811 lines
24 KiB
C++
811 lines
24 KiB
C++
/* ----------------------------------------------------------------------
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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: Mike Brown (SNL)
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------------------------------------------------------------------------- */
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#include "mpi.h"
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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 "prd.h"
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#include "universe.h"
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#include "update.h"
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#include "atom.h"
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#include "domain.h"
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#include "region.h"
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#include "comm.h"
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#include "velocity.h"
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#include "integrate.h"
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#include "min.h"
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#include "neighbor.h"
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#include "modify.h"
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#include "compute.h"
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#include "fix.h"
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#include "fix_event.h"
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#include "force.h"
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#include "pair.h"
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#include "random_park.h"
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#include "random_mars.h"
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#include "output.h"
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#include "dump.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 MAXINT 0x7FFFFFFF
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/* ---------------------------------------------------------------------- */
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PRD::PRD(LAMMPS *lmp) : Pointers(lmp) {}
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/* ----------------------------------------------------------------------
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perform PRD simulation on one or more replicas
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------------------------------------------------------------------------- */
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void PRD::command(int narg, char **arg)
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{
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int i,flag,allflag,ireplica;
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// error checks
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if (domain->box_exist == 0)
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error->all("PRD command before simulation box is defined");
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if (universe->nworlds != universe->nprocs &&
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atom->map_style == 0)
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error->all("Cannot use PRD with multi-proc replicas "
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"unless atom map exists");
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if (universe->nworlds == 1 && comm->me == 0)
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error->warning("Running PRD with only one replica");
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if (narg < 7) error->universe_all("Illegal prd command");
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nsteps = atoi(arg[0]);
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t_event = atoi(arg[1]);
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n_dephase = atoi(arg[2]);
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t_dephase = atoi(arg[3]);
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t_corr = atoi(arg[4]);
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char id_compute[strlen(arg[5])+1];
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strcpy(id_compute,arg[5]);
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int seed = atoi(arg[6]);
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options(narg-7,&arg[7]);
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// total # of timesteps must be multiple of t_event
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if (t_event <= 0) error->universe_all("Invalid t_event in prd command");
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if (nsteps % t_event)
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error->universe_all("PRD nsteps must be multiple of t_event");
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if (t_corr % t_event)
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error->universe_all("PRD t_corr must be multiple of t_event");
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// local storage
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int me_universe = universe->me;
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int nprocs_universe = universe->nprocs;
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int nreplica = universe->nworlds;
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int iworld = universe->iworld;
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MPI_Comm_rank(world,&me);
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MPI_Comm_size(world,&nprocs);
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// comm_replica = communicator between same proc across replicas
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// not used if replicas have unequal number of procs
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// equal_size_replicas = 1 if all replicas have same # of procs
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int color = me;
