schrodinger.application.qsite.output module

A class for parsing of QSite output files.

This module provides a class QSiteOutput that holds the information from a QSite run.

class schrodinger.application.qsite.output.QSiteResults

Bases: schrodinger.application.jaguar.results.JaguarResults

energy_precision = 1e-06

class schrodinger.application.qsite.output.QSiteTextParser(jaguar_output, file_iter=None)

Bases: schrodinger.application.jaguar.textparser.TextParser

A subclass of the Jaguar output text parser that adds QSite specific parsing.

callback = {'ssccb': {re.compile('Pair\\s(?P<atom_pair_index>\\d+)\\:\\s+(?P<atom1_name>[a-zA-Z]+\\d+)\\s+\\((?P<atom1_iso>\\d+\\-[a-zA-Z]+)\\s+(?P<atom1_nuc_spin>-?[\\.\\d]+)\\s+(?P<atom1_nuc_dip>-?[\\.\\d]+)\\)\\s+\\<\\-\\-\\>\\s+(): <function ssccb>, re.compile('Summary of total isotropic spin-spin coupling \\(Hz\\)\\:'): <function ssccb_summary>}, 'pre': {re.compile('^\\s*Using up to\\s+(\\d+) threads per process'): <function nthreads>, re.compile('^&gen'): <function gensec>, re.compile('^&atomic'): <function atomicsec>, re.compile('net molecular charge:\\s+(-?\\d+)'): <function molchg>, re.compile('multiplicity:\\s+(\\d+)'): <function multip>, re.compile('number of basis functions\\.\\.\\.\\.\\s+(\\d+)'): <function nbasis>, re.compile('Molecular weight:\\s+([0-9.]+)'): <function mol_weight>, re.compile('Stoichiometry:\\s+(\\w+)'): <function stoichiometry>, re.compile('basis set:\\s+(\\S+)'): <function basis_set>, re.compile('Number of optimization coordinates:\\s+(\\d+)'): <function coords_opt>, re.compile('Number of independent coordinates:\\s+(\\d+)'): <function coords_ind>, re.compile('Number of non-redundant coordinates:\\s+(\\d+)'): <function coords_nred>, re.compile('Number of constrained coordinates:\\s+(\\d+)'): <function coords_frozen1>, re.compile('Number of frozen coordinates:\\s+(\\d+)'): <function coords_frozen2>, re.compile('Number of harmonic constraints:\\s+(\\d+)'): <function coords_harmonic>, re.compile('Solvation energy will be computed'): <function solvation_job>, re.compile('Numerical 2nd derivatives will be computed'): <function numerical_freqs>, re.compile('Electrostatic potential fit to point charges on atomic centers'): <function esp_fit_atoms>, re.compile('and bond midpoints'): <function esp_fit_atoms_and_bonds>, re.compile('(Input|new) geometry:'): <function start_geometry>, re.compile('Path geometry: \\(interpolated\\, X\\=.*\\)'): <function path_geometry>, re.compile('Z-variables: (.*)$'): <function z_variables>, re.compile('Maestro file \\(output\\):\\s+(\\S.*)'): <function mae>, re.compile('Maestro file \\(input\\):\\s+(\\S.*)'): <function mae_in>, re.compile('Molecular Point Group:\\s+(\\w+)'): <function point_group>, re.compile('Point Group used:\\s+(\\w+)'): <function point_group_used>, re.compile('Number of atoms treated by QM:\\s+(\\w+)'): <function qm_atoms>, re.compile('SCF calculation type: ([A-Za-z0-9/_-]+)'): <function calc_type>, re.compile('Post-SCF correlation type: (\\w+)'): <function correlation_type>, re.compile('DFT=(\\S+)\\s*(\\(.