schrodinger.application.jaguar.textparser module

Classes for parsing Jaguar output files and accessing output properties programmatically.

Copyright Schrodinger, LLC. All rights reserved.

exception schrodinger.application.jaguar.textparser.JaguarParseError

Bases: exceptions.Exception

class schrodinger.application.jaguar.textparser.TextParser(jaguar_output, file_iter=None)

Bases: object

A parser to create a JaguarOutput object from a Jaguar output file.

The basic organization of this parser is that of a number of line processing callback functions triggered by regular expressions.

callback = {'pre': {<_sre.SRE_Pattern object at 0x63ea020>: <function solvation_job>, <_sre.SRE_Pattern object>: <function functional>, <_sre.SRE_Pattern object>: <function custom_functional>, <_sre.SRE_Pattern object at 0x7266050>: <function spin_splitting_score>, <_sre.SRE_Pattern object at 0x714a060>: <function total_lo_correction>, <_sre.SRE_Pattern object>: <function multip>, <_sre.SRE_Pattern object at 0x54840a0>: <function numerical_freqs>, <_sre.SRE_Pattern object at 0x498a8f0>: <function coords_ind>, <_sre.SRE_Pattern object>: <function z_variables>, <_sre.SRE_Pattern object at 0x5484950>: <function coords_nred>, <_sre.SRE_Pattern object at 0x4b01180>: <function coords_harmonic>, <_sre.SRE_Pattern object at 0x52ee1a0>: <function qst_geometries>, <_sre.SRE_Pattern object at 0x69ae9d0>: <function non_default_print_options>, <_sre.SRE_Pattern object>: <function stoichiometry>, <_sre.SRE_Pattern object>: <function point_group_used>, <_sre.SRE_Pattern object at 0x70b5260>: <function mae_in>, <_sre.SRE_Pattern object>: <function symmetrized_geometry>, <_sre.SRE_Pattern object at 0x7264b60>: <function scan_coordinates>, <_sre.SRE_Pattern object>: <function start_geometry>, <_sre.SRE_Pattern object at 0x725dc20>: <function calc_type>, <_sre.SRE_Pattern object at 0x71af470>: <function correlation_type>, <_sre.SRE_Pattern object at 0x5131cc0>: <function coords_frozen1>, <_sre.SRE_Pattern object at 0x6f914e0>: <function molchg>, <_sre.SRE_Pattern object>: <function esp_fit_atoms_and_bonds>, <_sre.SRE_Pattern object at 0x50d5d00>: <function nbasis>, <_sre.SRE_Pattern object at 0x63f9d20>: <function path_geometry>, <_sre.SRE_Pattern object at 0x55410f0>: <function coords_frozen2>, <_sre.SRE_Pattern object>: <function mol_weight>, <_sre.SRE_Pattern object at 0x5484640>: <function coords_opt>, <_sre.SRE_Pattern object at 0x71b1660>: <function point_group>, <_sre.SRE_Pattern object at 0x4d56eb0>: <function qst_initial_geometry>, <_sre.SRE_Pattern object at 0x725dec0>: <function esp_fit_atoms>, <_sre.SRE_Pattern object at 0x53a6520>: <function qm_atoms>, <_sre.SRE_Pattern object at 0x7260f50>: <function pseudospectral>, <_sre.SRE_Pattern object>: <function basis_set>, <_sre.SRE_Pattern object at 0x64037c0>: <function mae>}, 'ch': {<_sre.SRE_Pattern object at 0x7265650>: <function mulliken_charges>, <_sre.SRE_Pattern object at 0x7265d10>: <function multipole_esp>, <_sre.SRE_Pattern object>: <function fukui_indices>, <_sre.SRE_Pattern object at 0x7265380>: <function multipole_mulliken>, <_sre.SRE_Pattern object at 0x72613b0>: <function esp_charges>, <_sre.SRE_Pattern object at 0x72659d0>: <function multipole_qm>}, 'scanner': {<_sre.SRE_Pattern object>: <function start_geometry>, <_sre.SRE_Pattern object at 0x5acfcb0>: <function end_scan>, <_sre.SRE_Pattern object at 0x63f0ec0>: <function geometry_scan_step>}, 'scf': {<_sre.SRE_Pattern object>: <function electronic_e>, <_sre.SRE_Pattern object>: <function nucrep2>, <_sre.SRE_Pattern object at 0x61db020>: <function nops_on>, <_sre.SRE_Pattern object>: <function nucrep1>, <_sre.SRE_Pattern object>: <function gas_phase>, <_sre.SRE_Pattern