git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3951 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
@ -12,497 +12,56 @@
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------------------------------------------------------------------------- */
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#include "string.h"
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#include "stdlib.h"
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#include "math.h"
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#include "fix_npt_sphere.h"
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#include "atom.h"
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#include "atom_vec.h"
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#include "force.h"
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#include "compute.h"
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#include "kspace.h"
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#include "update.h"
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#include "domain.h"
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#include "modify.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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#define INERTIA 0.4 // moment of inertia for sphere
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enum{NOBIAS,BIAS};
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/* ---------------------------------------------------------------------- */
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FixNPTSphere::FixNPTSphere(LAMMPS *lmp, int narg, char **arg) :
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FixNPT(lmp, narg, arg)
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FixNHSphere(lmp, narg, arg)
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{
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// error checks
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if (!tstat_flag)
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error->all("Temperature control must be used with fix npt/sphere");
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if (!pstat_flag)
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error->all("Pressure control must be used with fix npt/sphere");
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if (!atom->omega_flag || !atom->torque_flag)
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error->all("Fix npt/sphere requires atom attributes omega, torque");
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if (!atom->radius_flag && !atom->avec->shape_type)
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error->all("Fix npt/sphere requires atom attribute radius or shape");
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}
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/* ---------------------------------------------------------------------- */
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void FixNPTSphere::init()
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{
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int i,itype;
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// check that all particles are finite-size and spherical
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// no point particles allowed
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if (atom->radius_flag) {
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double *radius = atom->radius;
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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if (igroup == atom->firstgroup) nlocal = atom->nfirst;
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for (i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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if (radius[i] == 0.0)
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error->one("Fix nvt/sphere requires extended particles");
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}
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} else {
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double **shape = atom->shape;
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int *type = atom->type;
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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if (igroup == atom->firstgroup) nlocal = atom->nfirst;
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for (i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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itype = type[i];
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if (shape[itype][0] == 0.0)
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error->one("Fix nvt/sphere requires extended particles");
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if (shape[itype][0] != shape[itype][1] ||
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shape[itype][0] != shape[itype][2])
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error->one("Fix nvt/sphere requires spherical particle shapes");
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}
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}
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FixNPT::init();
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}
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/* ---------------------------------------------------------------------- */
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void FixNPTSphere::initial_integrate(int vflag)
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{
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int i,itype;
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double dtfm,dtirotate;
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double delta = update->ntimestep - update->beginstep;
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delta /= update->endstep - update->beginstep;
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// update eta_dot
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t_target = t_start + delta * (t_stop-t_start);
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f_eta = t_freq*t_freq * (t_current/t_target - 1.0);
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eta_dot += f_eta*dthalf;
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eta_dot *= drag_factor;
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eta += dtv*eta_dot;
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// update omega_dot
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// for non-varying dims, p_freq is 0.0, so omega_dot doesn't change
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double f_omega,volume;
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if (dimension == 3) volume = domain->xprd*domain->yprd*domain->zprd;
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else volume = domain->xprd*domain->yprd;
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double denskt = atom->natoms*boltz*t_target / volume * nktv2p;
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for (i = 0; i < 3; i++) {
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p_target[i] = p_start[i] + delta * (p_stop[i]-p_start[i]);
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f_omega = p_freq[i]*p_freq[i] * (p_current[i]-p_target[i])/denskt;
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omega_dot[i] += f_omega*dthalf;
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omega_dot[i] *= drag_factor;
