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Merge pull request #3399 from akohlmey/lookup-molecules

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Refactor access to molecule templates
This commit is contained in:
Axel Kohlmeyer
2022-08-17 15:29:11 -04:00
committed by GitHub
parent 6e8db537c9 f592e3184e
commit ca4f7b6579
12 changed files with 72 additions and 61 deletions
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2
src/GRANULAR/fix_pour.cpp
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@ -131,7 +131,7 @@ FixPour::FixPour(LAMMPS *lmp, int narg, char **arg) :
if (atom->molecular == Atom::TEMPLATE && onemols != atom->avec->onemols)
error->all(FLERR, "Fix pour molecule template ID must be same as atom style template ID");
onemols[i]->check_attributes(0);
onemols[i]->check_attributes();
// fix pour uses geoemetric center of molecule for insertion

2
src/MC/fix_gcmc.cpp
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@ -177,7 +177,7 @@ FixGCMC::FixGCMC(LAMMPS *lmp, int narg, char **arg) :
if (atom->molecular == Atom::TEMPLATE && onemols != atom->avec->onemols)
error->all(FLERR,"Fix gcmc molecule template ID must be same "
"as atom_style template ID");
onemols[imol]->check_attributes(0);
onemols[imol]->check_attributes();
}
if (charge_flag && atom->q == nullptr)

2
src/MC/fix_widom.cpp
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@ -153,7 +153,7 @@ FixWidom::FixWidom(LAMMPS *lmp, int narg, char **arg) :
if (atom->molecular == Atom::TEMPLATE && onemols != atom->avec->onemols)
error->all(FLERR,"Fix widom molecule template ID must be same "
"as atom_style template ID");
onemols[imol]->check_attributes(0);
onemols[imol]->check_attributes();
}
if (charge_flag && atom->q == nullptr)

4
src/REACTION/fix_bond_react.cpp
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@ -471,8 +471,8 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
open(files[i]);
onemol = atom->molecules[unreacted_mol[i]];
twomol = atom->molecules[reacted_mol[i]];
onemol->check_attributes(0);
twomol->check_attributes(0);
onemol->check_attributes();
twomol->check_attributes();
get_molxspecials();
read(i);
fclose(fp);

21
src/atom.cpp
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@ -1900,6 +1900,18 @@ int Atom::find_molecule(char *id)
return -1;
}
/* ----------------------------------------------------------------------
return vector of molecules which match template ID
------------------------------------------------------------------------- */
std::vector<Molecule *>Atom::get_molecule_by_id(const std::string &id)
{
std::vector<Molecule *> result;
for (int imol = 0; imol < nmolecule; ++imol)
if (id == molecules[imol]->id) result.push_back(molecules[imol]);
return result;
}
/* ----------------------------------------------------------------------
add info to current atom ilocal from molecule template onemol and its iatom
offset = atom ID preceding IDs of atoms in this molecule
@ -1912,8 +1924,7 @@ void Atom::add_molecule_atom(Molecule *onemol, int iatom, int ilocal, tagint off
if (onemol->radiusflag && radius_flag) radius[ilocal] = onemol->radius[iatom];
if (onemol->rmassflag && rmass_flag) rmass[ilocal] = onemol->rmass[iatom];
else if (rmass_flag)
rmass[ilocal] = 4.0*MY_PI/3.0 *
radius[ilocal]*radius[ilocal]*radius[ilocal];
rmass[ilocal] = 4.0*MY_PI/3.0 * radius[ilocal]*radius[ilocal]*radius[ilocal];
if (onemol->bodyflag) {
body[ilocal] = 0; // as if a body read from data file
onemol->avec_body->data_body(ilocal,onemol->nibody,onemol->ndbody,
@ -1923,10 +1934,8 @@ void Atom::add_molecule_atom(Molecule *onemol, int iatom, int ilocal, tagint off
// initialize custom per-atom properties to zero if present
for (int i = 0; i < nivector; ++i)
ivector[i][ilocal] = 0;
for (int i = 0; i < ndvector; ++i)
dvector[i][ilocal] = 0.0;
for (int i = 0; i < nivector; ++i) ivector[i][ilocal] = 0;
for (int i = 0; i < ndvector; ++i) dvector[i][ilocal] = 0.0;
for (int i = 0; i < niarray; ++i)
for (int j = 0; j < icols[i]; ++j)
iarray[i][ilocal][j] = 0;

