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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7236 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2011-11-28 22:41:16 +00:00
parent 33f77e2917
commit c032f772ac
2 changed files with 124 additions and 25 deletions
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139
src/fix_langevin.cpp
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@ -31,6 +31,8 @@
#include "region.h"
#include "respa.h"
#include "comm.h"
#include "input.h"
#include "variable.h"
#include "random_mars.h"
#include "memory.h"
#include "error.h"
@ -39,6 +41,7 @@
using namespace LAMMPS_NS;
enum{NOBIAS,BIAS};
enum{CONSTANT,EQUAL,ATOM};
#define SINERTIA 0.4 // moment of inertia prefactor for sphere
#define EINERTIA 0.2 // moment of inertia prefactor for ellipsoid
@ -55,7 +58,16 @@ FixLangevin::FixLangevin(LAMMPS *lmp, int narg, char **arg) :
extscalar = 1;
nevery = 1;
t_start = atof(arg[3]);
tstr = NULL;
if (strstr(arg[3],"v_") == arg[3]) {
int n = strlen(&arg[3][2]) + 1;
tstr = new char[n];
strcpy(tstr,&arg[3][2]);
} else {
t_start = atof(arg[3]);
tstyle = CONSTANT;
}
t_stop = atof(arg[4]);
t_period = atof(arg[5]);
int seed = atoi(arg[6]);
@ -133,9 +145,10 @@ FixLangevin::FixLangevin(LAMMPS *lmp, int narg, char **arg) :
// flangevin is unallocated until first call to setup()
// compute_scalar checks for this and returns 0.0 if flangevin is NULL
flangevin = NULL;
nmax = 0;
energy = 0.0;
flangevin = NULL;
tforce = NULL;
maxatom1 = maxatom2 = 0;
}
/* ---------------------------------------------------------------------- */
@ -143,11 +156,13 @@ FixLangevin::FixLangevin(LAMMPS *lmp, int narg, char **arg) :
FixLangevin::~FixLangevin()
{
delete random;
delete [] tstr;
delete [] gfactor1;
delete [] gfactor2;
delete [] ratio;
delete [] id_temp;
memory->destroy(flangevin);
memory->destroy(tforce);
}
/* ---------------------------------------------------------------------- */
@ -171,6 +186,17 @@ void FixLangevin::init()
if (aflag && !atom->ellipsoid_flag)
error->all(FLERR,"Fix langevin angmom require atom style ellipsoid");
// check variable
if (tstr) {
tvar = input->variable->find(tstr);
if (tvar < 0)
error->all(FLERR,"Variable name for fix langevin does not exist");
if (input->variable->equalstyle(tvar)) tstyle = EQUAL;
else if (input->variable->atomstyle(tvar)) tstyle = ATOM;
else error->all(FLERR,"Variable for fix langevin is invalid style");
}
// if oflag or aflag set, check that all group particles are finite-size
if (oflag) {
@ -247,7 +273,7 @@ void FixLangevin::post_force_respa(int vflag, int ilevel, int iloop)
void FixLangevin::post_force_no_tally()
{
double gamma1,gamma2;
double gamma1,gamma2,t_target;
double **v = atom->v;
double **f = atom->f;
@ -258,8 +284,36 @@ void FixLangevin::post_force_no_tally()
double delta = update->ntimestep - update->beginstep;
delta /= update->endstep - update->beginstep;
double t_target = t_start + delta * (t_stop-t_start);
double tsqrt = sqrt(t_target);
// set current t_target and t_sqrt
// if variable temp, evaluate variable, wrap with clear/add
// reallocate tforce array if necessary
if (tstyle == CONSTANT) {
t_target = t_start + delta * (t_stop-t_start);
tsqrt = sqrt(t_target);
} else {
modify->clearstep_compute();
if (tstyle == EQUAL) {
t_target = input->variable->compute_equal(tvar);
if (t_target < 0.0)
error->one(FLERR,"Fix langevin variable returned negative temperature");
tsqrt = sqrt(t_target);
} else {
if (nlocal > maxatom2) {
maxatom2 = atom->nmax;
memory->destroy(tforce);
memory->create(tforce,maxatom2,"langevin:tforce");
}
input->variable->compute_atom(tvar,igroup,tforce,1,0);
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
if (tforce[i] < 0.0)
error->one(FLERR,
"Fix langevin variable returned negative temperature");
