From bb48c5ccdc0bed7fd6f89c8af72ead5c073caea2 Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Mon, 18 Jun 2012 23:49:36 +0000
Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8312
 f3b2605a-c512-4ea7-a41b-209d697bcdaa

---
 src/domain.cpp | 28 +++++++++++++---------------
 src/domain.h   |  2 +-
 src/min.cpp    |  4 ++++
 src/respa.cpp  |  3 +++
 src/verlet.cpp |  3 +++
 5 files changed, 24 insertions(+), 16 deletions(-)

diff --git a/src/domain.cpp b/src/domain.cpp
index 472da91734..c5a4b72d2b 100644
--- a/src/domain.cpp
+++ b/src/domain.cpp
@@ -98,12 +98,6 @@ Domain::~Domain()
 
 void Domain::init()
 {
-  // check for too small a periodic box for molecular system
-
-  if (atom->molecular && box_too_small())
-    error->all(FLERR,"Bond/angle/dihedral extent must be < "
-               "half of periodic box dimension");
-
   // set box_change if box dimensions/shape ever changes
   // due to shrink-wrapping, fixes that change volume (npt, vol/rescale, etc)
 
@@ -525,16 +519,16 @@ void Domain::pbc()
 /* ----------------------------------------------------------------------
    check that no pair of atoms in a bonded interaction
    are further apart than half a periodic box length
-   return 1 if any pair is, else 0
 ------------------------------------------------------------------------- */
 
-int Domain::box_too_small()
+void Domain::box_too_small_check()
 {
   int i,j,k;
 
-  // only need to check if some dimension is periodic
+  // only need to check if system is molecluar and some dimension is periodic
 
-  if (!xperiodic && !yperiodic && (dimension == 2 || !zperiodic)) return 0;
+  if (!atom->molecular) return;
+  if (!xperiodic && !yperiodic && (dimension == 2 || !zperiodic)) return;
 
   // maxbondall = longest current bond length
   // NOTE: if box is tiny (less than 2 * bond-length),
@@ -552,7 +546,7 @@ int Domain::box_too_small()
   for (i = 0; i < nlocal; i++)
     for (j = 0; j < num_bond[i]; j++) {
       k = atom->map(bond_atom[i][j]);
-      if (k < 0) error->one(FLERR,"Bond atom missing in box size check");
+      if (k == -1) error->one(FLERR,"Bond atom missing in box size check");
       delx = x[i][0] - x[k][0];
       dely = x[i][1] - x[k][1];
       delz = x[i][2] - x[k][2];
@@ -576,10 +570,14 @@ int Domain::box_too_small()
   // else when use minimg() in bond/angle/dihdral compute,
   // could calculate incorrect distance between 2 atoms
 
-  if (xperiodic && maxdelta > xprd_half) return 1;
-  if (yperiodic && maxdelta > yprd_half) return 1;
-  if (dimension == 3 && zperiodic && maxdelta > zprd_half) return 1;
-  return 0;
+  int flag = 0;
+  if (xperiodic && maxdelta > xprd_half) flag = 1;
+  if (yperiodic && maxdelta > yprd_half) flag = 1;
+  if (dimension == 3 && zperiodic && maxdelta > zprd_half) flag = 1;
+
+  if (flag)
+    error->all(FLERR,
+               "Bond/angle/dihedral extent > half of periodic box length");
 }
 
 /* ----------------------------------------------------------------------
diff --git a/src/domain.h b/src/domain.h
index 58303527c0..517fc565b6 100644
--- a/src/domain.h
+++ b/src/domain.h
@@ -93,7 +93,7 @@ class Domain : protected Pointers {
   virtual void set_local_box();
   virtual void reset_box();
   virtual void pbc();
-  int box_too_small();
+  void box_too_small_check();
   int minimum_image_check(double, double, double);
   void minimum_image(double &, double &, double &);
   void minimum_image(double *);
diff --git a/src/min.cpp b/src/min.cpp
index 629a895449..cc51460b99 100644
--- a/src/min.cpp
+++ b/src/min.cpp
@@ -234,6 +234,7 @@ void Min::setup()
   if (atom->sortfreq > 0) atom->sort();
   comm->borders();
   if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
+  domain->box_too_small_check();
   neighbor->build();
   neighbor->ncalls = 0;
 
@@ -319,6 +320,7 @@ void Min::setup_minimal(int flag)
     comm->exchange();
     comm->borders();
     if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
+    domain->box_too_small_check();
     neighbor->build();
     neighbor->ncalls = 0;
   }
@@ -432,6 +434,8 @@ void Min::cleanup()
   // delete fix at end of run, so its atom arrays won't persist
 
   modify->delete_fix("MINIMIZE");
+
+  domain->box_too_small_check();
 }
 
 /* ----------------------------------------------------------------------
diff --git a/src/respa.cpp b/src/respa.cpp
index fec5b10e89..a91037b8d1 100644
--- a/src/respa.cpp
+++ b/src/respa.cpp
@@ -363,6 +363,7 @@ void Respa::setup()
   if (atom->sortfreq > 0) atom->sort();
   comm->borders();
   if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
+  domain->box_too_small_check();
   neighbor->build();
   neighbor->ncalls = 0;
 
@@ -427,6 +428,7 @@ void Respa::setup_minimal(int flag)
     comm->exchange();
     comm->borders();
     if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
+    domain->box_too_small_check();
     neighbor->build();
     neighbor->ncalls = 0;
   }
@@ -501,6 +503,7 @@ void Respa::cleanup()
 {
   modify->post_run();
   modify->delete_fix("RESPA");
+  domain->box_too_small_check();
 }
 
 /* ---------------------------------------------------------------------- */
diff --git a/src/verlet.cpp b/src/verlet.cpp
index 20bc2d6112..ad8263d9a8 100644
--- a/src/verlet.cpp
+++ b/src/verlet.cpp
@@ -111,6 +111,7 @@ void Verlet::setup()
   if (atom->sortfreq > 0) atom->sort();
   comm->borders();
   if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
+  domain->box_too_small_check();
   neighbor->build();
   neighbor->ncalls = 0;
 
@@ -167,6 +168,7 @@ void Verlet::setup_minimal(int flag)
     comm->exchange();
     comm->borders();
     if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
+    domain->box_too_small_check();
     neighbor->build();
     neighbor->ncalls = 0;
   }
@@ -309,6 +311,7 @@ void Verlet::run(int n)
 void Verlet::cleanup()
 {
   modify->post_run();
+  domain->box_too_small_check();
 }
 
 /* ----------------------------------------------------------------------