git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3951 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
673
src/fix_nvt.cpp
673
src/fix_nvt.cpp
@ -11,693 +11,38 @@
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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/* ----------------------------------------------------------------------
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Contributing authors: Mark Stevens (SNL)
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Andy Ballard (U Maryland) for Nose/Hoover chains
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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_nvt.h"
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#include "atom.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 "respa.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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enum{NOBIAS,BIAS};
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/* ---------------------------------------------------------------------- */
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FixNVT::FixNVT(LAMMPS *lmp, int narg, char **arg) :
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Fix(lmp, narg, arg)
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FixNH(lmp, narg, arg)
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{
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if (narg < 6) error->all("Illegal fix nvt command");
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restart_global = 1;
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time_integrate = 1;
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scalar_flag = 1;
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global_freq = 1;
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extscalar = 1;
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t_start = atof(arg[3]);
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t_stop = atof(arg[4]);
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double t_period = atof(arg[5]);
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drag = 0.0;
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chain = 1;
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int iarg = 6;
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while (iarg < narg) {
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if (strcmp(arg[iarg],"drag") == 0) {
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if (iarg+2 > narg) error->all("Illegal fix nvt command");
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drag = atof(arg[iarg+1]);
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if (drag < 0.0) error->all("Illegal fix nvt command");
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iarg += 2;
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} else if (strcmp(arg[iarg],"chain") == 0) {
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if (iarg+2 > narg) error->all("Illegal fix nvt command");
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if (strcmp(arg[iarg+1],"yes") == 0) chain = 1;
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else if (strcmp(arg[iarg+1],"no") == 0) chain = 0;
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else error->all("Illegal fix nvt command");
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iarg += 2;
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} else error->all("Illegal fix nvt command");
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}
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// error checks
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// convert input period to frequency
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if (t_start < 0.0 || t_stop <= 0.0)
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error->all("Target T for fix nvt cannot be 0.0");
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if (t_period <= 0.0) error->all("Fix nvt period must be > 0.0");
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t_freq = 1.0 / t_period;
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if (!tstat_flag)
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error->all("Temperature control must be used with fix nvt");
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if (pstat_flag)
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error->all("Pressure control can not be used with fix nvt");
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// create a new compute temp style
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// id = fix-ID + temp, compute group = fix group
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// id = fix-ID + temp
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int n = strlen(id) + 6;
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id_temp = new char[n];
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strcpy(id_temp,id);
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strcat(id_temp,"_temp");
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char **newarg = new char*[3];
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newarg[0] = id_temp;
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newarg[1] = group->names[igroup];
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if (strcmp(style,"nvt") == 0)
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newarg[2] = (char *) "temp";
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else if (strcmp(style,"nvt/asphere") == 0)
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newarg[2] = (char *) "temp/asphere";
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else if (strcmp(style,"nvt/sllod") == 0)
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newarg[2] = (char *) "temp/deform";
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else if (strcmp(style,"nvt/sphere") == 0)
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newarg[2] = (char *) "temp/sphere";
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newarg[2] = (char *) "temp";
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modify->add_compute(3,newarg);
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delete [] newarg;
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tflag = 1;
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// Nose/Hoover temp init
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eta = eta_dot = 0.0;
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eta2 = eta2_dot = 0.0;
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}
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/* ---------------------------------------------------------------------- */
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FixNVT::~FixNVT()
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{
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// delete temperature if fix created it
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if (tflag) modify->delete_compute(id_temp);
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delete [] id_temp;
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}
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/* ---------------------------------------------------------------------- */
