Homec4science
Diffusion lammps (efficient_neuronet) Browse

lammps/src/MISC/fix_gld.cpp
1fac1d41fa78efficient_neuronet

Last Change
Raw File

fix_gld.cpp
View Options

/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors: Stephen Bond (SNL) and
Andrew Baczewski (Michigan State/SNL)
------------------------------------------------------------------------- */
#include "math.h"
#include "stdio.h"
#include "string.h"
#include "fix_gld.h"
#include "math_extra.h"
#include "atom.h"
#include "force.h"
#include "update.h"
#include "respa.h"
#include "comm.h"
#include "input.h"
#include "variable.h"
#include "random_mars.h"
#include "memory.h"
#include "error.h"
#include "group.h"
#define GLD_UNIFORM_DISTRO
using namespace LAMMPS_NS;
using namespace FixConst;
/* ----------------------------------------------------------------------
Parses parameters passed to the method, allocates some memory
------------------------------------------------------------------------- */
FixGLD::FixGLD(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
int narg_min = 8;
// Check to make sure we have the minimal number of inputs
if (narg < narg_min) error->all(FLERR,"Illegal fix gld command");
time_integrate = 1;
restart_peratom = 1;
// Parse the first set of required input arguments
// 0 = Fix ID (e.g., 1)
// 1 = Group ID (e.g., all)
// 2 = gld (name of this fix)
// 3 = t_start (Starting target temperature)
t_start = atof(arg[3]);
// 4 = t_stop (Stopping target temperature)
t_stop = atof(arg[4]);
// 5 = prony_terms (number of terms in Prony series)
prony_terms = atoi(arg[5]);
// 6 = seed (random seed)
int seed = atoi(arg[6]);
// 7 = series type
if(strcmp(arg[7],"pprony") == 0) {
series_type = 1; // series type 1 is 'positive Prony series'
} else {
error->all(FLERR,"Fix gld series type must be pprony for now");
}
// Error checking for the first set of required input arguments
if (seed <= 0) error->all(FLERR,"Illegal fix gld command");
if (prony_terms <= 0)
error->all(FLERR,"Fix gld prony terms must be > 0");
if (t_start < 0)
error->all(FLERR,"Fix gld start temperature must be >= 0");
if (t_stop < 0)
error->all(FLERR,"Fix gld stop temperature must be >= 0");
if (narg - narg_min < 2*(prony_terms) )
error->all(FLERR,"Fix gld needs more prony series coefficients");
// allocate memory for Prony series force coefficients
memory->create(prony_c, prony_terms, "gld:prony_c");
// allocate memory for Prony series timescale coefficients
memory->create(prony_tau, prony_terms, "gld:prony_tau");
// allocate memory for Prony series extended variables
s_gld = NULL;
grow_arrays(atom->nmax);
// add callbacks to enable restarts
atom->add_callback(0);
atom->add_callback(1);
// read in the Prony series coefficients
int iarg = narg_min;
int icoeff = 0;
while (iarg < narg && icoeff < prony_terms) {
double pc = atof(arg[iarg]);
double ptau = atof(arg[iarg+1]);
if (pc < 0)
error->all(FLERR,"Fix gld c coefficients must be >= 0");
if (ptau <= 0)
error->all(FLERR,"Fix gld tau coefficients must be > 0");
// All atom types to have the same Prony series
prony_c[icoeff] = pc;
prony_tau[icoeff] = ptau;
icoeff += 1;
iarg += 2;
}
// initialize Marsaglia RNG with processor-unique seed
random = new RanMars(lmp,seed + comm->me);
// initialize the extended variables
init_s_gld();
// optional arguments
freezeflag = 0;
zeroflag = 0;
while (iarg < narg) {
if (strcmp(arg[iarg],"zero") == 0) {
if (iarg+2 > narg) {
error->all(FLERR, "Illegal fix gld command");
}
if (strcmp(arg[iarg+1],"no") == 0) {
} else if (strcmp(arg[iarg+1],"yes") == 0) {
zeroflag = 1;
} else {
error->all(FLERR,"Illegal fix gld command");
}
iarg += 2;
}
else if (strcmp(arg[iarg],"frozen") == 0) {
if (iarg+2 > narg) {
error->all(FLERR, "Illegal fix gld command");
}
if (strcmp(arg[iarg+1],"no") == 0) {
} else if (strcmp(arg[iarg+1],"yes") == 0) {
freezeflag = 1;
for (int i = 0; i < atom->nlocal; i++) {
if (atom->mask[i] & groupbit) {
for (int k = 0; k < 3*prony_terms; k=k+3)
{