+\\))?'): <function functional>, re.compile('^ *User Defined Functional:'): <function custom_functional>, re.compile('Geometry from &zmat(2|3), &zvar(2|3)'): <function qst_geometries>, re.compile('Symmetrized geometry:'): <function symmetrized_geometry>, re.compile('Initial geometry: \\(interpolated\\)'): <function qst_initial_geometry>, re.compile('Geometry scan coordinates:(?:\\s*\\((angstroms|bohr) and (degrees|radians)\\))?'): <function scan_coordinates>, re.compile('Non-default print settings:'): <function non_default_print_options>, re.compile('Fully analytic SCF calculation: pseudospectral method not used'): <function pseudospectral>, re.compile('Total LO correction:\\s+(\\S+)\\s+kcal/mole'): <function total_lo_correction>, re.compile('Target molecule has a ligand field spin-splitting score of\\s+(\\S+)'): <function spin_splitting_score>, re.compile('rotational constants:'): <function rotational_constants>, re.compile('^Total number of atoms:\\s+(\\d+)'): <function total_atoms>, re.compile('^Number of atoms passed to Jaguar:\\s+(\\d+)'): <function jaguar_atoms>, re.compile('^Number of atoms treated by QM:\\s+(\\d+)'): <function qm_atoms>, re.compile('^Number of atoms treated by NDDO:\\s+(\\d+)'): <function nddo_atoms>, re.compile('^Number of hydrogen caps:\\s+(\\d+)'): <function nhcaps>, re.compile('^Number of NDDO hydrogen caps:\\s+(\\d+)'): <function nddo_hcaps>, re.compile('^Number of frozen orbital cuts:\\s+(\\d+)'): <function ncuts>, re.compile('^Number of constrained MM atoms:\\s+(\\d+)'): <function nconmm>, re.compile('^Number of frozen MM atoms:\\s+(\\d+)'): <function nfrzmm>}, 'scf': {re.compile('^\\s*number of electrons\\.+\\s+(\\d+)'): <function nelectron>, re.compile('^\\s*Sz\\*\\(Sz\\+1\\)[\\s\\.]+(\\S+)'): <function sz2>, re.compile('^\\s*<S\\*\\*2>[\\s\\.]+(\\S+)'): <function s2>, re.compile('^\\s*GVB:\\s+(\\S+)'): <function npair>, re.compile('(^etot.*$)'): <function etot>, re.compile('(?<!\\()SCFE.*\\s+(-?[\\.\\d]+)\\s+hartrees'): <function scfe>, re.compile('\\(B\\)\\s+Nuclear-nuclear\\.+\\s+(-?[\\.\\d]+)'): <function nucrep1>, re.compile('\\(A\\)\\s+Nuclear repulsion\\.+\\s+(-?[\\.\\d]+)'): <function nucrep2>, re.compile('\\(E\\)\\s+Total one-electron terms\\.+\\s+(-?[\\.\\d]+)'): <function one_e_terms>, re.compile('\\(I\\)\\s+Total two-electron terms\\.+\\s+(-?[\\.\\d]+)'): <function two_e_terms>, re.compile('\\(L\\)\\s+Electronic energy\\.+\\s+(-?[\\.\\d]+)'): <function electronic_e>, re.compile('\\(N0\\).*correction\\.+\\s+(-?[\\.\\d]+)'): <function aposteri_e>, re.compile('(Alpha|Beta)? HOMO energy:\\s+(\\S+)'): <function homo>, re.compile('(Alpha|Beta)? LUMO energy:\\s+(\\S+)'): <function lumo>, re.compile('(?P<type>Alpha|Beta)? Orbital energies( \\(hartrees\\))?(?P<label>/symmetry label)?:'): <function orbital_energies>, re.compile('Energy computed using (.*).'): <function nops_setting>, re.compile('Energy computed with NOPS on.'): <function nops_on>, re.compile('Energy computed with NOPS off.'): <function nops_off>, re.compile('\\s*No-fail mode: converged with (?P<settings>\\w+) settings'): <function nofail_mode>, re.compile('^\\sPCM solvation energy (electrostatic)\\.+\\s*(-?[\\.\\d]+)'): <function solvation>, re.compile('\\(V\\).*Solvation energy\\.+\\s*(-?[\\.\\d]+)'): <function solvation>, re.compile('^\\sSolution phase energy\\.+\\s*(-?[\\.\\d]+)'): <function solution_phase>, re.compile('\\(P\\).*Solution phase energy\\.+\\s*(-?[\\.\\d]+)'): <function solution_phase>, re.compile('^\\sGas phase energy\\.+\\s*(-?[\\.\\d]+)'): <function gas_phase>, re.compile('\\(O\\).*Gas phase energy\\.+\\s*(-?[\\.\\d]+)'): <function gas_phase>, re.compile('The zero point energy \\(ZPE\\):\\s+(\\S+) k(\\w+)/mol'): <function zpe>}, 'read_external_gradient': {re.compile('Energy From External Program \\(a\\.u\\.