git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8960 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/neigh_bond.cpp

@@ -66,6 +66,8 @@ void Neighbor::bond_all()
         nbondlist++;
       }
     }
+
+  if (cluster_check) bond_check();
 }
 
 /* ---------------------------------------------------------------------- */
@@ -106,6 +108,33 @@ void Neighbor::bond_partial()
         nbondlist++;
       }
     }
+
+  if (cluster_check) bond_check();
+}
+
+/* ---------------------------------------------------------------------- */
+
+void Neighbor::bond_check()
+{
+  int i,j;
+  double dx,dy,dz,dxstart,dystart,dzstart;
+  
+  double **x = atom->x;
+  int flag = 0;
+
+  for (int m = 0; m < nbondlist; m++) {
+    i = bondlist[m][0];
+    j = bondlist[m][1];
+    dxstart = dx = x[i][0] - x[j][0];
+    dystart = dy = x[i][1] - x[j][1];
+    dzstart = dz = x[i][2] - x[j][2];
+    domain->minimum_image(dx,dy,dz);
+    if (dx != dxstart || dy != dystart || dz != dzstart) flag = 1;
+  }
+
+  int flag_all;
+  MPI_Allreduce(&flag,&flag_all,1,MPI_INT,MPI_SUM,world);
+  if (flag_all) error->all(FLERR,"Bond extent > half of periodic box length");
 }
 
 /* ---------------------------------------------------------------------- */
@@ -153,6 +182,8 @@ void Neighbor::angle_all()
         nanglelist++;
       }
     }
+
+  if (cluster_check) angle_check();
 }
 
 /* ---------------------------------------------------------------------- */
@@ -201,6 +232,39 @@ void Neighbor::angle_partial()
         nanglelist++;
       }
     }
+
+  if (cluster_check) angle_check();
+}
+
+/* ---------------------------------------------------------------------- */
+
+void Neighbor::angle_check()
+{
+  int i,j,k;
+  double dx,dy,dz,dxstart,dystart,dzstart;
+  
+  double **x = atom->x;
+  int flag = 0;
+
+  for (int m = 0; m < nbondlist; m++) {
+    i = anglelist[m][0];
+    j = anglelist[m][1];
+    k = anglelist[m][1];
+    dxstart = dx = x[i][0] - x[j][0];
+    dystart = dy = x[i][1] - x[j][1];
+    dzstart = dz = x[i][2] - x[j][2];
+    domain->minimum_image(dx,dy,dz);
+    if (dx != dxstart || dy != dystart || dz != dzstart) flag = 1;
+    dxstart = dx = x[i][0] - x[k][0];
+    dystart = dy = x[i][1] - x[k][1];
+    dzstart = dz = x[i][2] - x[k][2];
+    domain->minimum_image(dx,dy,dz);
+    if (dx != dxstart || dy != dystart || dz != dzstart) flag = 1;
+  }
+
+  int flag_all;
+  MPI_Allreduce(&flag,&flag_all,1,MPI_INT,MPI_SUM,world);
+  if (flag_all) error->all(FLERR,"Angle extent > half of periodic box length");
 }
 
 /* ---------------------------------------------------------------------- */
@@ -254,6 +318,8 @@ void Neighbor::dihedral_all()
         ndihedrallist++;
       }
     }
+
+  if (cluster_check) dihedral_check(dihedrallist);
 }
 
 /* ---------------------------------------------------------------------- */
@@ -308,6 +374,46 @@ void Neighbor::dihedral_partial()
         ndihedrallist++;
       }
     }
+
+  if (cluster_check) dihedral_check(dihedrallist);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void Neighbor::dihedral_check(int **list)
+{
+  int i,j,k,l;
+  double dx,dy,dz,dxstart,dystart,dzstart;
+  
+  double **x = atom->x;
+  int flag = 0;
+
+  for (int m = 0; m < nbondlist; m++) {
+    i = list[m][0];
+    j = list[m][1];
+    k = list[m][1];
+    l = list[m][1];
+    dxstart = dx = x[i][0] - x[j][0];
+    dystart = dy = x[i][1] - x[j][1];
+    dzstart = dz = x[i][2] - x[j][2];
+    domain->minimum_image(dx,dy,dz);
+    if (dx != dxstart || dy != dystart || dz != dzstart) flag = 1;
+    dxstart = dx = x[i][0] - x[k][0];
+    dystart = dy = x[i][1] - x[k][1];
+    dzstart = dz = x[i][2] - x[k][2];
+    domain->minimum_image(dx,dy,dz);
+    if (dx != dxstart || dy != dystart || dz != dzstart) flag = 1;
+    dxstart = dx = x[i][0] - x[l][0];
+    dystart = dy = x[i][1] - x[l][1];
+    dzstart = dz = x[i][2] - x[l][2];
+    domain->minimum_image(dx,dy,dz);
+    if (dx != dxstart || dy != dystart || dz != dzstart) flag = 1;
+  }
+
+  int flag_all;
+  MPI_Allreduce(&flag,&flag_all,1,MPI_INT,MPI_SUM,world);
+  if (flag_all) 
+    error->all(FLERR,"Dihedral/improper extent > half of periodic box length");
 }
 
