git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8306 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/GRANULAR/fix_wall_gran.cpp

@@ -49,13 +49,8 @@ FixWallGran::FixWallGran(LAMMPS *lmp, int narg, char **arg) :
   if (!atom->sphere_flag)
     error->all(FLERR,"Fix wall/gran requires atom style sphere");
 
-  // set time_depend so that history will be preserved correctly
-  // across multiple runs via laststep setting in granular pair styles
-  // same as fix shear/history
-
   restart_peratom = 1;
   create_attribute = 1;
-  time_depend = 1;
 
   // wall/particle coefficients
 
@@ -184,7 +179,6 @@ FixWallGran::FixWallGran(LAMMPS *lmp, int narg, char **arg) :
     shear[i][0] = shear[i][1] = shear[i][2] = 0.0;
 
   time_origin = update->ntimestep;
-  laststep = -1;
 }
 
 /* ---------------------------------------------------------------------- */
@@ -289,8 +283,8 @@ void FixWallGran::post_force(int vflag)
   int *mask = atom->mask;
   int nlocal = atom->nlocal;
 
-  if (update->ntimestep > laststep) shearupdate = 1;
+  int shearupdate = 1;
-  else shearupdate = 0;
+  if (update->setupflag) shearupdate = 0;
 
   for (int i = 0; i < nlocal; i++) {
     if (mask[i] & groupbit) {
@@ -348,8 +342,6 @@ void FixWallGran::post_force(int vflag)
       }
     }
   }
-
-  laststep = update->ntimestep;
 }
 
 /* ---------------------------------------------------------------------- */

src/GRANULAR/fix_wall_gran.h

@@ -55,7 +55,6 @@ class FixWallGran : public Fix {
   int nlevels_respa;
   int time_origin;
 
-  bigint laststep;
   int *touch;
   double **shear;
   int shearupdate;

src/GRANULAR/pair_gran_hertz_history.cpp

@@ -53,8 +53,9 @@ void PairGranHertzHistory::compute(int eflag, int vflag)
   if (eflag || vflag) ev_setup(eflag,vflag);
   else evflag = vflag_fdotr = 0;
 
-  int shearupdate = 0;
+  computeflag = 1;
-  if (update->ntimestep > laststep) shearupdate = 1;
+  int shearupdate = 1;
+  if (update->setupflag) shearupdate = 0;
 
   double **x = atom->x;
   double **v = atom->v;
@@ -243,8 +244,6 @@ void PairGranHertzHistory::compute(int eflag, int vflag)
       }
     }
   }
-
-  laststep = update->ntimestep;
 }
 
 /* ----------------------------------------------------------------------

src/GRANULAR/pair_gran_hooke_history.cpp

@@ -51,7 +51,7 @@ PairGranHookeHistory::PairGranHookeHistory(LAMMPS *lmp) : Pair(lmp)
   single_extra = 4;
   svector = new double[4];
 
-  laststep = -1;
+  computeflag = 0;
   neighprev = 0;
 }
 
@@ -94,8 +94,9 @@ void PairGranHookeHistory::compute(int eflag, int vflag)
   if (eflag || vflag) ev_setup(eflag,vflag);
   else evflag = vflag_fdotr = 0;
 
-  int shearupdate = 0;
+  computeflag = 1;
-  if (update->ntimestep > laststep) shearupdate = 1;
+  int shearupdate = 1;
+  if (update->setupflag) shearupdate = 0;
 
   double **x = atom->x;
   double **v = atom->v;
@@ -283,8 +284,6 @@ void PairGranHookeHistory::compute(int eflag, int vflag)
       }
     }
   }
-
-  laststep = update->ntimestep;
 }
 
 /* ----------------------------------------------------------------------
@@ -393,7 +392,8 @@ void PairGranHookeHistory::init_style()
   // if first init, create Fix needed for storing shear history
 
   if (history && force->newton_pair == 1)
-    error->all(FLERR,"Pair granular with shear history requires newton pair off");
+    error->all(FLERR,
+               "Pair granular with shear history requires newton pair off");
 
   if (history && fix_history == NULL) {
     char **fixarg = new char*[3];

src/GRANULAR/pair_gran_hooke_history.h

@@ -26,6 +26,8 @@ namespace LAMMPS_NS {
 
 class PairGranHookeHistory : public Pair {
  public:
+  int computeflag;
+
   PairGranHookeHistory(class LAMMPS *);
   virtual ~PairGranHookeHistory();
   virtual void compute(int, int);
@@ -48,15 +50,12 @@ class PairGranHookeHistory : public Pair {
   int freeze_group_bit;
   int history;
 
