forked from lijiext/lammps
Merge pull request #1913 from jrgissing/molecule_template_moleculeIDs
Molecule template: molecule-IDs and fragments
This commit is contained in:
Axel Kohlmeyer
GitHub
commit
2b39c9968f
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@ -4724,6 +4724,12 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
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*Invalid Masses section in molecule file*
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Self-explanatory.
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*Invalid molecule ID in molecule file*
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Molecule ID must be a non-zero positive integer.
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*Invalid Molecules section in molecule file*
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Self-explanatory.
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*Invalid REAX atom type*
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There is a mis-match between LAMMPS atom types and the elements
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listed in the ReaxFF force field file.
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@ -4790,6 +4796,9 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
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Atom IDs must be positive integers and within range of defined
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atoms.
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*Invalid atom ID in Fragments section of molecule file*
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Self-explanatory.
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*Invalid atom ID in Impropers section of data file*
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Atom IDs must be positive integers and within range of defined
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atoms.
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@ -60,6 +60,7 @@ templates include:
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* :doc:`fix rigid/small <fix_rigid>`
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* :doc:`fix shake <fix_shake>`
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* :doc:`fix gcmc <fix_gcmc>`
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* :doc:`fix bond/react <fix_bond_react>`
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* :doc:`create_atoms <create_atoms>`
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* :doc:`atom_style template <atom_style>`
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@ -144,6 +145,7 @@ appear if the value(s) are different than the default.
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* Na *angles* = # of angles Na in molecule, default = 0
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* Nd *dihedrals* = # of dihedrals Nd in molecule, default = 0
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* Ni *impropers* = # of impropers Ni in molecule, default = 0
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* Nf *fragments* = # of fragments in molecule, default = 0
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* Mtotal *mass* = total mass of molecule
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* Xc Yc Zc *com* = coordinates of center-of-mass of molecule
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* Ixx Iyy Izz Ixy Ixz Iyz *inertia* = 6 components of inertia tensor of molecule
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@ -166,7 +168,7 @@ internally.
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These are the allowed section keywords for the body of the file.
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* *Coords, Types, Charges, Diameters, Masses* = atom-property sections
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* *Coords, Types, Molecules, Fragments, Charges, Diameters, Masses* = atom-property sections
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* *Bonds, Angles, Dihedrals, Impropers* = molecular topology sections
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* *Special Bond Counts, Special Bonds* = special neighbor info
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* *Shake Flags, Shake Atoms, Shake Bond Types* = SHAKE info
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@ -223,6 +225,26 @@ listed in order from 1 to Nlines, but LAMMPS does not check for this.
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----------
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*Molecules* section:
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* one line per atom
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* line syntax: ID molecule-ID
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* molecule-ID = molecule ID of atom
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----------
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*Fragments* section:
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* one line per fragment
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* line syntax: ID a b c d ...
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* a,b,c,d,... = IDs of atoms in fragment
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The ID of a fragment can only contain alphanumeric characters and
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underscores. The atom IDs should be values from 1 to Natoms, where
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Natoms = # of atoms in the molecule.
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----------
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*Charges* section:
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* one line per atom
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@ -632,7 +632,13 @@ void FixPour::pre_exchange()
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int n = atom->nlocal - 1;
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atom->tag[n] = maxtag_all + m+1;
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if (mode == MOLECULE) {
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if (atom->molecule_flag) atom->molecule[n] = maxmol_all+1;
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if (atom->molecule_flag) {
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if (onemols[imol]->moleculeflag) {
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atom->molecule[n] = maxmol_all + onemols[imol]->molecule[m];
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} else {
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atom->molecule[n] = maxmol_all+1;
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}
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}
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if (atom->molecular == 2) {
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atom->molindex[n] = 0;
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atom->molatom[n] = m;
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@ -666,7 +672,13 @@ void FixPour::pre_exchange()
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fixshake->set_molecule(nlocalprev,maxtag_all,imol,coord,vnew,quat);
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maxtag_all += natom;
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if (mode == MOLECULE && atom->molecule_flag) maxmol_all++;
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if (mode == MOLECULE && atom->molecule_flag) {
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if (onemols[imol]->moleculeflag) {
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maxmol_all += onemols[imol]->nmolecules;
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} else {
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maxmol_all++;
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}
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}
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}
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// warn if not successful with all insertions b/c too many attempts
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@ -539,7 +539,13 @@ void FixDeposit::pre_exchange()
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n = atom->nlocal - 1;
