forked from lijiext/lammps
Merge branch 'bond/react-delete_atoms' of https://github.com/jrgissing/lammps into collected-post-stable-patches
This commit is contained in:
commit
0ed4da0bf9
doc
src/USER-MISC
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@ -69,8 +69,9 @@ Initiate complex covalent bonding (topology) changes. These topology
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changes will be referred to as 'reactions' throughout this
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documentation. Topology changes are defined in pre- and post-reaction
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molecule templates and can include creation and deletion of bonds,
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angles, dihedrals, impropers, bond-types, angle-types, dihedral-types,
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atom-types, or atomic charges.
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angles, dihedrals, impropers, bond types, angle types, dihedral types,
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atom types, or atomic charges. In addition, reaction by-products or
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other molecules can be identified and deleted.
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Fix bond/react does not use quantum mechanical (eg. fix qmmm) or
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pairwise bond-order potential (eg. Tersoff or AIREBO) methods to
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@ -203,15 +204,16 @@ A discussion of correctly handling this is also provided on the
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The map file is a text document with the following format:
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A map file has a header and a body. The header of map file the
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contains one mandatory keyword and two optional keywords. The
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contains one mandatory keyword and three optional keywords. The
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mandatory keyword is 'equivalences' and the optional keywords are
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'edgeIDs' and 'customIDs':
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'edgeIDs' and 'deleteIDs' and 'customIDs':
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N {equivalences} = # of atoms N in the reaction molecule templates
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N {edgeIDs} = # of edge atoms N in the pre-reacted molecule template
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N {deleteIDs} = # of atoms N that are specified for deletion
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N {customIDs} = # of atoms N that are specified for a custom update :pre
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The body of the map file contains two mandatory sections and two
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The body of the map file contains two mandatory sections and three
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optional sections. The first mandatory section begins with the keyword
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'BondingIDs' and lists the atom IDs of the bonding atom pair in the
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pre-reacted molecule template. The second mandatory section begins
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@ -222,10 +224,12 @@ second column is the corresponding atom ID of the post-reacted
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molecule template. The first optional section begins with the keyword
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'EdgeIDs' and lists the atom IDs of edge atoms in the pre-reacted
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molecule template. The second optional section begins with the keyword
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'Custom Edges' and allows for forcing the update of a specific atom's
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atomic charge. The first column is the ID of an atom near the edge of
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the pre-reacted molecule template, and the value of the second column
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is either 'none' or 'charges.' Further details are provided in the
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'DeleteIDs' and lists the atom IDs of pre-reaction template atoms to
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delete. The third optional section begins with the keyword 'Custom
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Edges' and allows for forcing the update of a specific atom's atomic
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charge. The first column is the ID of an atom near the edge of the
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pre-reacted molecule template, and the value of the second column is
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either 'none' or 'charges.' Further details are provided in the
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discussion of the 'update_edges' keyword.
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A sample map file is given below:
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@ -309,7 +313,16 @@ edge are unaffected by this setting.
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A few other considerations:
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It may be beneficial to ensure reacting atoms are at a certain
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Many reactions result in one or more atoms that are considered
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unwanted by-products. Therefore, bond/react provides the option to
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delete a user-specified set of atoms. These pre-reaction atoms are
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identified in the map file. A deleted atom must still be included in
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the post-reaction molecule template, in which it cannot be bonded to
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an atom that is not deleted. In addition to deleting unwanted reaction
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by-products, this feature can be used to remove specific topologies,
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such as small rings, that may be otherwise indistinguishable.
