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add molecule IDs to molecule templates

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for when more than one molecule per file
This commit is contained in:
jrgissing
2020-03-02 00:53:19 -07:00
parent 8636e86f38
commit 90bfa6b783
2 changed files with 38 additions and 7 deletions
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39
src/molecule.cpp
View File

@ -146,19 +146,19 @@ Molecule::Molecule(LAMMPS *lmp, int narg, char **arg, int &index) :
if (me == 0) {
if (screen)
fprintf(screen,"Read molecule %s:\n"
fprintf(screen,"Read molecule template %s:\n %d molecules\n"
" %d atoms with max type %d\n %d bonds with max type %d\n"
" %d angles with max type %d\n %d dihedrals with max type %d\n"
" %d impropers with max type %d\n",
id,natoms,ntypes,
id,nmolecules,natoms,ntypes,
nbonds,nbondtypes,nangles,nangletypes,
ndihedrals,ndihedraltypes,nimpropers,nimpropertypes);
if (logfile)
fprintf(logfile,"Read molecule %s:\n"
fprintf(logfile,"Read molecule template %s:\n %d molecules\n"
" %d atoms with max type %d\n %d bonds with max type %d\n"
" %d angles with max type %d\n %d dihedrals with max type %d\n"
" %d impropers with max type %d\n",
id,natoms,ntypes,
id,nmolecules,natoms,ntypes,
nbonds,nbondtypes,nangles,nangletypes,
ndihedrals,ndihedraltypes,nimpropers,nimpropertypes);
}
@ -519,6 +519,10 @@ void Molecule::read(int flag)
typeflag = 1;
if (flag) types(line);
else skip_lines(natoms,line);
} else if (strcmp(keyword,"Molecules") == 0) {
moleculeflag = 1;
if (flag) molecules(line);
else skip_lines(natoms,line);
} else if (strcmp(keyword,"Charges") == 0) {
qflag = 1;
if (flag) charges(line);
@ -694,6 +698,29 @@ void Molecule::types(char *line)
ntypes = MAX(ntypes,type[i]);
}
/* ----------------------------------------------------------------------
read molecules from file
set nmolecules = max of any molecule type
------------------------------------------------------------------------- */
void Molecule::molecules(char *line)
{
int tmp;
for (int i = 0; i < natoms; i++) {
readline(line);
if (2 != sscanf(line,"%d %d",&tmp,&molecule[i]))
error->all(FLERR,"Invalid Molecules section in molecule file");
// molecule[i] += moffset; // placeholder for possible molecule offset
}
for (int i = 0; i < natoms; i++)
if (molecule[i] <= 0)
error->all(FLERR,"Invalid molecule ID in molecule file");
for (int i = 0; i < natoms; i++)
nmolecules = MAX(nmolecules,molecule[i]);
}
/* ----------------------------------------------------------------------
read charges from file
------------------------------------------------------------------------- */
@ -1432,13 +1459,14 @@ void Molecule::initialize()
natoms = 0;
nbonds = nangles = ndihedrals = nimpropers = 0;
ntypes = 0;
nmolecules = 1;
nbondtypes = nangletypes = ndihedraltypes = nimpropertypes = 0;
nibody = ndbody = 0;
bond_per_atom = angle_per_atom = dihedral_per_atom = improper_per_atom = 0;
maxspecial = 0;
xflag = typeflag = qflag = radiusflag = rmassflag = 0;
xflag = typeflag = moleculeflag = qflag = radiusflag = rmassflag = 0;
bondflag = angleflag = dihedralflag = improperflag = 0;
nspecialflag = specialflag = 0;
shakeflag = shakeflagflag = shakeatomflag = shaketypeflag = 0;
@ -1493,6 +1521,7 @@ void Molecule::allocate()
{
if (xflag) memory->create(x,natoms,3,"molecule:x");
if (typeflag) memory->create(type,natoms,"molecule:type");
if (moleculeflag) memory->create(molecule,natoms,"molecule:molecule");
if (qflag) memory->create(q,natoms,"molecule:q");
if (radiusflag) memory->create(radius,natoms,"molecule:radius");
if (rmassflag) memory->create(rmass,natoms,"molecule:rmass");

6
src/molecule.h
View File

@ -30,7 +30,7 @@ class Molecule : protected Pointers {
int natoms;
int nbonds,nangles,ndihedrals,nimpropers;
int ntypes;
int ntypes,nmolecules;
int nbondtypes,nangletypes,ndihedraltypes,nimpropertypes;
int nibody,ndbody;
@ -41,7 +41,7 @@ class Molecule : protected Pointers {
// 1 if attribute defined in file, 0 if not
int xflag,typeflag,qflag,radiusflag,rmassflag;
int xflag,typeflag,moleculeflag,qflag,radiusflag,rmassflag;
int bondflag,angleflag,dihedralflag,improperflag;
int nspecialflag,specialflag;
int shakeflag,shakeflagflag,shakeatomflag,shaketypeflag;
@ -59,6 +59,7 @@ class Molecule : protected Pointers {
double **x; // displacement of each atom from origin
int *type; // type of each atom
tagint *molecule; // molecule of each atom
double *q; // charge on each atom
double *radius; // radius of each atom
double *rmass; // mass of each atom
@ -131,6 +132,7 @@ class Molecule : protected Pointers {
void read(int);
void coords(char *);
void types(char *);
void molecules(char *);
void charges(char *);
void diameters(char *);
void masses(char *);