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atom->tag[n] = maxtag_all + m+1;
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if (mode == MOLECULE) {
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if (atom->molecule_flag) atom->molecule[n] = maxmol_all+1;
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if (atom->molecule_flag) {
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if (onemols[imol]->moleculeflag) {
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atom->molecule[n] = maxmol_all + onemols[imol]->molecule[m];
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} else {
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atom->molecule[n] = maxmol_all+1;
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}
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}
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if (atom->molecular == 2) {
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atom->molindex[n] = 0;
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atom->molatom[n] = m;
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@ -603,7 +609,13 @@ void FixDeposit::pre_exchange()
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maxtag_all += natom;
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if (maxtag_all >= MAXTAGINT)
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error->all(FLERR,"New atom IDs exceed maximum allowed ID");
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if (mode == MOLECULE && atom->molecule_flag) maxmol_all++;
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if (mode == MOLECULE && atom->molecule_flag) {
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if (onemols[imol]->moleculeflag) {
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maxmol_all += onemols[imol]->nmolecules;
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} else {
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maxmol_all++;
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}
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}
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if (atom->map_style) {
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atom->map_init();
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atom->map_set();
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@ -490,7 +490,13 @@ void CreateAtoms::command(int narg, char **arg)
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for (int i = 0; i < molcreate; i++) {
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if (tag) offset = tag[ilocal]-1;
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for (int m = 0; m < natoms; m++) {
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if (molecule_flag) molecule[ilocal] = moloffset + i+1;
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if (molecule_flag) {
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if (onemol->moleculeflag) {
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molecule[ilocal] = moloffset + onemol->molecule[m];
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} else {
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molecule[ilocal] = moloffset + 1;
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}
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}
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if (molecular == 2) {
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atom->molindex[ilocal] = 0;
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atom->molatom[ilocal] = m;
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@ -524,6 +530,13 @@ void CreateAtoms::command(int narg, char **arg)
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}
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ilocal++;
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}
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if (molecule_flag) {
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if (onemol->moleculeflag) {
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moloffset += onemol->nmolecules;
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} else {
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moloffset++;
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}
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}
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}
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// perform irregular comm to migrate atoms to new owning procs
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101
src/molecule.cpp
101
src/molecule.cpp
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@ -37,7 +37,7 @@ using namespace LAMMPS_NS;
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/* ---------------------------------------------------------------------- */
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Molecule::Molecule(LAMMPS *lmp, int narg, char **arg, int &index) :
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Pointers(lmp), id(NULL), x(NULL), type(NULL), q(NULL), radius(NULL),
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Pointers(lmp), id(NULL), x(NULL), type(NULL), molecule(NULL), q(NULL), radius(NULL),
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rmass(NULL), num_bond(NULL), bond_type(NULL), bond_atom(NULL),
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num_angle(NULL), angle_type(NULL), angle_atom1(NULL), angle_atom2(NULL),
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angle_atom3(NULL), num_dihedral(NULL), dihedral_type(NULL), dihedral_atom1(NULL),
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@ -46,7 +46,7 @@ Molecule::Molecule(LAMMPS *lmp, int narg, char **arg, int &index) :
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improper_atom3(NULL), improper_atom4(NULL), nspecial(NULL), special(NULL),
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shake_flag(NULL), shake_atom(NULL), shake_type(NULL), avec_body(NULL), ibodyparams(NULL),
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dbodyparams(NULL), dx(NULL), dxcom(NULL), dxbody(NULL), quat_external(NULL),
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fp(NULL), count(NULL)
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fp(NULL), count(NULL), fragmentmask(NULL)
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{
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me = comm->me;
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@ -146,19 +146,19 @@ Molecule::Molecule(LAMMPS *lmp, int narg, char **arg, int &index) :
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if (me == 0) {
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if (screen)
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fprintf(screen,"Read molecule %s:\n"
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fprintf(screen,"Read molecule template %s:\n %d molecules\n"
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" %d atoms with max type %d\n %d bonds with max type %d\n"
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" %d angles with max type %d\n %d dihedrals with max type %d\n"
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" %d impropers with max type %d\n",
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id,natoms,ntypes,
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id,nmolecules,natoms,ntypes,
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nbonds,nbondtypes,nangles,nangletypes,
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ndihedrals,ndihedraltypes,nimpropers,nimpropertypes);
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if (logfile)
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fprintf(logfile,"Read molecule %s:\n"
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fprintf(logfile,"Read molecule template %s:\n %d molecules\n"
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" %d atoms with max type %d\n %d bonds with max type %d\n"
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" %d angles with max type %d\n %d dihedrals with max type %d\n"
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" %d impropers with max type %d\n",
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id,natoms,ntypes,
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id,nmolecules,natoms,ntypes,
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nbonds,nbondtypes,nangles,nangletypes,
