schrodinger.application.jaguar.results module¶
Classes for parsing Jaguar output files and accessing output properties programmatically.
Copyright Schrodinger, LLC. All rights reserved.
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exception
schrodinger.application.jaguar.results.
IncompleteOutput
¶ Bases:
RuntimeError
Indicators that the output is incomplete.
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schrodinger.application.jaguar.results.
get_attribute_alias
(current_attr, old_attr)¶ Return a function to act as an attribute alias.
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schrodinger.application.jaguar.results.
add_attribute_aliases
(class_)¶ Add attribute aliases to a class based on what’s recorded in its _attributes list.
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class
schrodinger.application.jaguar.results.
JaguarAtomicResults
(index, name)¶ Bases:
object
A class for holding atomic level properties.
Attributes
- forces (list of floats, Hartree/Bohr)
- Atomic forces.
- charge_esp (float)
- Electrostatic potential charge.
- charge_mulliken (float)
- Mulliken charge.
- fukui_indices (FukuiIndices)
- Fukui indices.
- nmr_shielding (float)
- NMR shielding.
- maxat_esp (float)
- Max atomic ESP value on molecular surface.
- minat_esp (float)
- Min atomic ESP value on molecular surface.
- maxat_alie (float)
- Max atomic ALIE value on molecular surface.
- minat_alie (float)
- Min atomic ALIE value on molecular surface.
- epn (float)
- Electrostatic potential at the nucleus.
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forces_precision
= 0.0001¶
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charge_precision
= 5e-05¶
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nmr_precision
= 0.01¶
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esp_precision
= 0.01¶
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alie_precision
= 0.01¶
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epn_precision
= 0.01¶
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diff
(other, short_circuit=False, factor=1.0)¶ Return a list of differing attributes.
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class
schrodinger.application.jaguar.results.
BondCharge
(name, charge)¶ Bases:
object
A class to store bond-midpoint charges calculated in ESP fitting.
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precision
= 5e-05¶
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cmp
(other)¶
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class
schrodinger.application.jaguar.results.
FukuiIndices
(homo_nn, homo_ns, homo_sn, homo_ss, lumo_nn, lumo_ns, lumo_sn, lumo_ss)¶ Bases:
object
A class to store Atomic Fukui indices.
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precision
= 0.01¶
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class
schrodinger.application.jaguar.results.
Orbital
(energy, symmetry=None)¶ Bases:
object
A class for storing orbital information.
Attributes
energy (float, Hartrees)
symmetry (str)
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precision
= 0.0001¶
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cmp
(that)¶ Compare on orbital energy and the non-reduced symmetry.
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class
schrodinger.application.jaguar.results.
ScfIteration
(updt, diis, icut, grid, energy, energy_change, rms_density_change, max_diis_error)¶ Bases:
object
A simple storage class for storing info on an SCF iteration.
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header
= ' i u d i g\n t p i c r RMS maximum\n e d i u i energy density DIIS\n r t s t d total energy change change error\n\n'¶
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static
fromEtotString
(etot_string)¶ Create an instance from a standard etot string.
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toString
(iter=0)¶ Render as a string, with optional iteration number.
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class
schrodinger.application.jaguar.results.
Dipole
(x, y, z, magnitude=None)¶ Bases:
object
A class for storing dipole information.
Attributes:
- magnitude (float, Debye)
- The magnitude of the dipole moment.
- x, y, z (float, Debye)
- The x, y, z components of the dipole moment.
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precision
= 0.0001¶
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cmp
(other)¶
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class
schrodinger.application.jaguar.results.
ZVariables
(length_unit, angle_unit)¶ Bases:
dict
,object
A class to store Z-variables and their values, generated in scan jobs.
The class is basically a dictionary with added attributes indicating the length and angle units.
Attributes:
- length_unit (str)
- Either Angstrom or Bohr. (The value is equal to one of the module level constants unAngstrom or unBohr.)
- angle_unit (str)
- Either degree or radian. (The values is equal to one of the module level constants unDegree or unRadian.)
