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fix_property_atom.cpp
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Wed, Sep 4, 16:13

fix_property_atom.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 <stdlib.h>
#include <string.h>
#include "fix_property_atom.h"
#include "atom.h"
#include "comm.h"
#include "memory.h"
#include "error.h"
#include "update.h"
using namespace LAMMPS_NS;
using namespace FixConst;
enum{MOLECULE,CHARGE,RMASS,INTEGER,DOUBLE};
/* ---------------------------------------------------------------------- */
FixPropertyAtom::FixPropertyAtom(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg),
nvalue(0), style(NULL), index(NULL), astyle(NULL)
{
if (narg < 4) error->all(FLERR,"Illegal fix property/atom command");
restart_peratom = 1;
wd_section = 1;
int iarg = 3;
nvalue = narg-iarg;
style = new int[nvalue];
index = new int[nvalue];
molecule_flag = 0;
q_flag = 0;
rmass_flag = 0;
nvalue = 0;
while (iarg < narg) {
if (strcmp(arg[iarg],"mol") == 0) {
if (atom->molecule_flag)
error->all(FLERR,"Fix property/atom mol when atom_style "
"already has molecule attribute");
if (molecule_flag)
error->all(FLERR,"Fix property/atom cannot specify mol twice");
style[nvalue] = MOLECULE;
atom->molecule_flag = molecule_flag = 1;
nvalue++;
} else if (strcmp(arg[iarg],"q") == 0) {
if (atom->q_flag)
error->all(FLERR,"Fix property/atom q when atom_style "
"already has charge attribute");
if (q_flag)
error->all(FLERR,"Fix property/atom cannot specify q twice");
style[nvalue] = CHARGE;
atom->q_flag = q_flag = 1;
nvalue++;
} else if (strcmp(arg[iarg],"rmass") == 0) {
if (atom->rmass_flag)
error->all(FLERR,"Fix property/atom rmass when atom_style "
"already has rmass attribute");
if (rmass_flag)
error->all(FLERR,"Fix property/atom cannot specify rmass twice");
style[nvalue] = RMASS;
atom->rmass_flag = rmass_flag = 1;
nvalue++;
} else if (strstr(arg[iarg],"i_") == arg[iarg]) {
style[nvalue] = INTEGER;
int tmp;
index[nvalue] = atom->find_custom(&arg[iarg][2],tmp);
if (index[nvalue] >= 0)
error->all(FLERR,"Fix property/atom vector name already exists");
index[nvalue] = atom->add_custom(&arg[iarg][2],0);
nvalue++;
} else if (strstr(arg[iarg],"d_") == arg[iarg]) {
style[nvalue] = DOUBLE;
int tmp;
index[nvalue] = atom->find_custom(&arg[iarg][2],tmp);
if (index[nvalue] >= 0)
error->all(FLERR,"Fix property/atom vector name already exists");
index[nvalue] = atom->add_custom(&arg[iarg][2],1);
nvalue++;
} else break;
iarg++;
}
// optional args
border = 0;
while (iarg < narg) {
if (strcmp(arg[iarg],"ghost") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix property/atom command");
if (strcmp(arg[iarg+1],"no") == 0) border = 0;
else if (strcmp(arg[iarg+1],"yes") == 0) border = 1;
else error->all(FLERR,"Illegal fix property/atom command");
iarg += 2;
} else error->all(FLERR,"Illegal fix property/atom command");
}
if (border) comm_border = nvalue;
// warn if mol or charge keyword used without ghost yes
if (border == 0) {
int flag = 0;
for (int i = 0; i < nvalue; i++)
if (style[i] == MOLECULE
|| style[i] == CHARGE
|| style[i] == RMASS) flag = 1;
if (flag && comm->me == 0)
error->warning(FLERR,"Fix property/atom mol or charge or rmass "
"w/out ghost communication");
}
// store current atom style
int n = strlen(atom->atom_style) + 1;
astyle = new char[n];
strcpy(astyle,atom->atom_style);
// perform initial allocation of atom-based array
// register with Atom class
nmax_old = 0;
grow_arrays(atom->nmax);
atom->add_callback(0);
atom->add_callback(1);
if (border) atom->add_callback(2);
}
/* ---------------------------------------------------------------------- */