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ndihedrals,ndihedraltypes,nimpropers,nimpropertypes);
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}
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@ -447,6 +447,9 @@ void Molecule::read(int flag)
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} else if (strstr(line,"impropers")) {
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nmatch = sscanf(line,"%d",&nimpropers);
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nwant = 1;
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} else if (strstr(line,"fragments")) {
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nmatch = sscanf(line,"%d",&nfragments);
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nwant = 1;
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} else if (strstr(line,"mass")) {
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massflag = 1;
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nmatch = sscanf(line,"%lg",&masstotal);
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@ -519,6 +522,14 @@ void Molecule::read(int flag)
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typeflag = 1;
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if (flag) types(line);
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else skip_lines(natoms,line);
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} else if (strcmp(keyword,"Molecules") == 0) {
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moleculeflag = 1;
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if (flag) molecules(line);
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else skip_lines(natoms,line);
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} else if (strcmp(keyword,"Fragments") == 0) {
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fragmentflag = 1;
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if (flag) fragments(line);
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else skip_lines(nfragments,line);
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} else if (strcmp(keyword,"Charges") == 0) {
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qflag = 1;
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if (flag) charges(line);
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@ -694,6 +705,58 @@ void Molecule::types(char *line)
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ntypes = MAX(ntypes,type[i]);
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}
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/* ----------------------------------------------------------------------
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read molecules from file
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set nmolecules = max of any molecule type
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------------------------------------------------------------------------- */
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void Molecule::molecules(char *line)
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{
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int tmp;
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for (int i = 0; i < natoms; i++) {
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readline(line);
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if (2 != sscanf(line,"%d %d",&tmp,&molecule[i]))
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error->all(FLERR,"Invalid Molecules section in molecule file");
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// molecule[i] += moffset; // placeholder for possible molecule offset
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}
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for (int i = 0; i < natoms; i++)
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if (molecule[i] <= 0)
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error->all(FLERR,"Invalid molecule ID in molecule file");
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for (int i = 0; i < natoms; i++)
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nmolecules = MAX(nmolecules,molecule[i]);
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}
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/* ----------------------------------------------------------------------
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read fragments from file
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------------------------------------------------------------------------- */
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void Molecule::fragments(char *line)
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{
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int n,m,atomID,nwords;
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char **words = new char*[natoms+1];
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for (int i = 0; i < nfragments; i++) {
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readline(line);
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nwords = parse(line,words,natoms+1);
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if (nwords > natoms+1)
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error->all(FLERR,"Invalid atom ID in Fragments section of molecule file");
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n = strlen(words[0]) + 1;
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fragmentnames[i] = new char[n];
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strcpy(fragmentnames[i],words[0]);
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for (m = 1; m < nwords; m++) {
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atomID = atoi(words[m]);
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if (atomID <= 0 || atomID > natoms)
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error->all(FLERR,"Invalid atom ID in Fragments section of molecule file");
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fragmentmask[i][atomID-1] = 1;
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}
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}
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delete [] words;
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}
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/* ----------------------------------------------------------------------
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read charges from file
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------------------------------------------------------------------------- */
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@ -1359,6 +1422,17 @@ void Molecule::body(int flag, int pflag, char *line)
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}
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}
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/* ----------------------------------------------------------------------
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return fragment index if name matches existing fragment, -1 if no such fragment
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------------------------------------------------------------------------- */
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int Molecule::findfragment(const char *name)
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{
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for (int i = 0; i < nfragments; i++)
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if (fragmentnames[i] && strcmp(name,fragmentnames[i]) == 0) return i;
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return -1;
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}
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/* ----------------------------------------------------------------------
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error check molecule attributes and topology against system settings
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flag = 0, just check this molecule
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@ -1432,13 +1506,14 @@ void Molecule::initialize()
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natoms = 0;
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nbonds = nangles = ndihedrals = nimpropers = 0;