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int FixNVT::setmask()
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{
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int mask = 0;
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mask |= INITIAL_INTEGRATE;
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mask |= FINAL_INTEGRATE;
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mask |= THERMO_ENERGY;
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mask |= INITIAL_INTEGRATE_RESPA;
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mask |= FINAL_INTEGRATE_RESPA;
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return mask;
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}
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/* ---------------------------------------------------------------------- */
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void FixNVT::init()
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{
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int icompute = modify->find_compute(id_temp);
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if (icompute < 0) error->all("Temperature ID for fix nvt does not exist");
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temperature = modify->compute[icompute];
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if (temperature->tempbias) which = BIAS;
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else which = NOBIAS;
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// set timesteps and frequencies
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dtv = update->dt;
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dtf = 0.5 * update->dt * force->ftm2v;
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dthalf = 0.5 * update->dt;
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dt4 = 0.25 * update->dt;
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dt8 = 0.125 * update->dt;
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drag_factor = 1.0 - (update->dt * t_freq * drag);
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if (strcmp(update->integrate_style,"respa") == 0) {
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nlevels_respa = ((Respa *) update->integrate)->nlevels;
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step_respa = ((Respa *) update->integrate)->step;
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}
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}
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/* ---------------------------------------------------------------------- */
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void FixNVT::setup(int vflag)
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{
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t_target = t_start; // used by compute_scalar()
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t_current = temperature->compute_scalar();
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}
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/* ---------------------------------------------------------------------- */
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void FixNVT::initial_integrate(int vflag)
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{
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double dtfm;
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double delta = update->ntimestep - update->beginstep;
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delta /= update->endstep - update->beginstep;
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t_target = t_start + delta * (t_stop-t_start);
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// update eta, eta_dot, eta2, eta2_dot
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int nlocal = atom->nlocal;
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if (igroup == atom->firstgroup) nlocal = atom->nfirst;
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if (chain) {
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eta2_dot += (temperature->dof * eta_dot*eta_dot - t_freq*t_freq) * dt4;
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factor2 = exp(-dt8*eta2_dot);
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eta_dot *= factor2;
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f_eta = t_freq*t_freq * (t_current/t_target - 1.0);
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eta_dot += f_eta*dt4;
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eta_dot *= drag_factor;
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eta_dot *= factor2;
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eta += dthalf*eta_dot;
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eta2 += dthalf*eta2_dot;
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} else {
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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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}
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factor = exp(-dthalf*eta_dot);
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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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double *rmass = atom->rmass;
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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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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] = v[i][0]*factor + dtfm*f[i][0];
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v[i][1] = v[i][1]*factor + dtfm*f[i][1];
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v[i][2] = v[i][2]*factor + dtfm*f[i][2];
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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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} else {
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double tmp = temperature->compute_scalar();
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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] = v[i][0]*factor + dtfm*f[i][0];
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v[i][1] = v[i][1]*factor + dtfm*f[i][1];
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v[i][2] = v[i][2]*factor + dtfm*f[i][2];
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temperature->restore_bias(i,v[i]);
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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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}
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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] = v[i][0]*factor + dtfm*f[i][0];
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v[i][1] = v[i][1]*factor + dtfm*f[i][1];
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v[i][2] = v[i][2]*factor + dtfm*f[i][2];
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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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} else {
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double tmp = temperature->compute_scalar();
