qm_descriptors.py Command Help
Command: $SCHRODINGER/jaguar run qm_descriptors.py
usage: $SCHRODINGER/jaguar run qm_descriptors.py [-h] [-maes MAES]
[-config CONFIG]
[-outs OUTS [OUTS ...]]
[-props PROPS [PROPS ...]]
[-formats {mae,sdf,csv} [{mae,sdf,csv} ...]]
[-WAIT] [-DEBUG]
[-jobname <name>] [-subdir]
[-recover] [-no_subjob_files]
[-scr <absolute path>]
[-PARALLEL <N>]
[-max_threads <T>]
[-procs_per_node <N>]
[-use_one_node | -use_multiple_nodes]
[-HOST <host>:<M>]
[-SUBHOST <host>:<M>] [-SAVE]
[-NOJOBID]
[-OPLSDIR <oplsdir>]
Workflow to harvest quantum descriptors. Can harvest descriptors from completed
Jaguar .out files or, given a .mae containing structures, can generate a series
of jobs and harvest descriptors from each completed job. Mode of operation
determined by use of -outs/-maes, which are mutually exclusive and one must be
provided. With -outs, one can also specify -formats and -props.
With -maes, one can supply -config. -formats/-props/-config are optional and
have reasonable defaults detailed in online manual.
Harvested descriptors are output in requested formats, one file for each .out
along with a file containing descriptors from all .out files named
'all_calcs.<outputformat>', defaulting to .sdf format (the default for -formats).
options:
-h, --help show this help message and exit
.mae file cmdline argument set:
-maes MAES input .mae file containing structures to run
-config CONFIG configuration file with details of the workflow.
See online manual for specification of config file format and default values
.out file(s) cmdline argument set:
-outs OUTS [OUTS ...]
.out file(s) to harvest quantum descriptors from
-props PROPS [PROPS ...]
properties to harvest from provided .out file(s).
Defaults to all_descriptor_numeric. See online manual for list of all possible properties.
-formats {mae,sdf,csv} [{mae,sdf,csv} ...]
format(s) to output harvested properties in. Defaults to sdf
other options:
-WAIT Wait for job to finish before returning prompt.
-DEBUG, -D Print detailed information about job launch.
-jobname <name> Set the job name.
-subdir Run Jaguar in a sub-directory.
-recover Manually re-run a job using the recover mechanism. NOTE this option is not recommended for default recovery jobs.
Use "jaguar run <filename>.recover" instead (see documentation for more details).
-no_subjob_files Do not return subjob output files to launch directory.
-scr <absolute path> Specify a scratch directory (must not already exist). Directory must be given as an absolute path.
Note this will be used by the Fortran backend and is independent of the specification of -TMPDIR.
-PARALLEL <N> Use up to <N> CPUs simultaneously for the whole workflow, automatically allocated among subjobs, including threaded subjobs.
-max_threads <T> Use no more than <T> OpenMP threads for each Jaguar subjob. Default 8.
-procs_per_node <N> Use no more than <N> CPUs per node. Default is taken from the schrodinger.hosts file; if undefined 8.
-use_one_node Force CPU resources to be requested upfront on one node.
This pool of CPUs will be used for the duration of the job instead of resubmitting to the queue.
-use_multiple_nodes Force CPU resources to be requested dynamically from the queue (if available) instead of upfront on one node.
commonly used Schrodinger Suite options:
-HOST <host>:<M> Run job remotely on host <hostname>. The optional :<M> defines the maximum number of simultaneous subjobs.
May be combined with -PARALLEL <N>.
-SUBHOST <host>:<M> Run any subjobs remotely on subhost <hostname>. The optional :<M> defines the maximum number of simultaneous subjobs.
May be combined with -PARALLEL <N>.
-SAVE Return .zip file of scratch directory.
-NOJOBID Run Jaguar interactively without jobserver (not available with python workflows).
-OPLSDIR <oplsdir> Use custom FF parameters from specified directory for workflows which support it.
List of available Special Keywords
all: Returns all properties found in output file.
all_descriptor_numeric: Returns all numeric Molecular/Atomic properties found in output file.
all_numeric: Returns all numeric properties found in output file.
List of available Job Descriptors
<ROUTINE>_timing: User time for routine <ROUTINE> in seconds
_sm_n_points: number of string method points
atomicsec_dict: &atomic section parsed into dictionary mapping atom label to a dictionary of key:value
atomicsec_string: String that stores &atomic section, if printed to output
basis: Basis Set
charge: Molecular charge of Input Structure
coords_frozen: Number of frozen coordinates
coords_harmonic: number of harmonic constraints
coords_ind: Number of independent coordinates
coords_nred: Number of non-redundant coordinates
coords_opt: Number of optimization coordinates
cpu_duration: Total elapsed CPU Time used across all CPUs. CPU time is the time spent executing the process.
cpu_sys_duration: Total elapsed CPU and System Time used across all CPUs. CPU time is the time spent executing the process. System is the amount of time spent in the kernel.
fatal_error: Error message in the event the job failed
fatal_errorno: Error number in the event the job failed
functional: DFT Functional
gensec_string: String that stores &gen section, if printed to output
geopt_stuck: Whether the geopt or tsopt got stuck
glibc: Reported glibc version
host: Job Host
job_id: Job ID
lastexe: Last Jaguar Executable Used
mae_in: Maestro input file
mae_out: Maestro output file
method: Calculation Type
mol_weight: Molecular weight of input geometry
multiplicity: Spin Multiplicity of Input Structure
nbasis: Number of Basis Functions
nelectron: Number of Electrons
nthreads: Number of threads
num_occ_orbs: Number of Occupied Orbitals
num_occ_orbs_alpha: Number of Occupied Alpha Orbitals
num_occ_orbs_beta: Number of Occupied Beta Orbitals
point_group: Molecular point group of the input molecule
point_group_used: Point group used in the calculation
qm_atoms: Number of QM Atoms
solvent_params: Solvent parameters used in solvation entropy calculations
status: Job status - set to 0, 1, or 2 corresponding to UNKNOWN, OK, or SPLAT respectively
stoichiometry: Stoichiometry of input geometry
symmetrized: Whether the geometry has been symmetrized or not
ts_component_descriptions: Descriptions of the transition state vector components
List of available Molecular Descriptors
GTot_S_epsilon: Total Gibbs Free Energy with S_epsilon
GTot_S_epsilon_alpha: Total Gibbs Free Energy with S_epsilon_alpha
GTot_S_omega: Total Gibbs Free Energy with S_omega
GTotal: Total Gibbs Free Energy (HTotal - T*S)
HTotal: Total Enthalpy (UTotal + pV)
S_min_eval: Minimum value of S (overlap matrix)
UTotal: Total Internal Energy (SCFE + ZPE + U)
balance_alie: ALIE balance on isodensity surface
balance_esp: ESP balance on isodensity surface
bond_midpoint_charge: Bond-Midpoint Charges Calculated in ESP Fitting
canonical_orbitals: Number of canonical orbitals
deltaE: Geopt DeltaE
deltaE_thresh: DeltaE Geopt Convergence Threshold
density_isoval: Isodensity value for the surface in e/bohr**3
diamag_spin_orbit_isotropic: Diamagnetic Spin-Orbit Isotropic Value of Pairs
dipole_strength: Dipole Strengths of Normal Modes
dipolecomp_esp: ESP Dipole Moment Components Calc'd
dipolecomp_mulliken: Mulliken Dipole Moment Components Calc'd
dipolecomp_qm: Dipole Moment Components Calc'd
dipolemag_esp: ESP Dipole Moment Magnitude Calc'd
dipolemag_mulliken: Mulliken Dipole Moment Magnitude Calc'd
dipolemag_qm: Dipole Moment Magnitude Calc'd
dmax: Geopt Max Displacement
dmax_thresh: Geopt Max Displacement Convergence Threshold
doubted_geom: Indicates a geometry step was not expected to be good
drms: Geopt Displacement RMS
drms_thresh: Geopt Displacement RMS Convergence Threshold
energy_aposteri: a posteriori correction to the total energy (component (N0) in SCF summary)
energy_aposteri0: Uncorrected energy in the case of a posteri-corrected calculations (energy-energy_aposteri)
energy_electronic: Total electronic energy (component (L) in SCF summary)
energy_one_electron: Total one-electron energy (component (E) in SCF summary)
energy_two_electron: Total two-electron energy (component (I) in SCF summary)
enthalpy: Total Calculated Enthalpy
enthalpy_elec: Electronic Contribution to Enthalpy
enthalpy_rot: Rotational Contribution to Enthalpy
enthalpy_trans: Translational Contribution to Enthalpy
enthalpy_vib: Vibrational Contribution to Enthalpy
entropy: Total Calculated Entropy
entropy_elec: Electronic Contribution to Entropy
entropy_rot: Rotational Contribution to Entropy
entropy_trans: Translational Contribution to Entropy
entropy_vib: Vibrational Contribution to Entropy
et_H_if: Hamiltonian of initial to final state in e- transfer
et_H_ii: Hamiltonian of initial state in e- transfer
et_S_if: Overlap of initial and final state wfns in e- transfer
et_T_if: e- transfer transition energy
excitation_energies: Excitation energies
excited_dipole_moments: Excited state dipole moments
excited_esp_dipole_moments: Excited state ESP dipole moments
external_program_energy: Energy produced by external program
external_stability_eigenvalues: External WF Stability Eigenvalues
externally_stable: Indicates that the wave function is externally stable
fdpolar_alpha1: Frequency-Dependent Polarizability 1
fdpolar_alpha2: Frequency-Dependent Polarizability 2
fdpolar_beta: Frequency-Dependent First-Order Hyperpolarizability
fdpolar_freq1: Frequency of 'Freq-Dependent Polarizability 1'
fdpolar_freq2: Frequency of 'Freq-Dependent Polarizability 2'
fdpolar_freq3: Frequency used to calculate 'Frequency-Dependent First-Order Hyperpolarizability'
fdpolar_matrix1: Frequency-dependent polarizability matrix elements in xx, xy, xz, yx, yy, yz, zx, zy, zz order, first frequency
fdpolar_matrix2: Frequency-dependent polarizability matrix elements in xx, xy, xz, yx, yy, yz, zx, zy, zz order, second frequency
fermi_contact_isotropic: Fermi-Contact Isotropic Value of Pairs
fermi_contact_spin_dipole_isotropic: Isotropic value of Symmetric Combination of Fermi Contact Matrix and Spin Dipole Matrix of Atom Pair
force_constant: Force Constants of Normal Modes
frequency: Frequencies of Normal Modes
gas_phase_energy: Gas Phase Energy
geopt_step_num: Geometry optimization step number according to Jaguar (not necessarily monotonic since Jaguar sometimes restarts)
gibbs_free_energy: Total Calculated Gibbs Free Energy
gibbs_free_energy_elec: Electronic Contribution to Gibbs Free Energy
gibbs_free_energy_rot: Rotational Contribution to Gibbs Free Energy
gibbs_free_energy_trans: Translational Contribution to Gibbs Free Energy
gibbs_free_energy_vib: Vibrational Contribution to Gibbs Free Energy
gmax: Geopt Max Gradient
gmax_thresh: Geopt Max Gradient Convergence Threshold
grms: Geopt Gradient RMS
grms_thresh: Geopt Gradient RMS Convergence Threshold
heat_capacity: Total Calculated Heat Capacity
heat_capacity_elec: Electronic Contribution to Heat Capacity
heat_capacity_rot: Rotational Contribution to Heat Capacity
heat_capacity_trans: Translational Contribution to Heat Capacity
heat_capacity_vib: Vibrational Contribution to Heat Capacity
homo: HOMO energy (set to None for open-shell calcs)
homo_alpha: Alpha HOMO energy (set to None for closed-shell calcs)
homo_beta: Beta HOMO energy (set to None for closed-shell calcs)
homo_lumo_gap: HOMO-LUMO Gap energy. Calculated as lower of same-spin orbital differences in unrestricted calcs
hso_singlet_triplet_elements: Complex spin-orbit Hamiltonian (Hso) singlet-triplet matrix elements
internal_energy: Total Calculated Internal Energy
internal_energy_elec: Electronic Contribution to Internal Energy
internal_energy_rot: Rotational Contribution to Internal Energy
internal_energy_trans: Translational Contribution to Internal Energy
internal_energy_vib: Vibrational Contribution to Internal Energy
internal_stability_eigenvalues: Internal WF Stability Eigenvalues
internally_stable: Indicates that the wave function is internally stable
ir_intensity: IR Intensities of Normal Modes
isodensity_area: Area of the isodensity surface in angstrom**2
isodensity_volume: Volume of the isodensity surface angstrom**3
lambdamax_ev: Excitation energy (eV) of state with highest oscillator strength
lambdamax_nm: Excitation energy (nm) of state with highest oscillator strength
lmp2_energy: LMP2 Energy
lnq: Total Calculated lnQ
lnq_elec: Electronic Contribution to lnQ
lnq_rot: Rotational Contribution to lnQ
lnq_trans: Translational Contribution to lnQ
lnq_vib: Vibrational Contribution to lnQ
local_pol_alie: Avg deviation from mean ALIE on isodensity surface
local_pol_esp: Local polarity on isodensity surface
lumo: LUMO energy (set to None for open-shell calcs)
lumo_alpha: Alpha LUMO energy (set to None for closed-shell calcs)
lumo_beta: Beta LUMO energy (set to None for closed-shell calcs)
max_alie: Maximum ALIE value on isodensity surface
max_esp: Maximum ESP value on isodensity surface
mean_alie: Mean ALIE value on isodensity surface
mean_esp: Mean ESP value on isodensity surface
mean_neg_alie: Mean negative ALIE value on isodensity surface
mean_neg_esp: Mean negative ESP value on isodensity surface
mean_pos_alie: Mean positive ALIE value on isodensity surface
mean_pos_esp: Mean positive ESP value on isodensity surface
min_alie: Minimum ALIE value on isodensity surface
min_esp: Minimum ESP value on isodensity surface
nn_energy: neural network potential energy
nn_gas_energy: neural network gas-phase energy
nn_sol_energy: neural network solution-phase energy
nn_stddev: standard deviation in prediction of neural network energy
nops_on: Indicates a NOPS calculation
nuclear_repulsion: Nuclear Repulsion Energy
opt_excited_state_energy_1: Energy of first excited state geometry optimization
opt_rot: Specific Optical Rotation
orb_ener_alpha: Alpha Orbital Energies for UHF calculations
orb_ener_beta: Beta Orbital Energies for UHF calculations
orb_ener_rhf: Orbital Energies for RHF calculations
orb_symm_alpha: Alpha Orbital Energies for UHF calculations
orb_symm_beta: Beta Orbital Energies for UHF calculations
orb_symm_rhf: Orbital Energies for RHF calculations
oscillator_strengths: Excited state oscillator strengths
paramag_spin_orbit_isotropic: Paramagnetic Spin-Orbit Isotropic Value of Pairs
polar_alpha: Polarizability
polar_beta: First-Order Hyperpolarizability
polar_gamma: Second-Order Hyperpolarizability
raman_activity: Raman Activities of Normal Modes
raman_intensity: Raman Intensities of Normal Modes
reaction_coord: Reaction coordinate Number
reduced_mass: Reduced Masses of Normal Modes
rimp2_corr_energy: RI-MP2 Correlation Energy
rimp2_energy: RI-MP2 Energy
rimp2_os_energy: RI-MP2 Opposite-Spin Energy
rimp2_ss_energy: RI-MP2 Same-Spin Energy
rotational_constants: Rotational constants of molecule
rotational_strength: Rotational Strengths of Normal Modes
s2: Spin: <S**2>
s_epsilon: Total Calculated S_epsilon
s_epsilon_alpha: Total Calculated S_epsilon_alpha
s_epsilon_alpha_cav: Cavity Contribution to S_epsilon_alpha
s_epsilon_alpha_conc: Concentration Contribution to S_epsilon_alpha
s_epsilon_alpha_elec: Electronic Contribution to S_epsilon_alpha
s_epsilon_alpha_rot: Rotational Contribution to S_epsilon_alpha
s_epsilon_alpha_trans: Translational Contribution to S_epsilon_alpha
s_epsilon_alpha_vib: Vibrational Contribution to S_epsilon_alpha
s_epsilon_cav: Cavity Contribution to S_epsilon
s_epsilon_conc: Concentration Contribution to S_epsilon
s_epsilon_elec: Electronic Contribution to S_epsilon
s_epsilon_rot: Rotational Contribution to S_epsilon
s_epsilon_trans: Translational Contribution to S_epsilon
s_epsilon_vib: Vibrational Contribution to S_epsilon
s_omega: Total Calculated S_omega
s_omega_cav: Cavity Contribution to S_omega
s_omega_conc: Concentration Contribution to S_omega
s_omega_elec: Electronic Contribution to S_omega
s_omega_rot: Rotational Contribution to S_omega
s_omega_trans: Translational Contribution to S_omega
s_omega_vib: Vibrational Contribution to S_omega
scf_energy: SCF Energy
sig_neg_alie: Variance of negative ALIE on isodensity surface
sig_neg_esp: Variance of negative ESP on isodensity surface
sig_pos_alie: Variance of positive ALIE on isodensity surface
sig_pos_esp: Variance of positive ESP on isodensity surface
sig_tot_alie: Total ALIE variance on isodensity surface
sig_tot_esp: Total ESP variance on isodensity surface
singlet_excitation_energies: Restricted Singlet Electronic excitation energies
singlet_excited_dipole_moments: Restricted singlet excited state dipole moments
singlet_excited_esp_dipole_moments: Restricted singlet ESP excited state dipole moments
singlet_oscillator_strengths: Singlet excited state oscillator strengths
singlet_transition_dipole_moments: Restricted singlet transition dipole moments
sm_iter: Iteration number of string method
sm_point: Num of points along string method string
solution_phase_energy: Solution Phase Energy
solvation_energy: Solvation Energy
spin_dipole_isotropic: Spin-Dipole Isotropic Value of Pairs
spin_splitting_score: Ligand field spin-splitting score for DBLOC calculations
symmetry: Symmetries of Normal Modes
symmetry_number: symmetry number for molecule
sz2: Spin: Sz*<Sz+1>
total_lo_correction: Total localized orbital energy correction
total_spin_spin_isotropic: Total Spin-Spin Isotropic Value of Pairs
transition_dipole_moments: Transition dipole moments
transition_state_components: Transition State Components
triplet_excitation_energies: Restricted triplet electronic excitation energies
triplet_excited_dipole_moments: Restricted triplet excited state dipole moments
triplet_excited_esp_dipole_moments: Restricted triplet excited ESP state dipole moments
triplet_oscillator_strengths: Triplet excitation energy oscillator strengths
triplet_transition_dipole_moments: Restricted triplet transition dipole moments
zero_point_energy: Zero Point Energy
zvar: a mapping of scan variable names to values
List of available Atomic Descriptors
atom_name: Atom Name
charge_esp: Atomic Charges from ESP
charge_lowdin: Lowdin Atomic Charges
charge_mulliken: Mulliken Atomic Charges
charge_nbo: Atomic Charges from NBO
charge_stockholder: Stockholder Atomic Charges
epn: Electrostatic Potential at Atomic Nuclei
forces: Atomic Forces
homo_nn: Atomic Fukui Indices, f_NN HOMO
homo_ns: Atomic Fukui Indices, f_NS HOMO
homo_sn: Atomic Fukui Indices, f_SN HOMO
homo_ss: Atomic Fukui Indices, f_SS HOMO
isotope: Isotope of Atom
lumo_nn: Atomic Fukui Indices, f_NN LUMO
lumo_ns: Atomic Fukui Indices, f_NS LUMO
lumo_sn: Atomic Fukui Indices, f_SN LUMO
lumo_ss: Atomic Fukui Indices, f_SS LUMO
maxat_alie: Max Atomic ALIE Values
maxat_esp: Max Atomic ESP Values
minat_alie: Min Atomic ALIE Value
minat_esp: Min Atomic ESP Values
nmr_abs_shift: NMR Atomic Absolute Shifts
nmr_rel_shift: NMR Atomic Relative Shifts
nmr_shielding: NMR Isotropic Shielding per Atom
nmr_tensor: The NMR Shielding tensor (3x3 matrix)
nuclear_magnetic_dipole_moment: Nuclear Magnetic Dipole Moment of Atom
nuclear_spin: Nuclear Spin of Atom
spin_lowdin: Lowdin Spin Densities
spin_mulliken: Mulliken Spin Densities