git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11699 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/USER-OMP/fix_shear_history_omp.cpp

@@ -32,8 +32,8 @@ using namespace LAMMPS_NS;
 using namespace FixConst;
 
 /* ----------------------------------------------------------------------
-   copy shear partner info from neighbor lists to atom arrays
-   so can be exchanged with atoms
+   copy shear partner info from neighbor lists to per-atom arrays
+   so it can be exchanged with those atoms
 ------------------------------------------------------------------------- */
 
 void FixShearHistoryOMP::pre_exchange()
@@ -56,22 +56,11 @@ void FixShearHistoryOMP::pre_exchange()
     const int tid = 0;
 #endif
 
-    // each thread works on a fixed chunk of local and ghost atoms.
-    const int ldelta = 1 + nlocal/nthreads;
-    const int lfrom = tid*ldelta;
-    const int lmax = lfrom +ldelta;
-    const int lto = (lmax > nlocal) ? nlocal : lmax;
-
     int i,j,ii,jj,m,n,inum,jnum;
     int *ilist,*jlist,*numneigh,**firstneigh;
     int *touch,**firsttouch;
     double *shear,*allshear,**firstshear;
 
-    // zero npartners for all current atoms and
-    // clear page data structures for this thread
-
-    for (i = lfrom; i < lto; i++) npartner[i] = 0;
-
     MyPage <tagint> &ipg = ipage[tid];
     MyPage <double[3]> &dpg = dpage[tid];
     ipg.reset();
@@ -90,6 +79,21 @@ void FixShearHistoryOMP::pre_exchange()
     firsttouch = list->listgranhistory->firstneigh;
     firstshear = list->listgranhistory->firstdouble;
 
+    int nlocal_neigh = 0;
+    if (inum) nlocal_neigh = ilist[inum-1] + 1;
+
+    // each thread works on a fixed chunk of local and ghost atoms.
+    const int ldelta = 1 + nlocal_neigh/nthreads;
+    const int lfrom = tid*ldelta;
+    const int lmax = lfrom +ldelta;
+    const int lto = (lmax > nlocal_neigh) ? nlocal_neigh : lmax;
+
+    // zero npartners for all current atoms and
+    // clear page data structures for this thread
+
+    for (i = lfrom; i < lto; i++) npartner[i] = 0;
+
+
     for (ii = 0; ii < inum; ii++) {
       i = ilist[ii];
       jlist = firstneigh[i];
@@ -111,13 +115,15 @@ void FixShearHistoryOMP::pre_exchange()
 
     // get page chunks to store atom IDs and shear history for my atoms
 
-    for (ii = lfrom; ii < lto; ii++) {
+    for (ii = 0; ii < inum; ii++) {
       i = ilist[ii];
-      n = npartner[i];
-      partner[i] = ipg.get(n);
-      shearpartner[i] = dpg.get(n);
-      if (partner[i] == NULL || shearpartner[i] == NULL)
-        error->one(FLERR,"Shear history overflow, boost neigh_modify one");
+      if ((i >= lfrom) && (i < lto)) {
+        n = npartner[i];
+        partner[i] = ipg.get(n);
+        shearpartner[i] = dpg.get(n);
+        if (partner[i] == NULL || shearpartner[i] == NULL)
+          error->one(FLERR,"Shear history overflow, boost neigh_modify one");
+      }
     }
 
     // 2nd loop over neighbor list
@@ -161,7 +167,7 @@ void FixShearHistoryOMP::pre_exchange()
     }
 
     // set maxtouch = max # of partners of any owned atom
-    m = 0;
+    maxtouch = m = 0;
     for (i = lfrom; i < lto; i++)
       m = MAX(m,npartner[i]);
 

src/fix_recenter.cpp

@@ -42,6 +42,16 @@ FixRecenter::FixRecenter(LAMMPS *lmp, int narg, char **arg) :
   xcom = ycom = zcom = 0.0;
   xflag = yflag = zflag = 1;
   xinitflag = yinitflag = zinitflag = 0;
+  shift[0] = shift[1] = shift[2] = 0.0;
+  distance = 0.0;
+  scalar_flag = 1;
+  vector_flag = 1;
+  size_vector = 3;
+  extscalar = 1;
+  extvector = 1;
+  global_freq = 1;
+
+/* ---------------------------------------------------------------------- */
 
   if (strcmp(arg[3],"NULL") == 0) xflag = 0;
   else if (strcmp(arg[3],"INIT") == 0) xinitflag = 1;
@@ -177,10 +187,30 @@ void FixRecenter::initial_integrate(int vflag)
   int *mask = atom->mask;
   int nlocal = atom->nlocal;
 
+  shift[0] = xflag ? (xtarget - xcm[0]) : 0.0;
+  shift[1] = yflag ? (ytarget - xcm[1]) : 0.0;
+  shift[2] = zflag ? (ztarget - xcm[2]) : 0.0;
+  distance = sqrt(shift[0]*shift[0] + shift[1]*shift[1] + shift[2]*shift[2]);
+
   for (int i = 0; i < nlocal; i++)
     if (mask[i] & group2bit) {
-      if (xflag) x[i][0] += xtarget - xcm[0];
-      if (yflag) x[i][1] += ytarget - xcm[1];
-      if (zflag) x[i][2] += ztarget - xcm[2];
+      x[i][0] += shift[0];
+      x[i][1] += shift[1];
+      x[i][2] += shift[2];
     }
 }
+
+/* ---------------------------------------------------------------------- */
+
+double FixRecenter::compute_scalar()
+{
+  return distance;
+}
+
+/* ---------------------------------------------------------------------- */
+
+double FixRecenter::compute_vector(int n)
+{
+  return shift[n];
+}
+

src/fix_recenter.h

@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    http://lammps.sandia.gov, Sandia National Laboratories
    Steve Plimpton, sjplimp@sandia.gov
@@ -30,12 +30,14 @@ class FixRecenter : public Fix {
   int setmask();
   void init();
   void initial_integrate(int);
+  double compute_scalar();
+  double compute_vector(int);
 
  private:
   int group2bit,scaleflag;
   int xflag,yflag,zflag;
   int xinitflag,yinitflag,zinitflag;
-  double xcom,ycom,zcom,xinit,yinit,zinit,masstotal;
+  double xcom,ycom,zcom,xinit,yinit,zinit,masstotal,distance,shift[3];
 };
 
 }

src/irregular.cpp

@@ -145,7 +145,9 @@ void Irregular::migrate_atoms()
 
   // create irregular communication plan, perform comm, destroy plan
   // returned nrecv = size of buffer needed for incoming atoms
+  // debug: turn on sorting for repoducible irregular() via extra final arg
 
+  //int nrecv = create_atom(nsendatom,sizes,proclist,1);
   int nrecv = create_atom(nsendatom,sizes,proclist);
   if (nrecv > maxrecv) grow_recv(nrecv);
   exchange_atom(buf_send,sizes,buf_recv);