FixPropertyAtom::~FixPropertyAtom()
{
// unregister callbacks to this fix from Atom class
atom->delete_callback(id,0);
atom->delete_callback(id,1);
if (border) atom->delete_callback(id,2);
// deallocate per-atom vectors in Atom class
// set ptrs to NULL, so they no longer exist for Atom class
for (int m = 0; m < nvalue; m++) {
if (style[m] == MOLECULE) {
atom->molecule_flag = 0;
memory->destroy(atom->molecule);
atom->molecule = NULL;
} else if (style[m] == CHARGE) {
atom->q_flag = 0;
memory->destroy(atom->q);
atom->q = NULL;
} else if (style[m] == RMASS) {
atom->rmass_flag = 0;
memory->destroy(atom->rmass);
atom->rmass = NULL;
} else if (style[m] == INTEGER) {
atom->remove_custom(0,index[m]);
} else if (style[m] == DOUBLE) {
atom->remove_custom(1,index[m]);
}
}
delete [] style;
delete [] index;
delete [] astyle;
}
/* ---------------------------------------------------------------------- */
int FixPropertyAtom::setmask()
{
int mask = 0;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixPropertyAtom::init()
{
// error if atom style has changed since fix was defined
// don't allow this b/c user could change to style that defines molecule,q
if (strcmp(astyle,atom->atom_style) != 0)
error->all(FLERR,"Atom style was redefined after using fix property/atom");
}
/* ----------------------------------------------------------------------
unpack N lines in buf from section of data file labeled by keyword
id_offset is applied to first atomID field if multiple data files are read
------------------------------------------------------------------------- */
void FixPropertyAtom::read_data_section(char *keyword, int n, char *buf,
tagint id_offset)
{
int j,m;
tagint itag;
char *next;
int mapflag = 0;
if (atom->map_style == 0) {
mapflag = 1;
atom->map_init();
atom->map_set();
}
next = strchr(buf,'\n');
*next = '\0';
int nwords = atom->count_words(buf);
*next = '\n';
if (nwords != nvalue+1) {
char str[128];
sprintf(str,"Incorrect %s format in data file",keyword);
error->all(FLERR,str);
}
char **values = new char*[nwords];
// loop over lines of atom info
// tokenize the line into values
// if I own atom tag, unpack its values
tagint map_tag_max = atom->map_tag_max;
for (int i = 0; i < n; i++) {
next = strchr(buf,'\n');
values[0] = strtok(buf," \t\n\r\f");
if (values[0] == NULL) {
char str[128];
sprintf(str,"Too few lines in %s section of data file",keyword);
error->one(FLERR,str);
}
int format_ok = 1;
for (j = 1; j < nwords; j++) {
values[j] = strtok(NULL," \t\n\r\f");
if (values[j] == NULL) format_ok = 0;
}
if (!format_ok) {
char str[128];
sprintf(str,"Incorrect %s format in data file",keyword);
error->all(FLERR,str);
}
itag = ATOTAGINT(values[0]) + id_offset;
if (itag <= 0 || itag > map_tag_max) {
char str[128];
sprintf(str,"Invalid atom ID in %s section of data file",keyword);
error->one(FLERR,str);
}
// assign words in line to per-atom vectors
if ((m = atom->map(itag)) >= 0) {
for (j = 0; j < nvalue; j++) {
if (style[j] == MOLECULE) atom->molecule[m] = ATOTAGINT(values[j+1]);
else if (style[j] == CHARGE) atom->q[m] = atof(values[j+1]);
else if (style[j] == RMASS) atom->rmass[m] = atof(values[j+1]);
else if (style[j] == INTEGER)
atom->ivector[index[j]][m] = atoi(values[j+1]);
else if (style[j] == DOUBLE)
atom->dvector[index[j]][m] = atof(values[j+1]);
}
}
buf = next + 1;
}
delete [] values;
if (mapflag) {
atom->map_delete();
atom->map_style = 0;
}
}
/* ----------------------------------------------------------------------
return # of lines in section of data file labeled by keyword
------------------------------------------------------------------------- */
bigint FixPropertyAtom::read_data_skip_lines(char *keyword)
