Package schrodinger :: Package application :: Package jaguar :: Module output

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Module output

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

Classes

[hide private]

__metaclass__
type(object) -> the object's type type(name, bases, dict) -> a new type

IncompleteOutput
Indicators that the output is incomplete.

Dipole
A class for storing dipole information.

ZVariables
A class to store Z-variables and their values, generated in scan jobs.

ThermoProp
A class to store the components of calculated thermodynamic properties.

ThermoCollection
A class to store a full set of calculated thermodynamic properties at a given temperature.

NormalMode

JaguarOptions
A class for keeping track of specific calculation options.

_Attribute
A small utility class to automate and regularize handling of attributes.

JaguarResults
A class for holding results for a specific geometry.

JaguarAtomicResults
A class for holding atomic level properties.

BondCharge
A class to store bond-midpoint charges calculated in ESP fitting.

FukuiIndices
A class to store Atomic Fukui indices.

JaguarOutput

Orbital
A class for storing orbital information.

ScfIteration
A simple storage class for storing info on an SCF iteration.

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

JaguarParseError

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

CaseInsensitiveString
A class that behaves like a regular string except that comparisons are done on a case insensitive basis.

Functions

[hide private]

join_structure_files(name, files)
Pull the CTs out of each .mae file in the 'files' list and put them into a new .mae file called 'name', which is expected to already contain the .mae extension.

restart_name(name)
Generate a restart name from a job name.

compare_float(a, b, precision)
Compare two floats to the specified precision.

_diff(a, b, short_circuit=False, factor=1.0)
A general function for comparing the attributes of two objects.

get_attribute_alias(current_attr, old_attr)
Return a function to act as an attribute alias.

add_attribute_aliases(class_)
Add attribute aliases to a class based on what's recorded in its _attributes list.

textparser_trace(func)
A decorator that will print the callback function name when it is called.

callback(prog, regexp=None, debug=False, parser_class=TextParser)
A decorator to add a function to the TextParser callback dictionary.

molchg(tp, jo, m, it)

multip(tp, jo, m, it)

nbasis(tp, jo, m, it)

mol_weight(tp, jo, m, it)

stoichiometry(tp, jo, m, it)

basis_set(tp, jo, m, it)

coords_opt(tp, jo, m, it)

coords_ind(tp, jo, m, it)

coords_nred(tp, jo, m, it)

coords_frozen(tp, jo, m, it)

coords_harmonic(tp, jo, m, it)

solvation_job(tp, jo, m, it)

numerical_freqs(tp, jo, m, it)

esp_fit_atoms(tp, jo, m, it)

esp_fit_atoms_and_bonds(tp, jo, m, it)

etot(tp, jo, m, it)

scfe(tp, jo, m, it)

nucrep(tp, jo, m, it)

one_e_terms(tp, jo, m, it)

two_e_terms(tp, jo, m, it)

electronic_e(tp, jo, m, it)

aposteri_e(tp, jo, m, it)

homo(tp, jo, m, it)

lumo(tp, jo, m, it)

orbital_energies(tp, jo, m, it)

lmp2(tp, jo, m, it)

rolmp2(tp, jo, m, it)

gvblmp2(tp, jo, m, it)

start_geometry(tp, jo, m, it)

geopt_geometry(tp, jo, m, it)

path_geometry(tp, jo, m, it)

sm_geometry(tp, jo, m, it)

geometry_read(it, charge=None)
A utility function to read an input cartesian geometry from the output file.

end_geometry(tp, jo, m, it)

stopping_optimization(tp, jo, m, it)

geopt_stuck(tp, jo, m, it)

convergence_category(tp, jo, m, it)

irc_point(tp, jo, m, it)

irc_summary(tp, jo, m, it)

z_variables(tp, jo, m, it)

forces(tp, jo, m, it)

solvation(tp, jo, m, it)

solution_phase(tp, jo, m, it)

canorb(tp, jo, m, it)

s_min_eval(tp, jo, m, it)

end_scan(tp, jo, m, it)

mae(tp, jo, m, it)

mae_in(tp, jo, m, it)

point_group(tp, jo, m, it)

point_group_used(tp, jo, m, it)

qm_atoms(tp, jo, m, it)

calc_type(tp, jo, m, it)

correlation_type(tp, jo, m, it)

functional(tp, jo, m, it)

custom_functional(tp, jo, m, it)

qst_geometries(tp, jo, m, it)

