From 0723bf3db7751eafa59dd6c3b02fa737fc892716 Mon Sep 17 00:00:00 2001
From: Steve Plimpton <sjplimp@sandia.gov>
Date: Mon, 2 Mar 2020 13:32:05 -0700
Subject: [PATCH] setup issues with fix numdiff

---
 examples/numdiff/in.numdiff |  4 +--
 src/fix_numdiff.cpp         | 55 +++++++++++++++++++++++++++++--------
 src/fix_numdiff.h           |  3 ++
 3 files changed, 49 insertions(+), 13 deletions(-)

diff --git a/examples/numdiff/in.numdiff b/examples/numdiff/in.numdiff
index c42f80b94b..202e29279e 100644
--- a/examples/numdiff/in.numdiff
+++ b/examples/numdiff/in.numdiff
@@ -21,8 +21,8 @@ variable errx atom fx-f_numdiff[1]
 variable erry atom fy-f_numdiff[2]
 variable errz atom fz-f_numdiff[3]
 
+write_dump all custom tmp.error f_numdiff[1] f_numdiff[2] f_numdiff[3]
+
 dump forces all custom 200 force_error.dump v_errx v_erry v_errz
 thermo 200
 run 2000
-
-
diff --git a/src/fix_numdiff.cpp b/src/fix_numdiff.cpp
index 75dbf738d5..06a8a65364 100644
--- a/src/fix_numdiff.cpp
+++ b/src/fix_numdiff.cpp
@@ -71,7 +71,13 @@ FixNumDiff::FixNumDiff(LAMMPS *lmp, int narg, char **arg) :
   numdiff_forces = NULL;
   temp_x = NULL;
   temp_f = NULL;
-  array_atom = NULL;
+
+  // perform initial allocation of atom-based arrays
+  // zero numdiff_forces since dump may access it on timestep 0
+  // zero numdiff_forces since a variable may access it before first run
+
+  reallocate();
+  force_clear(numdiff_forces);
 }
 
 /* ---------------------------------------------------------------------- */
@@ -127,6 +133,26 @@ void FixNumDiff::init()
 
 /* ---------------------------------------------------------------------- */
 
+void FixNumDiff::setup(int vflag)
+{
+  if (strstr(update->integrate_style,"verlet"))
+    post_force(vflag);
+  else {
+    ((Respa *) update->integrate)->copy_flevel_f(ilevel_respa);
+    post_force_respa(vflag,ilevel_respa,0);
+    ((Respa *) update->integrate)->copy_f_flevel(ilevel_respa);
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixNumDiff::min_setup(int vflag)
+{
+  post_force(vflag);
+}
+
+/* ---------------------------------------------------------------------- */
+
 void FixNumDiff::post_force(int vflag)
 {
   if (update->ntimestep % nevery) return;
@@ -159,16 +185,7 @@ void FixNumDiff::calculate_forces()
 
   // grow arrays if necessary
 
-  if (atom->nlocal + atom->nghost > maxatom) {
-    memory->destroy(numdiff_forces);
-    memory->destroy(temp_x);
-    memory->destroy(temp_f);
-    maxatom = atom->nmax;
-    memory->create(numdiff_forces,maxatom,3,"numdiff:numdiff_force");
-    memory->create(temp_x,maxatom,3,"numdiff:temp_x");
-    memory->create(temp_f,maxatom,3,"numdiff:temp_f");
-    array_atom = numdiff_forces;
-  }
+  if (atom->nlocal + atom->nghost > maxatom) reallocate();
 
   // store copy of current forces for owned and ghost atoms
 
@@ -304,6 +321,22 @@ void FixNumDiff::force_clear(double **forces)
   if (nbytes) memset(&forces[0][0],0,3*nbytes);
 }
 
+/* ----------------------------------------------------------------------
+   reallocated local per-atoms arrays
+------------------------------------------------------------------------- */
+
+void FixNumDiff::reallocate()
+{
+  memory->destroy(numdiff_forces);
+  memory->destroy(temp_x);
+  memory->destroy(temp_f);
+  maxatom = atom->nmax;
+  memory->create(numdiff_forces,maxatom,3,"numdiff:numdiff_force");
+  memory->create(temp_x,maxatom,3,"numdiff:temp_x");
+  memory->create(temp_f,maxatom,3,"numdiff:temp_f");
+  array_atom = numdiff_forces;
+}
+
 /* ----------------------------------------------------------------------
    memory usage of local atom-based arrays
 ------------------------------------------------------------------------- */
diff --git a/src/fix_numdiff.h b/src/fix_numdiff.h
index a1a3ba15a2..1d09de8e54 100644
--- a/src/fix_numdiff.h
+++ b/src/fix_numdiff.h
@@ -30,6 +30,8 @@ class FixNumDiff : public Fix {
   ~FixNumDiff();
   int setmask();
   void init();
+  void setup(int);
+  void min_setup(int);
   void post_force(int);
   void post_force_respa(int, int, int);
   void min_post_force(int);
@@ -55,6 +57,7 @@ private:
   void restore_atoms(int, int);
   double update_energy();
   void force_clear(double **);
+  void reallocate();
 };
 
 }