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ntypes = 0;
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nmolecules = 1;
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nbondtypes = nangletypes = ndihedraltypes = nimpropertypes = 0;
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nibody = ndbody = 0;
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bond_per_atom = angle_per_atom = dihedral_per_atom = improper_per_atom = 0;
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maxspecial = 0;
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xflag = typeflag = qflag = radiusflag = rmassflag = 0;
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xflag = typeflag = moleculeflag = fragmentflag = qflag = radiusflag = rmassflag = 0;
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bondflag = angleflag = dihedralflag = improperflag = 0;
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nspecialflag = specialflag = 0;
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shakeflag = shakeflagflag = shakeatomflag = shaketypeflag = 0;
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@ -1493,6 +1568,11 @@ void Molecule::allocate()
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{
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if (xflag) memory->create(x,natoms,3,"molecule:x");
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if (typeflag) memory->create(type,natoms,"molecule:type");
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if (moleculeflag) memory->create(molecule,natoms,"molecule:molecule");
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if (fragmentflag) fragmentnames = new char*[nfragments];
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if (fragmentflag) memory->create(fragmentmask,nfragments,natoms,"molecule:fragmentmask");
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for (int i = 0; i < nfragments; i++)
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for (int j = 0; j < natoms; j++) fragmentmask[i][j] = 0;
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if (qflag) memory->create(q,natoms,"molecule:q");
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if (radiusflag) memory->create(radius,natoms,"molecule:radius");
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if (rmassflag) memory->create(rmass,natoms,"molecule:rmass");
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@ -1580,10 +1660,17 @@ void Molecule::deallocate()
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{
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memory->destroy(x);
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memory->destroy(type);
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memory->destroy(molecule);
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memory->destroy(q);
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memory->destroy(radius);
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memory->destroy(rmass);
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memory->destroy(fragmentmask);
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if (fragmentflag) {
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for (int i = 0; i < nfragments; i++) delete [] fragmentnames[i];
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delete [] fragmentnames;
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}
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memory->destroy(num_bond);
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memory->destroy(bond_type);
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memory->destroy(bond_atom);
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@ -30,10 +30,14 @@ class Molecule : protected Pointers {
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int natoms;
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int nbonds,nangles,ndihedrals,nimpropers;
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int ntypes;
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int ntypes,nmolecules,nfragments;
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int nbondtypes,nangletypes,ndihedraltypes,nimpropertypes;
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int nibody,ndbody;
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// fragment info
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char **fragmentnames;
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int **fragmentmask; // nfragments by natoms
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// max bond,angle,etc per atom
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int bond_per_atom,angle_per_atom,dihedral_per_atom,improper_per_atom;
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@ -41,7 +45,7 @@ class Molecule : protected Pointers {
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// 1 if attribute defined in file, 0 if not
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int xflag,typeflag,qflag,radiusflag,rmassflag;
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int xflag,typeflag,moleculeflag,fragmentflag,qflag,radiusflag,rmassflag;
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int bondflag,angleflag,dihedralflag,improperflag;
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int nspecialflag,specialflag;
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int shakeflag,shakeflagflag,shakeatomflag,shaketypeflag;
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@ -59,6 +63,7 @@ class Molecule : protected Pointers {
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double **x; // displacement of each atom from origin
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int *type; // type of each atom
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tagint *molecule; // molecule of each atom
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double *q; // charge on each atom
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double *radius; // radius of each atom
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double *rmass; // mass of each atom
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@ -118,6 +123,7 @@ class Molecule : protected Pointers {
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void compute_mass();
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void compute_com();
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void compute_inertia();
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int findfragment(const char *);
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void check_attributes(int);
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private:
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@ -131,6 +137,8 @@ class Molecule : protected Pointers {
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void read(int);
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void coords(char *);
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void types(char *);
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void molecules(char *);
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void fragments(char *);
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void charges(char *);
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void diameters(char *);
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void masses(char *);
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@ -363,6 +371,18 @@ E: Invalid improper type in impropers section of molecule file
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Self-explanatory.
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E: Invalid molecule ID in molecule file
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Molecule ID must be a non-zero positive integer.
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E: Invalid Molecules section in molecule file
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Self-explanatory.
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E: Invalid atom ID in Fragments section of molecule file
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: Invalid Special Bond Counts section in molecule file
|
||||
|
||||
Self-explanatory.
|
||||
|
|
|
|||
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Reference in New Issue