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omega[i] += dtv*omega_dot[i];
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factor[i] = exp(-dthalf*(eta_dot+omega_dot[i]));
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dilation[i] = exp(dthalf*omega_dot[i]);
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}
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factor_rotate = exp(-dthalf*eta_dot);
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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 **x = atom->x;
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double **v = atom->v;
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double **f = atom->f;
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double **omega = atom->omega;
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double **torque = atom->torque;
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double *radius = atom->radius;
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double *rmass = atom->rmass;
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double *mass = atom->mass;
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double **shape = atom->shape;
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int *type = atom->type;
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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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 (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] = v[i][0]*factor[0] + dtfm*f[i][0];
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v[i][1] = v[i][1]*factor[1] + dtfm*f[i][1];
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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 {
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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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dtfm = dtf / rmass[i];
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v[i][0] = v[i][0]*factor[0] + dtfm*f[i][0];
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v[i][1] = v[i][1]*factor[1] + dtfm*f[i][1];
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v[i][2] = v[i][2]*factor[2] + dtfm*f[i][2];
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temperature->restore_bias(i,v[i]);
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}
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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 (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] = v[i][0]*factor[0] + dtfm*f[i][0];
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v[i][1] = v[i][1]*factor[1] + dtfm*f[i][1];
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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 {
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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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dtfm = dtf / mass[type[i]];
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v[i][0] = v[i][0]*factor[0] + dtfm*f[i][0];
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v[i][1] = v[i][1]*factor[1] + dtfm*f[i][1];
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v[i][2] = v[i][2]*factor[2] + dtfm*f[i][2];
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temperature->restore_bias(i,v[i]);
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}
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}
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}
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}
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// remap simulation box by 1/2 step
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remap();
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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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x[i][0] += dtv * v[i][0];
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x[i][1] += dtv * v[i][1];
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x[i][2] += dtv * v[i][2];
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}
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}
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// set timestep here since dt may have changed or come via rRESPA
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double dtfrotate = dtf / INERTIA;
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// update omega for all particles
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// d_omega/dt = torque / inertia
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// 4 cases depending on radius vs shape and rmass vs mass
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if (radius) {
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if (rmass) {
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for (i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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dtirotate = dtfrotate / (radius[i]*radius[i]*rmass[i]);
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omega[i][0] = omega[i][0]*factor_rotate + dtirotate*torque[i][0];
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omega[i][1] = omega[i][1]*factor_rotate + dtirotate*torque[i][1];
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omega[i][2] = omega[i][2]*factor_rotate + dtirotate*torque[i][2];
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}
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}
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} else {
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for (i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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dtirotate = dtfrotate / (radius[i]*radius[i]*mass[type[i]]);
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omega[i][0] = omega[i][0]*factor_rotate + dtirotate*torque[i][0];
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omega[i][1] = omega[i][1]*factor_rotate + dtirotate*torque[i][1];
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omega[i][2] = omega[i][2]*factor_rotate + dtirotate*torque[i][2];
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}
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}
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}
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} else {
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if (rmass) {
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for (i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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itype = type[i];
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dtirotate = dtfrotate / (shape[itype][0]*shape[itype][0]*rmass[i]);
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omega[i][0] = omega[i][0]*factor_rotate + dtirotate*torque[i][0];
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omega[i][1] = omega[i][1]*factor_rotate + dtirotate*torque[i][1];
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omega[i][2] = omega[i][2]*factor_rotate + dtirotate*torque[i][2];
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}
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}
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} else {
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for (i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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itype = type[i];
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dtirotate = dtfrotate /
