added internal fix dummy command to enable more control of fix ordering

src/GRANULAR/pair_gran_hooke_history.cpp

@@ -24,6 +24,7 @@
 #include "update.h"
 #include "modify.h"
 #include "fix.h"
+#include "fix_dummy.h"
 #include "fix_neigh_history.h"
 #include "comm.h"
 #include "neighbor.h"
@@ -43,7 +44,6 @@ PairGranHookeHistory::PairGranHookeHistory(LAMMPS *lmp) : Pair(lmp)
   no_virial_fdotr_compute = 1;
   history = 1;
   size_history = 3;
-  fix_history = NULL;
 
   single_extra = 10;
   svector = new double[10];
@@ -60,6 +60,19 @@ PairGranHookeHistory::PairGranHookeHistory(LAMMPS *lmp) : Pair(lmp)
   // keep default behavior of history[i][j] = -history[j][i]
 
   nondefault_history_transfer = 0;
+
+  // create dummy fix as placeholder for FixNeighHistory
+  // this is so final order of Modify:fix will conform to input script
+
+  fix_history = NULL;
+
+  char **fixarg = new char*[3];
+  fixarg[0] = (char *) "NEIGH_HISTORY_DUMMY";
+  fixarg[1] = (char *) "all";
+  fixarg[2] = (char *) "DUMMY";
+  modify->add_fix(3,fixarg,1);
+  delete [] fixarg;
+  fix_dummy = (FixDummy *) modify->fix[modify->nfix-1];
 }
 
 /* ---------------------------------------------------------------------- */
@@ -69,7 +82,9 @@ PairGranHookeHistory::~PairGranHookeHistory()
   if (copymode) return;
 
   delete [] svector;
-  if (fix_history) modify->delete_fix("NEIGH_HISTORY");
+
+  if (!fix_history) modify->delete_fix("NEIGH_HISTORY_DUMMY");
+  else modify->delete_fix("NEIGH_HISTORY");
 
   if (allocated) {
     memory->destroy(setflag);
@@ -412,7 +427,9 @@ void PairGranHookeHistory::init_style()
 
   dt = update->dt;
 
-  // if first init, create Fix needed for storing shear history
+  // if history is stored and first init, create Fix to store history
+  // it replaces FixDummy, created in the constructor
+  // this is so its order in the fix list is preserved
 
   if (history && fix_history == NULL) {
     char dnumstr[16];
@@ -422,7 +439,7 @@ void PairGranHookeHistory::init_style()
     fixarg[1] = (char *) "all";
     fixarg[2] = (char *) "NEIGH_HISTORY";
     fixarg[3] = dnumstr;
-    modify->add_fix(4,fixarg,1);
+    modify->replace_fix("NEIGH_HISTORY_DUMMY",4,fixarg,1);
     delete [] fixarg;
     fix_history = (FixNeighHistory *) modify->fix[modify->nfix-1];
     fix_history->pair = this;

src/GRANULAR/pair_gran_hooke_history.h

@@ -56,6 +56,7 @@ class PairGranHookeHistory : public Pair {
 
   int size_history;
 
+  class FixDummy *fix_dummy;
   class FixNeighHistory *fix_history;
 
   // storage of rigid body masses for use in granular interactions

src/GRANULAR/pair_granular.cpp

@@ -1,4 +1,5 @@
 /* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    http://lammps.sandia.gov, Sandia National Laboratories
    Steve Plimpton, sjplimp@sandia.gov
 
