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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8226 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2012-06-06 22:47:51 +00:00
parent f46eb9dedb
commit ef9e700545
1408 changed files with 58053 additions and 57983 deletions
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154
src/output.cpp
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@ -5,7 +5,7 @@
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
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.
@ -39,7 +39,7 @@ using namespace LAMMPS_NS;
#define DELTA 1
/* ----------------------------------------------------------------------
initialize all output
initialize all output
------------------------------------------------------------------------- */
Output::Output(LAMMPS *lmp) : Pointers(lmp)
@ -71,10 +71,10 @@ Output::Output(LAMMPS *lmp) : Pointers(lmp)
newarg[0] = (char *) "one";
thermo = new Thermo(lmp,1,newarg);
delete [] newarg;
thermo_every = 0;
var_thermo = NULL;
ndump = 0;
max_dump = 0;
every_dump = NULL;
@ -92,7 +92,7 @@ Output::Output(LAMMPS *lmp) : Pointers(lmp)
}
/* ----------------------------------------------------------------------
free all memory
free all memory
------------------------------------------------------------------------- */
Output::~Output()
@ -136,9 +136,9 @@ void Output::init()
if (every_dump[i] == 0) {
ivar_dump[i] = input->variable->find(var_dump[i]);
if (ivar_dump[i] < 0)
error->all(FLERR,"Variable name for dump every does not exist");
error->all(FLERR,"Variable name for dump every does not exist");
if (!input->variable->equalstyle(ivar_dump[i]))
error->all(FLERR,"Variable for dump every is invalid style");
error->all(FLERR,"Variable for dump every is invalid style");
}
if (restart_flag_single && restart_every_single == 0) {
@ -182,26 +182,26 @@ void Output::setup(int flag)
for (int idump = 0; idump < ndump; idump++) {
if (dump[idump]->clearstep) modify->clearstep_compute();
writeflag = 0;
if (every_dump[idump] && ntimestep % every_dump[idump] == 0 &&
last_dump[idump] != ntimestep) writeflag = 1;
if (every_dump[idump] && ntimestep % every_dump[idump] == 0 &&
last_dump[idump] != ntimestep) writeflag = 1;
if (last_dump[idump] < 0 && dump[idump]->first_flag == 1) writeflag = 1;
if (writeflag) {
dump[idump]->write();
last_dump[idump] = ntimestep;
dump[idump]->write();
last_dump[idump] = ntimestep;
}
if (every_dump[idump])
next_dump[idump] =
(ntimestep/every_dump[idump])*every_dump[idump] + every_dump[idump];
next_dump[idump] =
(ntimestep/every_dump[idump])*every_dump[idump] + every_dump[idump];
else {
bigint nextdump = static_cast<bigint>
(input->variable->compute_equal(ivar_dump[idump]));
if (nextdump <= ntimestep)
error->all(FLERR,"Dump every variable returned a bad timestep");
next_dump[idump] = nextdump;
bigint nextdump = static_cast<bigint>
(input->variable->compute_equal(ivar_dump[idump]));
if (nextdump <= ntimestep)
error->all(FLERR,"Dump every variable returned a bad timestep");
next_dump[idump] = nextdump;
}
if (dump[idump]->clearstep) {
if (writeflag) modify->addstep_compute(next_dump[idump]);
else modify->addstep_compute_all(next_dump[idump]);
if (writeflag) modify->addstep_compute(next_dump[idump]);
else modify->addstep_compute_all(next_dump[idump]);
}
if (idump) next_dump_any = MIN(next_dump_any,next_dump[idump]);
else next_dump_any = next_dump[0];
@ -216,28 +216,28 @@ void Output::setup(int flag)
if (restart_flag && update->restrict_output == 0) {
if (restart_flag_single) {
if (restart_every_single)
next_restart_single =
(ntimestep/restart_every_single)*restart_every_single +
restart_every_single;
next_restart_single =
(ntimestep/restart_every_single)*restart_every_single +
restart_every_single;
else {
bigint nextrestart = static_cast<bigint>
(input->variable->compute_equal(ivar_restart_single));