\\)\\s+(-?[\\.\\d]+)'): <function external_program_energy>}, 'nn_energy': {re.compile('ANI Gas-Phase Energy \\(a\\.u\\.\\)\\s+(-?[\\.\\d]+)'): <function nn_gas_energy>, re.compile('QRNN Gas-Phase Energy \\(a\\.u\\.\\)\\s+(-?[\\.\\d]+)'): <function nn_gas_energy>, re.compile('GFN2-xTB Gas-Phase Energy \\(a\\.u\\.\\)\\s+(-?[\\.\\d]+)'): <function nn_gas_energy>, re.compile('QRNN Solution-Phase Energy \\(a\\.u\\.\\)\\s+(-?[\\.\\d]+)'): <function nn_sol_energy>, re.compile('GFN2-xTB Solution-Phase Energy \\(a\\.u\\.\\)\\s+(-?[\\.\\d]+)'): <function nn_sol_energy>, re.compile('ANI Committee Standard Deviation \\(a\\.u\\.\\)\\s+(-?[\\.\\d]+)'): <function external_program_nn_energy_stddev>, re.compile('QRNN Committee Standard Deviation \\(a\\.u\\.\\)\\s+(-?[\\.\\d]+)'): <function external_program_nn_energy_stddev>, re.compile('Gradients From QRNN \\(a.u.\\)'): <function qrnn_forces>}, 'rimp2': {re.compile('RI-MP2 Energies, in hartrees'): <function rimp2_energies>}, 'lmp2': {re.compile('Total LMP2.*\\s+(-?[\\.\\d]+)'): <function mp2>, re.compile('\\(V\\).*Solvation energy\\.+\\s*(-?[\\.\\d]+)'): <function solvation>, re.compile('\\(P\\).*Solution phase energy\\.+\\s*(-?[\\.\\d]+)'): <function solution_phase>, re.compile('\\(O\\).*Gas phase energy\\.+\\s*(-?[\\.\\d]+)'): <function gas_phase>}, 'gvblmp2': {re.compile('Total LMP2.*\\s+(-?[\\.\\d]+)'): <function mp2>, re.compile('Total GVB-LMP2.*\\s+(-?[\\.\\d]+)'): <function gvblmp2>}, 'rolmp2': {re.compile('Total LMP2.*\\s+(-?[\\.\\d]+)'): <function mp2>}, 'scanner': {re.compile('(Input|new) geometry:'): <function start_geometry>, re.compile('end of geometry scan step'): <function end_scan>, re.compile('Geometry scan step\\s+\\d+\\s*:'): <function geometry_scan_step>}, 'geopt': {re.compile('^  gradient maximum:\\s*(\\S+) .  \\(\\s*(\\S+)\\s+\\)'): <function geopt_convcrit>, re.compile('^  energy change:\\s*(\\S+) .  \\(\\s*(\\S+)\\s+\\)'): <function geopt_convcrit>, re.compile('new geometry:'): <function geopt_geometry>, re.compile('String geometry: \\(iteration=.* point=.*energy=.*\\)'): <function sm_geometry>, re.compile('end of geometry optimization iteration'): <function end_geometry>, re.compile('(stopping optimization: maximum number of iterations reached|Geometry optimization complete)'): <function stopping_optimization>, re.compile('optimization seems to be stuck'): <function geopt_stuck1>, re.compile('Convergence category (\\d+)'): <function convergence_category>, re.compile('IRC point found -\\s+(Forward|Reverse|Downhill)\\s+#\\s+(\\d+)'): <function irc_point>, re.compile('Summary of IRC Reaction Path:'): <function irc_summary>, re.compile('restarting optimization from step'): <function doubted_geom>, re.compile('[Gg]eometry optimization step\\s+(\\d+)'): <function geopt_step_number>, re.compile('Setting nops=0, recomputing energy'): <function geopt_nops_on>, re.compile('to be a stuck geometry'): <function geopt_stuck2>, re.compile('SCF will be redone to get proper energy & wavefunction.'): <function nofail_geopt_restart>, re.compile('Taking the geometry with the lowest energy \\(iteration (\\d+)\\)'): <function nofail_geopt>, re.compile('Z-variables: (.