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resolved merge conflicts with master

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This commit is contained in:
Steve Plimpton
2021-08-17 11:55:33 -06:00
parent b2f96d92df dad9942bb8
commit e6af1eecb8
8612 changed files with 510252 additions and 341930 deletions
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155
src/fix_property_atom.cpp
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@ -1,6 +1,7 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://lammps.sandia.gov/, Sandia National Laboratories
https://www.lammps.org/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
@ -13,11 +14,13 @@
#include "fix_property_atom.h"
#include <cstring>
#include "atom.h"
#include "comm.h"
#include "memory.h"
#include "error.h"
#include "memory.h"
#include "tokenizer.h"
#include <cstring>
using namespace LAMMPS_NS;
using namespace FixConst;
@ -85,21 +88,32 @@ FixPropertyAtom::FixPropertyAtom(LAMMPS *lmp, int narg, char **arg) :
values_peratom++;
nvalue++;
iarg++;
} else if (strstr(arg[iarg],"i_") == arg[iarg] ||
strstr(arg[iarg],"d_") == arg[iarg]) {
int which = 0;
if (arg[iarg][0] == 'd') which = 1;
if (which == 0) style[nvalue] = IVEC;
else style[nvalue] = DVEC;
int tmp1,tmp2;
index[nvalue] = atom->find_custom(&arg[iarg][2],tmp1,tmp2);
// custom atom vector
} else if (utils::strmatch(arg[iarg],"^i_")) {
style[nvalue] = IVEC;
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");
cols[nvalue] = 0;
index[nvalue] = atom->add_custom(&arg[iarg][2],which,cols[nvalue]);
values_peratom++;
index[nvalue] = atom->add_custom(&arg[iarg][2],0);
nvalue++;
iarg++
} else if (utils::strmatch(arg[iarg],"^d_")) {
style[nvalue] = DVEC;
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++;
iarg++;
// custom atom array
// OLDSTYLE code
} else if (strstr(arg[iarg],"i2_") == arg[iarg] ||
strstr(arg[iarg],"d2_") == arg[iarg]) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix property/atom command");
@ -118,6 +132,9 @@ FixPropertyAtom::FixPropertyAtom(LAMMPS *lmp, int narg, char **arg) :
values_peratom += cols[nvalue];
nvalue++;
iarg += 2;
// no match
} else break;
}
@ -151,9 +168,7 @@ FixPropertyAtom::FixPropertyAtom(LAMMPS *lmp, int narg, char **arg) :
// store current atom style
int n = strlen(atom->atom_style) + 1;
astyle = new char[n];
strcpy(astyle,atom->atom_style);
astyle = utils::strdup(atom->atom_style);
// perform initial allocation of atom-based array
// register with Atom class
@ -246,72 +261,60 @@ void FixPropertyAtom::read_data_section(char *keyword, int n, char *buf,
atom->map_set();
}
next = strchr(buf,'\n');
*next = '\0';
int nwords = utils::trim_and_count_words(buf);
*next = '\n';
if (nwords != values_peratom+1)
error->all(FLERR,fmt::format("Incorrect {} format in data file",keyword));
char **values = new char*[nwords];
// loop over lines of atom info
// tokenize the line into values
// if I own atom tag, unpack its values
// if I own atom tag, assign its values
tagint map_tag_max = atom->map_tag_max;
for (int i = 0; i < n; i++) {
next = strchr(buf,'\n');
*next = '\0';
values[0] = strtok(buf," \t\n\r\f");
if (values[0] == nullptr)
error->all(FLERR,fmt::format("Too few lines in {} section of data file",keyword));
try {
ValueTokenizer values(buf);
if ((int)values.count() != nvalue+1)
error->all(FLERR,"Incorrect format in {} section "
"of data file: {}",keyword,buf);
int format_ok = 1;
for (j = 1; j < nwords; j++) {