if (nextrestart <= ntimestep)
error->all(FLERR,"Restart variable returned a bad timestep");
next_restart_single = nextrestart;
bigint nextrestart = static_cast<bigint>
(input->variable->compute_equal(ivar_restart_single));
if (nextrestart <= ntimestep)
error->all(FLERR,"Restart variable returned a bad timestep");
next_restart_single = nextrestart;
}
} else next_restart_single = update->laststep + 1;
if (restart_flag_double) {
if (restart_every_double)
next_restart_double =
(ntimestep/restart_every_double)*restart_every_double +
restart_every_double;
next_restart_double =
(ntimestep/restart_every_double)*restart_every_double +
restart_every_double;
else {
bigint nextrestart = static_cast<bigint>
(input->variable->compute_equal(ivar_restart_double));
if (nextrestart <= ntimestep)
error->all(FLERR,"Restart variable returned a bad timestep");
next_restart_double = nextrestart;
bigint nextrestart = static_cast<bigint>
(input->variable->compute_equal(ivar_restart_double));
if (nextrestart <= ntimestep)
error->all(FLERR,"Restart variable returned a bad timestep");
next_restart_double = nextrestart;
}
} else next_restart_double = update->laststep + 1;
next_restart = MIN(next_restart_single,next_restart_double);
@ -262,7 +262,7 @@ void Output::setup(int flag)
next_thermo = (ntimestep/thermo_every)*thermo_every + thermo_every;
next_thermo = MIN(next_thermo,update->laststep);
} else if (var_thermo) {
next_thermo = static_cast<bigint>
next_thermo = static_cast<bigint>
(input->variable->compute_equal(ivar_thermo));
if (next_thermo <= ntimestep)
error->all(FLERR,"Thermo every variable returned a bad timestep");
@ -289,21 +289,21 @@ void Output::write(bigint ntimestep)
// download data from GPU if necessary
if (next_dump_any == ntimestep) {
if (lmp->cuda && !lmp->cuda->oncpu) lmp->cuda->downloadAll();
if (lmp->cuda && !lmp->cuda->oncpu) lmp->cuda->downloadAll();
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;
if (every_dump[idump]) next_dump[idump] += every_dump[idump];
else {
bigint nextdump = static_cast<bigint>
(input->variable->compute_equal(ivar_dump[idump]));
if (nextdump <= ntimestep)
error->all(FLERR,"Dump every variable returned a bad timestep");
next_dump[idump] = nextdump;
}
dump[idump]->write();
last_dump[idump] = ntimestep;
if (every_dump[idump]) next_dump[idump] += every_dump[idump];
else {
bigint nextdump = static_cast<bigint>
(input->variable->compute_equal(ivar_dump[idump]));
if (nextdump <= ntimestep)
error->all(FLERR,"Dump every variable returned a bad timestep");
next_dump[idump] = nextdump;
}
if (dump[idump]->clearstep) modify->addstep_compute(next_dump[idump]);
}
if (idump) next_dump_any = MIN(next_dump_any,next_dump[idump]);
@ -316,8 +316,8 @@ void Output::write(bigint ntimestep)
// download data from GPU if necessary
if (next_restart == ntimestep && last_restart != ntimestep) {
if (lmp->cuda && !lmp->cuda->oncpu) lmp->cuda->downloadAll();
if (lmp->cuda && !lmp->cuda->oncpu) lmp->cuda->downloadAll();
if (next_restart_single == ntimestep) {
char *file = new char[strlen(restart1) + 16];
char *ptr = strchr(restart1,'*');
@ -328,28 +328,28 @@ void Output::write(bigint ntimestep)
delete [] file;
if (restart_every_single) next_restart_single += restart_every_single;
else {
bigint nextrestart = static_cast<bigint>
(input->variable->compute_equal(ivar_restart_single));
if (nextrestart <= ntimestep)
error->all(FLERR,"Restart variable returned a bad timestep");
next_restart_single = nextrestart;
bigint nextrestart = static_cast<bigint>
(input->variable->compute_equal(ivar_restart_single));
if (nextrestart <= ntimestep)
error->all(FLERR,"Restart variable returned a bad timestep");
next_restart_single = nextrestart;
}
}
if (next_restart_double == ntimestep) {
if (restart_toggle == 0) {
restart->write(restart2a);
restart_toggle = 1;
