schrodinger.application.matsci.thermo_correction_utils module¶

Utilities for thermochemical correction in reaction workflow.

schrodinger.application.matsci.thermo_correction_utils.has_stage_separator(astr)¶

Return True if the given string has the STAGE_SEPARATOR.

Parameters:: astr (str) – string to check
Return type:: bool
Returns:: True if the given string has the STAGE_SEPARATOR

schrodinger.application.matsci.thermo_correction_utils.split_stage(astr)¶

Split the given string on STAGE_SEPARATOR.

Parameters:: astr (str) – string to split
Return type:: str, str
Returns:: the given string split on STAGE_SEPARATOR

schrodinger.application.matsci.thermo_correction_utils.split_stage_ext(astr)¶

Split the given string by the extension.

Parameters:: astr (str) – string to split
Return type:: str, str
Returns:: the given string split by the extension

schrodinger.application.matsci.thermo_correction_utils.split_stage_hash(astr)¶

Split the given string by the stage hash.

Parameters:: astr (str) – string to split
Return type:: str, str, str
Returns:: the given string split by the stage hash

schrodinger.application.matsci.thermo_correction_utils.insert_stage_hash(astr, stage_idx)¶

Insert the stage hash to the given string.

Parameters:

astr (str) – the string to which to insert the stage hash
stage_idx (int) – the stage index

Return type:

str

Returns:

the given string with the stage hash inserted

schrodinger.application.matsci.thermo_correction_utils.insert_temp_press(astr, temp, press)¶

Insert the temperature and pressure extension into the given string.

Parameters:

astr (str) – the string to which to insert the temperature and pressure extension
temp (float) – the temperature in K
press (float) – the pressure in atm

Raises:

ThermoCorrectionException – if there is an issue

Return type:

str

Returns:

the string with the temperature and pressure extension inserted

schrodinger.application.matsci.thermo_correction_utils.get_units(key)¶

Return units in the given key.

Parameters:: key (str) – the key
Return type:: str
Returns:: the units

schrodinger.application.matsci.thermo_correction_utils.insert_units(astr, units)¶

Insert the units extension into the given string.

Parameters:

astr (str) – the string to which to insert the units extension
units (str) – the units extension, for example ‘(au)’

Raises:

ThermoCorrectionException – if there is an issue

Return type:

str

Returns:

the string with the units extension inserted

schrodinger.application.matsci.thermo_correction_utils.get_stage_idx(astr)¶

Return the stage index from the given string.

Parameters:: astr (str) – the string from which to get the stage index
Return type:: int
Returns:: the stage index

schrodinger.application.matsci.thermo_correction_utils.get_restrain_distance_idxs(st)¶

Return a list of lists of indices of restrain distances in the given structure.

Parameters:: st (Structure) – the structure
Return type:: list
Returns:: contains lists of restrain distances

schrodinger.application.matsci.thermo_correction_utils.get_restrain_angle_idxs(st)¶

Return a list of lists of indices of restrain angles in the given structure.

Parameters:: st (Structure) – the structure
Return type:: list
Returns:: contains lists of restrain angles

schrodinger.application.matsci.thermo_correction_utils.get_restrain_dihedral_idxs(st)¶

Return a list of lists of indices of restrain dihedrals in the given structure.

Parameters:: st (Structure) – the structure
Return type:: list
Returns:: contains lists of restrain dihedrals

exception schrodinger.application.matsci.thermo_correction_utils.JaguarPostProcException¶: Bases: Exception

schrodinger.application.matsci.thermo_correction_utils.check_ts_vetting(out_file)¶

Return False if TS vetting failed in the given Jaguar out file.

Parameters:: out_file (str) – Jaguar out file
Return type:: bool
Returns:: False if TS vetting failed

schrodinger.application.matsci.thermo_correction_utils.check_jaguar_output(jag_out_dir, base_name, max_i_freq=0)¶

Check if the Jaguar job for the given base name is valid.

Parameters:

jag_out_dir (str) – path to the directory containing the Jaguar output files with the given base name
base_name (str) – base name of the Jaguar job
max_i_freq (float) – tolerate small imaginary frequencies less than this value in wavenumbers (cm^-1)

Raises:

JaguarPostProcException – if there is an issue

schrodinger.application.matsci.thermo_correction_utils.has_transition_state(rxnwf_file_path=None, rxnwf_sts=None)¶

Return True if the reaction workflow features a transition state, False otherwise.

Return type:: bool
Returns:: True if the reaction workflow features a transition state, False otherwise

schrodinger.application.matsci.thermo_correction_utils.check_anharmonic(sts)¶

Check if anharmonic corrections are applicable to the given structures.

Parameters:: sts (list[structure.Structure]) – the structures
Raises:: ThermoCorrectionException – if there is an issue

exception schrodinger.application.matsci.thermo_correction_utils.ThermoCorrectionException¶: Bases: Exception

class schrodinger.application.matsci.thermo_correction_utils.ThermoCorrection(sts, jag_out_dir, anharm=True, anharm_max_freq=300, anharm_factor_data=None, anharm_dir='anharmonic', return_anharm_zip=True, solvation_entropy=False, solvation_entropy_solvent='water', solvation_entropy_dir='solvation_entropy', return_solvation_entropy_zip=True, jaguar_keywords=None, max_i_freq=0, temp_press_data=None, host=None, n_subjobs=1, tpp=1, max_retries=0, logger=None)¶

Bases: object

Manage correcting thermochemical properties.

