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 repr_experiment_in_cif(experiment): """represents the entire experiment in .cif format""" return "\n".join([\ repr_angdeg_property_in_cif(experiment.get_direct_property('angdeg').value), repr_acell_property_in_cif(experiment.get_direct_property('acell').value), repr_atoms_in_cif(parse_atoms(experiment.meta['atoms']))\ ])
def main(): """ Displays the atoms from the meta attributes of the input experiment within a rhombal unit cell """ with handle_command_line_IO.get_input_file( display_help_function) as input_file: experiment = Experiment.load_from_json_file(input_file) atoms = parse_atoms(experiment.meta['atoms']) display_atoms_rhombus(atoms)
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 main(): """ Displays the atoms from the meta attributes of the input experiment within a rhombal unit cell """ with handle_command_line_IO.get_input_file(display_help_function) as input_file: experiment = Experiment.load_from_json_file(input_file) atoms = parse_atoms(experiment.meta['atoms']) rhomb_atoms = get_rhombal_cell(atoms) acell_raw = experiment.get_direct_property('acell') cell_size = [float(coord) for coord in acell_raw.value] correct_size_rhomb_atoms = [Atom(atom.znucl, atom.coord*cell_size) for atom in rhomb_atoms] print len(atoms) print '' #no comment on the file for atom in correct_size_rhomb_atoms: print repr_in_xyz(atom)
def main(): with handle_command_line_IO.get_input_file(display_help_message) as input_file: # get from stdin or first argument's file experiment = Experiment.load_from_json_file(input_file) if experiment.meta and 'atoms' in experiment.meta : #allow for pass-through if there's nothing to do atoms = sorted(parse_atoms(experiment.meta['atoms']), key=lambda atom: atom.znucl) # sorted so we can group by znucl experiment.meta['atoms'] = None atom_types = OrderedSet([atom.znucl for atom in atoms]) znucl_to_typat_mapping = dict((znucl, index+1) for index, znucl in enumerate(atom_types)) experiment.direct.append(SimpleAttribute(name="natom", value=len(atoms), comment=GENERATED_VALUE_COMMENT)) experiment.direct.append(SimpleAttribute(name="ntypat", value=len(atom_types), comment=GENERATED_VALUE_COMMENT)) experiment.direct.append(SimpleAttribute(name="znucl", value=list(atom_types), comment=GENERATED_VALUE_COMMENT)) experiment.direct.append(SimpleAttribute(name="typat", value=[znucl_to_typat_mapping[atom.znucl] for atom in atoms], comment=GENERATED_VALUE_COMMENT)) experiment.direct.append(SimpleAttribute(name="xred", value=[atom.coord.coordinate_array for atom in atoms], comment=GENERATED_VALUE_COMMENT)) 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)