def parse_band_eigenenergy_file(file_handler):
""" The main workhorse of this program.
Parses the given file with eigenenergy information from Abinit
The file format is as follows, with variables in <>:
Eigenvalues ( <energy_unit> ) for nkpt= <num_k_points> k points:
<k points>
Each k point is described on two lines, as follows
kpt# <number>, nband= <num_bands>, wtk= <wtk>, kpt= <x1> <x2> <x3> (<coord system>)
<band1_energy> <band2_energy> ...
This function returns an array of KPointWithEnergy objects
"""
first_line = file_handler.readline()
num_k_points, energy_unit = parse_num_k_points_and_energy_unit_from_first_line(
first_line)
k_points = []
for k_point in xrange(
1, num_k_points +
1): # +1 because range and xrange have exlusive maxes
line_one = file_handler.readline()
number, num_bands, wtk, coord = parse_k_point_line_one_for_number_nband_wtk_coord(
line_one)
assert number == k_point
band_energies = []
while len(band_energies) < num_bands:
band_energies.extend(
parse_line_for_k_point_band_energies(file_handler.readline()))
k_points.append(
KPointWithEnergy(number, num_bands, wtk, coord, band_energies,
energy_unit))
handle_command_line_IO.errprint(k_points)
return k_points
def display_help_function():
"""
displays usage information for this file
"""
handle_command_line_IO.errprint(\
'Usage: [echo input_file.abinit.json | ] '+\
'python generate_cell_xyz_rhombus.py [input_file.abinit.json]')
def main():
"""
Reads an experiment .abinit.json from stdin or from the file marked in the first argument,
and copies the unit cell in each cardinal direction according to the value
in "meta.repeat_cell", modifiying "meta.atoms" and "direct.acell".
Outputs in .abinit.json format to stdout.
"""
# Get input from stdin or first argument's file
with handle_command_line_IO.get_input_file(
display_help_message) as input_file:
experiment = Experiment.load_from_json_file(input_file)
# Make this transparent; if no scaling is specified, don't scale
if experiment.meta and 'dopings' in experiment.meta and 'atoms' in experiment.meta:
# Get the atoms and dopings, remove the dopings
experiment.meta['atoms'] = \
dope_atoms(parse_atoms(experiment.meta['atoms']),
parse_atoms(experiment.meta.pop('dopings', None)),
tolerance=1e-4)
else:
handle_command_line_IO.errprint(
"No doping of unit cell specified; taking no action")
# Echo the resulting experiment back to stdout
print json.dumps(experiment, cls=SimpleObjectJSONEncoder, indent=4)
def main():
"""
Reads an experiment .abinit.json from stdin or from the file marked in the first argument,
and copies the unit cell in each cardinal direction according to the value
in "meta.repeat_cell", modifiying "meta.atoms" and "direct.acell".
Outputs in .abinit.json format to stdout.
"""
# Get input from stdin or first argument's file
with handle_command_line_IO.get_input_file(
display_help_message) as input_file:
experiment = Experiment.load_from_json_file(input_file)
# Make this transparent; if no scaling is specified, don't scale
if experiment.meta and 'repeat_cell' in experiment.meta and 'atoms' in experiment.meta:
# Get the number of times to repeat
repeat_factor = experiment.meta['repeat_cell']
if isinstance(repeat_factor, list):
if len(repeat_factor) != 3:
raise RuntimeError("Unit cell must be 3-D.")
else:
# if this throws an error, just report it to the user
repeat_factor = [int(repeat_factor)] * 3
# Repeat the atoms
experiment.meta['atoms'] = \
repeat_atoms_in_unit_cell(parse_atoms(experiment.meta['atoms']), repeat_factor)
# Scale the unit cell
for attribute in experiment.direct:
if attribute.name == "acell":
attribute.value = [
float(attribute.value[i]) * repeat_factor[i]
for i in xrange(0, 3)
]
# Take out repetition of cell so it doesn't happen again somehow
experiment.meta.pop('repeat_cell', None)
else:
handle_command_line_IO.errprint(
"No repeat of unit cell specified; taking no action")
# Echo the resulting experiment back to stdout
print json.dumps(experiment, cls=SimpleObjectJSONEncoder, indent=4)
def main():
"""
Reads an experiment .abinit.json from stdin or from the file marked in the first argument,
and generates a 2-D chiral tesselation of the cell according to the values in
in "meta.make_chirality", modifiying "meta.atoms" and "direct.acell".
Outputs in .abinit.json format to stdout.
"""
# Get input from stdin or first argument's file
with handle_command_line_IO.get_input_file(display_help_message) as input_file:
experiment = Experiment.load_from_json_file(input_file)
# Make this transparent; if no scaling is specified, don't scale
if experiment.meta and 'make_chirality' in experiment.meta and 'atoms' in experiment.meta:
# Get the number of times to repeat
desired_chirality = experiment.meta.pop('make_chirality', None)
if not isinstance(desired_chirality, list) or len(desired_chirality) != 2:
raise RuntimeError("Desired chirality must be 2-D.")
rhombus_basis = [[1, 0.5, 0], [0, 3**0.5/2, 0], [0, 0, 1]]
original_number_of_atoms = len(experiment.meta['atoms'])
# Repeat the atoms
experiment.meta['atoms'] = \
generate_xy_chiral_cell(parse_atoms(experiment.meta['atoms']), desired_chirality, rhombus_basis)
# Scale the unit cell
normalization_factor = (desired_chirality[0] ** 2 + desired_chirality[1] ** 2) ** 0.5
for attribute in experiment.direct:
if attribute.name == "acell":
attribute.value = \
[attribute.value[0] * normalization_factor, \
attribute.value[1] * normalization_factor, \
attribute.value[2]]
# Validate (because chirality is easy to screw up)
# Make sure there are no collisions
for collision in get_collisions(experiment.meta['atoms']):
handle_command_line_IO.errprint(\
"collision between "+str(collision[0])+" and "+str(collision[1]))
# Make sure there are the right number of atoms
expected_number_of_atoms = original_number_of_atoms * sum([x*x for x in desired_chirality])
if expected_number_of_atoms != len(experiment.meta['atoms']):
handle_command_line_IO.errprint('WARNING\nExpected '+str(expected_number_of_atoms)+\
' atoms, found '+str(len(experiment.meta['atoms'])))
else:
handle_command_line_IO.errprint("No chirality of unit cell specified; taking no action")
# Echo the resulting experiment back to stdout
print json.dumps(experiment, cls=SimpleObjectJSONEncoder, indent=4)
def display_help():
handle_command_line_IO.errprint("Usage: python graph_band_eigenvalues.py [abinit_eigenvalue_data.json [point_label_index point_label ...]]> abinit_eigenvalue_data.svg")
def display_help_message():
"""Prints a help message with usage instructions to stderr"""
handle_command_line_IO.errprint(
"Usage: [cat input1.abinit.json | ] python merge.py [input2.abinit.json ... ] > [outfile.abinit.json]"
)
def err_print_help_message():
"""Prints a short help message describing how to use this program"""
handle_command_line_IO.errprint(
"Usage: parse_band_eigenvalues.py <filename>")
def display_help_message():
"""Prints a help message with usage instructions to stderr"""
handle_command_line_IO.errprint("Usage: python convert_abinit_input_from_atoms_to_direct.py"\
+" [infile.abinit.json] > [outfile.abinit.json]")
def display_help_message():
"""Prints a help message with usage instructions to stderr"""
handle_command_line_IO.errprint(
"Usage: python generate_abinit_input_file_from_json.py [filename.abinit.json] > outputfile.in"
)
