def _get_trajectories(self):
""" Internal method to make a Trajectory object """
atoms = self.get_atoms()
self.trajectory = Trajectory(num_steps=self.nsw,
timestep=self.potim,
atoms=atoms)
self.step_no = 0
status_text = "Parsing %s (%.2f MB)... " % (
self.filename, os.path.getsize(self.filename) / 1024.**2)
if imported['progressbar']:
self.pbar = ProgressBar(widgets=[status_text,
Percentage()],
maxval=self.nsw + 1).start()
parser = etree.XMLParser()
context = etree.iterparse(self.filename, tag='calculation')
try:
self._fast_iter(context, self._calculation_tag_found)
except etree.XMLSyntaxError:
type, message, traceback = sys.exc_info()
print "XML parsing halted:", message
for e in parser.error_log:
print "Warning: " + e.message
if imported['progressbar']:
self.pbar.finish()
print "Found %d out of %d steps" % (self.step_no, self.nsw)
self.trajectory.update_length(self.step_no)
print_memory_usage()
def read_trajectory(dir='', unwrap_pbcs=True, xml_file='vasprun.xml',
orig_file='traj_orig.h5', unwrapped_file='traj_unwrapped.h5',
poscar_file='POSCAR'):
"""
Convenience function for reading trajectory data from vasprun.xml.
- The first time a trajectory is read, the trajectory data is read from
vasprun.xml using lxml, and saved in a HDF5 binary file using PyTables.
- The next time the trajectory is read, the HDF5 file is read directly.
This is much faster.
If `unwrap_pbcs' is set to True, periodic boundary conditions (PBCs) will
be unwrapped, using initial positions from a specified POSCAR file.
Initial positions are taken from a POSCAR file instead of the initial
positions in the vasprun.xml file, because the latter are wrapped into the
cell, making visual comparison with the original structure difficult if the
POSCAR file contained coordinates out of the cell, such as may result from
a cell where the atoms were relaxed from initial positions at the edge of
the cell.
Parameters
----------
dir : str
Directory to read files from
Default is current directory
unwrap_pbcs : bool
Set to True to unwrap the periodic boundary conditions (PBCs) or False to leave them.
Default is True
xml_file : str
Name of the vasprun.xml file, default is "vasprun.xml"
orig_file : str
Name of the HDF5 file
unwrapped_file : str
Name of the HDF5 file containing unwrapped PBCs.
Only used if unwrap_pbcs is set to True
"""
if not os.path.isfile(dir + orig_file):
p = IterativeVasprunParser(dir + xml_file)
traj = p.get_trajectory()
traj.save(dir + orig_file)
if not unwrap_pbcs:
return traj
elif not unwrap_pbcs:
return Trajectory(filename = dir + orig_file)
if os.path.isfile(dir + unwrapped_file):
return Trajectory(filename = dir + unwrapped_file)
else:
poscar = PoscarParser(dir + poscar_file)
pos = poscar.get_positions(coords = 'direct')
try:
t = traj
except:
t = Trajectory(filename = dir + orig_file)
print "Unwrapping using initial pos from POSCAR"
t.unwrap_pbc(init_pos = pos)
t.save(dir + unwrapped_file)
return t
def _get_trajectories(self):
""" Internal method to make a Trajectory object """
atoms = self.get_atoms()
self.trajectory = Trajectory(num_steps = self.nsw, timestep = self.potim, atoms = atoms)
self.step_no = 0
status_text = "Parsing %s (%.2f MB)... " % (self.filename, os.path.getsize(self.filename)/1024.**2)
if imported['progressbar']:
self.pbar = ProgressBar(widgets=[status_text,Percentage()], maxval = self.nsw+1).start()
parser = etree.XMLParser()
context = etree.iterparse(self.filename, tag='calculation')
try:
self._fast_iter(context, self._calculation_tag_found)
except etree.XMLSyntaxError:
type, message, traceback = sys.exc_info()
print "XML parsing halted:",message
for e in parser.error_log:
print "Warning: "+e.message
if imported['progressbar']:
self.pbar.finish()
print "Found %d out of %d steps" % (self.step_no,self.nsw)
self.trajectory.update_length(self.step_no)
print_memory_usage()
def read_trajectory(dir='',
unwrap_pbcs=True,
xml_file='vasprun.xml',
orig_file='traj_orig.h5',
unwrapped_file='traj_unwrapped.h5',
poscar_file='POSCAR'):
"""
Convenience function for reading trajectory data from vasprun.xml.
