schrodinger.application.jaguar.results module¶
Classes for parsing Jaguar output files and accessing output properties programmatically.
Copyright Schrodinger, LLC. All rights reserved.
- exception schrodinger.application.jaguar.results.IncompleteOutput¶
Bases:
RuntimeError
Indicators that the output is incomplete.
- class schrodinger.application.jaguar.results.InputDeviation(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)¶
Bases:
enum.IntEnum
Deviations from input settings.
- NONE = 0¶
- NOPS = 1¶
- CUT20 = 2¶
- NOPS_AND_CUT20 = 3¶
- class schrodinger.application.jaguar.results.NofailResult(energy: float, cut20: float, nops: int, input_deviation: schrodinger.application.jaguar.results.InputDeviation)¶
Bases:
NamedTuple
Energy results from nofail measures taken to help SCF convergence.
- Parameters
energy – Energy in Hartree obtained with these settings
cut20 – Value of cut20 (basis set linear dependence threshold)
nops – Value of nops (turn on/off PS calculation)
input_deviation – Deviation from the input settings 0 = User input settings 1 = Set nops=1 2 = Used increased cut20 3 = Used both nops=1 and increased cut20
- energy: float¶
Alias for field number 0
- cut20: float¶
Alias for field number 1
- nops: int¶
Alias for field number 2
- input_deviation: schrodinger.application.jaguar.results.InputDeviation¶
Alias for field number 3
- class schrodinger.application.jaguar.results.FukuiIndices(index, atom_name, 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.
- precision = 0.01¶
- __init__(index, atom_name, homo_nn, homo_ns, homo_sn, homo_ss, lumo_nn, lumo_ns, lumo_sn, lumo_ss)¶
Initialization requires all N/S combinations for both the HOMO and the LUMO.
- class schrodinger.application.jaguar.results.JaguarAtomicResults(index, atom_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_nbo (float)
NBO charge.
- charge_stockholder (float)
Stockholder charge.
- charge_lowdin (float)
Lowdin charge.
- spin_lowdin (float)
Lowdin spin density.
- charge_mulliken (float)
Mulliken charge.
- spin_mulliken (float)
Mulliken spin density.
- fukui_indices (FukuiIndices)
Fukui indices.
- nmr_shielding (float)
NMR shielding.
- nmr_abs_shift (float)
NMR absolute shifts
- nmr_rel_shift (float)
NMR relative shifts, defined only for H/C/N/F.
- 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.
- isotope (string)
Atomic isotope label.
- nuclear_spin (float)
Nuclear spin of atom.
- nuclear_magnetic_dipole_moment (float)
Nuclear magnetic dipole moment of atom.
- forces_precision = 0.0001¶
- charge_precision = 5e-05¶
- nmr_precision = 0.01¶
- esp_precision = 0.01¶
- alie_precision = 0.01¶
- epn_precision = 0.01¶
- nuclear_spin_precision = 0.0001¶
- nuclear_magnetic_dipole_moment_precision = 0.0001¶
- __init__(index, atom_name)¶
- index (integer)
The 1-based index of the atom in the structure.
- atom_name (str)
The name of the atom. The name can have a trailing ‘@’ to indicate it’s a counterpoise atom.
- diff(other, short_circuit=False, factor=1.0)¶
Return a list of differing attributes.
- DEPRECATED = ['nmr_h_avg_shift', 'nmr_2d_avg_shift']¶
- class schrodinger.application.jaguar.results.BondCharge(name, charge)¶
Bases:
object
A class to store bond-midpoint charges calculated in ESP fitting.
- precision = 5e-05¶
- __init__(name, charge)¶
- cmp(other)¶
- class schrodinger.application.jaguar.results.Orbital(type_, index, energy, symmetry=None)¶
Bases:
object
A class for storing orbital information.
Attributes
energy (float, Hartrees)
symmetry (str)
- precision = 0.0001¶
- __init__(type_, index, energy, symmetry=None)¶
- cmp(that)¶
Compare on orbital energy and the non-reduced symmetry.