}
modify->addstep_compute(update->ntimestep + 1);
}
// apply damping and thermostat to atoms in group
// for BIAS:
@ -290,6 +344,7 @@ void FixLangevin::post_force_no_tally()
if (which == NOBIAS) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
if (tstyle == ATOM) tsqrt = sqrt(tforce[i]);
gamma1 = -rmass[i] / t_period / ftm2v;
gamma2 = sqrt(rmass[i]) * sqrt(24.0*boltz/t_period/dt/mvv2e) / ftm2v;
gamma1 *= 1.0/ratio[type[i]];
@ -310,6 +365,7 @@ void FixLangevin::post_force_no_tally()
temperature->compute_scalar();
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
if (tstyle == ATOM) tsqrt = sqrt(tforce[i]);
gamma1 = -rmass[i] / t_period / ftm2v;
gamma2 = sqrt(rmass[i]) * sqrt(24.0*boltz/t_period/dt/mvv2e) / ftm2v;
gamma1 *= 1.0/ratio[type[i]];
@ -337,6 +393,7 @@ void FixLangevin::post_force_no_tally()
if (which == NOBIAS) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
if (tstyle == ATOM) tsqrt = sqrt(tforce[i]);
gamma1 = gfactor1[type[i]];
gamma2 = gfactor2[type[i]] * tsqrt;
fran[0] = gamma2*(random->uniform()-0.5);
@ -355,6 +412,7 @@ void FixLangevin::post_force_no_tally()
temperature->compute_scalar();
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
if (tstyle == ATOM) tsqrt = sqrt(tforce[i]);
gamma1 = gfactor1[type[i]];
gamma2 = gfactor2[type[i]] * tsqrt;
temperature->remove_bias(i,v[i]);
@ -394,22 +452,22 @@ void FixLangevin::post_force_no_tally()
// thermostat omega and angmom
if (oflag) omega_thermostat(tsqrt);
if (aflag) angmom_thermostat(tsqrt);
if (oflag) omega_thermostat();
if (aflag) angmom_thermostat();
}
/* ---------------------------------------------------------------------- */
void FixLangevin::post_force_tally()
{
double gamma1,gamma2;
double gamma1,gamma2,t_target;
// reallocate flangevin if necessary
if (atom->nmax > nmax) {
if (atom->nlocal > maxatom1) {
memory->destroy(flangevin);
nmax = atom->nmax;
memory->create(flangevin,nmax,3,"langevin:flangevin");
maxatom1 = atom->nmax;
memory->create(flangevin,maxatom1,3,"langevin:flangevin");
}
double **v = atom->v;
@ -421,8 +479,36 @@ void FixLangevin::post_force_tally()
double delta = update->ntimestep - update->beginstep;
delta /= update->endstep - update->beginstep;
double t_target = t_start + delta * (t_stop-t_start);
double tsqrt = sqrt(t_target);
// set current t_target and t_sqrt
// if variable temp, evaluate variable, wrap with clear/add
// reallocate tforce array if necessary
if (tstyle == CONSTANT) {
t_target = t_start + delta * (t_stop-t_start);
tsqrt = sqrt(t_target);
} else {
modify->clearstep_compute();
if (tstyle == EQUAL) {
t_target = input->variable->compute_equal(tvar);
if (t_target < 0.0)
error->one(FLERR,"Fix langevin variable returned negative temperature");
tsqrt = sqrt(t_target);
} else {
if (nlocal > maxatom2) {
maxatom2 = atom->nmax;
memory->destroy(tforce);
memory->create(tforce,maxatom2,"langevin:tforce");
}
input->variable->compute_atom(tvar,igroup,tforce,1,0);
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
if (tforce[i] < 0.0)
error->one(FLERR,
"Fix langevin variable returned negative temperature");
}
modify->addstep_compute(update->ntimestep + 1);
}
// apply damping and thermostat to appropriate atoms
// for BIAS:
@ -440,6 +526,7 @@ void FixLangevin::post_force_tally()
if (which == NOBIAS) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
if (tstyle == ATOM) tsqrt = sqrt(tforce[i]);
gamma1 = -rmass[i] / t_period / ftm2v;
gamma2 = sqrt(rmass[i]) * sqrt(24.0*boltz/t_period/dt/mvv2e) / ftm2v;
gamma1 *= 1.0/ratio[type[i]];
@ -457,6 +544,7 @@ void FixLangevin::post_force_tally()
temperature->compute_scalar();
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
if (tstyle == ATOM) tsqrt = sqrt(tforce[i]);
gamma1 = -rmass[i] / t_period / ftm2v;
