git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11645 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2014-03-19 18:28:50 +00:00
parent e8154be88c
commit 48ce1b589e
2 changed files with 72 additions and 87 deletions

View File

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

View File

@ -33,13 +33,13 @@ class FixTempCSVR : public Fix {
void end_of_step();
int modify_param(int, char **);
void reset_target(double);
double compute_scalar();
virtual void *extract(const char *, int &);
private:
int which;
double t_start,t_stop,t_period,t_target;
double **vhold;
double energy;
int nmax,which;
int tstyle,tvar;
char *tstr;