- class schrodinger.application.jaguar.results.ConvCriteria(deltaE, deltaE_thresh, gmax, gmax_thresh, grms, grms_thresh, dmax, dmax_thresh, drms, drms_thresh)¶
Bases:
object
A simple storage class for storing info about the progress of convergence criteria for geometry optimizations. May add SCF convergence criterion later (but maybe that belongs in SCFIteration class)
- energy_prec = 1e-05¶
- grad_prec = 0.0001¶
- displacement_prec = 0.001¶
- thresh_prec = 0.0¶
- __init__(deltaE, deltaE_thresh, gmax, gmax_thresh, grms, grms_thresh, dmax, dmax_thresh, drms, drms_thresh)¶
Initialize.
- 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.
- 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'¶
- __init__(updt, diis, icut, grid, energy, energy_change, rms_density_change, max_diis_error)¶
Initialize.
- static fromEtotString(etot_string)¶
Create an instance from a standard etot string.
- toString(iter=0)¶
Render as a string, with optional iteration number.
- 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.)
- precision = 0.01¶
- __init__(length_unit, angle_unit)¶
- class schrodinger.application.jaguar.results.ThermoProp(type_, temp, press, energy_units, total, trans=None, rot=None, vib=None, elec=None)¶
Bases:
object
A class to store the components of calculated thermodynamic properties.
Attributes
- Variables
type_ (str) – Descriptive string indicating which thermodynamic property (U/Cv/S/H/G/lnQ) this instance refers to
temp (float) – The temperature at which the properties were calculated.
energy_units (str) – Units of provided values
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.
- precision = 0.001¶
- __init__(type_, temp, press, energy_units, total, trans=None, rot=None, vib=None, elec=None)¶
- cmp(other)¶
- class schrodinger.application.jaguar.results.ThermoCollection(temp, press, units, total, trans, rot, vib, elec, 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.
- press (float)
The pressure at which the properties were calculated. (in atm units)
- units (str)
Units that the energy values are in (if not in Hartrees)
- total (list of floats)
The total calculated thermodynamic properties for, in order, U/Cv/S/H/G
- trans (list of floats)
The translational contribution for, in order, U/Cv/S/H/G
- rot (list of floats)
The rotational contribution for, in order, U/Cv/S/H/G
- vib (list of floats)
The vibrational contribution for, in order, U/Cv/S/H/G
- elec (list of floats)
The electronic contribution for, in order, U/Cv/S/H/G
- 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)
- precision = 1e-06¶
- __init__(temp, press, units, total, trans, rot, vib, elec, UTotal, HTotal, GTotal)¶
- class schrodinger.application.jaguar.results.NormalMode(frequency, t_atoms, index)¶
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.
- frequency_precision = 0.1¶
- ir_intensity_precision = 0.1¶
- raman_activity_precision = 0.1¶
- raman_intensity_precision = 0.1¶
- reduced_mass_precision = 0.1¶
- force_constant_precision = 0.1¶
- dipole_strength_precision = 0.1¶
- rotational_strength_precision = 0.1¶
- __init__(frequency, t_atoms, index)¶
Arguments
- frequency (float)
The frequency of the normal mode.
- t_atoms (int)
The number of atoms in the molecule.
- 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)
True if the user did not enter
nops=1
in their input. This attribute tracks the users settings for the overall job, in contrast toJaguarResults.nops_on
which reports whether nops was used for various stages of the calculation (e.g. each step of a geometry optimization)- 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.
- ip_default = 1¶
- ESP_NONE = 0¶
- ESP_ATOMS = 1¶
- ESP_ATOMS_AND_BOND_MIDPOINTS = 2¶
- __init__()¶
- class schrodinger.application.jaguar.results.DerivedAttrs¶
Bases:
object
A class for building and holding properties derived from other _Attributes in JaguarResults. Designed only with single primitive valued _Attribute’s in mind (no lists). By its nature this class will be pretty manual, since every derived property will have its own logic. Class method buildDerivedAttrs called by JaguarOutput parent at end of init (after textparsing)
- energy_aposteri0 (float, Hartrees)
Uncorrected energy in the case of a posteri-corrected calculations (energy-energy_aposteri)
- homo_lumo_gap (float, Hartrees)
HOMO-LUMO Gap energy. Calculated as lower of same-spin orbital differences in unrestricted calcs
- lambdamax_ev (float, eV)
Excitation energy (ev) of state with highest oscillator strength
- lambdamax_nm (float, nm)
Excitation energy (nm) of state with highest oscillator strength
- energy_precision_hartree = 1e-06¶
- exc_energy_precision_ev = 0.0006¶
- exc_energy_precision_nm = 20¶
- orbe_precision = 0.0001¶
- osc_precision = 0.001¶
- __init__()¶
Create the _attributes list and define precisions so that _diff can be used.