restart->write(restart2a);
restart_toggle = 1;
} else {
restart->write(restart2b);
restart_toggle = 0;
restart->write(restart2b);
restart_toggle = 0;
}
if (restart_every_double) next_restart_double += restart_every_double;
else {
bigint nextrestart = static_cast<bigint>
(input->variable->compute_equal(ivar_restart_double));
if (nextrestart <= ntimestep)
error->all(FLERR,"Restart variable returned a bad timestep");
next_restart_double = nextrestart;
bigint nextrestart = static_cast<bigint>
(input->variable->compute_equal(ivar_restart_double));
if (nextrestart <= ntimestep)
error->all(FLERR,"Restart variable returned a bad timestep");
next_restart_double = nextrestart;
}
}
last_restart = ntimestep;
@ -365,10 +365,10 @@ void Output::write(bigint ntimestep)
last_thermo = ntimestep;
if (thermo_every) next_thermo += thermo_every;
else if (var_thermo) {
next_thermo = static_cast<bigint>
(input->variable->compute_equal(ivar_thermo));
next_thermo = static_cast<bigint>
(input->variable->compute_equal(ivar_thermo));
if (next_thermo <= ntimestep)
error->all(FLERR,"Thermo every variable returned a bad timestep");
error->all(FLERR,"Thermo every variable returned a bad timestep");
} else next_thermo = update->laststep;
next_thermo = MIN(next_thermo,update->laststep);
modify->addstep_compute(next_thermo);
@ -423,7 +423,7 @@ void Output::write_restart(bigint ntimestep)
}
/* ----------------------------------------------------------------------
add a Dump to list of Dumps
add a Dump to list of Dumps
------------------------------------------------------------------------- */
void Output::add_dump(int narg, char **arg)
@ -433,7 +433,7 @@ void Output::add_dump(int narg, char **arg)
// error checks
for (int idump = 0; idump < ndump; idump++)
if (strcmp(arg[0],dump[idump]->id) == 0)
if (strcmp(arg[0],dump[idump]->id) == 0)
error->all(FLERR,"Reuse of dump ID");
int igroup = group->find(arg[1]);
if (igroup == -1) error->all(FLERR,"Could not find dump group ID");
@ -473,7 +473,7 @@ void Output::add_dump(int narg, char **arg)
}
/* ----------------------------------------------------------------------
modify parameters of a Dump
modify parameters of a Dump
------------------------------------------------------------------------- */
void Output::modify_dump(int narg, char **arg)
@ -491,7 +491,7 @@ void Output::modify_dump(int narg, char **arg)
}
/* ----------------------------------------------------------------------
delete a Dump from list of Dumps
delete a Dump from list of Dumps
------------------------------------------------------------------------- */
void Output::delete_dump(char *id)
@ -520,7 +520,7 @@ void Output::delete_dump(char *id)
}
/* ----------------------------------------------------------------------
new Thermo style
new Thermo style
------------------------------------------------------------------------- */
void Output::create_thermo(int narg, char **arg)
@ -529,14 +529,14 @@ void Output::create_thermo(int narg, char **arg)
// don't allow this so that dipole style can safely allocate inertia vector
if (domain->box_exist == 0)
if (domain->box_exist == 0)
error->all(FLERR,"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(FLERR,"New thermo_style command, "
"previous thermo_modify settings will be lost");
"previous thermo_modify settings will be lost");
// set thermo = NULL in case new Thermo throws an error
@ -553,7 +553,7 @@ void Output::create_thermo(int narg, char **arg)
void Output::create_restart(int narg, char **arg)
{
if (narg < 1) error->all(FLERR,"Illegal restart command");
int every = 0;
int varflag = 0;
@ -642,7 +642,7 @@ void Output::memory_usage()
if (comm->me == 0) {
if (screen)
fprintf(screen,"Memory usage per processor = %g Mbytes\n",mbytes);
if (logfile)
if (logfile)
fprintf(logfile,"Memory usage per processor = %g Mbytes\n",mbytes);
}
}