schrodinger.application.matsci.bandshape_utils module

Utilities for bandshape calculations.

Copyright Schrodinger, LLC. All rights reserved.

class schrodinger.application.matsci.bandshape_utils.NormalMode(frequency, normal_mode)

Bases: tuple

__contains__

Return key in self.

__init__

Initialize self. See help(type(self)) for accurate signature.

__len__

Return len(self).

count(value) → integer -- return number of occurrences of value

frequency

Alias for field number 0

index(value[, start[, stop]]) → integer -- return first index of value.

Raises ValueError if the value is not present.

normal_mode

Alias for field number 1

class schrodinger.application.matsci.bandshape_utils.VibState(index, n_quantum, huang_rhys_f)

Bases: object

__init__(index, n_quantum, huang_rhys_f)

Initialize self. See help(type(self)) for accurate signature.

class schrodinger.application.matsci.bandshape_utils.Transition(index, energy, intensity, initial_vib_states, final_vib_states, max_n_imaginary)

Bases: object

__init__(index, energy, intensity, initial_vib_states, final_vib_states, max_n_imaginary)

Initialize self. See help(type(self)) for accurate signature.

schrodinger.application.matsci.bandshape_utils.is_bs_spectrum_file_key(key)

Return True if the given structure property key is a bandshape spectrum file key.

Parameters:key (str) – the structure property key to check Return type:bool Returns:True if the given key is a bandshape spectrum file key

schrodinger.application.matsci.bandshape_utils.get_temp_from_bs_spectrum_file_key(key)

Return the temperature from the given bandshape spectrum file structure property key.

Parameters:key (str) – the structure property key containing the temperature Return type:float Returns:the temperature in K

schrodinger.application.matsci.bandshape_utils.get_bs_spectrum_file_temps_keys(struct)

Return the bandshape spectrum file structure property keys and associated temperatures for the given structure.

Parameters:struct (schrodinger.structure.Structure) – the structure with the property keys Return type:list Returns:pair tuples of temperatures in K and bandshape spectrum file structure property keys

schrodinger.application.matsci.bandshape_utils.get_transition_type(atable)

Return the transition type of the given table.

Parameters:atable (table.Table) – the table to check Return type:str or None Returns:module constant ABSORPTION or EMISSION or None if it is unknown

class schrodinger.application.matsci.bandshape_utils.BandshapeSpectrumFile(data_file_name, spm_file_name, transition_type=None)

Bases: schrodinger.application.matsci.spectra.SpectrumFile

Manage a bandshape spectrum file.

ENERGY_KEY = 'r_j_Excitation_Energy_(eV)'

ENERGY_TITLE = 'Excitation Energy (eV)'

INTENSITY_KEY = 'r_j_Intensity'

INTENSITY_TITLE = 'Intensity'

SYMMETRY_KEY = 's_j_Symmetry'

SYMMETRY_TITLE = 'Symmetry'

SPECTRUM_KEY = 's_j_spectrum_type'

SPECTRUM_TITLE = 'Electronic Transition w/ Bandshape'

X_KEY = 's_j_x_label'

X_ALIAS = 'r_j_Excitation_Energy_(eV)'

Y_KEY = 's_j_y_label'

Y_ALIAS = 'r_j_Intensity'

HEADERS = {'s_j_spectrum_type': 'Electronic Transition w/ Bandshape', 's_j_x_label': 'r_j_Excitation_Energy_(eV)', 's_j_y_label': 'r_j_Intensity'}

COLUMNS = {'r_j_Excitation_Energy_(eV)': 'Excitation Energy (eV)', 'r_j_Intensity': 'Intensity', 's_j_Symmetry': 'Symmetry'}

EXT = '.uvv.spm'

DEFAULT_BIN_WIDTH = 400.0

__init__(data_file_name, spm_file_name, transition_type=None)

Create an instance.

Parameters:

• data_file_name (str) – the text file containing whitespace separated energies and intensities, one pair per line, energies in eV
• spm_file_name (str) – the name of the *spm file to create
• transition_type (str or None) – module constant ABSORPTION or EMISSION or None if it is unknown

static isBandshapeTable(atable)

Return True if the given table is a bandshape table.

Parameters:atable (table.Table) – the table to check Return type:bool Returns:True if the given table is a bandshape table

static getTrimmedTable(filepath, bin_width=None)

Return a table of trimmed data for the given file path and bin width.

Parameters:

• filepath (str) – the file path to the file with the data
• bin_width (float) – the bin width in wavenumbers (cm-1) used for binning

Raises:

ValueError – if there isn’t any data

Return type:

table.Table

Returns:

table of trimmed data

static getData(data_file_name, separator=None, types=None)

Return the data from the given data file.

Parameters:

• data_file_name (str) – the text file containing the data
• separator (str) – the data separator
• types (list) – a list of types used to type cast the data

Return type:

list

Returns:

contains data tuples

write()

Write the *spm file.

schrodinger.application.matsci.bandshape_utils.get_translated_xyz_vec(st)

Return a vector of cartesian coordinates of the given structure which have been translated so that the center of mass is at the (0, 0, 0) origin.

Parameters:st (schrodinger.structure.Structure) – the structure Return type:numpy.array Returns:the translated cartesian coordinates

schrodinger.application.matsci.bandshape_utils.get_mwc_to_nm_transform(jagout)

Return the mass-weighted Cartesian coordinate to normal mode transformation matrix.

