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fix.cpp
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Sat, Jun 28, 16:47

fix.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 "string.h"
#include "ctype.h"
#include "fix.h"
#include "atom.h"
#include "group.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
Fix::Fix(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
{
// fix 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("Fix ID must be alphanumeric or underscore characters");
igroup = group->find(arg[1]);
if (igroup == -1) error->all("Could not find fix group ID");
groupbit = group->bitmask[igroup];
n = strlen(arg[2]) + 1;
style = new char[n];
strcpy(style,arg[2]);
restart_global = 0;
restart_peratom = 0;
force_reneighbor = 0;
box_change = 0;
thermo_energy = 0;
rigid_flag = 0;
virial_flag = 0;
no_change_box = 0;
time_integrate = 0;
time_depend = 0;
restart_pbc = 0;
scalar_flag = vector_flag = peratom_flag = 0;
comm_forward = comm_reverse = 0;
maxvatom = 0;
vatom = NULL;
// mask settings - same as in modify.cpp
INITIAL_INTEGRATE = 1;
POST_INTEGRATE = 2;
PRE_EXCHANGE = 4;
PRE_NEIGHBOR = 8;
PRE_FORCE = 16;
POST_FORCE = 32;
FINAL_INTEGRATE = 64;
END_OF_STEP = 128;
THERMO_ENERGY = 256;
INITIAL_INTEGRATE_RESPA = 512;
POST_INTEGRATE_RESPA = 1024;
PRE_FORCE_RESPA = 2048;
POST_FORCE_RESPA = 4096;
FINAL_INTEGRATE_RESPA = 8192;
MIN_POST_FORCE = 16384;
MIN_ENERGY = 32768;
}
/* ---------------------------------------------------------------------- */
Fix::~Fix()
{
delete [] id;
delete [] style;
memory->destroy_2d_double_array(vatom);
}
/* ----------------------------------------------------------------------
process params common to all fixes here
if unknown param, call modify_param specific to the fix
------------------------------------------------------------------------- */
void Fix::modify_params(int narg, char **arg)
{
if (narg == 0) error->all("Illegal fix_modify command");
int iarg = 0;
while (iarg < narg) {
if (strcmp(arg[iarg],"energy") == 0) {
if (iarg+2 > narg) error->all("Illegal fix_modify command");
if (strcmp(arg[iarg+1],"no") == 0) thermo_energy = 0;
else if (strcmp(arg[iarg+1],"yes") == 0) thermo_energy = 1;
else error->all("Illegal fix_modify command");
iarg += 2;
} else {
int n = modify_param(narg-iarg,&arg[iarg]);
if (n == 0) error->all("Illegal fix_modify command");
iarg += n;
}
}
}
/* ----------------------------------------------------------------------
setup for virial computation
see integrate::ev_set() for values of vflag (0-6)
------------------------------------------------------------------------- */
void Fix::v_setup(int vflag)
{
int i,n;
evflag = 1;
vflag_global = vflag % 4;
vflag_atom = vflag / 4;
// reallocate per-atom array if necessary
if (vflag_atom && atom->nlocal > maxvatom) {
maxvatom = atom->nmax;
memory->destroy_2d_double_array(vatom);
vatom = memory->create_2d_double_array(maxvatom,6,"bond:vatom");
}
// zero accumulators
if (vflag_global) for (i = 0; i < 6; i++) virial[i] = 0.0;
if (vflag_atom) {
n = atom->nlocal;
for (i = 0; i < n; i++) {
vatom[i][0] = 0.0;
vatom[i][1] = 0.0;
vatom[i][2] = 0.0;
vatom[i][3] = 0.0;
vatom[i][4] = 0.0;
vatom[i][5] = 0.0;
}
}
}
/* ----------------------------------------------------------------------
tally virial into global and per-atom accumulators
v = total virial for the interaction involving total atoms
n = # of local atoms involved, with local indices in list
increment global virial by n/total fraction
increment per-atom virial of each atom in list by 1/total fraction
assumes other procs will tally left-over fractions
------------------------------------------------------------------------- */
void Fix::v_tally(int n, int *list, double total, double *v)
{
int m;
if (vflag_global) {
double fraction = n/total;
virial[0] += fraction*v[0];
virial[1] += fraction*v[1];
virial[2] += fraction*v[2];
virial[3] += fraction*v[3];
virial[4] += fraction*v[4];
virial[5] += fraction*v[5];
}
if (vflag_atom) {
double fraction = 1.0/total;
for (int i = 0; i < n; i++) {
m = list[i];
vatom[m][0] += fraction*v[0];
vatom[m][1] += fraction*v[1];
vatom[m][2] += fraction*v[2];
vatom[m][3] += fraction*v[3];
vatom[m][4] += fraction*v[4];
vatom[m][5] += fraction*v[5];
}
}
}

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