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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] = v[i][0]*factor + dtfm*f[i][0];
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v[i][1] = v[i][1]*factor + dtfm*f[i][1];
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v[i][2] = v[i][2]*factor + dtfm*f[i][2];
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temperature->restore_bias(i,v[i]);
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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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}
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}
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if (chain) {
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eta_dot *= factor2;
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f_eta = t_freq*t_freq * (factor * factor * t_current/t_target - 1.0);
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eta_dot += f_eta * dt4;
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eta_dot *= factor2;
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eta2_dot += (temperature->dof * eta_dot*eta_dot - t_freq*t_freq) * dt4;
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}
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}
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/* ---------------------------------------------------------------------- */
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void FixNVT::final_integrate()
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{
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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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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 (chain) factor = 1.0;
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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] * factor;
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v[i][0] = v[i][0]*factor + dtfm*f[i][0];
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v[i][1] = v[i][1]*factor + dtfm*f[i][1];
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v[i][2] = v[i][2]*factor + 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 (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] * factor;
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v[i][0] = v[i][0]*factor + dtfm*f[i][0];
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v[i][1] = v[i][1]*factor + dtfm*f[i][1];
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v[i][2] = v[i][2]*factor + 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 (int i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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dtfm = dtf / mass[type[i]] * factor;
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v[i][0] = v[i][0]*factor + dtfm*f[i][0];
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v[i][1] = v[i][1]*factor + dtfm*f[i][1];
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v[i][2] = v[i][2]*factor + 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 (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]] * factor;
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v[i][0] = v[i][0]*factor + dtfm*f[i][0];
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v[i][1] = v[i][1]*factor + dtfm*f[i][1];
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v[i][2] = v[i][2]*factor + 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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// compute current T
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t_current = temperature->compute_scalar();
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// update eta, eta_dot, eta2, eta2_dot
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// chains require additional velocity update and recompute of current T
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if (chain) {
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eta2_dot += (temperature->dof * eta_dot*eta_dot - t_freq*t_freq) * dt4;
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factor2 = exp(-dt8*eta2_dot);
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eta_dot *= factor2;
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f_eta = t_freq*t_freq * (t_current/t_target - 1.0);
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eta_dot += f_eta*dt4;
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eta_dot *= drag_factor;
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eta_dot *= factor2;
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eta += dthalf*eta_dot;
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eta2 += dthalf*eta2_dot;
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factor = exp(-dthalf*eta_dot);
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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 / mass[type[i]];
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v[i][0] *= factor;
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v[i][1] *= factor;
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v[i][2] *= factor;
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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 (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] *= factor;
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v[i][1] *= factor;
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v[i][2] *= factor;
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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 (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] *= factor;
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v[i][1] *= factor;
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v[i][2] *= factor;
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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 (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] *= factor;
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v[i][1] *= factor;
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v[i][2] *= factor;
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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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t_current = temperature->compute_scalar();
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eta_dot *= factor2;
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f_eta = t_freq*t_freq * (t_current/t_target - 1.0);
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eta_dot += f_eta * dt4;
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eta_dot *= factor2;
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eta2_dot += (temperature->dof * eta_dot*eta_dot - t_freq*t_freq) * dt4;
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} else {
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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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}
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||||
}
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||||
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/* ---------------------------------------------------------------------- */
