From 3b7123bec2a2e06c4d5afa2f3670af90d8b586b6 Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Fri, 2 May 2014 22:15:13 +0000
Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11908
 f3b2605a-c512-4ea7-a41b-209d697bcdaa

---
 src/CLASS2/dihedral_class2.cpp |  4 +---
 src/neighbor.cpp               | 16 ++++++++--------
 src/write_data.cpp             | 34 +++++++++++++++++++---------------
 3 files changed, 28 insertions(+), 26 deletions(-)

diff --git a/src/CLASS2/dihedral_class2.cpp b/src/CLASS2/dihedral_class2.cpp
index e4f58e0560..579e195c2a 100644
--- a/src/CLASS2/dihedral_class2.cpp
+++ b/src/CLASS2/dihedral_class2.cpp
@@ -230,9 +230,7 @@ void DihedralClass2::compute(int eflag, int vflag)
     sinphi = sqrt(1.0 - c*c);
     sinphi = MAX(sinphi,SMALL);
 
-    // addition by Andrew Jewett, Jan 2013
-    // adjust the sign of phi if necessary for negative input angles
-    // n123 = vb2 x vb1
+    // n123 = vb1 x vb2
 
     double n123x = vb1y*vb2z - vb1z*vb2y;
     double n123y = vb1z*vb2x - vb1x*vb2z;
diff --git a/src/neighbor.cpp b/src/neighbor.cpp
index 70807f475e..30ff8b3b0a 100644
--- a/src/neighbor.cpp
+++ b/src/neighbor.cpp
@@ -859,20 +859,20 @@ void Neighbor::init()
 
   // set ptrs to topology build functions
 
-  if (bond_off) bond_build = &Neighbor::bond_partial;
-  else if (atom->molecular == 2) bond_build = &Neighbor::bond_template;
+  if (atom->molecular == 2) bond_build = &Neighbor::bond_template;
+  else if (bond_off) bond_build = &Neighbor::bond_partial;
   else bond_build = &Neighbor::bond_all;
 
-  if (angle_off) angle_build = &Neighbor::angle_partial;
-  else if (atom->molecular == 2) angle_build = &Neighbor::angle_template;
+  if (atom->molecular == 2) angle_build = &Neighbor::angle_template;
+  else if (angle_off) angle_build = &Neighbor::angle_partial;
   else angle_build = &Neighbor::angle_all;
 
-  if (dihedral_off) dihedral_build = &Neighbor::dihedral_partial;
-  else if (atom->molecular == 2) dihedral_build = &Neighbor::dihedral_template;
+  if (atom->molecular == 2) dihedral_build = &Neighbor::dihedral_template;
+  else if (dihedral_off) dihedral_build = &Neighbor::dihedral_partial;
   else dihedral_build = &Neighbor::dihedral_all;
 
-  if (improper_off) improper_build = &Neighbor::improper_partial;
-  else if (atom->molecular == 2) improper_build = &Neighbor::improper_template;
+  if (atom->molecular == 2) improper_build = &Neighbor::improper_template;
+  else if (improper_off) improper_build = &Neighbor::improper_partial;
   else improper_build = &Neighbor::improper_all;
 
   // set topology neighbor list counts to 0
diff --git a/src/write_data.cpp b/src/write_data.cpp
index e9809692c9..6fd239461f 100644
--- a/src/write_data.cpp
+++ b/src/write_data.cpp
@@ -218,21 +218,25 @@ void WriteData::header()
   fprintf(fp,BIGINT_FORMAT " atoms\n",atom->natoms);
   fprintf(fp,"%d atom types\n",atom->ntypes);
 
-  if (atom->nbonds || atom->nbondtypes) {
-    fprintf(fp,BIGINT_FORMAT " bonds\n",nbonds);
-    fprintf(fp,"%d bond types\n",atom->nbondtypes);
-  }
-  if (atom->nangles || atom->nangletypes) {
-    fprintf(fp,BIGINT_FORMAT " angles\n",nangles);
-    fprintf(fp,"%d angle types\n",atom->nangletypes);
-  }
-  if (atom->ndihedrals || atom->ndihedraltypes) {
-    fprintf(fp,BIGINT_FORMAT " dihedrals\n",atom->ndihedrals);
-    fprintf(fp,"%d dihedral types\n",atom->ndihedraltypes);
-  }
-  if (atom->nimpropers || atom->nimpropertypes) {
-    fprintf(fp,BIGINT_FORMAT " impropers\n",atom->nimpropers);
-    fprintf(fp,"%d improper types\n",atom->nimpropertypes);
+  // do not write molecular topology info for atom_style template
+
+  if (atom->molecular == 1) {
+    if (atom->nbonds || atom->nbondtypes) {
+      fprintf(fp,BIGINT_FORMAT " bonds\n",nbonds);
+      fprintf(fp,"%d bond types\n",atom->nbondtypes);
+    }
+    if (atom->nangles || atom->nangletypes) {
+      fprintf(fp,BIGINT_FORMAT " angles\n",nangles);
+      fprintf(fp,"%d angle types\n",atom->nangletypes);
+    }
+    if (atom->ndihedrals || atom->ndihedraltypes) {
+      fprintf(fp,BIGINT_FORMAT " dihedrals\n",atom->ndihedrals);
+      fprintf(fp,"%d dihedral types\n",atom->ndihedraltypes);
+    }
+    if (atom->nimpropers || atom->nimpropertypes) {
+      fprintf(fp,BIGINT_FORMAT " impropers\n",atom->nimpropers);
+      fprintf(fp,"%d improper types\n",atom->nimpropertypes);
+    }
   }
 
   for (int i = 0; i < modify->nfix; i++)