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type label support for molecule files

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replace types directly for molecule files
This commit is contained in:
Jacob Gissinger
2021-01-12 17:52:55 -05:00
parent d7fb74f0be
commit 93c33ac4f4
2 changed files with 40 additions and 25 deletions
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21
src/label_map.cpp
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@ -36,27 +36,16 @@ LabelMap::~LabelMap()
// delete type labels
typelabel.clear();
delete [] lmap2lmap.atom;
if (force->bond) {
btypelabel.clear();
delete [] lmap2lmap.bond;
}
if (force->angle) {
atypelabel.clear();
delete [] lmap2lmap.angle;
}
if (force->dihedral) {
dtypelabel.clear();
delete [] lmap2lmap.dihedral;
}
if (force->improper) {
itypelabel.clear();
delete [] lmap2lmap.atom;
delete [] lmap2lmap.bond;
delete [] lmap2lmap.angle;
delete [] lmap2lmap.dihedral;
delete [] lmap2lmap.improper;
}
}
/* ----------------------------------------------------------------------

36
src/molecule.cpp
View File

@ -20,6 +20,7 @@
#include "domain.h"
#include "error.h"
#include "force.h"
#include "label_map.h"
#include "math_extra.h"
#include "math_eigen.h"
#include "memory.h"
@ -713,6 +714,7 @@ void Molecule::coords(char *line)
void Molecule::types(char *line)
{
std::string typestr;
for (int i = 0; i < natoms; i++) count[i] = 0;
try {
for (int i = 0; i < natoms; i++) {
@ -724,7 +726,11 @@ void Molecule::types(char *line)
int iatom = values.next_int() - 1;
if (iatom < 0 || iatom >= natoms) error->one(FLERR,"Invalid Types section in molecule file");
count[iatom]++;
type[iatom] = values.next_int();
typestr = values.next_string();
if (atom->labelmapflag) {
type[iatom] = atom->lmap->find(typestr,atom->lmap->typelabel,atom->ntypes);
if (type[iatom] == -1) error->one(FLERR,"Invalid Types section in molecule file");
} else type[iatom] = utils::inumeric(FLERR,typestr.c_str(),false,lmp);
type[iatom] += toffset;
}
} catch (TokenizerException &e) {
@ -917,6 +923,7 @@ void Molecule::bonds(int flag, char *line)
{
int itype;
tagint m,atom1,atom2;
std::string typestr;
int newton_bond = force->newton_bond;
if (flag == 0)
@ -931,7 +938,11 @@ void Molecule::bonds(int flag, char *line)
ValueTokenizer values(line);
if (values.count() != 4) error->one(FLERR,"Invalid Bonds section in molecule file");
values.next_int();
itype = values.next_int();
typestr = values.next_string();
if (atom->labelmapflag) {
itype = atom->lmap->find(typestr,atom->lmap->btypelabel,atom->nbondtypes);
if (itype == -1) error->one(FLERR,"Invalid Bonds section in molecule file");
} else itype = utils::inumeric(FLERR,typestr.c_str(),false,lmp);
atom1 = values.next_tagint();
atom2 = values.next_tagint();
} catch (TokenizerException &e) {
@ -985,6 +996,7 @@ void Molecule::angles(int flag, char *line)
{
int itype;
tagint m,atom1,atom2,atom3;
std::string typestr;
int newton_bond = force->newton_bond;
if (flag == 0)
@ -999,7 +1011,11 @@ void Molecule::angles(int flag, char *line)
ValueTokenizer values(line);
if (values.count() != 5) error->one(FLERR,"Invalid Angles section in molecule file");
values.next_int();
itype = values.next_int();
typestr = values.next_string();
if (atom->labelmapflag) {
itype = atom->lmap->find(typestr,atom->lmap->atypelabel,atom->nangletypes);
if (itype == -1) error->one(FLERR,"Invalid Angles section in molecule file");
} else itype = utils::inumeric(FLERR,typestr.c_str(),false,lmp);
atom1 = values.next_tagint();
atom2 = values.next_tagint();
atom3 = values.next_tagint();
@ -1069,6 +1085,7 @@ void Molecule::dihedrals(int flag, char *line)
{
int itype;
tagint m,atom1,atom2,atom3,atom4;
std::string typestr;
int newton_bond = force->newton_bond;
if (flag == 0)
@ -1083,7 +1100,11 @@ void Molecule::dihedrals(int flag, char *line)
ValueTokenizer values(line);
if (values.count() != 6) error->one(FLERR,"Invalid Dihedrals section in molecule file");
values.next_int();
itype = values.next_int();
typestr = values.next_string();
if (atom->labelmapflag) {
itype = atom->lmap->find(typestr,atom->lmap->dtypelabel,atom->ndihedraltypes);
if (itype == -1) error->one(FLERR,"Invalid Dihedrals section in molecule file");
} else itype = utils::inumeric(FLERR,typestr.c_str(),false,lmp);
atom1 = values.next_tagint();
atom2 = values.next_tagint();
atom3 = values.next_tagint();
@ -1168,6 +1189,7 @@ void Molecule::impropers(int flag, char *line)
{
int itype;
tagint m,atom1,atom2,atom3,atom4;
std::string typestr;
int newton_bond = force->newton_bond;
if (flag == 0)
@ -1182,7 +1204,11 @@ void Molecule::impropers(int flag, char *line)
ValueTokenizer values(line);
if (values.count() != 6) error->one(FLERR,"Invalid Impropers section in molecule file");
values.next_int();
itype = values.next_int();
typestr = values.next_string();
if (atom->labelmapflag) {
itype = atom->lmap->find(typestr,atom->lmap->itypelabel,atom->nimpropertypes);
if (itype == -1) error->one(FLERR,"Invalid Impropers section in molecule file");
} else itype = utils::inumeric(FLERR,typestr.c_str(),false,lmp);
atom1 = values.next_tagint();
atom2 = values.next_tagint();
atom3 = values.next_tagint();