git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4905 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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sjplimp
357
src/REPLICA/temper.cpp
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357
src/REPLICA/temper.cpp
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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/* ----------------------------------------------------------------------
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Contributing author: Mark Sears (SNL)
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------------------------------------------------------------------------- */
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#include "math.h"
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#include "stdlib.h"
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#include "string.h"
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#include "temper.h"
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#include "universe.h"
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#include "domain.h"
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#include "atom.h"
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#include "update.h"
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#include "integrate.h"
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#include "modify.h"
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#include "compute.h"
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#include "force.h"
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#include "output.h"
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#include "thermo.h"
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#include "fix.h"
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#include "random_park.h"
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#include "finish.h"
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#include "timer.h"
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#include "memory.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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// #define TEMPER_DEBUG 1
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/* ---------------------------------------------------------------------- */
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Temper::Temper(LAMMPS *lmp) : Pointers(lmp) {}
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/* ---------------------------------------------------------------------- */
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Temper::~Temper()
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{
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MPI_Comm_free(&roots);
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if (ranswap) delete ranswap;
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delete ranboltz;
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delete [] set_temp;
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delete [] temp2world;
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delete [] world2temp;
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delete [] world2root;
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}
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/* ----------------------------------------------------------------------
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perform tempering with inter-world swaps
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------------------------------------------------------------------------- */
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void Temper::command(int narg, char **arg)
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{
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if (universe->nworlds == 1)
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error->all("Must have more than one processor partition to temper");
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if (domain->box_exist == 0)
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error->all("Temper command before simulation box is defined");
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if (narg != 6 && narg != 7) error->universe_all("Illegal temper command");
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int nsteps = atoi(arg[0]);
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nevery = atoi(arg[1]);
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double temp = atof(arg[2]);
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for (whichfix = 0; whichfix < modify->nfix; whichfix++)
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if (strcmp(arg[3],modify->fix[whichfix]->id) == 0) break;
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if (whichfix == modify->nfix)
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error->universe_all("Tempering fix ID is not defined");
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seed_swap = atoi(arg[4]);
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seed_boltz = atoi(arg[5]);
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my_set_temp = universe->iworld;
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if (narg == 7) my_set_temp = atoi(arg[6]);
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// swap frequency must evenly divide total # of timesteps
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if (nevery == 0) error->universe_all("Invalid frequency in temper command");
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nswaps = nsteps/nevery;
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if (nswaps*nevery != nsteps)
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error->universe_all("Non integer # of swaps in temper command");
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// fix style must be appropriate for temperature control
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if ((strcmp(modify->fix[whichfix]->style,"nvt") != 0) &&
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(strcmp(modify->fix[whichfix]->style,"langevin") != 0) &&
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(strcmp(modify->fix[whichfix]->style,"temp/berendsen") != 0) &&
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(strcmp(modify->fix[whichfix]->style,"temp/rescale") != 0))
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error->universe_all("Tempering temperature fix is not valid");
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// setup for long tempering run
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update->whichflag = 1;
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update->nsteps = nsteps;
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update->beginstep = update->firststep = update->ntimestep;
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update->endstep = update->laststep = update->firststep + nsteps;
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lmp->init();
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// local storage
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me_universe = universe->me;
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MPI_Comm_rank(world,&me);
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nworlds = universe->nworlds;
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iworld = universe->iworld;
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boltz = force->boltz;
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// pe_compute = ptr to thermo_pe compute
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// notify compute it will be called at first swap
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int id = modify->find_compute("thermo_pe");
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if (id < 0) error->all("Tempering could not find thermo_pe compute");
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Compute *pe_compute = modify->compute[id];
