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toward multiple maps

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This commit is contained in:
Jacob Gissinger
2021-01-28 23:44:02 -05:00
parent add904ea4e
commit 797555b5ce
11 changed files with 85 additions and 63 deletions
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42
src/atom.cpp
View File

@ -204,7 +204,7 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
// type labels
lmap = nullptr;
lmaps = nullptr;
// custom atom arrays
@ -312,9 +312,10 @@ Atom::~Atom()
for (int i = 0; i < nmolecule; i++) delete molecules[i];
memory->sfree(molecules);
// delete label map
// delete label maps
delete lmap;
for (int i = 0; i < nlmap; i++) delete lmaps[i];
memory->sfree(lmaps);
// delete per-type arrays
@ -1989,16 +1990,35 @@ void Atom::add_molecule_atom(Molecule *onemol, int iatom,
allocate space for type label map
------------------------------------------------------------------------- */
void Atom::add_label_map()
void Atom::add_label_map(char *mapID)
{
labelmapflag = 1;
lmap = new LabelMap(lmp);
lmap->natomtypes = ntypes;
lmap->nbondtypes = nbondtypes;
lmap->nangletypes = nangletypes;
lmap->ndihedraltypes = ndihedraltypes;
lmap->nimpropertypes = nimpropertypes;
lmap->allocate_type_labels();
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++;
}
/* ----------------------------------------------------------------------
find label, first parsing prefix for label map-ID
return -1 if does not exist
------------------------------------------------------------------------- */
int Atom::find_label(std::string label, int mode)
{
// find label map ... in progress
int ilmap;
ilmap = 0;
return lmaps[ilmap]->find(label,mode);
}
/* ----------------------------------------------------------------------

9
src/atom.h
View File

@ -32,6 +32,7 @@ class Atom : protected Pointers {
enum{DOUBLE,INT,BIGINT};
enum{GROW=0,RESTART=1,BORDER=2};
enum{ATOMIC=0,MOLECULAR=1,TEMPLATE=2};
enum{ATOM=0,BOND=1,ANGLE=2,DIHEDRAL=3,IMPROPER=4};
enum{MAP_NONE=0,MAP_ARRAY=1,MAP_HASH=2,MAP_YES=3};
// atom counts
@ -229,9 +230,10 @@ class Atom : protected Pointers {
int nmolecule;
class Molecule **molecules;
// type labels
// type label maps
class LabelMap *lmap;
int nlmap;
class LabelMap **lmaps;
// extra peratom info in restart file destined for fix & diag
@ -327,7 +329,8 @@ class Atom : protected Pointers {
int find_molecule(char *);
void add_molecule_atom(class Molecule *, int, int, tagint);
void add_label_map();
void add_label_map(char *);
int find_label(std::string, int);
void first_reorder();
virtual void sort();

18
src/input.cpp
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@ -678,7 +678,7 @@ void Input::readtype(char *&str, int mode)
char typechar[256];
labelstr = str;
type = atom->lmap->find(labelstr,mode);
type = atom->find_label(labelstr,mode);
if (type == -1) error->all(FLERR,fmt::format("Invalid type {}",str));
sprintf(typechar,"%d",type);
@ -1332,7 +1332,7 @@ void Input::angle_coeff()
error->all(FLERR,"Angle_coeff command before angle_style is defined");
if (atom->avec->angles_allow == 0)
error->all(FLERR,"Angle_coeff command when no angles allowed");
readtype(arg[0],atom->lmap->ANGLE);
readtype(arg[0],atom->ANGLE);
force->angle->coeff(narg,arg);
}
@ -1374,7 +1374,7 @@ void Input::bond_coeff()
error->all(FLERR,"Bond_coeff command before bond_style is defined");
if (atom->avec->bonds_allow == 0)
error->all(FLERR,"Bond_coeff command when no bonds allowed");
readtype(arg[0],atom->lmap->BOND);
readtype(arg[0],atom->BOND);
force->bond->coeff(narg,arg);
}
@ -1478,7 +1478,7 @@ void Input::dihedral_coeff()
error->all(FLERR,"Dihedral_coeff command before dihedral_style is defined");
if (atom->avec->dihedrals_allow == 0)
error->all(FLERR,"Dihedral_coeff command when no dihedrals allowed");
readtype(arg[0],atom->lmap->DIHEDRAL);
readtype(arg[0],atom->DIHEDRAL);
force->dihedral->coeff(narg,arg);
}
@ -1556,7 +1556,7 @@ void Input::improper_coeff()
error->all(FLERR,"Improper_coeff command before improper_style is defined");
if (atom->avec->impropers_allow == 0)
error->all(FLERR,"Improper_coeff command when no impropers allowed");
readtype(arg[0],atom->lmap->IMPROPER);
readtype(arg[0],atom->IMPROPER);
force->improper->coeff(narg,arg);
}
@ -1593,8 +1593,8 @@ void Input::labelmap()
{
if (domain->box_exist == 0)
error->all(FLERR,"Labelmap command before simulation box is defined");
if (!atom->labelmapflag) atom->add_label_map();
atom->lmap->modify_lmap(narg,arg);
if (!atom->labelmapflag) atom->add_label_map("");
atom->lmaps[0]->modify_lmap(narg,arg);
}
/* ---------------------------------------------------------------------- */
@ -1734,8 +1734,8 @@ void Input::pair_coeff()
error->all(FLERR,"Pair_coeff command before simulation box is defined");
if (force->pair == nullptr)
error->all(FLERR,"Pair_coeff command before pair_style is defined");
readtype(arg[0],atom->lmap->ATOM);
readtype(arg[1],atom->lmap->ATOM);
readtype(arg[0],atom->ATOM);
readtype(arg[1],atom->ATOM);
force->pair->coeff(narg,arg);
}