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precision
= 0.01¶
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class
schrodinger.application.jaguar.results.
ThermoProp
(total, trans=None, rot=None, vib=None, elec=None)¶ Bases:
object
A class to store the components of calculated thermodynamic properties.
Attributes
- total (float)
- The total calculated thermodynamic property.
- translational (float)
- The translational contribution to the calculated property.
- rotational (float)
- The rotational contribution to the calculated property.
- vibrational (float)
- The vibrational contribution to the calculated property.
- electronic (float)
- The electronic contribution to the calculated property.
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precision
= 0.001¶
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cmp
(other)¶
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class
schrodinger.application.jaguar.results.
ThermoCollection
(temp, U, Cv, S, H, G, UTotal, HTotal, GTotal)¶ Bases:
object
A class to store a full set of calculated thermodynamic properties at a given temperature.
Attributes:
- temp (float)
- The temperature at which the properties were calculated.
- U (ThermoProp object, kcal/mol)
- Internal energy
- Cv (ThermoProp object, cal/(mol K))
- Heat capacity
- S (ThermoProp object, cal/(mol K))
- Entropy
- H (ThermoProp object, kcal/mol)
- Enthalpy
- G (ThermoProp object, kcal/mol)
- Free energy
- UTotal (float, Hartrees)
- Total internal energy (SCFE + ZPE + U)
- HTotal (float, Hartrees)
- Total enthalpy (UTotal + pV)
- GTotal (float, Hartrees)
- Total Gibbs free energy (HTotal - T*S)
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precision
= 1e-06¶
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class
schrodinger.application.jaguar.results.
NormalMode
(frequency, t_atoms)¶ Bases:
object
A class for storing normal mode results.
Attributes
frequency (float, 1/cm)
- symmetry (str)
- The symmetry type (Mulliken symbol) of the normal mode; None if symmetry is not present or used.
- ir_intensity (float, km/mol)
- The IR intensity; set to None if not calculated.
- raman_activity (float, Angstrom^4)
- The Raman activity; set to None if not calculated.
- raman_intensity (float, Angstrom^4)
- The Raman intensity; set to None if not calculated.
reduced_mass (float, amu)
force_constant (float, mDyne/Angstrom)
- dipole_strength (float, DSU)
- The dipole strength; set to None if not calculated.
- rotational_strength (float, RSU)
- The rotational strength; set to None if not calculated.
- displacement (float array)
- The atomic displacements, as an array with x, y, z columns for each atom row.
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frequency_precision
= 0.1¶
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ir_intensity_precision
= 0.1¶
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raman_activity_precision
= 0.1¶
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raman_intensity_precision
= 0.1¶
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reduced_mass_precision
= 0.1¶
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force_constant_precision
= 0.1¶
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dipole_strength_precision
= 0.1¶
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rotational_strength_precision
= 0.1¶
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class
schrodinger.application.jaguar.results.
JaguarOptions
¶ Bases:
object
A class for keeping track of specific calculation options.
Attributes
- ip (list of int)
- the values of all ip flags, indexed from 1
- pseudospectral (bool)
- whether the calculation used the pseudospectral method
- solvation (bool)
- whether the calculation used solvation
- analytic_gradients (bool)
- True if analytic gradients, False if calculated by finite difference. Is only meaningful when gradients are actually being calculated (i.e. when ‘forces’ of JaguarResults object is defined).
- analytic_frequencies (bool)
- True if analytic second derivatives are used, False if calculated by finite difference. Is only meaningful when frequencies are being calculated (i.e. when the JaguarResults normal_mode list attribute is non-empty).
- esp_fit (int)
- If no electrostatic potential fit is being done, this will be set to JaguarOutputs.ESP_NONE. If ESP atom centered fitting is being done, it will be set to JaguarOutputs.ESP_ATOMS. If ESP fitting is being done with atom centers and bond midpoints, esp_fit will be set to JaguarOptions.ESP_ATOMS_AND_BOND_MIDPOINTS.
