jneigh;
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j = *jneigh;
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@ -716,7 +716,7 @@ void PairBuckLongCoulLong::compute_middle()
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double qri, *cut_bucksqi, *buck1i, *buck2i, *rhoinvi;
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double qri, *cut_bucksqi, *buck1i, *buck2i, *rhoinvi;
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vector xi, d;
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vector xi, d;
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ineighn = (ineigh = list->ilist)+list->inum;
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ineighn = (ineigh = listmiddle->ilist)+listmiddle->inum;
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for (; ineigh<ineighn; ++ineigh) { // loop over my atoms
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for (; ineigh<ineighn; ++ineigh) { // loop over my atoms
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i = *ineigh; fi = f0+3*i;
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i = *ineigh; fi = f0+3*i;
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@ -724,7 +724,7 @@ void PairBuckLongCoulLong::compute_middle()
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memcpy(xi, x0+(i+(i<<1)), sizeof(vector));
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memcpy(xi, x0+(i+(i<<1)), sizeof(vector));
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cut_bucksqi = cut_bucksq[typei = type[i]];
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cut_bucksqi = cut_bucksq[typei = type[i]];
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buck1i = buck1[typei]; buck2i = buck2[typei]; rhoinvi = rhoinv[typei];
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buck1i = buck1[typei]; buck2i = buck2[typei]; rhoinvi = rhoinv[typei];
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jneighn = (jneigh = list->firstneigh[i])+list->numneigh[i];
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jneighn = (jneigh = listmiddle->firstneigh[i])+listmiddle->numneigh[i];
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for (; jneigh<jneighn; ++jneigh) { // loop over neighbors
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for (; jneigh<jneighn; ++jneigh) { // loop over neighbors
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j = *jneigh;
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j = *jneigh;
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@ -815,7 +815,7 @@ void PairBuckLongCoulLong::compute_outer(int eflag, int vflag)
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double cut_in_off_sq = cut_in_off*cut_in_off;
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double cut_in_off_sq = cut_in_off*cut_in_off;
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double cut_in_on_sq = cut_in_on*cut_in_on;
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double cut_in_on_sq = cut_in_on*cut_in_on;
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ineighn = (ineigh = list->ilist)+list->inum;
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ineighn = (ineigh = listouter->ilist)+listouter->inum;
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for (; ineigh<ineighn; ++ineigh) { // loop over my atoms
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for (; ineigh<ineighn; ++ineigh) { // loop over my atoms
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i = *ineigh; fi = f0+3*i;
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i = *ineigh; fi = f0+3*i;
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@ -825,7 +825,7 @@ void PairBuckLongCoulLong::compute_outer(int eflag, int vflag)
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buckai = buck_a[typei]; buckci = buck_c[typei]; rhoinvi = rhoinv[typei];
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buckai = buck_a[typei]; buckci = buck_c[typei]; rhoinvi = rhoinv[typei];
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cutsqi = cutsq[typei]; cut_bucksqi = cut_bucksq[typei];
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cutsqi = cutsq[typei]; cut_bucksqi = cut_bucksq[typei];
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memcpy(xi, x0+(i+(i<<1)), sizeof(vector));
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memcpy(xi, x0+(i+(i<<1)), sizeof(vector));
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jneighn = (jneigh = list->firstneigh[i])+list->numneigh[i];
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jneighn = (jneigh = listouter->firstneigh[i])+listouter->numneigh[i];
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for (; jneigh<jneighn; ++jneigh) { // loop over neighbors
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for (; jneigh<jneighn; ++jneigh) { // loop over neighbors
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j = *jneigh;
