Homec4science
Diffusion lammps (efficient_neuronet) Browse

lammps/src/REPLICA/temper.cpp
0f6d21acda7befficient_neuronet

Last Change
Raw File

temper.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 author: Mark Sears (SNL)
------------------------------------------------------------------------- */
#include <math.h>
#include <stdlib.h>
#include <string.h>
#include "temper.h"
#include "universe.h"
#include "domain.h"
#include "atom.h"
#include "update.h"
#include "integrate.h"
#include "modify.h"
#include "compute.h"
#include "force.h"
#include "output.h"
#include "thermo.h"
#include "fix.h"
#include "random_park.h"
#include "finish.h"
#include "timer.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
// #define TEMPER_DEBUG 1
/* ---------------------------------------------------------------------- */
Temper::Temper(LAMMPS *lmp) : Pointers(lmp) {}
/* ---------------------------------------------------------------------- */
Temper::~Temper()
{
MPI_Comm_free(&roots);
if (ranswap) delete ranswap;
delete ranboltz;
delete [] set_temp;
delete [] temp2world;
delete [] world2temp;
delete [] world2root;
}
/* ----------------------------------------------------------------------
perform tempering with inter-world swaps
------------------------------------------------------------------------- */
void Temper::command(int narg, char **arg)
{
if (universe->nworlds == 1)
error->all(FLERR,"Must have more than one processor partition to temper");
if (domain->box_exist == 0)
error->all(FLERR,"Temper command before simulation box is defined");
if (narg != 6 && narg != 7)
error->universe_all(FLERR,"Illegal temper command");
int nsteps = force->inumeric(FLERR,arg[0]);
nevery = force->inumeric(FLERR,arg[1]);
double temp = force->numeric(FLERR,arg[2]);
for (whichfix = 0; whichfix < modify->nfix; whichfix++)
if (strcmp(arg[3],modify->fix[whichfix]->id) == 0) break;
if (whichfix == modify->nfix)
error->universe_all(FLERR,"Tempering fix ID is not defined");
seed_swap = force->inumeric(FLERR,arg[4]);
seed_boltz = force->inumeric(FLERR,arg[5]);
my_set_temp = universe->iworld;
if (narg == 7) my_set_temp = force->inumeric(FLERR,arg[6]);
// swap frequency must evenly divide total # of timesteps
if (nevery <= 0)
error->universe_all(FLERR,"Invalid frequency in temper command");
nswaps = nsteps/nevery;
if (nswaps*nevery != nsteps)
error->universe_all(FLERR,"Non integer # of swaps in temper command");
// fix style must be appropriate for temperature control, i.e. it needs
// to provide a working Fix::reset_target() and must not change the volume.
if ((strcmp(modify->fix[whichfix]->style,"nvt") != 0) &&
(strcmp(modify->fix[whichfix]->style,"nvt/asphere") != 0) &&
(strcmp(modify->fix[whichfix]->style,"nvt/asphere/omp") != 0) &&
(strcmp(modify->fix[whichfix]->style,"nvt/body") != 0) &&
(strcmp(modify->fix[whichfix]->style,"nvt/eff") != 0) &&
(strcmp(modify->fix[whichfix]->style,"nvt/intel") != 0) &&
(strcmp(modify->fix[whichfix]->style,"nvt/kk") != 0) &&
(strcmp(modify->fix[whichfix]->style,"nvt/kk/host") != 0) &&
(strcmp(modify->fix[whichfix]->style,"nvt/kk/device") != 0) &&
(strcmp(modify->fix[whichfix]->style,"nvt/omp") != 0) &&
(strcmp(modify->fix[whichfix]->style,"nvt/sphere") != 0) &&
(strcmp(modify->fix[whichfix]->style,"nvt/sphere/omp") != 0) &&
(strcmp(modify->fix[whichfix]->style,"langevin") != 0) &&
(strcmp(modify->fix[whichfix]->style,"langevin/drude") != 0) &&
(strcmp(modify->fix[whichfix]->style,"langevin/eff") != 0) &&
(strcmp(modify->fix[whichfix]->style,"gld") != 0) &&
(strcmp(modify->fix[whichfix]->style,"gle") != 0) &&
(strcmp(modify->fix[whichfix]->style,"rigid/nvt") != 0) &&
(strcmp(modify->fix[whichfix]->style,"rigid/nvt/small") != 0) &&
(strcmp(modify->fix[whichfix]->style,"rigid/nvt/omp") != 0) &&
(strcmp(modify->fix[whichfix]->style,"rigid/nvt/small/omp") != 0) &&
