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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1591 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2008-03-11 17:15:30 +00:00
parent 07c6376bcf
commit d0e374e4c3
27 changed files with 412 additions and 206 deletions
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133
src/fix_npt.cpp
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@ -36,6 +36,8 @@ using namespace LAMMPS_NS;
#define MIN(A,B) ((A) < (B)) ? (A) : (B)
#define MAX(A,B) ((A) > (B)) ? (A) : (B)
enum{NOBIAS,BIAS};
/* ---------------------------------------------------------------------- */
FixNPT::FixNPT(LAMMPS *lmp, int narg, char **arg) :
@ -257,6 +259,9 @@ void FixNPT::init()
if (icompute < 0) error->all("Temp ID for fix npt does not exist");
temperature = modify->compute[icompute];
if (temperature->tempbias) which = BIAS;
else which = NOBIAS;
icompute = modify->find_compute(id_press);
if (icompute < 0) error->all("Press ID for fix npt does not exist");
pressure = modify->compute[icompute];
@ -365,7 +370,7 @@ void FixNPT::initial_integrate(int vflag)
dilation[i] = exp(dthalf*omega_dot[i]);
}
// v update only for atoms in NPT group
// v update only for atoms in group
double **x = atom->x;
double **v = atom->v;
@ -377,12 +382,27 @@ void FixNPT::initial_integrate(int vflag)
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
double dtfm;
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
dtfm = dtf / mass[type[i]];
v[i][0] = v[i][0]*factor[0] + dtfm*f[i][0];
v[i][1] = v[i][1]*factor[1] + dtfm*f[i][1];
v[i][2] = v[i][2]*factor[2] + dtfm*f[i][2];
if (which == NOBIAS) {
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
dtfm = dtf / mass[type[i]];
v[i][0] = v[i][0]*factor[0] + dtfm*f[i][0];
v[i][1] = v[i][1]*factor[1] + dtfm*f[i][1];
v[i][2] = v[i][2]*factor[2] + dtfm*f[i][2];
}
}
} else if (which == BIAS) {
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
temperature->remove_bias(i,v[i]);
dtfm = dtf / mass[type[i]];
v[i][0] = v[i][0]*factor[0] + dtfm*f[i][0];
v[i][1] = v[i][1]*factor[1] + dtfm*f[i][1];
v[i][2] = v[i][2]*factor[2] + dtfm*f[i][2];
temperature->restore_bias(v[i]);
}
}
}
@ -390,7 +410,7 @@ void FixNPT::initial_integrate(int vflag)
remap(0);
// x update by full step only for atoms in NPT group
// x update by full step only for atoms in group
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
@ -415,7 +435,7 @@ void FixNPT::final_integrate()
{
int i;
// v update only for atoms in NPT group
// v update only for atoms in group
double **v = atom->v;
double **f = atom->f;
@ -426,12 +446,27 @@ void FixNPT::final_integrate()
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
double dtfm;
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
dtfm = dtf / mass[type[i]];
v[i][0] = (v[i][0] + dtfm*f[i][0]) * factor[0];
v[i][1] = (v[i][1] + dtfm*f[i][1]) * factor[1];
v[i][2] = (v[i][2] + dtfm*f[i][2]) * factor[2];
if (which == NOBIAS) {
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
dtfm = dtf / mass[type[i]];
v[i][0] = (v[i][0] + dtfm*f[i][0]) * factor[0];
v[i][1] = (v[i][1] + dtfm*f[i][1]) * factor[1];
v[i][2] = (v[i][2] + dtfm*f[i][2]) * factor[2];
}
}
} else if (which == BIAS) {
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
temperature->remove_bias(i,v[i]);
dtfm = dtf / mass[type[i]];
v[i][0] = (v[i][0] + dtfm*f[i][0]) * factor[0];
v[i][1] = (v[i][1] + dtfm*f[i][1]) * factor[1];