_store_input_geometry(jo, it)
Store a Structure object at jo.input_geometry for the input geometry, then replace the initial geometry with the new one.

symmetrized_geometry(tp, jo, m, it)

qst_initial_geometry(tp, jo, m, it)

scan_coordinates(tp, jo, m, it)

geometry_scan_step(tp, jo, m, it)

non_default_print_options(tp, jo, m, it)

pseudospectral(tp, jo, m, it)

gen_charges(attr, tp, jo, m, it)

esp_charges(tp, jo, m, it)

mulliken_charges(tp, jo, m, it)

multipole_moments(type_, tp, jo, m, it)

multipole_qm(tp, jo, m, it)

multipole_esp(tp, jo, m, it)

multipole_mulliken(tp, jo, m, it)

fukui_indices(tp, jo, m, it)

electron_transfer(tp, jo, m, it)

alpha_polar(tp, jo, m, it)

beta_polar(tp, jo, m, it)

gamma_polar(tp, jo, m, it)

epn(tp, jo, m, it)

esp_analysis(tp, jo, m, it)

alie_analysis(tp, jo, m, it)

get_nmr(tp, jo, m, it)

cis_excitation_energies(tp, jo, m, it)

tddft_excitation_energies(tp, jo, m, it)

zpe(tp, jo, m, it)

thermo_helper(temp, it)
Parse a thermochemical properties section and return a ThermoCollection object.

frequencies(tp, jo, m, it)

jobid(tp, jo, m, it)

start_of_program(tp, jo, m, it)

glibc(tp, jo, m, it)

end_time(tp, jo, m, it)

fatal_error(tp, jo, m, it)

Variables

[hide private]

__cvs_version__ = "$Revision: 1.77 $"

restart_re = re.compile(r"^(.+)\.(\d\d)$")

blank_line_re = re.compile(r"^\s*$")

zvar_tags_re = re.compile(r"[\*#]")

input_geometry_re = re.compile(r"^\s+Input geometry:")

_log = logging.getLogger("schrodinger.application.jaguar.output")

unHartree = "Hartree"

unHartreePerBohr = "Hartree/Bohr"

unAtomicMassUnit = "amu"

unDebye = "Debye"

unKcalPerMol = "kcal/mol"

unAngstrom = "Angstrom"

unBohr = "Bohr"

unDegree = "degree"

unRadian = "radian"

unInverseCentimeter = "1/cm"

unMDynePerAngstrom = "mDyne/Angstrom"

unKilometersPerMol = "km/mol"

unDipoleStrength = "DSU"

unRotationalStrength = "RSU"

unAngstrom4 = "Angstrom^4"

ctHF = "HF"

ctUHF = "UHF"

ctROHF = "ROHF"

ctDFT = "DFT"

ctUDFT = "UDFT"

ctRODFT = "RODFT"

ctGVB = "GVB"

ctGVBLMP2 = "GVB/LMP2"

ctGVBRCI = "GVB/RCI"

ctLMP2 = "LMP2"

ctROHFLMP2 = "ROHF/LMP2"

ctUSER = "USER_HAM"

ctATOMICAVG = "ATOMIC-AVG"

ctOSS = "OSS"

ctNDDO = "NDDO"

_calc_types = set((ctHF, ctUHF, ctROHF, ctDFT, ctUDFT, ctRODFT...

textparser_debug = False
hash(x)

Function Details

[hide private]

join_structure_files(name, files)

Pull the CTs out of each .mae file in the 'files' list and put them into a new .mae file called 'name', which is expected to already contain the .mae extension. If a file called 'name' already exists, it will be overwritten.

restart_name(name)

Generate a restart name from a job name. If there is no number suffix for the job this will be jobname.01; otherwise the suffix will be incremented.