s_gld[i][k] = 0.0;
s_gld[i][k+1] = 0.0;
s_gld[i][k+2] = 0.0;
}
}
}
} else {
error->all(FLERR, "Illegal fix gld command");
}
iarg += 2;
}
else error->all(FLERR,"Illegal fix gld command");
}
// Initialize the target temperature
t_target = t_start;
}
/* ----------------------------------------------------------------------
Destroys memory allocated by the method
------------------------------------------------------------------------- */
FixGLD::~FixGLD()
{
delete random;
memory->destroy(prony_c);
memory->destroy(prony_tau);
memory->destroy(s_gld);
// remove callbacks to fix, so atom class stops calling it
atom->delete_callback(id,0);
atom->delete_callback(id,1);
}
/* ----------------------------------------------------------------------
Specifies when the fix is called during the timestep
------------------------------------------------------------------------- */
int FixGLD::setmask()
{
int mask = 0;
mask |= INITIAL_INTEGRATE;
mask |= FINAL_INTEGRATE;
mask |= INITIAL_INTEGRATE_RESPA;
mask |= FINAL_INTEGRATE_RESPA;
return mask;
}
/* ----------------------------------------------------------------------
Initialize the method parameters before a run
------------------------------------------------------------------------- */
void FixGLD::init()
{
dtv = update->dt;
dtf = 0.5 * update->dt * force->ftm2v;
if (strstr(update->integrate_style,"respa"))
step_respa = ((Respa *) update->integrate)->step;
}
/* ----------------------------------------------------------------------
First half of a timestep (V^{n} -> V^{n+1/2}; X^{n} -> X^{n+1})
------------------------------------------------------------------------- */
void FixGLD::initial_integrate(int vflag)
{
double dtfm;
double ftm2v = force->ftm2v;
double fran[3], fsum[3], fsumall[3];
bigint count;
int icoeff;
// update v and x of atoms in group
double **x = atom->x;
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;
// set kT to the temperature in mvvv units
double kT = (force->boltz)*t_target/(force->mvv2e);
// zero an accumulator for the total random force
fsum[0] = fsum[1] = fsum[2] = 0.0;
if (rmass) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
dtfm = dtf / rmass[i];
// Advance V by dt/2
v[i][0] += dtfm * f[i][0];
v[i][1] += dtfm * f[i][1];
v[i][2] += dtfm * f[i][2];
for (int k = 0; k < 3*prony_terms; k=k+3) {
v[i][0] += dtfm * s_gld[i][k];
v[i][1] += dtfm * s_gld[i][k+1];
v[i][2] += dtfm * s_gld[i][k+2];
}
// Advance X by dt
x[i][0] += dtv * v[i][0];
x[i][1] += dtv * v[i][1];
x[i][2] += dtv * v[i][2];
// Advance S by dt
icoeff = 0;
for (int k = 0; k < 3*prony_terms; k=k+3) {
double theta = exp(-dtv/prony_tau[icoeff]);
double ck = prony_c[icoeff];
double vmult = (theta-1.)*ck/ftm2v;
double rmult = sqrt(2.0*kT*ck/dtv)*(1.-theta)/ftm2v;
// random force
#ifdef GLD_GAUSSIAN_DISTRO
fran[0] = rmult*random->gaussian();
fran[1] = rmult*random->gaussian();
fran[2] = rmult*random->gaussian();
#endif
#ifdef GLD_UNIFORM_DISTRO
rmult *= sqrt(12.0); // correct variance of uniform distribution
fran[0] = rmult*(random->uniform() - 0.5);
fran[1] = rmult*(random->uniform() - 0.5);
fran[2] = rmult*(random->uniform() - 0.5);
#endif
// sum of random forces
fsum[0] += fran[0];
fsum[1] += fran[1];
fsum[2] += fran[2];
s_gld[i][k] *= theta;
s_gld[i][k+1] *= theta;
s_gld[i][k+2] *= theta;
s_gld[i][k] += vmult*v[i][0];
s_gld[i][k+1] += vmult*v[i][1];
s_gld[i][k+2] += vmult*v[i][2];
s_gld[i][k] += fran[0];
s_gld[i][k+1] += fran[1];
s_gld[i][k+2] += fran[2];
icoeff += 1;
}
}
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
dtfm = dtf / mass[type[i]];
// Advance V by dt/2
v[i][0] += dtfm * f[i][0];
v[i][1] += dtfm * f[i][1];
v[i][2] += dtfm * f[i][2];
for (int k = 0; k < 3*prony_terms; k=k+3) {
v[i][0] += dtfm * s_gld[i][k];
v[i][1] += dtfm * s_gld[i][k+1];
v[i][2] += dtfm * s_gld[i][k+2];
}
// Advance X by dt
x[i][0] += dtv * v[i][0];
x[i][1] += dtv * v[i][1];
x[i][2] += dtv * v[i][2];
// Advance S by dt
icoeff = 0;
for (int k = 0; k < 3*prony_terms; k=k+3) {
