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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15369 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2016-07-27 14:04:56 +00:00
parent 8c04540e8a
commit ddd85f006c
17 changed files with 527 additions and 389 deletions
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79
src/KSPACE/pair_lj_charmm_coul_long.cpp
View File

@ -172,9 +172,9 @@ void PairLJCharmmCoulLong::compute(int eflag, int vflag)
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
if (rsq > cut_lj_innersq) {
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) * denom_lj_inv;
switch2 = 12.0*rsq * (cut_ljsq-rsq) *
(rsq-cut_lj_innersq) / denom_lj;
(rsq-cut_lj_innersq) * denom_lj_inv;
philj = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]);
forcelj = forcelj*switch1 + philj*switch2;
}
@ -206,7 +206,7 @@ void PairLJCharmmCoulLong::compute(int eflag, int vflag)
evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);
if (rsq > cut_lj_innersq) {
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) * denom_lj_inv;
evdwl *= switch1;
}
evdwl *= factor_lj;
@ -247,13 +247,6 @@ void PairLJCharmmCoulLong::compute_inner()
numneigh = listinner->numneigh;
firstneigh = listinner->firstneigh;
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;
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
@ -289,7 +282,7 @@ void PairLJCharmmCoulLong::compute_inner()
fpair = (forcecoul + factor_lj*forcelj) * r2inv;
if (rsq > cut_out_on_sq) {
rsw = (sqrt(rsq) - cut_out_on)/cut_out_diff;
rsw = (sqrt(rsq) - cut_out_on)*cut_out_diff_inv;
fpair *= 1.0 + rsw*rsw*(2.0*rsw-3.0);
}
@ -332,18 +325,6 @@ void PairLJCharmmCoulLong::compute_middle()
numneigh = listmiddle->numneigh;
firstneigh = listmiddle->firstneigh;
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;
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
@ -378,20 +359,20 @@ void PairLJCharmmCoulLong::compute_middle()
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
if (rsq > cut_lj_innersq) {
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) * denom_lj_inv;
switch2 = 12.0*rsq * (cut_ljsq-rsq) *
(rsq-cut_lj_innersq) / denom_lj;
(rsq-cut_lj_innersq) * denom_lj_inv;
philj = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]);
forcelj = forcelj*switch1 + philj*switch2;
}
fpair = (forcecoul + factor_lj*forcelj) * r2inv;
if (rsq < cut_in_on_sq) {
rsw = (sqrt(rsq) - cut_in_off)/cut_in_diff;
rsw = (sqrt(rsq) - cut_in_off)*cut_in_diff_inv;
fpair *= rsw*rsw*(3.0 - 2.0*rsw);
}
if (rsq > cut_out_on_sq) {
rsw = (sqrt(rsq) - cut_out_on)/cut_out_diff;
rsw = (sqrt(rsq) - cut_out_on)*cut_out_diff_inv;
fpair *= 1.0 + rsw*rsw*(2.0*rsw - 3.0);
}
@ -441,13 +422,6 @@ void PairLJCharmmCoulLong::compute_outer(int eflag, int vflag)
numneigh = listouter->numneigh;
firstneigh = listouter->firstneigh;
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;
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
@ -518,9 +492,9 @@ void PairLJCharmmCoulLong::compute_outer(int eflag, int vflag)
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
if (rsq > cut_lj_innersq) {
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) * denom_lj_inv;
switch2 = 12.0*rsq * (cut_ljsq-rsq) *
(rsq-cut_lj_innersq) / denom_lj;
(rsq-cut_lj_innersq) * denom_lj_inv;
philj = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]);
forcelj = forcelj*switch1 + philj*switch2;
}
@ -562,7 +536,7 @@ void PairLJCharmmCoulLong::compute_outer(int eflag, int vflag)
evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);
if (rsq > cut_lj_innersq) {
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) * denom_lj_inv;
evdwl *= switch1;
}
evdwl *= factor_lj;
@ -590,9 +564,9 @@ void PairLJCharmmCoulLong::compute_outer(int eflag, int vflag)
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
if (rsq > cut_lj_innersq) {
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) * denom_lj_inv;
switch2 = 12.0*rsq * (cut_ljsq-rsq) *
(rsq-cut_lj_innersq) / denom_lj;
(rsq-cut_lj_innersq) * denom_lj_inv;
philj = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]);
forcelj = forcelj*switch1 + philj*switch2;
}
@ -601,9 +575,9 @@ void PairLJCharmmCoulLong::compute_outer(int eflag, int vflag)
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
if (rsq > cut_lj_innersq) {
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) * denom_lj_inv;
switch2 = 12.0*rsq * (cut_ljsq-rsq) *
(rsq-cut_lj_innersq) / denom_lj;
(rsq-cut_lj_innersq) * denom_lj_inv;
philj = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]);
forcelj = forcelj*switch1 + philj*switch2;
}
@ -759,14 +733,27 @@ void PairLJCharmmCoulLong::init_style()
cut_coulsq = cut_coul * cut_coul;
cut_bothsq = MAX(cut_ljsq,cut_coulsq);
denom_lj = (cut_ljsq-cut_lj_innersq) * (cut_ljsq-cut_lj_innersq) *
(cut_ljsq-cut_lj_innersq);
denom_lj_inv = 1.0 / ( (cut_ljsq-cut_lj_innersq) * (cut_ljsq-cut_lj_innersq) *
(cut_ljsq-cut_lj_innersq) );
// set & error check interior rRESPA cutoffs
if (strstr(update->integrate_style,"respa") &&
((Respa *) update->integrate)->level_inner >= 0) {
cut_respa = ((Respa *) update->integrate)->cutoff;
cut_in_off = cut_respa[0];
cut_in_on = cut_respa[1];
cut_out_on = cut_respa[2];
cut_out_off = cut_respa[3];
cut_in_diff = cut_in_on - cut_in_off;
cut_out_diff = cut_out_off - cut_out_on;
cut_in_diff_inv = 1.0 / (cut_in_diff);
cut_out_diff_inv = 1.0 / (cut_out_diff);
cut_in_off_sq = cut_in_off*cut_in_off;
cut_in_on_sq = cut_in_on*cut_in_on;
cut_out_on_sq = cut_out_on*cut_out_on;
cut_out_off_sq = cut_out_off*cut_out_off;
if (MIN(cut_lj,cut_coul) < cut_respa[3])
error->all(FLERR,"Pair cutoff < Respa interior cutoff");
if (cut_lj_inner < cut_respa[1])
@ -992,9 +979,9 @@ double PairLJCharmmCoulLong::single(int i, int j, int itype, int jtype,
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
if (rsq > cut_lj_innersq) {
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) * denom_lj_inv;
switch2 = 12.0*rsq * (cut_ljsq-rsq) *
(rsq-cut_lj_innersq) / denom_lj;
(rsq-cut_lj_innersq) * denom_lj_inv;
philj = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]);
forcelj = forcelj*switch1 + philj*switch2;
}
@ -1017,7 +1004,7 @@ double PairLJCharmmCoulLong::single(int i, int j, int itype, int jtype,
philj = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);
if (rsq > cut_lj_innersq) {
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) * denom_lj_inv;
philj *= switch1;
}
eng += factor_lj*philj;

6
src/KSPACE/pair_lj_charmm_coul_long.h
View File

@ -54,7 +54,11 @@ class PairLJCharmmCoulLong : public Pair {
double cut_lj_innersq,cut_ljsq;
double cut_coul,cut_coulsq;
double cut_bothsq;
double denom_lj;
double cut_in_off, cut_in_on, cut_out_off, cut_out_on;
double cut_in_diff, cut_out_diff;
double cut_in_diff_inv, cut_out_diff_inv;
double cut_in_off_sq, cut_in_on_sq, cut_out_off_sq, cut_out_on_sq;
double denom_lj, denom_lj_inv;
double **epsilon,**sigma,**eps14,**sigma14;
double **lj1,**lj2,**lj3,**lj4,**offset;
double **lj14_1,**lj14_2,**lj14_3,**lj14_4;