_diff(a, b, short_circuit=False, factor=1.0)


A general function for comparing the attributes of two objects.

Return a set of attribute names that fail the equality test.

The interface the objects must provide is as follows:
    1) A list of _Attribute instances stored under the attribute name
       '_attributes'.
    2) A named attribute for any named precision in _Attributes that
       have float or list comparisons.

Parameters

short_circuit (bool)
    If True, return as soon as a difference is found.

factor (float)
    A constant factor to use to loosen floating point comparisons by.

callback(prog, regexp=None, debug=False, parser_class=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.

molchg(tp, jo, m, it)

Decorators:

@callback("pre", r"net molecular charge:\s+(-?\d+)")

multip(tp, jo, m, it)

Decorators:

@callback("pre", r"multiplicity:\s+(\d+)")

nbasis(tp, jo, m, it)

Decorators:

@callback("pre", r"number of basis functions\.\.\.\.\s+(\d+)")

mol_weight(tp, jo, m, it)

Decorators:

@callback("pre", r"Molecular weight:\s+([0-9.]+)")

stoichiometry(tp, jo, m, it)

Decorators:

@callback("pre", r"Stoichiometry:\s+(\w+)")

basis_set(tp, jo, m, it)

Decorators:

@callback("pre", r"basis set:\s+(\S+)")

coords_opt(tp, jo, m, it)

Decorators:

@callback("pre", r"Number of optimization coordinates:\s+(\d+)")

coords_ind(tp, jo, m, it)

Decorators:

@callback("pre", r"Number of independent coordinates:\s+(\d+)")

coords_nred(tp, jo, m, it)

Decorators:

@callback("pre", r"Number of non-redundant coordinates:\s+(\d+)")

coords_frozen(tp, jo, m, it)

Decorators:

@callback("pre", r"Number of frozen coordinates:\s+(\d+)")

coords_harmonic(tp, jo, m, it)

Decorators:

@callback("pre", r"Number of harmonic constraints:\s+(\d+)")

solvation_job(tp, jo, m, it)

Decorators:

@callback("pre", r"Solvation energy will be computed")

numerical_freqs(tp, jo, m, it)

Decorators:

@callback("pre", "Numerical 2nd derivatives will be computed")

esp_fit_atoms(tp, jo, m, it)

Decorators:

@callback("pre", "Electrostatic potential fit to point charges on atomic centers")

esp_fit_atoms_and_bonds(tp, jo, m, it)

Decorators:

@callback("pre", "and bond midpoints")

etot(tp, jo, m, it)

Decorators:

@callback("scf", r"(^etot.*$)")

scfe(tp, jo, m, it)

Decorators:

@callback("scf", r"SCFE.*\s+(-?[\.\d]+)\s+hartrees")

nucrep(tp, jo, m, it)

Decorators:

@callback("scf", r"$A$\s+Nuclear repulsion\.+\s+(-?[\.\d]+)")

one_e_terms(tp, jo, m, it)

Decorators:

@callback("scf", r"$E$\s+Total one-electron terms\.+\s+(-?[\.\d]+)")

two_e_terms(tp, jo, m, it)

Decorators:

@callback("scf", r"$I$\s+Total two-electron terms\.+\s+(-?[\.\d]+)")

electronic_e(tp, jo, m, it)

Decorators:

@callback("scf", r"$L$\s+Electronic energy\.+\s+(-?[\.\d]+)")

aposteri_e(tp, jo, m, it)

Decorators:

@callback("scf", r"$N0$.*correction\.+\s+(-?[\.\d]+)")

homo(tp, jo, m, it)

Decorators:

@callback("scf", r"(Alpha|Beta)? HOMO energy:\s+(\S+)")

lumo(tp, jo, m, it)

Decorators:

@callback("scf", r"(Alpha|Beta)? LUMO energy:\s+(\S+)")

orbital_energies(tp, jo, m, it)

Decorators:

@callback("scf", r"(?PAlpha|Beta)? Orbital energies" r"( $hartrees$)?(?P/symmetry label)?:")

lmp2(tp, jo, m, it)

Decorators:

@callback("lmp2", r"Total LMP2.*\s+(-?[\.\d]+)")

rolmp2(tp, jo, m, it)

Decorators:

@callback("gvblmp2", r"Total LMP2.*\s+(-?[\.\d]+)")

gvblmp2(tp, jo, m, it)

Decorators:

@callback("gvblmp2", r"Total GVB-LMP2.*\s+(-?[\.\d]+)")

start_geometry(tp, jo, m, it)

Decorators:

@callback("pre")
@callback("scanner", r"(Input|new) geometry:")

geopt_geometry(tp, jo, m, it)

Decorators:

@callback("geopt", r"new geometry:")

path_geometry(tp, jo, m, it)

Decorators:

@callback("pre", r"Path geometry: $interpolated\, X\=.*$")

sm_geometry(tp, jo, m, it)

Decorators:

@callback("geopt", r"String geometry: $iteration=.* point=.*energy=.*$")

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.

end_geometry(tp, jo, m, it)

Decorators:

@callback("geopt", r"end of geometry optimization iteration")

stopping_optimization(tp, jo, m, it)

Decorators:

@callback("geopt", r"(stopping optimization: maximum number of iterations reached|Geometry optimization complete)")

geopt_stuck(tp, jo, m, it)

Decorators:

@callback("geopt", r"optimization seems to be stuck")

convergence_category(tp, jo, m, it)

Decorators:

@callback("geopt", r"Convergence category (\d+)")

irc_point(tp, jo, m, it)

Decorators:

@callback("geopt", r"IRC point found -\s+(Forward|Reverse|Downhill)\s+#\s+(\d+)")

irc_summary(tp, jo, m, it)

Decorators:

@callback("geopt", r"Summary of IRC Reaction Path:")

z_variables(tp, jo, m, it)

Decorators:

@callback("pre")
@callback("geopt", r"Z-variables: (.*)$")

forces(tp, jo, m, it)

Decorators:

@callback("nude")
@callback("lmp2gdb")
@callback("lmp2gb")
@callback("der1b", r"forces $hartrees/bohr$ : (total|numerical)")

solvation(tp, jo, m, it)

Decorators:

@callback("lmp2")
@callback("scf", r"$V$.*Solvation energy\.+\s*(-?[\.\d]+)")
@callback("sole", r"$V$.*Solvation energy\.+\s*(-?[\.\d]+).*$P-O$")

solution_phase(tp, jo, m, it)

Decorators:

@callback("lmp2")
@callback("scf", r"$P$.*Solution phase energy\.+\s*(-?[\.\d]+)")
@callback("sole", r"$P$.*Solution phase energy\.+\s*(-?[\.\d]+)")

canorb(tp, jo, m, it)

Decorators:

@callback("onee", r"number of canonical orbitals\.\.\.\.\.\s+(\d+)")

s_min_eval(tp, jo, m, it)

Decorators:

@callback("onee", r"smallest eigenvalue of S:\s+(\S+)")

end_scan(tp, jo, m, it)

Decorators:

@callback("scanner", r"end of geometry scan step")

mae(tp, jo, m, it)

Decorators:

@callback("pre", r"Maestro file $output$:\s+(\S+)")

mae_in(tp, jo, m, it)

Decorators:

@callback("pre", r"Maestro file $input$:\s+(\S+)")

point_group(tp, jo, m, it)

Decorators:

@callback("pre", r"Molecular Point Group:\s+(\w+)")

point_group_used(tp, jo, m, it)

Decorators:

@callback("pre", r"Point Group used:\s+(\w+)")

qm_atoms(tp, jo, m, it)

Decorators:

@callback("pre", r"Number of atoms treated by QM:\s+(\w+)")

calc_type(tp, jo, m, it)

Decorators:

@callback("pre", r"SCF calculation type: ([A-Z/_-]+)")

correlation_type(tp, jo, m, it)

Decorators:

@callback("pre", r"Post-SCF correlation type: (\w+)")

functional(tp, jo, m, it)

Decorators:

@callback("pre", r"DFT=(\S+)\s*($.+$)?")

custom_functional(tp, jo, m, it)

Decorators:

@callback("pre", r"^ *User Defined Functional:")

qst_geometries(tp, jo, m, it)

Decorators:

@callback("pre", r"Geometry from &zmat(2|3), &zvar(2|3)")

symmetrized_geometry(tp, jo, m, it)

Decorators:

@callback("pre", r"Symmetrized geometry:")

qst_initial_geometry(tp, jo, m, it)

Decorators:

@callback("pre", r"Initial geometry: $interpolated$")

scan_coordinates(tp, jo, m, it)

Decorators:

@callback("pre", r"Geometry scan coordinates:(?:\s*$(angstroms|bohr) and "+ r"(degrees|radians)$)?")

geometry_scan_step(tp, jo, m, it)

Decorators:

@callback("scanner", r"Geometry scan step\s+\d+\s*:")

non_default_print_options(tp, jo, m, it)

Decorators:

@callback("pre", r"Non-default print settings:")

pseudospectral(tp, jo, m, it)

Decorators:

@callback("pre", r"Fully analytic SCF calculation: pseudospectral method not used")

esp_charges(tp, jo, m, it)

Decorators:

@callback("ch", r"Atomic charges from electrostatic potential")

mulliken_charges(tp, jo, m, it)

Decorators:

@callback("ch", r"Atomic charges from Mulliken population analysis")

multipole_qm(tp, jo, m, it)

Decorators:

@callback("ch", r"Moments from quantum mechanical wavefunction")

multipole_esp(tp, jo, m, it)

Decorators:

@callback("ch", r"Moments from electrostatic potential charges")

multipole_mulliken(tp, jo, m, it)

Decorators:

@callback("ch", r"Moments from Mulliken charges")

fukui_indices(tp, jo, m, it)

Decorators:

@callback("ch", r"Atomic Fukui indices")

electron_transfer(tp, jo, m, it)

Decorators:

@callback("etit", r"^ Reading ")

alpha_polar(tp, jo, m, it)

Decorators:

@callback("cpolar", r"^ polarizability $in AU$:")

beta_polar(tp, jo, m, it)

Decorators:

@callback("cpolar", r"^ first hyperpolarizability $in AU$:")

gamma_polar(tp, jo, m, it)

Decorators:

@callback("cpolar", r"^ second hyperpolarizability $in AU$:")

epn(tp, jo, m, it)

Decorators:

@callback("elden", r"^ Electrostatic Potential at the Nuclei")

esp_analysis(tp, jo, m, it)

Decorators:

@callback("elden", r"^ Analysis of ESP on isodensity surface:")

alie_analysis(tp, jo, m, it)

Decorators:

@callback("elden", r"^ Analysis of ALIE on isodensity surface:")

get_nmr(tp, jo, m, it)

Decorators:

@callback("nmrcphf", r"solving first-order CPHF")

cis_excitation_energies(tp, jo, m, it)

Decorators:

@callback("cis", r"CI size =")

tddft_excitation_energies(tp, jo, m, it)

Decorators:

@callback("tdener", r"Excitation energy")

zpe(tp, jo, m, it)

Decorators:

@callback("freq", r"The zero point energy $ZPE$:\s+(\S+) kcal/mol")

frequencies(tp, jo, m, it)

Decorators:

@callback("freq", r"normal modes in cartesian coordinates:")

start_of_program(tp, jo, m, it)

Decorators:

@callback(None, r"start of program (\w+)")

glibc(tp, jo, m, it)

Decorators:

@callback(None, r"glibc:\s+(\S+)")

end_time(tp, jo, m, it)

Decorators:

@callback(None, r"Job \S+ completed on \S+ at (\w.*)$")

fatal_error(tp, jo, m, it)

Decorators:

@callback(None, r"ERROR *(\d+)?: fatal error( -- debug information follows)?")

Variables Details

[hide private]

_calc_types

Value:

set((ctHF, ctUHF, ctROHF, ctDFT, ctUDFT, ctRODFT, ctGVB, ctGVBLMP2, ct
GVBRCI, ctLMP2, ctROHFLMP2, ctUSER, ctATOMICAVG, ctOSS, ctNDDO))