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lammps/src/fix.cpp
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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 "force.h"
#include "comm.h"
#include "atom_masks.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace FixConst;
// allocate space for static class instance variable and initialize it
int Fix::instance_total = 0;
/* ---------------------------------------------------------------------- */
Fix::Fix(LAMMPS *lmp, int narg, char **arg) :
Pointers(lmp),
id(NULL), style(NULL), extlist(NULL), vector_atom(NULL), array_atom(NULL),
vector_local(NULL), array_local(NULL), eatom(NULL), vatom(NULL)
{
instance_me = instance_total++;
// 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(FLERR,"Fix ID must be alphanumeric or underscore characters");
igroup = group->find(arg[1]);
if (igroup == -1) error->all(FLERR,"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 = restart_peratom = restart_file = 0;
force_reneighbor = 0;
box_change_size = box_change_shape = box_change_domain = 0;
thermo_energy = 0;
thermo_virial = 0;
rigid_flag = 0;
peatom_flag = 0;
virial_flag = 0;
no_change_box = 0;
time_integrate = 0;
time_depend = 0;
create_attribute = 0;
restart_pbc = 0;
wd_header = wd_section = 0;
dynamic_group_allow = 0;
dynamic = 0;
dof_flag = 0;
special_alter_flag = 0;
enforce2d_flag = 0;
respa_level_support = 0;
respa_level = -1;
scalar_flag = vector_flag = array_flag = 0;
peratom_flag = local_flag = 0;
size_vector_variable = size_array_rows_variable = 0;
comm_forward = comm_reverse = comm_border = 0;
restart_reset = 0;
// reasonable defaults
// however, each fix that uses these values should explicitly set them
nevery = 1;
global_freq = 1;
// per-atom virial
// set vflag_atom = 0 b/c some fixes grow vatom in grow_arrays()
// which may occur outside of timestepping
maxeatom = maxvatom = 0;
vflag_atom = 0;
// KOKKOS per-fix data masks
execution_space = Host;
datamask_read = ALL_MASK;
datamask_modify = ALL_MASK;
kokkosable = 0;
copymode = 0;
}
/* ---------------------------------------------------------------------- */
Fix::~Fix()
{
if (copymode) return;
delete [] id;
delete [] style;
memory->destroy(eatom);
memory->destroy(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(FLERR,"Illegal fix_modify command");
int iarg = 0;
while (iarg < narg) {
if (strcmp(arg[iarg],"dynamic/dof") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix_modify command");
if (strcmp(arg[iarg+1],"no") == 0) dynamic = 0;
else if (strcmp(arg[iarg+1],"yes") == 0) dynamic = 1;
else error->all(FLERR,"Illegal fix_modify command");
iarg += 2;
} else if (strcmp(arg[iarg],"energy") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix_modify command");
if (strcmp(arg[iarg+1],"no") == 0) thermo_energy = 0;
else if (strcmp(arg[iarg+1],"yes") == 0) {
if (!(THERMO_ENERGY & setmask()))
error->all(FLERR,"Illegal fix_modify command");
thermo_energy = 1;
} else error->all(FLERR,"Illegal fix_modify command");
iarg += 2;
} else if (strcmp(arg[iarg],"virial") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix_modify command");
if (strcmp(arg[iarg+1],"no") == 0) thermo_virial = 0;
else if (strcmp(arg[iarg+1],"yes") == 0) {
if (virial_flag == 0)
error->all(FLERR,"Illegal fix_modify command");
thermo_virial = 1;
} else error->all(FLERR,"Illegal fix_modify command");
iarg += 2;
} else if (strcmp(arg[iarg],"respa") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix_modify command");
if (!respa_level_support) error->all(FLERR,"Illegal fix_modify command");
int lvl = force->inumeric(FLERR,arg[iarg+1]);
if (lvl < 0) error->all(FLERR,"Illegal fix_modify command");
respa_level = lvl-1;
iarg += 2;
} else {
int n = modify_param(narg-iarg,&arg[iarg]);
if (n == 0) error->all(FLERR,"Illegal fix_modify command");
iarg += n;
}
}
}
/* ----------------------------------------------------------------------
setup for energy, virial computation
see integrate::ev_set() for values of eflag (0-3) and vflag (0-6)
fixes call this if they use ev_tally()
------------------------------------------------------------------------- */
void Fix::ev_setup(int eflag, int vflag)
{
int i,n;
evflag = 1;
eflag_either = eflag;
eflag_global = eflag % 2;
eflag_atom = eflag / 2;
vflag_either = vflag;
vflag_global = vflag % 4;
vflag_atom = vflag / 4;
// reallocate per-atom arrays if necessary