- The first time a trajectory is read, the trajectory data is read from
vasprun.xml using lxml, and saved in a HDF5 binary file using PyTables.
- The next time the trajectory is read, the HDF5 file is read directly.
This is much faster.
If `unwrap_pbcs' is set to True, periodic boundary conditions (PBCs) will
be unwrapped, using initial positions from a specified POSCAR file.
Initial positions are taken from a POSCAR file instead of the initial
positions in the vasprun.xml file, because the latter are wrapped into the
cell, making visual comparison with the original structure difficult if the
POSCAR file contained coordinates out of the cell, such as may result from
a cell where the atoms were relaxed from initial positions at the edge of
the cell.
Parameters
----------
dir : str
Directory to read files from
Default is current directory
unwrap_pbcs : bool
Set to True to unwrap the periodic boundary conditions (PBCs) or False to leave them.
Default is True
xml_file : str
Name of the vasprun.xml file, default is "vasprun.xml"
orig_file : str
Name of the HDF5 file
unwrapped_file : str
Name of the HDF5 file containing unwrapped PBCs.
Only used if unwrap_pbcs is set to True
"""
if not os.path.isfile(dir + orig_file):
p = IterativeVasprunParser(dir + xml_file)
traj = p.get_trajectory()
traj.save(dir + orig_file)
if not unwrap_pbcs:
return traj
elif not unwrap_pbcs:
return Trajectory(filename=dir + orig_file)
if os.path.isfile(dir + unwrapped_file):
return Trajectory(filename=dir + unwrapped_file)
else:
poscar = PoscarParser(dir + poscar_file)
pos = poscar.get_positions(coords='direct')
try:
t = traj
except:
t = Trajectory(filename=dir + orig_file)
print "Unwrapping using initial pos from POSCAR"
t.unwrap_pbc(init_pos=pos)
t.save(dir + unwrapped_file)
return t
class IterativeVasprunParser(object):
"""
Parser for very large vasprun.xml files, based on iterative xml parsing.
The functionality of this parser is limited compared to VasprunParser.
"""
def __str__(self):
return "iterative vasprun parser"
def __init__(self, filename='vasprun.xml', verbose=False):
if not imported['lxml']:
print "Error: The module 'lxml' is needed!"
sys.exit(1)
self.filename = filename
self.verbose = verbose
if not os.path.isfile(self.filename):
print "Fatal error: The file '%s' was not found or is not a file." % (
self.filename)
sys.exit(1)
#print_memory_usage()
# read beginning of file to find number of ionic steps (NSW) and timestep (POTIM)
self.params = self._find_first_instance('parameters',
self._params_tag_found)
self.nsw = int(
self.params.xpath("separator[@name='ionic']/i[@name='NSW']")
[0].text)
if self.nsw == 0:
print "Note: This file contains no ionic motion (NSW=0)."