26
src/KSPACE/pair_lj_charmm_coul_msm.cpp
View File

@ -161,9 +161,9 @@ void PairLJCharmmCoulMSM::compute(int eflag, int vflag)
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
if (rsq > cut_lj_innersq) {
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) * denom_lj_inv;
switch2 = 12.0*rsq * (cut_ljsq-rsq) *
(rsq-cut_lj_innersq) / denom_lj;
(rsq-cut_lj_innersq) * denom_lj_inv;
philj = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]);
forcelj = forcelj*switch1 + philj*switch2;
}
@ -221,7 +221,7 @@ void PairLJCharmmCoulMSM::compute(int eflag, int vflag)
evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);
if (rsq > cut_lj_innersq) {
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) * denom_lj_inv;
evdwl *= switch1;
}
evdwl *= factor_lj;
@ -358,9 +358,9 @@ void PairLJCharmmCoulMSM::compute_outer(int eflag, int vflag)
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
if (rsq > cut_lj_innersq) {
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) * denom_lj_inv;
switch2 = 12.0*rsq * (cut_ljsq-rsq) *
(rsq-cut_lj_innersq) / denom_lj;
(rsq-cut_lj_innersq) * denom_lj_inv;
philj = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]);
forcelj = forcelj*switch1 + philj*switch2;
}
@ -402,7 +402,7 @@ void PairLJCharmmCoulMSM::compute_outer(int eflag, int vflag)
evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);
if (rsq > cut_lj_innersq) {
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) * denom_lj_inv;
evdwl *= switch1;
}
evdwl *= factor_lj;
@ -430,9 +430,9 @@ void PairLJCharmmCoulMSM::compute_outer(int eflag, int vflag)
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
if (rsq > cut_lj_innersq) {
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) * denom_lj_inv;
switch2 = 12.0*rsq * (cut_ljsq-rsq) *
(rsq-cut_lj_innersq) / denom_lj;
(rsq-cut_lj_innersq) * denom_lj_inv;
philj = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]);
forcelj = forcelj*switch1 + philj*switch2;
}
@ -441,9 +441,9 @@ void PairLJCharmmCoulMSM::compute_outer(int eflag, int vflag)
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
if (rsq > cut_lj_innersq) {
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) * denom_lj_inv;
switch2 = 12.0*rsq * (cut_ljsq-rsq) *
(rsq-cut_lj_innersq) / denom_lj;
(rsq-cut_lj_innersq) * denom_lj_inv;
philj = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]);
forcelj = forcelj*switch1 + philj*switch2;
}
@ -499,9 +499,9 @@ double PairLJCharmmCoulMSM::single(int i, int j, int itype, int jtype,
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
if (rsq > cut_lj_innersq) {
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) * denom_lj_inv;
switch2 = 12.0*rsq * (cut_ljsq-rsq) *
(rsq-cut_lj_innersq) / denom_lj;
(rsq-cut_lj_innersq) * denom_lj_inv;
philj = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]);
forcelj = forcelj*switch1 + philj*switch2;
}
@ -524,7 +524,7 @@ double PairLJCharmmCoulMSM::single(int i, int j, int itype, int jtype,
philj = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);
if (rsq > cut_lj_innersq) {
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) * denom_lj_inv;
philj *= switch1;
}
eng += factor_lj*philj;

14
src/USER-MISC/pair_lj_sf_dipole_sf.cpp
View File

@ -133,8 +133,9 @@ void PairLJSFDipoleSF::compute(int eflag, int vflag)
if (rsq < cut_coulsq[itype][jtype]) {
rcutcoul2inv=1.0/cut_coulsq[itype][jtype];
if (qtmp != 0.0 && q[j] != 0.0) {
pre1 = qtmp*q[j]*rinv*(r2inv-1.0/cut_coulsq[itype][jtype]);
pre1 = qtmp*q[j]*rinv*(r2inv-rcutcoul2inv);
forcecoulx += pre1*delx;
forcecouly += pre1*dely;
@ -144,7 +145,6 @@ void PairLJSFDipoleSF::compute(int eflag, int vflag)
if (mu[i][3] > 0.0 && mu[j][3] > 0.0) {
r3inv = r2inv*rinv;
r5inv = r3inv*r2inv;
rcutcoul2inv=1.0/cut_coulsq[itype][jtype];
pdotp = mu[i][0]*mu[j][0] + mu[i][1]*mu[j][1] + mu[i][2]*mu[j][2];
pidotr = mu[i][0]*delx + mu[i][1]*dely + mu[i][2]*delz;
@ -156,7 +156,7 @@ void PairLJSFDipoleSF::compute(int eflag, int vflag)
aforcecouly = pre1*dely;
aforcecoulz = pre1*delz;
bfac = 1.0 - 4.0*rsq*sqrt(rsq)*rcutcoul2inv*sqrt(rcutcoul2inv) +
bfac = 1.0 - 4.0*rsq*sqrt(rsq*rcutcoul2inv)*rcutcoul2inv +
3.0*rsq*rsq*rcutcoul2inv*rcutcoul2inv;
presf = 2.0 * r2inv * pidotr * pjdotr;
bforcecoulx = bfac * (pjdotr*mu[i][0]+pidotr*mu[j][0]-presf*delx);
@ -187,10 +187,9 @@ void PairLJSFDipoleSF::compute(int eflag, int vflag)
r3inv = r2inv*rinv;
r5inv = r3inv*r2inv;
pidotr = mu[i][0]*delx + mu[i][1]*dely + mu[i][2]*delz;
rcutcoul2inv=1.0/cut_coulsq[itype][jtype];
pre1 = 3.0 * q[j] * r5inv * pidotr * (1-rsq*rcutcoul2inv);
pqfac = 1.0 - 3.0*rsq*rcutcoul2inv +
2.0*rsq*sqrt(rsq)*rcutcoul2inv*sqrt(rcutcoul2inv);
2.0*rsq*sqrt(rsq*rcutcoul2inv)*rcutcoul2inv;
pre2 = q[j] * r3inv * pqfac;
forcecoulx += pre2*mu[i][0] - pre1*delx;
@ -205,10 +204,9 @@ void PairLJSFDipoleSF::compute(int eflag, int vflag)
r3inv = r2inv*rinv;
r5inv = r3inv*r2inv;
pjdotr = mu[j][0]*delx + mu[j][1]*dely + mu[j][2]*delz;
rcutcoul2inv=1.0/cut_coulsq[itype][jtype];
pre1 = 3.0 * qtmp * r5inv * pjdotr * (1-rsq*rcutcoul2inv);
qpfac = 1.0 - 3.0*rsq*rcutcoul2inv +
2.0*rsq*sqrt(rsq)*rcutcoul2inv*sqrt(rcutcoul2inv);
2.0*rsq*sqrt(rsq*rcutcoul2inv)*rcutcoul2inv;
pre2 = qtmp * r3inv * qpfac;
forcecoulx += pre1*delx - pre2*mu[j][0];
@ -261,7 +259,7 @@ void PairLJSFDipoleSF::compute(int eflag, int vflag)
if (eflag) {
if (rsq < cut_coulsq[itype][jtype]) {
ecoul = (1.0-sqrt(rsq)/sqrt(cut_coulsq[itype][jtype]));
ecoul = (1.0-sqrt(rsq/cut_coulsq[itype][jtype]));
ecoul *= ecoul;
ecoul *= qtmp * q[j] * rinv;
if (mu[i][3] > 0.0 && mu[j][3] > 0.0)

3
src/USER-OMP/fix_nh_sphere_omp.cpp
View File

@ -55,7 +55,7 @@ void FixNHSphereOMP::init()
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
if (radius[i] == 0.0)
error->one(FLERR,"Fix nvt/sphere requires extended particles");
error->one(FLERR,"Fix nvt/npt/nph/sphere/omp require extended particles");
FixNHOMP::init();
}
@ -97,6 +97,7 @@ void FixNHSphereOMP::nve_v()
v[i].x += dtfm*f[i].x;
v[i].y += dtfm*f[i].y;
v[i].z += dtfm*f[i].z;
const double dtirotate = dtfrotate / (radius[i]*radius[i]*rmass[i]);
omega[i].x += dtirotate*torque[i].x;
omega[i].y += dtirotate*torque[i].y;