@@ -25,6 +26,7 @@ See the README file in the top-level LAMMPS directory.
 #include "update.h"
 #include "modify.h"
 #include "fix.h"
+#include "fix_dummy.h"
 #include "fix_neigh_history.h"
 #include "comm.h"
 #include "neighbor.h"
@@ -62,7 +64,6 @@ PairGranular::PairGranular(LAMMPS *lmp) : Pair(lmp)
 {
   single_enable = 1;
   no_virial_fdotr_compute = 1;
-  fix_history = NULL;
 
   single_extra = 12;
   svector = new double[single_extra];
@@ -90,6 +91,19 @@ PairGranular::PairGranular(LAMMPS *lmp) : Pair(lmp)
   nondefault_history_transfer = 0;
   tangential_history_index = 0;
   roll_history_index = twist_history_index = 0;
+
+  // create dummy fix as placeholder for FixNeighHistory
+  // this is so final order of Modify:fix will conform to input script
+
+  fix_history = NULL;
+
+  char **fixarg = new char*[3];
+  fixarg[0] = (char *) "NEIGH_HISTORY_DUMMY";
+  fixarg[1] = (char *) "all";
+  fixarg[2] = (char *) "DUMMY";
+  modify->add_fix(3,fixarg,1);
+  delete [] fixarg;
+  fix_dummy = (FixDummy *) modify->fix[modify->nfix-1];
 }
 
 /* ---------------------------------------------------------------------- */
@@ -97,7 +111,9 @@ PairGranular::PairGranular(LAMMPS *lmp) : Pair(lmp)
 PairGranular::~PairGranular()
 {
   delete [] svector;
-  if (fix_history) modify->delete_fix("NEIGH_HISTORY");
+
+  if (!fix_history) modify->delete_fix("NEIGH_HISTORY_DUMMY");
+  else modify->delete_fix("NEIGH_HISTORY");
 
   if (allocated) {
     memory->destroy(setflag);
@@ -1021,8 +1037,9 @@ void PairGranular::init_style()
 
   dt = update->dt;
 
-  // if history is stored:
+  // if history is stored and first init, create Fix to store history
-  // if first init, create Fix needed for storing history
+  // it replaces FixDummy, created in the constructor
+  // this is so its order in the fix list is preserved
 
   if (use_history && fix_history == NULL) {
     char dnumstr[16];
@@ -1032,7 +1049,7 @@ void PairGranular::init_style()
     fixarg[1] = (char *) "all";
     fixarg[2] = (char *) "NEIGH_HISTORY";
     fixarg[3] = dnumstr;
-    modify->add_fix(4,fixarg,1);
+    modify->replace_fix("NEIGH_HISTORY_DUMMY",4,fixarg,1);
     delete [] fixarg;
     fix_history = (FixNeighHistory *) modify->fix[modify->nfix-1];
     fix_history->pair = this;

src/GRANULAR/pair_granular.h

@@ -51,6 +51,7 @@ class PairGranular : public Pair {
   double *maxrad_dynamic,*maxrad_frozen;
   double **cut;
 
+  class FixDummy *fix_dummy;
   class FixNeighHistory *fix_history;
 
   // storage of rigid body masses for use in granular interactions

src/USER-BOCS/fix_bocs.cpp

@@ -302,10 +302,10 @@ FixBocs::FixBocs(LAMMPS *lmp, int narg, char **arg) :
     // pre_exchange only required if flips can occur due to shape changes
 
     if (flipflag && (p_flag[3] || p_flag[4] || p_flag[5]))
-      pre_exchange_flag = 1;
+      pre_exchange_flag = pre_exchange_migrate = 1;
     if (flipflag && (domain->yz != 0.0 || domain->xz != 0.0 ||
                      domain->xy != 0.0))
-      pre_exchange_flag = 1;
+      pre_exchange_flag = pre_exchange_migrate = 1;
   }
 
   // convert input periods to frequencies

src/USER-MISC/fix_srp.cpp

@@ -22,6 +22,7 @@
 #include "atom.h"
 #include "force.h"
 #include "domain.h"
+#include "modify.h"
 #include "comm.h"
 #include "memory.h"
 #include "error.h"
@@ -112,19 +113,21 @@ void FixSRP::init()
   if ((bptype < 1) || (bptype > atom->ntypes))
     error->all(FLERR,"Illegal bond particle type");
 
-  // fix SRP should be the first fix running at the PRE_EXCHANGE step.
+  // this fix must come before any fix which migrates atoms in its pre_exchange()
-  // Otherwise it might conflict with, e.g. fix deform
+  // b/c this fix's pre_exchange() creates per-atom data structure
+  // that data must be current for atom migration to carry it along
 