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j = *jneigh;
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@ -236,7 +236,7 @@ void PairLJLongCoulLong::init_style()
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int irequest;
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int irequest;
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if (update->whichflag == 0 && strstr(update->integrate_style,"respa")) {
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if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) {
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int respa = 0;
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int respa = 0;
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if (((Respa *) update->integrate)->level_inner >= 0) respa = 1;
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if (((Respa *) update->integrate)->level_inner >= 0) respa = 1;
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if (((Respa *) update->integrate)->level_middle >= 0) respa = 2;
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if (((Respa *) update->integrate)->level_middle >= 0) respa = 2;
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@ -633,13 +633,13 @@ void PairLJLongCoulLong::compute_inner()
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double qri, *cut_ljsqi, *lj1i, *lj2i;
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double qri, *cut_ljsqi, *lj1i, *lj2i;
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vector xi, d;
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vector xi, d;
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ineighn = (ineigh = list->ilist)+list->inum;
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ineighn = (ineigh = listinner->ilist)+listinner->inum;
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for (; ineigh<ineighn; ++ineigh) { // loop over my atoms
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for (; ineigh<ineighn; ++ineigh) { // loop over my atoms
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i = *ineigh; fi = f0+3*i;
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i = *ineigh; fi = f0+3*i;
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memcpy(xi, x0+(i+(i<<1)), sizeof(vector));
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memcpy(xi, x0+(i+(i<<1)), sizeof(vector));
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cut_ljsqi = cut_ljsq[typei = type[i]];
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cut_ljsqi = cut_ljsq[typei = type[i]];
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lj1i = lj1[typei]; lj2i = lj2[typei];
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lj1i = lj1[typei]; lj2i = lj2[typei];
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jneighn = (jneigh = list->firstneigh[i])+list->numneigh[i];
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jneighn = (jneigh = listinner->firstneigh[i])+listinner->numneigh[i];
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for (; jneigh<jneighn; ++jneigh) { // loop over neighbors
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for (; jneigh<jneighn; ++jneigh) { // loop over neighbors
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j = *jneigh;
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j = *jneigh;
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ni = sbmask(j);
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ni = sbmask(j);
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@ -720,7 +720,7 @@ void PairLJLongCoulLong::compute_middle()
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double qri, *cut_ljsqi, *lj1i, *lj2i;
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double qri, *cut_ljsqi, *lj1i, *lj2i;
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vector xi, d;
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vector xi, d;
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ineighn = (ineigh = list->ilist)+list->inum;
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ineighn = (ineigh = listmiddle->ilist)+listmiddle->inum;
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for (; ineigh<ineighn; ++ineigh) { // loop over my atoms
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for (; ineigh<ineighn; ++ineigh) { // loop over my atoms
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i = *ineigh; fi = f0+3*i;
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i = *ineigh; fi = f0+3*i;
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@ -728,7 +728,7 @@ void PairLJLongCoulLong::compute_middle()
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memcpy(xi, x0+(i+(i<<1)), sizeof(vector));
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memcpy(xi, x0+(i+(i<<1)), sizeof(vector));
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cut_ljsqi = cut_ljsq[typei = type[i]];