135
src/USER-OMP/fix_nve_sphere_omp.cpp
View File

@ -21,13 +21,17 @@
#include "respa.h"
#include "force.h"
#include "error.h"
#include "math_vector.h"
#include "math_extra.h"
using namespace LAMMPS_NS;
using namespace FixConst;
using namespace MathExtra;
#define INERTIA 0.4 // moment of inertia prefactor for sphere
enum{NONE,DIPOLE};
enum{NODLM,DLM};
/* ---------------------------------------------------------------------- */
@ -77,21 +81,128 @@ void FixNVESphereOMP::initial_integrate(int vflag)
if (extra == DIPOLE) {
double * const * const mu = atom->mu;
if (dlm == NODLM) {
#if defined(_OPENMP)
#pragma omp parallel for private(i) default(none)
#endif
for (i = 0; i < nlocal; i++) {
double g0,g1,g2,msq,scale;
if (mask[i] & groupbit) {
if (mu[i][3] > 0.0) {
g0 = mu[i][0] + dtv * (omega[i][1]*mu[i][2]-omega[i][2]*mu[i][1]);
g1 = mu[i][1] + dtv * (omega[i][2]*mu[i][0]-omega[i][0]*mu[i][2]);
g2 = mu[i][2] + dtv * (omega[i][0]*mu[i][1]-omega[i][1]*mu[i][0]);
msq = g0*g0 + g1*g1 + g2*g2;
scale = mu[i][3]/sqrt(msq);
mu[i][0] = g0*scale;
mu[i][1] = g1*scale;
mu[i][2] = g2*scale;
for (i = 0; i < nlocal; i++) {
double g0,g1,g2,msq,scale;
if (mask[i] & groupbit) {
if (mu[i][3] > 0.0) {
g0 = mu[i][0] + dtv * (omega[i][1]*mu[i][2]-omega[i][2]*mu[i][1]);
g1 = mu[i][1] + dtv * (omega[i][2]*mu[i][0]-omega[i][0]*mu[i][2]);
g2 = mu[i][2] + dtv * (omega[i][0]*mu[i][1]-omega[i][1]*mu[i][0]);
msq = g0*g0 + g1*g1 + g2*g2;
scale = mu[i][3]/sqrt(msq);
mu[i][0] = g0*scale;
mu[i][1] = g1*scale;
mu[i][2] = g2*scale;
}
}
}
} else {
#if defined(_OPENMP)
#pragma omp parallel for private(i) default(none)
#endif
// Integrate orientation following Dullweber-Leimkuhler-Maclachlan scheme
for (i = 0; i < nlocal; i++) {
vector w, w_temp, a;
matrix Q, Q_temp, R;
if (mask[i] & groupbit && mu[i][3] > 0.0) {
// Construct Q from dipole:
// Q is the rotation matrix from space frame to body frame
// i.e. v_b = Q.v_s
// Define mu to lie along the z axis in the body frame
// We take the unit dipole to avoid getting a scaling matrix
const double inv_len_mu = 1.0/mu[i][3];
a[0] = mu[i][0]*inv_len_mu;
a[1] = mu[i][1]*inv_len_mu;
a[2] = mu[i][2]*inv_len_mu;
// v = a x [0 0 1] - cross product of mu in space and body frames
// s = |v|
// c = a.[0 0 1] = a[2]
// vx = [ 0 -v[2] v[1]
// v[2] 0 -v[0]
// -v[1] v[0] 0 ]
// then
// Q = I + vx + vx^2 * (1-c)/s^2
const double s2 = a[0]*a[0] + a[1]*a[1];
if (s2 != 0.0){ // i.e. the vectors are not parallel
const double scale = (1.0 - a[2])/s2;
Q[0][0] = 1.0 - scale*a[0]*a[0]; Q[0][1] = -scale*a[0]*a[1]; Q[0][2] = -a[0];
Q[1][0] = -scale*a[0]*a[1]; Q[1][1] = 1.0 - scale*a[1]*a[1]; Q[1][2] = -a[1];
Q[2][0] = a[0]; Q[2][1] = a[1]; Q[2][2] = 1.0 - scale*(a[0]*a[0] + a[1]*a[1]);
} else { // if parallel then we just have I or -I
Q[0][0] = 1.0/a[2]; Q[0][1] = 0.0; Q[0][2] = 0.0;
Q[1][0] = 0.0; Q[1][1] = 1.0/a[2]; Q[1][2] = 0.0;
Q[2][0] = 0.0; Q[2][1] = 0.0; Q[2][2] = 1.0/a[2];
}
// Local copy of this particle's angular velocity (in space frame)
w[0] = omega[i][0]; w[1] = omega[i][1]; w[2] = omega[i][2];
// Transform omega into body frame: w_temp= Q.w
matvec(Q,w,w_temp);
// Construct rotation R1
BuildRxMatrix(R, dtf/force->ftm2v*w_temp[0]);
// Apply R1 to w: w = R.w_temp
matvec(R,w_temp,w);
// Apply R1 to Q: Q_temp = R^T.Q
transpose_times3(R,Q,Q_temp);
// Construct rotation R2
BuildRyMatrix(R, dtf/force->ftm2v*w[1]);
// Apply R2 to w: w_temp = R.w
matvec(R,w,w_temp);
// Apply R2 to Q: Q = R^T.Q_temp
transpose_times3(R,Q_temp,Q);
// Construct rotation R3
BuildRzMatrix(R, 2.0*dtf/force->ftm2v*w_temp[2]);
// Apply R3 to w: w = R.w_temp
matvec(R,w_temp,w);
// Apply R3 to Q: Q_temp = R^T.Q
transpose_times3(R,Q,Q_temp);
// Construct rotation R4
BuildRyMatrix(R, dtf/force->ftm2v*w[1]);
// Apply R4 to w: w_temp = R.w
matvec(R,w,w_temp);
// Apply R4 to Q: Q = R^T.Q_temp
transpose_times3(R,Q_temp,Q);
// Construct rotation R5
BuildRxMatrix(R, dtf/force->ftm2v*w_temp[0]);
// Apply R5 to w: w = R.w_temp
matvec(R,w_temp,w);
// Apply R5 to Q: Q_temp = R^T.Q
transpose_times3(R,Q,Q_temp);
// Transform w back into space frame w_temp = Q^T.w
transpose_matvec(Q_temp,w,w_temp);
omega[i][0] = w_temp[0]; omega[i][1] = w_temp[1]; omega[i][2] = w_temp[2];
// Set dipole according to updated Q: mu = Q^T.[0 0 1] * |mu|
mu[i][0] = Q_temp[2][0] * mu[i][3];
mu[i][1] = Q_temp[2][1] * mu[i][3];
mu[i][2] = Q_temp[2][2] * mu[i][3];
}
}
}

16
src/USER-OMP/pair_lj_sf_dipole_sf_omp.cpp
View File

@ -123,8 +123,8 @@ void PairLJSFDipoleSFOMP::eval(int iifrom, int iito, ThrData * const thr)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
factor_coul = special_coul[sbmask(j)];
factor_lj = special_lj[sbmask(j)];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j].x;
@ -137,8 +137,6 @@ void PairLJSFDipoleSFOMP::eval(int iifrom, int iito, ThrData * const thr)
r2inv = 1.0/rsq;
rinv = sqrt(r2inv);
// atom can have both a charge and dipole
// i,j = charge-charge, dipole-dipole, dipole-charge, or charge-dipole
// atom can have both a charge and dipole
// i,j = charge-charge, dipole-dipole, dipole-charge, or charge-dipole
@ -148,8 +146,9 @@ void PairLJSFDipoleSFOMP::eval(int iifrom, int iito, ThrData * const thr)
if (rsq < cut_coulsq[itype][jtype]) {
rcutcoul2inv=1.0/cut_coulsq[itype][jtype];
if (qtmp != 0.0 && q[j] != 0.0) {
pre1 = qtmp*q[j]*rinv*(r2inv-1.0/cut_coulsq[itype][jtype]);
pre1 = qtmp*q[j]*rinv*(r2inv-rcutcoul2inv);
forcecoulx += pre1*delx;
forcecouly += pre1*dely;
@ -159,7 +158,6 @@ void PairLJSFDipoleSFOMP::eval(int iifrom, int iito, ThrData * const thr)
if (mu[i].w > 0.0 && mu[j].w > 0.0) {
r3inv = r2inv*rinv;
r5inv = r3inv*r2inv;
rcutcoul2inv=1.0/cut_coulsq[itype][jtype];
pdotp = mu[i].x*mu[j].x + mu[i].y*mu[j].y + mu[i].z*mu[j].z;
pidotr = mu[i].x*delx + mu[i].y*dely + mu[i].z*delz;
@ -171,7 +169,7 @@ void PairLJSFDipoleSFOMP::eval(int iifrom, int iito, ThrData * const thr)
aforcecouly = pre1*dely;
aforcecoulz = pre1*delz;
bfac = 1.0 - 4.0*rsq*sqrt(rsq)*rcutcoul2inv*sqrt(rcutcoul2inv) +
bfac = 1.0 - 4.0*rsq*sqrt(rsq*rcutcoul2inv)*rcutcoul2inv +
3.0*rsq*rsq*rcutcoul2inv*rcutcoul2inv;
presf = 2.0 * r2inv * pidotr * pjdotr;
bforcecoulx = bfac * (pjdotr*mu[i].x+pidotr*mu[j].x-presf*delx);
@ -202,10 +200,9 @@ void PairLJSFDipoleSFOMP::eval(int iifrom, int iito, ThrData * const thr)
r3inv = r2inv*rinv;
r5inv = r3inv*r2inv;
pidotr = mu[i].x*delx + mu[i].y*dely + mu[i].z*delz;
rcutcoul2inv=1.0/cut_coulsq[itype][jtype];
pre1 = 3.0 * q[j] * r5inv * pidotr * (1-rsq*rcutcoul2inv);
pqfac = 1.0 - 3.0*rsq*rcutcoul2inv +
2.0*rsq*sqrt(rsq)*rcutcoul2inv*sqrt(rcutcoul2inv);
2.0*rsq*sqrt(rsq*rcutcoul2inv)*rcutcoul2inv;
pre2 = q[j] * r3inv * pqfac;
forcecoulx += pre2*mu[i].x - pre1*delx;
@ -220,10 +217,9 @@ void PairLJSFDipoleSFOMP::eval(int iifrom, int iito, ThrData * const thr)
r3inv = r2inv*rinv;
r5inv = r3inv*r2inv;
pjdotr = mu[j].x*delx + mu[j].y*dely + mu[j].z*delz;
rcutcoul2inv=1.0/cut_coulsq[itype][jtype];
pre1 = 3.0 * qtmp * r5inv * pjdotr * (1-rsq*rcutcoul2inv);
qpfac = 1.0 - 3.0*rsq*rcutcoul2inv +
2.0*rsq*sqrt(rsq)*rcutcoul2inv*sqrt(rcutcoul2inv);
2.0*rsq*sqrt(rsq*rcutcoul2inv)*rcutcoul2inv;
pre2 = qtmp * r3inv * qpfac;
forcecoulx += pre1*delx - pre2*mu[j].x;

