git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8621 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/MAKE/Makefile.redsky

@@ -2,25 +2,17 @@
 
 SHELL = /bin/sh
 
-# this Makefile builds LAMMPS for RedSky with OpenMPI
+# This Makefile builds LAMMPS for RedSky with OpenMPI.
-# to invoke this Makefile, you need these modules loaded:
+# To use this Makefile, you need appropriate modules loaded.
-#   mpi/openmpi-1.4.1_oobpr_intel-11.1-f064-c064
+# You can determine which modules are loaded by typing:
-#   misc/env-openmpi-1.4-oobpr
-#   compilers/intel-11.1-f064-c064
-#   libraries/intel-mkl-11.1.064
-#   libraries/fftw-2.1.5_openmpi-1.4.1_oobpr_intel-11.1-f064-c064
-# you can determine which modules are loaded by typing:
 #   module list
-# these modules are not the default ones, but can be enabled by 
+# These modules can be enabled by lines like this in your .cshrc or 
-#   lines like this in your .cshrc or other start-up shell file
+# other start-up shell file or by typing them before you build LAMMPS:
-#   or by typing them before you build LAMMPS:
+#   module load mpi/openmpi-1.4.2_oobpr_intel-11.1-f064-c064
-#     module load mpi/openmpi-1.4.3_oobpr_intel-11.1-f064-c064
+#   module load libraries/intel-mkl-11.1.064
-#     module load misc/env-openmpi-1.4-oobpr
+#   module load libraries/fftw-2.1.5_openmpi-1.4.2_oobpr_intel-11.1-f064-c064
-#     module load compilers/intel-11.1-f064-c064
+# These same modules need to be loaded to submit a LAMMPS job,
-#     module load libraries/intel-mkl-11.1.064
+#   either interactively or via a batch script.
-#     module load libraries/fftw-2.1.5_openmpi-1.4.3_oobpr_intel-11.1-f064-c064
-# these same modules need to be loaded to submit a LAMMPS job,
-#   either interactively or via a batch script
 
 # IMPORTANT NOTE:
 # to run efficiently on RedSky, use the "numa_wrapper" mpiexec option,

src/finish.cpp

@@ -618,8 +618,10 @@ void Finish::end(int flag)
         if (atom->molecular && atom->natoms > 0)
           fprintf(screen,"Ave special neighs/atom = %g\n",
                   nspec_all/atom->natoms);
-        fprintf(screen,"Neighbor list builds = %d\n",neighbor->ncalls);
+        fprintf(screen,"Neighbor list builds = " BIGINT_FORMAT "\n",
-        fprintf(screen,"Dangerous builds = %d\n",neighbor->ndanger);
+                neighbor->ncalls);
+        fprintf(screen,"Dangerous builds = " BIGINT_FORMAT "\n",
+                neighbor->ndanger);
       }
       if (logfile) {
         if (nall < 2.0e9)
@@ -631,8 +633,10 @@ void Finish::end(int flag)
         if (atom->molecular && atom->natoms > 0)
           fprintf(logfile,"Ave special neighs/atom = %g\n",
                   nspec_all/atom->natoms);
-        fprintf(logfile,"Neighbor list builds = %d\n",neighbor->ncalls);
+        fprintf(logfile,"Neighbor list builds = " BIGINT_FORMAT "\n",
-        fprintf(logfile,"Dangerous builds = %d\n",neighbor->ndanger);
+                neighbor->ncalls);
+        fprintf(logfile,"Dangerous builds = " BIGINT_FORMAT "\n",
+                neighbor->ndanger);
       }
     }
   }

src/library.cpp

@@ -161,7 +161,7 @@ void *lammps_extract_atom(void *ptr, char *name)
      for the entity which the caller can cast to the proper data type
    returns a NULL if id is not recognized or style/type not supported
    IMPORTANT: if the compute is not current it will be invoked
-     LAMMPS cannot easily check if it is valid to invoke the compute,
+     LAMMPS cannot easily check here if it is valid to invoke the compute,
      so caller must insure that it is OK
 ------------------------------------------------------------------------- */
 