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cut_ljsqi = cut_ljsq[typei = type[i]];
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lj1i = lj1[typei]; lj2i = lj2[typei];
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lj1i = lj1[typei]; lj2i = lj2[typei];
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jneighn = (jneigh = list->firstneigh[i])+list->numneigh[i];
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jneighn = (jneigh = listmiddle->firstneigh[i])+listmiddle->numneigh[i];
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for (; jneigh<jneighn; ++jneigh) {
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for (; jneigh<jneighn; ++jneigh) {
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j = *jneigh;
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j = *jneigh;
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@ -817,7 +817,7 @@ void PairLJLongCoulLong::compute_outer(int eflag, int vflag)
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double cut_in_off_sq = cut_in_off*cut_in_off;
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double cut_in_off_sq = cut_in_off*cut_in_off;
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double cut_in_on_sq = cut_in_on*cut_in_on;
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double cut_in_on_sq = cut_in_on*cut_in_on;
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ineighn = (ineigh = list->ilist)+list->inum;
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ineighn = (ineigh = listouter->ilist)+listouter->inum;
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for (; ineigh<ineighn; ++ineigh) { // loop over my atoms
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for (; ineigh<ineighn; ++ineigh) { // loop over my atoms
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i = *ineigh; fi = f0+3*i;
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i = *ineigh; fi = f0+3*i;
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@ -826,7 +826,7 @@ void PairLJLongCoulLong::compute_outer(int eflag, int vflag)
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lj1i = lj1[typei]; lj2i = lj2[typei]; lj3i = lj3[typei]; lj4i = lj4[typei];
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lj1i = lj1[typei]; lj2i = lj2[typei]; lj3i = lj3[typei]; lj4i = lj4[typei];
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cutsqi = cutsq[typei]; cut_ljsqi = cut_ljsq[typei];
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cutsqi = cutsq[typei]; cut_ljsqi = cut_ljsq[typei];
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memcpy(xi, x0+(i+(i<<1)), sizeof(vector));
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memcpy(xi, x0+(i+(i<<1)), sizeof(vector));
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jneighn = (jneigh = list->firstneigh[i])+list->numneigh[i];
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jneighn = (jneigh = listouter->firstneigh[i])+listouter->numneigh[i];
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for (; jneigh<jneighn; ++jneigh) { // loop over neighbors
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for (; jneigh<jneighn; ++jneigh) { // loop over neighbors
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j = *jneigh;
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j = *jneigh;
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@ -53,7 +53,7 @@ PairLJLongTIP4PLong::PairLJLongTIP4PLong(LAMMPS *lmp) :
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{
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{
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dispersionflag = tip4pflag = 1;
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dispersionflag = tip4pflag = 1;
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single_enable = 0;
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single_enable = 0;
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respa_enable = 0;
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respa_enable = 1;
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nmax = 0;
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nmax = 0;
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hneigh = NULL;
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hneigh = NULL;
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@ -184,22 +184,40 @@ void PairLJLongTIP4PLong::compute(int eflag, int vflag)
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if (rsq < cut_ljsq[itype][jtype]) { // lj
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if (rsq < cut_ljsq[itype][jtype]) { // lj
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r2inv = 1.0/rsq;
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r2inv = 1.0/rsq;
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if (order6) { // long-range lj
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if (order6) { // long-range lj