1
src/atom.h
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@ -345,6 +345,7 @@ class Atom : protected Pointers {
void add_molecule(int, char **);
int find_molecule(char *);
std::vector<Molecule *>get_molecule_by_id(const std::string &);
void add_molecule_atom(class Molecule *, int, int, tagint);
void first_reorder();

2
src/create_atoms.cpp
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@ -299,7 +299,7 @@ void CreateAtoms::command(int narg, char **arg)
if (onemol->tag_require && !atom->tag_enable)
error->all(FLERR, "Create_atoms molecule has atom IDs, but system does not");
onemol->check_attributes(0);
onemol->check_attributes();
// use geometric center of molecule for insertion
// molecule random number generator, different for each proc

2
src/fix_deposit.cpp
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@ -117,7 +117,7 @@ FixDeposit::FixDeposit(LAMMPS *lmp, int narg, char **arg) :
if (atom->molecular == Atom::TEMPLATE && onemols != atom->avec->onemols)
error->all(FLERR,"Fix deposit molecule template ID must be same "
"as atom_style template ID");
onemols[i]->check_attributes(0);
onemols[i]->check_attributes();
// fix deposit uses geoemetric center of molecule for insertion

76
src/molecule.cpp
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@ -1671,64 +1671,48 @@ int Molecule::findfragment(const char *name)
/* ----------------------------------------------------------------------
error check molecule attributes and topology against system settings
flag = 0, just check this molecule
flag = 1, check all molecules in set, this is 1st molecule in set
------------------------------------------------------------------------- */
void Molecule::check_attributes(int flag)
void Molecule::check_attributes()
{
int n = 1;
if (flag) n = nset;
int imol = atom->find_molecule(id);
// check per-atom attributes of molecule
// warn if not a match
for (int i = imol; i < imol+n; i++) {
Molecule *onemol = atom->molecules[imol];
int mismatch = 0;
if (qflag && !atom->q_flag) mismatch = 1;
if (radiusflag && !atom->radius_flag) mismatch = 1;
if (rmassflag && !atom->rmass_flag) mismatch = 1;
// check per-atom attributes of molecule
// warn if not a match
if (mismatch && me == 0)
error->warning(FLERR,"Molecule attributes do not match system attributes");
int mismatch = 0;
if (onemol->qflag && !atom->q_flag) mismatch = 1;
if (onemol->radiusflag && !atom->radius_flag) mismatch = 1;
if (onemol->rmassflag && !atom->rmass_flag) mismatch = 1;
// for all atom styles, check nbondtype,etc
if (mismatch && me == 0)
error->warning(FLERR,"Molecule attributes do not match system attributes");
mismatch = 0;
if (atom->nbondtypes < nbondtypes) mismatch = 1;
if (atom->nangletypes < nangletypes) mismatch = 1;
if (atom->ndihedraltypes < ndihedraltypes) mismatch = 1;
if (atom->nimpropertypes < nimpropertypes) mismatch = 1;
// for all atom styles, check nbondtype,etc
if (mismatch) error->all(FLERR,"Molecule topology type exceeds system topology type");
mismatch = 0;
if (atom->nbondtypes < onemol->nbondtypes) mismatch = 1;
if (atom->nangletypes < onemol->nangletypes) mismatch = 1;
if (atom->ndihedraltypes < onemol->ndihedraltypes) mismatch = 1;
if (atom->nimpropertypes < onemol->nimpropertypes) mismatch = 1;
// for molecular atom styles, check bond_per_atom,etc + maxspecial
// do not check for atom style template, since nothing stored per atom
if (mismatch)
error->all(FLERR,"Molecule topology type exceeds system topology type");
if (atom->molecular == Atom::MOLECULAR) {
if (atom->avec->bonds_allow && atom->bond_per_atom < bond_per_atom) mismatch = 1;
if (atom->avec->angles_allow && atom->angle_per_atom < angle_per_atom) mismatch = 1;
if (atom->avec->dihedrals_allow && atom->dihedral_per_atom < dihedral_per_atom) mismatch = 1;
if (atom->avec->impropers_allow && atom->improper_per_atom < improper_per_atom) mismatch = 1;
if (atom->maxspecial < maxspecial) mismatch = 1;
// for molecular atom styles, check bond_per_atom,etc + maxspecial
// do not check for atom style template, since nothing stored per atom
if (atom->molecular == Atom::MOLECULAR) {
if (atom->avec->bonds_allow &&
atom->bond_per_atom < onemol->bond_per_atom) mismatch = 1;
if (atom->avec->angles_allow &&
atom->angle_per_atom < onemol->angle_per_atom) mismatch = 1;
if (atom->avec->dihedrals_allow &&
atom->dihedral_per_atom < onemol->dihedral_per_atom) mismatch = 1;
if (atom->avec->impropers_allow &&
atom->improper_per_atom < onemol->improper_per_atom) mismatch = 1;
if (atom->maxspecial < onemol->maxspecial) mismatch = 1;
if (mismatch)
error->all(FLERR,"Molecule topology/atom exceeds system topology/atom");
}
// warn if molecule topology defined but no special settings
if (onemol->bondflag && !onemol->specialflag)
if (me == 0) error->warning(FLERR,"Molecule has bond topology but no special bond settings");
if (mismatch) error->all(FLERR,"Molecule topology/atom exceeds system topology/atom");
}
// warn if molecule topology defined but no special settings
if (bondflag && !specialflag)
if (me == 0) error->warning(FLERR,"Molecule has bond topology but no special bond settings");
}
/* ----------------------------------------------------------------------

