From 65e93cbaab76aec1165096ee302bdd973f1230ef Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Mon, 26 Oct 2020 17:06:27 -0400
Subject: [PATCH] decrement/increment molindex and atomindex to have 1-based
 indices in files and 0-based internally

---
 src/MOLECULE/atom_vec_template.cpp | 25 +++++++++++++++++++++++--
 src/MOLECULE/atom_vec_template.h   |  2 ++
 2 files changed, 25 insertions(+), 2 deletions(-)

diff --git a/src/MOLECULE/atom_vec_template.cpp b/src/MOLECULE/atom_vec_template.cpp
index 3b05a9a139..d21bd39cf9 100644
--- a/src/MOLECULE/atom_vec_template.cpp
+++ b/src/MOLECULE/atom_vec_template.cpp
@@ -112,6 +112,27 @@ void AtomVecTemplate::create_atom_post(int ilocal)
   molatom[ilocal] = -1;
 }
 
+/* ----------------------------------------------------------------------
+   modify values for AtomVec::pack_data() to pack
+------------------------------------------------------------------------- */
+
+void AtomVecTemplate::pack_data_pre(int ilocal)
+{
+  molindex[ilocal]++;
+  molatom[ilocal]++;
+}
+
+/* ----------------------------------------------------------------------
+   unmodify values packed by AtomVec::pack_data()
+------------------------------------------------------------------------- */
+
+void AtomVecTemplate::pack_data_post(int ilocal)
+{
+  molindex[ilocal]--;
+  molatom[ilocal]--;
+}
+
+
 /* ----------------------------------------------------------------------
    modify what AtomVec::data_atom() just unpacked
    or initialize other atom quantities
@@ -119,8 +140,8 @@ void AtomVecTemplate::create_atom_post(int ilocal)
 
 void AtomVecTemplate::data_atom_post(int ilocal)
 {
-  int molindex_one = molindex[ilocal];
-  int molatom_one = molatom[ilocal];
+  int molindex_one = --molindex[ilocal];
+  int molatom_one = --molatom[ilocal];
 
   if (molindex_one < 0 || molindex_one >= nset)
     error->one(FLERR,"Invalid template index in Atoms section of data file");
diff --git a/src/MOLECULE/atom_vec_template.h b/src/MOLECULE/atom_vec_template.h
index 3bf2ec6273..99acf5d855 100644
--- a/src/MOLECULE/atom_vec_template.h
+++ b/src/MOLECULE/atom_vec_template.h
@@ -31,6 +31,8 @@ class AtomVecTemplate : public AtomVec {
   void grow_pointers();
   void process_args(int, char **);
   void create_atom_post(int);
+  void pack_data_pre(int);
+  void pack_data_post(int);
   void data_atom_post(int);
 
  private: