Adding compatability with MC fixes, set_array to property/atom, faster update/special/bonds, single methods, and misc small changes

src/fix_update_special_bonds.cpp

@@ -0,0 +1,195 @@
+// clang-format off
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://www.lammps.org/, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "fix_update_special_bonds.h"
+
+#include "atom.h"
+#include "atom_vec.h"
+#include "comm.h"
+#include "error.h"
+#include "force.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "pair.h"
+
+#include <cstring>
+#include <vector>
+#include <utility>
+
+using namespace LAMMPS_NS;
+using namespace FixConst;
+
+/* ---------------------------------------------------------------------- */
+
+FixUpdateSpecialBonds::FixUpdateSpecialBonds(LAMMPS *lmp, int narg, char **arg) :
+  Fix(lmp, narg, arg)
+{
+  if (narg != 3) error->all(FLERR,"Illegal fix update/special/bonds command");
+}
+
+/* ---------------------------------------------------------------------- */
+
+FixUpdateSpecialBonds::~FixUpdateSpecialBonds()
+{
+}
+
+/* ---------------------------------------------------------------------- */
+
+int FixUpdateSpecialBonds::setmask()
+{
+  int mask = 0;
+  mask |= PRE_EXCHANGE;
+  mask |= PRE_FORCE;
+  return mask;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixUpdateSpecialBonds::setup(int /*vflag*/)
+{
+  // Require atoms know about all of their bonds and if they break
+  if (force->newton_bond)
+    error->all(FLERR,"Fix update/special/bonds requires Newton bond off");
+
+  if (!atom->avec->bonds_allow)
+    error->all(FLERR,"Fix update/special/bonds requires atom bonds");
+
+  // special lj must be 0 1 1 to censor pair forces between bonded particles
+  // special coulomb must be 1 1 1 to ensure all pairs are included in the
+  //   neighbor list and 1-3 and 1-4 special bond lists are skipped
+  if (force->special_lj[1] != 0.0 || force->special_lj[2] != 1.0 ||
+      force->special_lj[3] != 1.0)
+    error->all(FLERR,"Fix update/special/bonds requires special LJ weights = 0,1,1");
+  if (force->special_coul[1] != 1.0 || force->special_coul[2] != 1.0 ||
+      force->special_coul[3] != 1.0)
+    error->all(FLERR,"Fix update/special/bonds requires special Coulomb weights = 1,1,1");
+
+  new_broken_pairs.clear();
+  broken_pairs.clear();
+}
+
+/* ----------------------------------------------------------------------
+  Update special bond list and atom bond arrays, empty broken bond list
+------------------------------------------------------------------------- */
+
+void FixUpdateSpecialBonds::pre_exchange()
+{
+  int i, j, key, m, n1, n3;
+  tagint tagi, tagj;
+  int nlocal = atom->nlocal;
+
+  tagint *tag = atom->tag;
+  tagint *slist;
+  int **nspecial = atom->nspecial;
+  tagint **special = atom->special;
+
+  for (auto const &it : broken_pairs) {
+    tagi = it.first;
+    tagj = it.second;
+
+    i = atom->map(tagi);
+    j = atom->map(tagj);
+
+    // remove i from special bond list for atom j and vice versa
+    if (i < nlocal) {
+      slist = special[i];
+      n1 = nspecial[i][0];
+      for (m = 0; m < n1; m++)
+        if (slist[m] == tagj) break;
+      n3 = nspecial[i][2];
+      for (; m < n3-1; m++) slist[m] = slist[m+1];
+      nspecial[i][0]--;
+      nspecial[i][1]--;
+      nspecial[i][2]--;
+    }
+
+    if (j < nlocal) {
+      slist = special[j];
+      n1 = nspecial[j][0];
+      for (m = 0; m < n1; m++)
+        if (slist[m] == tagi) break;
+      n3 = nspecial[j][2];
+      for (; m < n3-1; m++) slist[m] = slist[m+1];
+      nspecial[j][0]--;
+      nspecial[j][1]--;
+      nspecial[j][2]--;
+    }
+  }
+
+  broken_pairs.clear();
+}
+
+/* ----------------------------------------------------------------------
+  Loop neighbor list and update special bond lists for recently broken bonds
+------------------------------------------------------------------------- */
+
+void FixUpdateSpecialBonds::pre_force(int /*vflag*/)
+{
+  int i1,i2,j,jj,jnum;
+  int *jlist,*numneigh,**firstneigh;
+  tagint tag1, tag2;
+
+  int nlocal = atom->nlocal;
+
+  tagint *tag = atom->tag;
+  NeighList *list = force->pair->list; // may need to be generalized to work with pair hybrid*
+  numneigh = list->numneigh;
+  firstneigh = list->firstneigh;
+
+  // In theory could communicate a list of broken bonds to neighboring processors here
+  // to remove restriction that users use Newton bond off
+
+  for (auto const &it : new_broken_pairs) {
+    tag1 = it.first;
+    tag2 = it.second;
+    i1 = atom->map(tag1);
+    i2 = atom->map(tag2);
+    
+    // Loop through atoms of owned atoms i j
+    if (i1 < nlocal) {
+      jlist = firstneigh[i1];
+      jnum = numneigh[i1];    
+      for (jj = 0; jj < jnum; jj++) {
+        j = jlist[jj];
+        j &= SPECIALMASK; // Clear special bond bits
+        if (tag[j] == tag2)
+          jlist[jj] = j;
+      }
+    }
+
+    if (i2 < nlocal) {
+      jlist = firstneigh[i2];
+      jnum = numneigh[i2];
+      for (jj = 0; jj < jnum; jj++) {
+        j = jlist[jj];
+        j &= SPECIALMASK; // Clear special bond bits
+        if (tag[j] == tag1)
+          jlist[jj] = j;
+      }
+    }
+  }
+
+  new_broken_pairs.clear();
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixUpdateSpecialBonds::add_broken_bond(int i, int j)
+{
+  tagint *tag = atom->tag;
+  std::pair <tagint, tagint> tag_pair = std::make_pair(tag[i],tag[j]);
+
+  new_broken_pairs.push_back(tag_pair);
+  broken_pairs.push_back(tag_pair);
+}