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MPI_Comm_split(universe->uworld,color,0,&comm_replica);
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flag = 0;
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if (nreplica*nprocs == nprocs_universe) flag = 1;
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MPI_Allreduce(&flag,&equal_size_replicas,1,MPI_INT,MPI_MIN,universe->uworld);
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// workspace for inter-replica communication via gathers
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natoms = static_cast<int> (atom->natoms);
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displacements = NULL;
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tagall = NULL;
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xall = NULL;
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imageall = NULL;
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if (nreplica != nprocs_universe) {
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displacements = new int[nprocs];
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tagall = (int *) memory->smalloc(natoms*sizeof(int),"prd:tagall");
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xall = memory->create_2d_double_array(natoms,3,"prd:xall");
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imageall = (int *) memory->smalloc(natoms*sizeof(int),"prd:imageall");
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}
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// random_select = same RNG for each replica for multiple event selection
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// random_dephase = unique RNG for each replica for dephasing
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random_select = new RanPark(lmp,seed);
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random_dephase = new RanMars(lmp,seed+iworld);
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// create ComputeTemp class to monitor temperature
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char **args = new char*[3];
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args[0] = (char *) "prd_temp";
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args[1] = (char *) "all";
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args[2] = (char *) "temp";
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modify->add_compute(3,args);
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temperature = modify->compute[modify->ncompute-1];
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// create Velocity class for velocity creation in dephasing
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// pass it temperature compute, loop_setting, dist_setting settings
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atom->check_mass();
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velocity = new Velocity(lmp);
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velocity->init_external("all");
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args[0] = (char *) "temp";
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args[1] = (char *) "prd_temp";
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velocity->options(2,args);
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args[0] = (char *) "loop";
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args[1] = (char *) loop_setting;
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if (loop_setting) velocity->options(2,args);
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args[0] = (char *) "dist";
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args[1] = (char *) dist_setting;
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if (dist_setting) velocity->options(2,args);
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// create FixEvent class to store event and pre-quench states
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args[0] = (char *) "prd_event";
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args[1] = (char *) "all";
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args[2] = (char *) "EVENT";
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modify->add_fix(3,args);
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fix_event = (FixEvent *) modify->fix[modify->nfix-1];
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// create Finish for timing output
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finish = new Finish(lmp);
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// string clean-up
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delete [] args;
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delete [] loop_setting;
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delete [] dist_setting;
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// assign FixEvent to event-detection compute
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// necessary so it will know atom coords at last event
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int icompute = modify->find_compute(id_compute);
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if (icompute < 0) error->all("Could not find compute ID for PRD");
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compute_event = modify->compute[icompute];
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compute_event->reset_extra_compute_fix("prd_event");
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// reset reneighboring criteria since will perform minimizations
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neigh_every = neighbor->every;
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neigh_delay = neighbor->delay;
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neigh_dist_check = neighbor->dist_check;
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if (neigh_every != 1 || neigh_delay != 0 || neigh_dist_check != 1) {
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if (me == 0)
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error->warning("Resetting reneighboring criteria during PRD");
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}
