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: future.types.newobject.newobject

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 0x80eb0a0>: <function esp_fit_atoms>, <_sre.SRE_Pattern object at 0x80f00c0>: <function pseudospectral>, <_sre.SRE_Pattern object at 0x7eb7420>: <function coords_frozen1>, <_sre.SRE_Pattern object at 0x88f4ed0>: <function mae>, <_sre.SRE_Pattern object>: <function z_variables>, <_sre.SRE_Pattern object>: <function start_geometry>, <_sre.SRE_Pattern object at 0x80ef430>: <function scan_coordinates>, <_sre.SRE_Pattern object at 0x89746e0>: <function total_lo_correction>, <_sre.SRE_Pattern object at 0x89b6160>: <function point_group>, <_sre.SRE_Pattern object>: <function functional>, <_sre.SRE_Pattern object at 0x765c990>: <function solvation_job>, <_sre.SRE_Pattern object at 0x66d41a0>: <function correlation_type>, <_sre.SRE_Pattern object>: <function point_group_used>, <_sre.SRE_Pattern object at 0x5341210>: <function qst_initial_geometry>, <_sre.SRE_Pattern object at 0x7612a60>: <function mae_in>, <_sre.SRE_Pattern object at 0x579a320>: <function molchg>, <_sre.SRE_Pattern object at 0x634c320>: <function coords_frozen2>, <_sre.SRE_Pattern object at 0x7fe13a0>: <function path_geometry>, <_sre.SRE_Pattern object>: <function symmetrized_geometry>, <_sre.SRE_Pattern object>: <function mol_weight>, <_sre.SRE_Pattern object at 0x66d4420>: <function coords_opt>, <_sre.SRE_Pattern object>: <function custom_functional>, <_sre.SRE_Pattern object at 0x80ee440>: <function spin_splitting_score>, <_sre.SRE_Pattern object>: <function esp_fit_atoms_and_bonds>, <_sre.SRE_Pattern object at 0x694a500>: <function qst_geometries>, <_sre.SRE_Pattern object at 0x57b8d10>: <function nbasis>, <_sre.SRE_Pattern object at 0x6270520>: <function non_default_print_options>, <_sre.SRE_Pattern object>: <function stoichiometry>, <_sre.SRE_Pattern object at 0x73f5dd0>: <function coords_ind>, <_sre.SRE_Pattern object at 0x80eb630>: <function numerical_freqs>, <_sre.SRE_Pattern object at 0x66d3e80>: <function coords_nred>, <_sre.SRE_Pattern object at 0x4f576b0>: <function qm_atoms>, <_sre.SRE_Pattern object>: <function multip>, <_sre.SRE_Pattern object at 0x665dee0>: <function coords_harmonic>, <_sre.SRE_Pattern object at 0x62b7e80>: <function calc_type>, <_sre.SRE_Pattern object>: <function basis_set>}, 'ch': {<_sre.SRE_Pattern object at 0x80ef800>: <function esp_charges>, <_sre.SRE_Pattern object at 0x828ac80>: <function multipole_esp>, <_sre.SRE_Pattern object at 0x6b6eec0>: <function multipole_mulliken>, <_sre.SRE_Pattern object>: <function fukui_indices>, <_sre.SRE_Pattern object at 0x80efb30>: <function mulliken_charges>, <_sre.SRE_Pattern object at 0x828a940>: <function multipole_qm>}, 'scanner': {<_sre.SRE_Pattern object at 0x7db1e80>: <function end_scan>, <_sre.SRE_Pattern object at 0x6e49790>: <function geometry_scan_step>, <_sre.SRE_Pattern object>: <function start_geometry>}, 'scf': {<_sre.SRE_Pattern object>: <function electronic_e>, <_sre.SRE_Pattern object at 0x7c87060>: <function two_e_terms>, <_sre.SRE_Pattern object>: <function aposteri_e>, <_sre.SRE_Pattern object>: <function solvation>, <_sre.SRE_Pattern object>: <function scfe>, <_sre.SRE_Pattern object at 0x8655ee0>: <function nops_on>, <_sre.SRE_Pattern object at 0x7dd5f10>: <function solution_phase>, <_sre.SRE_Pattern object>: <function homo>, <_sre.SRE_Pattern object>: <function gas_phase>, <_sre.SRE_Pattern object at 0x7e921f0>: <function nops_on>, <_sre.SRE_Pattern object>: <function etot>, <_sre.SRE_Pattern