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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13320 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2015-03-27 20:39:27 +00:00
parent bc06bcf854
commit 9435c9dcb1
14 changed files with 566 additions and 96 deletions
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166
src/fix_temp_csvr.cpp
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@ -12,7 +12,8 @@
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Axel Kohlmeyer (ICTP, Italy)
Contributing author: Axel Kohlmeyer (Temple U)
Based on code by Paulo Raiteri (Curtin U) and Giovanni Bussi (SISSA)
------------------------------------------------------------------------- */
#include "string.h"
@ -38,6 +39,78 @@ using namespace FixConst;
enum{NOBIAS,BIAS};
enum{CONSTANT,EQUAL};
double FixTempCSVR::gamdev(const int ia)
{
int j;
double am,e,s,v1,v2,x,y;
if (ia < 1) return 0.0;
if (ia < 6) {
x=1.0;
for (j=1; j<=ia; j++)
x *= random->uniform();
x = -log(x);
} else {
restart:
do {
do {
do {
v1 = random->uniform();
v2 = 2.0*random->uniform() - 1.0;
} while (v1*v1 + v2*v2 > 1.0);
y=v2/v1;
am=ia-1;
s=sqrt(2.0*am+1.0);
x=s*y+am;
} while (x <= 0.0);
if (am*log(x/am)-s*y < -700 || v1<0.00001) {
goto restart;
}
e=(1.0+y*y)*exp(am*log(x/am)-s*y);
} while (random->uniform() > e);
}
return x;
}
/* -------------------------------------------------------------------
returns the sum of n independent gaussian noises squared
(i.e. equivalent to summing the square of the return values of nn
calls to gasdev)
---------------------------------------------------------------------- */
double FixTempCSVR::sumnoises(int nn) {
if (nn == 0) {
return 0.0;
} else if (nn == 1) {
const double rr = random->gaussian();
return rr*rr;
} else if (nn % 2 == 0) {
return 2.0 * gamdev(nn / 2);
} else {
const double rr = random->gaussian();
return 2.0 * gamdev((nn-1) / 2) + rr*rr;
}
return 0.0;
}
/* -------------------------------------------------------------------
returns the scaling factor for velocities to thermalize
the system so it samples the canonical ensemble
---------------------------------------------------------------------- */
double FixTempCSVR::resamplekin(double ekin_old, double ekin_new){
const double tdof = temperature->dof;
const double c1 = exp(-update->dt/t_period);
const double c2 = (1.0-c1)*ekin_new/ekin_old/tdof;
const double r1 = random->gaussian();
const double r2 = sumnoises(tdof - 1);
const double scale = c1 + c2*(r1*r1+r2) + 2.0*r1*sqrt(c1*c2);
return sqrt(scale);
}
/* ---------------------------------------------------------------------- */
FixTempCSVR::FixTempCSVR(LAMMPS *lmp, int narg, char **arg) :
@ -48,8 +121,10 @@ FixTempCSVR::FixTempCSVR(LAMMPS *lmp, int narg, char **arg) :
// CSVR thermostat should be applied every step
nevery = 1;
scalar_flag = 1;
global_freq = nevery;
dynamic_group_allow = 1;
extscalar = 1;
tstr = NULL;
if (strstr(arg[3],"v_") == arg[3]) {
@ -72,6 +147,8 @@ FixTempCSVR::FixTempCSVR(LAMMPS *lmp, int narg, char **arg) :
if (t_period <= 0.0) error->all(FLERR,"Illegal fix temp/csvr command");
if (seed <= 0) error->all(FLERR,"Illegal fix temp/csvr command");
random = new RanMars(lmp,seed + comm->me);
// create a new compute temp style
// id = fix-ID + temp, compute group = fix group
@ -88,9 +165,6 @@ FixTempCSVR::FixTempCSVR(LAMMPS *lmp, int narg, char **arg) :
delete [] newarg;
tflag = 1;
random = new RanMars(lmp,seed + comm->me);
vhold = NULL;
nmax = -1;
energy = 0.0;
}
@ -107,8 +181,6 @@ FixTempCSVR::~FixTempCSVR()
delete [] id_temp;
delete random;
memory->destroy(vhold);
vhold = NULL;
nmax = -1;
}
@ -118,6 +190,7 @@ int FixTempCSVR::setmask()
{
int mask = 0;
mask |= END_OF_STEP;
mask |= THERMO_ENERGY;
return mask;
}
@ -125,15 +198,7 @@ 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) {
@ -175,65 +240,45 @@ void FixTempCSVR::end_of_step()
modify->addstep_compute(update->ntimestep + nevery);
}
const double t_current = temperature->compute_scalar();
const double efactor = 0.5 * temperature->dof * force->boltz;
const double ekin_old = t_current * efactor;
const double ekin_new = t_target * efactor;
// compute velocity scaling factor on root node and broadcast
double lamda;
if (comm->me == 0) {
lamda = resamplekin(ekin_old, ekin_new);
}
MPI_Bcast(&lamda,1,MPI_DOUBLE,0,world);
double * const * const v = atom->v;
const int * const mask = atom->mask;
const int * const type = atom->type;
const int nlocal = atom->nlocal;
// adjust holding space, if needed and copy existing velocities
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;
}
}
// 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;
v[i][0] *= lamda;
v[i][1] *= lamda;
v[i][2] *= lamda;
}
}
} 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->remove_bias(i,v[i]);
v[i][0] *= lamda;
v[i][1] *= lamda;
v[i][2] *= lamda;
temperature->restore_bias(i,v[i]);
}
}
}
// tally the kinetic energy transferred between heat bath and system
energy += ekin_old * (1.0 - lamda*lamda);
}
/* ---------------------------------------------------------------------- */
@ -273,6 +318,13 @@ void FixTempCSVR::reset_target(double t_new)
t_target = t_start = t_stop = t_new;
}
/* ---------------------------------------------------------------------- */
double FixTempCSVR::compute_scalar()
{
return energy;
}
/* ----------------------------------------------------------------------
extract thermostat properties
------------------------------------------------------------------------- */