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neighbor->every = 1;
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neighbor->delay = 0;
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neighbor->dist_check = 1;
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// initialize PRD as if one long dynamics 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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update->restrict_output = 1;
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lmp->init();
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// init minimizer settings and minimizer itself
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update->etol = etol;
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update->ftol = ftol;
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update->max_eval = maxeval;
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update->minimize->init();
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// cannot use PRD with time-dependent fixes or regions or atom sorting
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for (int i = 0; i < modify->nfix; i++)
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if (modify->fix[i]->time_depend)
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error->all("Cannot use PRD with a time-dependent fix defined");
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for (int i = 0; i < domain->nregion; i++)
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if (domain->regions[i]->dynamic_check())
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error->all("Cannot use PRD with a time-dependent region defined");
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if (atom->sortfreq > 0)
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error->all("Cannot use PRD with atom_modify sort enabled");
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// perform PRD simulation
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if (me_universe == 0 && universe->uscreen)
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fprintf(universe->uscreen,"Setting up PRD ...\n");
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if (me_universe == 0) {
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if (universe->uscreen)
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fprintf(universe->uscreen,"Step CPU Clock Event "
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"Correlated Coincident Replica\n");
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if (universe->ulogfile)
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fprintf(universe->ulogfile,"Step CPU Clock Event "
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"Correlated Coincident Replica\n");
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}
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// store hot state and quenched event for replica 0
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// use share_event() to copy that info to all replicas
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// this insures all start from same place
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// need this line if quench() does only setup_minimal()
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// update->minimize->setup();
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fix_event->store_state();
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quench();
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ncoincident = 0;
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share_event(0,0);
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timer->barrier_start(TIME_LOOP);
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time_start = timer->array[TIME_LOOP];
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log_event();
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// do full init/setup since are starting all replicas after event
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// replica 0 bcasts temp to all replicas if temp_dephase is not set
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update->whichflag = 1;
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lmp->init();
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update->integrate->setup();
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if (temp_flag == 0) {
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if (universe->iworld == 0) temp_dephase = temperature->compute_scalar();
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MPI_Bcast(&temp_dephase,1,MPI_DOUBLE,universe->root_proc[0],
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universe->uworld);
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}
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// main loop: look for events until out of time
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// (1) dephase independently on each proc after event
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// (2) loop: dynamics, store state, quench, check event, restore state
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// (3) share and record event
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nbuild = ndanger = 0;
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time_dephase = time_dynamics = time_quench = time_comm = time_output = 0.0;
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timer->barrier_start(TIME_LOOP);
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time_start = timer->array[TIME_LOOP];
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while (update->ntimestep < update->endstep) {
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dephase();
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ireplica = -1;
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while (update->ntimestep < update->endstep) {
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dynamics();
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fix_event->store_state();
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quench();
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ireplica = check_event();