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register double rn = r2inv*r2inv*r2inv;
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if (!ndisptablebits || rsq <= tabinnerdispsq) {
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register double x2 = g2*rsq, a2 = 1.0/x2;
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register double rn = r2inv*r2inv*r2inv;
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x2 = a2*exp(-x2)*lj4i[jtype];
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register double x2 = g2*rsq, a2 = 1.0/x2;
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if (ni == 0) {
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x2 = a2*exp(-x2)*lj4i[jtype];
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forcelj =
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if (ni == 0) {
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(rn*=rn)*lj1i[jtype]-g8*(((6.0*a2+6.0)*a2+3.0)*a2+1.0)*x2*rsq;
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forcelj =
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if (eflag)
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(rn*=rn)*lj1i[jtype]-g8*(((6.0*a2+6.0)*a2+3.0)*a2+1.0)*x2*rsq;
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evdwl = rn*lj3i[jtype]-g6*((a2+1.0)*a2+0.5)*x2;
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if (eflag)
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}
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evdwl = rn*lj3i[jtype]-g6*((a2+1.0)*a2+0.5)*x2;
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else { // special case
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}
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register double f = special_lj[ni], t = rn*(1.0-f);
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else { // special case
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forcelj = f*(rn *= rn)*lj1i[jtype]-
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register double f = special_lj[ni], t = rn*(1.0-f);
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g8*(((6.0*a2+6.0)*a2+3.0)*a2+1.0)*x2*rsq+t*lj2i[jtype];
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forcelj = f*(rn *= rn)*lj1i[jtype]-
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if (eflag)
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g8*(((6.0*a2+6.0)*a2+3.0)*a2+1.0)*x2*rsq+t*lj2i[jtype];
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evdwl = f*rn*lj3i[jtype]-g6*((a2+1.0)*a2+0.5)*x2+t*lj4i[jtype];
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if (eflag)
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}
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evdwl = f*rn*lj3i[jtype]-g6*((a2+1.0)*a2+0.5)*x2+t*lj4i[jtype];
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}
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}
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else { // table real space
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register union_int_float_t disp_t;
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disp_t.f = rsq;
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register const int disp_k = (disp_t.i & ndispmask)>>ndispshiftbits;
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register double f_disp = (rsq-rdisptable[disp_k])*drdisptable[disp_k];
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register double rn = r2inv*r2inv*r2inv;
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if (ni == 0) {
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forcelj = (rn*=rn)*lj1i[jtype]-(fdisptable[disp_k]+f_disp*dfdisptable[disp_k])*lj4i[jtype];
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if (eflag) evdwl = rn*lj3i[jtype]-(edisptable[disp_k]+f_disp*dedisptable[disp_k])*lj4i[jtype];
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}
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else { // special case
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register double f = special_lj[ni], t = rn*(1.0-f);
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forcelj = f*(rn *= rn)*lj1i[jtype]-(fdisptable[disp_k]+f_disp*dfdisptable[disp_k])*lj4i[jtype]+t*lj2i[jtype];
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if (eflag) evdwl = f*rn*lj3i[jtype]-(edisptable[disp_k]+f_disp*dedisptable[disp_k])*lj4i[jtype]+t*lj4i[jtype];
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}
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}
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}
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}
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else { // cut lj
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else { // cut lj
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register double rn = r2inv*r2inv*r2inv;
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register double rn = r2inv*r2inv*r2inv;