object at 0x3db34b0>: <function two_e_terms>, <_sre.SRE_Pattern object at 0x4b48220>: <function solution_phase>, <_sre.SRE_Pattern object>: <function solvation>, <_sre.SRE_Pattern object>: <function lumo>, <_sre.SRE_Pattern object at 0x4c26030>: <function orbital_energies>, <_sre.SRE_Pattern object>: <function homo>, <_sre.SRE_Pattern object at 0x7081b60>: <function nops_on>, <_sre.SRE_Pattern object>: <function etot>, <_sre.SRE_Pattern object>: <function aposteri_e>, <_sre.SRE_Pattern object at 0x54843c0>: <function one_e_terms>, <_sre.SRE_Pattern object>: <function scfe>}, 'elden': {<_sre.SRE_Pattern object>: <function esp_analysis>, <_sre.SRE_Pattern object>: <function epn>, <_sre.SRE_Pattern object>: <function alie_analysis>}, 'tdener': {<_sre.SRE_Pattern object>: <function tddft_excitation_energies>, <_sre.SRE_Pattern object>: <function tddft_excitation_energies_old>, <_sre.SRE_Pattern object at 0x69a24f0>: <function reset_tddft_excitation_energies>}, 'lmp2': {<_sre.SRE_Pattern object>: <function gas_phase>, <_sre.SRE_Pattern object>: <function lmp2>, <_sre.SRE_Pattern object at 0x4b48220>: <function solution_phase>, <_sre.SRE_Pattern object>: <function solvation>}, 'etit': {<_sre.SRE_Pattern object>: <function electron_transfer>}, 'gvblmp2': {<_sre.SRE_Pattern object>: <function gvblmp2>, <_sre.SRE_Pattern object>: <function rolmp2>}, None: {<_sre.SRE_Pattern object>: <function start_of_program>, <_sre.SRE_Pattern object>: <function glibc>, <_sre.SRE_Pattern object at 0x71494d0>: <function fatal_error>, <_sre.SRE_Pattern object>: <function end_time>}, 'geopt': {<_sre.SRE_Pattern object>: <function z_variables>, <_sre.SRE_Pattern object>: <function convergence_category>, <_sre.SRE_Pattern object at 0x725fc70>: <function irc_point>, <_sre.SRE_Pattern object at 0x56ce4a0>: <function geopt_stuck1>, <_sre.SRE_Pattern object at 0x4b10470>: <function nops_on>, <_sre.SRE_Pattern object at 0x4aa0cf0>: <function end_geometry>, <_sre.SRE_Pattern object at 0x7261730>: <function nofail_geopt>, <_sre.SRE_Pattern object at 0x725e320>: <function nofail_geopt_restart>, <_sre.SRE_Pattern object at 0x5209730>: <function irc_summary>, <_sre.SRE_Pattern object>: <function geopt_geometry>, <_sre.SRE_Pattern object at 0x69c7370>: <function tddft_geopt_energy>, <_sre.SRE_Pattern object>: <function geopt_stuck2>, <_sre.SRE_Pattern object at 0x725ffb0>: <function stopping_optimization>, <_sre.SRE_Pattern object at 0x582e8f0>: <function sm_geometry>}, 'der1b': {<_sre.SRE_Pattern object at 0x4b56650>: <function forces>}, 'tddft_g': {<_sre.SRE_Pattern object at 0x4b56650>: <function forces>}, 'lmp2gb': {<_sre.SRE_Pattern object at 0x4b56650>: <function forces>}, 'onee': {<_sre.SRE_Pattern object at 0x6c242b0>: <function s_min_eval>, <_sre.SRE_Pattern object at 0x48e09b0>: <function canorb>}, 'sole': {<_sre.SRE_Pattern object at 0x5424120>: <function solvation>, <_sre.SRE_Pattern object at 0x4b48220>: <function solution_phase>}, 'before pre': {<_sre.SRE_Pattern object>: <function jobid>}, 'cpolar': {<_sre.SRE_Pattern object>: <function beta_polar>, <_sre.SRE_Pattern object>: <function alpha_polar>, <_sre.SRE_Pattern object>: <function gamma_polar>}, 'freq': {<_sre.SRE_Pattern object at 0x7264f30>: <function frequencies>, <_sre.SRE_Pattern object at 0x51ef4d0>: <function zpe>, <_sre.SRE_Pattern object at 0x7266650>: <function frequencies_old>, <_sre.SRE_Pattern object at 0x71101d0>: <function get_vetted_vec_index>}, 'lmp2gdb': {<_sre.SRE_Pattern object at 0x4b56650>: <function forces>}, 'nude': {<_sre.SRE_Pattern object at 0x4b56650>: <function forces>}, 'cis': {<_sre.SRE_Pattern object>: <function cis_excitation_energies>}, 'nmrcphf': {<_sre.SRE_Pattern object>: <function get_nmr>}}

endGeopt(jo)

Clean up at the end of a geopt step.

Adds the current results to the geopt list and creates a new current results object if appropriate.

endIRC(direction)

Set state indicating the end of an IRC step and its direction.

direction (str)

Must be ‘Forward’ or ‘Reverse’.

endScan(jo)

Clean up at the end of a scan step.

Adds the current results to the scan list and creates a new current results object. Or, if this a relaxed scan, archives the geopt steps to the scan list and creates an empty geopt_step list.

first_line_re = <_sre.SRE_Pattern object>

parse(file_iter=None, jaguar_output=None)

Parse the provided file iterator.

Return a JaguarOutput instance populated with properties parsed from the output file.

Parameters

file_iter (iterator returning lines of Jaguar output)

jaguar_output (JaguarOutput instance)

If jaguar_output is provided, that instance will be populated with the properties parsed from the output file. Otherwise, the object provided to the TextParser constructor will be used.

schrodinger.application.jaguar.textparser.alie_analysis(tp, jo, m, it)

schrodinger.application.jaguar.textparser.alpha_polar(tp, jo, m, it)

schrodinger.application.jaguar.textparser.aposteri_e(tp, jo, m, it)

schrodinger.application.jaguar.textparser.basis_set(tp, jo, m, it)

schrodinger.application.jaguar.textparser.beta_polar(tp, jo, m, it)

schrodinger.application.jaguar.textparser.calc_type(tp, jo, m, it)

schrodinger.application.jaguar.textparser.callback(prog, regexp=None, debug=False, parser_class=<class 'schrodinger.application.jaguar.textparser.TextParser'>)

A decorator to add a function to the TextParser callback dictionary.

The ‘callback’ dictionary consists of dictionaries for individual programs, each one indexed by the regular expression that needs to be satisfied to invoke the function.

Arguments

prog (str)

A Jaguar subprogram to which searching will be restricted. Set to None if the whole file needs to be searched.

regexp (str)

The regular expression that needs to be matched. This can be None if multiple decorators are being applied (to restrict to multiple subprograms) and the inner decorator specified a regexp.

schrodinger.application.jaguar.textparser.canorb(tp, jo, m, it)

schrodinger.application.jaguar.textparser.cis_excitation_energies(tp, jo, m, it)

schrodinger.application.jaguar.textparser.convergence_category(tp, jo, m, it)

schrodinger.application.jaguar.textparser.coords_frozen1(tp, jo, m, it)

schrodinger.application.jaguar.textparser.coords_frozen2(tp, jo, m, it)

schrodinger.application.jaguar.textparser.coords_harmonic(tp, jo, m, it)

schrodinger.application.jaguar.textparser.coords_ind(tp, jo, m, it)

schrodinger.application.jaguar.textparser.coords_nred(tp, jo, m, it)

schrodinger.application.jaguar.textparser.coords_opt(tp, jo, m, it)

schrodinger.application.jaguar.textparser.correlation_type(tp, jo, m, it)

schrodinger.application.jaguar.textparser.custom_functional(tp, jo, m, it)

schrodinger.application.jaguar.textparser.electron_transfer(tp, jo, m, it)

schrodinger.application.jaguar.textparser.electronic_e(tp, jo, m, it)

schrodinger.application.jaguar.textparser.end_geometry(tp, jo, m, it)

schrodinger.application.jaguar.textparser.end_scan(tp, jo, m, it)

schrodinger.application.jaguar.textparser.end_time(tp, jo, m, it)

schrodinger.application.jaguar.textparser.epn(tp, jo, m, it)

schrodinger.application.jaguar.textparser.esp_analysis(tp, jo, m, it)

schrodinger.application.jaguar.textparser.esp_charges(tp, jo, m, it)

schrodinger.application.jaguar.textparser.esp_fit_atoms(tp, jo, m, it)

schrodinger.application.jaguar.textparser.esp_fit_atoms_and_bonds(tp, jo, m, it)

schrodinger.application.jaguar.textparser.etot(tp, jo, m, it)

schrodinger.application.jaguar.textparser.fatal_error(tp, jo, m, it)

schrodinger.application.jaguar.textparser.forces(tp, jo, m, it)

schrodinger.application.jaguar.textparser.frequencies(tp, jo, m, it)

schrodinger.application.jaguar.textparser.frequencies_old(tp, jo, m, it)

schrodinger.application.jaguar.textparser.fukui_indices(tp, jo, m, it)

schrodinger.application.jaguar.textparser.functional(tp, jo, m, it)

schrodinger.application.jaguar.textparser.gamma_polar(tp, jo, m, it)

schrodinger.application.jaguar.textparser.gas_phase(tp, jo, m, it)

schrodinger.application.jaguar.textparser.gen_charges(attr, tp, jo, m, it)

schrodinger.application.jaguar.textparser.geometry_read(it, charge=None)

A utility function to read an input cartesian geometry from the output file.

Return a tuple of (JaguarAtomicResults list, mmjag_handle). The mmjag_handle containing the parsed geometry in MMJAG_ZMAT1 if charge is provided. If not, the mmjag handle is None.

schrodinger.application.jaguar.textparser.geometry_scan_step(tp, jo, m, it)

schrodinger.application.jaguar.textparser.geopt_geometry(tp, jo, m, it)

schrodinger.application.jaguar.textparser.geopt_stuck1(tp, jo, m, it)

schrodinger.application.jaguar.textparser.geopt_stuck2(tp, jo, m, it)

schrodinger.application.jaguar.textparser.get_nmr(tp, jo, m, it)

schrodinger.application.jaguar.textparser.get_vetted_vec_index(tp, jo, m, it)

schrodinger.application.jaguar.textparser.glibc(tp, jo, m, it)

schrodinger.application.jaguar.textparser.gvblmp2(tp, jo, m, it)

schrodinger.application.jaguar.textparser.homo(tp, jo, m, it)

schrodinger.application.jaguar.textparser.irc_point(tp, jo, m, it)

schrodinger.application.jaguar.textparser.irc_summary(tp, jo, m, it)

schrodinger.application.jaguar.textparser.jobid(tp, jo, m, it)

class schrodinger.application.jaguar.textparser.line_enumerate(iter_)

Bases: object

A simple wrapper class to keep track of the line iteration count.

The builtin enumerate function isn’t practical for TextParser since it passes around the iterator and uses explicit next() calls.

Public attributes:

line_num

The line number of the last line returned.

line

The last line returned.

iter

The underlying iterator.