@@ -244,7 +244,7 @@ void *lammps_extract_compute(void *ptr, char *id, int style, int type)
        double *dptr = (double *) lammps_extract_fix();
        double value = *dptr;
        free(dptr);
-   IMPORTANT: LAMMPS cannot easily check when info extracted from
+   IMPORTANT: LAMMPS cannot easily check here when info extracted from
      the fix is valid, so caller must insure that it is OK
 ------------------------------------------------------------------------- */
 
@@ -313,7 +313,7 @@ void *lammps_extract_fix(void *ptr, char *id, int style, int type,
        double *vector = (double *) lammps_extract_variable();
        use the vector values
        free(vector);
-   IMPORTANT: LAMMPS cannot easily check when it is valid to evaluate
+   IMPORTANT: LAMMPS cannot easily check here when it is valid to evaluate
      the variable or any fixes or computes or thermodynamic info it references,
      so caller must insure that it is OK
 ------------------------------------------------------------------------- */

src/neighbor.cpp

@@ -1259,14 +1259,16 @@ int Neighbor::check_distance()
 /* ----------------------------------------------------------------------
    build all perpetual neighbor lists every few timesteps
    pairwise & topology lists are created as needed
+   topology lists only built if topoflag = 1
 ------------------------------------------------------------------------- */
 
-void Neighbor::build()
+void Neighbor::build(int topoflag)
 {
   int i;
 
   ago = 0;
   ncalls++;
+  lastcall = update->ntimestep;
 
   // store current atom positions and box size if needed
 
@@ -1336,12 +1338,20 @@ void Neighbor::build()
   for (i = 0; i < nblist; i++)
     (this->*pair_build[blist[i]])(lists[blist[i]]);
 
-  if (atom->molecular) {
+  if (atom->molecular && topoflag) build_topology();
-    if (force->bond) (this->*bond_build)();
+}
-    if (force->angle) (this->*angle_build)();
+
-    if (force->dihedral) (this->*dihedral_build)();
+/* ----------------------------------------------------------------------
-    if (force->improper) (this->*improper_build)();
+   build all topology neighbor lists every few timesteps
-  }
+   normally built with pair lists, but USER-CUDA separates them
+------------------------------------------------------------------------- */
+
+void Neighbor::build_topology()
+{
+  if (force->bond) (this->*bond_build)();
+  if (force->angle) (this->*angle_build)();
+  if (force->dihedral) (this->*dihedral_build)();
+  if (force->improper) (this->*improper_build)();
 }
 
 /* ----------------------------------------------------------------------

src/neighbor.h

@@ -38,8 +38,9 @@ class Neighbor : protected Pointers {
   double cutneighmax;              // max neighbor cutoff for all type pairs
   double *cuttype;                 // for each type, max neigh cut w/ others
 
-  int ncalls;                      // # of times build has been called
+  bigint ncalls;                   // # of times build has been called
-  int ndanger;                     // # of dangerous builds
+  bigint ndanger;                  // # of dangerous builds
+  bigint lastcall;                 // timestep of last neighbor::build() call
 
   int nrequest;                    // requests for pairwise neighbor lists
   class NeighRequest **requests;   // from Pair, Fix, Compute, Command classes
@@ -70,7 +71,8 @@ class Neighbor : protected Pointers {
   int decide();                     // decide whether to build or not
   virtual int check_distance();     // check max distance moved since last build
   void setup_bins();                // setup bins based on box and cutoff
-  virtual void build();             // create all neighbor lists (pair,bond)
+  virtual void build(int topoflag=1);  // create all neighbor lists (pair,bond)
+  virtual void build_topology();    // create all topology neighbor lists
   void build_one(int);              // create a single neighbor list
   void set(int, char **);           // set neighbor style and skin distance
   void modify_params(int, char**);  // modify parameters that control builds