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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14163 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2015-10-22 21:48:05 +00:00
parent 1eeeb028f9
commit b229c719d0
6 changed files with 160 additions and 70 deletions
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81
src/molecule.cpp
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@ -35,11 +35,12 @@ using namespace MathConst;
/* ---------------------------------------------------------------------- */
Molecule::Molecule(LAMMPS *lmp, int narg, char **arg, int ifile) : Pointers(lmp)
Molecule::Molecule(LAMMPS *lmp, int narg, char **arg, int &index) :
Pointers(lmp)
{
me = comm->me;
if (ifile >= narg) error->all(FLERR,"Illegal molecule command");
if (index >= narg) error->all(FLERR,"Illegal molecule command");
int n = strlen(arg[0]) + 1;
id = new char[n];
@ -50,21 +51,14 @@ Molecule::Molecule(LAMMPS *lmp, int narg, char **arg, int ifile) : Pointers(lmp)
error->all(FLERR,"Molecule template ID must be "
"alphanumeric or underscore characters");
// scan args past ifile to reach optional args
// set last = 1 if no more files in list
last = 0;
int iarg = ifile+1;
while (iarg < narg) {
if (strcmp(arg[iarg],"offset") == 0) break;
iarg++;
}
if (iarg == ifile+1) last = 1;
// parse optional args
// parse args until reach unknown arg (next file)
toffset = 0;
boffset = aoffset = doffset = ioffset = 0;
sizescale = 1.0;
int ifile = index;
int iarg = ifile+1;
while (iarg < narg) {
if (strcmp(arg[iarg],"offset") == 0) {
@ -78,9 +72,45 @@ Molecule::Molecule(LAMMPS *lmp, int narg, char **arg, int ifile) : Pointers(lmp)
doffset < 0 || ioffset < 0)
error->all(FLERR,"Illegal molecule command");
iarg += 6;
} else error->all(FLERR,"Illegal molecule command");
} else if (strcmp(arg[iarg],"toff") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal molecule command");
toffset = force->inumeric(FLERR,arg[iarg+1]);
if (toffset < 0) error->all(FLERR,"Illegal molecule command");
iarg += 2;
} else if (strcmp(arg[iarg],"boff") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal molecule command");
boffset = force->inumeric(FLERR,arg[iarg+1]);
if (boffset < 0) error->all(FLERR,"Illegal molecule command");
iarg += 2;
} else if (strcmp(arg[iarg],"aoff") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal molecule command");
aoffset = force->inumeric(FLERR,arg[iarg+1]);
if (aoffset < 0) error->all(FLERR,"Illegal molecule command");
iarg += 2;
} else if (strcmp(arg[iarg],"doff") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal molecule command");
doffset = force->inumeric(FLERR,arg[iarg+1]);
if (doffset < 0) error->all(FLERR,"Illegal molecule command");
iarg += 2;
} else if (strcmp(arg[iarg],"ioff") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal molecule command");
ioffset = force->inumeric(FLERR,arg[iarg+1]);
if (ioffset < 0) error->all(FLERR,"Illegal molecule command");
iarg += 2;
} else if (strcmp(arg[iarg],"scale") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal molecule command");
sizescale = force->numeric(FLERR,arg[iarg+1]);
if (sizescale <= 0.0) error->all(FLERR,"Illegal molecule command");
iarg += 2;
} else break;
}
index = iarg;
// last molecule if have scanned all args
if (iarg == narg) last = 1;
// initialize all fields to empty
initialize();
@ -392,10 +422,14 @@ void Molecule::read(int flag)
else if (strstr(line,"mass")) {
massflag = 1;
sscanf(line,"%lg",&masstotal);
masstotal *= sizescale*sizescale*sizescale;
}
else if (strstr(line,"com")) {
comflag = 1;
sscanf(line,"%lg %lg %lg",&com[0],&com[1],&com[2]);
com[0] *= sizescale;
com[1] *= sizescale;
com[2] *= sizescale;
if (domain->dimension == 2 && com[2] != 0.0)
error->all(FLERR,"Molecule file z center-of-mass must be 0.0 for 2d");
}
@ -404,6 +438,12 @@ void Molecule::read(int flag)
sscanf(line,"%lg %lg %lg %lg %lg %lg",
&itensor[0],&itensor[1],&itensor[2],
&itensor[3],&itensor[4],&itensor[5]);
itensor[0] *= sizescale*sizescale*sizescale*sizescale*sizescale;
itensor[1] *= sizescale*sizescale*sizescale*sizescale*sizescale;
itensor[2] *= sizescale*sizescale*sizescale*sizescale*sizescale;
itensor[3] *= sizescale*sizescale*sizescale*sizescale*sizescale;
itensor[4] *= sizescale*sizescale*sizescale*sizescale*sizescale;
itensor[5] *= sizescale*sizescale*sizescale*sizescale*sizescale;
}
else break;
@ -414,8 +454,10 @@ void Molecule::read(int flag)
if (natoms < 1) error->all(FLERR,"No or invalid atom count in molecule file");
if (nbonds < 0) error->all(FLERR,"Invalid bond count in molecule file");
if (nangles < 0) error->all(FLERR,"Invalid angle count in molecule file");
if (ndihedrals < 0) error->all(FLERR,"Invalid dihedral count in molecule file");
if (nimpropers < 0) error->all(FLERR,"Invalid improper count in molecule file");
if (ndihedrals < 0)
error->all(FLERR,"Invalid dihedral count in molecule file");
if (nimpropers < 0)
error->all(FLERR,"Invalid improper count in molecule file");
// count = vector for tallying bonds,angles,etc per atom
@ -544,6 +586,9 @@ void Molecule::coords(char *line)
error->all(FLERR,"Invalid Coords section in molecule file");
}
sscanf(line,"%d %lg %lg %lg",&tmp,&x[i][0],&x[i][1],&x[i][2]);
x[i][0] *= sizescale;
x[i][1] *= sizescale;
x[i][2] *= sizescale;
}
if (domain->dimension == 2) {
@ -614,6 +659,7 @@ void Molecule::diameters(char *line)
error->all(FLERR,"Invalid Diameters section in molecule file");
}
sscanf(line,"%d %lg",&tmp,&radius[i]);
radius[i] *= sizescale;
radius[i] *= 0.5;
maxradius = MAX(maxradius,radius[i]);
}
@ -638,6 +684,7 @@ void Molecule::masses(char *line)
error->all(FLERR,"Invalid Masses section in molecule file");
}
sscanf(line,"%d %lg",&tmp,&rmass[i]);
rmass[i] *= sizescale*sizescale*sizescale;
}
for (int i = 0; i < natoms; i++)