-  if (modify->n_pre_exchange > 1) {
+  for (int i = 0; i < modify->nfix; i++) {
-    char *first = modify->fix[modify->list_pre_exchange[0]]->id;
+    if (modify->fix[i] == this) break;
-    if ((comm->me == 0) && (strcmp(id,first) != 0))
+    if (modify->fix[i]->pre_exchange_migrate)
-      error->warning(FLERR,"Internal fix for pair srp defined too late."
+      error->all(FLERR,"Fix SRP comes after a fix which "
-                     " May lead to incorrect behavior.");
+                 "migrates atoms in pre_exchange");
   }
 
   // setup neigh exclusions for diff atom types
   // bond particles do not interact with other types
   // type bptype only interacts with itself
+
   char* arg1[4];
   arg1[0] = (char *) "exclude";
   arg1[1] = (char *) "type";

src/USER-MISC/pair_srp.cpp

@@ -79,13 +79,18 @@ PairSRP::PairSRP(LAMMPS *lmp) : Pair(lmp)
   segment = NULL;
 
   // generate unique fix-id for this pair style instance
+
   fix_id = strdup("XX_FIX_SRP");
   fix_id[0] = '0' + srp_instance / 10;
   fix_id[1] = '0' + srp_instance % 10;
   ++srp_instance;
 
-  // create fix SRP instance here, as it has to
+  // create fix SRP instance here
-  // be executed before all other fixes
+  // similar to granular pair styles with history,
+  //   this should be early enough that FixSRP::pre_exchange()
+  //   will be invoked before other fixes that migrate atoms
+  //   this is checked for in FixSRP
+
   char **fixarg = new char*[3];
   fixarg[0] = fix_id;
   fixarg[1] = (char *) "all";
@@ -143,7 +148,6 @@ PairSRP::~PairSRP()
  ------------------------------------------------------------------------- */
 
 void PairSRP::compute(int eflag, int vflag)
-
 {
     // setup energy and virial
     ev_init(eflag, vflag);
@@ -458,6 +462,7 @@ void PairSRP::init_style()
     error->all(FLERR,"PairSRP: Pair srp requires newton pair on");
 
   // verify that fix SRP is still defined and has not been changed.
+
   int ifix = modify->find_fix(fix_id);
   if (f_srp != (FixSRP *)modify->fix[ifix])
     error->all(FLERR,"Fix SRP has been changed unexpectedly");
@@ -471,6 +476,7 @@ void PairSRP::init_style()
   // bonds of this type will be represented by bond particles
   // if bond type is 0, then all bonds have bond particles
   // btype = bond type
+
   char c0[20];
   char* arg0[2];
   sprintf(c0, "%d", btype);
@@ -506,7 +512,6 @@ void PairSRP::init_style()
 
 double PairSRP::init_one(int i, int j)
 {
-
  if (setflag[i][j] == 0) error->all(FLERR,"PairSRP: All pair coeffs are not set");
 
   cut[j][i] = cut[i][j];

src/fix.cpp

@@ -79,6 +79,7 @@ Fix::Fix(LAMMPS *lmp, int /*narg*/, char **arg) :
   respa_level = -1;
   maxexchange = 0;
   maxexchange_dynamic = 0;
+  pre_exchange_migrate = 0;
 
   scalar_flag = vector_flag = array_flag = 0;
   peratom_flag = local_flag = 0;

src/fix.h

@@ -58,6 +58,7 @@ class Fix : protected Pointers {
   int respa_level;               // which respa level to apply fix (1-Nrespa)
   int maxexchange;               // max # of per-atom values for Comm::exchange()
   int maxexchange_dynamic;       // 1 if fix sets maxexchange dynamically
+  int pre_exchange_migrate;      // 1 if fix migrates atoms in pre_exchange()
 
   int scalar_flag;               // 0/1 if compute_scalar() function exists
   int vector_flag;               // 0/1 if compute_vector() function exists