values[j] = strtok(nullptr," \t\n\r\f");
if (values[j] == nullptr) format_ok = 0;
}
if (!format_ok)
error->all(FLERR,fmt::format("Incorrect {} format in data file",keyword));
itag = values.next_tagint() + id_offset;
if (itag <= 0 || itag > map_tag_max)
error->all(FLERR,"Invalid atom ID {} in {} section of "
"data file",itag, keyword);
itag = ATOTAGINT(values[0]) + id_offset;
if (itag <= 0 || itag > map_tag_max)
error->all(FLERR,fmt::format("Invalid atom ID {} in {} section of "
"data file",itag, keyword));
// assign words in line to per-atom vectors
// assign words in line to per-atom vectors
// iword = position in vector of words
if ((m = atom->map(itag)) >= 0) {
iword = 1;
for (nv = 0; nv < nvalue; nv++) {
if (style[nv] == MOLECULE) atom->molecule[m] = ATOTAGINT(values[iword++]);
else if (style[nv] == CHARGE) atom->q[m] = atof(values[iword++]);
else if (style[nv] == RMASS) atom->rmass[m] = atof(values[iword++]);
else if (style[nv] == IVEC)
atom->ivector[index[nv]][m] = atoi(values[iword++]);
else if (style[nv] == DVEC)
atom->dvector[index[nv]][m] = atof(values[iword++]);
else if (style[nv] == IARRAY) {
ncol = cols[nv];
for (k = 0; k < ncol; k++)
atom->iarray[index[nv]][m][k] = atoi(values[iword++]);
} else if (style[nv] == DARRAY) {
ncol = cols[nv];
for (k = 0; k < ncol; k++)
atom->darray[index[nv]][m][k] = atof(values[iword++]);
}
if ((m = atom->map(itag)) >= 0) {
for (j = 0; j < nvalue; j++) {
if (style[j] == MOLECULE) {
atom->molecule[m] = values.next_tagint();
} else if (style[j] == CHARGE) {
atom->q[m] = values.next_double();
} else if (style[j] == RMASS) {
atom->rmass[m] = values.next_double();
} else if (style[j] == IVEC) {
atom->ivector[index[j]][m] = values.next_int();
} else if (style[j] == DVEC) {
atom->dvector[index[j]][m] = values.next_double();
// NOTE: Axel please check these lines of array code
} else if (style[j] == IARRAY) {
ncol = cols[j];
for (k = 0; k < ncol; k++)
atom->iarray[index[j]][m][k] = values.next_int();
} else if (style[j] == DARRAY) {
ncol = cols[j];
for (k = 0; k < ncol; k++)
atom->darray[index[j]][m][k] = values.next_double();
}
}
}
} catch (TokenizerException &e) {
error->all(FLERR,"Invalid format in {} section of data "
"file '{}': {}",keyword, buf,e.what());
}
buf = next + 1;
}
delete [] values;
if (mapflag) {
atom->map_delete();
atom->map_style = 0;
@ -398,8 +401,9 @@ void FixPropertyAtom::write_data_section_pack(int /*mth*/, double **buf)
}
/* ----------------------------------------------------------------------
write section keyword for Mth data section to file
use Molecules or Charges if that is only field, else use fix ID
write a Molecules or Charges section if that is only field
manages by this fix instance. Otherwise write everything
to the section labeled by the fix ID
only called by proc 0
------------------------------------------------------------------------- */
@ -407,7 +411,18 @@ 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);
else {
fprintf(fp,"\n%s #",id);
// write column hint as comment
for (int i = 0; i < nvalue; ++i) {
if (style[i] == MOLECULE) fputs(" mol",fp);
else if (style[i] == CHARGE) fputs(" q",fp);
else if (style[i] == RMASS) fputs(" rmass",fp);
else if (style[i] == INTEGER) fprintf(fp," i_%s", atom->iname[index[i]]);
else if (style[i] == DOUBLE) fprintf(fp, " d_%s", atom->dname[index[i]]);
}
fputs("\n\n",fp);
}
}
/* ----------------------------------------------------------------------