*)$'): <function z_variables>, re.compile('First excited state energy:\\s+(\\S+) hartrees'): <function tddft_geopt_energy>, re.compile('rotational constants:'): <function rotational_constants>}, 'tddft_g': {re.compile('forces \\(hartrees/bohr\\) : (total|numerical)'): <function forces>}, 'rimp2g': {re.compile('forces \\(hartrees/bohr\\) : (total|numerical)'): <function forces>}, 'der1b': {re.compile('forces \\(hartrees/bohr\\) : (total|numerical)'): <function forces>}, 'lmp2gb': {re.compile('forces \\(hartrees/bohr\\) : (total|numerical)'): <function forces>}, 'lmp2gdb': {re.compile('forces \\(hartrees/bohr\\) : (total|numerical)'): <function forces>}, 'nude': {re.compile('forces \\(hartrees/bohr\\) : (total|numerical)'): <function forces>}, 'sole': {re.compile('\\(V\\).*Solvation energy\\.+\\s*(-?[\\.\\d]+).*\\(P-O\\)'): <function solvation>, re.compile('\\(P\\).*Solution phase energy\\.+\\s*(-?[\\.\\d]+)'): <function solution_phase>}, 'onee': {re.compile('number of canonical orbitals\\.\\.\\.\\.\\.\\s+(\\d+)'): <function canorb>, re.compile('smallest eigenvalue of S:\\s+(\\S+)'): <function s_min_eval>, re.compile('^  bond-charge repulsion energy\\.+\\s+(\\S+) '): <function bondchg_repulsion_energy>}, 'ch': {re.compile('Atomic charges from electrostatic potential'): <function esp_charges>, re.compile('Atomic charges from Lowdin population analysis'): <function lowdin_charges>, re.compile('Atomic Spin Densities from Lowdin analysis'): <function lowdin_spins>, re.compile('Atomic charges from Mulliken population analysis'): <function mulliken_charges>, re.compile('Atomic Spin Densities from Mulliken analysis'): <function mulliken_spins>, re.compile('Stockholder charges from Hirshfeld partitioning'): <function stockholder_charges>, re.compile('Moments from quantum mechanical wavefunction'): <function multipole_qm>, re.compile('Moments from electrostatic potential charges'): <function multipole_esp>, re.compile('Moments from Mulliken charges'): <function multipole_mulliken>, re.compile('Atomic Fukui indices'): <function fukui_indices>}, 'etit': {re.compile('^   Reading '): <function electron_transfer>}, 'fdpol': {re.compile('polarizability \\(in AU\\) alpha\\(\\s+([0-9.-]+) eV;\\s+([0-9.-]+) eV'): <function alpha_fdpolar>, re.compile('hyperpolarizability \\(in AU\\) beta\\(\\s+([0-9.-]+) eV;'): <function beta_fdpolar>}, 'polar': {re.compile('^  polarizability \\(in AU\\):'): <function alpha_polar>}, 'cpolar': {re.compile('^  polarizability \\(in AU\\):'): <function alpha_polar>, re.compile('^  first hyperpolarizability \\(in AU\\):'): <function beta_polar>, re.compile('^  second hyperpolarizability \\(in AU\\):'): <function gamma_polar>}, 'elden': {re.compile('\\s+Density isovalue:\\s+(-?\\d+.\\d+) electrons/bohr\\*\\*3,'): <function isovalue>, re.compile('\\s+Area of molecular surface:\\s+(-?\\d+.\\d+) bohr\\*\\*2,\\s+(-?\\d+.\\d+) A\\*\\*2'): <function mol_area>, re.compile('\\s+Volume of molecular surface:\\s+(-?\\d+.\\d+) bohr\\*\\*3,\\s+(-?\\d+.\\d+) A\\*\\*3'): <function mol_volume>, re.compile('^  Electrostatic Potential at the Nuclei'): <function epn>, re.compile('^  Analysis of ESP on isodensity surface:'): <function esp_analysis>, re.compile('^  Analysis of ALIE on isodensity surface:'): <function alie_analysis>}, 'nmrcphf': {re.compile('NMR Properties for atom\\s+(\\S+)'): <function get_nmr>}, 'cis': {re.compile('CI size ='): <function cis_excitation_energies>}, 'sotdener': {re.compile('Ground State Dipole Moments'): <function initialize_tddft>, re.compile('(.*)Excited State\\s+\\d+:\\s+$'): <function tddft_excitation_properties>}, 'tdener': {re.compile('Ground State Dipole Moments'): <function initialize_tddft>, re.compile('(.