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@ -437,6 +455,922 @@ void PairLJLongTIP4PLong::compute(int eflag, int vflag)
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}
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}
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}
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}
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/* --------------------------------------------------------------------- */
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void PairLJLongTIP4PLong::compute_inner()
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{
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int i,j,ii,jj,inum,jnum,itype,jtype,itable;
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int iH1,iH2,jH1,jH2;
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double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul;
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double r,r2inv,forcecoul,forcelj,cforce;
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double factor_coul,factor_lj;
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double grij,expm2,prefactor,t,erfc;
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double xiM[3],xjM[3],fO[3],fH[3],fd[3],v[6],xH1[3],xH2[3];// f1[3];
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double *x1,*x2;
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int *ilist,*jlist,*numneigh,**firstneigh;
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double rsq, qri;
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double cut_out_on = cut_respa[0];
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double cut_out_off = cut_respa[1];
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double cut_out_diff = cut_out_off - cut_out_on;
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double cut_out_on_sq = cut_out_on*cut_out_on;
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double cut_out_off_sq = cut_out_off*cut_out_off;
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// reallocate hneigh & newsite if necessary
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// initialize hneigh[0] to -1 on steps when reneighboring occurred
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// initialize hneigh[2] to 0 every step
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int nlocal = atom->nlocal;
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int nall = nlocal + atom->nghost;
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if (atom->nmax > nmax) {
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nmax = atom->nmax;
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memory->destroy(hneigh);
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memory->create(hneigh,nmax,3,"pair:hneigh");
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memory->destroy(newsite);
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memory->create(newsite,nmax,3,"pair:newsite");
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}
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if (neighbor->ago == 0)
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for (i = 0; i < nall; i++) hneigh[i][0] = -1;
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for (i = 0; i < nall; i++) hneigh[i][2] = 0;
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double **f = atom->f;
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double **x = atom->x;
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double *q = atom->q;
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int *type = atom->type;
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double *special_coul = force->special_coul;
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double *special_lj = force->special_lj;
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int newton_pair = force->newton_pair;
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double qqrd2e = force->qqrd2e;
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double cut_coulsqplus = (cut_coul+2.0*qdist)*(cut_coul+2.0*qdist);
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int order1 = ewald_order&(1<<1);
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int ni;
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double *cut_ljsqi, *lj1i, *lj2i, *lj3i, *lj4i, *offseti;
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inum = listinner->inum;
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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
|
global settings
|
||||||
------------------------------------------------------------------------- */
|
------------------------------------------------------------------------- */
|
||||||
|
|||||||
@ -29,6 +29,9 @@ class PairLJLongTIP4PLong : public PairLJLongCoulLong {
|
|||||||
PairLJLongTIP4PLong(class LAMMPS *);
|