double theta = exp(-dtv/prony_tau[icoeff]);
double ck = prony_c[icoeff];
double vmult = (theta-1.)*ck/ftm2v;
double rmult = sqrt(2.0*kT*ck/dtv)*(1.-theta)/ftm2v;
// random force
#ifdef GLD_GAUSSIAN_DISTRO
fran[0] = rmult*random->gaussian();
fran[1] = rmult*random->gaussian();
fran[2] = rmult*random->gaussian();
#endif
#ifdef GLD_UNIFORM_DISTRO
rmult *= sqrt(12.0); // correct variance of uniform distribution
fran[0] = rmult*(random->uniform() - 0.5);
fran[1] = rmult*(random->uniform() - 0.5);
fran[2] = rmult*(random->uniform() - 0.5);
#endif
// sum of random forces
fsum[0] += fran[0];
fsum[1] += fran[1];
fsum[2] += fran[2];
s_gld[i][k] *= theta;
s_gld[i][k+1] *= theta;
s_gld[i][k+2] *= theta;
s_gld[i][k] += vmult*v[i][0];
s_gld[i][k+1] += vmult*v[i][1];
s_gld[i][k+2] += vmult*v[i][2];
s_gld[i][k] += fran[0];
s_gld[i][k+1] += fran[1];
s_gld[i][k+2] += fran[2];
icoeff += 1;
}
}
}
// correct the random force, if zeroflag is set
if (zeroflag) {
count = group->count(igroup);
if (count == 0) error->all(FLERR,"Cannot zero gld force for zero atoms");
MPI_Allreduce(fsum,fsumall,3,MPI_DOUBLE,MPI_SUM,world);
fsumall[0] /= (count*prony_terms);
fsumall[1] /= (count*prony_terms);
fsumall[2] /= (count*prony_terms);
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
for (int k = 0; k < 3*prony_terms; k=k+3) {
s_gld[i][k] -= fsumall[0];
s_gld[i][k+1] -= fsumall[1];
s_gld[i][k+2] -= fsumall[2];
}
}
}
}
}
/* ----------------------------------------------------------------------
Second half of a timestep (V^{n+1/2} -> V^{n+1})
------------------------------------------------------------------------- */
void FixGLD::final_integrate()
{
double dtfm;
// update v of atoms in group
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];
for (int k = 0; k < 3*prony_terms; k=k+3) {
v[i][0] += dtfm * s_gld[i][k];
v[i][1] += dtfm * s_gld[i][k+1];
v[i][2] += dtfm * s_gld[i][k+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];
for (int k = 0; k < 3*prony_terms; k=k+3) {
v[i][0] += dtfm * s_gld[i][k];
v[i][1] += dtfm * s_gld[i][k+1];
v[i][2] += dtfm * s_gld[i][k+2];
}
}
}
// Change the temperature for the next step
double delta = update->ntimestep - update->beginstep;
delta /= update->endstep - update->beginstep;
t_target = t_start + delta * (t_stop - t_start);
}
/* ---------------------------------------------------------------------- */
void FixGLD::initial_integrate_respa(int vflag, int ilevel, int iloop)
{
dtv = step_respa[ilevel];
dtf = 0.5 * step_respa[ilevel] * (force->ftm2v);
// innermost level - GLD update of v and x
// all other levels - GLD update of v
if (ilevel == 0) initial_integrate(vflag);
else final_integrate();
}
/* ---------------------------------------------------------------------- */
void FixGLD::final_integrate_respa(int ilevel, int iloop)
{
dtf = 0.5 * step_respa[ilevel] * (force->ftm2v);
final_integrate();
}
/* ----------------------------------------------------------------------
Called when a change to the target temperature is requested mid-run
------------------------------------------------------------------------- */
void FixGLD::reset_target(double t_new)
{
t_target = t_start = t_stop = t_new;
}
/* ----------------------------------------------------------------------
Called when a change to the timestep is requested mid-run
------------------------------------------------------------------------- */
void FixGLD::reset_dt()
{
// set the time integration constants
dtv = update->dt;
dtf = 0.5 * update->dt * (force->ftm2v);
}
/* ----------------------------------------------------------------------
memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double FixGLD::memory_usage()
{
double bytes = atom->nmax*3*prony_terms*sizeof(double);
return bytes;
}
/* ----------------------------------------------------------------------
allocate local atom-based arrays
------------------------------------------------------------------------- */
void FixGLD::grow_arrays(int nmax)
{