- buildDerivedAttrs(jresults, joutput)¶
Fill in the values of self._attributes if ingredients exist
jresults is parent JaguarResults, use to obtain ingredients joutput is parent JaguarOutput, use to obtain job options needed for logic (ie - homo_lumo_gap)
- diff(other, short_circuit=False, factor=1.0)¶
Return a list of differing attributes.
- 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
- nn_gas_energy (float, Hartrees)
Neural network potential energy
- nn_sol_energy (float, Hartrees)
Neural network potential energy
- nn_energy (float, Hartrees)
Neural network potential energy
- nn_stddev (float, Hartrees)
Neural network potential energy std deviation across models
- rimp2_ss_energy (float, Hartrees)
RI-MP2 same-spin energy
- rimp2_os_energy (float, Hartrees)
RI-MP2 opposite-spin energy
- rimp2_corr_energy (float, Hartrees)
RI-MP2 correlation energy
- rimp2_energy (float, Hartrees)
RI-MP2 energy
- gas_phase_energy (float, Hartrees)
Gas phase total energy
- conv_crit (ConvCriteria)
Details on convergence criterion for a geopt step
- 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)
Zero point from a frequency calculation
- canonical_orbitals (int)
Number of canonical orbitals for a given job
- doubted_geom (bool)
Indicates that the Jaguar output contained an indication that this was a bad step
- geopt_step_num (int)
Nominal geometry optimization step according to Jaguar, which is not necessarily monotonic because Jaguar sometimes restarts optimizations
- nofail_results (list of NofailResult objects)
Converged energies obtained in a nofail calculation, along with the settings used and whether those were the users original settings.
- nops_on (bool)
True if this stage of the calculation is not using pseudospectral methods.
- 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
- spin_spin_couplings (list of SpinSpinCoupling objects)
Spin-spin coupling information
- scan_value (dict of floats)
A dictionary with zvar keys and float values indicating the scan coordinate values for this geometry
- fdpolar_matrix1 (list of floats)
- Frequency-dependent polarizability matrix elements in xx, xy, xz,
yx, yy, yz, zx, zy, zz order, first frequency
- fdpolar_alpha1 (float)
Frequency-dependent polarizability, first frequency
- fdpolar_freq1 (float)
Frequency used for fdpolar_alpha1
- fdpolar_matrix2 (list of floats)
- Frequency-dependent polarizability matrix elements in xx, xy, xz,
yx, yy, yz, zx, zy, zz order, second frequency
- fdpolar_alpha2 (float)
Frequency-dependent polarizability, second frequency
- fdpolar_freq2 (float)
Frequency used for fdpolar_alpha2
- fdpolar_beta (float)
frequency-dependent first-order hyperpolarizability, reported as mean of beta-tensor orientations
- fdpolar_freq3 (float)
third frequency used for frequency-dependent hyperpolarizability calcs
- 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 of 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
- hso_singlet_triplet_elements (list of HsoSingletTripletElement)
Hso singlet-triplet elements
- 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
- internally_stable (bool)
Indicates that the wave function is internally stable
- internal_stability_eigenvalues (list of floats)
Eigenvalues of wave function internal stability analysis
- externally_stable (bool)
Indicates that the wave function is externally stable
- external_stability_eigenvalues (list of floats)
Eigenvalues of wave function external stability analysis
- s2 (float)
Spin: <S**2>
- sz2 (float)
Spin: Sz*<Sz+1>
- derived_attrs (DerivedAttrs object)
Container for simple attributes derived from ones explicitly found in output file
- energy_precision = 1e-06¶
- nucrep_precision = 1e-08¶
- zpe_precision = 0.01¶
- lo_precision = 0.01¶
- spin_splitting_precision = 0.01¶
- rxn_coord_precision = 0.001¶
- ts_component_precision = 0.1¶
- alpha_polar_precision = 0.001¶
- beta_polar_precision = 0.001¶
- gamma_polar_precision = 0.1¶
- esp_analysis_precision = 0.01¶
- balance_esp_precision = 0.001¶
- alie_analysis_precision = 0.01¶
- balance_alie_precision = 0.001¶
- exc_precision = 0.0006¶
- osc_precision = 0.001¶
- tdm_precision = 0.02¶
- __init__()¶
Create a JaguarResults object.
