git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5105 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/pair_soft.cpp

@@ -289,38 +289,6 @@ void PairSoft::read_restart_settings(FILE *fp)
   MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
 }
 
-/* ----------------------------------------------------------------------
-   check if name is recognized, return integer index for that name
-   if name not recognized, return -1
-   if type pair setting, return -2 if no type pairs are set
-------------------------------------------------------------------------- */
-
-int PairSoft::pre_adapt(char *name, int ilo, int ihi, int jlo, int jhi)
-{
-  int count = 0;
-  for (int i = ilo; i <= ihi; i++)
-    for (int j = MAX(jlo,i); j <= jhi; j++)
-      count++;
-  if (count == 0) return -2;
-
-  if (strcmp(name,"a") == 0) return 0;
-  return -1;
-}
-
-/* ----------------------------------------------------------------------
-   adapt parameter indexed by which
-   change all pair variables affected by the reset parameter
-   if type pair setting, set I-J and J-I coeffs
-------------------------------------------------------------------------- */
-
-void PairSoft::adapt(int which, int ilo, int ihi, int jlo, int jhi,
-		     double value)
-{
-  for (int i = ilo; i <= ihi; i++)
-    for (int j = MAX(jlo,i); j <= jhi; j++)
-      prefactor[i][j] = prefactor[j][i] = value;
-}
-
 /* ---------------------------------------------------------------------- */
 
 double PairSoft::single(int i, int j, int itype, int jtype, double rsq,
@@ -337,3 +305,12 @@ double PairSoft::single(int i, int j, int itype, int jtype, double rsq,
   philj = prefactor[itype][jtype] * (1.0+cos(arg));
   return factor_lj*philj;
 }
+
+/* ---------------------------------------------------------------------- */
+
+void *PairSoft::extract(char *str, int &dim)
+{
+  dim = 2;
+  if (strcmp(str,"a") == 0) return (void *) prefactor;
+  return NULL;
+}

src/pair_soft.h

@@ -38,9 +38,8 @@ class PairSoft : public Pair {
   void read_restart(FILE *);
   void write_restart_settings(FILE *);
   void read_restart_settings(FILE *);
-  int pre_adapt(char *, int, int, int, int);
-  void adapt(int, int, int, int, int, double);
   double single(int, int, int, int, double, double, double, double &);
+  void *extract(char *, int &);
 
  private:
   double PI;

src/respa.cpp

@@ -466,11 +466,12 @@ void Respa::run(int n)
 }
 
 /* ----------------------------------------------------------------------
-   delete fix at end of run, so its atom arrays won't persist
+   delete rRESPA fix at end of run, so its atom arrays won't persist
 ------------------------------------------------------------------------- */
 
 void Respa::cleanup()
 {
+  modify->post_run();
   modify->delete_fix("RESPA");
 }
 

src/verlet.cpp

@@ -286,6 +286,13 @@ void Verlet::run(int n)
   }
 }
 
+/* ---------------------------------------------------------------------- */
+
+void Verlet::cleanup()
+{
+  modify->post_run();
+}
+
 /* ----------------------------------------------------------------------
    clear force on own & ghost atoms
    setup and clear other arrays as needed

src/verlet.h

@@ -32,6 +32,7 @@ class Verlet : public Integrate {
   void setup();
   void setup_minimal(int);
   void run(int);
+  void cleanup();
 
  private:
   int triclinic;                    // 0 if domain is orthog, 1 if triclinic