v[i][2] = (v[i][2] + dtfm*f[i][2]) * factor[2];
temperature->restore_bias(v[i]);
}
}
}
@ -505,7 +540,7 @@ void FixNPT::initial_integrate_respa(int vflag, int ilevel, int flag)
// outermost level - update eta_dot and omega_dot, apply to v, remap box
// all other levels - NVE update of v
// x,v updates only performed for atoms in NPT group
// x,v updates only performed for atoms in group
if (ilevel == nlevels_respa-1) {
@ -538,7 +573,7 @@ void FixNPT::initial_integrate_respa(int vflag, int ilevel, int flag)
dilation[i] = exp(dthalf*omega_dot[i]);
}
// v update only for atoms in NPT group
// v update only for atoms in group
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
@ -555,19 +590,33 @@ void FixNPT::initial_integrate_respa(int vflag, int ilevel, int flag)
} else {
// v update only for atoms in NPT group
// v update only for atoms in group
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
dtfm = dtf / mass[type[i]];
v[i][0] += dtfm*f[i][0];
v[i][1] += dtfm*f[i][1];
v[i][2] += dtfm*f[i][2];
if (which == NOBIAS) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
dtfm = dtf / mass[type[i]];
v[i][0] += dtfm*f[i][0];
v[i][1] += dtfm*f[i][1];
v[i][2] += dtfm*f[i][2];
}
}
} else if (which == BIAS) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
temperature->remove_bias(i,v[i]);
dtfm = dtf / mass[type[i]];
v[i][0] += dtfm*f[i][0];
v[i][1] += dtfm*f[i][1];
v[i][2] += dtfm*f[i][2];
temperature->restore_bias(v[i]);
}
}
}
}
// innermost level - also update x only for atoms in NPT group
// innermost level - also update x only for atoms in group
if (ilevel == 0) {
for (int i = 0; i < nlocal; i++) {
@ -594,12 +643,12 @@ void FixNPT::final_integrate_respa(int ilevel)
// outermost level - update eta_dot and omega_dot,
// apply to v via final_integrate()
// all other levels - NVE update of v
// v update only performed for atoms in NPT group
// v update only performed for atoms in group
if (ilevel == nlevels_respa-1) final_integrate();
else {
// v update only for atoms in NPT group
// v update only for atoms in group
double **v = atom->v;
double **f = atom->f;
@ -609,12 +658,26 @@ void FixNPT::final_integrate_respa(int ilevel)
int nlocal = atom->nlocal;
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
dtfm = dtf / mass[type[i]];
v[i][0] += dtfm*f[i][0];
v[i][1] += dtfm*f[i][1];
v[i][2] += dtfm*f[i][2];
if (which == NOBIAS) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
dtfm = dtf / mass[type[i]];
v[i][0] += dtfm*f[i][0];
v[i][1] += dtfm*f[i][1];
v[i][2] += dtfm*f[i][2];
}
}
} else if (which == BIAS) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
temperature->remove_bias(i,v[i]);
dtfm = dtf / mass[type[i]];
v[i][0] += dtfm*f[i][0];
v[i][1] += dtfm*f[i][1];
v[i][2] += dtfm*f[i][2];
temperature->restore_bias(v[i]);
}
}
}
}
@ -763,7 +826,7 @@ int FixNPT::modify_param(int narg, char **arg)
id_temp = new char[n];
strcpy(id_temp,arg[1]);
int icompute = modify->find_compute(id_temp);
int icompute = modify->find_compute(arg[1]);
if (icompute < 0) error->all("Could not find fix_modify temp ID");
temperature = modify->compute[icompute];
@ -793,7 +856,7 @@ int FixNPT::modify_param(int narg, char **arg)
id_press = new char[n];
strcpy(id_press,arg[1]);
int icompute = modify->find_compute(id_press);
int icompute = modify->find_compute(arg[1]);
if (icompute < 0) error->all("Could not find fix_modify press ID");
pressure = modify->compute[icompute];