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if (ireplica >= 0) break;
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fix_event->restore_state();
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}
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if (ireplica < 0) break;
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// potentially more efficient for correlated events if don't
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// share until correlated check has completed
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// this will complicate the dump (always on replica 0)
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share_event(ireplica,1);
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log_event();
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int restart_flag = 0;
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if (output->restart_every && universe->iworld == 0)
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if (fix_event->event_number % output->restart_every == 0)
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restart_flag = 1;
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// correlated event loop
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// other procs could be dephasing during this time
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int corr_endstep = update->ntimestep + t_corr;
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while (update->ntimestep < corr_endstep) {
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if (update->ntimestep == update->endstep) {
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restart_flag = 0;
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break;
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}
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dynamics();
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fix_event->store_state();
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quench();
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int corr_event_check = check_event(ireplica);
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if (corr_event_check >= 0) {
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share_event(ireplica,2);
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log_event();
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corr_endstep = update->ntimestep + t_corr;
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} else fix_event->restore_state();
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}
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// full init/setup since are starting all replicas after event
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// event replica bcasts temp to all replicas if temp_dephase is not set
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update->whichflag = 1;
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lmp->init();
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update->integrate->setup();
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timer->barrier_start(TIME_LOOP);
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if (t_corr > 0) replicate(ireplica);
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if (temp_flag == 0) {
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if (ireplica == universe->iworld)
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temp_dephase = temperature->compute_scalar();
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MPI_Bcast(&temp_dephase,1,MPI_DOUBLE,universe->root_proc[ireplica],
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universe->uworld);
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}
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timer->barrier_stop(TIME_LOOP);
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time_comm += timer->array[TIME_LOOP];
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// write restart file of hot coords
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if (restart_flag) {
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timer->barrier_start(TIME_LOOP);
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output->write_restart(update->ntimestep);
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timer->barrier_stop(TIME_LOOP);
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time_output += timer->array[TIME_LOOP];
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}
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}
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// set total timers and counters so Finish() will process them
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timer->array[TIME_LOOP] = time_start;
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timer->barrier_stop(TIME_LOOP);
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timer->array[TIME_PAIR] = time_dephase;
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timer->array[TIME_BOND] = time_dynamics;
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timer->array[TIME_KSPACE] = time_quench;
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timer->array[TIME_COMM] = time_comm;
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timer->array[TIME_OUTPUT] = time_output;
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neighbor->ncalls = nbuild;
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neighbor->ndanger = ndanger;
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if (me_universe == 0) {
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if (universe->uscreen)
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fprintf(universe->uscreen,
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"Loop time of %g on %d procs for %d steps with %.15g atoms\n",
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timer->array[TIME_LOOP],nprocs_universe,nsteps,atom->natoms);
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if (universe->ulogfile)
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fprintf(universe->ulogfile,
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"Loop time of %g on %d procs for %d steps with %.15g atoms\n",
