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compute.cpp
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Fri, Jun 28, 20:27

compute.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 <mpi.h>
#include <stdlib.h>
#include <string.h>
#include <ctype.h>
#include "compute.h"
#include "atom.h"
#include "domain.h"
#include "force.h"
#include "comm.h"
#include "group.h"
#include "modify.h"
#include "fix.h"
#include "atom_masks.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define DELTA 4
#define BIG MAXTAGINT
// allocate space for static class instance variable and initialize it
int Compute::instance_total = 0;
/* ---------------------------------------------------------------------- */
Compute::Compute(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
{
instance_me = instance_total++;
if (narg < 3) error->all(FLERR,"Illegal compute command");
// compute ID, group, and style
// ID must be all alphanumeric chars or underscores
int n = strlen(arg[0]) + 1;
id = new char[n];
strcpy(id,arg[0]);
for (int i = 0; i < n-1; i++)
if (!isalnum(id[i]) && id[i] != '_')
error->all(FLERR,
"Compute ID must be alphanumeric or underscore characters");
igroup = group->find(arg[1]);
if (igroup == -1) error->all(FLERR,"Could not find compute group ID");
groupbit = group->bitmask[igroup];
n = strlen(arg[2]) + 1;
style = new char[n];
strcpy(style,arg[2]);
// set child class defaults
scalar_flag = vector_flag = array_flag = 0;
peratom_flag = local_flag = 0;
size_vector_variable = size_array_rows_variable = 0;
tempflag = pressflag = peflag = 0;
pressatomflag = peatomflag = 0;
create_attribute = 0;
tempbias = 0;
timeflag = 0;
comm_forward = comm_reverse = 0;
dynamic = 0;
dynamic_group_allow = 1;
invoked_scalar = invoked_vector = invoked_array = -1;
invoked_peratom = invoked_local = -1;
invoked_flag = 0;
// set modify defaults
extra_dof = domain->dimension;
dynamic_user = 0;
fix_dof = 0;
// setup list of timesteps
ntime = maxtime = 0;
tlist = NULL;
// data masks
datamask = ALL_MASK;
datamask_ext = ALL_MASK;
execution_space = Host;
datamask_read = ALL_MASK;
datamask_modify = ALL_MASK;
copymode = 0;
// force init to zero in case these are used as logicals
vector = vector_atom = vector_local = NULL;
array = array_atom = array_local = NULL;
}
/* ---------------------------------------------------------------------- */
Compute::~Compute()
{
if (copymode) return;
delete [] id;
delete [] style;
memory->destroy(tlist);
}
/* ---------------------------------------------------------------------- */
void Compute::modify_params(int narg, char **arg)
{
if (narg == 0) error->all(FLERR,"Illegal compute_modify command");
int iarg = 0;
while (iarg < narg) {
if (strcmp(arg[iarg],"extra") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal compute_modify command");
extra_dof = force->numeric(FLERR,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"dynamic") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal compute_modify command");
if (strcmp(arg[iarg+1],"no") == 0) dynamic_user = 0;
else if (strcmp(arg[iarg+1],"yes") == 0) dynamic_user = 1;
else error->all(FLERR,"Illegal compute_modify command");
iarg += 2;
} else error->all(FLERR,"Illegal compute_modify command");
}
}
/* ----------------------------------------------------------------------
calculate adjustment in DOF due to fixes
------------------------------------------------------------------------- */
void Compute::adjust_dof_fix()
{
Fix **fix = modify->fix;
int nfix = modify->nfix;
fix_dof = 0;
for (int i = 0; i < nfix; i++)
if (fix[i]->dof_flag)
fix_dof += fix[i]->dof(igroup);
}
/* ----------------------------------------------------------------------
reset extra_dof to its default value
------------------------------------------------------------------------- */
void Compute::reset_extra_dof()
{
extra_dof = domain->dimension;
}
/* ---------------------------------------------------------------------- */
void Compute::reset_extra_compute_fix(const char *)
{
error->all(FLERR,
"Compute does not allow an extra compute or fix to be reset");
}
/* ----------------------------------------------------------------------
add ntimestep to list of timesteps the compute will be called on
do not add if already in list
search from top downward, since list of times is in decreasing order
------------------------------------------------------------------------- */
void Compute::addstep(bigint ntimestep)
{
// i = location in list to insert ntimestep
int i;
for (i = ntime-1; i >= 0; i--) {
if (ntimestep == tlist[i]) return;
if (ntimestep < tlist[i]) break;
}
i++;
// extend list as needed
if (ntime == maxtime) {
maxtime += DELTA;
memory->grow(tlist,maxtime,"compute:tlist");
}
// move remainder of list upward and insert ntimestep
for (int j = ntime-1; j >= i; j--) tlist[j+1] = tlist[j];
tlist[i] = ntimestep;
ntime++;
}
/* ----------------------------------------------------------------------
return 1/0 if ntimestep is or is not in list of calling timesteps
if value(s) on top of list are less than ntimestep, delete them
search from top downward, since list of times is in decreasing order
------------------------------------------------------------------------- */
int Compute::matchstep(bigint ntimestep)
{
for (int i = ntime-1; i >= 0; i--) {
if (ntimestep < tlist[i]) return 0;
if (ntimestep == tlist[i]) return 1;
if (ntimestep > tlist[i]) ntime--;
}
return 0;
}
/* ----------------------------------------------------------------------
clean out list of timesteps to call the compute on
------------------------------------------------------------------------- */
void Compute::clearstep()
{
ntime = 0;
}

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