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pe_compute->addstep(update->ntimestep + nevery);
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// create MPI communicator for root proc from each world
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int color;
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if (me == 0) color = 0;
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else color = 1;
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MPI_Comm_split(universe->uworld,color,0,&roots);
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// RNGs for swaps and Boltzmann test
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// warm up Boltzmann RNG
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if (seed_swap) ranswap = new RanPark(lmp,seed_swap);
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else ranswap = NULL;
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ranboltz = new RanPark(lmp,seed_boltz + me_universe);
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for (int i = 0; i < 100; i++) ranboltz->uniform();
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// world2root[i] = global proc that is root proc of world i
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world2root = new int[nworlds];
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if (me == 0)
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MPI_Allgather(&me_universe,1,MPI_INT,world2root,1,MPI_INT,roots);
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MPI_Bcast(world2root,nworlds,MPI_INT,0,world);
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// create static list of set temperatures
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// allgather tempering arg "temp" across root procs
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// bcast from each root to other procs in world
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set_temp = new double[nworlds];
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if (me == 0) MPI_Allgather(&temp,1,MPI_DOUBLE,set_temp,1,MPI_DOUBLE,roots);
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MPI_Bcast(set_temp,nworlds,MPI_DOUBLE,0,world);
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// create world2temp only on root procs from my_set_temp
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// create temp2world on root procs from world2temp,
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// then bcast to all procs within world
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world2temp = new int[nworlds];
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temp2world = new int[nworlds];
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if (me == 0) {
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MPI_Allgather(&my_set_temp,1,MPI_INT,world2temp,1,MPI_INT,roots);
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for (int i = 0; i < nworlds; i++) temp2world[world2temp[i]] = i;
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}
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MPI_Bcast(temp2world,nworlds,MPI_INT,0,world);
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// if restarting tempering, reset temp target of Fix to current my_set_temp
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if (narg == 7) {
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double new_temp = set_temp[my_set_temp];
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modify->fix[whichfix]->reset_target(new_temp);
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}
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// setup tempering runs
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int i,which,partner,swap,partner_set_temp,partner_world;
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double pe,pe_partner,boltz_factor,new_temp;
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MPI_Status status;
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if (me_universe == 0 && universe->uscreen)
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fprintf(universe->uscreen,"Setting up tempering ...\n");
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update->integrate->setup();
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if (me_universe == 0) {
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if (universe->uscreen) {
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fprintf(universe->uscreen,"Step");
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for (int i = 0; i < nworlds; i++)
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fprintf(universe->uscreen," T%d",i);
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fprintf(universe->uscreen,"\n");
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}
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if (universe->ulogfile) {
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fprintf(universe->ulogfile,"Step");
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for (int i = 0; i < nworlds; i++)
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fprintf(universe->ulogfile," T%d",i);
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fprintf(universe->ulogfile,"\n");
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}
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print_status();
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}
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timer->barrier_start(TIME_LOOP);
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for (int iswap = 0; iswap < nswaps; iswap++) {
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// run for nevery timesteps
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update->integrate->run(nevery);
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// compute PE
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// notify compute it will be called at next swap
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pe = pe_compute->compute_scalar();
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pe_compute->addstep(update->ntimestep + nevery);
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// which = which of 2 kinds of swaps to do (0,1)
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if (!ranswap) which = iswap % 2;
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else if (ranswap->uniform() < 0.5) which = 0;
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else which = 1;
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// partner_set_temp = which set temp I am partnering with for this swap
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if (which == 0) {
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if (my_set_temp % 2 == 0) partner_set_temp = my_set_temp + 1;
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else partner_set_temp = my_set_temp - 1;
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} else {
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if (my_set_temp % 2 == 1) partner_set_temp = my_set_temp + 1;
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else partner_set_temp = my_set_temp - 1;
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}
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// partner = proc ID to swap with
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// if partner = -1, then I am not a proc that swaps
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partner = -1;
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if (me == 0 && partner_set_temp >= 0 && partner_set_temp < nworlds) {
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partner_world = temp2world[partner_set_temp];
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partner = world2root[partner_world];
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}
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// swap with a partner, only root procs in each world participate
