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_angle_template.cpp
+++ b/src/ntopo_angle_template.cpp
@ -0,0 +1,119 @@
+/* ----------------------------------------------------------------------
+   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_angle_template.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "force.h"
+#include "domain.h"
+#include "update.h"
+#include "output.h"
+#include "thermo.h"
+#include "molecule.h"
+#include "memory.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+#define DELTA 10000
+
+/* ---------------------------------------------------------------------- */
+
+NTopoAngleTemplate::NTopoAngleTemplate(LAMMPS *lmp) : NTopo(lmp)
+{
+  allocate_angle();
+}
+
+/* ---------------------------------------------------------------------- */
+
+void NTopoAngleTemplate::build()
+{
+  int i,m,atom1,atom2,atom3;
+  int imol,iatom;
+  tagint tagprev;
+  int *num_angle;
+  tagint **angle_atom1,**angle_atom2,**angle_atom3;
+  int **angle_type;
+
+  Molecule **onemols = atom->avec->onemols;
+
+  tagint *tag = atom->tag;
+  int *molindex = atom->molindex;
+  int *molatom = atom->molatom;
+  int nlocal = atom->nlocal;
+  int newton_bond = force->newton_bond;
+
+  int lostbond = output->thermo->lostbond;
+  int nmissing = 0;
+  nanglelist = 0;
+
+  for (i = 0; i < nlocal; i++) {
+    if (molindex[i] < 0) continue;
+    imol = molindex[i];
+    iatom = molatom[i];
+    tagprev = tag[i] - iatom - 1;
+    num_angle = onemols[imol]->num_angle;
+    angle_atom1 = onemols[imol]->angle_atom1;
+    angle_atom2 = onemols[imol]->angle_atom2;
+    angle_atom3 = onemols[imol]->angle_atom3;
+    angle_type = onemols[imol]->angle_type;
+
+    for (m = 0; m < num_angle[iatom]; m++) {
+      if (angle_type[iatom][m] <= 0) continue;
+      atom1 = atom->map(angle_atom1[iatom][m]+tagprev);
+      atom2 = atom->map(angle_atom2[iatom][m]+tagprev);
+      atom3 = atom->map(angle_atom3[iatom][m]+tagprev);
+      if (atom1 == -1 || atom2 == -1 || atom3 == -1) {
+        nmissing++;
+        if (lostbond == ERROR) {
+          char str[128];
+          sprintf(str,"Angle atoms "
+                  TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT
+                  " missing on proc %d at step " BIGINT_FORMAT,
+                  angle_atom1[iatom][m]+tagprev,angle_atom2[iatom][m]+tagprev,
+                  angle_atom3[iatom][m]+tagprev,
+                  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);
+      if (newton_bond || (i <= atom1 && i <= atom2 && i <= atom3)) {
+        if (nanglelist == maxangle) {
+          maxangle += DELTA;
+          memory->grow(anglelist,maxangle,4,"neigh_topo:anglelist");
+        }
+        anglelist[nanglelist][0] = atom1;
+        anglelist[nanglelist][1] = atom2;
+        anglelist[nanglelist][2] = atom3;
+        anglelist[nanglelist][3] = angle_type[iatom][m];
+        nanglelist++;
+      }
+    }
+  }
+
+  if (cluster_check) angle_check();
+  if (lostbond == IGNORE) return;
+
+  int all;
+  MPI_Allreduce(&nmissing,&all,1,MPI_INT,MPI_SUM,world);
+  if (all) {
+    char str[128];
+    sprintf(str,
+            "Angle atoms missing at step " BIGINT_FORMAT,update->ntimestep);
+    if (me == 0) error->warning(FLERR,str);
+  }
+}