267
src/USER-QMMM/fix_qmmm.cpp
View File

@ -34,7 +34,8 @@
// have to match with those from the QM code
enum {QMMM_TAG_OTHER=0, QMMM_TAG_SIZE=1, QMMM_TAG_COORD=2,
QMMM_TAG_FORCE=3, QMMM_TAG_FORCE2=4, QMMM_TAG_CELL=5,
QMMM_TAG_RADII=6, QMMM_TAG_CHARGE=7};
QMMM_TAG_RADII=6, QMMM_TAG_CHARGE=7, QMMM_TAG_TYPE=8,
QMMM_TAG_MASS=9};
using namespace LAMMPS_NS;
using namespace FixConst;
@ -406,8 +407,10 @@ void FixQMMM::exchange_positions()
double *charge = atom->q;
const int * const mask = atom->mask;
const int * const type = atom->type;
const double * const mass = atom->mass;
const tagint * const tag = atom->tag;
const int nlocal = atom->nlocal;
const int ntypes = atom->ntypes;
const int natoms = (int) atom->natoms;
if (atom->natoms > MAXSMALLINT)
@ -422,12 +425,8 @@ void FixQMMM::exchange_positions()
- create hash table that connects master list index with tag
- collect necessary data and get master list index via hash table
*/
if (comm->me == 0) { // AK: make aradii a per-atom property managed by
// fix qmmm so it migrates with the local atoms.
double *aradii = (double *) calloc(natoms, sizeof(double));
ec_fill_radii( aradii, natoms );
// This array will pack all details about the cell
if (comm->me == 0) {
// Pack various cell dimension properties into one chunk.
double celldata[9];
celldata[0] = domain->boxlo[0];
celldata[1] = domain->boxlo[1];
@ -440,14 +439,13 @@ void FixQMMM::exchange_positions()
celldata[8] = domain->yz;
if (qmmm_role == QMMM_ROLE_MASTER) {
int isend_buf[3];
int isend_buf[4];
isend_buf[0] = natoms;
isend_buf[1] = num_qm;
isend_buf[2] =num_mm;
MPI_Send( isend_buf, 3, MPI_INTEGER,1, QMMM_TAG_SIZE, qm_comm );
MPI_Send( celldata, 9, MPI_DOUBLE, 1, QMMM_TAG_CELL, qm_comm );
MPI_Send( aradii, natoms, MPI_DOUBLE, 1, QMMM_TAG_RADII, qm_comm );
free(aradii);
isend_buf[2] = num_mm;
isend_buf[3] = ntypes;
MPI_Send(isend_buf, 4, MPI_INTEGER,1, QMMM_TAG_SIZE, qm_comm);
MPI_Send(celldata, 9, MPI_DOUBLE, 1, QMMM_TAG_CELL, qm_comm);
}
if (verbose > 0) {
if (screen) fputs("QMMM: exchange positions\n",screen);
@ -497,6 +495,8 @@ void FixQMMM::exchange_positions()
MPI_Send(mm_charge_all, natoms, MPI_DOUBLE, 1, QMMM_TAG_COORD, qm_comm);
MPI_Send(mm_coord_all, 3*natoms, MPI_DOUBLE, 1, QMMM_TAG_COORD, qm_comm);
MPI_Send(mm_mask_all, natoms, MPI_INT, 1, QMMM_TAG_COORD, qm_comm);
MPI_Send(type, natoms, MPI_INT, 1, QMMM_TAG_TYPE, qm_comm);
MPI_Send(mass, ntypes+1, MPI_DOUBLE, 1, QMMM_TAG_MASS, qm_comm);
/* to MM slave code */
MPI_Send(qm_coord, 3*num_qm, MPI_DOUBLE, 1, QMMM_TAG_COORD, mm_comm);
@ -838,247 +838,6 @@ double FixQMMM::memory_usage(void)
}
/* ---------------------------------------------------------------------- */
/* Manage the atomic number */
#define QMMM_ISOTOPES 351
static const int FixQMMM_Z[QMMM_ISOTOPES] = {
1, 1, 1, 2, 2, 3, 3, 4, 5, 5, 6, 6, 6, 7, 7, 8, 8, 8, 9,
10, 10, 10, 11, 12, 12, 12, 13, 14, 14, 14, 15, 16, 16, 16,
16, 17, 17, 18, 18, 18, 19, 19, 19, 20, 20, 20, 20, 20, 20,
21, 22, 22, 22, 22, 22, 23, 23, 24, 24, 24, 24, 25, 26, 26,
26, 26, 27, 28, 28, 28, 28, 28, 29, 29, 30, 30, 30, 30, 30,
31, 31, 32, 32, 32, 32, 32, 33, 34, 34, 34, 34, 34, 34, 35,
35, 36, 36, 36, 36, 36, 36, 37, 37, 38, 38, 38, 38, 39, 40,
40, 40, 40, 40, 41, 42, 42, 42, 42, 42, 42, 42, 43, 43, 43,
44, 44, 44, 44, 44, 44, 44, 45, 46, 46, 46, 46, 46, 46, 47,
47, 48, 48, 48, 48, 48, 48, 48, 48, 49, 49, 50, 50, 50, 50,
50, 50, 50, 50, 50, 50, 51, 51, 52, 52, 52, 52, 52, 52, 52,
52, 53, 54, 54, 54, 54, 54, 54, 54, 54, 54, 55, 56, 56, 56,
56, 56, 56, 56, 57, 57, 58, 58, 58, 58, 59, 60, 60, 60, 60,
60, 60, 60, 61, 61, 62, 62, 62, 62, 62, 62, 62, 63, 63, 64,
64, 64, 64, 64, 64, 64, 65, 66, 66, 66, 66, 66, 66, 66, 67,
68, 68, 68, 68, 68, 68, 69, 70, 70, 70, 70, 70, 70, 70, 71,
71, 72, 72, 72, 72, 72, 72, 73, 73, 74, 74, 74, 74, 74, 75,
75, 76, 76, 76, 76, 76, 76, 76, 77, 77, 78, 78, 78, 78, 78,
78, 79, 80, 80, 80, 80, 80, 80, 80, 81, 81, 82, 82, 82, 82,
83, 84, 84, 85, 85, 86, 86, 86, 87, 88, 88, 88, 88, 89, 90,
90, 91, 92, 92, 92, 92, 92, 93, 93, 94, 94, 94, 94, 94, 94,
95, 95, 96, 96, 96, 96, 96, 96, 97, 97, 98, 98, 98, 98, 99,
100, 101, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110,
111, 112, 113, 114, 115};
static const char FixQMMM_EL[QMMM_ISOTOPES][4] = {
"H", "H", "H", "He", "He", "Li", "Li", "Be", "B", "B",
"C", "C", "C", "N", "N", "O", "O", "O", "F", "Ne", "Ne",
"Ne", "Na", "Mg", "Mg", "Mg", "Al", "Si", "Si", "Si",
"P", "S", "S", "S", "S", "Cl", "Cl", "Ar", "Ar", "Ar",
"K", "K", "K", "Ca", "Ca", "Ca", "Ca", "Ca", "Ca", "Sc",
"Ti", "Ti", "Ti", "Ti", "Ti", "V", "V", "Cr", "Cr", "Cr",
"Cr", "Mn", "Fe", "Fe", "Fe", "Fe", "Co", "Ni", "Ni",
"Ni", "Ni", "Ni", "Cu", "Cu", "Zn", "Zn", "Zn", "Zn", "Zn",
"Ga", "Ga", "Ge", "Ge", "Ge", "Ge", "Ge", "As", "Se",
"Se", "Se", "Se", "Se", "Se", "Br", "Br", "Kr", "Kr",
"Kr", "Kr", "Kr", "Kr", "Rb", "Rb", "Sr", "Sr", "Sr",
"Sr", "Y", "Zr", "Zr", "Zr", "Zr", "Zr", "Nb", "Mo", "Mo",
"Mo", "Mo", "Mo", "Mo", "Mo", "Tc", "Tc", "Tc", "Ru", "Ru",
"Ru", "Ru", "Ru", "Ru", "Ru", "Rh", "Pd", "Pd", "Pd", "Pd",
"Pd", "Pd", "Ag", "Ag", "Cd", "Cd", "Cd", "Cd", "Cd", "Cd",
"Cd", "Cd", "In", "In", "Sn", "Sn", "Sn", "Sn", "Sn", "Sn",
"Sn", "Sn", "Sn", "Sn", "Sb", "Sb", "Te", "Te", "Te", "Te",
"Te", "Te", "Te", "Te", "I", "Xe", "Xe", "Xe", "Xe", "Xe",
"Xe", "Xe", "Xe", "Xe", "Cs", "Ba", "Ba", "Ba", "Ba", "Ba",
"Ba", "Ba", "La", "La", "Ce", "Ce", "Ce", "Ce", "Pr", "Nd",
"Nd", "Nd", "Nd", "Nd", "Nd", "Nd", "Pm", "Pm", "Sm", "Sm",
"Sm", "Sm", "Sm", "Sm", "Sm", "Eu", "Eu", "Gd", "Gd", "Gd",
"Gd", "Gd", "Gd", "Gd", "Tb", "Dy", "Dy", "Dy", "Dy", "Dy",
"Dy", "Dy", "Ho", "Er", "Er", "Er", "Er", "Er", "Er", "Tm",
"Yb", "Yb", "Yb", "Yb", "Yb", "Yb", "Yb", "Lu", "Lu", "Hf",
"Hf", "Hf", "Hf", "Hf", "Hf", "Ta", "Ta", "W", "W", "W", "W",
"W", "Re", "Re", "Os", "Os", "Os", "Os", "Os", "Os", "Os",
"Ir", "Ir", "Pt", "Pt", "Pt", "Pt", "Pt", "Pt", "Au", "Hg",
"Hg", "Hg", "Hg", "Hg", "Hg", "Hg", "Tl", "Tl", "Pb", "Pb",
"Pb", "Pb", "Bi", "Po", "Po", "At", "At", "Rn", "Rn", "Rn",
"Fr", "Ra", "Ra", "Ra", "Ra", "Ac", "Th", "Th", "Pa", "U",
"U", "U", "U", "U", "Np", "Np", "Pu", "Pu", "Pu", "Pu", "Pu",
"Pu", "Am", "Am", "Cm", "Cm", "Cm", "Cm", "Cm", "Cm", "Bk",
"Bk", "Cf", "Cf", "Cf", "Cf", "Es", "Fm", "Md", "Md", "No",
"Lr", "Rf", "Db", "Sg", "Bh", "Hs", "Mt", "Ds", "Rg", "Cn",
"Uut", "Uuq", "Uup"};
static const int FixQMMM_A[QMMM_ISOTOPES] = {
1, 2, 3, 3, 4, 6, 7, 9, 10, 11, 12, 13, 14, 14, 15, 16, 17, 18,
19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34,
36, 35, 37, 36, 38, 40, 39, 40, 41, 40, 42, 43, 44, 46, 48, 45,
46, 47, 48, 49, 50, 50, 51, 50, 52, 53, 54, 55, 54, 56, 57, 58,
59, 58, 60, 61, 62, 64, 63, 65, 64, 66, 67, 68, 70, 69, 71, 70,
72, 73, 74, 76, 75, 74, 76, 77, 78, 80, 82, 79, 81, 78, 80, 82,
83, 84, 86, 85, 87, 84, 86, 87, 88, 89, 90, 91, 92, 94, 96, 93,
92, 94, 95, 96, 97, 98, 100, 97, 98, 99, 96, 98, 99, 100, 101,
102, 104, 103, 102, 104, 105, 106, 108, 110, 107, 109, 106, 108,
110, 111, 112, 113, 114, 116, 113, 115, 112, 114, 115, 116, 117,
118, 119, 120, 122, 124, 121, 123, 120, 122, 123, 124, 125, 126,
128, 130, 127, 124, 126, 128, 129, 130, 131, 132, 134, 136, 133,
130, 132, 134, 135, 136, 137, 138, 138, 139, 136, 138, 140, 142,
141, 142, 143, 144, 145, 146, 148, 150, 145, 147, 144, 147, 148,
149, 150, 152, 154, 151, 153, 152, 154, 155, 156, 157, 158, 160,
159, 156, 158, 160, 161, 162, 163, 164, 165, 162, 164, 166, 167,
168, 170, 169, 168, 170, 171, 172, 173, 174, 176, 175, 176, 174,
176, 177, 178, 179, 180, 180, 181, 180, 182, 183, 184, 186, 185,
187, 184, 186, 187, 188, 189, 190, 192, 191, 193, 190, 192, 194,
195, 196, 198, 197, 196, 198, 199, 200, 201, 202, 204, 203, 205,
204, 206, 207, 208, 209, 209, 210, 210, 211, 211, 220, 222, 223,