PairLJLongTIP4PLong(class LAMMPS *);
|
||||||
~PairLJLongTIP4PLong();
|
~PairLJLongTIP4PLong();
|
||||||
virtual void compute(int, int);
|
virtual void compute(int, int);
|
||||||
|
virtual void compute_inner();
|
||||||
|
virtual void compute_middle();
|
||||||
|
virtual void compute_outer(int, int);
|
||||||
void settings(int, char **);
|
void settings(int, char **);
|
||||||
void init_style();
|
void init_style();
|
||||||
double init_one(int, int);
|
double init_one(int, int);
|
||||||
|
|||||||
@ -168,6 +168,8 @@ PPPMDisp::PPPMDisp(LAMMPS *lmp, int narg, char **arg) : KSpace(lmp, narg, arg)
|
|||||||
cg_peratom = NULL;
|
cg_peratom = NULL;
|
||||||
cg_6 = NULL;
|
cg_6 = NULL;
|
||||||
cg_peratom_6 = NULL;
|
cg_peratom_6 = NULL;
|
||||||
|
|
||||||
|
memset(function, 0, EWALD_FUNCS*sizeof(int));
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
|
|||||||
@ -726,7 +726,7 @@ void PairLJLongCoulLongOpt::eval_outer()
|
|||||||
double cut_in_off_sq = cut_in_off*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;
|
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
|
for (; ineigh<ineighn; ++ineigh) { // loop over my atoms
|
||||||
i = *ineigh; fi = f0+3*i;
|
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];
|
lj1i = lj1[typei]; lj2i = lj2[typei]; lj3i = lj3[typei]; lj4i = lj4[typei];
|
||||||
cutsqi = cutsq[typei]; cut_ljsqi = cut_ljsq[typei];
|
cutsqi = cutsq[typei]; cut_ljsqi = cut_ljsq[typei];
|
||||||
memcpy(xi, x0+(i+(i<<1)), sizeof(vector));
|
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
|
for (; jneigh<jneighn; ++jneigh) { // loop over neighbors
|
||||||
j = *jneigh;
|
j = *jneigh;
|
||||||
|
|||||||
@ -100,37 +100,33 @@ void Neighbor::respa_nsq_no_newton_omp(NeighList *list)
|
|||||||
#if defined(_OPENMP)
|
#if defined(_OPENMP)
|
||||||
#pragma omp critical
|
#pragma omp critical
|
||||||
#endif
|
#endif
|
||||||
|
{
|
||||||
if (pgsize - npnt < oneatom) {
|
if (pgsize - npnt < oneatom) {
|
||||||
npnt = 0;
|
npnt = 0;
|
||||||
npage += nthreads;
|
npage += nthreads;
|
||||||
if (npage == list->maxpage) list->add_pages(nthreads);
|
if (npage >= list->maxpage) list->add_pages(nthreads);
|
||||||
}
|
}
|
||||||
neighptr = &(list->pages[npage][npnt]);
|
neighptr = &(list->pages[npage][npnt]);
|
||||||
n = 0;
|
n = 0;
|
||||||
|
|
||||||
#if defined(_OPENMP)
|
|
||||||
#pragma omp critical
|
|
||||||
#endif
|
|
||||||
if (pgsize - npnt_inner < oneatom) {
|
if (pgsize - npnt_inner < oneatom) {
|
||||||
npnt_inner = 0;
|
npnt_inner = 0;
|
||||||
npage_inner += nthreads;
|
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]);
|
neighptr_inner = &(listinner->pages[npage_inner][npnt_inner]);
|
||||||
n_inner = 0;
|
n_inner = 0;
|
||||||
|
|
||||||
#if defined(_OPENMP)
|
|
||||||
#pragma omp critical
|
|
||||||
#endif
|
|
||||||
if (respamiddle) {
|
if (respamiddle) {
|
||||||
if (pgsize - npnt_middle < oneatom) {
|
if (pgsize - npnt_middle < oneatom) {
|
||||||
npnt_middle = 0;
|
npnt_middle = 0;
|
||||||
npage_middle += nthreads;
|
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]);
|
neighptr_middle = &(listmiddle->pages[npage_middle][npnt_middle]);
|
||||||
n_middle = 0;
|
n_middle = 0;
|
||||||
}
|
}
|
||||||
|
}
|
||||||
|
|
||||||
itype = type[i];
|
itype = type[i];
|
||||||
xtmp = x[i][0];
|
xtmp = x[i][0];
|
||||||
@ -281,37 +277,33 @@ void Neighbor::respa_nsq_newton_omp(NeighList *list)
|
|||||||
#if defined(_OPENMP)
|
#if defined(_OPENMP)
|
||||||
#pragma omp critical
|
#pragma omp critical
|
||||||
#endif
|
#endif
|
||||||
|
{
|
||||||
if (pgsize - npnt < oneatom) {
|
if (pgsize - npnt < oneatom) {
|
||||||
npnt = 0;
|
npnt = 0;
|
||||||
npage += nthreads;
|
npage += nthreads;
|
||||||
if (npage == list->maxpage) list->add_pages(nthreads);
|
if (npage >= list->maxpage) list->add_pages(nthreads);
|
||||||
}
|
}
|
||||||
neighptr = &(list->pages[npage][npnt]);
|
neighptr = &(list->pages[npage][npnt]);
|
||||||
n = 0;
|
n = 0;
|
||||||
|
|
||||||
#if defined(_OPENMP)
|
|
||||||
#pragma omp critical
|
|
||||||
#endif
|
|
||||||
if (pgsize - npnt_inner < oneatom) {
|
if (pgsize - npnt_inner < oneatom) {
|
||||||
npnt_inner = 0;
|
npnt_inner = 0;
|
||||||
npage_inner += nthreads;
|
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]);
|
neighptr_inner = &(listinner->pages[npage_inner][npnt_inner]);
|
||||||
n_inner = 0;
|
n_inner = 0;
|
||||||
|
|
||||||
#if defined(_OPENMP)
|
|
||||||
#pragma omp critical
|
|
||||||
#endif
|
|
||||||
if (respamiddle) {
|
if (respamiddle) {
|
||||||
if (pgsize - npnt_middle < oneatom) {
|
if (pgsize - npnt_middle < oneatom) {
|
||||||
npnt_middle = 0;
|
npnt_middle = 0;
|
||||||
npage_middle += nthreads;
|
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]);
|
neighptr_middle = &(listmiddle->pages[npage_middle][npnt_middle]);
|
||||||
n_middle = 0;
|
n_middle = 0;
|
||||||
}
|
}
|
||||||
|
}
|
||||||
|
|
||||||
itag = tag[i];
|