if (eflag_atom && atom->nlocal > maxeatom) {
maxeatom = atom->nmax;
memory->destroy(eatom);
memory->create(eatom,maxeatom,"fix:eatom");
}
if (vflag_atom && atom->nlocal > maxvatom) {
maxvatom = atom->nmax;
memory->destroy(vatom);
memory->create(vatom,maxvatom,6,"fix:vatom");
}
// zero accumulators
// no global energy variable to zero (unlike pair,bond,angle,etc)
// fixes tally it individually via fix_modify energy yes and compute_scalar()
if (vflag_global) for (i = 0; i < 6; i++) virial[i] = 0.0;
if (eflag_atom) {
n = atom->nlocal;
for (i = 0; i < n; i++) eatom[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;
}
}
}
/* ----------------------------------------------------------------------
if thermo_virial is on:
setup for virial computation
see integrate::ev_set() for values of vflag (0-6)
fixes call this if use v_tally()
else: set evflag=0
------------------------------------------------------------------------- */
void Fix::v_setup(int vflag)
{
int i,n;
if (!thermo_virial) {
evflag = 0;
return;
}
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(vatom);
memory->create(vatom,maxvatom,6,"fix: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 per-atom energy and global/per-atom virial into accumulators
n = # of local owned atoms involved, with local indices in list
eng = total energy for the interaction involving total atoms
v = total virial for the interaction involving total atoms
increment per-atom energy of each atom in list by 1/total fraction
v_tally tallies virial
this method can be used when fix computes energy/forces in post_force()
e.g. fix cmap: compute energy and virial only on owned atoms
whether newton_bond is on or off
other procs will tally left-over fractions for atoms they own
------------------------------------------------------------------------- */
void Fix::ev_tally(int n, int *list, double total, double eng, double *v)
{
if (eflag_atom) {
double fraction = eng/total;
for (int i = 0; i < n; i++)
eatom[list[i]] += fraction;
}
v_tally(n,list,total,v);
}
/* ----------------------------------------------------------------------
tally virial into global and per-atom accumulators
n = # of local owned atoms involved, with local indices in list
v = total virial for the interaction involving total atoms
increment global virial by n/total fraction
increment per-atom virial of each atom in list by 1/total fraction
this method can be used when fix computes forces in post_force()
e.g. fix shake, fix rigid: compute virial only on owned atoms
whether newton_bond is on or off
other procs will tally left-over fractions for atoms they own
------------------------------------------------------------------------- */
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];
}
}
}
/* ----------------------------------------------------------------------
tally virial into global and per-atom accumulators
i = local index of atom
v = total virial for the interaction
increment global virial by v
increment per-atom virial by v
this method can be used when fix computes forces in post_force()
and the force depends on a distance to some external object
e.g. fix wall/lj93: compute virial only on owned atoms
------------------------------------------------------------------------- */
void Fix::v_tally(int i, double *v)
{
if (vflag_global) {
virial[0] += v[0];
virial[1] += v[1];
virial[2] += v[2];
virial[3] += v[3];
virial[4] += v[4];
virial[5] += v[5];
}
if (vflag_atom) {
vatom[i][0] += v[0];
vatom[i][1] += v[1];
vatom[i][2] += v[2];
vatom[i][3] += v[3];
vatom[i][4] += v[4];
vatom[i][5] += v[5];
}
}
/* ----------------------------------------------------------------------
tally virial component into global and per-atom accumulators
n = index of virial component (0-5)
i = local index of atom
vn = nth component of virial for the interaction
increment nth component of global virial by vn
increment nth component of per-atom virial by vn
this method can be used when fix computes forces in post_force()
and the force depends on a distance to some external object
e.g. fix wall/lj93: compute virial only on owned atoms
------------------------------------------------------------------------- */
void Fix::v_tally(int n, int i, double vn)
{
if (vflag_global)
virial[n] += vn;
if (vflag_atom)
vatom[i][n] += vn;
}
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