(strcmp(modify->fix[whichfix]->style,"temp/berendsen") != 0) &&
(strcmp(modify->fix[whichfix]->style,"temp/berendsen/cuda") != 0) &&
(strcmp(modify->fix[whichfix]->style,"temp/csvr") != 0) &&
(strcmp(modify->fix[whichfix]->style,"temp/csld") != 0) &&
(strcmp(modify->fix[whichfix]->style,"temp/rescale") != 0) &&
(strcmp(modify->fix[whichfix]->style,"temp/rescale/cuda") != 0) &&
(strcmp(modify->fix[whichfix]->style,"temp/rescale/eff") != 0))
error->universe_all(FLERR,"Tempering temperature fix is not supported");
// setup for long tempering run
update->whichflag = 1;
update->nsteps = nsteps;
update->beginstep = update->firststep = update->ntimestep;
update->endstep = update->laststep = update->firststep + nsteps;
if (update->laststep < 0)
error->all(FLERR,"Too many timesteps");
lmp->init();
// local storage
me_universe = universe->me;
MPI_Comm_rank(world,&me);
nworlds = universe->nworlds;
iworld = universe->iworld;
boltz = force->boltz;
// pe_compute = ptr to thermo_pe compute
// notify compute it will be called at first swap
int id = modify->find_compute("thermo_pe");
if (id < 0) error->all(FLERR,"Tempering could not find thermo_pe compute");
Compute *pe_compute = modify->compute[id];
pe_compute->addstep(update->ntimestep + nevery);
// create MPI communicator for root proc from each world
int color;
if (me == 0) color = 0;
else color = 1;
MPI_Comm_split(universe->uworld,color,0,&roots);
// RNGs for swaps and Boltzmann test
// warm up Boltzmann RNG
if (seed_swap) ranswap = new RanPark(lmp,seed_swap);
else ranswap = NULL;
ranboltz = new RanPark(lmp,seed_boltz + me_universe);
for (int i = 0; i < 100; i++) ranboltz->uniform();
// world2root[i] = global proc that is root proc of world i
world2root = new int[nworlds];
if (me == 0)
MPI_Allgather(&me_universe,1,MPI_INT,world2root,1,MPI_INT,roots);
MPI_Bcast(world2root,nworlds,MPI_INT,0,world);
// create static list of set temperatures
// allgather tempering arg "temp" across root procs
// bcast from each root to other procs in world
set_temp = new double[nworlds];
if (me == 0) MPI_Allgather(&temp,1,MPI_DOUBLE,set_temp,1,MPI_DOUBLE,roots);
MPI_Bcast(set_temp,nworlds,MPI_DOUBLE,0,world);
// create world2temp only on root procs from my_set_temp
// create temp2world on root procs from world2temp,
// then bcast to all procs within world
world2temp = new int[nworlds];
temp2world = new int[nworlds];
if (me == 0) {
MPI_Allgather(&my_set_temp,1,MPI_INT,world2temp,1,MPI_INT,roots);
for (int i = 0; i < nworlds; i++) temp2world[world2temp[i]] = i;
}
MPI_Bcast(temp2world,nworlds,MPI_INT,0,world);
// if restarting tempering, reset temp target of Fix to current my_set_temp
if (narg == 7) {
double new_temp = set_temp[my_set_temp];
modify->fix[whichfix]->reset_target(new_temp);
}
// setup tempering runs
int i,which,partner,swap,partner_set_temp,partner_world;
double pe,pe_partner,boltz_factor,new_temp;
if (me_universe == 0 && universe->uscreen)
fprintf(universe->uscreen,"Setting up tempering ...\n");
update->integrate->setup();
if (me_universe == 0) {
if (universe->uscreen) {
fprintf(universe->uscreen,"Step");
for (int i = 0; i < nworlds; i++)
fprintf(universe->uscreen," T%d",i);
fprintf(universe->uscreen,"\n");
}
if (universe->ulogfile) {
fprintf(universe->ulogfile,"Step");
for (int i = 0; i < nworlds; i++)
fprintf(universe->ulogfile," T%d",i);
fprintf(universe->ulogfile,"\n");
}
print_status();
}
timer->init();
timer->barrier_start();
for (int iswap = 0; iswap < nswaps; iswap++) {
// run for nevery timesteps
update->integrate->run(nevery);
// compute PE
// notify compute it will be called at next swap
pe = pe_compute->compute_scalar();
pe_compute->addstep(update->ntimestep + nevery);
// which = which of 2 kinds of swaps to do (0,1)
if (!ranswap) which = iswap % 2;
else if (ranswap->uniform() < 0.5) which = 0;