{
return atom->natoms;
}
/* ----------------------------------------------------------------------
return size I own for Mth data section
# of data sections = 1 for this fix
nx = # of local atoms
ny = columns = tag + nvalues
------------------------------------------------------------------------- */
void FixPropertyAtom::write_data_section_size(int mth, int &nx, int &ny)
{
nx = atom->nlocal;
ny = nvalue + 1;
}
/* ----------------------------------------------------------------------
pack values for Mth data section into 2d buf
buf allocated by caller as Nlocal by Nvalues+1
------------------------------------------------------------------------- */
void FixPropertyAtom::write_data_section_pack(int mth, double **buf)
{
int i;
// 1st column = atom tag
// rest of columns = per-atom values
tagint *tag = atom->tag;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++) buf[i][0] = ubuf(tag[i]).d;
for (int m = 0; m < nvalue; m++) {
int mp1 = m+1;
if (style[m] == MOLECULE) {
tagint *molecule = atom->molecule;
for (i = 0; i < nlocal; i++) buf[i][mp1] = ubuf(molecule[i]).d;
} else if (style[m] == CHARGE) {
double *q = atom->q;
for (i = 0; i < nlocal; i++) buf[i][mp1] = q[i];
} else if (style[m] == RMASS) {
double *rmass = atom->rmass;
for (i = 0; i < nlocal; i++) buf[i][mp1] = rmass[i];
} else if (style[m] == INTEGER) {
int *ivec = atom->ivector[index[m]];
for (i = 0; i < nlocal; i++) buf[i][mp1] = ubuf(ivec[i]).d;
} else if (style[m] == DOUBLE) {
double *dvec = atom->dvector[index[m]];
for (i = 0; i < nlocal; i++) buf[i][mp1] = dvec[i];
}
}
}
/* ----------------------------------------------------------------------
write section keyword for Mth data section to file
use Molecules or Charges if that is only field, else use fix ID
only called by proc 0
------------------------------------------------------------------------- */
void FixPropertyAtom::write_data_section_keyword(int mth, FILE *fp)
{
if (nvalue == 1 && style[0] == MOLECULE) fprintf(fp,"\nMolecules\n\n");
else if (nvalue == 1 && style[0] == CHARGE) fprintf(fp,"\nCharges\n\n");
else fprintf(fp,"\n%s\n\n",id);
}
/* ----------------------------------------------------------------------
write N lines from buf to file
convert buf fields to int or double depending on styles
index can be used to prepend global numbering
only called by proc 0
------------------------------------------------------------------------- */
void FixPropertyAtom::write_data_section(int mth, FILE *fp,
int n, double **buf, int index)
{
int m;
for (int i = 0; i < n; i++) {
fprintf(fp,TAGINT_FORMAT,(tagint) ubuf(buf[i][0]).i);
for (m = 0; m < nvalue; m++) {
if (style[m] == MOLECULE)
fprintf(fp," " TAGINT_FORMAT,(tagint) ubuf(buf[i][m+1]).i);
else if (style[m] == INTEGER)
fprintf(fp," %d",(int) ubuf(buf[i][m+1]).i);
else fprintf(fp," %g",buf[i][m+1]);
}
fprintf(fp,"\n");
}
}
/* ----------------------------------------------------------------------
memory usage of local atom-based array
------------------------------------------------------------------------- */
double FixPropertyAtom::memory_usage()
{
double bytes = 0.0;
for (int m = 0; m < nvalue; m++) {
if (style[m] == MOLECULE) bytes = atom->nmax * sizeof(tagint);
else if (style[m] == CHARGE) bytes = atom->nmax * sizeof(double);
else if (style[m] == RMASS) bytes = atom->nmax * sizeof(double);
else if (style[m] == INTEGER) bytes = atom->nmax * sizeof(int);
else if (style[m] == DOUBLE) bytes = atom->nmax * sizeof(double);
}
return bytes;
}
/* ----------------------------------------------------------------------
allocate atom-based arrays
initialize new values to 0,