223, 224, 226, 228, 227, 230, 232, 231, 233, 234, 235, 236, 238,
236, 237, 238, 239, 240, 241, 242, 244, 241, 243, 243, 244, 245,
246, 247, 248, 247, 249, 249, 250, 251, 252, 252, 257, 258, 260,
259, 262, 265, 268, 271, 272, 270, 276, 281, 280, 285, 284, 289,
288};
static const double FixQMMM_MASS[QMMM_ISOTOPES] = {
1.00782503207, 2.0141017778, 3.0160492777, 3.0160293191, 4.00260325415, 6.015122795, 7.01600455, 9.0121822,
10.0129370, 11.0093054, 12.0000000, 13.0033548378, 14.003241989, 14.0030740048, 15.0001088982, 15.99491461956,
16.99913170, 17.9991610, 18.99840322, 19.9924401754, 20.99384668, 21.991385114, 22.9897692809, 23.985041700,
24.98583692, 25.982592929, 26.98153863, 27.9769265325, 28.976494700, 29.97377017, 30.97376163, 31.97207100,
32.97145876, 33.96786690, 35.96708076, 34.96885268, 36.96590259, 35.967545106, 37.9627324, 39.9623831225,
38.96370668, 39.96399848, 40.96182576, 39.96259098, 41.95861801, 42.9587666, 43.9554818, 45.9536926,
47.952534, 44.9559119, 45.9526316, 46.9517631, 47.9479463, 48.9478700, 49.9447912, 49.9471585,
50.9439595, 49.9460442, 51.9405075, 52.9406494, 53.9388804, 54.9380451, 53.9396105, 55.9349375,
56.9353940, 57.9332756, 58.9331950, 57.9353429, 59.9307864, 60.9310560, 61.9283451, 63.9279660,
62.9295975, 64.9277895, 63.9291422, 65.9260334, 66.9271273, 67.9248442, 69.9253193, 68.9255736,
70.9247013, 69.9242474, 71.9220758, 72.9234589, 73.9211778, 75.9214026, 74.9215965, 73.9224764,
75.9192136, 76.9199140, 77.9173091, 79.9165213, 81.9166994, 78.9183371, 80.9162906, 77.9203648,
79.9163790, 81.9134836, 82.914136, 83.911507, 85.91061073, 84.911789738, 86.909180527, 83.913425,
85.9092602, 86.9088771, 87.9056121, 88.9058483, 89.9047044, 90.9056458, 91.9050408, 93.9063152,
95.9082734, 92.9063781, 91.906811, 93.9050883, 94.9058421, 95.9046795, 96.9060215, 97.9054082,
99.907477, 96.906365, 97.907216, 98.9062547, 95.907598, 97.905287, 98.9059393, 99.9042195,
100.9055821, 101.9043493, 103.905433, 102.905504, 101.905609, 103.904036, 104.905085, 105.903486,
107.903892, 109.905153, 106.905097, 108.904752, 105.906459, 107.904184, 109.9030021, 110.9041781,
111.9027578, 112.9044017, 113.9033585, 115.904756, 112.904058, 114.903878, 111.904818, 113.902779,
114.903342, 115.901741, 116.902952, 117.901603, 118.903308, 119.9021947, 121.9034390, 123.9052739,
120.9038157, 122.9042140, 119.904020, 121.9030439, 122.9042700, 123.9028179, 124.9044307, 125.9033117,
127.9044631, 129.9062244, 126.904473, 123.9058930, 125.904274, 127.9035313, 128.9047794, 129.9035080,
130.9050824, 131.9041535, 133.9053945, 135.907219, 132.905451933, 129.9063208, 131.9050613, 133.9045084,
134.9056886, 135.9045759, 136.9058274, 137.9052472, 137.907112, 138.9063533, 135.907172, 137.905991,
139.9054387, 141.909244, 140.9076528, 141.9077233, 142.9098143, 143.9100873, 144.9125736, 145.9131169,
147.916893, 149.920891, 144.912749, 146.9151385, 143.911999, 146.9148979, 147.9148227, 148.9171847,
149.9172755, 151.9197324, 153.9222093, 150.9198502, 152.9212303, 151.9197910, 153.9208656, 154.9226220,
155.9221227, 156.9239601, 157.9241039, 159.9270541, 158.9253468, 155.924283, 157.924409, 159.9251975,
160.9269334, 161.9267984, 162.9287312, 163.9291748, 164.9303221, 161.928778, 163.929200, 165.9302931,
166.9320482, 167.9323702, 169.9354643, 168.9342133, 167.933897, 169.9347618, 170.9363258, 171.9363815,
172.9382108, 173.9388621, 175.9425717, 174.9407718, 175.9426863, 173.940046, 175.9414086, 176.9432207,
177.9436988, 178.9458161, 179.9465500, 179.9474648, 180.9479958, 179.946704, 181.9482042, 182.9502230,
183.9509312, 185.9543641, 184.9529550, 186.9557531, 183.9524891, 185.9538382, 186.9557505, 187.9558382,
188.9581475, 189.9584470, 191.9614807, 190.9605940, 192.9629264, 189.959932, 191.9610380, 193.9626803,
194.9647911, 195.9649515, 197.967893, 196.9665687, 195.965833, 197.9667690, 198.9682799, 199.9683260,
200.9703023, 201.9706430, 203.9734939, 202.9723442, 204.9744275, 203.9730436, 205.9744653, 206.9758969,
207.9766521, 208.9803987, 208.9824304, 209.9828737, 209.987148, 210.9874963, 210.990601, 220.0113940,
222.0175777, 223.0197359, 223.0185022, 224.0202118, 226.0254098, 228.0310703, 227.0277521, 230.0331338,
232.0380553, 231.0358840, 233.0396352, 234.0409521, 235.0439299, 236.0455680, 238.0507882, 236.046570,
237.0481734, 238.0495599, 239.0521634, 240.0538135, 241.0568515, 242.0587426, 244.064204, 241.0568291,
243.0613811, 243.0613891, 244.0627526, 245.0654912, 246.0672237, 247.070354, 248.072349, 247.070307,
249.0749867, 249.0748535, 250.0764061, 251.079587, 252.081626, 252.082980, 257.095105, 258.098431,
260.10365, 259.10103, 262.10963, 265.11670, 268.12545, 271.13347, 272.13803, 270.13465,
276.15116, 281.16206, 280.16447, 285.17411, 284.17808, 289.18728, 288.19249};
/*
* This function matches the element which has the least absolute
* difference between the masses. delta is set to the difference
* between the mass provided and the best match.
*
* THIS FUNCTION RELIES ON THE CORRECT ORDER OF THE DATA TABLES
* IN ORDER TO SKIP ISOTOPES FROM THE MATCH
*
* */
int match_element(double mass, int search_isotopes, double &delta)
{
int i;
int bestcandidate;
double diff, mindiff;
int lastz;
mindiff = 1e6;
bestcandidate = -1;
lastz = -1;
for(i=0; i<QMMM_ISOTOPES; i++) {
if(!search_isotopes && lastz == FixQMMM_Z[i])
continue;
diff = fabs(FixQMMM_MASS[i] - mass);
if(diff < mindiff) {
mindiff = diff;
bestcandidate = i;
}
lastz = FixQMMM_Z[i];
}
delta = mindiff;
return bestcandidate;
}
/* ---------------------------------------------------------------------- */
//! Atomic radii of all atoms. Master/QM only
//
//
/*
* Source: wikipedia
* [ http://en.wikipedia.org/wiki/Atomic_radii_of_the_elements_(data_page) ]
*
* Atomic radii for the various elements in picometers.
*
* A value of -1 has the meaning of "data not available".
*
* */
/// Number of elements in the arrays
#define EC_ELEMENTS 116
static const double ec_r_covalent[EC_ELEMENTS+1] = {
-1 /* Z=0 */,
0.38, 0.32, 1.34, 0.90, 0.82, 0.77, 0.75, 0.73, 0.71, 0.69, 1.54, 1.30, 1.18, 1.11, 1.06, 1.02, 0.99, 0.97, 1.96, 1.74,
1.44, 1.36, 1.25, 1.27, 1.39, 1.25, 1.26, 1.21, 1.38, 1.31, 1.26, 1.22, 1.19, 1.16, 1.14, 1.10, 2.11, 1.92, 1.62, 1.48,
1.37, 1.45, 1.56, 1.26, 1.35, 1.31, 1.53, 1.48, 1.44, 1.41, 1.38, 1.35, 1.33, 1.30, 2.25, 1.98, 1.69, -1, -1, -1,
-1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 1.60, 1.50, 1.38, 1.46, 1.59, 1.28, 1.37, 1.28, 1.44, 1.49,
1.48, 1.47, 1.46, -1, -1, 1.45, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1
};
int FixQMMM::ec_fill_radii( double *aradii, int ndata )
{
int i, el;
char errmsg[150];
int *type2element;
memory->create(type2element,atom->ntypes+1,"qmmm:type2element");
type2element[0] = 0;
for (i=1; i <= atom->ntypes; ++i) {
double delta;
el = match_element(atom->mass[i], 0, delta);
sprintf(errmsg,"FixQMMM: type %2d (mass: %8g) matches %2s with:"
" Z = %-3d A = %-3d r_cov = %5.2f (error = %-8.2g -> %-.2g%%)\n",
i, atom->mass[i], FixQMMM_EL[el], FixQMMM_Z[el], FixQMMM_A[el],
ec_r_covalent[FixQMMM_Z[el]], delta, delta/atom->mass[i] * 100.0);
type2element[i] = FixQMMM_Z[el];
if(screen) fprintf(screen, "%s", errmsg);
if(logfile) fprintf(logfile, "%s", errmsg);
}
for (i=0; i<ndata; i++) {
el = type2element[atom->type[i]];
if (el < 0 || el > EC_ELEMENTS) {
sprintf(errmsg,"Unable to find element Z=%d in table of covalent radii", el);
error->one(FLERR,errmsg);
}
aradii[i] = ec_r_covalent[el];
if (ec_r_covalent[el] < 0.0) {
sprintf(errmsg, "Covalent radius for atom of element Z=%d not availabe", el);
error->one(FLERR,errmsg);
}
}
memory->destroy(type2element);
return 0;
}
// Local Variables:
// mode: c++
// compile-command: "make -j4 openmpi"