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Also, it may be beneficial to ensure reacting atoms are at a certain
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temperature before being released to the overall thermostat. For this,
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you can use the internally-created dynamic group named
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"bond_react_MASTER_group." For example, adding the following command
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@ -506,6 +506,7 @@ deepskyblue
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defgrad
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deformable
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del
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deleteIDs
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Dellago
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delocalization
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delocalized
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@ -275,12 +275,14 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
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memory->create(edge,max_natoms,nreacts,"bond/react:edge");
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memory->create(landlocked_atoms,max_natoms,nreacts,"bond/react:landlocked_atoms");
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memory->create(custom_edges,max_natoms,nreacts,"bond/react:custom_edges");
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memory->create(delete_atoms,max_natoms,nreacts,"bond/react:delete_atoms");
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for (int j = 0; j < nreacts; j++)
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for (int i = 0; i < max_natoms; i++) {
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edge[i][j] = 0;
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if (update_edges_flag[j] == 1) custom_edges[i][j] = 1;
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else custom_edges[i][j] = 0;
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delete_atoms[i][j] = 0;
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}
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// read all map files afterward
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@ -393,6 +395,7 @@ FixBondReact::~FixBondReact()
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memory->destroy(equivalences);
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memory->destroy(reverse_equiv);
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memory->destroy(custom_edges);
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memory->destroy(delete_atoms);
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memory->destroy(nevery);
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memory->destroy(cutsq);
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@ -1650,6 +1653,18 @@ void FixBondReact::find_landlocked_atoms(int myrxn)
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}
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}
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// additionally, if a deleted atom is bonded to an atom that is not deleted, bad
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for (int i = 0; i < onemol->natoms; i++) {
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if (delete_atoms[i][myrxn] == 1) {
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int ii = reverse_equiv[i][1][myrxn] - 1;
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for (int j = 0; j < twomol_nxspecial[ii][0]; j++) {
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if (delete_atoms[equivalences[twomol_xspecial[ii][j]-1][1][myrxn]-1][myrxn] == 0) {
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error->one(FLERR,"A deleted atom cannot remain bonded to an atom that is not deleted");
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}
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}
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}
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}
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// also, if atoms change number of bonds, but aren't landlocked, that could be bad
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if (me == 0)
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for (int i = 0; i < twomol->natoms; i++) {
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@ -2053,6 +2068,13 @@ void FixBondReact::update_everything()
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tagint **bond_atom = atom->bond_atom;
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int *num_bond = atom->num_bond;
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// used when deleting atoms
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int ndel,ndelone;
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int *mark = new int[nlocal];
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for (int i = 0; i < nlocal; i++) mark[i] = 0;
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tagint *tag = atom->tag;
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AtomVec *avec = atom->avec;
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// update atom->nbonds, etc.
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// TODO: correctly tally with 'newton off'
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int delta_bonds = 0;
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@ -2086,6 +2108,18 @@ void FixBondReact::update_everything()
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}
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}
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// mark to-delete atoms
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for (int i = 0; i < update_num_mega; i++) {
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rxnID = update_mega_glove[0][i];
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onemol = atom->molecules[unreacted_mol[rxnID]];
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for (int j = 0; j < onemol->natoms; j++) {
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int iatom = atom->map(update_mega_glove[j+1][i]);
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if (delete_atoms[j][rxnID] == 1 && iatom >= 0 && iatom < nlocal) {
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mark[iatom] = 1;
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}
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}
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}
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// update charges and types of landlocked atoms
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for (int i = 0; i < update_num_mega; i++) {
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rxnID = update_mega_glove[0][i];
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@ -2486,6 +2520,59 @@ void FixBondReact::update_everything()
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memory->destroy(update_mega_glove);
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// delete atoms. taken from fix_evaporate. but don't think it needs to be in pre_exchange
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// loop in reverse order to avoid copying marked atoms
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ndel = ndelone = 0;
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for (int i = atom->nlocal-1; i >= 0; i--) {
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if (mark[i] == 1) {
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avec->copy(atom->nlocal-1,i,1);
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atom->nlocal--;
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ndelone++;
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if (atom->avec->bonds_allow) {
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if (force->newton_bond) delta_bonds += atom->num_bond[i];
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else {
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for (int j = 0; j < atom->num_bond[i]; j++) {