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(shape[itype][0]*shape[itype][0]*mass[itype]);
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omega[i][0] = omega[i][0]*factor_rotate + dtirotate*torque[i][0];
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omega[i][1] = omega[i][1]*factor_rotate + dtirotate*torque[i][1];
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omega[i][2] = omega[i][2]*factor_rotate + dtirotate*torque[i][2];
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}
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}
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}
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}
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// remap simulation box by 1/2 step
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// redo KSpace coeffs since volume has changed
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remap();
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if (kspace_flag) force->kspace->setup();
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}
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/* ---------------------------------------------------------------------- */
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void FixNPTSphere::final_integrate()
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{
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int i,itype;
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double dtfm,dtirotate;
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double **v = atom->v;
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double **f = atom->f;
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double **omega = atom->omega;
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double **torque = atom->torque;
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double *radius = atom->radius;
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double *rmass = atom->rmass;
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double *mass = atom->mass;
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double **shape = atom->shape;
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int *type = atom->type;
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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if (igroup == atom->firstgroup) nlocal = atom->nfirst;
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// set timestep here since dt may have changed or come via rRESPA
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double dtfrotate = dtf / INERTIA;
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// update v,omega of atoms in group
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// d_omega/dt = torque / inertia
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// 8 cases depending on radius vs shape, rmass vs mass, bias vs nobias
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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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if (radius) {
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if (rmass) {
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if (which == NOBIAS) {
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for (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] = (v[i][0] + dtfm*f[i][0]) * factor[0];
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v[i][1] = (v[i][1] + dtfm*f[i][1]) * factor[1];
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v[i][2] = (v[i][2] + dtfm*f[i][2]) * factor[2];
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dtirotate = dtfrotate / (radius[i]*radius[i]*rmass[i]);
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omega[i][0] = (omega[i][0] + dtirotate*torque[i][0]) *
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factor_rotate;
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omega[i][1] = (omega[i][1] + dtirotate*torque[i][1]) *
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factor_rotate;
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omega[i][2] = (omega[i][2] + dtirotate*torque[i][2]) *
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factor_rotate;
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}
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}
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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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dtfm = dtf / rmass[i];
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v[i][0] = (v[i][0] + dtfm*f[i][0]) * factor[0];
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v[i][1] = (v[i][1] + dtfm*f[i][1]) * factor[1];
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v[i][2] = (v[i][2] + dtfm*f[i][2]) * factor[2];
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temperature->restore_bias(i,v[i]);
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dtirotate = dtfrotate / (radius[i]*radius[i]*rmass[i]);
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omega[i][0] = (omega[i][0] + dtirotate*torque[i][0]) *
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factor_rotate;
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omega[i][1] = (omega[i][1] + dtirotate*torque[i][1]) *
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factor_rotate;
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omega[i][2] = (omega[i][2] + dtirotate*torque[i][2]) *
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factor_rotate;
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}
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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 (i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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itype = type[i];
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dtfm = dtf / mass[itype];
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v[i][0] = (v[i][0] + dtfm*f[i][0]) * factor[0];
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v[i][1] = (v[i][1] + dtfm*f[i][1]) * factor[1];
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v[i][2] = (v[i][2] + dtfm*f[i][2]) * factor[2];
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dtirotate = dtfrotate / (radius[i]*radius[i]*mass[itype]);
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omega[i][0] = (omega[i][0] + dtirotate*torque[i][0]) *
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factor_rotate;
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omega[i][1] = (omega[i][1] + dtirotate*torque[i][1]) *
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factor_rotate;
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omega[i][2] = (omega[i][2] + dtirotate*torque[i][2]) *
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factor_rotate;
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}
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}
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} else {
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for (i = 0; i < nlocal; i++) {
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double tmp = temperature->compute_scalar();
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if (mask[i] & groupbit) {
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itype = type[i];
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temperature->remove_bias(i,v[i]);
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dtfm = dtf / mass[itype];
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v[i][0] = (v[i][0] + dtfm*f[i][0]) * factor[0];
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v[i][1] = (v[i][1] + dtfm*f[i][1]) * factor[1];
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v[i][2] = (v[i][2] + dtfm*f[i][2]) * factor[2];
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temperature->restore_bias(i,v[i]);
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dtirotate = dtfrotate / (radius[i]*radius[i]*mass[itype]);
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omega[i][0] = (omega[i][0] + dtirotate*torque[i][0]) *
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factor_rotate;
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omega[i][1] = (omega[i][1] + dtirotate*torque[i][1]) *
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factor_rotate;
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omega[i][2] = (omega[i][2] + dtirotate*torque[i][2]) *
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factor_rotate;
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}
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}
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}
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}
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} else {
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if (rmass) {
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if (which == NOBIAS) {
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for (i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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itype = type[i];
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dtfm = dtf / rmass[i];
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v[i][0] = (v[i][0] + dtfm*f[i][0]) * factor[0];
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v[i][1] = (v[i][1] + dtfm*f[i][1]) * factor[1];
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v[i][2] = (v[i][2] + dtfm*f[i][2]) * factor[2];
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dtirotate = dtfrotate / (shape[itype][0]*shape[itype][0]*rmass[i]);
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omega[i][0] = (omega[i][0] + dtirotate*torque[i][0]) *
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factor_rotate;
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omega[i][1] = (omega[i][1] + dtirotate*torque[i][1]) *
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factor_rotate;
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omega[i][2] = (omega[i][2] + dtirotate*torque[i][2]) *
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factor_rotate;
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}
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}
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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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itype = type[i];
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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] = (v[i][0] + dtfm*f[i][0]) * factor[0];
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v[i][1] = (v[i][1] + dtfm*f[i][1]) * factor[1];
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v[i][2] = (v[i][2] + dtfm*f[i][2]) * factor[2];
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temperature->restore_bias(i,v[i]);
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dtirotate = dtfrotate / (shape[itype][0]*shape[itype][0]*rmass[i]);
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omega[i][0] = (omega[i][0] + dtirotate*torque[i][0]) *
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factor_rotate;
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omega[i][1] = (omega[i][1] + dtirotate*torque[i][1]) *
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factor_rotate;
|
||||
omega[i][2] = (omega[i][2] + dtirotate*torque[i][2]) *
|
||||
factor_rotate;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
} else {
|
||||
if (which == NOBIAS) {
|
||||
for (i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & groupbit) {
|
||||
itype = type[i];
|
||||
dtfm = dtf / mass[itype];
|
||||
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];
|
||||
|
||||
dtirotate = dtfrotate /
|
||||
(shape[itype][0]*shape[itype][0]*mass[itype]);
|
||||
omega[i][0] = (omega[i][0] + dtirotate*torque[i][0]) *
|
||||
factor_rotate;
|
||||
omega[i][1] = (omega[i][1] + dtirotate*torque[i][1]) *
|
||||
factor_rotate;
|
||||
omega[i][2] = (omega[i][2] + dtirotate*torque[i][2]) *
|
||||
factor_rotate;
|
||||
}
|
||||
}
|
||||
} else {
|
||||
double tmp = temperature->compute_scalar();
|
||||
for (i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & groupbit) {
|
||||
itype = type[i];
|
||||
temperature->remove_bias(i,v[i]);
|
||||
dtfm = dtf / mass[itype];
|
||||
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(i,v[i]);
|
||||
|
||||
dtirotate = dtfrotate /
|
||||
(shape[itype][0]*shape[itype][0]*mass[itype]);
|
||||
omega[i][0] = (omega[i][0] + dtirotate*torque[i][0]) *
|
||||
factor_rotate;
|
||||
omega[i][1] = (omega[i][1] + dtirotate*torque[i][1]) *
|
||||
factor_rotate;
|
||||
omega[i][2] = (omega[i][2] + dtirotate*torque[i][2]) *
|
||||
factor_rotate;
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
// compute new T,P
|
||||
|
||||
t_current = temperature->compute_scalar();
|
||||
if (press_couple == 0) {
|
||||
double tmp = pressure->compute_scalar();
|
||||
} else {
|
||||
temperature->compute_vector();
|
||||
pressure->compute_vector();
|
||||
}
|
||||
couple();
|
||||
|
||||
// trigger virial computation on next timestep
|
||||
|
||||
pressure->addstep(update->ntimestep+1);
|
||||
|
||||
// update eta_dot
|
||||
|
||||
f_eta = t_freq*t_freq * (t_current/t_target - 1.0);
|
||||
eta_dot += f_eta*dthalf;
|
||||
eta_dot *= drag_factor;
|
||||
|
||||
// update omega_dot
|
||||
// for non-varying dims, p_freq is 0.0, so omega_dot doesn't change
|
||||
|
||||
double f_omega,volume;
|
||||
if (dimension == 3) volume = domain->xprd*domain->yprd*domain->zprd;
|
||||
else volume = domain->xprd*domain->yprd;
|
||||
double denskt = atom->natoms*boltz*t_target / volume * nktv2p;
|
||||
|
||||
for (i = 0; i < 3; i++) {
|
||||
f_omega = p_freq[i]*p_freq[i] * (p_current[i]-p_target[i])/denskt;
|
||||
omega_dot[i] += f_omega*dthalf;
|
||||
omega_dot[i] *= drag_factor;
|
||||
}
|
||||
// create a new compute temp style
|
||||
// id = fix-ID + temp
|
||||
// compute group = all since pressure is always global (group all)
|
||||
// and thus its KE/temperature contribution should use group all
|
||||
|
||||
int n = strlen(id) + 6;
|
||||
id_temp = new char[n];
|
||||
strcpy(id_temp,id);
|
||||
strcat(id_temp,"_temp");
|
||||
|
||||
char **newarg = new char*[3];
|
||||
newarg[0] = id_temp;
|
||||
newarg[1] = (char *) "all";
|
||||
newarg[2] = (char *) "temp/sphere";
|
||||
|
||||
modify->add_compute(3,newarg);
|
||||
delete [] newarg;
|
||||
tflag = 1;
|
||||
|
||||
// create a new compute pressure style
|
||||
// id = fix-ID + press, compute group = all
|
||||
// pass id_temp as 4th arg to pressure constructor
|
||||
|
||||
n = strlen(id) + 7;
|
||||
id_press = new char[n];
|
||||
strcpy(id_press,id);
|
||||
strcat(id_press,"_press");
|
||||
|
||||
newarg = new char*[4];
|
||||
newarg[0] = id_press;
|
||||
newarg[1] = (char *) "all";
|
||||
newarg[2] = (char *) "pressure";
|
||||
newarg[3] = id_temp;
|
||||
modify->add_compute(4,newarg);
|
||||
delete [] newarg;
|
||||
pflag = 1;
|
||||
}
|
||||
|
||||
Reference in New Issue
Block a user