8
src/fix_nh.cpp
View File

@ -79,6 +79,7 @@ FixNH::FixNH(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
etap_mass_flag = 0;
flipflag = 1;
dipole_flag = 0;
dlm_flag = 0;
tcomputeflag = 0;
pcomputeflag = 0;
@ -330,7 +331,10 @@ FixNH::FixNH(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
} else if (strcmp(arg[iarg],"update") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
if (strcmp(arg[iarg+1],"dipole") == 0) dipole_flag = 1;
else error->all(FLERR,"Illegal fix nvt/npt/nph command");
else if (strcmp(arg[iarg],"dipole/dlm") == 0) {
dipole_flag = 1;
dlm_flag = 1;
} else error->all(FLERR,"Illegal fix nvt/npt/nph command");
iarg += 2;
} else if (strcmp(arg[iarg],"fixedpoint") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
@ -434,7 +438,7 @@ FixNH::FixNH(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
if (!atom->mu_flag)
error->all(FLERR,"Using update dipole flag requires atom attribute mu");
}
if ((tstat_flag && t_period <= 0.0) ||
(p_flag[0] && p_period[0] <= 0.0) ||
(p_flag[1] && p_period[1] <= 0.0) ||

5
src/fix_nh.h
View File

@ -111,6 +111,7 @@ class FixNH : public Fix {
int omega_mass_flag; // 1 if omega_mass updated, 0 if not.
int etap_mass_flag; // 1 if etap_mass updated, 0 if not.
int dipole_flag; // 1 if dipole is updated, 0 if not.
int dlm_flag; // 1 if using the DLM rotational integrator, 0 if not
int scaleyz; // 1 if yz scaled with lz
int scalexz; // 1 if xz scaled with lz
@ -219,6 +220,10 @@ Self-explanatory.
E: Using update dipole flag requires atom attribute mu
Self-explanatory.
E: The dlm flag must be used with update dipole
Self-explanatory.
E: Fix nvt/npt/nph damping parameters must be > 0.0

