Added QSO python tools qso.py, qso2qbox.py, qso2qe.py

git-svn-id: http://qboxcode.org/svn/qb/trunk@1820 cba15fb0-1239-40c8-b417-11db7ca47a34

util/qso.py

+#!/usr/bin/python
+import xml.sax
+# quantum-simulation.org (QSO) definitions
+class Atom:
+  def __init__(self,name,species,pos,vel):
+    self.name = name
+    self.species = species
+    self.position = pos
+    self.velocity = vel
+
+class Species:
+  def __init__(self,name,href,symbol,atomic_number,mass):
+    self.name = name
+    self.href = href
+    self.symbol = symbol
+    self.atomic_number = atomic_number
+    self.mass = mass
+
+class UnitCell:
+  def __init__(self):
+    a = []
+    b = []
+    c = []
+
+class AtomSet:
+  def __init__(self):
+    self.atom_list = []
+    self.species_list = []
+    self.cell = UnitCell()
+
+  def add_atom(self,atom):
+    self.atom_list.append(atom)
+
+  def add_species(self,species):
+    # add species to the species list, only if name is not a duplicate
+    if not self.find_species(species.name):
+      self.species_list.append(species)
+
+  def find_species(self,species_name):
+    found = False
+    for sp in range(len(self.species_list)):
+      found |= (self.species_list[sp].name == species_name)
+    return found
+
+class Sample:
+  def __init__(self):
+    self.atoms = AtomSet()
+ 
+# The following handler processes the <atomset> element of
+# an XML document and updates the AtomSet data of the Sample
+# If multiple instances of <atomset> are found, the 
+# handler overwrites the AtomSet data
+class QSOAtomSetHandler(xml.sax.handler.ContentHandler):
+  def __init__(self,sample):
+    self.s = sample
+    self.inAtomSet = False
+    self.inAtom = False
+    self.inPosition = False
+    self.inVelocity = False
+    self.inSpecies = False
+    self.inSymbol = False
+    self.inAtomicNumber = False
+    self.inMass = False
+    self.buffer = ""
+    # flag to signal that the first <atomset> has been processed
+    self.done_first = False
+
+  def startElement(self, name, attributes):
+    if name == "atomset":
+      self.s.atoms.atom_list = []
+      self.inAtomSet = True
+    elif (name == "unit_cell") and self.inAtomSet:
+      self.s.atoms.cell.a = attributes["a"]
+      self.s.atoms.cell.b = attributes["b"]
+      self.s.atoms.cell.c = attributes["c"]
+    elif (name == "species"): 
+      self.inSpecies = True
+      self.species_name = "species_name"
+      if "name" in attributes:
+        self.species_name = attributes["name"]
+      self.species_href = self.species_name+"_href"
+      if "href" in attributes:
+        self.species_href = attributes["href"]
+      self.species_symbol = self.species_name+"_symbol"
+      self.species_atomic_number = self.species_name+"_atomic_number"
+      self.species_mass = self.species_name+"_mass" 
+    elif (name == "atom") and self.inAtomSet:
+      self.inAtom = True 
+      self.atom_name = attributes["name"]
+      self.atom_species = attributes["species"]
+      sp = Species(self.species_name,self.species_href,self.species_symbol,
+           self.species_atomic_number,self.species_mass)
+      self.s.atoms.add_species(sp)
+      self.atom_position = []
+      self.atom_velocity = []
+    elif (name == "position") and self.inAtom:
+      self.buffer = ""
+      self.inPosition = True
+    elif (name == "velocity") and self.inAtom:
+      self.buffer = ""
+      self.inVelocity = True
+    elif (name == "symbol") and self.inSpecies:
+      self.buffer = ""
+      self.inSymbol = True
+    elif (name == "atomic_number") and self.inSpecies:
+      self.buffer = ""
+      self.inAtomicNumber = True
+    elif (name == "mass") and self.inSpecies:
+      self.buffer = ""
+      self.inMass = True
+
+  def characters(self, data):
+    if self.inPosition or self.inVelocity or self.inSymbol or self.inAtomicNumber or self.inMass:
+      self.buffer += data
+
+  def endElement(self, name):
+    if (name == "atom") and self.inAtomSet:
+      a = Atom(self.atom_name,self.atom_species,self.atom_position,
+      self.atom_velocity)
+      self.s.atoms.add_atom(a)
+      self.inAtom = False
+    if (name == "position") and self.inAtom:
+      pos = self.buffer.split()
+      x = float(pos[0])
+      y = float(pos[1])
+      z = float(pos[2])
+      self.atom_position = [x,y,z] 
+      self.inPosition = False
+    if (name == "velocity") and self.inAtom:
+      vel = self.buffer.split()
+      vx = float(vel[0])
+      vy = float(vel[1])
+      vz = float(vel[2])
+      self.atom_velocity = [vx,vy,vz]
+      self.inVelocity = False
+    elif name == "atomset":
+      self.done_first = True
+      self.inAtomSet = False
+    elif name == "species":
+      sp = Species(self.species_name,self.species_href,self.species_symbol,
+           self.species_atomic_number,self.species_mass)
+      self.s.atoms.add_species(sp)
+      self.inSpecies = False
+    elif (name == "symbol") and self.inSpecies:
+      self.species_symbol = self.buffer
+      self.inSymbol = False
+    elif name == ("atomic_number") and self.inSpecies:
+      self.species_atomic_number = int(self.buffer)
+      self.inAtomicNumber = False
+    elif (name == "mass") and self.inSpecies:
+      self.species_mass = float(self.buffer)
+      self.inMass = False
+