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||||
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void FixNVT::initial_integrate_respa(int vflag, int ilevel, int iloop)
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{
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// set timesteps by level
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||||
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double dtfm;
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dtv = step_respa[ilevel];
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dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
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||||
dthalf = 0.5 * step_respa[ilevel];
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||||
|
||||
// atom quantities
|
||||
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||||
double **x = atom->x;
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||||
double **v = atom->v;
|
||||
double **f = atom->f;
|
||||
double *rmass = atom->rmass;
|
||||
double *mass = atom->mass;
|
||||
int *type = atom->type;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
|
||||
|
||||
// outermost level - update eta_dot and apply to v with factor
|
||||
// all other levels - NVE update of v (factor = 1)
|
||||
// innermost level - also update x
|
||||
|
||||
if (ilevel == nlevels_respa-1) {
|
||||
double delta = update->ntimestep - update->beginstep;
|
||||
delta /= update->endstep - update->beginstep;
|
||||
t_target = t_start + delta * (t_stop-t_start);
|
||||
|
||||
if (chain) {
|
||||
eta2_dot += (temperature->dof * eta_dot*eta_dot - t_freq*t_freq) * dt4;
|
||||
factor2 = exp(-dt8*eta2_dot);
|
||||
eta_dot *= factor2;
|
||||
f_eta = t_freq*t_freq * (t_current/t_target - 1.0);
|
||||
eta_dot += f_eta*dt4;
|
||||
eta_dot *= drag_factor;
|
||||
eta_dot *= factor2;
|
||||
eta += dthalf*eta_dot;
|
||||
eta2 += dthalf*eta2_dot;
|
||||
|
||||
} else {
|
||||
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);
|
||||
|
||||
} else factor = 1.0;
|
||||
|
||||
if (rmass) {
|
||||
if (which == NOBIAS) {
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & groupbit) {
|
||||
dtfm = dtf / rmass[i];
|
||||
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];
|
||||
}
|
||||
}
|
||||
} else {
|
||||
double tmp = temperature->compute_scalar();
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & groupbit) {
|
||||
temperature->remove_bias(i,v[i]);
|
||||
dtfm = dtf / rmass[i];
|
||||
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]);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
} else {
|
||||
if (which == NOBIAS) {
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & groupbit) {
|
||||
dtfm = dtf / mass[type[i]];
|
||||
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];
|
||||
}
|
||||
}
|
||||
|
||||
} else {
|
||||
double tmp = temperature->compute_scalar();
|
||||
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] = 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]);
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
if (ilevel == 0) {
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & groupbit) {
|
||||
x[i][0] += dtv * v[i][0];
|
||||
x[i][1] += dtv * v[i][1];
|
||||
x[i][2] += dtv * v[i][2];
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
if (ilevel == nlevels_respa-1 && chain) {
|
||||
eta_dot *= factor2;
|
||||
f_eta = t_freq*t_freq * (factor * factor * t_current/t_target - 1.0);
|
||||
eta_dot += f_eta * dt4;
|
||||
eta_dot *= factor2;
|
||||
eta2_dot += (temperature->dof * eta_dot*eta_dot - t_freq*t_freq) * dt4;
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixNVT::final_integrate_respa(int ilevel, int iloop)
|
||||
{
|
||||
// set timesteps by level
|
||||
|
||||
double dtfm;
|
||||
dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
|
||||
dthalf = 0.5 * step_respa[ilevel];
|
||||
|
||||
// outermost level - update eta_dot and apply to v via final_integrate()
|
||||
// all other levels - NVE update of v
|
||||
|
||||
if (ilevel == nlevels_respa-1) final_integrate();
|
||||
else {
|
||||
double **v = atom->v;
|
||||
double **f = atom->f;
|
||||
double *rmass = atom->rmass;
|
||||
double *mass = atom->mass;
|
||||
int *type = atom->type;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
|
||||
|
||||
if (rmass) {
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & groupbit) {
|
||||
dtfm = dtf / rmass[i];
|
||||
v[i][0] += dtfm*f[i][0];
|
||||
v[i][1] += dtfm*f[i][1];
|
||||
v[i][2] += dtfm*f[i][2];
|
||||
}
|
||||
}
|
||||
|
||||
} else {
|
||||
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];
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
pack entire state of Fix into one write
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void FixNVT::write_restart(FILE *fp)
|
||||
{
|
||||
int n = 0;
|
||||
double list[4];
|
||||
list[n++] = eta;
|
||||
list[n++] = eta_dot;
|
||||
list[n++] = eta2;
|
||||
list[n++] = eta2_dot;
|
||||
|
||||
if (comm->me == 0) {
|
||||
int size = n * sizeof(double);
|
||||
fwrite(&size,sizeof(int),1,fp);
|
||||
fwrite(list,sizeof(double),n,fp);
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
use state info from restart file to restart the Fix
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void FixNVT::restart(char *buf)
|
||||
{
|
||||
int n = 0;
|
||||
double *list = (double *) buf;
|
||||
eta = list[n++];
|
||||
eta_dot = list[n++];
|
||||
eta2 = list[n++];
|
||||
eta2_dot = list[n++];
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
int FixNVT::modify_param(int narg, char **arg)
|
||||
{
|
||||
if (strcmp(arg[0],"temp") == 0) {
|
||||
if (narg < 2) error->all("Illegal fix_modify command");
|
||||
if (tflag) {
|
||||
modify->delete_compute(id_temp);
|
||||
tflag = 0;
|
||||
}
|
||||
delete [] id_temp;
|
||||
int n = strlen(arg[1]) + 1;
|
||||
id_temp = new char[n];
|
||||
strcpy(id_temp,arg[1]);
|
||||
|
||||
int icompute = modify->find_compute(id_temp);
|
||||
if (icompute < 0) error->all("Could not find fix_modify temperature ID");
|
||||
temperature = modify->compute[icompute];
|
||||
|
||||
if (temperature->tempflag == 0)
|
||||
error->all("Fix_modify temperature ID does not compute temperature");
|
||||
if (temperature->igroup != igroup && comm->me == 0)
|
||||
error->warning("Group for fix_modify temp != fix group");
|
||||
return 2;
|
||||
}
|
||||
|
||||
return 0;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixNVT::reset_target(double t_new)
|
||||
{
|
||||
t_start = t_stop = t_new;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixNVT::reset_dt()
|
||||
{
|
||||
dtv = update->dt;
|
||||
dtf = 0.5 * update->dt * force->ftm2v;
|
||||
dthalf = 0.5 * update->dt;
|
||||
dt4 = 0.25 * update->dt;
|
||||
dt8 = 0.125 * update->dt;
|
||||
|
||||
drag_factor = 1.0 - (update->dt * t_freq * drag);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double FixNVT::compute_scalar()
|
||||
{
|
||||
double ke = temperature->dof * force->boltz * t_target;
|
||||
double energy = ke * (eta + 0.5*eta_dot*eta_dot/(t_freq*t_freq));
|
||||
return energy;
|
||||
}
|
||||
|
||||
Reference in New Issue
Block a user