143
src/fix_nh_sphere.cpp
View File

@ -21,9 +21,13 @@
#include "atom_vec.h"
#include "group.h"
#include "error.h"
#include "force.h"
#include "math_vector.h"
#include "math_extra.h"
using namespace LAMMPS_NS;
using namespace FixConst;
using namespace MathExtra;
#define INERTIA 0.4 // moment of inertia prefactor for sphere
@ -50,7 +54,7 @@ void FixNHSphere::init()
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
if (radius[i] == 0.0)
error->one(FLERR,"Fix nvt/sphere requires extended particles");
error->one(FLERR,"Fix nvt/npt/nph/sphere require extended particles");
FixNH::init();
}
@ -102,28 +106,133 @@ void FixNHSphere::nve_x()
FixNH::nve_x();
// update mu for dipoles
// d_mu/dt = omega cross mu
// renormalize mu to dipole length
if (dipole_flag) {
double msq,scale,g[3];
double **mu = atom->mu;
double **omega = atom->omega;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
if (mu[i][3] > 0.0) {
g[0] = mu[i][0] + dtv * (omega[i][1]*mu[i][2]-omega[i][2]*mu[i][1]);
g[1] = mu[i][1] + dtv * (omega[i][2]*mu[i][0]-omega[i][0]*mu[i][2]);
g[2] = mu[i][2] + dtv * (omega[i][0]*mu[i][1]-omega[i][1]*mu[i][0]);
msq = g[0]*g[0] + g[1]*g[1] + g[2]*g[2];
scale = mu[i][3]/sqrt(msq);
mu[i][0] = g[0]*scale;
mu[i][1] = g[1]*scale;
mu[i][2] = g[2]*scale;
if (dlm_flag == 0){
// d_mu/dt = omega cross mu
// renormalize mu to dipole length
double msq,scale,g[3];
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
if (mu[i][3] > 0.0) {
g[0] = mu[i][0] + dtv * (omega[i][1]*mu[i][2]-omega[i][2]*mu[i][1]);
g[1] = mu[i][1] + dtv * (omega[i][2]*mu[i][0]-omega[i][0]*mu[i][2]);
g[2] = mu[i][2] + dtv * (omega[i][0]*mu[i][1]-omega[i][1]*mu[i][0]);
msq = g[0]*g[0] + g[1]*g[1] + g[2]*g[2];
scale = mu[i][3]/sqrt(msq);
mu[i][0] = g[0]*scale;
mu[i][1] = g[1]*scale;
mu[i][2] = g[2]*scale;
}
} else {
// Integrate orientation following Dullweber-Leimkuhler-Maclachlan scheme
vector w, w_temp, a;
matrix Q, Q_temp, R;
double scale,s2,inv_len_mu;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit && mu[i][3] > 0.0) {
// Construct Q from dipole:
// Q is the rotation matrix from space frame to body frame
// i.e. v_b = Q.v_s
// Define mu to lie along the z axis in the body frame
// We take the unit dipole to avoid getting a scaling matrix
inv_len_mu = 1.0/mu[i][3];
a[0] = mu[i][0]*inv_len_mu;
a[1] = mu[i][1]*inv_len_mu;
a[2] = mu[i][2]*inv_len_mu;
// v = a x [0 0 1] - cross product of mu in space and body frames
// s = |v|
// c = a.[0 0 1] = a[2]
// vx = [ 0 -v[2] v[1]
// v[2] 0 -v[0]
// -v[1] v[0] 0 ]
// then
// Q = I + vx + vx^2 * (1-c)/s^2
s2 = a[0]*a[0] + a[1]*a[1];
if (s2 != 0.0){ // i.e. the vectors are not parallel
scale = (1.0 - a[2])/s2;
Q[0][0] = 1.0 - scale*a[0]*a[0]; Q[0][1] = -scale*a[0]*a[1]; Q[0][2] = -a[0];
Q[1][0] = -scale*a[0]*a[1]; Q[1][1] = 1.0 - scale*a[1]*a[1]; Q[1][2] = -a[1];
Q[2][0] = a[0]; Q[2][1] = a[1]; Q[2][2] = 1.0 - scale*(a[0]*a[0] + a[1]*a[1]);
} else { // if parallel then we just have I or -I
Q[0][0] = 1.0/a[2]; Q[0][1] = 0.0; Q[0][2] = 0.0;
Q[1][0] = 0.0; Q[1][1] = 1.0/a[2]; Q[1][2] = 0.0;
Q[2][0] = 0.0; Q[2][1] = 0.0; Q[2][2] = 1.0/a[2];
}
// Local copy of this particle's angular velocity (in space frame)
w[0] = omega[i][0]; w[1] = omega[i][1]; w[2] = omega[i][2];
// Transform omega into body frame: w_temp= Q.w
matvec(Q,w,w_temp);
// Construct rotation R1
BuildRxMatrix(R, dtf/force->ftm2v*w_temp[0]);
// Apply R1 to w: w = R.w_temp
matvec(R,w_temp,w);
// Apply R1 to Q: Q_temp = R^T.Q
transpose_times3(R,Q,Q_temp);
// Construct rotation R2
BuildRyMatrix(R, dtf/force->ftm2v*w[1]);
// Apply R2 to w: w_temp = R.w
matvec(R,w,w_temp);
// Apply R2 to Q: Q = R^T.Q_temp
transpose_times3(R,Q_temp,Q);
// Construct rotation R3
BuildRzMatrix(R, 2.0*dtf/force->ftm2v*w_temp[2]);
// Apply R3 to w: w = R.w_temp
matvec(R,w_temp,w);
// Apply R3 to Q: Q_temp = R^T.Q
transpose_times3(R,Q,Q_temp);
// Construct rotation R4
BuildRyMatrix(R, dtf/force->ftm2v*w[1]);
// Apply R4 to w: w_temp = R.w
matvec(R,w,w_temp);
// Apply R4 to Q: Q = R^T.Q_temp
transpose_times3(R,Q_temp,Q);
// Construct rotation R5
BuildRxMatrix(R, dtf/force->ftm2v*w_temp[0]);
// Apply R5 to w: w = R.w_temp
matvec(R,w_temp,w);
// Apply R5 to Q: Q_temp = R^T.Q
transpose_times3(R,Q,Q_temp);
// Transform w back into space frame w_temp = Q^T.w
transpose_matvec(Q_temp,w,w_temp);
omega[i][0] = w_temp[0]; omega[i][1] = w_temp[1]; omega[i][2] = w_temp[2];
// Set dipole according to updated Q: mu = Q^T.[0 0 1] * |mu|
mu[i][0] = Q_temp[2][0] * mu[i][3];
mu[i][1] = Q_temp[2][1] * mu[i][3];
mu[i][2] = Q_temp[2][2] * mu[i][3];
}
}
}
}
}