object at 0x7636fa0>: <function one_e_terms>, <_sre.SRE_Pattern object>: <function lumo>, <_sre.SRE_Pattern object at 0x73efdc0>: <function orbital_energies>, <_sre.SRE_Pattern object>: <function nucrep1>, <_sre.SRE_Pattern object>: <function nucrep2>}, 'elden': {<_sre.SRE_Pattern object>: <function esp_analysis>, <_sre.SRE_Pattern object>: <function alie_analysis>, <_sre.SRE_Pattern object>: <function epn>}, 'tdener': {<_sre.SRE_Pattern object at 0x69458c0>: <function reset_tddft_excitation_energies>, <_sre.SRE_Pattern object>: <function tddft_excitation_energies>, <_sre.SRE_Pattern object>: <function tddft_excitation_energies_old>}, 'lmp2': {<_sre.SRE_Pattern object>: <function lmp2>, <_sre.SRE_Pattern object>: <function solvation>, <_sre.SRE_Pattern object>: <function gas_phase>, <_sre.SRE_Pattern object at 0x7dd5f10>: <function solution_phase>}, 'etit': {<_sre.SRE_Pattern object>: <function electron_transfer>}, 'gvblmp2': {<_sre.SRE_Pattern object>: <function rolmp2>, <_sre.SRE_Pattern object>: <function gvblmp2>}, None: {<_sre.SRE_Pattern object at 0x63c57c0>: <function fatal_error>, <_sre.SRE_Pattern object>: <function start_of_program>, <_sre.SRE_Pattern object>: <function glibc>, <_sre.SRE_Pattern object>: <function end_time>}, 'geopt': {<_sre.SRE_Pattern object at 0x80ef010>: <function nofail_geopt>, <_sre.SRE_Pattern object at 0x80eec20>: <function nofail_geopt_restart>, <_sre.SRE_Pattern object>: <function convergence_category>, <_sre.SRE_Pattern object at 0x6896190>: <function tddft_geopt_energy>, <_sre.SRE_Pattern object>: <function geopt_geometry>, <_sre.SRE_Pattern object at 0x8936490>: <function end_geometry>, <_sre.SRE_Pattern object at 0x80ed4a0>: <function stopping_optimization>, <_sre.SRE_Pattern object at 0x7af70c0>: <function nops_on>, <_sre.SRE_Pattern object>: <function z_variables>, <_sre.SRE_Pattern object at 0x8925b30>: <function sm_geometry>, <_sre.SRE_Pattern object at 0x807d290>: <function irc_summary>, <_sre.SRE_Pattern object at 0x80ec590>: <function irc_point>, <_sre.SRE_Pattern object>: <function geopt_stuck2>, <_sre.SRE_Pattern object at 0x6aad7f0>: <function geopt_stuck1>}, 'der1b': {<_sre.SRE_Pattern object at 0x6efa4f0>: <function forces>}, 'tddft_g': {<_sre.SRE_Pattern object at 0x6efa4f0>: <function forces>}, 'lmp2gb': {<_sre.SRE_Pattern object at 0x6efa4f0>: <function forces>}, 'onee': {<_sre.SRE_Pattern object at 0x8105600>: <function s_min_eval>, <_sre.SRE_Pattern object at 0x65927f0>: <function canorb>}, 'sole': {<_sre.SRE_Pattern object at 0x7dd5f10>: <function solution_phase>, <_sre.SRE_Pattern object at 0x6b8a1d0>: <function solvation>}, 'before pre': {<_sre.SRE_Pattern object>: <function jobid>}, 'cpolar': {<_sre.SRE_Pattern object>: <function beta_polar>, <_sre.SRE_Pattern object>: <function gamma_polar>, <_sre.SRE_Pattern object>: <function alpha_polar>}, 'freq': {<_sre.SRE_Pattern object at 0x80ea6c0>: <function frequencies_old>, <_sre.SRE_Pattern object at 0x61f73a0>: <function zpe>, <_sre.SRE_Pattern object at 0x828afc0>: <function frequencies>, <_sre.SRE_Pattern object at 0x6265f70>: <function get_vetted_vec_index>}, 'lmp2gdb': {<_sre.SRE_Pattern object at 0x6efa4f0>: <function forces>}, 'nude': {<_sre.SRE_Pattern object at 0x6efa4f0>: <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(jaguar_output=None)

Parse the provided file iterator.

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

Parameters

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)

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)