-  bigint laststep;
-  class FixShearHistory *fix_history;
-
   char *suffix;
-
+  int neighprev;
   double *onerad_dynamic,*onerad_frozen;
   double *maxrad_dynamic,*maxrad_frozen;
 
-  int neighprev;
+  class FixShearHistory *fix_history;
 
   void allocate();
 };

src/fix.h

@@ -117,6 +117,7 @@ class Fix : protected Pointers {
   virtual void post_force_respa(int, int, int) {}
   virtual void final_integrate_respa(int, int) {}
 
+  virtual void min_setup_pre_exchange() {}
   virtual void min_setup_pre_force(int) {}
   virtual void min_pre_exchange() {}
   virtual void min_pre_force(int) {}

src/fix_shear_history.cpp

@@ -18,7 +18,7 @@
 #include "neighbor.h"
 #include "neigh_list.h"
 #include "force.h"
-#include "pair.h"
+#include "pair_gran_hooke_history.h"
 #include "update.h"
 #include "modify.h"
 #include "memory.h"
@@ -34,12 +34,8 @@ using namespace FixConst;
 FixShearHistory::FixShearHistory(LAMMPS *lmp, int narg, char **arg) :
   Fix(lmp, narg, arg)
 {
-  // set time_depend so that history will be preserved correctly
-  // across multiple runs via laststep setting in granular pair styles
-
   restart_peratom = 1;
   create_attribute = 1;
-  time_depend = 1;
 
   // perform initial allocation of atom-based arrays
   // register with atom class
@@ -79,6 +75,7 @@ int FixShearHistory::setmask()
 {
   int mask = 0;
   mask |= PRE_EXCHANGE;
+  mask |= MIN_PRE_EXCHANGE;
   return mask;
 }
 
@@ -91,16 +88,30 @@ void FixShearHistory::init()
                "Pair style granular with history requires atoms have IDs");
 }
 
-/* ---------------------------------------------------------------------- */
+/* ----------------------------------------------------------------------
+   called by setup of run or minimize
+   called by write_restart as input script command
+   only invoke pre_exchange() if neigh list stores more current history info
+     than npartner/partner arrays in this fix
+   that will only be case if pair->compute() has been invoked since
+     upate of npartner/npartner
+   this logic avoids 2 problems:
+     run 100; write_restart; run 100
+       setup_pre_exchange is called twice (by write_restart and 2nd run setup)
+       w/out a neighbor list being created in between
+     read_restart; run 100
+       setup_pre_exchange called by run setup whacks restart shear history info
+------------------------------------------------------------------------- */
 
 void FixShearHistory::setup_pre_exchange()
 {
-  pre_exchange();
+  if (pair->computeflag) pre_exchange();
+  pair->computeflag = 0;
 }
 
 /* ----------------------------------------------------------------------
    copy shear partner info from neighbor lists to atom arrays
-   so can be exchanged with atoms
+   so can be migrated or stored with atoms
 ------------------------------------------------------------------------- */
 
 void FixShearHistory::pre_exchange()
@@ -111,23 +122,14 @@ void FixShearHistory::pre_exchange()
   double *shear,*allshear,**firstshear;
 
   // zero npartner for all current atoms
-  // do not do this if inum = 0, since will wipe out npartner counts
-  // inum is 0 when pre_exchange() is called from integrate->setup()
-  //   before first run when no neighbor lists yet exist
-  //   partner info may have just been read from restart file
-  //     and won't be used until granular neighbor lists are built
-  //   if nothing read from restart file, constructor sets npartner = 0
 
-  NeighList *list = pair->list;
   int nlocal = atom->nlocal;
-
+  for (i = 0; i < nlocal; i++) npartner[i] = 0;
-  if (list->inum)
-    for (i = 0; i < nlocal; i++)
-      npartner[i] = 0;
 
   // copy shear info from neighbor list atoms to atom arrays
 
   int *tag = atom->tag;
+  NeighList *list = pair->list;
   inum = list->inum;
   ilist = list->ilist;
   numneigh = list->numneigh;
@@ -180,6 +182,21 @@ void FixShearHistory::pre_exchange()
     error->all(FLERR,"Too many touching neighbors - boost MAXTOUCH");
 }
 
