git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@254 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
355
src/lammps.cpp
355
src/lammps.cpp
@ -1,7 +1,7 @@
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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www.cs.sandia.gov/~sjplimp/lammps.html
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Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
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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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@ -11,54 +11,325 @@
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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// parent class for all of LAMMPS
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// all other classes inherit from this
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// contains static ptrs to single instance of other classes
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// contains MPI communicator and file handles for my world of procs
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#include "mpi.h"
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#include "stdlib.h"
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#include "string.h"
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#include "lammps.h"
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#include "system.h"
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#include "memory.h"
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#include "error.h"
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#include "universe.h"
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#include "input.h"
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#include "atom.h"
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#include "update.h"
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#include "neighbor.h"
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#include "comm.h"
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#include "domain.h"
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#include "force.h"
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#include "modify.h"
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#include "group.h"
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#include "output.h"
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#include "timer.h"
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// set static ptrs to NULL
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using namespace LAMMPS_NS;
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System *LAMMPS::sys = NULL;
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Universe *LAMMPS::universe = NULL;
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Input *LAMMPS::input = NULL;
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Memory *LAMMPS::memory = NULL;
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Error *LAMMPS::error = NULL;
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/* ----------------------------------------------------------------------
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start up LAMMPS
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allocate fundamental classes (memory, error, universe, input)
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parse input switches
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initialize communicators, screen & logfile output
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input is allocated at end after MPI info is setup
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------------------------------------------------------------------------- */
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Atom *LAMMPS::atom = NULL;
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Update *LAMMPS::update = NULL;
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Neighbor *LAMMPS::neighbor = NULL;
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Comm *LAMMPS::comm = NULL;
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Domain *LAMMPS::domain = NULL;
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Force *LAMMPS::force = NULL;
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Modify *LAMMPS::modify = NULL;
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Group *LAMMPS::group = NULL;
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Output *LAMMPS::output = NULL;
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Timer *LAMMPS::timer = NULL;
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MPI_Comm LAMMPS::world = 0;
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FILE *LAMMPS::infile = NULL;
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FILE *LAMMPS::screen = NULL;
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FILE *LAMMPS::logfile = NULL;
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/* ---------------------------------------------------------------------- */
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void LAMMPS::open(int narg, char **arg, MPI_Comm communicator)
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LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator)
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{
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sys = new System();
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sys->open(narg,arg,communicator);
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sys->create();
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memory = new Memory(this);
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error = new Error(this);
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universe = new Universe(this,communicator);
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// parse input switches
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int inflag = 0;
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int screenflag = 0;
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int logflag = 0;
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int iarg = 1;
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while (iarg < narg) {
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if (strcmp(arg[iarg],"-partition") == 0) {
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if (iarg+1 > narg)
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error->universe_all("Invalid command-line argument");
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iarg++;
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while (iarg < narg && arg[iarg][0] != '-') {
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universe->add_world(arg[iarg]);
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iarg++;
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}
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} else if (strcmp(arg[iarg],"-in") == 0) {
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if (iarg+2 > narg)
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error->universe_all("Invalid command-line argument");
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inflag = iarg + 1;
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iarg += 2;
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} else if (strcmp(arg[iarg],"-screen") == 0) {
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if (iarg+2 > narg)
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error->universe_all("Invalid command-line argument");
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screenflag = iarg + 1;
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iarg += 2;
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} else if (strcmp(arg[iarg],"-log") == 0) {
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if (iarg+2 > narg)
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error->universe_all("Invalid command-line argument");
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logflag = iarg + 1;
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iarg += 2;
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} else if (strcmp(arg[iarg],"-var") == 0) {
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if (iarg+3 > narg)
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error->universe_all("Invalid command-line argument");
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iarg += 3;
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} else if (strcmp(arg[iarg],"-echo") == 0) {
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if (iarg+2 > narg)
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error->universe_all("Invalid command-line argument");
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iarg += 2;
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} else error->universe_all("Invalid command-line argument");
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}
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// if procs was not a command-line switch, universe is one world w/ all procs
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if (universe->nworlds == 0) universe->add_world(NULL);
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// sum of procs in all worlds must equal total # of procs
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if (!universe->consistent())
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error->universe_all("Processor partitions are inconsistent");
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// multiple-world universe must define input file
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if (universe->nworlds > 1 && inflag == 0)
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error->universe_all("Must use -in switch with multiple partitions");
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// set universe screen and logfile
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if (universe->me == 0) {
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if (screenflag == 0)
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universe->uscreen = stdout;
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else if (strcmp(arg[screenflag],"none") == 0)
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universe->uscreen = NULL;
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else {
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universe->uscreen = fopen(arg[screenflag],"w");
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if (universe->uscreen == NULL)
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error->universe_one("Cannot open universe screen file");
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}
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if (logflag == 0) {
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universe->ulogfile = fopen("log.lammps","w");
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if (universe->ulogfile == NULL)
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error->universe_one("Cannot open log.lammps");
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} else if (strcmp(arg[logflag],"none") == 0)
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universe->ulogfile = NULL;
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else {
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universe->ulogfile = fopen(arg[logflag],"w");
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if (universe->ulogfile == NULL)
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error->universe_one("Cannot open universe log file");
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}
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}
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if (universe->me > 0) {
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if (screenflag == 0) universe->uscreen = stdout;
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else universe->uscreen = NULL;
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universe->ulogfile = NULL;
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}
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// universe is single world
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// inherit settings from universe
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// set world screen, logfile, communicator, infile
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// open input script if from file
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if (universe->nworlds == 1) {
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screen = universe->uscreen;
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logfile = universe->ulogfile;
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world = universe->uworld;
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infile = NULL;
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if (universe->me == 0) {
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if (inflag == 0) infile = stdin;
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else infile = fopen(arg[inflag],"r");
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if (infile == NULL) {
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char str[128];
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sprintf(str,"Cannot open input script %s",arg[inflag]);
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error->one(str);
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}
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}
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if (universe->me == 0) {