itag = tag[i];
|
||||||
itype = type[i];
|
itype = type[i];
|
||||||
@ -484,37 +476,33 @@ void Neighbor::respa_bin_no_newton_omp(NeighList *list)
|
|||||||
#if defined(_OPENMP)
|
#if defined(_OPENMP)
|
||||||
#pragma omp critical
|
#pragma omp critical
|
||||||
#endif
|
#endif
|
||||||
|
{
|
||||||
if (pgsize - npnt < oneatom) {
|
if (pgsize - npnt < oneatom) {
|
||||||
npnt = 0;
|
npnt = 0;
|
||||||
npage += nthreads;
|
npage += nthreads;
|
||||||
if (npage == list->maxpage) list->add_pages(nthreads);
|
if (npage >= list->maxpage) list->add_pages(nthreads);
|
||||||
}
|
}
|
||||||
neighptr = &(list->pages[npage][npnt]);
|
neighptr = &(list->pages[npage][npnt]);
|
||||||
n = 0;
|
n = 0;
|
||||||
|
|
||||||
#if defined(_OPENMP)
|
|
||||||
#pragma omp critical
|
|
||||||
#endif
|
|
||||||
if (pgsize - npnt_inner < oneatom) {
|
if (pgsize - npnt_inner < oneatom) {
|
||||||
npnt_inner = 0;
|
npnt_inner = 0;
|
||||||
npage_inner += nthreads;
|
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]);
|
neighptr_inner = &(listinner->pages[npage_inner][npnt_inner]);
|
||||||
n_inner = 0;
|
n_inner = 0;
|
||||||
|
|
||||||
#if defined(_OPENMP)
|
|
||||||
#pragma omp critical
|
|
||||||
#endif
|
|
||||||
if (respamiddle) {
|
if (respamiddle) {
|
||||||
if (pgsize - npnt_middle < oneatom) {
|
if (pgsize - npnt_middle < oneatom) {
|
||||||
npnt_middle = 0;
|
npnt_middle = 0;
|
||||||
npage_middle += nthreads;
|
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]);
|
neighptr_middle = &(listmiddle->pages[npage_middle][npnt_middle]);
|
||||||
n_middle = 0;
|
n_middle = 0;
|
||||||
}
|
}
|
||||||
|
}
|
||||||
|
|
||||||
itype = type[i];
|
itype = type[i];
|
||||||
xtmp = x[i][0];
|
xtmp = x[i][0];
|
||||||
@ -677,37 +665,33 @@ void Neighbor::respa_bin_newton_omp(NeighList *list)
|
|||||||
#if defined(_OPENMP)
|
#if defined(_OPENMP)
|
||||||
#pragma omp critical
|
#pragma omp critical
|
||||||
#endif
|
#endif
|
||||||
|
{
|
||||||
if (pgsize - npnt < oneatom) {
|
if (pgsize - npnt < oneatom) {
|
||||||
npnt = 0;
|
npnt = 0;
|
||||||
npage += nthreads;
|
npage += nthreads;
|
||||||
if (npage == list->maxpage) list->add_pages(nthreads);
|
if (npage >= list->maxpage) list->add_pages(nthreads);
|
||||||
}
|
}
|
||||||
neighptr = &(list->pages[npage][npnt]);
|
neighptr = &(list->pages[npage][npnt]);
|
||||||
n = 0;
|
n = 0;
|
||||||
|
|
||||||
#if defined(_OPENMP)
|
|
||||||
#pragma omp critical
|
|
||||||
#endif
|
|
||||||
if (pgsize - npnt_inner < oneatom) {
|
if (pgsize - npnt_inner < oneatom) {
|
||||||
npnt_inner = 0;
|
npnt_inner = 0;
|
||||||
npage_inner += nthreads;
|
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]);
|
neighptr_inner = &(listinner->pages[npage_inner][npnt_inner]);
|
||||||
n_inner = 0;
|
n_inner = 0;
|
||||||
|
|
||||||
#if defined(_OPENMP)
|
|
||||||
#pragma omp critical
|
|
||||||
#endif
|
|
||||||
if (respamiddle) {
|
if (respamiddle) {
|
||||||
if (pgsize - npnt_middle < oneatom) {
|
if (pgsize - npnt_middle < oneatom) {
|
||||||
npnt_middle = 0;
|
npnt_middle = 0;
|
||||||
npage_middle += nthreads;
|
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]);
|
neighptr_middle = &(listmiddle->pages[npage_middle][npnt_middle]);
|
||||||
n_middle = 0;
|
n_middle = 0;
|
||||||
}
|
}
|
||||||
|
}
|
||||||
|
|
||||||
itype = type[i];
|
itype = type[i];
|
||||||
xtmp = x[i][0];
|
xtmp = x[i][0];
|
||||||
@ -911,37 +895,33 @@ void Neighbor::respa_bin_newton_tri_omp(NeighList *list)
|
|||||||
#if defined(_OPENMP)
|
#if defined(_OPENMP)
|
||||||
#pragma omp critical
|
#pragma omp critical
|
||||||
#endif
|
#endif
|
||||||
|
{
|
||||||
if (pgsize - npnt < oneatom) {
|
if (pgsize - npnt < oneatom) {
|
||||||
npnt = 0;
|
npnt = 0;
|
||||||
npage += nthreads;
|
npage += nthreads;
|
||||||
if (npage == list->maxpage) list->add_pages(nthreads);
|
if (npage >= list->maxpage) list->add_pages(nthreads);
|
||||||
}
|
}
|
||||||
neighptr = &(list->pages[npage][npnt]);
|
neighptr = &(list->pages[npage][npnt]);
|
||||||
n = 0;
|
n = 0;
|
||||||
|
|
||||||
#if defined(_OPENMP)
|
|
||||||
#pragma omp critical
|
|
||||||
#endif
|
|
||||||
if (pgsize - npnt_inner < oneatom) {
|
if (pgsize - npnt_inner < oneatom) {
|
||||||
npnt_inner = 0;
|
npnt_inner = 0;
|
||||||
npage_inner += nthreads;
|
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]);
|
neighptr_inner = &(listinner->pages[npage_inner][npnt_inner]);
|
||||||
n_inner = 0;
|
n_inner = 0;
|
||||||
|
|
||||||
#if defined(_OPENMP)
|
|
||||||
#pragma omp critical
|
|
||||||
#endif
|
|
||||||
if (respamiddle) {
|
if (respamiddle) {
|
||||||
if (pgsize - npnt_middle < oneatom) {
|
if (pgsize - npnt_middle < oneatom) {
|
||||||
npnt_middle = 0;
|
npnt_middle = 0;
|
||||||
npage_middle += nthreads;
|
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]);
|
neighptr_middle = &(listmiddle->pages[npage_middle][npnt_middle]);
|
||||||
n_middle = 0;
|
n_middle = 0;
