From 6ec332feea4b59eca58c7dae05955acf53449d8e Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Fri, 22 Oct 2010 21:27:16 +0000
Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5105
 f3b2605a-c512-4ea7-a41b-209d697bcdaa

---
 src/pair_soft.cpp | 41 +++++++++--------------------------------
 src/pair_soft.h   |  3 +--
 src/respa.cpp     |  3 ++-
 src/verlet.cpp    |  7 +++++++
 src/verlet.h      |  1 +
 5 files changed, 20 insertions(+), 35 deletions(-)

diff --git a/src/pair_soft.cpp b/src/pair_soft.cpp
index 8add30e678..e9e6bd0d8e 100644
--- a/src/pair_soft.cpp
+++ b/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;
+}
diff --git a/src/pair_soft.h b/src/pair_soft.h
index eceb98ec6f..fbfd3ca43d 100644
--- a/src/pair_soft.h
+++ b/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;
diff --git a/src/respa.cpp b/src/respa.cpp
index 708b0ec754..209c7dd163 100644
--- a/src/respa.cpp
+++ b/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");
 }
 
diff --git a/src/verlet.cpp b/src/verlet.cpp
index 844234171f..c7a6180d64 100644
--- a/src/verlet.cpp
+++ b/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
diff --git a/src/verlet.h b/src/verlet.h
index 02a5c1704e..211b5653f6 100644
--- a/src/verlet.h
+++ b/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