src/fix_balance.cpp

@@ -40,6 +40,7 @@ FixBalance::FixBalance(LAMMPS *lmp, int narg, char **arg) :
   if (narg < 6) error->all(FLERR,"Illegal fix balance command");
 
   box_change_domain = 1;
+  pre_exchange_migrate = 1;
   scalar_flag = 1;
   extscalar = 0;
   vector_flag = 1;

src/fix_deform.cpp

@@ -48,6 +48,7 @@ rfix(NULL), irregular(NULL), set(NULL)
 
   no_change_box = 1;
   restart_global = 1;
+  pre_exchange_migrate = 1;
 
   nevery = force->inumeric(FLERR,arg[3]);
   if (nevery <= 0) error->all(FLERR,"Illegal fix deform command");

src/fix_dummy.cpp

@@ -0,0 +1,65 @@
+/* ----------------------------------------------------------------------
+   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 "fix_dummy.h"
+#include <cstring>
+#include "error.h"
+
+using namespace LAMMPS_NS;
+using namespace FixConst;
+
+/* ---------------------------------------------------------------------- */
+
+FixDummy::FixDummy(LAMMPS *lmp, int narg, char **arg) :
+  Fix(lmp, narg, arg)
+{
+  // process optional args
+  // customize here and in setmask() by adding a new keyword from fix.h
+  // only necessary if both of these are true:
+  // (a) the real fix you are placeholding for defines the method
+  // (b) the real fix will be defined so late in run initialization
+  //     that the dummy fix will have already been processed by Modify::init()
+  //     to add its index to its lists of fixes to invoke during timestepping
+
+  initial_integrate_flag = final_integrate_flag = 0;
+  pre_exchange_flag = pre_neighbor_flag = 0;
+  pre_force_flag = post_force_flag = 0;
+  end_of_step_flag = 0;
+
+  int iarg = 3;
+  while (iarg < narg) {
+    if (strcmp(arg[iarg],"initial_integrate") == 0) initial_integrate_flag = 1;
+    else if (strcmp(arg[iarg],"final_integrate") == 0) final_integrate_flag = 1;
+    else if (strcmp(arg[iarg],"final_integrate") == 0) final_integrate_flag = 1;
+    else if (strcmp(arg[iarg],"final_integrate") == 0) final_integrate_flag = 1;
+    else if (strcmp(arg[iarg],"final_integrate") == 0) final_integrate_flag = 1;
+    else if (strcmp(arg[iarg],"final_integrate") == 0) final_integrate_flag = 1;
+    else error->all(FLERR,"Illegal fix DUMMY command");
+    iarg++;
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+int FixDummy::setmask()
+{
+  int mask = 0;
+  if (initial_integrate_flag) mask |= INITIAL_INTEGRATE;
+  if (final_integrate_flag) mask |= FINAL_INTEGRATE;
+  if (pre_exchange_flag) mask |= PRE_EXCHANGE;
+  if (pre_neighbor_flag) mask |= PRE_NEIGHBOR;
+  if (pre_force_flag) mask |= PRE_FORCE;
+  if (post_force_flag) mask |= POST_FORCE;
+  if (end_of_step_flag) mask |= END_OF_STEP;
+  return mask;
+}

src/fix_dummy.h

@@ -0,0 +1,53 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   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.
+------------------------------------------------------------------------- */
+
+#ifdef FIX_CLASS
+
+FixStyle(DUMMY,FixDummy)
+
+#else
+
+#ifndef LMP_FIX_DUMMY_H
+#define LMP_FIX_DUMMY_H
+
+#include "fix.h"
+
+namespace LAMMPS_NS {
+
+class FixDummy : public Fix {
+ public:
+  FixDummy(class LAMMPS *, int, char **);
+  virtual ~FixDummy() {}
+  int setmask();
+
+ protected:
+  int initial_integrate_flag,final_integrate_flag;
+  int pre_exchange_flag,pre_neighbor_flag;
+  int pre_force_flag,post_force_flag;
+  int end_of_step_flag;
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+E: Illegal ... command
+
+Self-explanatory.  Check the input script syntax and compare to the
+documentation for the command.  You can use -echo screen as a
+command-line option when running LAMMPS to see the offending line.
+
+*/

src/fix_neigh_history.cpp

@@ -19,6 +19,7 @@
 #include "comm.h"
 #include "neighbor.h"
 #include "neigh_list.h"
+#include "modify.h"
 #include "force.h"
 #include "pair.h"
 #include "memory.h"
@@ -147,6 +148,19 @@ void FixNeighHistory::init()
   if (atom->tag_enable == 0)
     error->all(FLERR,"Neighbor history requires atoms have IDs");
 
