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begin unfeaturing multiple label maps feature

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This commit is contained in:
Jacob Gissinger
2022-08-09 01:01:31 -04:00
parent 8c8084a027
commit 363b80f85c
10 changed files with 49 additions and 86 deletions
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76
src/atom.cpp
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@ -226,8 +226,7 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
// type labels
nlmap = 0;
lmaps = nullptr;
lmap = nullptr;
// custom atom arrays
@ -348,8 +347,7 @@ Atom::~Atom()
// delete label maps
for (int i = 0; i < nlmap; i++) delete lmaps[i];
memory->sfree(lmaps);
memory->sfree(lmap);
// delete per-type arrays
@ -1166,7 +1164,7 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset,
if (mol_offset) molecule[nlocal-1] += mol_offset;
if (!isdigit(typestr[0])) {
if (!atom->labelmapflag) error->one(FLERR,"Invalid Atoms section in data file");
type[nlocal-1] = find_label(typestr,Atom::ATOM);
type[nlocal-1] = lmap->find(typestr,Atom::ATOM);
if (type[nlocal-1] == -1) error->one(FLERR,"Invalid Atoms section in data file");
} else {
type[nlocal-1] = utils::inumeric(FLERR,typestr.c_str(),true,lmp);
@ -1254,7 +1252,7 @@ void Atom::data_bonds(int n, char *buf, int *count, tagint id_offset,
}
if (!isdigit(typestr[0])) {
if (!atom->labelmapflag) error->one(FLERR,"Invalid Bonds section in data file");
itype = find_label(typestr,Atom::BOND);
itype = lmap->find(typestr,Atom::BOND);
if (itype == -1) error->one(FLERR,"Invalid Bonds section in data file");
} else {
itype = utils::inumeric(FLERR,typestr,true,lmp);
@ -1333,7 +1331,7 @@ void Atom::data_angles(int n, char *buf, int *count, tagint id_offset,
}
if (!isdigit(typestr[0])) {
if (!atom->labelmapflag) error->one(FLERR,"Invalid Angles section in data file");
itype = find_label(typestr,Atom::ANGLE);
itype = lmap->find(typestr,Atom::ANGLE);
if (itype == -1) error->one(FLERR,"Invalid Angles section in data file");
} else {
itype = utils::inumeric(FLERR,typestr,true,lmp);
@ -1428,7 +1426,7 @@ void Atom::data_dihedrals(int n, char *buf, int *count, tagint id_offset,
}
if (!isdigit(typestr[0])) {
if (!atom->labelmapflag) error->one(FLERR,"Invalid Dihedrals section in data file");
itype = find_label(typestr,Atom::DIHEDRAL);
itype = lmap->find(typestr,Atom::DIHEDRAL);
if (itype == -1) error->one(FLERR,"Invalid Dihedrals section in data file");
} else {
itype = utils::inumeric(FLERR,typestr,true,lmp);
@ -1539,7 +1537,7 @@ void Atom::data_impropers(int n, char *buf, int *count, tagint id_offset,
}
if (!isdigit(typestr[0])) {
if (!atom->labelmapflag) error->one(FLERR,"Invalid Impropers section in data file");
itype = find_label(typestr,Atom::IMPROPER);
itype = lmap->find(typestr,Atom::IMPROPER);
if (itype == -1) error->one(FLERR,"Invalid Impropers section in data file");
} else {
itype = utils::inumeric(FLERR,typestr,true,lmp);
@ -1814,7 +1812,7 @@ void Atom::set_mass(const char *file, int line, int /*narg*/, char **arg)
if (!isdigit(arg[0][0]) && arg[0][0] != '*') {
std::string typestr(arg[0]);
int itype = find_label(typestr,Atom::ATOM);
int itype = lmap->find(typestr,Atom::ATOM);
if (itype == -1) error->all(file,line,"Invalid type for mass set");
mass[itype] = utils::numeric(FLERR,arg[1],false,lmp);
mass_setflag[itype] = 1;
@ -2062,54 +2060,20 @@ void Atom::add_molecule_atom(Molecule *onemol, int iatom, int ilocal, tagint off
allocate space for type label map
------------------------------------------------------------------------- */
int Atom::add_label_map(const std::string &mapID)
void Atom::add_label_map(const std::string &mapID)
{
labelmapflag = 1;
lmaps = (LabelMap **)
memory->srealloc(lmaps,(nlmap+1)*sizeof(LabelMap *),
"atom::lmaps");
lmaps[nlmap] = new LabelMap(lmp);
lmaps[nlmap]->id = mapID;
lmaps[nlmap]->natomtypes = ntypes;
lmaps[nlmap]->nbondtypes = nbondtypes;
lmaps[nlmap]->nangletypes = nangletypes;
lmaps[nlmap]->ndihedraltypes = ndihedraltypes;
lmaps[nlmap]->nimpropertypes = nimpropertypes;
lmaps[nlmap]->allocate_type_labels();
nlmap++;
return nlmap - 1;
}
/* ----------------------------------------------------------------------
find label, first parsing prefix for label map-ID
return -1 if does not exist
------------------------------------------------------------------------- */
int Atom::find_label(const std::string &label, int mode)
{
// check for auxiliary map prefix
std::string::size_type pos = label.find("::");
if (pos != std::string::npos) {
int ilmap = find_labelmap(label.substr(0,pos));
if (ilmap == -1) return -1;
auto slabel = label.substr(pos+2);
return lmaps[ilmap]->find(slabel,mode);
}
return lmaps[0]->find(label,mode);
}
/* ----------------------------------------------------------------------
find first label map in set with ID
return -1 if does not exist
------------------------------------------------------------------------- */
int Atom::find_labelmap(const std::string &id)
{
for (int ilmap = 0; ilmap < nlmap; ilmap++)
if (id == lmaps[ilmap]->id) return ilmap;
return -1;
lmap = (LabelMap *)
memory->srealloc(lmap,sizeof(LabelMap *),
"atom::lmap");
lmap = new LabelMap(lmp);
if (mapID != "") lmap->id = mapID;
lmap->natomtypes = ntypes;
lmap->nbondtypes = nbondtypes;
lmap->nangletypes = nangletypes;
lmap->ndihedraltypes = ndihedraltypes;
lmap->nimpropertypes = nimpropertypes;
lmap->allocate_type_labels();
}
/* ----------------------------------------------------------------------