31
src/label_map.cpp
View File

@ -13,6 +13,7 @@
#include "label_map.h"
#include "atom.h"
#include "force.h"
#include "memory.h"
#include "error.h"
@ -118,23 +119,23 @@ void LabelMap::modify_lmap(int narg, char **arg)
void LabelMap::merge_lmap(LabelMap *lmap2, int mode)
{
if (mode == ATOM)
if (mode == atom->ATOM)
for (int i = 0; i < lmap2->natomtypes; i++)
find_or_create(lmap2->typelabel[i],typelabel,natomtypes);
if (mode == BOND)
if (mode == atom->BOND)
for (int i = 0; i < lmap2->nbondtypes; i++)
find_or_create(lmap2->btypelabel[i],btypelabel,nbondtypes);
if (mode == ANGLE)
if (mode == atom->ANGLE)
for (int i = 0; i < lmap2->nangletypes; i++)
find_or_create(lmap2->atypelabel[i],atypelabel,nangletypes);
if (mode == DIHEDRAL)
if (mode == atom->DIHEDRAL)
for (int i = 0; i < lmap2->ndihedraltypes; i++)
find_or_create(lmap2->dtypelabel[i],dtypelabel,ndihedraltypes);
if (mode == IMPROPER)
if (mode == atom->IMPROPER)
for (int i = 0; i < lmap2->nimpropertypes; i++)
find_or_create(lmap2->itypelabel[i],itypelabel,nimpropertypes);
}
@ -146,27 +147,27 @@ void LabelMap::merge_lmap(LabelMap *lmap2, int mode)
void LabelMap::create_lmap2lmap(LabelMap *lmap2, int mode)
{
if (mode == ATOM)
if (mode == atom->ATOM)
for (int i = 0; i < natomtypes; i++)
lmap2lmap.atom[i] = search(typelabel[i],lmap2->typelabel,
lmap2->natomtypes);
if (mode == BOND)
if (mode == atom->BOND)
for (int i = 0; i < nbondtypes; i++)
lmap2lmap.bond[i] = search(btypelabel[i],lmap2->btypelabel,
lmap2->nbondtypes);
if (mode == ANGLE)
if (mode == atom->ANGLE)
for (int i = 0; i < nangletypes; i++)
lmap2lmap.angle[i] = search(atypelabel[i],lmap2->atypelabel,
lmap2->nangletypes);
if (mode == DIHEDRAL)
if (mode == atom->DIHEDRAL)
for (int i = 0; i < ndihedraltypes; i++)
lmap2lmap.dihedral[i] = search(dtypelabel[i],lmap2->dtypelabel,
lmap2->ndihedraltypes);
if (mode == IMPROPER)
if (mode == atom->IMPROPER)
for (int i = 0; i < nimpropertypes; i++)
lmap2lmap.improper[i] = search(itypelabel[i],lmap2->itypelabel,
lmap2->nimpropertypes);
@ -205,19 +206,19 @@ int LabelMap::find_or_create(std::string mylabel, std::vector<std::string> &labe
int LabelMap::find(std::string mylabel, int mode)
{
if (mode == ATOM)
if (mode == atom->ATOM)
return search(mylabel,typelabel,natomtypes);
if (mode == BOND)
if (mode == atom->BOND)
return search(mylabel,btypelabel,nbondtypes);
if (mode == ANGLE)
if (mode == atom->ANGLE)
return search(mylabel,atypelabel,nangletypes);
if (mode == DIHEDRAL)
if (mode == atom->DIHEDRAL)
return search(mylabel,dtypelabel,ndihedraltypes);
if (mode == IMPROPER)
if (mode == atom->IMPROPER)
return search(mylabel,itypelabel,nimpropertypes);
return -1;

