autofile.schema¶

autofile.schema.loc_maps¶

specifier mappings for naming directories in a DataSeries

autofile.schema.loc_maps.species_trunk()¶: species trunk directory name

autofile.schema.loc_maps.species_leaf(ich, chg, mul)¶: species leaf directory name

autofile.schema.loc_maps.reaction_trunk()¶: reaction trunk directory name

autofile.schema.loc_maps.reaction_leaf(rxn_ichs, rxn_chgs, rxn_muls, ts_mul)¶: reaction leaf directory name

autofile.schema.loc_maps.reaction_is_reversed(rxn_ichs, rxn_chgs, rxn_muls)¶: sort inchis, chgs, and muliplicities together

autofile.schema.loc_maps.sort_together(rxn_ichs, rxn_chgs, rxn_muls)¶: sort inchis, chgs, and muliplicities together

autofile.schema.loc_maps.transition_state_trunk()¶: transition state trunk directory name

autofile.schema.loc_maps.transition_state_leaf(num)¶: transition state leaf directory name

autofile.schema.loc_maps.theory_leaf(method, basis, orb_type)¶

theory leaf directory name

This need not be tied to elstruct – just take out the name checks.

Parameters

method (str) – the name of the electronic structure method
basis (str) – the atomic orbital basis set
orb_type (str) – ‘R’ indicates restricted orbitals, ‘U’ indicates unrestricted orbitals

autofile.schema.loc_maps.conformer_trunk()¶: conformer trunk directory name

autofile.schema.loc_maps.conformer_branch(rid)¶: ring conformer leaf directory name

autofile.schema.loc_maps.conformer_leaf(cid)¶: torsion conformer leaf directory name

autofile.schema.loc_maps.generate_new_conformer_id()¶: generate a new conformer identifier

autofile.schema.loc_maps.generate_new_ring_id()¶: generate a new conformer identifier

autofile.schema.loc_maps.single_point_trunk()¶: single point trunk directory name

autofile.schema.loc_maps.high_spin_trunk()¶: high spin, single point trunk directory name

autofile.schema.loc_maps.symmetry_trunk()¶: symmetric-conformer trunk directory name

autofile.schema.loc_maps.zmatrix_trunk()¶: zmatrix trunk directory name

autofile.schema.loc_maps.zmatrix_leaf(num)¶: zmatrix leaf directory name

autofile.schema.loc_maps.scan_trunk()¶: scan trunk directory name

autofile.schema.loc_maps.scan_branch(coo_names)¶: scan branch directory name

autofile.schema.loc_maps.scan_leaf(coo_vals)¶: scan leaf directory name

autofile.schema.loc_maps.cscan_trunk()¶: constrained scan trunk directory name

autofile.schema.loc_maps.cscan_branch1(cons_coo_val_dct)¶

constrained scan branch 1 directory name

Parameters: cons_coo_val_dct (dict) – a dictionary of the constraint values, keyed by coordinate name

autofile.schema.loc_maps.cscan_branch2(coo_names)¶: constrained scan branch 2 directory name

autofile.schema.loc_maps.cscan_leaf(coo_vals)¶: constrained scan leaf directory name

autofile.schema.loc_maps.tau_trunk()¶: tau trunk directory name

autofile.schema.loc_maps.tau_leaf(tid)¶: tau leaf directory name

autofile.schema.loc_maps.generate_new_tau_id()¶: generate a new conformer identifier

autofile.schema.loc_maps.energy_transfer_trunk()¶: energy_transfer trunk directory name

autofile.schema.loc_maps.vrctst_trunk()¶: vrctst trunk directory name

autofile.schema.loc_maps.vrctst_leaf(num)¶: vrctst leaf directory name

autofile.schema.loc_maps.run_trunk()¶: run trunk directory name

autofile.schema.loc_maps.run_leaf(job)¶: run leaf directory name

autofile.schema.loc_maps.subrun_leaf(macro_idx, micro_idx)¶: run leaf directory name

autofile.schema.loc_maps.build_trunk(head)¶: build trunk directory name

autofile.schema.loc_maps.build_branch(_string)¶: build branch directory name

autofile.schema.loc_maps.build_leaf(val)¶: build leaf directory name

autofile.schema.loc_maps.get_next_build_number(num)¶: determine the next build number

autofile.schema.data_series¶

DataSeriess

autofile.schema.data_series.species_trunk(prefix, root_ds=None)¶

species trunk DataSeries

Parameters: prefix (string) – path to trunk
Returns: dataseries filesystem object for trunk
Type: DataSeries

autofile.schema.data_series.species_leaf(prefix, root_ds=None)¶

species leaf DataSeries

Parameters: prefix (string) – path to leaf
Returns: dataseries filesystem object for leaf
Type: DataSeries

autofile.schema.data_series.reaction_trunk(prefix, root_ds=None)¶

reaction trunk DataSeries

Parameters: prefix (string) – path to trunk
Returns: dataseries filesystem object for trunk
Type: DataSeries

autofile.schema.data_series.reaction_leaf(prefix, root_ds=None)¶

reaction leaf DataSeries

Parameters: prefix (string) – path to leaf
Returns: dataseries filesystem object for leaf
Type: DataSeries

autofile.schema.data_series.transition_state_trunk(prefix, root_ds=None)¶

transition state trunk DataSeries

Parameters: prefix (string) – path to trunk
Returns: dataseries filesystem object for trunk
Type: DataSeries

autofile.schema.data_series.transition_state_leaf(prefix, root_ds=None)¶

transition state leaf DataSeries

Parameters: prefix (string) – path to leaf
Returns: dataseries filesystem object for leaf
Type: DataSeries

autofile.schema.data_series.theory_leaf(prefix, root_ds=None)¶

theory leaf DataSeries

Parameters: prefix (string) – path to leaf
Returns: dataseries filesystem object for leaf
Type: DataSeries

autofile.schema.data_series.conformer_trunk(prefix, root_ds=None)¶

conformer trunk DataSeries

Parameters: prefix (string) – path to trunk
Returns: dataseries filesystem object for trunk
Type: DataSeries

autofile.schema.data_series.conformer_branch(prefix, root_ds=None)¶

conformer branch DataSeries

Parameters: prefix (string) – path to branch
Returns: dataseries filesystem object for branch
Type: DataSeries

autofile.schema.data_series.conformer_leaf(prefix, root_ds=None)¶

conformer leaf DataSeries

Parameters: prefix (string) – path to leaf
Returns: dataseries filesystem object for leaf
Type: DataSeries

autofile.schema.data_series.single_point_trunk(prefix, root_ds=None)¶

single point trunk DataSeries

Parameters: prefix (string) – path to trunk
Returns: dataseries filesystem object for trunk
Type: DataSeries

autofile.schema.data_series.single_point_leaf(prefix, root_ds=None)¶

single-point leaf DataSeries

Parameters: prefix (string) – path to leaf
Returns: dataseries filesystem object for leaf
Type: DataSeries

autofile.schema.data_series.high_spin_trunk(prefix, root_ds=None)¶

high spin, single point trunk DataSeries

Parameters: prefix (string) – path to trunk
Returns: dataseries filesystem object for trunk
Type: DataSeries

autofile.schema.data_series.high_spin_leaf(prefix, root_ds=None)¶

high-spin, single-point leaf DataSeries

Parameters: prefix (string) – path to leaf
Returns: dataseries filesystem object for leaf
Type: DataSeries

autofile.schema.data_series.symmetry_trunk(prefix, root_ds=None)¶

symmetric-conformer trunk DataSeries

Parameters: prefix (string) – path to trunk
Returns: dataseries filesystem object for trunk
Type: DataSeries

autofile.schema.data_series.zmatrix_trunk(prefix, root_ds=None)¶

zmatrix trunk DataSeries

Parameters: prefix (string) – path to trunk
Returns: dataseries filesystem object for trunk
Type: DataSeries

autofile.schema.data_series.zmatrix_leaf(prefix, root_ds=None)¶

zmatrix leaf DataSeries

Parameters: prefix (string) – path to leaf
Returns: dataseries filesystem object for leaf
Type: DataSeries

autofile.schema.data_series.scan_trunk(prefix, root_ds=None)¶

scan trunk DataSeries

Parameters: prefix (string) – path to trunk
Returns: dataseries filesystem object for trunk
Type: DataSeries

autofile.schema.data_series.scan_branch(prefix, root_ds=None)¶

scan branch DataSeries

Parameters: prefix (string) – path to branch
Returns: dataseries filesystem object for branch
Type: DataSeries

autofile.schema.data_series.scan_leaf(prefix, root_ds=None)¶

scan leaf DataSeries

Parameters: prefix (string) – path to leaf
Returns: dataseries filesystem object for leaf
Type: DataSeries

autofile.schema.data_series.cscan_trunk(prefix, root_ds=None)¶

constrained scan trunk DataSeries

Parameters: prefix (string) – path to trunk
Returns: dataseries filesystem object for trunk
Type: DataSeries

autofile.schema.data_series.cscan_branch1(prefix, root_ds=None)¶

constrained scan branch 2 DataSeries

Parameters: prefix (string) – path to branch
Returns: dataseries filesystem object for branch
Type: DataSeries

autofile.schema.data_series.cscan_branch2(prefix, root_ds=None)¶

constrained scan branch 1 DataSeries

Parameters: prefix (string) – path to branch
Returns: dataseries filesystem object for branch
Type: DataSeries

autofile.schema.data_series.cscan_leaf(prefix, root_ds=None)¶

constrained scan leaf DataSeries

Parameters: prefix (string) – path to leaf
Returns: dataseries filesystem object for leaf
Type: DataSeries

autofile.schema.data_series.tau_trunk(prefix, root_ds=None)¶

tau trunk DataSeries

Parameters: prefix (string) – path to trunk
Returns: dataseries filesystem object for trunk
Type: DataSeries

autofile.schema.data_series.tau_leaf(prefix, root_ds=None)¶

tau leaf DataSeries

Parameters: prefix (string) – path to leaf
Returns: dataseries filesystem object for leaf
Type: DataSeries

autofile.schema.data_series.energy_transfer_trunk(prefix, root_ds=None)¶

energy transfer trunk DataSeries

Parameters: prefix (string) – path to trunk
Returns: dataseries filesystem object for trunk
Type: DataSeries

autofile.schema.data_series.energy_transfer_branch(prefix, root_ds=None)¶

energy transfer branch DataSeries

Parameters: prefix (string) – path to branch
Returns: dataseries filesystem object for branch
Type: DataSeries

autofile.schema.data_series.energy_transfer_leaf(prefix, root_ds=None)¶

energy transfer leaf DataSeries

Parameters: prefix (string) – path to leaf
Returns: dataseries filesystem object for leaf
Type: DataSeries

autofile.schema.data_series.vrctst_trunk(prefix, root_ds=None)¶

vrctst trunk DataSeries

Parameters: prefix (string) – path to trunk
Returns: dataseries filesystem object for trunk
Type: DataSeries

autofile.schema.data_series.vrctst_leaf(prefix, root_ds=None)¶

vrctst leaf DataSeries

Parameters: prefix (string) – path to leaf
Returns: dataseries filesystem object for leaf
Type: DataSeries

autofile.schema.data_series.run_trunk(prefix, root_ds=None)¶

run trunk DataSeries

Parameters: prefix (string) – path to trunk
Returns: dataseries filesystem object for trunk
Type: DataSeries

autofile.schema.data_series.run_leaf(prefix, root_ds=None)¶

run leaf DataSeries

Parameters: prefix (string) – path to leaf
Returns: dataseries filesystem object for leaf
Type: DataSeries

autofile.schema.data_series.subrun_leaf(prefix, root_ds=None)¶

subrun leaf DataSeries

Parameters: prefix (string) – path to leaf
Returns: dataseries filesystem object for leaf
Type: DataSeries

autofile.schema.data_series.build_trunk(prefix, root_ds=None)¶

build trunk DataSeries

Parameters: prefix (string) – path to trunk
Returns: dataseries filesystem object for trunk
Type: DataSeries

autofile.schema.data_series.build_branch(prefix, root_ds=None)¶

build trunk DataSeries

Parameters: prefix (string) – path to trunk
Returns: dataseries filesystem object for trunk
Type: DataSeries

autofile.schema.data_series.build_leaf(prefix, root_ds=None)¶

build leaf DataSeries

Parameters: prefix (string) – path to leaf
Returns: dataseries filesystem object for leaf
Type: DataSeries

autofile.schema.data_files¶

DataFiles

autofile.schema.data_files.information(file_prefix, function=None)¶

information DataFile

Parameters

file_prefix (str) – path to file
function (callable) – optional information-generator function, for checking the function signature against the information object

Returns

instance of DataFile class

Return type

Datafile

autofile.schema.data_files.locator(file_prefix, map_dct_, loc_keys)¶

locator DataFile

Specifiers are stored in information files according to map_dct_ and read back out according to loc_keys_. The file may contain auxiliary information (such as SMILES along with InChI), but for the read to work it must contain each locator value.

Parameters

map_dct (dict[key: callable]) – Maps on the locator list to the values stored in the information file, by key.
loc_keys (tuple[str]) – Keys to the original locator values.

autofile.schema.data_files.input_file(file_prefix)¶

generate input file DataFile

Parameters: file_prefix (str) – path to file
Returns: instance of DataFile class
Return type: Datafile

autofile.schema.data_files.output_file(file_prefix)¶

generate output file DataFile

Parameters: file_prefix (str) – path to file
Returns: instance of DataFile class
Return type: Datafile

autofile.schema.data_files.instability(file_prefix)¶: Generate a data file for instabiliy

autofile.schema.data_files.energy(file_prefix)¶

generate energy DataFile

Parameters: file_prefix (str) – path to file
Returns: instance of DataFile class
Return type: Datafile

autofile.schema.data_files.geometry(file_prefix)¶

generate geometry DataFile

Parameters: file_prefix (str) – path to file
Returns: instance of DataFile class
Return type: Datafile

autofile.schema.data_files.gradient(file_prefix)¶

generate gradient DataFile

Parameters: file_prefix (str) – path to file
Returns: instance of DataFile class
Return type: Datafile

autofile.schema.data_files.hessian(file_prefix)¶

generate hessian DataFile

Parameters: file_prefix (str) – path to file
Returns: instance of DataFile class
Return type: Datafile

autofile.schema.data_files.harmonic_frequencies(file_prefix)¶

generate harmonic_frequencies DataFile

Parameters: file_prefix (str) – path to file
Returns: instance of DataFile class
Return type: Datafile

autofile.schema.data_files.anharmonic_frequencies(file_prefix)¶

generate anharmonic_frequencies DataFile

Parameters: file_prefix (str) – path to file
Returns: instance of DataFile class
Return type: Datafile

autofile.schema.data_files.anharmonic_zpve(file_prefix)¶

generate anharmonic_zpve DataFile

Parameters: file_prefix (str) – path to file
Returns: instance of DataFile class
Return type: Datafile

autofile.schema.data_files.cubic_force_constants(file_prefix)¶

generate cubic_force_constants DataFile

Parameters: file_prefix (str) – path to file
Returns: instance of DataFile class
Return type: Datafile

autofile.schema.data_files.quartic_force_constants(file_prefix)¶

generate quartic_force_constants DataFile

Parameters: file_prefix (str) – path to file
Returns: instance of DataFile class
Return type: Datafile

autofile.schema.data_files.anharmonicity_matrix(file_prefix)¶

generate anharmonicity matrix DataFile

Parameters: file_prefix (str) – path to file
Returns: instance of DataFile class
Return type: Datafile

autofile.schema.data_files.vibro_rot_alpha_matrix(file_prefix)¶

generate vibro_rot_alpha matrix DataFile

Parameters: file_prefix (str) – path to file
Returns: instance of DataFile class
Return type: Datafile

autofile.schema.data_files.quartic_centrifugal_dist_consts(file_prefix)¶

generate vibro_rot_alpha matrix DataFile

Parameters: file_prefix (str) – path to file
Returns: instance of DataFile class
Return type: Datafile

autofile.schema.data_files.zmatrix(file_prefix)¶

generate zmatrix DataFile

Parameters: file_prefix (str) – path to file
Returns: instance of DataFile class
Return type: Datafile

autofile.schema.data_files.vmatrix(file_prefix)¶

generate vmatrix DataFile

Parameters: file_prefix (str) – path to file
Returns: instance of DataFile class
Return type: Datafile

autofile.schema.data_files.ring_torsions(file_prefix)¶: generate ring torsions DataFile

autofile.schema.data_files.torsions(file_prefix)¶: generate torsions DataFile

autofile.schema.data_files.trajectory(file_prefix)¶

generate trajectory DataFile

Parameters: file_prefix (str) – path to file
Returns: instance of DataFile class
Return type: Datafile

autofile.schema.data_files.reaction(file_prefix)¶

generate reaction DataFile

Parameters: file_prefix (str) – path to file
Returns: instance of DataFile class
Return type: Datafile

autofile.schema.data_files.lennard_jones_epsilon(file_prefix)¶

generate lennard_jones_epsilon DataFile

Parameters: file_prefix (str) – path to file
Returns: instance of DataFile class
Return type: Datafile

autofile.schema.data_files.lennard_jones_sigma(file_prefix)¶

generate lennard_jones_sigma DataFile

Parameters: file_prefix (str) – path to file
Returns: instance of DataFile class
Return type: Datafile

autofile.schema.data_files.external_symmetry_number(file_prefix)¶

generate external_symmetry_number DataFile

Parameters: file_prefix (str) – path to file
Returns: instance of DataFile class
Return type: Datafile

autofile.schema.data_files.internal_symmetry_number(file_prefix)¶

generate internal_symmetry_number DataFile

Parameters: file_prefix (str) – path to file
Returns: instance of DataFile class
Return type: Datafile

autofile.schema.data_files.lennard_jones_input(file_prefix)¶

generate input file for the LJ params program

Parameters: file_prefix (str) – path to file
Returns: instance of DataFile class
Return type: Datafile

autofile.schema.data_files.lennard_jones_elstruct(file_prefix)¶

generate elec struct template file for the LJ params program

Parameters: file_prefix (str) – path to file
Returns: instance of DataFile class
Return type: Datafile

autofile.schema.data_files.dipole_moment(file_prefix)¶

generate dipole_moment DataFile

Parameters: file_prefix (str) – path to file
Returns: instance of DataFile class
Return type: Datafile

autofile.schema.data_files.polarizability(file_prefix)¶

generate polarizability DataFile

Parameters: file_prefix (str) – path to file
Returns: instance of DataFile class
Return type: Datafile

autofile.schema.data_files.vrctst_tst(file_prefix)¶

generate vrcttst_tst DataFile

Parameters: file_prefix (str) – path to file
Returns: instance of DataFile class
Return type: Datafile

autofile.schema.data_files.vrctst_divsur(file_prefix)¶

generate vrctst_divsur DataFile

Parameters: file_prefix (str) – path to file
Returns: instance of DataFile class
Return type: Datafile

autofile.schema.data_files.vrctst_molpro(file_prefix)¶

generate vrctst_molpro DataFile

Parameters: file_prefix (str) – path to file
Returns: instance of DataFile class
Return type: Datafile

autofile.schema.data_files.vrctst_tml(file_prefix)¶

generate vrctst_tml DataFile

Parameters: file_prefix (str) – path to file
Returns: instance of DataFile class
Return type: Datafile

autofile.schema.data_files.vrctst_struct(file_prefix)¶

generate vrctst_struct DataFile

Parameters: file_prefix (str) – path to file
Returns: instance of DataFile class
Return type: Datafile

autofile.schema.data_files.vrctst_pot(file_prefix)¶

generate vrctst_pot DataFile

Parameters: file_prefix (str) – path to file
Returns: instance of DataFile class
Return type: Datafile

autofile.schema.data_files.vrctst_flux(file_prefix)¶

generate vrctst_flux DataFile

Parameters: file_prefix (str) – path to file
Returns: instance of DataFile class
Return type: Datafile

autofile.schema.info_objects¶

Info objects

autofile.schema.info_objects.conformer_trunk(nsamp)¶

conformer trunk information

Parameters: nsamp (int) – the number of samples

autofile.schema.info_objects.conformer_branch(nsamp)¶

conformer trunk information

Parameters: nsamp (int) – the number of samples

autofile.schema.info_objects.tau_trunk(nsamp, tors_ranges)¶

tau trunk information

Parameters

nsamp (int) – the number of samples
tors_ranges (dict[str: (float, float)]) – sampling ranges [(start, end)] for each torsional coordinate, by z-matrix coordinate name

autofile.schema.info_objects.scan_branch(grids)¶

scan trunk information

Parameters: grids (dict[str: list[float]]) – sampling grids, [val1, val2, …], for each coordinate, by coordinate name

autofile.schema.info_objects.vpt2(fermi_treatment)¶

vpt2 information

Parameters: fermi (str) – description of fermi resonance treatment

autofile.schema.info_objects.lennard_jones(nsamp, program, version)¶: energy transfer trunk

class autofile.schema.info_objects.RunStatus¶: run statuses

autofile.schema.info_objects.run(job, prog, version, method, basis, status, utc_start_time=None, utc_end_time=None)¶: run information

autofile.schema.info_objects.utc_time()¶: current run time

autofile.schema¶

designs the file system schema for automech

autofile.schema.generate_new_conformer_id()¶: generate a new conformer identifier

autofile.schema.generate_new_ring_id()¶: generate a new conformer identifier

autofile.schema.generate_new_tau_id()¶: generate a new conformer identifier

autofile.schema.sort_together(rxn_ichs, rxn_chgs, rxn_muls)¶: sort inchis, chgs, and muliplicities together

autofile.schema.reaction_is_reversed(rxn_ichs, rxn_chgs, rxn_muls)¶: sort inchis, chgs, and muliplicities together

autofile.schema.utc_time()¶: current run time

class autofile.schema.RunStatus¶: run statuses

autofile.schema¶

autofile.schema.loc_maps¶

autofile.schema.data_series¶

autofile.schema.data_files¶

autofile.schema.info_objects¶

autofile.schema¶

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