new neighbor list changes

2016-09-07 13:42:58 -06:00
parent 0252347d43
commit c9c2ae6c61
259 changed files with 23076 additions and 14650 deletions
--- a/src/ntopo_dihedral_partial.cpp
+++ b/src/ntopo_dihedral_partial.cpp
@ -0,0 +1,108 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, 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 <mpi.h>
+#include "ntopo_dihedral_partial.h"
+#include "atom.h"
+#include "force.h"
+#include "domain.h"
+#include "update.h"
+#include "output.h"
+#include "thermo.h"
+#include "memory.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+#define DELTA 10000
+
+/* ---------------------------------------------------------------------- */
+
+NTopoDihedralPartial::NTopoDihedralPartial(LAMMPS *lmp) : 
+  NTopo(lmp)
+{
+  allocate_dihedral();
+}
+
+/* ---------------------------------------------------------------------- */
+
+void NTopoDihedralPartial::build()
+{
+  int i,m,atom1,atom2,atom3,atom4;
+
+  int nlocal = atom->nlocal;
+  int *num_dihedral = atom->num_dihedral;
+  tagint **dihedral_atom1 = atom->dihedral_atom1;
+  tagint **dihedral_atom2 = atom->dihedral_atom2;
+  tagint **dihedral_atom3 = atom->dihedral_atom3;
+  tagint **dihedral_atom4 = atom->dihedral_atom4;
+  int **dihedral_type = atom->dihedral_type;
+  int newton_bond = force->newton_bond;
+
+  int lostbond = output->thermo->lostbond;
+  int nmissing = 0;
+  ndihedrallist = 0;
+
+  for (i = 0; i < nlocal; i++)
+    for (m = 0; m < num_dihedral[i]; m++) {
+      if (dihedral_type[i][m] <= 0) continue;
+      atom1 = atom->map(dihedral_atom1[i][m]);
+      atom2 = atom->map(dihedral_atom2[i][m]);
+      atom3 = atom->map(dihedral_atom3[i][m]);
+      atom4 = atom->map(dihedral_atom4[i][m]);
+      if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) {
+        nmissing++;
+        if (lostbond == ERROR) {
+          char str[128];
+          sprintf(str,"Dihedral atoms "
+                  TAGINT_FORMAT " " TAGINT_FORMAT " "
+                  TAGINT_FORMAT " " TAGINT_FORMAT
+                  " missing on proc %d at step " BIGINT_FORMAT,
+                  dihedral_atom1[i][m],dihedral_atom2[i][m],
+                  dihedral_atom3[i][m],dihedral_atom4[i][m],
+                  me,update->ntimestep);
+          error->one(FLERR,str);
+        }
+        continue;
+      }
+      atom1 = domain->closest_image(i,atom1);
+      atom2 = domain->closest_image(i,atom2);
+      atom3 = domain->closest_image(i,atom3);
+      atom4 = domain->closest_image(i,atom4);
+      if (newton_bond ||
+          (i <= atom1 && i <= atom2 && i <= atom3 && i <= atom4)) {
+        if (ndihedrallist == maxdihedral) {
+          maxdihedral += DELTA;
+          memory->grow(dihedrallist,maxdihedral,5,"neigh_topo:dihedrallist");
+        }
+        dihedrallist[ndihedrallist][0] = atom1;
+        dihedrallist[ndihedrallist][1] = atom2;
+        dihedrallist[ndihedrallist][2] = atom3;
+        dihedrallist[ndihedrallist][3] = atom4;
+        dihedrallist[ndihedrallist][4] = dihedral_type[i][m];
+        ndihedrallist++;
+      }
+    }
+
+  if (cluster_check) dihedral_check(ndihedrallist,dihedrallist);
+  if (lostbond == IGNORE) return;
+
+  int all;
+  MPI_Allreduce(&nmissing,&all,1,MPI_INT,MPI_SUM,world);
+  if (all) {
+    char str[128];
+    sprintf(str,
+            "Dihedral atoms missing at step " BIGINT_FORMAT,update->ntimestep);
+    if (me == 0) error->warning(FLERR,str);
+  }
+}