*)Excited State\\s+\\d+:\\s+$'): <function tddft_excitation_properties>, re.compile('  Total number of HSOs between singlet and triplet:\\s*\\d+$'): <function hso_singlet_triplet>}, 'stdener': {re.compile('Ground State Dipole Moments'): <function initialize_tddft>, re.compile('(.*)Excited State\\s+\\d+:\\s+$'): <function tddft_excitation_properties>}, 'stability_analysis': {re.compile('.HF/.KS solution is (\\S+)\\s+(\\S+)'): <function wf_stability_eigenvalues>}, 'freq': {re.compile('The zero point energy \\(ZPE\\):\\s+(\\S+) k(\\w+)/mol'): <function zpe>, re.compile('Valid transition vector #\\s+(\\b[0-9]+\\b)'): <function get_vetted_vec_index>, re.compile('normal modes in mass-weighted cartesian coordinates:\\s+(\\d+)'): <function frequencies>, re.compile('normal modes in cartesian coordinates:\\s+(\\d+)'): <function frequencies>, re.compile('normal modes in cartesian coordinates:\\s+$'): <function frequencies_old>, re.compile('\\s*rotational symmetry number:\\s+([0-9]+)'): <function symmetry_number>}, 'before pre': {re.compile('^JobId:\\s+(\\S+)', re.IGNORECASE|re.MULTILINE): <function jobid>}, None: {re.compile('start of program (\\w+)'): <function start_of_program>, re.compile('glibc:\\s+(\\S+)'): <function glibc>, re.compile('\\s+Summary of Natural Population Analysis:'): <function nbo_charges>, re.compile('\\s+Total cpu seconds\\s+user:\\s+(?P<cpu_duration>[\\.\\d]+)\\s+user\\+sys:\\s+(?P<cpu_sys_duration>[\\.\\d]+)'): <function cpu_time>, re.compile('Time\\((?P<routine>\\w+)\\)\\s+user:\\s+(?P<utime>\\d+\\.\\d+)\\s+user\\+sys:\\s+(?P<systime>\\d+\\.\\d+)\\s+wallclock:\\s+(?P<clocktime>\\d+\\.\\d+)'): <function routine_time>, re.compile('Job .+ completed on \\S+ at (\\w.*)$'): <function end_time>, re.compile('ERROR *(\\d+)?: fatal error( -- debug information follows)?'): <function fatal_error>, re.compile('\\s+MEMINIT: failed to allocate *(\\d+)? words of dynamic memory'): <function nbo_mem_failure>}, 'impact': {re.compile(' calling (\\S+)\\s+atomtyping'): <function ffld>, re.compile('^ Cutoff radius:\\s+(\\S+)'): <function nb_cutoff>, re.compile('^ Update frequency: every\\s+(\\d+) '): <function nb_update>, re.compile('^ Total Energy of the system\\.+\\s+(\\S+) '): <function total_energy>, re.compile('^ Total Potential Energy\\.+\\s+(\\S+) '): <function total_potential_energy>, re.compile('^ Total Kinetic Energy\\.+\\s+(\\S+) '): <function total_kinetic_energy>, re.compile('^ Bond Stretch Energy\\.+\\s+(\\S+) '): <function bond_stretch_energy>, re.compile('^ Angle Bending Energy\\.+\\s+(\\S+) '): <function angle_bend_energy>, re.compile('^ Torsion Angle Energy\\.+\\s+(\\S+) '): <function torsion_energy>, re.compile('^ 1,4 Lennard Jones Energy\\.+\\s+(\\S+) '): <function lj14_energy>, re.compile('^ 1,4 Electrostatic Energy\\.+\\s+(\\S+) '): <function electrostatic14_energy>, re.compile('^ Lennard Jones Energy\\.+\\s+(\\S+) '): <function lj_energy>, re.compile('^ Electrostatic Energy\\.+\\s+(\\S+) '): <function electrostatic_energy>, re.compile('^ H-bond Energy\\.+\\s+(\\S+) '): <function hbond_energy>, re.compile('^ QM/MM Electrostatic Energy\\.+\\s+(\\S+) '): <function qmmm_electrostatic_energy>, re.compile('^ QM/MM Stretch Energy\\.+\\s+(\\S+) '): <function qmmm_stretch_energy>, re.compile('^ QM/MM Bend Energy\\.+\\s+(\\S+) '): <function qmmm_bend_energy>, re.compile('^ QM/MM Torsion Energy\\.+\\s+(\\S+) '): <function qmmm_torsion_energy>}}

