From 9bf573d9733cb0862e40a194473cc97030849f30 Mon Sep 17 00:00:00 2001
From: "Fattebert J.-L" <fattebertj@ornl.gov>
Date: Mon, 3 Jun 2024 22:32:36 -0400
Subject: [PATCH 1/2] Add possible periodic dimensions to xyz2in.py

---
 util/xyz2in.py | 40 ++++++++++++++++++++++++++++++++++------
 1 file changed, 34 insertions(+), 6 deletions(-)

diff --git a/util/xyz2in.py b/util/xyz2in.py
index 3555e138..8877ea27 100644
--- a/util/xyz2in.py
+++ b/util/xyz2in.py
@@ -15,6 +15,16 @@
 
 #read file
 ifile=open(sys.argv[1],'r')
+
+lx = 0.
+ly = 0.
+lz = 0.
+if( len(sys.argv) > 2 ):
+  lx = eval(sys.argv[2])
+  ly = eval(sys.argv[3])
+  lz = eval(sys.argv[4])
+
+
 lines=ifile.readlines()
 
 count=0
@@ -22,13 +32,31 @@
 dummy=0   #unused flag set to 0
 
 for line in lines: ## loop over lines of file
-  words=line.split()
-  if len(words)>1:
-    if words[0][0:1]!='#':
-      name=words[0]+str(count)
+  if count>1:
+    words=line.split()
+    if len(words)>1:
+      name=words[0]+str(count-2)
       x=eval(words[1])*ang2bohr
       y=eval(words[2])*ang2bohr
       z=eval(words[3])*ang2bohr
-      
+
+      if lx > 0.:
+        if x<0:
+          x = x +lx
+        if x>lx:
+          x = x -lx
+
+      if ly > 0.:
+        if y<0:
+          y = y +ly
+        if y>ly:
+          y = y -ly
+
+      if lz > 0.:
+        if z<0:
+          z = z +lz
+        if z>lz:
+          z = z -lz
+
       print(name,'\t',dummy,'\t',x,'\t',y,'\t',z,'\t',movable)
-      count=count+1
+  count=count+1

From 07f6c4d7b382c42ed7796a51c1c62eafcd3662a9 Mon Sep 17 00:00:00 2001
From: Jean-Luc Fattebert <fattebertj@ornl.gov>
Date: Tue, 4 Jun 2024 09:44:09 -0400
Subject: [PATCH 2/2] Update xyz2in.py

---
 util/xyz2in.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/util/xyz2in.py b/util/xyz2in.py
index 8877ea27..bb2e022d 100644
--- a/util/xyz2in.py
+++ b/util/xyz2in.py
@@ -5,9 +5,11 @@
 # This file is part of MGmol. For details, see https://github.com/llnl/mgmol.
 # Please also read this link https://github.com/llnl/mgmol/LICENSE
 #
-# Python program to convert .xyz file into mgmol input
+# Python program to convert .xyz file into mgmol input coordinates file
+# Optional arguments: [lx ly lz] to define box size and map all atoms into
+#                     box (0,0,0)-(lx,ly,lz) using periodic boundary conditions
 #
-# use: python coords.xyz > coords.in
+# use: python coords.xyz [lx ly lz] > coords.in
 #-------------------------------------------------------------------------------
 import sys, string