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timer->array[TIME_LOOP],nprocs_universe,nsteps,atom->natoms);
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}
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finish->end(2);
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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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update->restrict_output = 0;
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// reset reneighboring criteria
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neighbor->every = neigh_every;
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neighbor->delay = neigh_delay;
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neighbor->dist_check = neigh_dist_check;
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// clean up
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delete [] displacements;
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memory->sfree(tagall);
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memory->destroy_2d_double_array(xall);
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memory->sfree(imageall);
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MPI_Comm_free(&comm_replica);
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delete random_select;
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delete random_dephase;
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delete velocity;
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delete finish;
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modify->delete_compute("prd_temp");
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modify->delete_fix("prd_event");
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compute_event->reset_extra_compute_fix(NULL);
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}
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/* ----------------------------------------------------------------------
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dephasing = one or more short runs with new random velocities
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------------------------------------------------------------------------- */
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void PRD::dephase()
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{
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int ntimestep_hold = update->ntimestep;
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update->whichflag = 1;
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update->nsteps = n_dephase*t_dephase;
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timer->barrier_start(TIME_LOOP);
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for (int i = 0; i < n_dephase; i++) {
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int seed = static_cast<int> (random_dephase->uniform() * MAXINT);
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if (seed == 0) seed = 1;
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velocity->create(temp_dephase,seed);
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update->integrate->run(t_dephase);
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if (temp_flag == 0) temp_dephase = temperature->compute_scalar();
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}
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timer->barrier_stop(TIME_LOOP);
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time_dephase += timer->array[TIME_LOOP];
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update->integrate->cleanup();
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finish->end(0);
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// reset timestep as if dephase did not occur
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// clear timestep storage from computes, since now invalid
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update->ntimestep = ntimestep_hold;
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for (int i = 0; i < modify->ncompute; i++)
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if (modify->compute[i]->timeflag) modify->compute[i]->clearstep();
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}
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/* ----------------------------------------------------------------------
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single short dynamics run
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------------------------------------------------------------------------- */
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void PRD::dynamics()
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{
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update->whichflag = 1;
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update->nsteps = t_event;
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lmp->init();
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update->integrate->setup();
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// this may be needed if don't do full init
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//modify->addstep_compute_all(update->ntimestep);
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int ncalls = neighbor->ncalls;
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timer->barrier_start(TIME_LOOP);
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update->integrate->run(t_event);
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timer->barrier_stop(TIME_LOOP);
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time_dynamics += timer->array[TIME_LOOP];
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nbuild += neighbor->ncalls - ncalls;
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ndanger += neighbor->ndanger;
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update->integrate->cleanup();
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finish->end(0);
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}
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/* ----------------------------------------------------------------------
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quench minimization
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------------------------------------------------------------------------- */
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void PRD::quench()
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{
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int ntimestep_hold = update->ntimestep;
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int endstep_hold = update->endstep;
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// need to change whichflag so that minimize->setup() calling
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// modify->setup() will call fix->min_setup()
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update->whichflag = 2;
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update->nsteps = maxiter;
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update->endstep = update->laststep = update->firststep + maxiter;
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// full init works
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lmp->init();
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update->minimize->setup();
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// partial init does not work
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//modify->addstep_compute_all(update->ntimestep);
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//update->minimize->setup_minimal(1);
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int ncalls = neighbor->ncalls;
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timer->barrier_start(TIME_LOOP);
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update->minimize->run(maxiter);
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timer->barrier_stop(TIME_LOOP);
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time_quench += timer->array[TIME_LOOP];
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if (neighbor->ncalls == ncalls) quench_reneighbor = 0;
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else quench_reneighbor = 1;
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update->minimize->cleanup();
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finish->end(0);
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// reset timestep as if dephase did not occur
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// clear timestep storage from computes, since now invalid
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update->ntimestep = ntimestep_hold;
|
|
update->endstep = update->laststep = endstep_hold;
|
|
for (int i = 0; i < modify->ncompute; i++)
|
|
if (modify->compute[i]->timeflag) modify->compute[i]->clearstep();
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
check for an event in any replica
|
|
if replica_num is non-negative only check for event on replica_num
|
|
if multiple events, choose one at random
|
|
return -1 if no event
|
|
else return ireplica = world in which event occured
|
|
------------------------------------------------------------------------- */
|
|
|
|
int PRD::check_event(int replica_num)
|
|
{
|
|
int worldflag,universeflag,scanflag,replicaflag,ireplica;
|
|
|
|
worldflag = 0;
|
|
if (compute_event->compute_scalar() > 0.0) worldflag = 1;
|
|
if (replica_num >= 0 && replica_num != universe->iworld) worldflag = 0;
|
|
|
|
timer->barrier_start(TIME_LOOP);
|
|
if (me == 0) MPI_Allreduce(&worldflag,&universeflag,1,
|
|
MPI_INT,MPI_SUM,comm_replica);
|
|
MPI_Bcast(&universeflag,1,MPI_INT,0,world);
|
|
ncoincident = universeflag;
|
|
if (!universeflag) ireplica = -1;
|
|
else {
|
|
if (universeflag > 1) {
|
|
int iwhich = static_cast<int>
|
|
(universeflag*random_select->uniform()) + 1;
|
|
if (me == 0) MPI_Scan(&worldflag,&scanflag,1,
|
|
MPI_INT,MPI_SUM,comm_replica);
|
|
MPI_Bcast(&scanflag,1,MPI_INT,0,world);
|
|
if (scanflag != iwhich) worldflag = 0;
|
|
}
|
|
|
|
if (worldflag) replicaflag = universe->iworld;
|
|
else replicaflag = 0;
|
|
if (me == 0) MPI_Allreduce(&replicaflag,&ireplica,1,
|
|
MPI_INT,MPI_SUM,comm_replica);
|
|
MPI_Bcast(&ireplica,1,MPI_INT,0,world);
|
|
}
|
|
timer->barrier_stop(TIME_LOOP);
|
|
time_comm += timer->array[TIME_LOOP];
|
|
return ireplica;
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
share quenched and hot coords owned by ireplica with all replicas
|
|
all replicas store event in fix_event
|
|
replica 0 dumps event snapshot
|
|
flag = 0 = called before PRD run
|
|
flag = 1 = called during PRD run = not correlated event
|
|
flag = 2 = called during PRD run = correlated event
|
|
------------------------------------------------------------------------- */
|
|
|
|
void PRD::share_event(int ireplica, int flag)
|
|
{
|
|
timer->barrier_start(TIME_LOOP);
|
|
|
|
// communicate quenched coords to all replicas and store as event
|
|
// decrement event counter if flag = 0 since not really an event
|
|
|
|
replicate(ireplica);
|
|
timer->barrier_stop(TIME_LOOP);
|
|
time_comm += timer->array[TIME_LOOP];
|
|
|
|
// adjust time for last correlated event check (not on first event)
|
|
|
|
int corr_adjust = t_corr;
|
|
if (fix_event->event_number < 1 || flag == 2) corr_adjust = 0;
|
|
|
|
// delta = time since last correlated event check
|
|
|
|
int delta = update->ntimestep - fix_event->event_timestep - corr_adjust;
|
|
|
|
// if this is a correlated event, time elapsed only on one partition
|
|
|
|
if (flag != 2) delta *= universe->nworlds;
|
|
delta += corr_adjust;
|
|
|
|
// don't change the clock or timestep if this is a restart
|
|
|
|
if (flag == 0 && fix_event->event_number != 0)
|
|
fix_event->store_event(fix_event->event_timestep,0);
|
|
else {
|
|
fix_event->store_event(update->ntimestep,delta);
|
|
fix_event->replica_number = ireplica;
|
|
fix_event->correlated_event = 0;
|
|
if (flag == 2) fix_event->correlated_event = 1;
|
|
fix_event->ncoincident = ncoincident;
|
|
}
|
|
if (flag == 0) fix_event->event_number--;
|
|
|
|
// dump snapshot of quenched coords
|
|
// must reneighbor and compute forces before dumping
|
|
// since replica 0 possibly has new state from another replica
|
|
// addstep_compute_all insures eng/virial are calculated if needed
|
|
|
|
if (output->ndump && universe->iworld == 0) {
|
|
timer->barrier_start(TIME_LOOP);
|
|
modify->addstep_compute_all(update->ntimestep);
|
|
update->integrate->setup_minimal(1);
|
|
output->write_dump(update->ntimestep);
|
|
timer->barrier_stop(TIME_LOOP);
|
|
time_output += timer->array[TIME_LOOP];
|
|
}
|
|
|
|
// restore and communicate hot coords to all replicas
|
|
|
|
fix_event->restore_state();
|
|
timer->barrier_start(TIME_LOOP);
|
|
replicate(ireplica);
|
|
timer->barrier_stop(TIME_LOOP);
|
|
time_comm += timer->array[TIME_LOOP];
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
universe proc 0 prints event info
|
|
------------------------------------------------------------------------- */
|
|
|
|
void PRD::log_event()
|
|
{
|
|
timer->array[TIME_LOOP] = time_start;
|
|
if (universe->me == 0) {
|
|
if (universe->uscreen)
|
|
fprintf(universe->uscreen,"%d %.3f %d %d %d %d %d\n",
|
|
fix_event->event_timestep,
|
|
timer->elapsed(TIME_LOOP),
|
|
fix_event->clock,
|
|
fix_event->event_number,fix_event->correlated_event,
|
|
fix_event->ncoincident,
|
|
fix_event->replica_number);
|
|
if (universe->ulogfile)
|
|
fprintf(universe->ulogfile,"%d %.3f %d %d %d %d %d\n",
|
|
fix_event->event_timestep,
|
|
timer->elapsed(TIME_LOOP),
|
|
fix_event->clock,
|
|
fix_event->event_number,fix_event->correlated_event,
|
|
fix_event->ncoincident,
|
|
fix_event->replica_number);
|
|
}
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
communicate atom coords and image flags in ireplica to all other replicas
|
|
one proc per replica:
|
|
direct overwrite via bcast
|
|
equal procs per replica and no replica reneighbored:
|
|
direct overwrite via bcast
|
|
unequal procs per replica or reneighboring occurred:
|
|
collect to root proc of event replica
|
|
bcast to roots of other replicas
|
|
bcast within each replica
|
|
each proc extracts info for atoms it owns using atom IDs
|
|
------------------------------------------------------------------------- */
|
|
|
|
void PRD::replicate(int ireplica)
|
|
{
|
|
int nreplica = universe->nworlds;
|
|
int nprocs_universe = universe->nprocs;
|
|
int i,m,flag,commflag;
|
|
int counts[nprocs];
|
|
|
|
if (nreplica == nprocs_universe) commflag = 0;
|
|
else if (equal_size_replicas) {
|
|
flag = 0;
|
|
if (quench_reneighbor) flag = 1;
|
|
MPI_Allreduce(&flag,&commflag,1,MPI_INT,MPI_MAX,universe->uworld);
|
|
} else commflag = 1;
|
|
|
|
if (commflag == 0) {
|
|
MPI_Bcast(atom->image,atom->nlocal,MPI_INT,ireplica,comm_replica);
|
|
MPI_Bcast(atom->x[0],3*atom->nlocal,MPI_DOUBLE,ireplica,comm_replica);
|
|
} else {
|
|
if (universe->iworld == ireplica) {
|
|
MPI_Gather(&atom->nlocal,1,MPI_INT,counts,1,MPI_INT,0,world);
|
|
displacements[0] = 0;
|
|
for (i = 0; i < nprocs-1; i++)
|
|
displacements[i+1] = displacements[i] + counts[i];
|
|
MPI_Gatherv(atom->tag,atom->nlocal,MPI_INT,
|
|
tagall,counts,displacements,MPI_INT,0,world);
|
|
MPI_Gatherv(atom->image,atom->nlocal,MPI_INT,
|
|
imageall,counts,displacements,MPI_INT,0,world);
|
|
for (i = 0; i < nprocs; i++) counts[i] *= 3;
|
|
for (i = 0; i < nprocs-1; i++)
|
|
displacements[i+1] = displacements[i] + counts[i];
|
|
MPI_Gatherv(atom->x[0],3*atom->nlocal,MPI_DOUBLE,
|
|
xall[0],counts,displacements,MPI_DOUBLE,0,world);
|
|
}
|
|
|
|
if (me == 0) {
|
|
MPI_Bcast(tagall,natoms,MPI_INT,ireplica,comm_replica);
|
|
MPI_Bcast(imageall,natoms,MPI_INT,ireplica,comm_replica);
|
|
MPI_Bcast(xall[0],3*natoms,MPI_DOUBLE,ireplica,comm_replica);
|
|
}
|
|
|
|
MPI_Bcast(tagall,natoms,MPI_INT,0,world);
|
|
MPI_Bcast(imageall,natoms,MPI_INT,0,world);
|
|
MPI_Bcast(xall[0],3*natoms,MPI_DOUBLE,0,world);
|
|
|
|
double **x = atom->x;
|
|
int nlocal = atom->nlocal;
|
|
|
|
for (i = 0; i < natoms; i++) {
|
|
m = atom->map(tagall[i]);
|
|
if (m >= 0 && m < nlocal) {
|
|
x[m][0] = xall[i][0];
|
|
x[m][1] = xall[i][1];
|
|
x[m][2] = xall[i][2];
|
|
atom->image[m] = imageall[i];
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
parse optional parameters at end of PRD input line
|
|
------------------------------------------------------------------------- */
|
|
|
|
void PRD::options(int narg, char **arg)
|
|
{
|
|
if (narg < 0) error->all("Illegal prd command");
|
|
|
|
// set defaults
|
|
|
|
etol = 0.1;
|
|
ftol = 0.1;
|
|
maxiter = 40;
|
|
maxeval = 50;
|
|
temp_flag = 0;
|
|
|
|
char *str = "geom";
|
|
int n = strlen(str) + 1;
|
|
loop_setting = new char[n];
|
|
strcpy(loop_setting,str);
|
|
|
|
str = "gaussian";
|
|
n = strlen(str) + 1;
|
|
dist_setting = new char[n];
|
|
strcpy(dist_setting,str);
|
|
|
|
int iarg = 0;
|
|
while (iarg < narg) {
|
|
if (strcmp(arg[iarg],"min") == 0) {
|
|
if (iarg+5 > narg) error->all("Illegal prd command");
|
|
etol = atof(arg[iarg+1]);
|
|
ftol = atof(arg[iarg+2]);
|
|
maxiter = atoi(arg[iarg+3]);
|
|
maxeval = atoi(arg[iarg+4]);
|
|
if (maxiter < 0) error->all("Illegal prd command");
|
|
iarg += 5;
|
|
|
|
} else if (strcmp(arg[iarg],"temp") == 0) {
|
|
if (iarg+2 > narg) error->all("Illegal prd command");
|
|
temp_flag = 1;
|
|
temp_dephase = atof(arg[iarg+1]);
|
|
if (temp_dephase <= 0.0) error->all("Illegal prd command");
|
|
iarg += 2;
|
|
|
|
} else if (strcmp(arg[iarg],"vel") == 0) {
|
|
if (iarg+3 > narg) error->all("Illegal prd command");
|
|
delete [] loop_setting;
|
|
delete [] dist_setting;
|
|
|
|
if (strcmp(arg[iarg+1],"all") == 0) loop_setting = NULL;
|
|
else if (strcmp(arg[iarg+1],"local") == 0) loop_setting = NULL;
|
|
else if (strcmp(arg[iarg+1],"geom") == 0) loop_setting = NULL;
|
|
else error->all("Illegal prd command");
|
|
int n = strlen(arg[iarg+1]) + 1;
|
|
loop_setting = new char[n];
|
|
strcpy(loop_setting,arg[iarg+1]);
|
|
|
|
if (strcmp(arg[iarg+2],"uniform") == 0) dist_setting = NULL;
|
|
else if (strcmp(arg[iarg+2],"gaussian") == 0) dist_setting = NULL;
|
|
else error->all("Illegal prd command");
|
|
n = strlen(arg[iarg+2]) + 1;
|
|
dist_setting = new char[n];
|
|
strcpy(dist_setting,arg[iarg+2]);
|
|
|
|
iarg += 3;
|
|
} else error->all("Illegal prd command");
|
|
}
|
|
}
|