Merge branch 'bond/react-delete_atoms' of https://github.com/jrgissing/lammps into collected-post-stable-patches

doc/src/fix_bond_react.txt

@@ -69,8 +69,9 @@ Initiate complex covalent bonding (topology) changes. These topology
 changes will be referred to as 'reactions' throughout this
 documentation. Topology changes are defined in pre- and post-reaction
 molecule templates and can include creation and deletion of bonds,
-angles, dihedrals, impropers, bond-types, angle-types, dihedral-types,
+angles, dihedrals, impropers, bond types, angle types, dihedral types,
-atom-types, or atomic charges.
+atom types, or atomic charges. In addition, reaction by-products or
+other molecules can be identified and deleted.
 
 Fix bond/react does not use quantum mechanical (eg. fix qmmm) or
 pairwise bond-order potential (eg. Tersoff or AIREBO) methods to
@@ -203,15 +204,16 @@ A discussion of correctly handling this is also provided on the
 The map file is a text document with the following format:
 
 A map file has a header and a body. The header of map file the
-contains one mandatory keyword and two optional keywords. The
+contains one mandatory keyword and three optional keywords. The
 mandatory keyword is 'equivalences' and the optional keywords are
-'edgeIDs' and 'customIDs':
+'edgeIDs' and 'deleteIDs' and 'customIDs':
 
 N {equivalences} = # of atoms N in the reaction molecule templates
 N {edgeIDs} = # of edge atoms N in the pre-reacted molecule template
+N {deleteIDs} = # of atoms N that are specified for deletion
 N {customIDs} = # of atoms N that are specified for a custom update :pre
 
-The body of the map file contains two mandatory sections and two
+The body of the map file contains two mandatory sections and three
 optional sections. The first mandatory section begins with the keyword
 'BondingIDs' and lists the atom IDs of the bonding atom pair in the
 pre-reacted molecule template. The second mandatory section begins
@@ -222,10 +224,12 @@ second column is the corresponding atom ID of the post-reacted
 molecule template. The first optional section begins with the keyword
 'EdgeIDs' and lists the atom IDs of edge atoms in the pre-reacted
 molecule template. The second optional section begins with the keyword
-'Custom Edges' and allows for forcing the update of a specific atom's
+'DeleteIDs' and lists the atom IDs of pre-reaction template atoms to
-atomic charge. The first column is the ID of an atom near the edge of
+delete. The third optional section begins with the keyword 'Custom
-the pre-reacted molecule template, and the value of the second column
+Edges' and allows for forcing the update of a specific atom's atomic
-is either 'none' or 'charges.' Further details are provided in the
+charge. The first column is the ID of an atom near the edge of the
+pre-reacted molecule template, and the value of the second column is
+either 'none' or 'charges.' Further details are provided in the
 discussion of the 'update_edges' keyword.
 
 A sample map file is given below:
@@ -309,7 +313,16 @@ edge are unaffected by this setting.
 
 A few other considerations:
 
-It may be beneficial to ensure reacting atoms are at a certain
+Many reactions result in one or more atoms that are considered
+unwanted by-products. Therefore, bond/react provides the option to
+delete a user-specified set of atoms. These pre-reaction atoms are
+identified in the map file. A deleted atom must still be included in
+the post-reaction molecule template, in which it cannot be bonded to
+an atom that is not deleted. In addition to deleting unwanted reaction
+by-products, this feature can be used to remove specific topologies,
+such as small rings, that may be otherwise indistinguishable.
+
+Also, it may be beneficial to ensure reacting atoms are at a certain
 temperature before being released to the overall thermostat. For this,
 you can use the internally-created dynamic group named
 "bond_react_MASTER_group." For example, adding the following command

doc/utils/sphinx-config/false_positives.txt

@@ -506,6 +506,7 @@ deepskyblue
 defgrad
 deformable
 del
+deleteIDs
 Dellago
 delocalization
 delocalized

src/USER-MISC/fix_bond_react.cpp

@@ -275,12 +275,14 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
   memory->create(edge,max_natoms,nreacts,"bond/react:edge");
   memory->create(landlocked_atoms,max_natoms,nreacts,"bond/react:landlocked_atoms");
   memory->create(custom_edges,max_natoms,nreacts,"bond/react:custom_edges");
+  memory->create(delete_atoms,max_natoms,nreacts,"bond/react:delete_atoms");
 
   for (int j = 0; j < nreacts; j++)
     for (int i = 0; i < max_natoms; i++) {
       edge[i][j] = 0;
       if (update_edges_flag[j] == 1) custom_edges[i][j] = 1;
       else custom_edges[i][j] = 0;
+      delete_atoms[i][j] = 0;
     }
 