next()

schrodinger.application.jaguar.textparser.lmp2(tp, jo, m, it)

schrodinger.application.jaguar.textparser.lumo(tp, jo, m, it)

schrodinger.application.jaguar.textparser.mae(tp, jo, m, it)

schrodinger.application.jaguar.textparser.mae_in(tp, jo, m, it)

schrodinger.application.jaguar.textparser.mol_weight(tp, jo, m, it)

schrodinger.application.jaguar.textparser.molchg(tp, jo, m, it)

schrodinger.application.jaguar.textparser.mulliken_charges(tp, jo, m, it)

schrodinger.application.jaguar.textparser.multip(tp, jo, m, it)

schrodinger.application.jaguar.textparser.multipole_esp(tp, jo, m, it)

schrodinger.application.jaguar.textparser.multipole_moments(type_, tp, jo, m, it)

schrodinger.application.jaguar.textparser.multipole_mulliken(tp, jo, m, it)

schrodinger.application.jaguar.textparser.multipole_qm(tp, jo, m, it)

schrodinger.application.jaguar.textparser.nbasis(tp, jo, m, it)

schrodinger.application.jaguar.textparser.nofail_geopt(tp, jo, m, it)

schrodinger.application.jaguar.textparser.nofail_geopt_restart(tp, jo, m, it)

schrodinger.application.jaguar.textparser.non_default_print_options(tp, jo, m, it)

schrodinger.application.jaguar.textparser.nops_on(tp, jo, m, it)

schrodinger.application.jaguar.textparser.nucrep1(tp, jo, m, it)

schrodinger.application.jaguar.textparser.nucrep2(tp, jo, m, it)

schrodinger.application.jaguar.textparser.numerical_freqs(tp, jo, m, it)

schrodinger.application.jaguar.textparser.one_e_terms(tp, jo, m, it)

schrodinger.application.jaguar.textparser.orbital_energies(tp, jo, m, it)

schrodinger.application.jaguar.textparser.path_geometry(tp, jo, m, it)

schrodinger.application.jaguar.textparser.point_group(tp, jo, m, it)

schrodinger.application.jaguar.textparser.point_group_used(tp, jo, m, it)

schrodinger.application.jaguar.textparser.pseudospectral(tp, jo, m, it)

schrodinger.application.jaguar.textparser.qm_atoms(tp, jo, m, it)

schrodinger.application.jaguar.textparser.qst_geometries(tp, jo, m, it)

schrodinger.application.jaguar.textparser.qst_initial_geometry(tp, jo, m, it)

schrodinger.application.jaguar.textparser.reset_tddft_excitation_energies(tp, jo, m, it)

schrodinger.application.jaguar.textparser.rolmp2(tp, jo, m, it)

schrodinger.application.jaguar.textparser.s_min_eval(tp, jo, m, it)

schrodinger.application.jaguar.textparser.scan_coordinates(tp, jo, m, it)

schrodinger.application.jaguar.textparser.scfe(tp, jo, m, it)

schrodinger.application.jaguar.textparser.sm_geometry(tp, jo, m, it)

schrodinger.application.jaguar.textparser.solution_phase(tp, jo, m, it)

schrodinger.application.jaguar.textparser.solvation(tp, jo, m, it)

schrodinger.application.jaguar.textparser.solvation_job(tp, jo, m, it)

schrodinger.application.jaguar.textparser.spin_splitting_score(tp, jo, m, it)

schrodinger.application.jaguar.textparser.start_geometry(tp, jo, m, it)

schrodinger.application.jaguar.textparser.start_of_program(tp, jo, m, it)

schrodinger.application.jaguar.textparser.stoichiometry(tp, jo, m, it)

schrodinger.application.jaguar.textparser.stopping_optimization(tp, jo, m, it)

schrodinger.application.jaguar.textparser.symmetrized_geometry(tp, jo, m, it)

schrodinger.application.jaguar.textparser.tddft_excitation_energies(tp, jo, m, it)

schrodinger.application.jaguar.textparser.tddft_excitation_energies_old(tp, jo, m, it)

schrodinger.application.jaguar.textparser.tddft_geopt_energy(tp, jo, m, it)

schrodinger.application.jaguar.textparser.textparser_trace(func)

A decorator that will print the callback function name when it is called.

schrodinger.application.jaguar.textparser.thermo_helper(temp, it)

Parse a thermochemical properties section and return a ThermoCollection object.

schrodinger.application.jaguar.textparser.total_lo_correction(tp, jo, m, it)

schrodinger.application.jaguar.textparser.two_e_terms(tp, jo, m, it)

schrodinger.application.jaguar.textparser.z_variables(tp, jo, m, it)

schrodinger.application.jaguar.textparser.zpe(tp, jo, m, it)