self.nsw = 1 # to read the static structure
# should make a try clause
self.potim = float(
self.params.xpath("separator[@name='ionic']/i[@name='POTIM']")
[0].text)
self.atoms = self._find_first_instance('atominfo', self._get_atoms)
self.natoms = len(self.atoms)
try:
self.nsw
#print "Number of ionic steps: %d" % (self.nsw)
except AttributeError:
print "Could not find incar:NSW in vasprun.xml"
sys.exit(1)
def _params_tag_found(self, elem):
return copy(elem)
def _get_atoms(self, elem):
atoms = []
for rc in elem.xpath("array[@name='atoms']/set/rc"):
atoms.append(get_atomic_number_from_symbol(rc[0].text))
return np.array(atoms, dtype=int)
def _fast_iter(self, context, func):
for event, elem in context:
func(elem)
elem.clear()
while elem.getprevious() is not None:
del elem.getparent()[0]
del context
def _find_first_instance(self, tag, func):
parser = etree.XMLParser()
context = etree.iterparse(self.filename, tag=tag)
ret = None
try:
for event, elem in context:
ret = func(elem)
elem.clear()
while elem.getprevious() is not None:
del elem.getparent()[0]
break
except etree.XMLSyntaxError:
print "XML parsing failed:"
type, message, traceback = sys.exc_info()
print message
for e in parser.error_log:
print "XML Error: " + e.message
if str(message).split()[0] == 'Char':
ZapControlCharacters(self.filename)
print
print "You may now try to re-run the script."
print
sys.exit(1)
del context
return ret
def get_num_ionic_steps(self):
""" Returns the number of ionic steps """
return self.nsw
def get_num_atoms(self):
""" Returns the number of atoms """
return self.natoms
def get_atoms(self):
""" Returns an array with the types of the atoms """
return self.atoms
def _get_initial_structure(self, elem):
basis = elem.xpath("crystal/varray[@name='basis']/v")
basis = [[float(x) for x in p.text.split()] for p in basis]
pos = elem.xpath("varray[@name='positions']/v")
pos = [[float(x) for x in p.text.split()] for p in pos]
vel = elem.xpath("varray[@name='velocities']/v")
vel = [[float(x) for x in p.text.split()] for p in vel]
return {'basis': basis, 'positions': pos, 'velocities': vel}
def get_initial_structure(self):
"""
Returns a dictionary containing 'basis', 'positions' and 'velocities'
"""
return self._find_first_instance('structure',
self._get_initial_structure)
def _calculation_tag_found(self, elem):
bas = elem.xpath("structure/crystal/varray[@name='basis']/v")
self.trajectory.set_basis(
self.step_no,
np.array([[float(x) for x in b.text.split()] for b in bas]))
if self.trajectory.num_atoms == 1:
pos = elem.xpath("structure/varray[@name='positions']/v[%d]" %
(self.atom_no + 1))
forces = elem.xpath("structure/varray[@name='forces']/v[%d]" %
(self.atom_no + 1))
else:
pos = elem.xpath("structure/varray[@name='positions']/v")
forces = elem.xpath("varray[@name='forces']/v")
pos = [[float(x) for x in ap.text.split()] for ap in pos]
forces = [[float(x) for x in ap.text.split()] for ap in forces]
self.trajectory.set_positions(self.step_no, pos)
self.trajectory.set_forces(self.step_no, forces)
e_kin = elem.xpath("energy/i[@name='kinetic']")
if e_kin:
self.trajectory.set_e_kinetic(self.step_no, float(e_kin[0].text))
e_pot = elem.xpath("energy/i[@name='e_fr_energy']")
self.trajectory.set_e_total(self.step_no, float(e_pot[0].text))
self.step_no += 1
if imported['progressbar']:
self.pbar.update(self.step_no)
#print pos
def _get_trajectories(self):
""" Internal method to make a Trajectory object """
atoms = self.get_atoms()
self.trajectory = Trajectory(num_steps=self.nsw,
timestep=self.potim,
atoms=atoms)
self.step_no = 0
status_text = "Parsing %s (%.2f MB)... " % (
self.filename, os.path.getsize(self.filename) / 1024.**2)
if imported['progressbar']:
self.pbar = ProgressBar(widgets=[status_text,
Percentage()],
maxval=self.nsw + 1).start()
parser = etree.XMLParser()
context = etree.iterparse(self.filename, tag='calculation')
try:
self._fast_iter(context, self._calculation_tag_found)
except etree.XMLSyntaxError:
type, message, traceback = sys.exc_info()
print "XML parsing halted:", message
for e in parser.error_log:
print "Warning: " + e.message
if imported['progressbar']:
self.pbar.finish()
print "Found %d out of %d steps" % (self.step_no, self.nsw)
self.trajectory.update_length(self.step_no)
print_memory_usage()
def get_trajectory(self):
"""
Returns a oppvasp.trajectory.Trajectory object
"""
self.atom_no = -1
self._get_trajectories()
return self.trajectory
def get_all_trajectories(self):
print "DEPRECATED: get_all_trajectories is deprectated! Use get_trajectory instead"
return self.get_trajectory()
def ionic_steps(self, step=0):
try:
parser
except:
parser = etree.XMLParser()
context = etree.iterparse(self.filename, tag='atominfo')
for event, elem in context:
atominfo = []
for rc in elem.xpath("array[@name='atoms']/set/rc"):
atominfo.append(
get_atomic_number_from_symbol(rc[0].text.strip()))
break # avoid scanning the whole file!
