git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1660 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
278
src/fix_npt_sphere.cpp
Normal file
278
src/fix_npt_sphere.cpp
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@ -0,0 +1,278 @@
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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||||
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Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
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||||
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||||
See the README file in the top-level LAMMPS directory.
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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 "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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{
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if (!atom->omega_flag || !atom->torque_flag)
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error->all("Fix nvt/sphere requires atom attributes omega, torque");
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dttype = new double[atom->ntypes+1];
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}
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/* ---------------------------------------------------------------------- */
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FixNPTSphere::~FixNPTSphere()
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{
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delete [] dttype;
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}
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/* ---------------------------------------------------------------------- */
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void FixNPTSphere::init()
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{
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FixNPT::init();
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dtfrotate = dtf / INERTIA;
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if (!atom->shape)
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error->all("Fix npt/sphere requires atom attribute shape");
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double *mass = atom->mass;
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double **shape = atom->shape;
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for (int i = 1; i <= atom->ntypes; i++) {
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if (shape[i][0] != shape[i][1] || shape[i][0] != shape[i][2])
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error->all("Fix npt/sphere requires spherical particle shapes");
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dttype[i] = dtfrotate / (0.25*shape[i][0]*shape[i][0]*mass[i]);
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}
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}
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/* ----------------------------------------------------------------------
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1st half of Verlet update
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------------------------------------------------------------------------- */
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void FixNPTSphere::initial_integrate(int vflag)
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{
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int i;
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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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// v update only for atoms in group
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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 *mass = atom->mass;
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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 (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 if (which == BIAS) {
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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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// remap simulation box and all owned atoms by 1/2 step
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remap(0);
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// x update by full step only 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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// update angular momentum by 1/2 step
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// update quaternion a full step via Richardson iteration
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// returns new normalized quaternion
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for (i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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dtirotate = dttype[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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// remap simulation box and all owned atoms by 1/2 step
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// redo KSpace coeffs since volume has changed
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remap(0);
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if (kspace_flag) force->kspace->setup();
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}
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/* ----------------------------------------------------------------------
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2nd half of Verlet update
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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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// v update only for atoms in group
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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 *mass = atom->mass;
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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 (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 = dttype[itype];
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omega[i][0] = (omega[i][0] + dtirotate*torque[i][0]) * factor_rotate;
