From f3b32ed0c55d5a576a2adc111e200e1bc53012c9 Mon Sep 17 00:00:00 2001
From: Francois Gygi <fgygi@ucdavis.edu>
Date: Wed, 11 Jul 2018 13:47:09 -0700
Subject: [PATCH] Add qbox_move_to.py script

---
 util/qbox_move_to.py | 115 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 115 insertions(+)
 create mode 100755 util/qbox_move_to.py

diff --git a/util/qbox_move_to.py b/util/qbox_move_to.py
new file mode 100755
index 0000000..b862136
--- /dev/null
+++ b/util/qbox_move_to.py
@@ -0,0 +1,115 @@
+#!/usr/bin/python
+# Copyright 2018 The Regents of the University of California
+# This file is part of Qbox
+#
+# qbox_move_to.py: create a qbox input file moving atoms to the positions
+# of a given iteration of a simulation, or of a restart file.
+#
+# use: qbox_move_to.py [iter] {file|URL}
+import os.path
+import xml.sax
+import sys
+import urllib2
+
+def usage():
+  print "use: ",sys.argv[0]," [-iter i] {file|URL}"
+  sys.exit()
+
+argc=len(sys.argv)
+if ( argc != 2 and argc != 4 ):
+  usage()
+
+# check if option -iter is used
+# "iter" option: extract atomset of iteration iter
+# default: iter = 1
+iter = 1
+iter_option = False
+input_source = sys.argv[1]
+if ( sys.argv[1] == "-iter" ):
+  if ( argc != 4 ):
+    usage()
+  iter_option = True
+  iter = int(sys.argv[2])
+  input_source = sys.argv[3]
+
+# Qbox output handler to extract and process data
+class QboxOutputHandler(xml.sax.handler.ContentHandler):
+  def __init__(self):
+    self.step = 0
+    self.inAtomset = 0
+    self.inAtom = 0
+    self.inPosition = 0
+    self.done = False
+
+  def startElement(self, name, attributes):
+    if name == "atomset":
+      self.tau=[]
+      self.atomname=[]
+      self.inAtomset = 1
+    elif (name == "unit_cell") & self.inAtomset:
+      self.cell_a = attributes["a"]
+      self.cell_b = attributes["b"]
+      self.cell_c = attributes["c"]
+    elif (name == "atom") & self.inAtomset:
+      self.atomname.append(attributes["name"])
+      self.inAtom = 1
+    elif (name == "position") & self.inAtom:
+        self.buffer = ""
+        self.inPosition = 1
+
+  def characters(self, data):
+    if self.inPosition:
+      self.buffer += data
+
+  def endElement(self, name):
+    if (name == "atom") and self.inAtomset:
+      self.inAtom = 0
+    if (name == "position") & self.inAtom:
+      pos = self.buffer.split()
+      self.tau.append([pos[0],pos[1],pos[2]])
+      self.inPosition = 0
+    elif name == "atomset":
+      self.step += 1
+      if ( self.step == iter ):
+        if ( iter_option ):
+          print "#",input_source,"iteration",iter
+        else:
+          print "#",input_source
+        avec = self.cell_a.split()
+        bvec = self.cell_b.split()
+        cvec = self.cell_c.split()
+        print "set cell ",avec[0],avec[1],avec[2],\
+          bvec[0],bvec[1],bvec[2],\
+          cvec[0],cvec[1],cvec[2]
+        for i in range(len(self.tau)):
+          print "move ",self.atomname[i]," to ",\
+            self.tau[i][0],self.tau[i][1],self.tau[i][2]
+      self.inAtomset = 0
+      self.done = ( self.step >= iter )
+
+parser = xml.sax.make_parser()
+handler = QboxOutputHandler()
+parser.setContentHandler(handler)
+# test if input_source is a local file
+# if not, process as a URL
+if ( os.path.isfile(input_source) ):
+  file = open(input_source)
+  s = file.read(8192)
+  while ( s !="" and not handler.done ):
+    parser.feed(s)
+    s = file.read(8192)
+  file.close()
+else:
+  # attempt to open as a URL
+  try:
+    f = urllib2.urlopen(input_source)
+    s = f.read(8192)
+    while ( s !="" and not handler.done ):
+      parser.feed(s)
+      s = f.read(8192)
+    f.close()
+  except (ValueError,urllib2.HTTPError) as e:
+    print e
+    sys.exit()
+
+parser.reset()
--
libgit2 0.26.0