2
src/label_map.h
View File

@ -20,9 +20,9 @@ namespace LAMMPS_NS {
class LabelMap : protected Pointers {
public:
enum{ATOM,BOND,ANGLE,DIHEDRAL,IMPROPER};
int natomtypes,nbondtypes,nangletypes;
int ndihedraltypes,nimpropertypes;
std::string id;
std::vector<std::string> typelabel,btypelabel,atypelabel;
std::vector<std::string> dtypelabel,itypelabel;

11
src/molecule.cpp
View File

@ -20,7 +20,6 @@
#include "domain.h"
#include "error.h"
#include "force.h"
#include "label_map.h"
#include "math_extra.h"
#include "math_eigen.h"
#include "memory.h"
@ -729,7 +728,7 @@ void Molecule::types(char *line)
typestr = values.next_string();
if (!isdigit(typestr[0])) {
if (!atom->labelmapflag) error->one(FLERR,"Invalid Types section in molecule file");
type[iatom] = atom->lmap->find(typestr,atom->lmap->ATOM);
type[iatom] = atom->find_label(typestr,atom->ATOM);
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;
@ -942,7 +941,7 @@ void Molecule::bonds(int flag, char *line)
typestr = values.next_string();
if (!isdigit(typestr[0])) {
if (!atom->labelmapflag) error->one(FLERR,"Invalid Bonds section in molecule file");
itype = atom->lmap->find(typestr,atom->lmap->BOND);
itype = atom->find_label(typestr,atom->BOND);
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();
@ -1016,7 +1015,7 @@ void Molecule::angles(int flag, char *line)
typestr = values.next_string();
if (!isdigit(typestr[0])) {
if (!atom->labelmapflag) error->one(FLERR,"Invalid Angles section in molecule file");
itype = atom->lmap->find(typestr,atom->lmap->ANGLE);
itype = atom->find_label(typestr,atom->ANGLE);
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();
@ -1106,7 +1105,7 @@ void Molecule::dihedrals(int flag, char *line)
typestr = values.next_string();
if (!isdigit(typestr[0])) {
if (!atom->labelmapflag) error->one(FLERR,"Invalid Dihedrals section in molecule file");
itype = atom->lmap->find(typestr,atom->lmap->DIHEDRAL);
itype = atom->find_label(typestr,atom->DIHEDRAL);
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();
@ -1211,7 +1210,7 @@ void Molecule::impropers(int flag, char *line)
typestr = values.next_string();
if (!isdigit(typestr[0])) {
if (!atom->labelmapflag) error->one(FLERR,"Invalid Impropers section in molecule file");
itype = atom->lmap->find(typestr,atom->lmap->IMPROPER);
itype = atom->find_label(typestr,atom->IMPROPER);
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();