 /* ---------------------------------------------------------------------- */
@@ -346,7 +452,7 @@ void Neighbor::improper_all()
       atom1 = domain->closest_image(i,atom1);
       atom2 = domain->closest_image(i,atom2);
       atom3 = domain->closest_image(i,atom3);
-      atom4 = domain->closest_image(i,atom4);
+      atom4 = domain-> closest_image(i,atom4);
       if (newton_bond ||
           (i <= atom1 && i <= atom2 && i <= atom3 && i <= atom4)) {
         if (nimproperlist == maximproper) {
@@ -361,6 +467,8 @@ void Neighbor::improper_all()
         nimproperlist++;
       }
     }
+
+  if (cluster_check) dihedral_check(improperlist);
 }
 
 /* ---------------------------------------------------------------------- */
@@ -415,4 +523,6 @@ void Neighbor::improper_partial()
         nimproperlist++;
       }
     }
+
+  if (cluster_check) dihedral_check(improperlist);
 }

src/neighbor.cpp

@@ -68,6 +68,7 @@ Neighbor::Neighbor(LAMMPS *lmp) : Pointers(lmp)
   oneatom = 2000;
   binsizeflag = 0;
   build_once = 0;
+  cluster_check = 0;
 
   cutneighsq = NULL;
   cutneighghostsq = NULL;
@@ -1672,6 +1673,13 @@ void Neighbor::modify_params(int narg, char **arg)
       if (binsize_user <= 0.0) binsizeflag = 0;
       else binsizeflag = 1;
       iarg += 2;
+    } else if (strcmp(arg[iarg],"cluster") == 0) {
+      if (iarg+2 > narg) error->all(FLERR,"Illegal neigh_modify command");
+      if (strcmp(arg[iarg+1],"yes") == 0) cluster_check = 1;
+      else if (strcmp(arg[iarg+1],"no") == 0) cluster_check = 0;
+      else error->all(FLERR,"Illegal neigh_modify command");
+      iarg += 2;
+
     } else if (strcmp(arg[iarg],"include") == 0) {
       if (iarg+2 > narg) error->all(FLERR,"Illegal neigh_modify command");
       includegroup = group->find(arg[iarg+1]);
@@ -1682,6 +1690,7 @@ void Neighbor::modify_params(int narg, char **arg)
         error->all(FLERR,
                    "Neigh_modify include group != atom_modify first group");
       iarg += 2;
+
     } else if (strcmp(arg[iarg],"exclude") == 0) {
       if (iarg+2 > narg) error->all(FLERR,"Illegal neigh_modify command");
 
@@ -1729,6 +1738,7 @@ void Neighbor::modify_params(int narg, char **arg)
       } else if (strcmp(arg[iarg+1],"none") == 0) {
         nex_type = nex_group = nex_mol = 0;
         iarg += 2;
+
       } else error->all(FLERR,"Illegal neigh_modify command");
 
     } else error->all(FLERR,"Illegal neigh_modify command");

src/neighbor.h

@@ -97,6 +97,7 @@ class Neighbor : protected Pointers {
   double *cuttypesq;               // cuttype squared
 
   double triggersq;                // trigger = build when atom moves this dist
+  int cluster_check;               // 1 if check bond/angle/etc satisfies minimg
 
   double **xhold;                      // atom coords at last neighbor build
   int maxhold;                         // size of xhold array
@@ -255,14 +256,17 @@ class Neighbor : protected Pointers {
   BondPtr bond_build;                 // ptr to bond list functions
   void bond_all();                    // bond list with all bonds
   void bond_partial();                // exclude certain bonds
+  void bond_check();
 
   BondPtr angle_build;                // ptr to angle list functions
   void angle_all();                   // angle list with all angles
   void angle_partial();               // exclude certain angles
+  void angle_check();
 
   BondPtr dihedral_build;             // ptr to dihedral list functions
   void dihedral_all();                // dihedral list with all dihedrals
   void dihedral_partial();            // exclude certain dihedrals
+  void dihedral_check(int **);
 
   BondPtr improper_build;             // ptr to improper list functions
   void improper_all();                // improper list with all impropers