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// hi proc sends PE to low proc
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// lo proc make Boltzmann decision on whether to swap
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// lo proc communicates decision back to hi proc
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swap = 0;
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if (partner != -1) {
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if (me_universe > partner)
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MPI_Send(&pe,1,MPI_DOUBLE,partner,0,universe->uworld);
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else
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MPI_Recv(&pe_partner,1,MPI_DOUBLE,partner,0,universe->uworld,&status);
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if (me_universe < partner) {
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boltz_factor = (pe - pe_partner) *
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(1.0/(boltz*set_temp[my_set_temp]) -
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1.0/(boltz*set_temp[partner_set_temp]));
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if (boltz_factor >= 0.0) swap = 1;
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else if (ranboltz->uniform() < exp(boltz_factor)) swap = 1;
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}
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if (me_universe < partner)
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MPI_Send(&swap,1,MPI_INT,partner,0,universe->uworld);
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else
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MPI_Recv(&swap,1,MPI_INT,partner,0,universe->uworld,&status);
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#ifdef TEMPER_DEBUG
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if (me_universe < partner)
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printf("SWAP %d & %d: yes = %d,Ts = %d %d, PEs = %g %g, Bz = %g %g\n",
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me_universe,partner,swap,my_set_temp,partner_set_temp,
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pe,pe_partner,boltz_factor,exp(boltz_factor));
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#endif
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}
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// bcast swap result to other procs in my world
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MPI_Bcast(&swap,1,MPI_INT,0,world);
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// rescale kinetic energy via velocities if move is accepted
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if (swap) scale_velocities(partner_set_temp,my_set_temp);
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// if my world swapped, all procs in world reset temp target of Fix
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if (swap) {
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new_temp = set_temp[partner_set_temp];
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modify->fix[whichfix]->reset_target(new_temp);
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}
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// update my_set_temp and temp2world on every proc
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// root procs update their value if swap took place
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// allgather across root procs
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// bcast within my world
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if (swap) my_set_temp = partner_set_temp;
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if (me == 0) {
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MPI_Allgather(&my_set_temp,1,MPI_INT,world2temp,1,MPI_INT,roots);
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for (i = 0; i < nworlds; i++) temp2world[world2temp[i]] = i;
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}
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MPI_Bcast(temp2world,nworlds,MPI_INT,0,world);
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// print out current swap status
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if (me_universe == 0) print_status();
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}
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timer->barrier_stop(TIME_LOOP);
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update->integrate->cleanup();
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Finish finish(lmp);
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finish.end(1);
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update->whichflag = 0;
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update->firststep = update->laststep = 0;
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update->beginstep = update->endstep = 0;
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}
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/* ----------------------------------------------------------------------
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scale kinetic energy via velocities a la Sugita
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------------------------------------------------------------------------- */
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void Temper::scale_velocities(int t_partner, int t_me)
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{
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double sfactor = sqrt(set_temp[t_partner]/set_temp[t_me]);
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double **v = atom->v;
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int nlocal = atom->nlocal;
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for (int i = 0; i < nlocal; i++) {
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v[i][0] = v[i][0]*sfactor;
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v[i][1] = v[i][1]*sfactor;
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v[i][2] = v[i][2]*sfactor;
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}
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}
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/* ----------------------------------------------------------------------
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proc 0 prints current tempering status
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------------------------------------------------------------------------- */
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void Temper::print_status()
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{
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if (universe->uscreen) {
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fprintf(universe->uscreen,"%d ",update->ntimestep);
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for (int i = 0; i < nworlds; i++)
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fprintf(universe->uscreen,"%d ",world2temp[i]);
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fprintf(universe->uscreen,"\n");
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}
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if (universe->ulogfile) {
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fprintf(universe->ulogfile,"%d ",update->ntimestep);
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for (int i = 0; i < nworlds; i++)
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fprintf(universe->ulogfile,"%d ",world2temp[i]);
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fprintf(universe->ulogfile,"\n");
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fflush(universe->ulogfile);
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}
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}
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