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lammps/src/output.cpp
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output.cpp
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "stdio.h"
#include "stdlib.h"
#include "string.h"
#include "output.h"
#include "style_dump.h"
#include "atom.h"
#include "neighbor.h"
#include "comm.h"
#include "update.h"
#include "group.h"
#include "domain.h"
#include "thermo.h"
#include "modify.h"
#include "compute.h"
#include "force.h"
#include "dump.h"
#include "write_restart.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define DELTA 1
#define MYMIN(a,b) ((a) < (b) ? (a) : (b))
#define MYMAX(a,b) ((a) > (b) ? (a) : (b))
/* ----------------------------------------------------------------------
initialize all output
------------------------------------------------------------------------- */
Output::Output(LAMMPS *lmp) : Pointers(lmp)
{
// create default computes for temp,pressure,pe
char **newarg = new char*[4];
newarg[0] = (char *) "thermo_temp";
newarg[1] = (char *) "all";
newarg[2] = (char *) "temp";
modify->add_compute(3,newarg);
newarg[0] = (char *) "thermo_press";
newarg[1] = (char *) "all";
newarg[2] = (char *) "pressure";
newarg[3] = (char *) "thermo_temp";
modify->add_compute(4,newarg);
newarg[0] = (char *) "thermo_pe";
newarg[1] = (char *) "all";
newarg[2] = (char *) "pe";
modify->add_compute(3,newarg);
delete [] newarg;
// create default Thermo class
newarg = new char*[1];
newarg[0] = (char *) "one";
thermo = new Thermo(lmp,1,newarg);
delete [] newarg;
thermo_every = 0;
ndump = 0;
max_dump = 0;
next_dump = NULL;
last_dump = NULL;
dump_every = NULL;
dump = NULL;
restart = NULL;
restart1 = restart2 = NULL;
restart_every = 0;
last_restart = -1;
}
/* ----------------------------------------------------------------------
free all memory
------------------------------------------------------------------------- */
Output::~Output()
{
if (thermo) delete thermo;
memory->sfree(next_dump);
memory->sfree(last_dump);
memory->sfree(dump_every);
for (int i = 0; i < ndump; i++) delete dump[i];
memory->sfree(dump);
delete restart;
delete [] restart1;
delete [] restart2;
}
/* ---------------------------------------------------------------------- */
void Output::init()
{
thermo->init();
for (int i = 0; i < ndump; i++) dump[i]->init();
}
/* ----------------------------------------------------------------------
perform output for setup of run/min
do dump first, so memory_usage will include dump allocation
do thermo last, so will print after memory_usage
------------------------------------------------------------------------- */
void Output::setup(int flag)
{
int ntimestep = update->ntimestep;
// perform dump at start of run if current timestep is multiple of every
// and last dump was not on this timestep
// set next_dump to multiple of every
// will not write on last step of run unless multiple of every
// set next_dump_any to smallest next_dump
// if no dumps, set next_dump_any to last+1 so will not influence next
// wrap dumps that invoke computes with clear/add
if (ndump && update->restrict_output == 0) {
for (int idump = 0; idump < ndump; idump++) {
if (dump[idump]->clearstep) modify->clearstep_compute();
if ((ntimestep % dump_every[idump] == 0 &&
last_dump[idump] != ntimestep) || last_dump[idump] < 0) {
dump[idump]->write();
last_dump[idump] = ntimestep;
}
next_dump[idump] =
(ntimestep/dump_every[idump])*dump_every[idump] + dump_every[idump];
if (dump[idump]->clearstep) modify->addstep_compute(next_dump[idump]);
if (idump) next_dump_any = MYMIN(next_dump_any,next_dump[idump]);
else next_dump_any = next_dump[0];
}
} else next_dump_any = update->laststep + 1;
// do not write a restart file at start of run
// set next_restart to multiple of every
// will not write on last step of run unless multiple of every
// if every = 0, set next_restart to last+1 so will not influence next
if (restart_every && update->restrict_output == 0)
next_restart = (ntimestep/restart_every)*restart_every + restart_every;
else next_restart = update->laststep + 1;
// print memory usage unless being called between multiple runs
if (flag) memory_usage();
// always do thermo with header at start of run
// set next_thermo to multiple of every or last step of run (if smaller)
// if every = 0, set next_thermo to last step of run