since AtomVec class won't do it as atoms are added,
e.g. in create_atom() or data_atom()
------------------------------------------------------------------------- */
void FixPropertyAtom::grow_arrays(int nmax)
{
for (int m = 0; m < nvalue; m++) {
if (style[m] == MOLECULE) {
memory->grow(atom->molecule,nmax,"atom:molecule");
size_t nbytes = (nmax-nmax_old) * sizeof(tagint);
memset(&atom->molecule[nmax_old],0,nbytes);
} else if (style[m] == CHARGE) {
memory->grow(atom->q,nmax,"atom:q");
size_t nbytes = (nmax-nmax_old) * sizeof(double);
memset(&atom->q[nmax_old],0,nbytes);
} else if (style[m] == RMASS) {
memory->grow(atom->rmass,nmax,"atom:rmass");
size_t nbytes = (nmax-nmax_old) * sizeof(double);
memset(&atom->rmass[nmax_old],0,nbytes);
} else if (style[m] == INTEGER) {
memory->grow(atom->ivector[index[m]],nmax,"atom:ivector");
size_t nbytes = (nmax-nmax_old) * sizeof(int);
memset(&atom->ivector[index[m]][nmax_old],0,nbytes);
} else if (style[m] == DOUBLE) {
memory->grow(atom->dvector[index[m]],nmax,"atom:dvector");
size_t nbytes = (nmax-nmax_old) * sizeof(double);
memset(&atom->dvector[index[m]][nmax_old],0,nbytes);
}
}
nmax_old = nmax;
}
/* ----------------------------------------------------------------------
copy values within local atom-based arrays
------------------------------------------------------------------------- */
void FixPropertyAtom::copy_arrays(int i, int j, int delflag)
{
for (int m = 0; m < nvalue; m++) {
if (style[m] == MOLECULE)
atom->molecule[j] = atom->molecule[i];
else if (style[m] == CHARGE)
atom->q[j] = atom->q[i];
else if (style[m] == RMASS)
atom->rmass[j] = atom->rmass[i];
else if (style[m] == INTEGER)
atom->ivector[index[m]][j] = atom->ivector[index[m]][i];
else if (style[m] == DOUBLE)
atom->dvector[index[m]][j] = atom->dvector[index[m]][i];
}
}
/* ----------------------------------------------------------------------
pack values for border communication at re-neighboring
------------------------------------------------------------------------- */
int FixPropertyAtom::pack_border(int n, int *list, double *buf)
{
int i,j,k;
int m = 0;
for (k = 0; k < nvalue; k++) {
if (style[k] == MOLECULE) {
tagint *molecule = atom->molecule;
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = ubuf(molecule[j]).d;
}
} else if (style[k] == CHARGE) {
double *q = atom->q;
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = q[j];
}
} else if (style[k] == RMASS) {
double *rmass = atom->rmass;
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = rmass[j];
}
} else if (style[k] == INTEGER) {
int *ivector = atom->ivector[index[k]];
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = ubuf(ivector[j]).d;
}
} else if (style[k] == DOUBLE) {
double *dvector = atom->dvector[index[k]];
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = dvector[j];
}
}
}
return m;
}
/* ----------------------------------------------------------------------
unpack values for border communication at re-neighboring
------------------------------------------------------------------------- */
int FixPropertyAtom::unpack_border(int n, int first, double *buf)
{
int i,k,last;
int m = 0;
for (k = 0; k < nvalue; k++) {
if (style[k] == MOLECULE) {
tagint *molecule = atom->molecule;
last = first + n;
for (i = first; i < last; i++)
molecule[i] = (tagint) ubuf(buf[m++]).i;
} else if (style[k] == CHARGE) {
double *q = atom->q;
last = first + n;
for (i = first; i < last; i++)
q[i] = buf[m++];
} else if (style[k] == RMASS) {
double *rmass = atom->rmass;
last = first + n;
for (i = first; i < last; i++)
rmass[i] = buf[m++];
} else if (style[k] == INTEGER) {
int *ivector = atom->ivector[index[k]];
last = first + n;