context = etree.iterparse(self.filename, tag='calculation')
for event, elem in context:
step = IonicStep(elem, atominfo)
elem.clear()
while elem.getprevious() is not None:
del elem.getparent()[0]
yield step
class IterativeVasprunParser(object):
"""
Parser for very large vasprun.xml files, based on iterative xml parsing.
The functionality of this parser is limited compared to VasprunParser.
"""
def __str__(self):
return "iterative vasprun parser"
def __init__(self, filename = 'vasprun.xml', verbose = False):
if not imported['lxml']:
print "Error: The module 'lxml' is needed!"
sys.exit(1)
self.filename = filename
self.verbose = verbose
if not os.path.isfile(self.filename):
print "Fatal error: The file '%s' was not found or is not a file." % (self.filename)
sys.exit(1)
#print_memory_usage()
# read beginning of file to find number of ionic steps (NSW) and timestep (POTIM)
self.params = self._find_first_instance('parameters', self._params_tag_found)
self.nsw = int(self.params.xpath("separator[@name='ionic']/i[@name='NSW']")[0].text)
if self.nsw == 0:
print "Note: This file contains no ionic motion (NSW=0)."
self.nsw = 1 # to read the static structure
# should make a try clause
self.potim = float(self.params.xpath("separator[@name='ionic']/i[@name='POTIM']")[0].text)
self.atoms = self._find_first_instance('atominfo',self._get_atoms)
self.natoms = len(self.atoms)
try:
self.nsw
#print "Number of ionic steps: %d" % (self.nsw)
except AttributeError:
print "Could not find incar:NSW in vasprun.xml"
sys.exit(1)
def _params_tag_found(self, elem):
return copy(elem)
def _get_atoms(self, elem):
atoms = []
for rc in elem.xpath("array[@name='atoms']/set/rc"):
atoms.append(get_atomic_number_from_symbol(rc[0].text))
return np.array(atoms, dtype=int)
def _fast_iter(self, context, func):
for event, elem in context:
func(elem)
elem.clear()
while elem.getprevious() is not None:
del elem.getparent()[0]
del context
def _find_first_instance(self, tag, func):
parser = etree.XMLParser()
context = etree.iterparse(self.filename, tag=tag)
ret = None
try:
for event, elem in context:
ret = func(elem)
elem.clear()
while elem.getprevious() is not None:
del elem.getparent()[0]
break
except etree.XMLSyntaxError:
print "XML parsing failed:"
type, message, traceback = sys.exc_info()
print message
for e in parser.error_log:
print "XML Error: "+e.message
if str(message).split()[0] == 'Char':
ZapControlCharacters(self.filename)
print
print "You may now try to re-run the script."