Parameters:jagout (JaguarOutput) – the Jaguar output class Return type:numpy.array or None Returns:the transformation matrix or None if there isn’t one

schrodinger.application.matsci.bandshape_utils.get_huang_rhys_fs(ground_jo, excited_jo)

Return the Huang-Rhys factors for the ground and excited states.

Parameters:

• ground_jo (JaguarOutput) – the Jaguar output class for the ground state
• excited_jo (JaguarOutput) – the Jaguar output class for the excited state

Return type:

list, list

Returns:

Huang-Rhys factors for ground and excited states

schrodinger.application.matsci.bandshape_utils.get_transitions(bs_out_file_name, initial_jo=None, final_jo=None)

Return a list of transitions from the given band shape output file.

Parameters:

• bs_out_file_name (str) – the band shape output file name
• initial_jo (JaguarOutput or None) – the Jaguar output class for the initial state
• final_jo (JaguarOutput or None) – the Jaguar output class for the final state

Return type:

list

Returns:

contains Transition

exception schrodinger.application.matsci.bandshape_utils.NormalModeAnalysisException

Bases: Exception

__init__

Initialize self. See help(type(self)) for accurate signature.

args

with_traceback()

Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

class schrodinger.application.matsci.bandshape_utils.NormalModeAnalysis(bs_out_file_name)

Bases: object

Manage normal mode analysis.

TAG = 'normal_mode_analysis'

N_ATOMS_KEY = 'i_j_atom_total'

FREQ_KEY = 'r_j_Frequency'

FREQ_TITLE = 'Frequency'

SYMM_KEY = 's_j_Symmetry'

SYMM_TITLE = 'Symmetry'

INTENSITY_KEY = 'r_j_Intensity'

INTENSITY_TITLE = 'Intensity'

RAMAN_ACT_KEY = 'r_j_Raman_Act'

RAMAN_ACT_TITLE = 'Raman Act'

RAMAN_INT_KEY = 'r_j_Raman_Int'

RAMAN_INT_TITLE = 'Raman Int'

X_KEY = 'r_j_x%s'

X_TITLE = 'x%s'

Y_KEY = 'r_j_y%s'

Y_TITLE = 'y%s'

Z_KEY = 'r_j_z%s'

Z_TITLE = 'z%s'

COLUMNS = {'r_j_Frequency': 'Frequency', 'r_j_Intensity': 'Intensity', 'r_j_Raman_Act': 'Raman Act', 'r_j_Raman_Int': 'Raman Int', 's_j_Symmetry': 'Symmetry'}

__init__(bs_out_file_name)

Create an instance.

Parameters:bs_out_file_name (str) – the band shape output file name Raises:NormalModeAnalysisException – if there is an issue

getVibStates(energy_start, energy_stop)

Get all vibrational states within the given energy window for the initial and final states.

Parameters:

• energy_start (float) – the lower bound on the energy in eV
• energy_stop (float) – the upper bound on the energy in eV

Return type:

dict, dict

Returns:

initial and final vibrational states, keys are indices, values are sets of VibState

getVibStateWeight(state)

Return the weight of the given vibrational state.

Parameters:state (VibState) – the vibrational state Return type:float Returns:the weight

getAllVibData(all_states, jagout, include_n_quantum)

Return all frequencies and normal modes from the given vibrational states.

Parameters:

• all_states (dict) – vibrational states, keys are indices, values are sets of VibState
• jagout (JaguarOutput) – the Jaguar output class
• include_n_quantum (bool) – whether to include effects due to vibrational quantum numbers

Return type:

list

Returns:

contains NormalMode

getAvgVibData(all_states, jagout, include_n_quantum)

Return an averaged frequency and normal mode from the given vibrational states.

Parameters:

• all_states (dict) – vibrational states, keys are indices, values are sets of VibState
• jagout (JaguarOutput) – the Jaguar output class
• include_n_quantum (bool) – whether to include effects due to vibrational quantum numbers

Return type:

NormalMode

Returns:

the averaged NormalMode

getMaxVibData(all_states, jagout, include_n_quantum)

Return the frequency and normal mode with the largest weight from the given vibrational states.

Parameters:

• all_states (dict) – vibrational states, keys are indices, values are sets of VibState
• jagout (JaguarOutput) – the Jaguar output class
• include_n_quantum (bool) – whether to include effects due to vibrational quantum numbers

Return type:

NormalMode

Returns:

the max (largest weight) NormalMode

writeVibFile(file_name, n_atoms, normal_modes)

Write the *.vib file for the given normal modes.

Parameters:

• file_name (str) – the file name
• n_atoms (int) – the number of atoms
• normal_modes (list) – contains NormalMode

writeFiles(base_name, initial_normal_modes, final_normal_modes, title=None)

Write normal mode analysis files.

Parameters:

• base_name (str) – a base name for the files
• initial_normal_modes (list or None) – contains NormalMode for the initial state
• final_normal_modes (list or None) – contains NormalMode for the final state
• title (str) – a title to use for structures in the normal mode analysis output files

run(energy_start, energy_stop, average=False, maximum=False, include_n_quantum=False, base_name=None, title=None)

Run it.

Parameters:

• energy_start (float) – the lower bound on the energy in eV
• energy_stop (float) – the upper bound on the energy in eV
• average (bool) – whether to average the normal modes
• maximum (bool) – whether to report only the normal mode with the largest weight
• include_n_quantum (bool) – whether to include effects due to vibrational quantum numbers
• base_name (str) – a base name to use for the normal mode analysis output files
• title (str) – a title to use for structures in the normal mode analysis output files

Raises:

NormalModeAnalysisException – if there is an issue

Return type:

str

Returns:

the name of the Maestro file written