git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3419 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
138
src/fix_npt.cpp
138
src/fix_npt.cpp
@ -388,6 +388,12 @@ void FixNPT::initial_integrate(int vflag)
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dilation[i] = exp(dthalf*omega_dot[i]);
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}
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// update v and x of atoms in group
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// for BIAS:
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// calculate temperature since some computes require temp
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// computed on current nlocal atoms to remove bias
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// OK to not test returned v = 0, since factor is multiplied by v
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double **x = atom->x;
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double **v = atom->v;
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double **f = atom->f;
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@ -408,7 +414,8 @@ void FixNPT::initial_integrate(int vflag)
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v[i][2] = v[i][2]*factor[2] + dtfm*f[i][2];
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}
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}
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} else if (which == BIAS) {
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} else {
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double tmp = temperature->compute_scalar();
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for (i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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temperature->remove_bias(i,v[i]);
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@ -431,7 +438,8 @@ void FixNPT::initial_integrate(int vflag)
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v[i][2] = v[i][2]*factor[2] + dtfm*f[i][2];
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}
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}
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} else if (which == BIAS) {
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} else {
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double tmp = temperature->compute_scalar();
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for (i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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temperature->remove_bias(i,v[i]);
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@ -449,7 +457,7 @@ void FixNPT::initial_integrate(int vflag)
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remap(0);
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// x update by full step only for atoms in group
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// update x by full step for atoms in group
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for (i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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@ -475,6 +483,12 @@ void FixNPT::final_integrate()
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int i;
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double dtfm;
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// update v of atoms in group
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// for BIAS:
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// calculate temperature since some computes require temp
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// computed on current nlocal atoms to remove bias
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// OK to not test returned v = 0, since factor is multiplied by v
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double **v = atom->v;
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double **f = atom->f;
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double *rmass = atom->rmass;
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@ -494,7 +508,8 @@ void FixNPT::final_integrate()
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v[i][2] = (v[i][2] + dtfm*f[i][2]) * factor[2];
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}
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}
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} else if (which == BIAS) {
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} else {
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double tmp = temperature->compute_scalar();
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for (i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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temperature->remove_bias(i,v[i]);
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@ -517,7 +532,8 @@ void FixNPT::final_integrate()
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v[i][2] = (v[i][2] + dtfm*f[i][2]) * factor[2];
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}
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}
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} else if (which == BIAS) {
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} else {
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double tmp = temperature->compute_scalar();
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for (i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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temperature->remove_bias(i,v[i]);
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@ -602,7 +618,7 @@ void FixNPT::initial_integrate_respa(int vflag, int ilevel, int flag)
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// outermost level - update eta_dot and omega_dot, apply to v, remap box
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// all other levels - NVE update of v
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// x,v updates only performed for atoms in group
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// x,v updates performed for atoms in group
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if (ilevel == nlevels_respa-1) {
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@ -635,7 +651,7 @@ void FixNPT::initial_integrate_respa(int vflag, int ilevel, int flag)
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dilation[i] = exp(dthalf*omega_dot[i]);
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}
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// v update only for atoms in group
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// update v for atoms in group
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if (rmass) {
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for (int i = 0; i < nlocal; i++) {
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@ -663,57 +679,31 @@ void FixNPT::initial_integrate_respa(int vflag, int ilevel, int flag)
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} else {
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// v update only for atoms in group
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// update v for atoms in group
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if (rmass) {
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if (which == NOBIAS) {
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for (int i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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dtfm = dtf / rmass[i];
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v[i][0] += dtfm*f[i][0];
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v[i][1] += dtfm*f[i][1];
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v[i][2] += dtfm*f[i][2];
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}
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}
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} else if (which == BIAS) {
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for (int i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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temperature->remove_bias(i,v[i]);
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dtfm = dtf / rmass[i];
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v[i][0] += dtfm*f[i][0];
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v[i][1] += dtfm*f[i][1];
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v[i][2] += dtfm*f[i][2];
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temperature->restore_bias(i,v[i]);
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}
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for (int i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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dtfm = dtf / rmass[i];
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v[i][0] += dtfm*f[i][0];
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v[i][1] += dtfm*f[i][1];
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v[i][2] += dtfm*f[i][2];
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}
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}
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} else {
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if (which == NOBIAS) {
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for (int i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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dtfm = dtf / mass[type[i]];
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v[i][0] += dtfm*f[i][0];
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v[i][1] += dtfm*f[i][1];
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v[i][2] += dtfm*f[i][2];
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}
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}
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} else if (which == BIAS) {
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for (int i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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temperature->remove_bias(i,v[i]);
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dtfm = dtf / mass[type[i]];
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v[i][0] += dtfm*f[i][0];
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v[i][1] += dtfm*f[i][1];
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v[i][2] += dtfm*f[i][2];
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temperature->restore_bias(i,v[i]);
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}
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for (int i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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dtfm = dtf / mass[type[i]];
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v[i][0] += dtfm*f[i][0];
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v[i][1] += dtfm*f[i][1];
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v[i][2] += dtfm*f[i][2];
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}
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}
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}
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}
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// innermost level - also update x only for atoms in group
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// innermost level - also update x for atoms in group
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if (ilevel == 0) {
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for (int i = 0; i < nlocal; i++) {
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@ -740,12 +730,12 @@ void FixNPT::final_integrate_respa(int ilevel)
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// outermost level - update eta_dot and omega_dot,
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// apply to v via final_integrate()
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// all other levels - NVE update of v
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// v update only performed for atoms in group
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// update v for atoms in group
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if (ilevel == nlevels_respa-1) final_integrate();
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else {
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// v update only for atoms in group
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// update v for atoms in group
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double **v = atom->v;
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double **f = atom->f;
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@ -757,48 +747,22 @@ void FixNPT::final_integrate_respa(int ilevel)
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if (igroup == atom->firstgroup) nlocal = atom->nfirst;
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if (rmass) {
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if (which == NOBIAS) {
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for (int i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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dtfm = dtf / rmass[i];
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v[i][0] += dtfm*f[i][0];
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v[i][1] += dtfm*f[i][1];
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v[i][2] += dtfm*f[i][2];
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}
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}
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} else if (which == BIAS) {
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for (int i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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temperature->remove_bias(i,v[i]);
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dtfm = dtf / rmass[i];
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v[i][0] += dtfm*f[i][0];
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v[i][1] += dtfm*f[i][1];
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v[i][2] += dtfm*f[i][2];
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temperature->restore_bias(i,v[i]);
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}
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for (int i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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dtfm = dtf / rmass[i];
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v[i][0] += dtfm*f[i][0];
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v[i][1] += dtfm*f[i][1];
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v[i][2] += dtfm*f[i][2];
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}
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}
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} else {
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if (which == NOBIAS) {
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for (int i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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dtfm = dtf / mass[type[i]];
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v[i][0] += dtfm*f[i][0];
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v[i][1] += dtfm*f[i][1];
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v[i][2] += dtfm*f[i][2];
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}
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}
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} else if (which == BIAS) {
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for (int i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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temperature->remove_bias(i,v[i]);
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dtfm = dtf / mass[type[i]];
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v[i][0] += dtfm*f[i][0];
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v[i][1] += dtfm*f[i][1];
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v[i][2] += dtfm*f[i][2];
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temperature->restore_bias(i,v[i]);
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}
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for (int i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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dtfm = dtf / mass[type[i]];
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v[i][0] += dtfm*f[i][0];
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v[i][1] += dtfm*f[i][1];
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v[i][2] += dtfm*f[i][2];
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}
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}
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}
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