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ip_default
= 1¶
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ESP_NONE
= 0¶
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ESP_ATOMS
= 1¶
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ESP_ATOMS_AND_BOND_MIDPOINTS
= 2¶
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class
schrodinger.application.jaguar.results.
JaguarResults
¶ Bases:
object
A class for holding results for a specific geometry.
Attributes
- scf_energy (float, Hartrees)
- SCF energy
- external_program_energy (float, Hartrees)
- Energy produced by an external program
- gas_phase_energy (float, Hartrees)
- Gas phase total energy
- scf_iter (list of ScfIterations)
- details on the scf iterations
- lmp2_energy (float, Hartrees)
- LMP2 energy
- solvation_energy (float, Hartrees)
- solvation energy
- solution_phase_energy (float, Hartrees)
- solution phase energy
- energy_one_electron (float, Hartrees)
- total one-electron energy (component (E) in SCF summary)
- energy_two_electron (float, Hartrees)
- total two-electron energy (component (I) in SCF summary)
- energy_electronic (float, Hartrees)
- total electronic energy (component (L) in SCF summary)
- energy_aposteri (float, Hartrees)
- a posteriori correction to the total energy (component (N0) in SCF summary)
- energy_aposteri0 (float, Hartrees)
- uncorrected energy in the case of a posteri-corrected calculations (derived quantity not in output file)
- nuclear_repulsion (float, Hartrees)
- nuclear repulsion energy
- homo (float, Hartrees)
- HOMO energy (set to None for open shell calcs)
- homo_alpha (float, Hartrees)
- alpha HOMO energy (set to None for closed shell calcs)
- homo_beta (float, Hartrees)
- beta HOMO energy (set to None for closed shell calcs)
- lumo (float, Hartrees)
- LUMO energy (set to None for open shell calcs)
- lumo_alpha (float, Hartrees)
- alpha LUMO energy (set to None for closed shell calcs)
- lumo_beta (float, Hartrees)
- beta LUMO energy (set to None for closed shell calcs)
zero_point_energy (float, kcal/mol)
- nops_on (bool)
- indicates this is a NOPS calculation
- sm_point (integer)
- number of point along string method string.
- sm_iter (integer)
- iteration number of string method.
- S_min_eval (float)
- minimum eigenvalue of S (overlap matrix)
- orbital (list of Orbitals)
- orbitals (defined for closed shell only)
- orbital_alpha (list of Orbitals)
- alpha orbitals (defined for open shell only)
- orbital_beta (list of Orbitals)
- beta orbitals (defined for open shell only)
- zvar (ZVariables)
- a mapping of scan variable names to values; ZVariables is a dict subclass.
- thermo (list of ThermoCollection)
- a list of ThermoCollection objects, each representing thermochemical properties at a given temperature
reaction_coord (float)
transition_state_components (list of floats)
- vetted_ts_vector_index (integer)
- index eigenvector of TS geometry that has been vetted with vet_ts != 0
- vetted_ts_vector (NormalMode instance)
- NormalMode instance representing eigenvector of TS geometry that has been vetted with vet_ts != 0
- dipole_qm (Dipole)
- dipole calculated from the wavefunction
- dipole_esp (Dipole)
- dipole calculated from the electrostatic potential charges
- dipole_mulliken (Dipole)
- dipole calculated from the Mulliken charges
- charge_bond_midpoint (list of BondCharge)
- ESP charges for bond midpoints
- atom (list of JaguarAtomicResults)
- atom based properties for this JaguarResults object
- normal_mode (list of NormalMode objects)
- normal mode information
- scan_value (dict of floats)
- a dictionary with zvar keys and float values indicating the scan coordinate values for this geometry
- polar_alpha (float)
- polarizability
- polar_beta (float)
- first-order hyperpolarizability
- polar_gamma (float)
- second-order hyperpolarizability
- et_S_if (float)
- overlap of initial and final state wfns in electron transfer
- et_H_ii (float)
- hamiltonian of initial state in electron transfer
- et_H_if (float)
- hamiltonian if initial->final state in electron transfer
- et_T_if (float)
- electron transfer transition energy
- min_esp (float)
- Minimum ESP value on isodensity surface
- max_esp (float)
- Maximum ESP value on isodensity surface
- mean_esp (float)
- Mean ESP value on isodensity surface
- mean_pos_esp (float)
- Mean positive ESP value on isodensity surface
- mean_neg_esp (float)
- Mean negative ESP value on isodensity surface
- sig_pos_esp (float)
- Variance of positive ESP values on isodensity surface
- sig_neg_esp (float)
- Variance of negative ESP values on isodensity surface
- sig_tot_esp (float)
- Total ESP variance on isodensity surface
- balance_esp (float)
- ESP balance on isodensity surface