memory->grow(s_gld, nmax, 3*prony_terms,"gld:s_gld");
}
/* ----------------------------------------------------------------------
copy values within local atom-based arrays
------------------------------------------------------------------------- */
void FixGLD::copy_arrays(int i, int j, int delflag)
{
for (int k = 0; k < 3*prony_terms; k++) {
s_gld[j][k] = s_gld[i][k];
}
}
/* ----------------------------------------------------------------------
Pack extended variables assoc. w/ atom i into buffer for exchange
with another processor
------------------------------------------------------------------------- */
int FixGLD::pack_exchange(int i, double *buf)
{
int m = 0;
for (int k = 0; k < 3*prony_terms; k++) {
buf[m++] = s_gld[i][k];
}
return m;
}
/* ----------------------------------------------------------------------
Unpack extended variables from exchange with another processor
------------------------------------------------------------------------- */
int FixGLD::unpack_exchange(int nlocal, double *buf)
{
int m = 0;
for (int k = 0; k < 3*prony_terms; k++) {
s_gld[nlocal][k] = buf[m++];
}
return m;
}
/* ----------------------------------------------------------------------
Pack extended variables assoc. w/ atom i into buffer for
writing to a restart file
------------------------------------------------------------------------- */
int FixGLD::pack_restart(int i, double *buf)
{
int m = 0;
buf[m++] = 3*prony_terms + 1;
for (int k = 0; k < 3*prony_terms; k=k+3)
{
buf[m++] = s_gld[i][k];
buf[m++] = s_gld[i][k+1];
buf[m++] = s_gld[i][k+2];
}
return m;
}
/* ----------------------------------------------------------------------
Unpack extended variables to restart the fix from a restart file
------------------------------------------------------------------------- */
void FixGLD::unpack_restart(int nlocal, int nth)
{
double **extra = atom->extra;
// skip to the nth set of extended variables
int m = 0;
for (int i = 0; i< nth; i++) m += static_cast<int> (extra[nlocal][m]);
m++;
for (int k = 0; k < 3*prony_terms; k=k+3)
{
s_gld[nlocal][k] = extra[nlocal][m++];
s_gld[nlocal][k+1] = extra[nlocal][m++];
s_gld[nlocal][k+2] = extra[nlocal][m++];
}
}
/* ----------------------------------------------------------------------
Returns the number of items in atomic restart data associated with
local atom nlocal. Used in determining the total extra data stored by
fixes on a given processor.
------------------------------------------------------------------------- */
int FixGLD::size_restart(int nlocal)
{
return 3*prony_terms+1;
}
/* ----------------------------------------------------------------------
Returns the maximum number of items in atomic restart data
Called in Modify::restart for peratom restart.
------------------------------------------------------------------------- */
int FixGLD::maxsize_restart()
{
return 3*prony_terms+1;
}
/* ----------------------------------------------------------------------
Initializes the extended variables to equilibrium distribution
at t_start.
------------------------------------------------------------------------- */
void FixGLD::init_s_gld()
{
int icoeff;
double eq_sdev=0.0;
// set kT to the temperature in mvvv units
double kT = (force->boltz)*t_start/(force->mvv2e);
#ifdef GLD_GAUSSIAN_DISTRO
double scale = sqrt(kT)/(force->ftm2v);
#endif
#ifdef GLD_UNIFORM_DISTRO
double scale = sqrt(12.0*kT)/(force->ftm2v);
#endif
for (int i = 0; i < atom->nlocal; i++) {
if (atom->mask[i] & groupbit) {
icoeff = 0;
for (int k = 0; k < 3*prony_terms; k=k+3) {
eq_sdev = scale*sqrt(prony_c[icoeff]/prony_tau[icoeff]);
#ifdef GLD_GAUSSIAN_DISTRO
s_gld[i][k] = eq_sdev*random->gaussian();
s_gld[i][k+1] = eq_sdev*random->gaussian();
s_gld[i][k+2] = eq_sdev*random->gaussian();
#endif
#ifdef GLD_UNIFORM_DISTRO
s_gld[i][k] = eq_sdev*(random->uniform()-0.5);
s_gld[i][k+1] = eq_sdev*(random->uniform()-0.5);
s_gld[i][k+2] = eq_sdev*(random->uniform()-0.5);
#endif
icoeff += 1;
}
}
}
return;
}
c4science · Help