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if (tag[i] < atom->bond_atom[i][j]) delta_bonds++;
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}
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}
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}
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if (atom->avec->angles_allow) {
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if (force->newton_bond) delta_angle += atom->num_angle[i];
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else {
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for (int j = 0; j < atom->num_angle[i]; j++) {
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int m = atom->map(atom->angle_atom2[i][j]);
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if (m >= 0 && m < nlocal) delta_angle++;
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}
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}
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}
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if (atom->avec->dihedrals_allow) {
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if (force->newton_bond) delta_dihed += atom->num_dihedral[i];
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else {
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for (int j = 0; j < atom->num_dihedral[i]; j++) {
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int m = atom->map(atom->dihedral_atom2[i][j]);
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if (m >= 0 && m < nlocal) delta_dihed++;
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}
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}
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}
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if (atom->avec->impropers_allow) {
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if (force->newton_bond) delta_imprp += atom->num_improper[i];
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else {
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for (int j = 0; j < atom->num_improper[i]; j++) {
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int m = atom->map(atom->improper_atom2[i][j]);
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if (m >= 0 && m < nlocal) delta_imprp;
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}
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}
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}
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}
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}
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delete [] mark;
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MPI_Allreduce(&ndelone,&ndel,1,MPI_INT,MPI_SUM,world);
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atom->natoms -= ndel;
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// done deleting atoms
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// something to think about: this could done much more concisely if
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// all atom-level info (bond,angles, etc...) were kinda inherited from a common data struct --JG
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@ -2536,6 +2623,7 @@ void FixBondReact::read(int myrxn)
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if (strstr(line,"edgeIDs")) sscanf(line,"%d",&nedge);
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else if (strstr(line,"equivalences")) sscanf(line,"%d",&nequivalent);
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else if (strstr(line,"customIDs")) sscanf(line,"%d",&ncustom);
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else if (strstr(line,"deleteIDs")) sscanf(line,"%d",&ndelete);
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else break;
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}
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@ -2565,6 +2653,8 @@ void FixBondReact::read(int myrxn)
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} else if (strcmp(keyword,"Custom Edges") == 0) {
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customedgesflag = 1;
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CustomEdges(line, myrxn);
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} else if (strcmp(keyword,"DeleteIDs") == 0) {
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DeleteAtoms(line, myrxn);
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} else error->one(FLERR,"Unknown section in superimpose file");
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parse_keyword(1,line,keyword);
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@ -2630,6 +2720,16 @@ void FixBondReact::CustomEdges(char *line, int myrxn)
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delete [] edgemode;
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}
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void FixBondReact::DeleteAtoms(char *line, int myrxn)
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{
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int tmp;
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for (int i = 0; i < ndelete; i++) {
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readline(line);
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sscanf(line,"%d",&tmp);
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delete_atoms[tmp-1][myrxn] = 1;
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}
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}
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void FixBondReact::open(char *file)
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{
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fp = fopen(file,"r");
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@ -101,7 +101,7 @@ class FixBondReact : public Fix {
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int *ibonding,*jbonding;
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int *closeneigh; // indicates if bonding atoms of a rxn are 1-2, 1-3, or 1-4 neighbors
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int nedge,nequivalent,ncustom; // number of edge, equivalent, custom atoms in mapping file
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int nedge,nequivalent,ncustom,ndelete; // number of edge, equivalent, custom atoms in mapping file
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int attempted_rxn; // there was an attempt!
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int *local_rxn_count;
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int *ghostly_rxn_count;
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@ -116,6 +116,7 @@ class FixBondReact : public Fix {
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int ***reverse_equiv; // re-ordered equivalences
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int **landlocked_atoms; // all atoms at least three bonds away from edge atoms
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int **custom_edges; // atoms in molecule templates with incorrect valences
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int **delete_atoms; // atoms in pre-reacted templates to delete
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int **nxspecial,**onemol_nxspecial,**twomol_nxspecial; // full number of 1-4 neighbors
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tagint **xspecial,**onemol_xspecial,**twomol_xspecial; // full 1-4 neighbor list
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@ -138,6 +139,7 @@ class FixBondReact : public Fix {
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void EdgeIDs(char *,int);
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void Equivalences(char *,int);
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void CustomEdges(char *,int);
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void DeleteAtoms(char *,int);
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void make_a_guess ();
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void neighbor_loop();
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