   // read all map files afterward
@@ -393,6 +395,7 @@ FixBondReact::~FixBondReact()
   memory->destroy(equivalences);
   memory->destroy(reverse_equiv);
   memory->destroy(custom_edges);
+  memory->destroy(delete_atoms);
 
   memory->destroy(nevery);
   memory->destroy(cutsq);
@@ -1650,6 +1653,18 @@ void FixBondReact::find_landlocked_atoms(int myrxn)
     }
   }
 
+  // additionally, if a deleted atom is bonded to an atom that is not deleted, bad
+  for (int i = 0; i < onemol->natoms; i++) {
+    if (delete_atoms[i][myrxn] == 1) {
+      int ii = reverse_equiv[i][1][myrxn] - 1;
+      for (int j = 0; j < twomol_nxspecial[ii][0]; j++) {
+        if (delete_atoms[equivalences[twomol_xspecial[ii][j]-1][1][myrxn]-1][myrxn] == 0) {
+         error->one(FLERR,"A deleted atom cannot remain bonded to an atom that is not deleted");
+        }
+      }
+    }
+  }
+
   // also, if atoms change number of bonds, but aren't landlocked, that could be bad
   if (me == 0)
     for (int i = 0; i < twomol->natoms; i++) {
@@ -2053,6 +2068,13 @@ void FixBondReact::update_everything()
   tagint **bond_atom = atom->bond_atom;
   int *num_bond = atom->num_bond;
 
+  // used when deleting atoms
+  int ndel,ndelone;
+  int *mark = new int[nlocal];
+  for (int i = 0; i < nlocal; i++) mark[i] = 0;
+  tagint *tag = atom->tag;
+  AtomVec *avec = atom->avec;
+
   // update atom->nbonds, etc.
   // TODO: correctly tally with 'newton off'
   int delta_bonds = 0;
@@ -2086,6 +2108,18 @@ void FixBondReact::update_everything()
       }
     }
 
+    // mark to-delete atoms
+    for (int i = 0; i < update_num_mega; i++) {
+      rxnID = update_mega_glove[0][i];
+      onemol = atom->molecules[unreacted_mol[rxnID]];
+      for (int j = 0; j < onemol->natoms; j++) {
+        int iatom = atom->map(update_mega_glove[j+1][i]);
+        if (delete_atoms[j][rxnID] == 1 && iatom >= 0 && iatom < nlocal) {
+          mark[iatom] = 1;
+        }
+      }
+    }
+
     // update charges and types of landlocked atoms
     for (int i = 0; i < update_num_mega; i++) {
       rxnID = update_mega_glove[0][i];
@@ -2486,6 +2520,59 @@ void FixBondReact::update_everything()
 
   memory->destroy(update_mega_glove);
 