149
src/fix_nve_sphere.cpp
View File

@ -21,13 +21,17 @@
#include "respa.h"
#include "force.h"
#include "error.h"
#include "math_vector.h"
#include "math_extra.h"
using namespace LAMMPS_NS;
using namespace FixConst;
using namespace MathExtra;
#define INERTIA 0.4 // moment of inertia prefactor for sphere
enum{NONE,DIPOLE};
enum{NODLM,DLM};
/* ---------------------------------------------------------------------- */
@ -41,13 +45,17 @@ FixNVESphere::FixNVESphere(LAMMPS *lmp, int narg, char **arg) :
// process extra keywords
extra = NONE;
dlm = NODLM;
int iarg = 3;
while (iarg < narg) {
if (strcmp(arg[iarg],"update") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix nve/sphere command");
if (strcmp(arg[iarg+1],"dipole") == 0) extra = DIPOLE;
else error->all(FLERR,"Illegal fix nve/sphere command");
else if (strcmp(arg[iarg+1],"dipole/dlm") == 0) {
extra = DIPOLE;
dlm = DLM;
} else error->all(FLERR,"Illegal fix nve/sphere command");
iarg += 2;
} else error->all(FLERR,"Illegal fix nve/sphere command");
}
@ -57,7 +65,7 @@ FixNVESphere::FixNVESphere(LAMMPS *lmp, int narg, char **arg) :
if (!atom->sphere_flag)
error->all(FLERR,"Fix nve/sphere requires atom style sphere");
if (extra == DIPOLE && !atom->mu_flag)
error->all(FLERR,"Fix nve/sphere dipole requires atom attribute mu");
error->all(FLERR,"Fix nve/sphere update dipole requires atom attribute mu");
}
/* ---------------------------------------------------------------------- */
@ -83,8 +91,10 @@ void FixNVESphere::init()
void FixNVESphere::initial_integrate(int vflag)
{
double dtfm,dtirotate,msq,scale;
double dtfm,dtirotate,msq,scale,s2,inv_len_mu;
double g[3];
vector w, w_temp, a;
matrix Q, Q_temp, R;
double **x = atom->x;
double **v = atom->v;
@ -120,25 +130,127 @@ void FixNVESphere::initial_integrate(int vflag)
omega[i][2] += dtirotate * torque[i][2];
}
}
// update mu for dipoles
// d_mu/dt = omega cross mu
// renormalize mu to dipole length
if (extra == DIPOLE) {
double **mu = atom->mu;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
if (mu[i][3] > 0.0) {
g[0] = mu[i][0] + dtv * (omega[i][1]*mu[i][2]-omega[i][2]*mu[i][1]);
g[1] = mu[i][1] + dtv * (omega[i][2]*mu[i][0]-omega[i][0]*mu[i][2]);
g[2] = mu[i][2] + dtv * (omega[i][0]*mu[i][1]-omega[i][1]*mu[i][0]);
msq = g[0]*g[0] + g[1]*g[1] + g[2]*g[2];
scale = mu[i][3]/sqrt(msq);
mu[i][0] = g[0]*scale;
mu[i][1] = g[1]*scale;
mu[i][2] = g[2]*scale;
if (dlm == NODLM) {
// d_mu/dt = omega cross mu
// renormalize mu to dipole length
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
if (mu[i][3] > 0.0) {
g[0] = mu[i][0] + dtv * (omega[i][1]*mu[i][2]-omega[i][2]*mu[i][1]);
g[1] = mu[i][1] + dtv * (omega[i][2]*mu[i][0]-omega[i][0]*mu[i][2]);
g[2] = mu[i][2] + dtv * (omega[i][0]*mu[i][1]-omega[i][1]*mu[i][0]);
msq = g[0]*g[0] + g[1]*g[1] + g[2]*g[2];
scale = mu[i][3]/sqrt(msq);
mu[i][0] = g[0]*scale;
mu[i][1] = g[1]*scale;
mu[i][2] = g[2]*scale;
}
} else {
// Integrate orientation following Dullweber-Leimkuhler-Maclachlan scheme
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit && mu[i][3] > 0.0) {
// Construct Q from dipole:
// Q is the rotation matrix from space frame to body frame
// i.e. v_b = Q.v_s
// Define mu to lie along the z axis in the body frame
// We take the unit dipole to avoid getting a scaling matrix
inv_len_mu = 1.0/mu[i][3];
a[0] = mu[i][0]*inv_len_mu;
a[1] = mu[i][1]*inv_len_mu;
a[2] = mu[i][2]*inv_len_mu;
// v = a x [0 0 1] - cross product of mu in space and body frames
// s = |v|
// c = a.[0 0 1] = a[2]
// vx = [ 0 -v[2] v[1]
// v[2] 0 -v[0]
// -v[1] v[0] 0 ]
// then
// Q = I + vx + vx^2 * (1-c)/s^2
s2 = a[0]*a[0] + a[1]*a[1];
if (s2 != 0.0){ // i.e. the vectors are not parallel
scale = (1.0 - a[2])/s2;
Q[0][0] = 1.0 - scale*a[0]*a[0]; Q[0][1] = -scale*a[0]*a[1]; Q[0][2] = -a[0];
Q[1][0] = -scale*a[0]*a[1]; Q[1][1] = 1.0 - scale*a[1]*a[1]; Q[1][2] = -a[1];
Q[2][0] = a[0]; Q[2][1] = a[1]; Q[2][2] = 1.0 - scale*(a[0]*a[0] + a[1]*a[1]);
} else { // if parallel then we just have I or -I
Q[0][0] = 1.0/a[2]; Q[0][1] = 0.0; Q[0][2] = 0.0;
Q[1][0] = 0.0; Q[1][1] = 1.0/a[2]; Q[1][2] = 0.0;
Q[2][0] = 0.0; Q[2][1] = 0.0; Q[2][2] = 1.0/a[2];
}
// Local copy of this particle's angular velocity (in space frame)
w[0] = omega[i][0]; w[1] = omega[i][1]; w[2] = omega[i][2];
// Transform omega into body frame: w_temp= Q.w
matvec(Q,w,w_temp);
// Construct rotation R1
BuildRxMatrix(R, dtf/force->ftm2v*w_temp[0]);
// Apply R1 to w: w = R.w_temp
matvec(R,w_temp,w);
// Apply R1 to Q: Q_temp = R^T.Q
transpose_times3(R,Q,Q_temp);
// Construct rotation R2
BuildRyMatrix(R, dtf/force->ftm2v*w[1]);
// Apply R2 to w: w_temp = R.w
matvec(R,w,w_temp);
// Apply R2 to Q: Q = R^T.Q_temp
transpose_times3(R,Q_temp,Q);
// Construct rotation R3
BuildRzMatrix(R, 2.0*dtf/force->ftm2v*w_temp[2]);
// Apply R3 to w: w = R.w_temp
matvec(R,w_temp,w);
// Apply R3 to Q: Q_temp = R^T.Q
transpose_times3(R,Q,Q_temp);
// Construct rotation R4
BuildRyMatrix(R, dtf/force->ftm2v*w[1]);
// Apply R4 to w: w_temp = R.w
matvec(R,w,w_temp);
// Apply R4 to Q: Q = R^T.Q_temp
transpose_times3(R,Q_temp,Q);
// Construct rotation R5
BuildRxMatrix(R, dtf/force->ftm2v*w_temp[0]);
// Apply R5 to w: w = R.w_temp
matvec(R,w_temp,w);
// Apply R5 to Q: Q_temp = R^T.Q
transpose_times3(R,Q,Q_temp);
// Transform w back into space frame w_temp = Q^T.w
transpose_matvec(Q_temp,w,w_temp);
omega[i][0] = w_temp[0]; omega[i][1] = w_temp[1]; omega[i][2] = w_temp[2];
// Set dipole according to updated Q: mu = Q^T.[0 0 1] * |mu|
mu[i][0] = Q_temp[2][0] * mu[i][3];
mu[i][1] = Q_temp[2][1] * mu[i][3];
mu[i][2] = Q_temp[2][2] * mu[i][3];
}
}
}
}
}
@ -165,6 +277,7 @@ void FixNVESphere::final_integrate()
// update v,omega for all particles
// d_omega/dt = torque / inertia
double rke = 0.0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
dtfm = dtf / rmass[i];
@ -176,5 +289,7 @@ void FixNVESphere::final_integrate()
omega[i][0] += dtirotate * torque[i][0];
omega[i][1] += dtirotate * torque[i][1];
omega[i][2] += dtirotate * torque[i][2];
rke += (omega[i][0]*omega[i][0] + omega[i][1]*omega[i][1] + omega[i][2]*omega[i][2])*radius[i]*radius[i]*rmass[i];
}
}

8
src/fix_nve_sphere.h
View File

@ -34,6 +34,7 @@ class FixNVESphere : public FixNVE {
protected:
int extra;
int dlm;
};
}
@ -53,12 +54,17 @@ E: Fix nve/sphere requires atom style sphere
Self-explanatory.
E: Fix nve/sphere dipole requires atom attribute mu
E: Fix nve/sphere update dipole requires atom attribute mu
An atom style with this attribute is needed.
E: Fix nve/sphere requires extended particles
This fix can only be used for particles of a finite size.
E: Fix nve/sphere dlm must be used with update dipole
The DLM algorithm can only be used in conjunction with update dipole.
*/

6
src/force.cpp
View File

@ -260,12 +260,6 @@ char *Force::pair_match_ptr(Pair *ptr)
if (ptr == hybrid->styles[i]) return hybrid->keywords[i];
}
if (strstr(pair_style,"hybrid/overlay")) {
PairHybridOverlay *hybrid = (PairHybridOverlay *) pair;
for (int i = 0; i < hybrid->nstyles; i++)
if (ptr == hybrid->styles[i]) return hybrid->keywords[i];
}
return NULL;
}

45
src/math_extra.cpp
View File

@ -607,6 +607,51 @@ void inertia_triangle(double *idiag, double *quat, double mass,
inertia[5] = tensor[0][1];
}
/* ----------------------------------------------------------------------
Build rotation matrix for a small angle rotation around the X axis
------------------------------------------------------------------------- */
void BuildRxMatrix(double R[3][3], const double angle)
{
const double angleSq = angle * angle;
const double cosAngle = (1.0 - angleSq * 0.25) / (1.0 + angleSq * 0.25);
const double sinAngle = angle / (1.0 + angleSq * 0.25);
R[0][0] = 1.0; R[0][1] = 0.0; R[0][2] = 0.0;
R[1][0] = 0.0; R[1][1] = cosAngle; R[1][2] = -sinAngle;
R[2][0] = 0.0; R[2][1] = sinAngle; R[2][2] = cosAngle;
}
/* ----------------------------------------------------------------------
Build rotation matrix for a small angle rotation around the Y axis
------------------------------------------------------------------------- */
void BuildRyMatrix(double R[3][3], const double angle)
{
const double angleSq = angle * angle;
const double cosAngle = (1.0 - angleSq * 0.25) / (1.0 + angleSq * 0.25);
const double sinAngle = angle / (1.0 + angleSq * 0.25);
R[0][0] = cosAngle; R[0][1] = 0.0; R[0][2] = sinAngle;
R[1][0] = 0.0; R[1][1] = 1.0; R[1][2] = 0.0;
R[2][0] = -sinAngle; R[2][1] = 0.0; R[2][2] = cosAngle;
}
/* ----------------------------------------------------------------------
Build rotation matrix for a small angle rotation around the Y axis
------------------------------------------------------------------------- */
void BuildRzMatrix(double R[3][3], const double angle)
{
const double angleSq = angle * angle;
const double cosAngle = (1.0 - angleSq * 0.25) / (1.0 + angleSq * 0.25);
const double sinAngle = angle / (1.0 + angleSq * 0.25);
R[0][0] = cosAngle; R[0][1] = -sinAngle; R[0][2] = 0.0;
R[1][0] = sinAngle; R[1][1] = cosAngle; R[1][2] = 0.0;
R[2][0] = 0.0; R[2][1] = 0.0; R[2][2] = 1.0;
}
/* ---------------------------------------------------------------------- */
}

4
src/math_extra.h
View File

@ -111,6 +111,10 @@ namespace MathExtra {
inline void rotation_generator_x(const double m[3][3], double ans[3][3]);
inline void rotation_generator_y(const double m[3][3], double ans[3][3]);
inline void rotation_generator_z(const double m[3][3], double ans[3][3]);
void BuildRxMatrix(double R[3][3], const double angle);
void BuildRyMatrix(double R[3][3], const double angle);
void BuildRzMatrix(double R[3][3], const double angle);
// moment of inertia operations

2
src/thermo.cpp
View File

@ -991,7 +991,7 @@ int Thermo::add_variable(const char *id)
}
/* ----------------------------------------------------------------------
compute a single thermodyanmic value, word is any keyword in custom list
compute a single thermodynamic value, word is any keyword in custom list
called when a variable is evaluated by Variable class
return value as double in answer
return 0 if str is recoginzed keyword, 1 if unrecognized