util/qso2qbox.py

+#!/usr/bin/python
+# Convert <atomset> elements from quantum-simulation.org (QSO) format 
+# to Qbox input file
+# use: qso2qbox.py [-last] {file|URL}
+# Default: only the first <atomset> element is processed
+# If using -last, only the last <atomset> element is processed
+
+from qso import *
+import os.path
+import xml.sax
+import sys
+import urllib2
+import datetime 
+
+def usage():
+  print "use: ",sys.argv[0]," [-last] {file|URL}"
+  sys.exit()
+
+argc=len(sys.argv)
+if ( argc < 2 or argc > 3 ):
+  usage()
+
+# check if option "-last" is used
+# "-last" option: process all <atomset> and return only the last
+# default: extract first atomset only
+first_only = True
+input_source = sys.argv[1]
+if ( sys.argv[1] == "-last" ):
+  if ( argc != 3 ):
+    usage()
+  first_only = False
+  input_source = sys.argv[2]
+
+s = Sample()
+parser = xml.sax.make_parser()
+handler = QSOAtomSetHandler(s)
+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)
+  str = file.read(8192)
+  while ( str !="" and not (first_only and handler.done_first) ):
+    parser.feed(str)
+    str = file.read(8192)
+  file.close()
+else:
+  # attempt to open as a URL
+  try:
+    f = urllib2.urlopen(input_source)
+    str = f.read(8192)
+    while ( str !="" and not (first_only and handler.done_first) ):
+      parser.feed(str)
+      str = f.read(8192)
+    f.close()
+  except (ValueError,urllib2.HTTPError) as e:
+    print e
+    sys.exit()
+
+parser.reset()
+
+# write Qbox input file
+datestr=datetime.datetime.utcnow().isoformat()+'Z'
+print "# converted",datestr,"from",input_source
+print "set cell ",s.atoms.cell.a,s.atoms.cell.b,s.atoms.cell.c
+for sp in s.atoms.species_list:
+  print "species",sp.name,sp.href
+for a in s.atoms.atom_list:
+  print "atom",a.name,a.species,a.position[0],a.position[1],a.position[2],a.velocity[0],a.velocity[1],a.velocity[2]
+

util/qso2qe.py

+#!/usr/bin/python
+# Convert from quantum-simulation.org format to QuantumEspresso input format
+# use: env ECUT=ecut qso2qe.py [-last] {file|URL}
+
+from qso import *
+import sys
+import os.path
+import urllib2
+
+# Get Ecut from environment variable, default=25
+ecut = os.getenv("ECUT",25.0)
+
+def usage():
+  print "use: ",sys.argv[0]," [-last] {file|URL}"
+  sys.exit()
+
+argc=len(sys.argv)
+if ( argc < 2 or argc > 3 ):
+  usage()
+
+# check if option "-last" is used
+# "-last" option: process all <atomset> and return only the last
+# default: extract first atomset only
+first_only = True
+input_source = sys.argv[1]
+if ( sys.argv[1] == "-last" ):
+  if ( argc != 3 ):
+    usage()
+  first_only = False
+  input_source = sys.argv[2]
+
+s = Sample()
+parser = xml.sax.make_parser()
+handler = QSOAtomSetHandler(s)
+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)
+  str = file.read(8192)
+  while ( str !="" and not (first_only and handler.done_first) ):
+    parser.feed(str)
+    str = file.read(8192)
+  file.close()
+else:
+  # attempt to open as a URL
+  try:
+    f = urllib2.urlopen(input_source)
+    str = f.read(8192)
+    while ( str !="" and not (first_only and handler.done_first) ):
+      parser.feed(str)
+      str = f.read(8192)
+    f.close()
+  except (ValueError,urllib2.HTTPError) as e:
+    print e
+    sys.exit()
+
+parser.reset()
+
+# write QE input file
+
+print "&control"
+print "  calculation = 'scf'"
+print "  pseudo_dir = './'"
+print "/"
+print "&system"
+print "  ibrav=0"
+print "  nat=",len(s.atoms.atom_list),", ntyp=",len(s.atoms.species_list),","
+print "  ecutwfc=",ecut
+print "/"
+print "&electrons"
+print "/"
+print "ATOMIC_SPECIES"
+for sp in s.atoms.species_list:
+  print sp.name,sp.mass,sp.href
+print "ATOMIC_POSITIONS {bohr}"
+for a in s.atoms.atom_list:
+  print a.species,a.position[0],a.position[1],a.position[2]
+print "CELL_PARAMETERS bohr"
+print s.atoms.cell.a
+print s.atoms.cell.b
+print s.atoms.cell.c
+print "K_POINTS {gamma}"