print
sys.exit(1)
del context
return ret
def get_num_ionic_steps(self):
""" Returns the number of ionic steps """
return self.nsw
def get_num_atoms(self):
""" Returns the number of atoms """
return self.natoms
def get_atoms(self):
""" Returns an array with the types of the atoms """
return self.atoms
def _get_initial_structure(self,elem):
basis= elem.xpath("crystal/varray[@name='basis']/v")
basis = [[float(x) for x in p.text.split()] for p in basis]
pos = elem.xpath("varray[@name='positions']/v")
pos = [[float(x) for x in p.text.split()] for p in pos]
vel = elem.xpath("varray[@name='velocities']/v")
vel = [[float(x) for x in p.text.split()] for p in vel]
return { 'basis': basis, 'positions': pos, 'velocities': vel }
def get_initial_structure(self):
"""
Returns a dictionary containing 'basis', 'positions' and 'velocities'
"""
return self._find_first_instance('structure',self._get_initial_structure)
def _calculation_tag_found(self, elem):
bas = elem.xpath("structure/crystal/varray[@name='basis']/v")
self.trajectory.set_basis(self.step_no, np.array([[float(x) for x in b.text.split()] for b in bas]))
if self.trajectory.num_atoms == 1:
pos = elem.xpath("structure/varray[@name='positions']/v[%d]" % (self.atom_no+1))
forces = elem.xpath("structure/varray[@name='forces']/v[%d]" % (self.atom_no+1))
else:
pos = elem.xpath("structure/varray[@name='positions']/v")
forces = elem.xpath("varray[@name='forces']/v")
pos = [[float(x) for x in ap.text.split()] for ap in pos]
forces = [[float(x) for x in ap.text.split()] for ap in forces]
self.trajectory.set_positions(self.step_no, pos)
self.trajectory.set_forces(self.step_no, forces)
e_kin = elem.xpath("energy/i[@name='kinetic']")
if e_kin:
self.trajectory.set_e_kinetic(self.step_no, float(e_kin[0].text))
e_pot = elem.xpath("energy/i[@name='e_fr_energy']")
self.trajectory.set_e_total(self.step_no, float(e_pot[0].text))
self.step_no += 1
if imported['progressbar']:
self.pbar.update(self.step_no)
#print pos
def _get_trajectories(self):
""" Internal method to make a Trajectory object """
atoms = self.get_atoms()
self.trajectory = Trajectory(num_steps = self.nsw, timestep = self.potim, atoms = atoms)
self.step_no = 0
status_text = "Parsing %s (%.2f MB)... " % (self.filename, os.path.getsize(self.filename)/1024.**2)
if imported['progressbar']:
self.pbar = ProgressBar(widgets=[status_text,Percentage()], maxval = self.nsw+1).start()
parser = etree.XMLParser()
context = etree.iterparse(self.filename, tag='calculation')
try:
self._fast_iter(context, self._calculation_tag_found)
except etree.XMLSyntaxError:
type, message, traceback = sys.exc_info()
print "XML parsing halted:",message
for e in parser.error_log:
print "Warning: "+e.message
if imported['progressbar']:
self.pbar.finish()
print "Found %d out of %d steps" % (self.step_no,self.nsw)
self.trajectory.update_length(self.step_no)
print_memory_usage()
def get_trajectory(self):
"""
Returns a oppvasp.trajectory.Trajectory object
"""
self.atom_no = -1
self._get_trajectories()
return self.trajectory
def get_all_trajectories(self):
print "DEPRECATED: get_all_trajectories is deprectated! Use get_trajectory instead"
return self.get_trajectory()
def ionic_steps(self, step = 0):
try:
parser
except:
parser = etree.XMLParser()
context = etree.iterparse(self.filename, tag='atominfo')
for event, elem in context:
atominfo = []
for rc in elem.xpath("array[@name='atoms']/set/rc"):
atominfo.append(get_atomic_number_from_symbol(rc[0].text.strip()))
break # avoid scanning the whole file!
context = etree.iterparse(self.filename, tag='calculation')
for event, elem in context:
step = IonicStep(elem, atominfo)
elem.clear()
while elem.getprevious() is not None:
del elem.getparent()[0]
yield step