// thermo may invoke computes so wrap with clear/add
modify->clearstep_compute();
thermo->header();
thermo->compute(0);
last_thermo = ntimestep;
if (thermo_every) {
next_thermo = (ntimestep/thermo_every)*thermo_every + thermo_every;
next_thermo = MYMIN(next_thermo,update->laststep);
} else next_thermo = update->laststep;
modify->addstep_compute(next_thermo);
// next = next timestep any output will be done
next = MYMIN(next_dump_any,next_restart);
next = MYMIN(next,next_thermo);
}
/* ----------------------------------------------------------------------
perform all output for this timestep
only perform output if next matches current step and last doesn't
do dump/restart before thermo so thermo CPU time will include them
------------------------------------------------------------------------- */
void Output::write(int ntimestep)
{
// next_dump does not force output on last step of run
// wrap dumps that invoke computes with clear/add
if (next_dump_any == ntimestep) {
for (int idump = 0; idump < ndump; idump++) {
if (next_dump[idump] == ntimestep && last_dump[idump] != ntimestep) {
if (dump[idump]->clearstep) modify->clearstep_compute();
dump[idump]->write();
last_dump[idump] = ntimestep;
next_dump[idump] += dump_every[idump];
if (dump[idump]->clearstep) modify->addstep_compute(next_dump[idump]);
}
if (idump) next_dump_any = MYMIN(next_dump_any,next_dump[idump]);
else next_dump_any = next_dump[0];
}
}
// next_restart does not force output on last step of run
// for toggle = 0, replace "*" with current timestep in restart filename
if (next_restart == ntimestep && last_restart != ntimestep) {
if (restart_toggle == 0) {
char *file = new char[strlen(restart1) + 16];
char *ptr = strchr(restart1,'*');
*ptr = '\0';
sprintf(file,"%s%d%s",restart1,ntimestep,ptr+1);
*ptr = '*';
restart->write(file);
delete [] file;
} else if (restart_toggle == 1) {
restart->write(restart1);
restart_toggle = 2;
} else if (restart_toggle == 2) {
restart->write(restart2);
restart_toggle = 1;
}
last_restart = ntimestep;
next_restart += restart_every;
}
// insure next_thermo forces output on last step of run
// thermo may invoke computes so wrap with clear/add
if (next_thermo == ntimestep && last_thermo != ntimestep) {
modify->clearstep_compute();
thermo->compute(1);
last_thermo = ntimestep;
next_thermo += thermo_every;
next_thermo = MYMIN(next_thermo,update->laststep);
modify->addstep_compute(next_thermo);
}
// next = next timestep any output will be done
next = MYMIN(next_dump_any,next_restart);
next = MYMIN(next,next_thermo);
}
/* ----------------------------------------------------------------------
force a snapshot to be written for all dumps
------------------------------------------------------------------------- */
void Output::write_dump(int ntimestep)
{
for (int idump = 0; idump < ndump; idump++) {
dump[idump]->write();
last_dump[idump] = ntimestep;
}
}
/* ----------------------------------------------------------------------
force a restart file to be written
------------------------------------------------------------------------- */
void Output::write_restart(int ntimestep)
{
if (restart_toggle == 0) {
char *file = new char[strlen(restart1) + 16];
char *ptr = strchr(restart1,'*');
*ptr = '\0';
sprintf(file,"%s%d%s",restart1,ntimestep,ptr+1);
*ptr = '*';
restart->write(file);
delete [] file;
} else if (restart_toggle == 1) {
restart->write(restart1);
restart_toggle = 2;
} else if (restart_toggle == 2) {
restart->write(restart2);
restart_toggle = 1;
}
last_restart = ntimestep;
}
/* ----------------------------------------------------------------------
add a Dump to list of Dumps
------------------------------------------------------------------------- */
void Output::add_dump(int narg, char **arg)
{
if (narg < 5) error->all("Illegal dump command");
// error checks
for (int idump = 0; idump < ndump; idump++)
if (strcmp(arg[0],dump[idump]->id) == 0) error->all("Reuse of dump ID");
int igroup = group->find(arg[1]);
if (igroup == -1) error->all("Could not find dump group ID");
if (atoi(arg[3]) <= 0) error->all("Invalid dump frequency");
// extend Dump list if necessary
if (ndump == max_dump) {
max_dump += DELTA;
dump = (Dump **)
memory->srealloc(dump,max_dump*sizeof(Dump *),"output:dump");
dump_every = (int *)
memory->srealloc(dump_every,max_dump*sizeof(int *),"output:dump_every");