- property energy¶
The overall/final energy for the calculation. Meant to be a simple handle for one to get the energy of a calculation, since there are many different types of energies in JaguarResults. The energy types range from general to method-specific - energy, solution_phase_energy, gas_phase energy, scf_energy, RI-MP2, LMP2, Neural Net (NN), external. More general energy types can be assigned the value of other energy types depending on the calculation.
For instance, a gas-phase HF job has energy = scf_energy. But a gas-phase RI-MP2 job has energy = rimp2_energy, since that is the “final” energy of the calculation. Solution-phase calculations have more layers.
The code that assigns values to the various energy types is split between _getEnergy() and the various functions in textparser.py. For instance see the rimp2_energies, nn_gas/sol_energy fxns.
- property forces¶
Convenient access to forces for all atoms as a numpy array.
- getAtomTotal()¶
- property atom_total¶
Return the number of atoms in the structure geometry.
- 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.
- 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.
- class schrodinger.application.jaguar.results.Dipole(source, x=None, y=None, z=None, magnitude=None)¶
Bases:
object
A class for storing dipole information.
Attributes:
- source (string)
Descriptor of what set of charges or wavefunction were used to compute the dipole
- magnitude (float, Debye)
The magnitude of the dipole moment.
- x, y, z (float, Debye)
The x, y, z components of the dipole moment.
- precision = 0.0001¶
- tdm_precision = 0.02¶
- __init__(source, x=None, y=None, z=None, magnitude=None)¶
- cmp(other)¶
- class schrodinger.application.jaguar.results.SpinSpinCoupling(atom_pair, total_spin_spin=None, total_spin_spin_isotropic=None, fermi_contact=None, fermi_contact_isotropic=None, spin_dipole=None, spin_dipole_isotropic=None, fermi_contact_spin_dipole=None, fermi_contact_spin_dipole_isotropic=None, paramag_spin_orbit=None, paramag_spin_orbit_isotropic=None, diamag_spin_orbit=None, diamag_spin_orbit_isotropic=None)¶
Bases:
object
A class for storing Spin-Spin Coupling results.
Attributes
- atom_pair (list(JaguarAtomicResults))
The atom pair used to calculate the spin-spin coupling constants
- total_spin_spin (np.array(float), Hz)
The total spin-spin coupling tensor (3x3 matrix)
- total_spin_spin_isotropic (float, Hz)
The isotropic value of the spin-spin coupling tensor
- fermi_contact (np.array(float), Hz)
The Fermi-Contact Matrix (3x3 matrix)
- fermi_contact_isotropic (float, Hz)
The isotropic value of the Fermi-Contact Matrix
- spin_dipole (np.array(float), Hz)
The Spin-Dipole Matrix (3x3 matrix)
- spin_dipole_isotropic (float, Hz)
The isotropic value of the Spin-Dipole Matrix
- fermi_contact_spin_dipole (np.array(float), Hz)
The Fermi-Contact / Spin-Dipole Matrix (3x3 matrix)
- fermi_contact_spin_dipole_isotropic (float, Hz)
The isotropic value of the Fermi-Contact / Spin-Dipole Matrix
- paramag_spin_orbit (np.array(float), Hz)
The Paramagnetic Spin-Orbit Matrix (3x3 matrix)
- paramag_spin_orbit_isotropic (float, Hz)
The isotropic value of the Paramagnetic Spin-Orbit Matrix
- diamag_spin_orbit (np.array(float), Hz)
The Diamagnetic Spin-Orbit Matrix (3x3 matrix)
- diamag_spin_orbit_isotropic (float, Hz)
The isotropic value of the Diamagnetic Spin-Orbit Matrix
- __init__(atom_pair, total_spin_spin=None, total_spin_spin_isotropic=None, fermi_contact=None, fermi_contact_isotropic=None, spin_dipole=None, spin_dipole_isotropic=None, fermi_contact_spin_dipole=None, fermi_contact_spin_dipole_isotropic=None, paramag_spin_orbit=None, paramag_spin_orbit_isotropic=None, diamag_spin_orbit=None, diamag_spin_orbit_isotropic=None)¶
Arguments
- Parameters
atom_pair (np.array(JaguarAtomicResults)) – The atom pair used to calculate the spin-spin coupling constants
total_spin_spin (np.array(float)) – The total spin-spin coupling tensor (3x3 matrix) in Hz units
total_spin_spin_isotropic (float) – The isotropic value of the spin-spin coupling tensor in Hz units
fermi_contact (np.array(float)) – The Fermi-Contact Matrix in Hz units
fermi_contact_isotropic (float) – The isotropic value of the Fermi-Contact Matrix in Hz units
spin_dipole (np.array(float)) – The Spin-Dipole Matrix in Hz units
spin_dipole_isotropic (float) – The isotropic value of the Spin-Dipole Matrix in Hz units
fermi_contact_spin_dipole (np.array(float)) – The Fermi-Contact and Spin-Dipole symmetric combination Matrix in Hz units
fermi_contact_spin_dipole_isotropic (float) – The isotropic value of the Fermi-Contact and Spin-Dipole symmetric combination Matrix in Hz units
paramag_spin_orbit (np.array(float)) – The Paramagnetic Spin-Orbit Matrix in Hz units
paramag_spin_orbit_isotropic (float) – The isotropic value of the Paramagnetic Spin-Orbit Matrix in Hz units
diamag_spin_orbit (np.array(float)) – The Diamagnetic Spin-Orbit Matrix in Hz units
diamag_spin_orbit_isotropic (float) – The isotropic value of the Diamagnetic Spin-Orbit Matrix in Hz units
- class schrodinger.application.jaguar.results.HsoSingletTripletElement(singlet_idx, triplet_idx, ms, hso_element_re, hso_element_im)¶
Bases:
object
A class for storing an Hso singlet-triplet element.
Attributes:
- singlet_idx (int)
- The index of the singlet state 0 (ground state), 1 (first
excited state), etc.
- triplet_idx (int)
The index of the triplet state 1 (first excited state), etc.
- ms (int)
The magnetic quantum number of the triplet state, either -1, 0, or 1
- hso_element_re (float)
The Hso element real component
- hso_element_im (float)
The Hso element imaginary component
- PRECISION = 0.0001¶
- __init__(singlet_idx, triplet_idx, ms, hso_element_re, hso_element_im)¶
- Parameters
singlet_idx (int) – index of the singlet state 0 (ground state), 1 (first excited state), etc.
triplet_idx (int) – index of the triplet state 1 (first excited state), etc.
ms (int) – magnetic quantum number of the triplet state, either -1, 0, or 1
hso_element_re (float) – Hso element real component
hso_element_im (float) – Hso element imaginary component
- class schrodinger.application.jaguar.results.RoutineTimes(thresh: Optional[Dict[str, float]] = None)¶
Bases:
collections.abc.MutableMapping
- __init__(thresh: Optional[Dict[str, float]] = None)¶
Collection of routine times for a Jaguar calculation
Stores timings in a defaultdict and, once filled, can create a set of attributes for the available times.
Accessing from the times array can be done as if RoutineTimes were a dictionary and will return
datetime.timedelta
times. Once attributes have been generated, float values of the times can be accessed fromRoutineTimes.{routine}_timing
attributes.thresh
stores thresholds for comparing times of given routines. If a routine is not specified, its corresponding attribute will not be compared via JaguarDiff
- __len__()¶
- generate_attributes()¶
Create list of
_Attributes
and assign attribute values usingself.times
We create the attributes dynamically to avoid the need to maintain a complete list of all Jaguar routines.
- diff(other, short_circuit: bool = False, factor: float = 1.0) bool ¶
Return a set of attributes that differ.
- Parameters
other – The instance to compare against.
short_circuit – If True, return immediately upon finding a difference.
factor – A fudge factor to apply to most comparison precision values. The allowed difference between values is multiplied by factor.