else which = 1;
// partner_set_temp = which set temp I am partnering with for this swap
if (which == 0) {
if (my_set_temp % 2 == 0) partner_set_temp = my_set_temp + 1;
else partner_set_temp = my_set_temp - 1;
} else {
if (my_set_temp % 2 == 1) partner_set_temp = my_set_temp + 1;
else partner_set_temp = my_set_temp - 1;
}
// partner = proc ID to swap with
// if partner = -1, then I am not a proc that swaps
partner = -1;
if (me == 0 && partner_set_temp >= 0 && partner_set_temp < nworlds) {
partner_world = temp2world[partner_set_temp];
partner = world2root[partner_world];
}
// swap with a partner, only root procs in each world participate
// hi proc sends PE to low proc
// lo proc make Boltzmann decision on whether to swap
// lo proc communicates decision back to hi proc
swap = 0;
if (partner != -1) {
if (me_universe > partner)
MPI_Send(&pe,1,MPI_DOUBLE,partner,0,universe->uworld);
else
MPI_Recv(&pe_partner,1,MPI_DOUBLE,partner,0,universe->uworld,MPI_STATUS_IGNORE);
if (me_universe < partner) {
boltz_factor = (pe - pe_partner) *
(1.0/(boltz*set_temp[my_set_temp]) -
1.0/(boltz*set_temp[partner_set_temp]));
if (boltz_factor >= 0.0) swap = 1;
else if (ranboltz->uniform() < exp(boltz_factor)) swap = 1;
}
if (me_universe < partner)
MPI_Send(&swap,1,MPI_INT,partner,0,universe->uworld);
else
MPI_Recv(&swap,1,MPI_INT,partner,0,universe->uworld,MPI_STATUS_IGNORE);
#ifdef TEMPER_DEBUG
if (me_universe < partner)
printf("SWAP %d & %d: yes = %d,Ts = %d %d, PEs = %g %g, Bz = %g %g\n",
me_universe,partner,swap,my_set_temp,partner_set_temp,
pe,pe_partner,boltz_factor,exp(boltz_factor));
#endif
}
// bcast swap result to other procs in my world
MPI_Bcast(&swap,1,MPI_INT,0,world);
// rescale kinetic energy via velocities if move is accepted
if (swap) scale_velocities(partner_set_temp,my_set_temp);
// if my world swapped, all procs in world reset temp target of Fix
if (swap) {
new_temp = set_temp[partner_set_temp];
modify->fix[whichfix]->reset_target(new_temp);
}
// update my_set_temp and temp2world on every proc
// root procs update their value if swap took place
// allgather across root procs
// bcast within my world
if (swap) my_set_temp = partner_set_temp;
if (me == 0) {
MPI_Allgather(&my_set_temp,1,MPI_INT,world2temp,1,MPI_INT,roots);
for (i = 0; i < nworlds; i++) temp2world[world2temp[i]] = i;
}
MPI_Bcast(temp2world,nworlds,MPI_INT,0,world);
// print out current swap status
if (me_universe == 0) print_status();
}
timer->barrier_stop();
update->integrate->cleanup();
Finish finish(lmp);
finish.end(1);
update->whichflag = 0;
update->firststep = update->laststep = 0;
update->beginstep = update->endstep = 0;
}
/* ----------------------------------------------------------------------
scale kinetic energy via velocities a la Sugita
------------------------------------------------------------------------- */
void Temper::scale_velocities(int t_partner, int t_me)
{
double sfactor = sqrt(set_temp[t_partner]/set_temp[t_me]);
double **v = atom->v;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
v[i][0] = v[i][0]*sfactor;
v[i][1] = v[i][1]*sfactor;
v[i][2] = v[i][2]*sfactor;
}
}
/* ----------------------------------------------------------------------
proc 0 prints current tempering status
------------------------------------------------------------------------- */
void Temper::print_status()
{
if (universe->uscreen) {
fprintf(universe->uscreen,BIGINT_FORMAT,update->ntimestep);
for (int i = 0; i < nworlds; i++)
fprintf(universe->uscreen," %d",world2temp[i]);
fprintf(universe->uscreen,"\n");
}
if (universe->ulogfile) {
fprintf(universe->ulogfile,BIGINT_FORMAT,update->ntimestep);
for (int i = 0; i < nworlds; i++)
fprintf(universe->ulogfile," %d",world2temp[i]);
fprintf(universe->ulogfile,"\n");
fflush(universe->ulogfile);
}
}
c4science · Help