schrodinger.application.matsci.bandshape_utils module¶

Utilities for bandshape calculations.

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

Bases: tuple

frequency¶: Alias for field number 0

normal_mode¶: Alias for field number 1

schrodinger.application.matsci.bandshape_utils.get_spectrum_type(inp_fp)¶

Return the spectrum type.

Parameters:: inp_fp (str) – the bandshape input .inp file path
Return type:: str
Returns:: bandshape_utils.ABSORPTION or bandshape_utils.EMISSION

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: 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

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

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