schrodinger.application.matsci.bandshape_utils module¶

Utilities for bandshape calculations.

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

Bases: tuple

__contains__(key, /)¶: Return key in self.

__len__()¶: Return len(self).

count(value, /)¶: Return number of occurrences of value.

frequency¶: Alias for field number 0

index(value, start=0, stop=9223372036854775807, /)¶

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)¶

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)¶

static getSimplified(vib_states)¶

Return a simplified representation of the transition.

Parameters: vib_states (list) – contains VibState
Return type: str
Returns: the simplified representation of the transition

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
transition_type (str or None) – module constant ABSORPTION or EMISSION or None if it is unknown

Param

spm_file_name: the name of the *spm file to create

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(spectrum_type, initial_vib_jo, final_vib_jo, geoms_base_name=None)¶

Return the Huang-Rhys factors for the initial and final states.

Parameters

spectrum_type (str) – the spectrum type, either module constant ABSORPTION or EMISSION
initial_vib_jo (JaguarOutput) – the Jaguar output class for the initial state frequency calculation
final_vib_jo (JaguarOutput) – the Jaguar output class for the final state frequency calculation
geoms_base_name (str or None) – if given use geometries from Jaguar restart .01.in files rather than from the input Jaguar objects

Return type

list, list

Returns

Huang-Rhys factors for initial and final 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

schrodinger.application.matsci.bandshape_utils.get_bs_base_name(name)¶

Return the base name of the given bandshape name.

Parameters: name (str) – the bandshape name
Return type: str
Returns: the base name

schrodinger.application.matsci.bandshape_utils.get_bs_ext(name)¶

Return the extension of the given bandshape name.

Parameters: name (str) – the bandshape name
Return type: str
Returns: the extension

schrodinger.application.matsci.bandshape_utils.get_out_file_paths(source_path, patterns)¶

Return the output file paths.

Parameters

source_path (str) – the source path to the output files
patterns (list) – the glob patterns of the output files

Raises

NormalModeAnalysisException – if there is an issue

Return type

list

Returns

contains the output file paths in the same order as patterns

exception schrodinger.application.matsci.bandshape_utils.NormalModeAnalysisException¶

Bases: Exception

__init__(*args, **kwargs)¶

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

classmethod 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

schrodinger.application.matsci.bandshape_utils.write_simplified_transitions_file(bs_out_file_name, s_bs_out_file_name=None)¶

Write a simplified transitions file.

Parameters

bs_out_file_name (str) – the band shape output file name
s_bs_out_file_name (str or None) – the simplified band shape output file name, if None then it will be determined from bs_out_file_name