16
src/read_data.cpp
View File

@ -729,7 +729,7 @@ void ReadData::command(int narg, char **arg)
if (firstpass) {
if (atomflag == 1)
error->all(FLERR,"Must read Atom Type Labels before Atoms");
typelabels(lmap->typelabel,ntypes,lmap->ATOM);
typelabels(lmap->typelabel,ntypes,atom->ATOM);
} else skip_lines(ntypes);
} else if (strcmp(keyword,"Bond Type Labels") == 0) {
@ -737,7 +737,7 @@ void ReadData::command(int narg, char **arg)
if (firstpass) {
if (bondflag == 1)
error->all(FLERR,"Must read Bond Type Labels before Bonds");
typelabels(lmap->btypelabel,nbondtypes,lmap->BOND);
typelabels(lmap->btypelabel,nbondtypes,atom->BOND);
} else skip_lines(nbondtypes);
}
@ -746,7 +746,7 @@ void ReadData::command(int narg, char **arg)
if (firstpass) {
if (angleflag == 1)
error->all(FLERR,"Must read Angle Type Labels before Angles");
typelabels(lmap->atypelabel,nangletypes,lmap->ANGLE);
typelabels(lmap->atypelabel,nangletypes,atom->ANGLE);
} else skip_lines(nangletypes);
}
@ -755,7 +755,7 @@ void ReadData::command(int narg, char **arg)
if (firstpass) {
if (dihedralflag == 1)
error->all(FLERR,"Must read Dihedral Type Labels before Dihedrals");
typelabels(lmap->dtypelabel,ndihedraltypes,lmap->DIHEDRAL);
typelabels(lmap->dtypelabel,ndihedraltypes,atom->DIHEDRAL);
} else skip_lines(ndihedraltypes);
}
@ -764,7 +764,7 @@ void ReadData::command(int narg, char **arg)
if (firstpass) {
if (improperflag == 1)
error->all(FLERR,"Must read Improper Type Labels before Impropers");
typelabels(lmap->itypelabel,nimpropertypes,lmap->IMPROPER);
typelabels(lmap->itypelabel,nimpropertypes,atom->IMPROPER);
} else skip_lines(nimpropertypes);
}
@ -1974,7 +1974,7 @@ void ReadData::typelabels(std::vector<std::string> &mytypelabel, int myntypes, i
char *buf = new char[myntypes*MAXLINE];
labelflag = 1;
if (!atom->labelmapflag) atom->add_label_map();
if (!atom->labelmapflag) atom->add_label_map("");
int eof = comm->read_lines_from_file(fp,myntypes,MAXLINE,buf);
if (eof) error->all(FLERR,"Unexpected end of data file");
@ -1994,8 +1994,8 @@ void ReadData::typelabels(std::vector<std::string> &mytypelabel, int myntypes, i
// determine mapping to let labels override numeric types
// valid operations for first or subsequent data files
atom->lmap->merge_lmap(lmap,mode);
lmap->create_lmap2lmap(atom->lmap,mode);
atom->lmaps[0]->merge_lmap(lmap,mode);
lmap->create_lmap2lmap(atom->lmaps[0],mode);
}
/* ----------------------------------------------------------------------

4
src/read_restart.cpp
View File

@ -932,8 +932,8 @@ void ReadRestart::type_arrays()
} else if (flag == LABELMAP) {
read_int();
atom->add_label_map();
atom->lmap->read_restart(fp);
atom->add_label_map("");
atom->lmaps[0]->read_restart(fp);
} else error->all(FLERR,
"Invalid flag in type arrays section of restart file");

11
src/variable.cpp
View File

@ -24,7 +24,6 @@
#include "info.h"
#include "input.h"
#include "lmppython.h"
#include "label_map.h"
#include "math_const.h"
#include "memory.h"
#include "modify.h"
@ -4541,19 +4540,19 @@ int Variable::labelmap_function(char *word, char *contents, Tree **tree,
std::string typestr = contents;
if (strcmp(word,"label") == 0) {
value = atom->lmap->find(typestr,atom->lmap->ATOM);
value = atom->find_label(typestr,atom->ATOM);
} else if (strcmp(word,"blabel") == 0) {
value = atom->lmap->find(typestr,atom->lmap->BOND);
value = atom->find_label(typestr,atom->BOND);
} else if (strcmp(word,"alabel") == 0) {
value = atom->lmap->find(typestr,atom->lmap->ANGLE);
value = atom->find_label(typestr,atom->ANGLE);
} else if (strcmp(word,"dlabel") == 0) {
value = atom->lmap->find(typestr,atom->lmap->DIHEDRAL);
value = atom->find_label(typestr,atom->DIHEDRAL);
} else if (strcmp(word,"ilabel") == 0) {
value = atom->lmap->find(typestr,atom->lmap->IMPROPER);
value = atom->find_label(typestr,atom->IMPROPER);
}
if (value == -1)

2
src/write_data.cpp
View File

@ -186,7 +186,7 @@ void WriteData::write(const std::string &file)
if (me == 0) {
header();
if (atom->labelmapflag) atom->lmap->write_data(fp);
if (atom->labelmapflag) atom->lmaps[0]->write_data(fp);
type_arrays();
if (coeffflag) force_fields();
}

2
src/write_restart.cpp
View File

@ -523,7 +523,7 @@ void WriteRestart::type_arrays()
if (atom->mass) write_double_vec(MASS,atom->ntypes,&atom->mass[1]);
if (atom->labelmapflag) {
write_int(LABELMAP,atom->labelmapflag);
atom->lmap->write_restart(fp);
atom->lmaps[0]->write_restart(fp);
}
// -1 flag signals end of type arrays