2
src/molecule.h
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@ -125,7 +125,7 @@ class Molecule : protected Pointers {
void compute_com();
void compute_inertia();
int findfragment(const char *);
void check_attributes(int);
void check_attributes();
private:
int me;

5
src/read_data.cpp
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@ -866,7 +866,10 @@ void ReadData::command(int narg, char **arg)
// insure nbondtypes,etc are still consistent with template molecules,
// in case data file re-defined them
if (atom->molecular == Atom::TEMPLATE) atom->avec->onemols[0]->check_attributes(1);
if (atom->molecular == Atom::TEMPLATE) {
int nset = MAX(1, atom->avec->onemols[0]->nset);
for (int i = 0; i < nset; ++i) atom->avec->onemols[i]->check_attributes();
}
// if adding atoms, migrate atoms to new processors
// use irregular() b/c box size could have changed dramaticaly

14
unittest/formats/test_molecule_file.cpp
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@ -216,6 +216,9 @@ TEST_F(MoleculeFileTest, twomols)
auto output = END_CAPTURE_OUTPUT();
ASSERT_THAT(output, ContainsRegex(".*Read molecule template.*\n.*2 molecules.*\n"
".*0 fragments.*\n.*2 atoms with max type 2.*\n.*0 bonds.*"));
ASSERT_EQ(lmp->atom->nmolecule, 1);
auto mols = lmp->atom->get_molecule_by_id(test_name);
ASSERT_EQ(mols.size(), 1);
}
TEST_F(MoleculeFileTest, twofiles)
@ -231,6 +234,17 @@ TEST_F(MoleculeFileTest, twofiles)
".*Read molecule template twomols:.*\n.*1 molecules.*\n"
".*0 fragments.*\n.*3 atoms with max type 4.*\n.*2 bonds with max type 2.*\n"
".*1 angles with max type 2.*\n.*0 dihedrals.*"));
BEGIN_CAPTURE_OUTPUT();
command("molecule h2o moltest.h2o.mol");
command("molecule co2 moltest.co2.mol");
output = END_CAPTURE_OUTPUT();
ASSERT_EQ(lmp->atom->nmolecule, 4);
auto mols = lmp->atom->get_molecule_by_id("twomols");
ASSERT_EQ(mols.size(), 2);
mols = lmp->atom->get_molecule_by_id("h2o");
ASSERT_EQ(mols.size(), 1);
mols = lmp->atom->get_molecule_by_id("co2");
ASSERT_EQ(mols.size(), 1);
}
TEST_F(MoleculeFileTest, bonds)