Merge pull request #3558 from jtclemm/BPM

Small patch to BPM package

doc/src/bond_bpm_rotational.rst

@@ -69,7 +69,7 @@ which is proportional to the tangential shear displacement with a
 stiffness of :math:`k_s`. This tangential force also induces a torque.
 In addition, bending and twisting torques are also applied to
 particles which are proportional to angular bending and twisting
-displacements with stiffnesses of :math`k_b` and :math:`k_t',
+displacements with stiffnesses of :math:`k_b` and :math:`k_t`,
 respectively.  Details on the calculations of shear displacements and
 angular displacements can be found in :ref:`(Wang) <Wang2009>` and
 :ref:`(Wang and Mora) <Wang2009b>`.

src/fix_bond_history.cpp

@@ -264,6 +264,9 @@ void FixBondHistory::write_restart(FILE *fp)
   double list[1];
   list[n++] = stored_flag;
 
+  // Update stored values if needed
+  pre_exchange();
+
   if (comm->me == 0) {
     int size = n * sizeof(double);
     fwrite(&size, sizeof(int), 1, fp);

src/fix_update_special_bonds.cpp

@@ -15,6 +15,7 @@
 
 #include "atom.h"
 #include "atom_vec.h"
+#include "comm.h"
 #include "error.h"
 #include "force.h"
 #include "modify.h"
@@ -34,6 +35,8 @@ FixUpdateSpecialBonds::FixUpdateSpecialBonds(LAMMPS *lmp, int narg, char **arg)
     Fix(lmp, narg, arg)
 {
   if (narg != 3) error->all(FLERR, "Illegal fix update/special/bonds command");
+
+  restart_global = 1;
 }
 
 /* ---------------------------------------------------------------------- */
@@ -69,12 +72,6 @@ void FixUpdateSpecialBonds::setup(int /*vflag*/)
       force->special_coul[3] != 1.0)
     error->all(FLERR, "Fix update/special/bonds requires special Coulomb weights = 1,1,1");
   // Implies neighbor->special_flag = [X, 2, 1, 1]
-
-  new_broken_pairs.clear();
-  broken_pairs.clear();
-
-  new_created_pairs.clear();
-  created_pairs.clear();
 }
 
 /* ----------------------------------------------------------------------
@@ -246,3 +243,18 @@ void FixUpdateSpecialBonds::add_created_bond(int i, int j)
   new_created_pairs.push_back(tag_pair);
   created_pairs.push_back(tag_pair);
 }
+
+/* ----------------------------------------------------------------------
+   Use write_restart to invoke pre_exchange
+------------------------------------------------------------------------- */
+
+void FixUpdateSpecialBonds::write_restart(FILE *fp)
+{
+  // Call pre-exchange to process any broken/created bonds
+
+  pre_exchange();
+  if (comm->me == 0) {
+    int size = 0;
+    fwrite(&size,sizeof(int),1,fp);
+  }
+}

src/fix_update_special_bonds.h

@@ -35,6 +35,7 @@ class FixUpdateSpecialBonds : public Fix {
   void pre_force(int) override;
   void add_broken_bond(int, int);
   void add_created_bond(int, int);
+  void write_restart(FILE *) override;
 
  protected:
   // Create two arrays to store bonds broken this timestep (new)