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omega[i][1] = (omega[i][1] + dtirotate*torque[i][1]) * factor_rotate;
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omega[i][2] = (omega[i][2] + dtirotate*torque[i][2]) * factor_rotate;
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}
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}
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} else if (which == BIAS) {
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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 / 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 = dttype[itype];
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omega[i][0] = (omega[i][0] + dtirotate*torque[i][0]) * factor_rotate;
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omega[i][1] = (omega[i][1] + dtirotate*torque[i][1]) * factor_rotate;
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omega[i][2] = (omega[i][2] + dtirotate*torque[i][2]) * factor_rotate;
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}
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}
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}
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// compute new T,P
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t_current = temperature->compute_scalar();
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if (press_couple == 0) {
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double tmp = pressure->compute_scalar();
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} else {
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temperature->compute_vector();
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pressure->compute_vector();
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}
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couple();
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// trigger virial computation on next timestep
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pressure->addstep(update->ntimestep+1);
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// update eta_dot
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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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// 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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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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}
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}
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/* ---------------------------------------------------------------------- */
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void FixNPTSphere::reset_dt()
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{
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FixNPT::reset_dt();
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dtfrotate = dtf / INERTIA;
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}
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38
src/fix_npt_sphere.h
Normal file
38
src/fix_npt_sphere.h
Normal file
@ -0,0 +1,38 @@
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
|
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Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#ifndef FIX_NPT_SPHERE_H
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#define FIX_NPT_SPHERE_H
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#include "fix_npt.h"
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namespace LAMMPS_NS {
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class FixNPTSphere : public FixNPT {
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public:
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FixNPTSphere(class LAMMPS *, int, char **);
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~FixNPTSphere();
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void init();
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void initial_integrate(int);
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void final_integrate();
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void reset_dt();
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private:
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double dtfrotate;
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double *dttype;
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double factor_rotate;
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};
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}
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#endif
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221
src/fix_nvt_sphere.cpp
Normal file
221
src/fix_nvt_sphere.cpp
Normal file
@ -0,0 +1,221 @@
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/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "string.h"
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#include "stdlib.h"
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||||
#include "math.h"
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#include "fix_nvt_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 "comm.h"
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#include "group.h"
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||||
#include "update.h"
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#include "modify.h"
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#include "compute.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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||||
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enum{NOBIAS,BIAS};
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/* ---------------------------------------------------------------------- */
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FixNVTSphere::FixNVTSphere(LAMMPS *lmp, int narg, char **arg) :
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FixNVT(lmp, narg, arg)
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{
|
||||
if (!atom->omega_flag || !atom->torque_flag)
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error->all("Fix nvt/sphere requires atom attributes omega, torque");