|
||||||
}
|
}
|
||||||
|
}
|
||||||
|
|
||||||
itype = type[i];
|
itype = type[i];
|
||||||
xtmp = x[i][0];
|
xtmp = x[i][0];
|
||||||
|
|||||||
@ -317,7 +317,7 @@ void PairBuckLongCoulLongOMP::compute_inner()
|
|||||||
|
|
||||||
const int nall = atom->nlocal + atom->nghost;
|
const int nall = atom->nlocal + atom->nghost;
|
||||||
const int nthreads = comm->nthreads;
|
const int nthreads = comm->nthreads;
|
||||||
const int inum = list->inum;
|
const int inum = listinner->inum;
|
||||||
#if defined(_OPENMP)
|
#if defined(_OPENMP)
|
||||||
#pragma omp parallel default(none)
|
#pragma omp parallel default(none)
|
||||||
#endif
|
#endif
|
||||||
@ -339,7 +339,7 @@ void PairBuckLongCoulLongOMP::compute_middle()
|
|||||||
|
|
||||||
const int nall = atom->nlocal + atom->nghost;
|
const int nall = atom->nlocal + atom->nghost;
|
||||||
const int nthreads = comm->nthreads;
|
const int nthreads = comm->nthreads;
|
||||||
const int inum = list->inum;
|
const int inum = listmiddle->inum;
|
||||||
|
|
||||||
#if defined(_OPENMP)
|
#if defined(_OPENMP)
|
||||||
#pragma omp parallel default(none)
|
#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 nall = atom->nlocal + atom->nghost;
|
||||||
const int nthreads = comm->nthreads;
|
const int nthreads = comm->nthreads;
|
||||||
const int inum = list->inum;
|
const int inum = listouter->inum;
|
||||||
|
|
||||||
#if defined(_OPENMP)
|
#if defined(_OPENMP)
|
||||||
#pragma omp parallel default(none) shared(eflag,vflag)
|
#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];
|
const double *x0 = x[0];
|
||||||
double *f0 = f[0], *fi = 0;
|
double *f0 = f[0], *fi = 0;
|
||||||
|
|
||||||
int *ilist = list->ilist;
|
int *ilist = listinner->ilist;
|
||||||
|
|
||||||
const int newton_pair = force->newton_pair;
|
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));
|
memcpy(xi, x0+(i+(i<<1)), sizeof(vector));
|
||||||
cut_bucksqi = cut_bucksq[typei = type[i]];
|
cut_bucksqi = cut_bucksq[typei = type[i]];
|
||||||
buck1i = buck1[typei]; buck2i = buck2[typei]; rhoinvi = rhoinv[typei];
|
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
|
for (; jneigh<jneighn; ++jneigh) { // loop over neighbors
|
||||||
j = *jneigh;
|
j = *jneigh;
|
||||||
@ -896,7 +896,7 @@ void PairBuckLongCoulLongOMP::eval_middle(int iifrom, int iito, ThrData * const
|
|||||||
const double *x0 = x[0];
|
const double *x0 = x[0];
|
||||||
double *f0 = f[0], *fi = 0;
|
double *f0 = f[0], *fi = 0;
|
||||||
|
|
||||||
int *ilist = list->ilist;
|
int *ilist = listmiddle->ilist;
|
||||||
|
|
||||||
const int newton_pair = force->newton_pair;
|
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));
|
memcpy(xi, x0+(i+(i<<1)), sizeof(vector));
|
||||||
cut_bucksqi = cut_bucksq[typei = type[i]];
|
cut_bucksqi = cut_bucksq[typei = type[i]];
|
||||||
buck1i = buck1[typei]; buck2i = buck2[typei]; rhoinvi = rhoinv[typei];
|
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
|
for (; jneigh<jneighn; ++jneigh) { // loop over neighbors
|
||||||
j = *jneigh;
|
j = *jneigh;
|
||||||
@ -1001,7 +1001,7 @@ void PairBuckLongCoulLongOMP::eval_outer(int iiform, int iito, ThrData * const t
|
|||||||
const double *x0 = x[0];
|
const double *x0 = x[0];
|
||||||
double *f0 = f[0], *fi = f0;
|
double *f0 = f[0], *fi = f0;
|
||||||
|
|
||||||
int *ilist = list->ilist;
|
int *ilist = listouter->ilist;
|
||||||
|
|
||||||
int i, j, ii;
|
int i, j, ii;
|
||||||
int *jneigh, *jneighn, typei, typej, ni, respa_flag;
|
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];
|
buckai = buck_a[typei]; buckci = buck_c[typei]; rhoinvi = rhoinv[typei];
|
||||||
cutsqi = cutsq[typei]; cut_bucksqi = cut_bucksq[typei];
|
cutsqi = cutsq[typei]; cut_bucksqi = cut_bucksq[typei];
|
||||||
memcpy(xi, x0+(i+(i<<1)), sizeof(vector));
|
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
|
for (; jneigh<jneighn; ++jneigh) { // loop over neighbors
|
||||||
j = *jneigh;
|
j = *jneigh;
|
||||||
|
|||||||
File diff suppressed because it is too large
Load Diff
@ -35,11 +35,28 @@ class PairLJLongCoulLongOMP : public PairLJLongCoulLong, public ThrOMP {
|
|||||||
PairLJLongCoulLongOMP(class LAMMPS *);
|
PairLJLongCoulLongOMP(class LAMMPS *);
|
||||||
|
|
||||||
virtual void compute(int, int);
|
virtual void compute(int, int);
|
||||||
|
virtual void compute_inner();
|
||||||
|
virtual void compute_middle();
|
||||||
|
virtual void compute_outer(int, int);
|
||||||
virtual double memory_usage();
|
virtual double memory_usage();
|
||||||
|
|
||||||
private:
|
private:
|
||||||
template <int EVFLAG, int EFLAG, int NEWTON_PAIR>
|
template <const int EVFLAG, const int EFLAG,
|
||||||
void eval(int ifrom, int ito, ThrData * const thr);
|
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);
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
};
|
};
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|||||||
Reference in New Issue
Block a user