class schrodinger.application.qsite.output.QSiteOutput(output: Optional[str] = None, partial_ok: bool = False, timing_thresh: Optional[Dict[str, float]] = None)

Bases: schrodinger.application.jaguar.output.JaguarOutput

A class to hold output information from a QSite run.

schrodinger.application.qsite.output.callback(prog, regexp=None, debug=False)

A decorator based on the Jaguar output callback decorator, but that adds the callbacks to the QSiteTextParser instead.

schrodinger.application.qsite.output.ffld(tp, qo, m, it)

schrodinger.application.qsite.output.nb_cutoff(tp, qo, m, it)

schrodinger.application.qsite.output.nb_update(tp, qo, m, it)

schrodinger.application.qsite.output.total_energy(tp, qo, m, it)

schrodinger.application.qsite.output.total_potential_energy(tp, qo, m, it)

schrodinger.application.qsite.output.total_kinetic_energy(tp, qo, m, it)

schrodinger.application.qsite.output.bond_stretch_energy(tp, qo, m, it)

schrodinger.application.qsite.output.angle_bend_energy(tp, qo, m, it)

schrodinger.application.qsite.output.torsion_energy(tp, qo, m, it)

schrodinger.application.qsite.output.lj14_energy(tp, qo, m, it)

schrodinger.application.qsite.output.electrostatic14_energy(tp, qo, m, it)

schrodinger.application.qsite.output.lj_energy(tp, qo, m, it)

schrodinger.application.qsite.output.electrostatic_energy(tp, qo, m, it)

schrodinger.application.qsite.output.hbond_energy(tp, qo, m, it)

schrodinger.application.qsite.output.qmmm_electrostatic_energy(tp, qo, m, it)

schrodinger.application.qsite.output.qmmm_stretch_energy(tp, qo, m, it)

schrodinger.application.qsite.output.qmmm_bend_energy(tp, qo, m, it)

schrodinger.application.qsite.output.qmmm_torsion_energy(tp, qo, m, it)

schrodinger.application.qsite.output.total_atoms(tp, qo, m, it)

schrodinger.application.qsite.output.jaguar_atoms(tp, qo, m, it)

schrodinger.application.qsite.output.qm_atoms(tp, qo, m, it)

schrodinger.application.qsite.output.nddo_atoms(tp, qo, m, it)

schrodinger.application.qsite.output.nhcaps(tp, qo, m, it)

schrodinger.application.qsite.output.nddo_hcaps(tp, qo, m, it)

schrodinger.application.qsite.output.ncuts(tp, qo, m, it)

schrodinger.application.qsite.output.nconmm(tp, qo, m, it)

schrodinger.application.qsite.output.nfrzmm(tp, qo, m, it)

schrodinger.application.qsite.output.bondchg_repulsion_energy(tp, qo, m, it)