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if (screen) fprintf(screen,"LAMMPS (%s)\n",universe->version);
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if (logfile) fprintf(logfile,"LAMMPS (%s)\n",universe->version);
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}
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// universe is multiple worlds
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// split into separate communicators
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// set world screen, logfile, communicator, infile
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// open input script
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} else {
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int me;
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MPI_Comm_split(universe->uworld,universe->iworld,0,&world);
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MPI_Comm_rank(world,&me);
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if (me == 0) {
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if (screenflag == 0) {
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char str[32];
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sprintf(str,"screen.%d",universe->iworld);
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screen = fopen(str,"w");
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if (screen == NULL) error->one("Cannot open screen file");
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} else if (strcmp(arg[screenflag],"none") == 0)
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screen = NULL;
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else {
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char str[128];
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sprintf(str,"%s.%d",arg[screenflag],universe->iworld);
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screen = fopen(str,"w");
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if (screen == NULL) error->one("Cannot open screen file");
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}
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} else screen = NULL;
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if (me == 0) {
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if (logflag == 0) {
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char str[32];
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sprintf(str,"log.lammps.%d",universe->iworld);
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logfile = fopen(str,"w");
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if (logfile == NULL) error->one("Cannot open logfile");
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} else if (strcmp(arg[logflag],"none") == 0)
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logfile = NULL;
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else {
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char str[128];
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sprintf(str,"%s.%d",arg[logflag],universe->iworld);
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logfile = fopen(str,"w");
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if (logfile == NULL) error->one("Cannot open logfile");
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}
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} else logfile = NULL;
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if (me == 0) {
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infile = fopen(arg[inflag],"r");
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if (infile == NULL) {
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char str[128];
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sprintf(str,"Cannot open input script %s",arg[inflag]);
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error->one(str);
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}
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} else infile = NULL;
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// screen and logfile messages for universe and world
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if (universe->me == 0) {
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if (universe->uscreen) {
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fprintf(universe->uscreen,"LAMMPS (%s)\n",universe->version);
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fprintf(universe->uscreen,"Running on %d partitions of processors\n",
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universe->nworlds);
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}
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if (universe->ulogfile) {
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fprintf(universe->ulogfile,"LAMMPS (%s)\n",universe->version);
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fprintf(universe->ulogfile,"Running on %d partitions of processors\n",
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universe->nworlds);
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}
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}
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if (me == 0) {
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if (screen) {
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fprintf(screen,"LAMMPS (%s)\n",universe->version);
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fprintf(screen,"Processor partition = %d\n",universe->iworld);
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}
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if (logfile) {
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fprintf(logfile,"LAMMPS (%s)\n",universe->version);
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fprintf(logfile,"Processor partition = %d\n",universe->iworld);
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}
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}
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}
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// allocate input class now that MPI is fully setup
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input = new Input(this,narg,arg);
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// allocate top-level classes
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create();
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}
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/* ---------------------------------------------------------------------- */
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/* ----------------------------------------------------------------------
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shutdown LAMMPS
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delete top-level classes
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close screen and log files in world and universe
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output files were already closed in destroy()
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delete fundamental classes
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------------------------------------------------------------------------- */
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void LAMMPS::close()
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LAMMPS::~LAMMPS()
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{
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sys->destroy();
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sys->close();
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delete sys;
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destroy();
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if (universe->nworlds == 1) {
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if (logfile) fclose(logfile);
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} else {
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if (screen && screen != stdout) fclose(screen);
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if (logfile) fclose(logfile);
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if (universe->ulogfile) fclose(universe->ulogfile);
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}
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if (world != universe->uworld) MPI_Comm_free(&world);
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delete input;
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delete universe;
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delete error;
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delete memory;
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}
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/* ----------------------------------------------------------------------
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allocate single instance of top-level classes
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fundamental classes are allocated in constructor
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------------------------------------------------------------------------- */
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void LAMMPS::create()
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{
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atom = new Atom(this);
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neighbor = new Neighbor(this);
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comm = new Comm(this);
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domain = new Domain(this);
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group = new Group(this);
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force = new Force(this); // must be after group, to create temperature
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modify = new Modify(this);
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output = new Output(this); // must be after group, so "all" exists
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// must be after modify so can create Computes
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update = new Update(this); // must be after output, force, neighbor
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timer = new Timer(this);
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}
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/* ----------------------------------------------------------------------
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initialize top-level classes
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------------------------------------------------------------------------- */
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void LAMMPS::init()
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{
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update->init();
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force->init();
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domain->init();
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atom->init(); // atom must come after force:
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// atom deletes extra array
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// used by fix shear_history::unpack_restart()
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// when force->pair->gran_history creates fix ??
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modify->init(); // modify must come after update, force, atom
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neighbor->init(); // neighbor must come after force, modify (due to min)
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output->init(); // output must come after domain, force, modify
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comm->init(); // comm must come after force, modify
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timer->init();
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}
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/* ----------------------------------------------------------------------
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delete single instance of top-level classes
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fundamental classes are deleted in destructor
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------------------------------------------------------------------------- */
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void LAMMPS::destroy()
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{
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delete update;
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delete neighbor;
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delete comm;
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delete domain;
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delete force;
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delete group;
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delete output;
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delete modify; // modify must come after output, force, update
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// since they delete fixes
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delete atom; // must come after modify
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// since fixes delete callbacks in atom
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delete timer;
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}
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