next_dump = (int *)
memory->srealloc(next_dump,max_dump*sizeof(int *),"output:next_dump");
last_dump = (int *)
memory->srealloc(last_dump,max_dump*sizeof(int *),"output:last_dump");
}
// create the Dump
if (0) return; // dummy line to enable else-if macro expansion
#define DUMP_CLASS
#define DumpStyle(key,Class) \
else if (strcmp(arg[2],#key) == 0) dump[ndump] = new Class(lmp,narg,arg);
#include "style_dump.h"
#undef DUMP_CLASS
else error->all("Invalid dump style");
dump_every[ndump] = atoi(arg[3]);
if (dump_every[ndump] <= 0) error->all("Illegal dump command");
last_dump[ndump] = -1;
ndump++;
}
/* ----------------------------------------------------------------------
modify parameters of a Dump
------------------------------------------------------------------------- */
void Output::modify_dump(int narg, char **arg)
{
if (narg < 1) error->all("Illegal dump_modify command");
// find which dump it is
int idump;
for (idump = 0; idump < ndump; idump++)
if (strcmp(arg[0],dump[idump]->id) == 0) break;
if (idump == ndump) error->all("Cound not find dump_modify ID");
dump[idump]->modify_params(narg-1,&arg[1]);
}
/* ----------------------------------------------------------------------
delete a Dump from list of Dumps
------------------------------------------------------------------------- */
void Output::delete_dump(char *id)
{
// find which dump it is and delete it
int idump;
for (idump = 0; idump < ndump; idump++)
if (strcmp(id,dump[idump]->id) == 0) break;
if (idump == ndump) error->all("Could not find undump ID");
delete dump[idump];
// move other dumps down in list one slot
for (int i = idump+1; i < ndump; i++) {
dump[i-1] = dump[i];
dump_every[i-1] = dump_every[i];
next_dump[i-1] = next_dump[i];
last_dump[i-1] = last_dump[i];
}
ndump--;
}
/* ----------------------------------------------------------------------
new Thermo style
------------------------------------------------------------------------- */
void Output::create_thermo(int narg, char **arg)
{
if (narg < 1) error->all("Illegal thermo_style command");
// don't allow this so that dipole style can safely allocate inertia vector
if (domain->box_exist == 0)
error->all("Thermo_style command before simulation box is defined");
// warn if previous thermo had been modified via thermo_modify command
if (thermo->modified && comm->me == 0)
error->warning("New thermo_style command, "
"previous thermo_modify settings will be lost");
// set thermo = NULL in case new Thermo throws an error
delete thermo;
thermo = NULL;
thermo = new Thermo(lmp,narg,arg);
}
/* ----------------------------------------------------------------------
setup restart capability
if only one filename and it contains no "*", then append ".*"
------------------------------------------------------------------------- */
void Output::create_restart(int narg, char **arg)
{
if (narg < 1) error->all("Illegal restart command");
if (restart) delete restart;
delete [] restart1;
delete [] restart2;
restart = NULL;
restart1 = restart2 = NULL;
last_restart = -1;
restart_every = atoi(arg[0]);
if (restart_every == 0) {
if (narg != 1) error->all("Illegal restart command");
return;
}
restart = new WriteRestart(lmp);
int n = strlen(arg[1]) + 3;
restart1 = new char[n];
strcpy(restart1,arg[1]);
if (narg == 2) {
restart_toggle = 0;
restart2 = NULL;
if (strchr(restart1,'*') == NULL) strcat(restart1,".*");
} else if (narg == 3) {
restart_toggle = 1;
n = strlen(arg[2]) + 1;
restart2 = new char[n];
strcpy(restart2,arg[2]);
} else error->all("Illegal restart command");
}
/* ----------------------------------------------------------------------
sum and print memory usage
is only memory on proc 0, not averaged across procs
------------------------------------------------------------------------- */
void Output::memory_usage()
{
double bytes = 0.0;
bytes += atom->memory_usage();
bytes += neighbor->memory_usage();
bytes += comm->memory_usage();
bytes += update->memory_usage();
bytes += force->memory_usage();
bytes += modify->memory_usage();
for (int i = 0; i < ndump; i++) bytes += dump[i]->memory_usage();
double mbytes = bytes/1024.0/1024.0;
if (comm->me == 0) {
if (screen)
fprintf(screen,"Memory usage per processor = %g Mbytes\n",mbytes);
if (logfile)
fprintf(logfile,"Memory usage per processor = %g Mbytes\n",mbytes);
}
}
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