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modernize using get_fix_by_id()

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This commit is contained in:
Axel Kohlmeyer
2022-08-13 01:49:00 -04:00
parent 894b053ef4
commit a4faa3aced
2 changed files with 34 additions and 37 deletions
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65
src/read_data.cpp
View File

@ -17,6 +17,7 @@
#include "angle.h"
#include "atom.h"
#include "atom_vec.h"
#include "atom_vec_body.h"
#include "atom_vec_ellipsoid.h"
#include "atom_vec_line.h"
#include "atom_vec_tri.h"
@ -99,30 +100,30 @@ ReadData::ReadData(LAMMPS *lmp) : Command(lmp)
// pointers to atom styles that store bonus info
nellipsoids = 0;
avec_ellipsoid = dynamic_cast<AtomVecEllipsoid *>( atom->style_match("ellipsoid"));
avec_ellipsoid = dynamic_cast<AtomVecEllipsoid *>(atom->style_match("ellipsoid"));
nlines = 0;
avec_line = dynamic_cast<AtomVecLine *>( atom->style_match("line"));
avec_line = dynamic_cast<AtomVecLine *>(atom->style_match("line"));
ntris = 0;
avec_tri = dynamic_cast<AtomVecTri *>( atom->style_match("tri"));
avec_tri = dynamic_cast<AtomVecTri *>(atom->style_match("tri"));
nbodies = 0;
avec_body = (AtomVecBody *) atom->style_match("body");
avec_body = dynamic_cast<AtomVecBody *>(atom->style_match("body"));
}
/* ---------------------------------------------------------------------- */
ReadData::~ReadData()
{
delete [] line;
delete [] keyword;
delete [] style;
delete [] buffer;
delete[] line;
delete[] keyword;
delete[] style;
delete[] buffer;
memory->sfree(coeffarg);
for (int i = 0; i < nfix; i++) {
delete [] fix_header[i];
delete [] fix_section[i];
delete[] fix_header[i];
delete[] fix_section[i];
}
memory->destroy(fix_index);
memory->sfree(fix_index);
memory->sfree(fix_header);
memory->sfree(fix_section);
}
@ -285,16 +286,13 @@ void ReadData::command(int narg, char **arg)
} else if (strcmp(arg[iarg],"fix") == 0) {
if (iarg+4 > narg)
error->all(FLERR,"Illegal read_data command");
memory->grow(fix_index,nfix+1,"read_data:fix_index");
fix_header = (char **) memory->srealloc(fix_header,(nfix+1)*sizeof(char *),
"read_data:fix_header");
fix_section = (char **) memory->srealloc(fix_section,(nfix+1)*sizeof(char *),
"read_data:fix_section");
fix_index = (Fix **)memory->srealloc(fix_index,(nfix+1)*sizeof(Fix *),"read_data:fix_index");
fix_header = (char **) memory->srealloc(fix_header,(nfix+1)*sizeof(char *),"read_data:fix_header");
fix_section = (char **) memory->srealloc(fix_section,(nfix+1)*sizeof(char *),"read_data:fix_section");
if (is_data_section(arg[iarg+3]))
error->all(FLERR,"Custom data section name {} for fix {} collides with existing "
"data section",arg[iarg+3],arg[iarg+1]);
fix_index[nfix] = modify->find_fix(arg[iarg+1]);
if (fix_index[nfix] < 0) error->all(FLERR,"Fix ID for read_data does not exist");
error->all(FLERR,"Custom data section name {} for fix {} collides with existing data section",arg[iarg+3],arg[iarg+1]);
fix_index[nfix] = modify->get_fix_by_id(arg[iarg+1]);
if (!fix_index[nfix]) error->all(FLERR,"Fix ID {} for read_data does not exist",arg[iarg+1]);
if (strcmp(arg[iarg+2],"NULL") == 0) fix_header[nfix] = nullptr;
else fix_header[nfix] = utils::strdup(arg[iarg+2]);
if (strcmp(arg[iarg+3],"NULL") == 0) fix_section[nfix] = utils::strdup(arg[iarg+1]);
@ -743,8 +741,7 @@ void ReadData::command(int narg, char **arg)
for (i = 0; i < nfix; i++)
if (strcmp(keyword,fix_section[i]) == 0) {
