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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13696 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2015-07-23 15:47:57 +00:00
parent 6c84ca5377
commit 54ad69177c
1 changed files with 9 additions and 23 deletions
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32
src/molecule.cpp
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@ -57,7 +57,6 @@ Molecule::Molecule(LAMMPS *lmp, int narg, char **arg, int ifile) : Pointers(lmp)
int iarg = ifile+1; int iarg = ifile+1;
while (iarg < narg) { while (iarg < narg) {
if (strcmp(arg[iarg],"offset") == 0) break; if (strcmp(arg[iarg],"offset") == 0) break;
if (strcmp(arg[iarg],"auto") == 0) break;
iarg++; iarg++;
} }
if (iarg == ifile+1) last = 1; if (iarg == ifile+1) last = 1;
@ -66,7 +65,6 @@ Molecule::Molecule(LAMMPS *lmp, int narg, char **arg, int ifile) : Pointers(lmp)
toffset = 0; toffset = 0;
boffset = aoffset = doffset = ioffset = 0; boffset = aoffset = doffset = ioffset = 0;
autospecial = 0;
while (iarg < narg) { while (iarg < narg) {
if (strcmp(arg[iarg],"offset") == 0) { if (strcmp(arg[iarg],"offset") == 0) {
@ -80,9 +78,6 @@ Molecule::Molecule(LAMMPS *lmp, int narg, char **arg, int ifile) : Pointers(lmp)
doffset < 0 || ioffset < 0) doffset < 0 || ioffset < 0)
error->all(FLERR,"Illegal molecule command"); error->all(FLERR,"Illegal molecule command");
iarg += 6; iarg += 6;
} else if (strcmp(arg[iarg],"auto") == 0) {
autospecial = 1;
iarg++;
} else error->all(FLERR,"Illegal molecule command"); } else error->all(FLERR,"Illegal molecule command");
} }
@ -476,15 +471,9 @@ void Molecule::read(int flag)
impropers(flag,line); impropers(flag,line);
} else if (strcmp(keyword,"Special Bond Counts") == 0) { } else if (strcmp(keyword,"Special Bond Counts") == 0) {
if (autospecial)
error->all(FLERR,"Molecule file with auto keyword cannot list "
"explict special bonds");
nspecialflag = 1; nspecialflag = 1;
nspecial_read(flag,line); nspecial_read(flag,line);
} else if (strcmp(keyword,"Special Bonds") == 0) { } else if (strcmp(keyword,"Special Bonds") == 0) {
if (autospecial)
error->all(FLERR,"Molecule file with auto keyword cannot list "
"explict special bonds");
specialflag = tag_require = 1; specialflag = tag_require = 1;
if (flag) special_read(line); if (flag) special_read(line);
else skip_lines(natoms,line); else skip_lines(natoms,line);
@ -513,14 +502,6 @@ void Molecule::read(int flag)
parse_keyword(1,line,keyword); parse_keyword(1,line,keyword);
} }
// auto-generate special bonds
if (autospecial) {
specialflag = 1;
nspecialflag = 1;
if (flag) special_generate();
}
// clean up // clean up
memory->destroy(count); memory->destroy(count);
@ -532,12 +513,18 @@ void Molecule::read(int flag)
error->all(FLERR,"Molecule file needs both Special Bond sections"); error->all(FLERR,"Molecule file needs both Special Bond sections");
if (specialflag && !bondflag) if (specialflag && !bondflag)
error->all(FLERR,"Molecule file has special flags but no bonds"); error->all(FLERR,"Molecule file has special flags but no bonds");
if (!specialflag && bondflag)
error->all(FLERR,"Molecule file has bonds but no special flags");
if ((shakeflagflag || shakeatomflag || shaketypeflag) && !shakeflag) if ((shakeflagflag || shakeatomflag || shaketypeflag) && !shakeflag)
error->all(FLERR,"Molecule file shake info is incomplete"); error->all(FLERR,"Molecule file shake info is incomplete");
} }
// auto-generate special bonds
if (bondflag && !specialflag) {
specialflag = 1;
nspecialflag = 1;
maxspecial = atom->maxspecial;
if (flag) special_generate();
}
} }
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
@ -1301,7 +1288,6 @@ void Molecule::allocate()
memory->create(num_improper,natoms,"molecule:num_improper"); memory->create(num_improper,natoms,"molecule:num_improper");
for (int i = 0; i < natoms; i++) num_improper[i] = 0; for (int i = 0; i < natoms; i++) num_improper[i] = 0;
if (autospecial) maxspecial = atom->maxspecial;
memory->create(special,natoms,maxspecial,"molecule:special"); memory->create(special,natoms,maxspecial,"molecule:special");
memory->create(nspecial,natoms,3,"molecule:nspecial"); memory->create(nspecial,natoms,3,"molecule:nspecial");