+  // this fix must come before any fix which migrates atoms in its pre_exchange()
+  // b/c this fix's pre_exchange() creates per-atom data structure
+  // that data must be current for atom migration to carry it along
+
+  for (int i = 0; i < modify->nfix; i++) {
+    if (modify->fix[i] == this) break;
+    if (modify->fix[i]->pre_exchange_migrate)
+      error->all(FLERR,"Fix neigh_history comes after a fix which "
+                 "migrates atoms in pre_exchange");
+  }
+
+  // setup data struct
+
   allocate_pages();
 }
 

src/fix_nh.cpp

@@ -492,10 +492,10 @@ FixNH::FixNH(LAMMPS *lmp, int narg, char **arg) :
     // pre_exchange only required if flips can occur due to shape changes
 
     if (flipflag && (p_flag[3] || p_flag[4] || p_flag[5]))
-      pre_exchange_flag = 1;
+      pre_exchange_flag = pre_exchange_migrate = 1;
     if (flipflag && (domain->yz != 0.0 || domain->xz != 0.0 ||
                      domain->xy != 0.0))
-      pre_exchange_flag = 1;
+      pre_exchange_flag = pre_exchange_migrate = 1;
   }
 
   // convert input periods to frequencies

src/modify.cpp

@@ -953,6 +953,46 @@ void Modify::add_fix(int narg, char **arg, int trysuffix)
   fix[ifix]->post_constructor();
 }
 
+/* ----------------------------------------------------------------------
+   replace replaceID fix with a new fix
+   this is used by callers to preserve ordering of fixes
+   e.g. create replaceID as a FixDummy instance early in the input script
+        replace it later with the desired Fix instance
+------------------------------------------------------------------------- */
+
+void Modify::replace_fix(const char *replaceID, 
+                         int narg, char **arg, int trysuffix)
+{
+  int ifix = find_fix(replaceID);
+  if (ifix < 0) error->all(FLERR,"Modify replace_fix ID could not be found");
+ 
+  // change ID, igroup, style of fix being replaced to match new fix
+  // requires some error checking on arguments for new fix
+
+  if (narg < 3) error->all(FLERR,"Illegal replace_fix invocation");
+  int jfix = find_fix(arg[0]);
+  if (jfix >= 0) error->all(FLERR,"Replace_fix ID is already in use");
+
+  delete [] fix[ifix]->id;
+  int n = strlen(arg[0]) + 1;
+  fix[ifix]->id = new char[n];
+  strcpy(fix[ifix]->id,arg[0]);
+
+  int jgroup = group->find(arg[1]);
+  if (jgroup == -1) error->all(FLERR,"Could not find replace_fix group ID");
+  fix[ifix]->igroup = jgroup;
+
+  delete [] fix[ifix]->style;
+  n = strlen(arg[2]) + 1;
+  fix[ifix]->style = new char[n];
+  strcpy(fix[ifix]->style,arg[2]);
+
+  // invoke add_fix
+  // it will find and overwrite the replaceID fix
+
+  add_fix(narg,arg,trysuffix);
+}
+
 /* ----------------------------------------------------------------------
    one instance per fix in style_fix.h
 ------------------------------------------------------------------------- */

src/modify.h

@@ -96,6 +96,7 @@ class Modify : protected Pointers {
   virtual int min_reset_ref();
 
   void add_fix(int, char **, int trysuffix=1);
+  void replace_fix(const char *, int, char **, int trysuffix=1);
   void modify_fix(int, char **);
   void delete_fix(const char *);
   void delete_fix(int);