if (firstpass) fix(fix_index[i],keyword);
else skip_lines(modify->fix[fix_index[i]]->
read_data_skip_lines(keyword));
else skip_lines(fix_index[i]->read_data_skip_lines(keyword));
break;
}
if (i == nfix)
@ -1008,7 +1005,7 @@ void ReadData::header(int firstpass)
for (n = 0; n < nfix; n++) {
if (!fix_header[n]) continue;
if (strstr(line,fix_header[n])) {
modify->fix[fix_index[n]]->read_data_header(line);
fix_index[n]->read_data_header(line);
break;
}
}
@ -1754,7 +1751,7 @@ void ReadData::mass()
atom->set_mass(FLERR,buf,toffset);
buf = next + 1;
}
delete [] original;
delete[] original;
}
/* ---------------------------------------------------------------------- */
@ -1777,7 +1774,7 @@ void ReadData::paircoeffs()
force->pair->coeff(ncoeffarg,coeffarg);
buf = next + 1;
}
delete [] original;
delete[] original;
}
/* ---------------------------------------------------------------------- */
@ -1804,7 +1801,7 @@ void ReadData::pairIJcoeffs()
force->pair->coeff(ncoeffarg,coeffarg);
buf = next + 1;
}
delete [] original;
delete[] original;
}
/* ---------------------------------------------------------------------- */
@ -1829,7 +1826,7 @@ void ReadData::bondcoeffs()
force->bond->coeff(ncoeffarg,coeffarg);
buf = next + 1;
}
delete [] original;
delete[] original;
}
/* ---------------------------------------------------------------------- */
@ -1856,7 +1853,7 @@ void ReadData::anglecoeffs(int which)
force->angle->coeff(ncoeffarg,coeffarg);
buf = next + 1;
}
delete [] original;
delete[] original;
}
/* ---------------------------------------------------------------------- */
@ -1886,7 +1883,7 @@ void ReadData::dihedralcoeffs(int which)
force->dihedral->coeff(ncoeffarg,coeffarg);
buf = next + 1;
}
delete [] original;
delete[] original;
}
/* ---------------------------------------------------------------------- */
@ -1911,7 +1908,7 @@ void ReadData::impropercoeffs(int which)
force->improper->coeff(ncoeffarg,coeffarg);
buf = next + 1;
}
delete [] original;
delete[] original;
}
/* ----------------------------------------------------------------------
@ -1919,18 +1916,18 @@ void ReadData::impropercoeffs(int which)
n = index of fix
------------------------------------------------------------------------- */
void ReadData::fix(int ifix, char *keyword)
void ReadData::fix(Fix *ifix, char *keyword)
{
int nchunk,eof;
bigint nline = modify->fix[ifix]->read_data_skip_lines(keyword);
bigint nline = ifix->read_data_skip_lines(keyword);
bigint nread = 0;
while (nread < nline) {
nchunk = MIN(nline-nread,CHUNK);
eof = utils::read_lines_from_file(fp,nchunk,MAXLINE,buffer,me,world);
if (eof) error->all(FLERR,"Unexpected end of data file");
modify->fix[ifix]->read_data_section(keyword,nchunk,buffer,id_offset);
if (eof) error->all(FLERR,"Unexpected end of data file while reading section {}",keyword);
ifix->read_data_section(keyword,nchunk,buffer,id_offset);
nread += nchunk;
}
}

6
src/read_data.h
View File

@ -23,7 +23,7 @@ CommandStyle(read_data,ReadData);
#include "command.h"
namespace LAMMPS_NS {
class Fix;
class ReadData : public Command {
public:
ReadData(class LAMMPS *);
@ -73,7 +73,7 @@ class ReadData : public Command {
int groupbit;
int nfix;
int *fix_index;
Fix **fix_index;
char **fix_header;
char **fix_section;
@ -108,7 +108,7 @@ class ReadData : public Command {
void dihedralcoeffs(int);
void impropercoeffs(int);
void fix(int, char *);
void fix(Fix *, char *);
};
} // namespace LAMMPS_NS