+/* ---------------------------------------------------------------------- */
+
+void FixShearHistory::min_setup_pre_exchange()
+{
+  if (pair->computeflag) pre_exchange();
+  pair->computeflag = 0;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixShearHistory::min_pre_exchange()
+{
+  pre_exchange();
+}
+
 /* ----------------------------------------------------------------------
    memory usage of local atom-based arrays
 ------------------------------------------------------------------------- */

src/fix_shear_history.h

@@ -36,6 +36,8 @@ class FixShearHistory : public Fix {
   void init();
   void setup_pre_exchange();
   virtual void pre_exchange();
+  void min_setup_pre_exchange();
+  void min_pre_exchange();
 
   double memory_usage();
   void grow_arrays(int);
@@ -53,7 +55,7 @@ class FixShearHistory : public Fix {
   int **partner;                // tags for the partners
   double ***shearpartner;       // 3 shear values with the partner
 
-  class Pair *pair;
+  class PairGranHookeHistory *pair;
 };
 
 }

src/min.cpp

@@ -189,6 +189,8 @@ void Min::setup()
 {
   if (comm->me == 0 && screen) fprintf(screen,"Setting up minimization ...\n");
 
+  update->setupflag = 1;
+
   // setup extra global dof due to fixes
   // cannot be done in init() b/c update init() is before modify init()
 
@@ -222,6 +224,7 @@ void Min::setup()
   // build neighbor lists
 
   atom->setup();
+  modify->setup_pre_exchange();
   if (triclinic) domain->x2lamda(atom->nlocal);
   domain->pbc();
   domain->reset_box();
@@ -279,6 +282,7 @@ void Min::setup()
 
   modify->setup(vflag);
   output->setup();
+  update->setupflag = 0;
 
   // stats for Finish to print
 
@@ -299,11 +303,14 @@ void Min::setup()
 
 void Min::setup_minimal(int flag)
 {
+  update->setupflag = 1;
+
   // setup domain, communication and neighboring
   // acquire ghosts
   // build neighbor lists
 
   if (flag) {
+    modify->setup_pre_exchange();
     if (triclinic) domain->x2lamda(atom->nlocal);
     domain->pbc();
     domain->reset_box();
@@ -351,6 +358,7 @@ void Min::setup_minimal(int flag)
       requestor[m]->min_xf_get(m);
 
   modify->setup(vflag);
+  update->setupflag = 0;
 
   // stats for Finish to print
 

src/modify.cpp

@@ -235,8 +235,12 @@ void Modify::setup(int vflag)
 
 void Modify::setup_pre_exchange()
 {
+  if (update->whichflag == 1)
     for (int i = 0; i < n_pre_exchange; i++)
       fix[list_pre_exchange[i]]->setup_pre_exchange();
+  else if (update->whichflag == 2)
+    for (int i = 0; i < n_min_pre_exchange; i++)
+      fix[list_min_pre_exchange[i]]->min_setup_pre_exchange();
 }
 
 /* ----------------------------------------------------------------------

src/modify.h

@@ -64,7 +64,6 @@ class Modify : protected Pointers {
   void post_force_respa(int, int, int);
   void final_integrate_respa(int, int);
 
-  void setup_min_pre_force(int);
   void min_pre_exchange();
   void min_pre_force(int);
   void min_post_force(int);

src/respa.cpp

@@ -418,6 +418,7 @@ void Respa::setup_minimal(int flag)
   // build neighbor lists
 
   if (flag) {
+    modify->setup_pre_exchange();
     if (triclinic) domain->x2lamda(atom->nlocal);
     domain->pbc();
     domain->reset_box();

src/verlet.cpp

@@ -158,6 +158,7 @@ void Verlet::setup_minimal(int flag)
   // build neighbor lists
 
   if (flag) {
+    modify->setup_pre_exchange();
     if (triclinic) domain->x2lamda(atom->nlocal);
     domain->pbc();
     domain->reset_box();

src/write_restart.cpp

@@ -95,12 +95,11 @@ void WriteRestart::command(int narg, char **arg)
   lmp->init();
 
   // move atoms to new processors before writing file
-  // do pre_exchange so FixShearHistory will store 
+  // do setup_pre_exchange to force update of per-atom info if needed
-  //   current neigh info with atoms
   // enforce PBC in case atoms are outside box
   // call borders() to rebuild atom map since exchange() destroys map
 
-  if (modify->n_pre_exchange) modify->pre_exchange();
+  modify->setup_pre_exchange();
   if (domain->triclinic) domain->x2lamda(atom->nlocal);
   domain->pbc();
   domain->reset_box();