forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11645 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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sjplimp
parent
e8154be88c
commit
48ce1b589e
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@ -21,6 +21,7 @@
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#include "fix_temp_csvr.h"
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#include "atom.h"
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#include "force.h"
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#include "memory.h"
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#include "comm.h"
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#include "input.h"
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#include "variable.h"
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@ -47,9 +48,7 @@ FixTempCSVR::FixTempCSVR(LAMMPS *lmp, int narg, char **arg) :
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// CSVR thermostat should be applied every step
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nevery = 1;
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scalar_flag = 1;
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global_freq = nevery;
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extscalar = 1;
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tstr = NULL;
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if (strstr(arg[3],"v_") == arg[3]) {
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@ -90,6 +89,8 @@ FixTempCSVR::FixTempCSVR(LAMMPS *lmp, int narg, char **arg) :
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random = new RanMars(lmp,seed + comm->me);
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vhold = NULL;
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nmax = -1;
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energy = 0.0;
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}
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@ -105,6 +106,9 @@ FixTempCSVR::~FixTempCSVR()
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delete [] id_temp;
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delete random;
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memory->destroy(vhold);
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vhold = NULL;
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nmax = -1;
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}
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/* ---------------------------------------------------------------------- */
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@ -113,7 +117,6 @@ int FixTempCSVR::setmask()
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{
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int mask = 0;
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mask |= END_OF_STEP;
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mask |= THERMO_ENERGY;
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return mask;
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}
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@ -121,6 +124,16 @@ int FixTempCSVR::setmask()
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void FixTempCSVR::init()
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{
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// we cannot handle shake correctly at the moment.
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int has_shake = 0;
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for (int i = 0; i < modify->nfix; i++)
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if (strcmp(modify->fix[i]->style,"shake") == 0) ++has_shake;
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if (has_shake > 0)
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error->all(FLERR,"Fix temp/csvr is not compatible with fix shake");
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// check variable
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if (tstr) {
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@ -144,14 +157,13 @@ void FixTempCSVR::init()
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void FixTempCSVR::end_of_step()
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{
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double t_current = temperature->compute_scalar();
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double delta = update->ntimestep - update->beginstep;
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if (delta != 0.0) delta /= update->endstep - update->beginstep;
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// set current t_target
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// if variable temp, evaluate variable, wrap with clear/add
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double delta = update->ntimestep - update->beginstep;
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if (delta != 0.0) delta /= update->endstep - update->beginstep;
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if (tstyle == CONSTANT)
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t_target = t_start + delta * (t_stop-t_start);
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else {
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@ -163,82 +175,62 @@ void FixTempCSVR::end_of_step()
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modify->addstep_compute(update->ntimestep + nevery);
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}
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// Langevin thermostat, implemented as decribed in
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// Bussi and Parrinello, Phys. Rev. E (2007).
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// it is a linear combination of old velocities and new,
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// randomly chosen, velocity, with proper coefficients
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double * const * const v = atom->v;
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const int * const mask = atom->mask;
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const int * const type = atom->type;
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const int nlocal = atom->nlocal;
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double **v = atom->v;
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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const double c1 = exp(-update->dt/t_period);
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// adjust holding space, if needed and copy existing velocities
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if (atom->rmass_flag) { // per atom masses
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const double * const rmass = atom->rmass;
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if (nmax < atom->nlocal) {
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nmax = atom->nlocal + 1;
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memory->destroy(vhold);
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memory->create(vhold,nmax,3,"csvr:vhold");
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}
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// The CSVR thermostat is a linear combination of old and new velocities,
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// where the new ones are randomly chosen from a gaussian distribution.
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// see Bussi and Parrinello, Phys. Rev. E (2007).
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for (int i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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double m;
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if (atom->rmass_flag) m = atom->rmass[i];
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else m = atom->mass[type[i]];
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const double factor = 1.0/sqrt(m);
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const double vx = random->gaussian() * factor;
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vhold[i][0] = v[i][0];
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v[i][0] = vx;
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const double vy = random->gaussian() * factor;
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vhold[i][1] = v[i][1];
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v[i][1] = vy;
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const double vz = random->gaussian() * factor;
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vhold[i][2] = v[i][2];
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v[i][2] = vz;
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}
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}
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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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const double m = rmass[i];
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const double c2 = sqrt((1.0-c1*c1)*t_target/m);
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for (int j = 0; j < 3; ++j) {
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energy += 0.5*m*v[i][j]*v[i][j];
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v[i][j] *= c1;
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v[i][j] += c2*random->gaussian();
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energy -= 0.5*m*v[i][j]*v[i][j];
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}
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}
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}
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} else {
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for (int i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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const double m = rmass[i];
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const double c2 = sqrt((1.0-c1*c1)*t_target/m);
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temperature->remove_bias(i,v[i]);
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for (int j = 0; j < 3; ++j) {
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energy += 0.5*rmass[i]*v[i][j]*v[i][j];
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v[i][j] *= c1;
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v[i][j] += c2*random->gaussian();
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energy -= 0.5*rmass[i]*v[i][j]*v[i][j];
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}
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temperature->restore_bias(i,v[i]);
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}
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// mixing factors
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const double c1 = exp(-update->dt/t_period);
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const double c2 = sqrt((1.0-c1*c1)*t_target/temperature->compute_scalar());
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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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v[i][0] = vhold[i][0]*c1 + v[i][0]*c2;
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v[i][1] = vhold[i][1]*c1 + v[i][1]*c2;
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v[i][2] = vhold[i][2]*c1 + v[i][2]*c2;
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}
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}
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} else { // per atom type masses
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const double * const mass = atom->mass;
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const int * const type = atom->type;
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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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const double m = mass[type[i]];
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const double c2 = sqrt((1.0-c1*c1)*t_target/m);
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for (int j = 0; j < 3; ++j) {
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energy += 0.5*m*v[i][j]*v[i][j];
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v[i][j] *= c1;
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v[i][j] += c2*random->gaussian();
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energy -= 0.5*m*v[i][j]*v[i][j];
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}
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}
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}
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} else {
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for (int i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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const double m = mass[type[i]];
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const double c2 = sqrt((1.0-c1*c1)*t_target/m);
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temperature->remove_bias(i,v[i]);
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for (int j = 0; j < 3; ++j) {
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energy += 0.5*m*v[i][j]*v[i][j];
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v[i][j] *= c1;
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v[i][j] += c2*random->gaussian();
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energy -= 0.5*m*v[i][j]*v[i][j];
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}
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temperature->restore_bias(i,v[i]);
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}
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} else {
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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,vhold[i]);
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v[i][0] = vhold[i][0]*c1 + v[i][0]*c2;
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v[i][1] = vhold[i][1]*c1 + v[i][1]*c2;
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v[i][2] = vhold[i][2]*c1 + v[i][2]*c2;
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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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@ -281,13 +273,6 @@ void FixTempCSVR::reset_target(double t_new)
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t_target = t_start = t_stop = t_new;
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}
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/* ---------------------------------------------------------------------- */
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double FixTempCSVR::compute_scalar()
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{
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return energy;
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}
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/* ----------------------------------------------------------------------
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extract thermostat properties
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------------------------------------------------------------------------- */
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@ -33,13 +33,13 @@ class FixTempCSVR : public Fix {
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void end_of_step();
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int modify_param(int, char **);
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void reset_target(double);
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double compute_scalar();
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virtual void *extract(const char *, int &);
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private:
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int which;
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double t_start,t_stop,t_period,t_target;
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double **vhold;
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double energy;
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int nmax,which;
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int tstyle,tvar;
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char *tstr;
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