+  // delete atoms. taken from fix_evaporate. but don't think it needs to be in pre_exchange
+  // loop in reverse order to avoid copying marked atoms
+  ndel = ndelone = 0;
+  for (int i = atom->nlocal-1; i >= 0; i--) {
+    if (mark[i] == 1) {
+      avec->copy(atom->nlocal-1,i,1);
+      atom->nlocal--;
+      ndelone++;
+
+      if (atom->avec->bonds_allow) {
+        if (force->newton_bond) delta_bonds += atom->num_bond[i];
+        else {
+          for (int j = 0; j < atom->num_bond[i]; j++) {
+            if (tag[i] < atom->bond_atom[i][j]) delta_bonds++;
+          }
+        }
+      }
+      if (atom->avec->angles_allow) {
+        if (force->newton_bond) delta_angle += atom->num_angle[i];
+        else {
+          for (int j = 0; j < atom->num_angle[i]; j++) {
+            int m = atom->map(atom->angle_atom2[i][j]);
+            if (m >= 0 && m < nlocal) delta_angle++;
+          }
+        }
+      }
+      if (atom->avec->dihedrals_allow) {
+        if (force->newton_bond) delta_dihed += atom->num_dihedral[i];
+        else {
+          for (int j = 0; j < atom->num_dihedral[i]; j++) {
+            int m = atom->map(atom->dihedral_atom2[i][j]);
+            if (m >= 0 && m < nlocal) delta_dihed++;
+          }
+        }
+      }
+      if (atom->avec->impropers_allow) {
+        if (force->newton_bond) delta_imprp += atom->num_improper[i];
+        else {
+          for (int j = 0; j < atom->num_improper[i]; j++) {
+            int m = atom->map(atom->improper_atom2[i][j]);
+            if (m >= 0 && m < nlocal) delta_imprp;
+          }
+        }
+      }
+    }
+  }
+  delete [] mark;
+
+  MPI_Allreduce(&ndelone,&ndel,1,MPI_INT,MPI_SUM,world);
+
+  atom->natoms -= ndel;
+  // done deleting atoms
+
   // something to think about: this could done much more concisely if
   // all atom-level info (bond,angles, etc...) were kinda inherited from a common data struct --JG
 
@@ -2536,6 +2623,7 @@ void FixBondReact::read(int myrxn)
     if (strstr(line,"edgeIDs")) sscanf(line,"%d",&nedge);
     else if (strstr(line,"equivalences")) sscanf(line,"%d",&nequivalent);
     else if (strstr(line,"customIDs")) sscanf(line,"%d",&ncustom);
+    else if (strstr(line,"deleteIDs")) sscanf(line,"%d",&ndelete);
     else break;
   }
 
@@ -2565,6 +2653,8 @@ void FixBondReact::read(int myrxn)
     } else if (strcmp(keyword,"Custom Edges") == 0) {
       customedgesflag = 1;
       CustomEdges(line, myrxn);
+    } else if (strcmp(keyword,"DeleteIDs") == 0) {
+      DeleteAtoms(line, myrxn);
     } else error->one(FLERR,"Unknown section in superimpose file");
 
     parse_keyword(1,line,keyword);
@@ -2630,6 +2720,16 @@ void FixBondReact::CustomEdges(char *line, int myrxn)
   delete [] edgemode;
 }
 
+void FixBondReact::DeleteAtoms(char *line, int myrxn)
+{
+  int tmp;
+  for (int i = 0; i < ndelete; i++) {
+    readline(line);
+    sscanf(line,"%d",&tmp);
+    delete_atoms[tmp-1][myrxn] = 1;
+  }
+}
+
 void FixBondReact::open(char *file)
 {
   fp = fopen(file,"r");

src/USER-MISC/fix_bond_react.h

@@ -101,7 +101,7 @@ class FixBondReact : public Fix {
 
   int *ibonding,*jbonding;
   int *closeneigh; // indicates if bonding atoms of a rxn are 1-2, 1-3, or 1-4 neighbors
-  int nedge,nequivalent,ncustom; // number of edge, equivalent, custom atoms in mapping file
+  int nedge,nequivalent,ncustom,ndelete; // number of edge, equivalent, custom atoms in mapping file
   int attempted_rxn; // there was an attempt!
   int *local_rxn_count;
   int *ghostly_rxn_count;
@@ -116,6 +116,7 @@ class FixBondReact : public Fix {
   int ***reverse_equiv; // re-ordered equivalences
   int **landlocked_atoms; // all atoms at least three bonds away from edge atoms
   int **custom_edges; // atoms in molecule templates with incorrect valences
+  int **delete_atoms; // atoms in pre-reacted templates to delete
 
   int **nxspecial,**onemol_nxspecial,**twomol_nxspecial; // full number of 1-4 neighbors
   tagint **xspecial,**onemol_xspecial,**twomol_xspecial; // full 1-4 neighbor list
@@ -138,6 +139,7 @@ class FixBondReact : public Fix {
   void EdgeIDs(char *,int);
   void Equivalences(char *,int);
   void CustomEdges(char *,int);
+  void DeleteAtoms(char *,int);
 
   void make_a_guess ();
   void neighbor_loop();