- local_pol_esp (float)
- Local polarity on isodensity surface
- min_alie (float)
- Minimum ALIE value on isodensity surface
- max_alie (float)
- Maximum ALIE value on isodensity surface
- mean_alie (float)
- Mean ALIE value on isodensity surface
- mean_pos_alie (float)
- Mean positive ALIE value on isodensity surface
- mean_neg_alie (float)
- Mean negative ALIE value on isodensity surface
- sig_pos_alie (float)
- Variance of positive ALIE values on isodensity surface
- sig_neg_alie (float)
- Variance of negative ALIE values on isodensity surface
- sig_tot_alie (float)
- Total ALIE variance on isodensity surface
- balance_alie (float)
- ALIE balance on isodensity surface
- local_pol_alie (float)
- Average deviation from mean ALIE on isodensity surface
- excitation_energies (list of floats)
- electronic excitation energies
- singlet_excitation_energies (list of floats)
- restricted singlet electronic excitation energies
- triplet_excitation_energies (list of floats)
- restricted triplet electronic excitation energies
- oscillator_strengths (list of floats)
- excitation energy oscillator strengths
- singlet_oscillator_strengths (list of floats)
- singlet excitation energy oscillator strengths
- triplet_oscillator_strengths (list of floats)
- triplet excitation energy oscillator strengths
- opt_excited_state_energy_1 (float)
- energy of first excited state geometry optimization
- total_lo_correction (float, kcal/mol)
- total localized orbital energy correction
- spin_splitting_score (float)
- ligand field spin-splitting score for DBLOC calculations
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energy_precision
= 1e-06¶
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nucrep_precision
= 1e-08¶
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zpe_precision
= 0.01¶
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lo_precision
= 0.01¶
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spin_splitting_precision
= 0.01¶
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rxn_coord_precision
= 0.001¶
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ts_component_precision
= 0.1¶
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alpha_polar_precision
= 0.001¶
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beta_polar_precision
= 0.001¶
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gamma_polar_precision
= 0.1¶
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esp_analysis_precision
= 0.01¶
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balance_esp_precision
= 0.001¶
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alie_analysis_precision
= 0.01¶
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balance_alie_precision
= 0.001¶
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exc_precision
= 0.0006¶
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osc_precision
= 0.001¶
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energy
¶ The overall energy for the calculation. For LMP2 calculations this is the LMP2 energy, otherwise it is the SCF energy. If this calculation includes solvation it is the solution phase energy.
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forces
¶ Convenient access to forces for all atoms as a numpy array.
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getAtomTotal
()¶
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atom_total
¶ Return the number of atoms in the structure geometry.
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getStructure
(properties=None)¶ Get a schrodinger.Structure object for a specific geometry.
- property_names (list of tuples of (string, object))
- A list of properties names and values belonging to the overall job these results are a part of.
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diff
(other, short_circuit=False, factor=1.0)¶ Return a set of attributes that differ.
Parameters other (JaguarResults)
The instance to compare against.- short_circuit (bool)
- If True, return immediately upon finding a difference.
- factor (float)
- A fudge factor to apply to most comparison precision values. The allowed difference between values is multiplied by factor.
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esp_balance
¶
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esp_local_polarity
¶
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espmax
¶
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espmean_n
¶
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espmean_p
¶
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espmin
¶
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sig_n
¶
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sig_p
¶
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sigtot
¶