gamma2 = sqrt(rmass[i]) * sqrt(24.0*boltz/t_period/dt/mvv2e) / ftm2v;
gamma1 *= 1.0/ratio[type[i]];
@ -480,6 +568,7 @@ void FixLangevin::post_force_tally()
if (which == NOBIAS) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
if (tstyle == ATOM) tsqrt = sqrt(tforce[i]);
gamma1 = gfactor1[type[i]];
gamma2 = gfactor2[type[i]] * tsqrt;
flangevin[i][0] = gamma1*v[i][0] + gamma2*(random->uniform()-0.5);
@ -495,6 +584,7 @@ void FixLangevin::post_force_tally()
temperature->compute_scalar();
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
if (tstyle == ATOM) tsqrt = sqrt(tforce[i]);
gamma1 = gfactor1[type[i]];
gamma2 = gfactor2[type[i]] * tsqrt;
temperature->remove_bias(i,v[i]);
@ -515,15 +605,15 @@ void FixLangevin::post_force_tally()
// thermostat omega and angmom
if (oflag) omega_thermostat(tsqrt);
if (aflag) angmom_thermostat(tsqrt);
if (oflag) omega_thermostat();
if (aflag) angmom_thermostat();
}
/* ----------------------------------------------------------------------
thermostat rotational dof via omega
------------------------------------------------------------------------- */
void FixLangevin::omega_thermostat(double tsqrt)
void FixLangevin::omega_thermostat()
{
double gamma1,gamma2;
@ -546,6 +636,7 @@ void FixLangevin::omega_thermostat(double tsqrt)
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
inertiaone = SINERTIA*radius[i]*radius[i]*rmass[i];
if (tstyle == ATOM) tsqrt = sqrt(tforce[i]);
gamma1 = -inertiaone / t_period / ftm2v;
gamma2 = sqrt(inertiaone) * sqrt(24.0*boltz/t_period/dt/mvv2e) / ftm2v;
gamma1 *= 1.0/ratio[type[i]];
@ -564,7 +655,7 @@ void FixLangevin::omega_thermostat(double tsqrt)
thermostat rotational dof via angmom
------------------------------------------------------------------------- */
void FixLangevin::angmom_thermostat(double tsqrt)
void FixLangevin::angmom_thermostat()
{
double gamma1,gamma2;
@ -594,6 +685,7 @@ void FixLangevin::angmom_thermostat(double tsqrt)
quat = bonus[ellipsoid[i]].quat;
MathExtra::mq_to_omega(angmom[i],quat,inertia,omega);
if (tstyle == ATOM) tsqrt = sqrt(tforce[i]);
gamma1 = -1.0 / t_period / ftm2v;
gamma2 = sqrt(24.0*boltz/t_period/dt/mvv2e) / ftm2v;
gamma1 *= 1.0/ratio[type[i]];
@ -663,11 +755,13 @@ int FixLangevin::modify_param(int narg, char **arg)
strcpy(id_temp,arg[1]);
int icompute = modify->find_compute(id_temp);
if (icompute < 0) error->all(FLERR,"Could not find fix_modify temperature ID");
if (icompute < 0)
error->all(FLERR,"Could not find fix_modify temperature ID");
temperature = modify->compute[icompute];
if (temperature->tempflag == 0)
error->all(FLERR,"Fix_modify temperature ID does not compute temperature");
error->all(FLERR,
"Fix_modify temperature ID does not compute temperature");
if (temperature->igroup != igroup && comm->me == 0)
error->warning(FLERR,"Group for fix_modify temp != fix group");
return 2;
@ -709,7 +803,8 @@ double FixLangevin::compute_scalar()
double FixLangevin::memory_usage()
{
if (!tally) return 0.0;
double bytes = atom->nmax*3 * sizeof(double);
double bytes = 0.0;
if (tally) double bytes = atom->nmax*3 * sizeof(double);
if (tforce) bytes = atom->nmax * sizeof(double);
return bytes;
}

10
src/fix_langevin.h
View File

@ -45,11 +45,15 @@ class FixLangevin : public Fix {
double t_start,t_stop,t_period;
double *gfactor1,*gfactor2,*ratio;
double energy,energy_onestep;
double tsqrt;
int tstyle,tvar;
char *tstr;
class AtomVecEllipsoid *avec;
int nmax;
int maxatom1,maxatom2;
double **flangevin;
double *tforce;
char *id_temp;
class Compute *temperature;
@ -59,8 +63,8 @@ class FixLangevin : public Fix {
virtual void post_force_no_tally();
virtual void post_force_tally();
void omega_thermostat(double);
void angmom_thermostat(double);
void omega_thermostat();
void angmom_thermostat();
};
}