for (i = first; i < last; i++)
ivector[i] = (int) ubuf(buf[m++]).i;
} else if (style[k] == DOUBLE) {
double *dvector = atom->dvector[index[k]];
last = first + n;
for (i = first; i < last; i++)
dvector[i] = buf[m++];
}
}
return m;
}
/* ----------------------------------------------------------------------
pack values in local atom-based array for exchange with another proc
------------------------------------------------------------------------- */
int FixPropertyAtom::pack_exchange(int i, double *buf)
{
for (int m = 0; m < nvalue; m++) {
if (style[m] == MOLECULE) buf[m] = ubuf(atom->molecule[i]).d;
else if (style[m] == CHARGE) buf[m] = atom->q[i];
else if (style[m] == RMASS) buf[m] = atom->rmass[i];
else if (style[m] == INTEGER) buf[m] = ubuf(atom->ivector[index[m]][i]).d;
else if (style[m] == DOUBLE) buf[m] = atom->dvector[index[m]][i];
}
return nvalue;
}
/* ----------------------------------------------------------------------
unpack values in local atom-based array from exchange with another proc
------------------------------------------------------------------------- */
int FixPropertyAtom::unpack_exchange(int nlocal, double *buf)
{
for (int m = 0; m < nvalue; m++) {
if (style[m] == MOLECULE)
atom->molecule[nlocal] = (tagint) ubuf(buf[m]).i;
else if (style[m] == CHARGE)
atom->q[nlocal] = buf[m];
else if (style[m] == RMASS)
atom->rmass[nlocal] = buf[m];
else if (style[m] == INTEGER)
atom->ivector[index[m]][nlocal] = (int) ubuf(buf[m]).i;
else if (style[m] == DOUBLE)
atom->dvector[index[m]][nlocal] = buf[m];
}
return nvalue;
}
/* ----------------------------------------------------------------------
pack values in local atom-based arrays for restart file
------------------------------------------------------------------------- */
int FixPropertyAtom::pack_restart(int i, double *buf)
{
buf[0] = nvalue+1;
int m = 1;
for (int j = 0; j < nvalue; j++) {
if (style[j] == MOLECULE) buf[m++] = ubuf(atom->molecule[i]).d;
else if (style[j] == CHARGE) buf[m++] = atom->q[i];
else if (style[j] == RMASS) buf[m++] = atom->rmass[i];
else if (style[j] == INTEGER) buf[m++] = ubuf(atom->ivector[index[j]][i]).d;
else if (style[j] == DOUBLE) buf[m++] = atom->dvector[index[j]][i];
}
return nvalue+1;
}
/* ----------------------------------------------------------------------
unpack values from atom->extra array to restart the fix
------------------------------------------------------------------------- */
void FixPropertyAtom::unpack_restart(int nlocal, int nth)
{
double **extra = atom->extra;
// skip to Nth set of extra values
int m = 0;
for (int i = 0; i < nth; i++) m += static_cast<int> (extra[nlocal][m]);
m++;
for (int i = 0; i < nvalue; i++) {
if (style[i] == MOLECULE)
atom->molecule[nlocal] = (tagint) ubuf(extra[nlocal][m++]).i;
else if (style[i] == CHARGE)
atom->q[nlocal] = extra[nlocal][m++];
else if (style[i] == RMASS)
atom->rmass[nlocal] = extra[nlocal][m++];
else if (style[i] == INTEGER)
atom->ivector[index[i]][nlocal] = (int) ubuf(extra[nlocal][m++]).i;
else if (style[i] == DOUBLE)
atom->dvector[index[i]][nlocal] = extra[nlocal][m++];
}
}
/* ----------------------------------------------------------------------
maxsize of any atom's restart data
------------------------------------------------------------------------- */
int FixPropertyAtom::maxsize_restart()
{
return nvalue+1;
}
/* ----------------------------------------------------------------------
size of atom nlocal's restart data
------------------------------------------------------------------------- */
int FixPropertyAtom::size_restart(int nlocal)
{
return nvalue+1;
}

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