mirror of https://github.com/phonopy/phonopy.git
write_FORCE_SETS is modified to recieve displacement_dataset
This commit is contained in:
Atsushi Togo
parent
3fc3bbc6b0
commit
dcce5fe198
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@ -109,25 +109,26 @@ def write_FORCE_SETS_wien2k(forces_filenames,
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is_distribute=True,
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symprec=1e-5):
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forces = []
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natom = supercell.get_number_of_atoms()
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lattice = supercell.get_cell()
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for wien2k_filename, disp in zip(forces_filenames, displacements):
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for wien2k_filename, disp in zip(forces_filenames,
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displacements['first_atoms']):
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# Parse wien2k case.scf file
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wien2k_forces = wien2k.get_forces_wien2k(wien2k_filename, lattice)
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if is_distribute:
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force_set = wien2k.distribute_forces(supercell,
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disp,
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wien2k_forces,
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wien2k_filename,
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symprec)
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force_set = wien2k.distribute_forces(
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supercell,
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[disp['number'], disp['displacement']],
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wien2k_forces,
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wien2k_filename,
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symprec)
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if not force_set:
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return False
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else:
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if not (natom == len(wien2k_forces)):
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print "%s contains only forces of %d atoms" % (wien2k_filename,
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len(wien2k_forces))
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print "%s contains only forces of %d atoms" % (
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wien2k_filename, len(wien2k_forces))
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return False
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else:
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force_set = wien2k_forces
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@ -136,26 +137,31 @@ def write_FORCE_SETS_wien2k(forces_filenames,
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print "Drift force of %s" % wien2k_filename
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print "%12.8f %12.8f %12.8f" % tuple(drift_force)
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print "This drift force was subtracted from forces."
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print
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print
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forces.append(np.array(force_set) - drift_force)
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disp['forces'] = np.array(force_set) - drift_force
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write_FORCE_SETS(filename, natom, displacements, forces)
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write_FORCE_SETS(displacements, filename=filename)
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return True
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def write_FORCE_SETS_vasp(forces_filenames,
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displacements,
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num_atom,
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filename='FORCE_SETS',
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is_zero_point=False,
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verbose=True):
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try:
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from lxml import etree
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except ImportError:
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print "You need to install python-lxml."
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sys.exit(1)
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if verbose:
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print "counter (file index):",
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num_atom = displacements['natom']
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count = 0
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are_files_correct = True
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if is_zero_point:
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force_files = forces_filenames[1:]
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if vasp.is_version528(forces_filenames[0]):
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@ -164,103 +170,72 @@ def write_FORCE_SETS_vasp(forces_filenames,
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else:
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zero_forces = vasp.get_forces_vasprun_xml(
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etree.iterparse(forces_filenames[0], tag='varray'))
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if verbose:
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print "%d" % (count + 1),
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count += 1
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if not check_forces(zero_forces, num_atom, forces_filenames[0]):
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are_files_correct = False
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else:
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force_files = forces_filenames
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zero_forces = None
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forces = []
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# Show progress
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for i in range(len(displacements)):
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for i, disp in enumerate(displacements['first_atoms']):
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if vasp.is_version528(force_files[i]):
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forces.append(vasp.get_forces_vasprun_xml(etree.iterparse(
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vasp.VasprunWrapper(force_files[i]), tag='varray')))
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disp['forces'] = vasp.get_forces_vasprun_xml(etree.iterparse(
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vasp.VasprunWrapper(force_files[i]), tag='varray'))
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else:
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forces.append(vasp.get_forces_vasprun_xml(
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etree.iterparse(force_files[i], tag='varray')))
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disp['forces'] = vasp.get_forces_vasprun_xml(
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etree.iterparse(force_files[i], tag='varray'))
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if is_zero_point:
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dummy_forces = [zero_forces] + forces
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else:
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dummy_forces = forces
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if is_forces_read(dummy_forces, num_atom, forces_filenames):
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if verbose:
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print >> sys.stderr, "counter (file index):",
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write_FORCE_SETS(filename,
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num_atom,
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displacements,
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forces,
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zero_forces,
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verbose)
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return True
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else:
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print "%d" % (count + 1),
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count += 1
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if not check_forces(disp['forces'], num_atom, force_files[i]):
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are_files_correct = False
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if verbose:
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print
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write_FORCE_SETS(displacements,
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filename=filename,
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zero_forces=zero_forces)
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return are_files_correct
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def check_forces(forces, num_atom, filename):
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if len(forces) != num_atom:
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print " \"%s\" does not contain necessary information." % filename,
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return False
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else:
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return True
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def is_forces_read(force_sets, num_atom, filenames):
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is_read = True
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for i, forces in enumerate(force_sets):
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if not len(forces)==num_atom:
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is_read = False
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print "\'%s\' does not contain necessary information." % filenames[i]
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return is_read
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def write_FORCE_SETS_from_dataset(dataset,
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filename='FORCE_SETS',
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verbose=False):
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displacements = [[x['number'], x['displacement']]
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for x in dataset['first_atoms']]
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def write_FORCE_SETS(dataset, filename='FORCE_SETS', zero_forces=None):
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num_atom = dataset['natom']
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displacements = dataset['first_atoms']
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forces = [x['forces'] for x in dataset['first_atoms']]
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write_FORCE_SETS(filename,
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dataset['natom'],
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displacements,
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forces,
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verbose=verbose)
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def write_FORCE_SETS(filename,
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natom,
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displacements,
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forces,
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zero_forces=None,
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verbose=True):
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disps = sort_displacements(displacements)
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# Write FORCE_SETS
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file = open(filename, 'w')
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file.write("%-5d\n" % natom)
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file.write("%-5d\n" % len(disps))
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for count, disp in enumerate(disps):
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# Show progress
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if verbose:
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print >> sys.stderr, "%d (%d) " % (count+1, disp[2] + 1),
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file.write("\n%-5d\n" % (disp[0] + 1))
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file.write("%20.16f %20.16f %20.16f\n" % (tuple(disp[1])))
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fp = open(filename, 'w')
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fp.write("%-5d\n" % num_atom)
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fp.write("%-5d\n" % len(displacements))
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for count, disp in enumerate(displacements):
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fp.write("\n%-5d\n" % (disp['number'] + 1))
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fp.write("%20.16f %20.16f %20.16f\n" % (tuple(disp['displacement'])))
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# Subtract residual forces
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if not zero_forces==None:
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forces[disp[2]] -= zero_forces
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if zero_forces is not None:
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forces[count] -= zero_forces
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for f in forces[disp[2]]:
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file.write("%15.10f %15.10f %15.10f\n" % (tuple(f)))
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# Show progress
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if verbose:
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print >> sys.stderr, "\n"
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for f in forces[count]:
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fp.write("%15.10f %15.10f %15.10f\n" % (tuple(f)))
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def mycmp(x, y):
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return cmp(x[0], y[0])
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# Sort by the atom numbering
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# To remember the original order, the original index is added at 5th element.
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def sort_displacements(displacements):
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for i, disp in enumerate(displacements):
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disp.append(i)
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displacements.sort(mycmp)
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return displacements
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def parse_disp_yaml_with_supercell(filename='disp.yaml'):
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def parse_disp_yaml(filename="disp.yaml", return_cell=False):
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try:
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import yaml
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except ImportError:
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@ -269,45 +244,38 @@ def parse_disp_yaml_with_supercell(filename='disp.yaml'):
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try:
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from yaml import CLoader as Loader
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from yaml import CDumper as Dumper
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except ImportError:
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from yaml import Loader, Dumper
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from yaml import Loader
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data = yaml.load(open(filename).read(), Loader=Loader)
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lattice = data['lattice']
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displacements = []
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for x in data['displacements']:
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displacements.append([x['atom']-1, x['displacement']])
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positions = [x['position'] for x in data['atoms']]
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symbols = [x['symbol'] for x in data['atoms']]
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cell = Atoms(cell=lattice,
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scaled_positions=positions,
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symbols=symbols,
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pbc=True)
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dataset = yaml.load(open(filename), Loader=Loader)
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natom = dataset['natom']
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new_dataset = {}
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new_dataset['natom'] = natom
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new_first_atoms = []
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for first_atoms in dataset['displacements']:
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first_atoms['atom'] -= 1
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atom1 = first_atoms['atom']
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disp1 = first_atoms['displacement']
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if 'direction' in first_atoms:
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direct1 = first_atoms['direction']
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new_first_atoms.append({'number': atom1,
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'displacement': disp1,
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'direction':direct1})
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else:
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new_first_atoms.append({'number': atom1, 'displacement': disp1})
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new_dataset['first_atoms'] = new_first_atoms
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return displacements, cell
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def parse_disp_yaml(filename='disp.yaml'):
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try:
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import yaml
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except ImportError:
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print "You need to install python-yaml."
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exit(1)
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try:
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from yaml import CLoader as Loader
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from yaml import CDumper as Dumper
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except ImportError:
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from yaml import Loader, Dumper
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data = yaml.load(open(filename).read(), Loader=Loader)
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natom = data['natom']
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lattice = data['lattice']
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displacements = []
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for x in data['displacements']:
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displacements.append([x['atom']-1, x['displacement']])
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return displacements, natom
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if return_cell:
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lattice = dataset['lattice']
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positions = [x['position'] for x in dataset['atoms']]
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symbols = [x['symbol'] for x in dataset['atoms']]
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cell = Atoms(cell=lattice,
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scaled_positions=positions,
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symbols=symbols,
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pbc=True)
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return new_dataset, cell
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else:
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return new_dataset
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def parse_DISP(filename='DISP'):
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disp = open(filename)
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@ -411,29 +411,28 @@ if options.force_sets_mode or options.force_sets_zero_mode:
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if file_exists('disp.yaml', log_level):
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if interface_mode == 'vasp':
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displacements, natom = file_IO.parse_disp_yaml('disp.yaml')
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displacements = file_IO.parse_disp_yaml('disp.yaml')
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if interface_mode == 'wien2k':
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displacements, supercell = file_IO.parse_disp_yaml_with_supercell('disp.yaml')
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displacements, supercell = file_IO.parse_disp_yaml(
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'disp.yaml', return_cell=True)
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for filename in args:
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file_exists(filename, log_level)
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num_disp_files = len(args)
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if options.force_sets_zero_mode:
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num_disp_files -= 1
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if not len(displacements)== num_disp_files:
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if len(displacements['first_atoms']) != num_disp_files:
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print_error_message("Number of files to be read don't match "
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"to number of displacements in disp.yaml.")
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if log_level > 0:
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print_end()
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sys.exit(1)
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if interface_mode == 'vasp':
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is_created = file_IO.write_FORCE_SETS_vasp(
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args,
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displacements,
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natom,
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'FORCE_SETS',
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is_zero_point=options.force_sets_zero_mode)
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@ -450,7 +449,6 @@ if options.force_sets_mode or options.force_sets_zero_mode:
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is_zero_point=options.force_sets_zero_mode,
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is_distribute=(not options.is_wien2k_p1),
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symprec=options.symprec)
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if log_level > 0:
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if is_created:
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@ -460,6 +458,9 @@ if options.force_sets_mode or options.force_sets_zero_mode:
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print_end()
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sys.exit(0)
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##########################
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# Read crystal structure #
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##########################
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# Parse VASP-type crystal structure
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if interface_mode=='vasp':
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if options.cell_poscar == None:
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