python xyz script with 6 digit precision for positions

git-svn-id: http://qboxcode.org/svn/qb/trunk@1629 cba15fb0-1239-40c8-b417-11db7ca47a34

util/qbox_xyz.py

+#!/usr/bin/python
+# qbox_xyz_cell.py: extract atomic positions with cell info
+# from Qbox output
+# use: qbox_xyz_cell.py file.r
+
+import xml.sax
+import sys
+import math
+
+if len(sys.argv) != 2:
+  print "use: ",sys.argv[0]," file.r"
+  sys.exit()
+
+infile = sys.argv[1]
+a0=0.529177
+
+# 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
+
+  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()
+      x = a0*float(pos[0])
+      y = a0*float(pos[1])
+      z = a0*float(pos[2])
+      self.tau.append([x,y,z])
+      self.inPosition = 0
+    elif name == "atomset":
+      self.step += 1
+      print len(self.tau)
+      avec = self.cell_a.split()
+      bvec = self.cell_b.split()
+      cvec = self.cell_c.split()
+      print self.step,\
+      '%.6f'%(a0*float(avec[0])),\
+      '%.6f'%(a0*float(avec[1])),\
+      '%.6f'%(a0*float(avec[2])),\
+      '%.6f'%(a0*float(bvec[0])),\
+      '%.6f'%(a0*float(bvec[1])),\
+      '%.6f'%(a0*float(bvec[2])),\
+      '%.6f'%(a0*float(cvec[0])),\
+      '%.6f'%(a0*float(cvec[1])),\
+      '%.6f'%(a0*float(cvec[2]))
+      for i in range(len(self.tau)):
+        print self.atomname[i],'%.6f'%self.tau[i][0],\
+                               '%.6f'%self.tau[i][1],\
+                               '%.6f'%self.tau[i][2]
+      self.inAtomset = 0
+
+parser = xml.sax.make_parser()
+handler = QboxOutputHandler()
+parser.setContentHandler(handler)
+parser.parse(infile)