|
||||
|
||||
dttype = new double[atom->ntypes+1];
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
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FixNVTSphere::~FixNVTSphere()
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{
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||||
delete [] dttype;
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||||
}
|
||||
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||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixNVTSphere::init()
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{
|
||||
FixNVT::init();
|
||||
dtfrotate = dtf / INERTIA;
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||||
|
||||
if (!atom->shape)
|
||||
error->all("Fix nvt/sphere requires atom attribute shape");
|
||||
|
||||
double *mass = atom->mass;
|
||||
double **shape = atom->shape;
|
||||
for (int i = 1; i <= atom->ntypes; i++) {
|
||||
if (shape[i][0] != shape[i][1] || shape[i][0] != shape[i][2])
|
||||
error->all("Fix nvt/sphere requires spherical particle shapes");
|
||||
dttype[i] = dtfrotate / (0.25*shape[i][0]*shape[i][0]*mass[i]);
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixNVTSphere::initial_integrate(int vflag)
|
||||
{
|
||||
int itype;
|
||||
double dtfm,dtirotate;
|
||||
|
||||
double delta = update->ntimestep - update->beginstep;
|
||||
delta /= update->endstep - update->beginstep;
|
||||
t_target = t_start + delta * (t_stop-t_start);
|
||||
|
||||
// update eta_dot
|
||||
|
||||
f_eta = t_freq*t_freq * (t_current/t_target - 1.0);
|
||||
eta_dot += f_eta*dthalf;
|
||||
eta_dot *= drag_factor;
|
||||
eta += dtv*eta_dot;
|
||||
factor = exp(-dthalf*eta_dot);
|
||||
|
||||
// update v and x of only atoms in group
|
||||
|
||||
double **x = atom->x;
|
||||
double **v = atom->v;
|
||||
double **f = atom->f;
|
||||
double **quat = atom->quat;
|
||||
double **omega = atom->omega;
|
||||
double **torque = atom->torque;
|
||||
double *mass = atom->mass;
|
||||
int *type = atom->type;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
|
||||
|
||||
if (which == NOBIAS) {
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & groupbit) {
|
||||
itype = type[i];
|
||||
|
||||
dtfm = dtf / mass[itype];
|
||||
v[i][0] = v[i][0]*factor + dtfm*f[i][0];
|
||||
v[i][1] = v[i][1]*factor + dtfm*f[i][1];
|
||||
v[i][2] = v[i][2]*factor + dtfm*f[i][2];
|
||||
x[i][0] += dtv * v[i][0];
|
||||
x[i][1] += dtv * v[i][1];
|
||||
x[i][2] += dtv * v[i][2];
|
||||
|
||||
dtirotate = dttype[itype];
|
||||
omega[i][0] = omega[i][0]*factor + dtirotate*torque[i][0];
|
||||
omega[i][1] = omega[i][1]*factor + dtirotate*torque[i][1];
|
||||
omega[i][2] = omega[i][2]*factor + dtirotate*torque[i][2];
|
||||
}
|
||||
}
|
||||
|
||||
} else if (which == BIAS) {
|
||||
for (int 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]*factor + dtfm*f[i][0];
|
||||
v[i][1] = v[i][1]*factor + dtfm*f[i][1];
|
||||
v[i][2] = v[i][2]*factor + dtfm*f[i][2];
|
||||
temperature->restore_bias(i,v[i]);
|
||||
x[i][0] += dtv * v[i][0];
|
||||
x[i][1] += dtv * v[i][1];
|
||||
x[i][2] += dtv * v[i][2];
|
||||
|
||||
dtirotate = dttype[itype];
|
||||
omega[i][0] = omega[i][0]*factor + dtirotate*torque[i][0];
|
||||
omega[i][1] = omega[i][1]*factor + dtirotate*torque[i][1];
|
||||
omega[i][2] = omega[i][2]*factor + dtirotate*torque[i][2];
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixNVTSphere::final_integrate()
|
||||
{
|
||||
int itype;
|
||||
double dtfm,dtirotate;
|
||||
|
||||
// update v of only atoms in group
|
||||
|
||||
double **v = atom->v;
|
||||
double **f = atom->f;
|
||||
double **omega = atom->omega;
|
||||
double **torque = atom->torque;
|
||||
double *mass = atom->mass;
|
||||
int *type = atom->type;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
|
||||
|
||||
if (which == NOBIAS) {
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & groupbit) {
|
||||
itype = type[i];
|
||||
|
||||
dtfm = dtf / mass[itype] * factor;
|
||||
v[i][0] = v[i][0]*factor + dtfm*f[i][0];
|
||||
v[i][1] = v[i][1]*factor + dtfm*f[i][1];
|
||||
v[i][2] = v[i][2]*factor + dtfm*f[i][2];
|
||||
|
||||
dtirotate = dttype[itype];
|
||||
omega[i][0] = (omega[i][0] + dtirotate*torque[i][0]) * factor;
|
||||
omega[i][1] = (omega[i][1] + dtirotate*torque[i][1]) * factor;
|
||||
omega[i][2] = (omega[i][2] + dtirotate*torque[i][2]) * factor;
|
||||
}
|
||||
}
|
||||
|
||||
} else {
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & groupbit) {
|
||||
itype = type[i];
|
||||
|
||||
temperature->remove_bias(i,v[i]);
|
||||
dtfm = dtf / mass[itype] * factor;
|
||||
v[i][0] = v[i][0]*factor + dtfm*f[i][0];
|
||||
v[i][1] = v[i][1]*factor + dtfm*f[i][1];
|
||||
v[i][2] = v[i][2]*factor + dtfm*f[i][2];
|
||||
temperature->restore_bias(i,v[i]);
|
||||
|
||||
dtirotate = dttype[itype];
|
||||
omega[i][0] = (omega[i][0] + dtirotate*torque[i][0]) * factor;
|
||||
omega[i][1] = (omega[i][1] + dtirotate*torque[i][1]) * factor;
|
||||
omega[i][2] = (omega[i][2] + dtirotate*torque[i][2]) * factor;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
// compute current T
|
||||
|
||||
t_current = temperature->compute_scalar();
|
||||
|
||||
// update eta_dot
|
||||
|
||||
f_eta = t_freq*t_freq * (t_current/t_target - 1.0);
|
||||
eta_dot += f_eta*dthalf;
|
||||
eta_dot *= drag_factor;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixNVTSphere::reset_dt()
|
||||
{
|
||||
FixNVT::reset_dt();
|
||||
dtfrotate = dtf / INERTIA;
|
||||
}
|
||||
37
src/fix_nvt_sphere.h
Normal file
37
src/fix_nvt_sphere.h
Normal file
@ -0,0 +1,37 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifndef FIX_NVT_SPHERE_H
|
||||
#define FIX_NVT_SPHERE_H
|
||||
|
||||
#include "fix_nvt.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class FixNVTSphere : public FixNVT {
|
||||
public:
|
||||
FixNVTSphere(class LAMMPS *, int, char **);
|
||||
~FixNVTSphere();
|
||||
void init();
|
||||
void initial_integrate(int);
|
||||
void final_integrate();
|
||||
void reset_dt();
|
||||
|
||||
private:
|
||||
double dtfrotate;
|
||||
double *dttype;
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
Reference in New Issue
Block a user