THERMO_CORR_FINAL = 'thermo_corr_final'¶

PROP_STARTER = 'r_matsci_thermo_corr_final'¶

FREE_ENERGY_STARTER = 'r_matsci_thermo_corr_final{type_key}G_tot_(au)'¶

FREE_ENERGY_PROP = 'r_matsci_thermo_corr_final{type_key}G_tot_(au){temp_press}_stage_{idx}'¶

LNQ_STARTER = 'r_matsci_thermo_corr_final{type_key}lnQ_tot'¶

LNQ_PROP = 'r_matsci_thermo_corr_final{type_key}lnQ_tot{temp_press}_stage_{idx}'¶

__init__(sts, jag_out_dir, anharm=True, anharm_max_freq=300, anharm_factor_data=None, anharm_dir='anharmonic', return_anharm_zip=True, solvation_entropy=False, solvation_entropy_solvent='water', solvation_entropy_dir='solvation_entropy', return_solvation_entropy_zip=True, jaguar_keywords=None, max_i_freq=0, temp_press_data=None, host=None, n_subjobs=1, tpp=1, max_retries=0, logger=None)¶

Parameters:

sts (list[structure.Structure]) – the structures
jag_out_dir (str) – path to a directory containing output files of Jaguar jobs, the .out, .01.in, and .01.mae files are required, base names of files should be title_stage_n where title are the titles of the given structures and n is the stage number, stage being the Jaguar multistage workflow stage from which the output came, .01.mae files should be from auto-rxnwf and have certain properties related to that workflow
anharm (bool) – whether to calculate the anharmonic correction
anharm_max_freq (float) – anharmonic potentials are created for normal modes with harmonic frequencies less than this value in wavenumbers (cm^-1)
anharm_factor_data (SeqData or None) – unitless factor data for factors that multiply a normal mode displacement, if None then the defaults are used, the number of points is in the positive direction only, excluding zero and the negative direction, for example using a value of 4 in turn means 2 * 4 + 1 = 9 points total
return_anharm_zip (bool) – whether to return zipped up directories of all anharmonic subjobs
solvation_entropy (bool) – whether to correct thermochemical properties for solvation entropy
solvation_entropy_solvent (str) – solvent to use for solvation entropy calculation
solvation_entropy_dir (str) – path to a directory to hold results from solvation entropy corrections
return_solvation_entropy_zip (bool) – whether to return zipped up directories of all solvation entropy subjobs
jaguar_keywords (dict) – Jaguar keywords
max_i_freq (float) – tolerate small imaginary frequencies less than this value in wavenumbers (cm^-1)
temp_press_data (seu.TempPressData) – the temperature and pressure data for thermochemical properties
host (str) – the host on which to run subjobs, by default it will be determined automatically by job control from the toplevel -HOST and -SUBHOST arguments
n_subjobs (int) – the maximum number of simulatanous subjobs
tpp (int) – the number of threads to use for Jaguar subjobs, i.e. -TPP (threads-per-process)
max_retries (int) – maximum number of times to try relaunching subjobs
logger (logging.Logger or None) – output logger or None if there isn’t one

setFreqStageIdxs()¶: Set the indices of frequency stages.

getJagOutFileName(st, stage_idx)¶

Return the Jaguar output file name.

Parameters:

st (schrodinger.structure.Structure) – the structure
stage_idx (int) – the stage index

Return type:

str

Returns:

the Jaguar output file name

setUpDirs()¶

Set up the directories.

Raises:: ThermoCorrectionException – if there is an issue

addSolvationEntropyJobs(job_dj, host)¶

Add solvation entropy subjobs.

Parameters:

jobs_dj (schrodinger.job.queue.JobDJ) – the JobDJ object
host (str or None) – the host string or None if it is determined by the backend

Raises:

ThermoCorrectionException – if there is an issue

processSolvationEntropy()¶

Process the solvation entropy.

Raises:: ThermoCorrectionException – if there is an issue

addAnharmonicJobs(job_dj, host)¶

Add anharmonic subjobs.

Parameters:

jobs_dj (schrodinger.job.queue.JobDJ) – the JobDJ object
host (str or None) – the host string or None if it is determined by the backend

processAnharmonic()¶

Process the anharmonic workflow.

Raises:: ThermoCorrectionException – if there is an issue

getFinalThermoProps(st, stage_idx, temperature, pressure)¶

Return final thermochemical properties.

Parameters:

st (schrodinger.structure.Structure) – the structure
stage_idx (int) – the stage index
temperature (float) – temperature in K
pressure (float) – pressure in atm

Raises:

ThermoCorrectionException – if there is an issue

Return type:

dict[seu.StructurePropertyInfo]=float

Returns:

dictionary of seu.StructurePropertyInfo to values

setFinalThermoProps()¶: Set the final thermochemical properties.

run()¶: Run it.