autofile.fs¶

This module generates managers for the various layers in the file system.

The overall file system layout is as follows:

PREFIX/
    SPECIES/THEORY
        CONFORMER*/ [SINGLE POINT*/ or HIGH SPIN*/]
            SYMMETRY/
            ZMATRIX/
                SCAN*/ [SINGLE POINT*/ or HIGH SPIN*/]
                CSCAN*/ [SINGLE POINT*/ or HIGH SPIN*/]
    REACTION/THEORY/
        ZMATRIX/
            SCAN*/
        TRANSITION STATE*/
            CONFORMER*/ [SINGLE POINT*/ or HIGH SPIN*/]
                SYMMETRY/
                ZMATRIX/
                    SCAN*/ [SINGLE POINT*/ or HIGH SPIN*/]
                    CSCAN*/

* Directory layer where electronic structure jobs are run.

Manager for the species-specific layer:

SPECIES: autofile.fs.species()

Managers for the reaction-specific layers:

REACTION: autofile.fs.reaction()
TRANSITION STATE: autofile.fs.transition_state()

Managers for layers used by both species and reaction file systems:

THEORY: autofile.fs.theory()
CONFORMER: autofile.fs.conformer()
SYMMETRY: autofile.fs.symmetry()
SINGLE POINT: autofile.fs.single_point()
HIGH SPIN: autofile.fs.high_spin()
ZMATRIX: autofile.fs.zmatrix()
SCAN: autofile.fs.scan()
CSCAN: autofile.fs.cscan()
VRCTST: autofile.fs.vrctst()

Each function in this module returns a tuple of autofile.model.DataSeries objects for interacting with successive layers in a file system.

class autofile.fs.FileAttributeName¶: DataFile attribute names

autofile.fs.species(prefix)¶

Create a species file system manager for a given path.

Layers:

[0] The species “trunk” layer.

Specifiers: []

(no files)

Generated by autofile.schema.data_series.species_trunk()

[1] The species “leaf” layer.

Specifiers: [InChI String, Charge, Spin Multiplicity]

(no files)

Generated by autofile.schema.data_series.species_leaf()

Parameters: prefix (str) – Path to where the file system will be created
Returns: A tuple of DataSeries objects. Each item in this tuple manages a different layer in the file system, as described above.

autofile.fs.reaction(prefix)¶

construct the reaction filesystem (2 layers)

locators:

0 - []: (no files)
1 - [rxn_ichs, rxn_chgs, rxn_muls, ts_mul]: (no files)

Parameters: prefix (str) – sets the path where this filesystem will sit

autofile.fs.transition_state(prefix)¶

construct the ts filesystem (1 layer)

locators:

0 - []: files: - energy - geometry - zmatrix

1 - [TS Number]

Parameters: prefix (str) – sets the path where this filesystem will sit

autofile.fs.theory(prefix)¶

construct the theory filesystem (1 layer)

locators:

[0] “leaf” layer”: Specifiers: [method, basis, orb_type]

Parameters: prefix (str) – sets the path where this filesystem will sit

autofile.fs.conformer(prefix)¶

Create a conformer file system manager for a given path.

Layers:

[0] The “trunk” layer.

Specifiers: []

Generated by autofile.schema.data_series.conformer_trunk()

[1] The “branch” layer.

Specifiers: [Ring ID]

Files:

info
energy
trajectory

Generated by autofile.schema.data_series.conformer_branch()

[2] The “leaf” layer.

Specifiers: [Conformer ID]

Files:

geometry_info
gradient_info
hessian_info
geometry_input
gradient_input
hessian_input
geometry
gradient
hessian
harmonic_frequencies
vpt2_info
vpt2_input
anharmonic_frequencies
anharmonic_zpve
anharmonicity_matrix
vibro_rot_alpha_matrix
quartic_centrifugal_dist_consts
cubic_force_constants
quartic_force_constants
dipole_moment
polarizability

Generated by autofile.schema.data_series.conformer_leaf()

Parameters: prefix (str) – Path to where the file system will be created
Returns: A tuple of DataSeries objects. Each item in this tuple manages a different layer in the file system, as described above.

autofile.fs.single_point(prefix, json_layer=None)¶

construct the single-point filesystem (2 layers)

locators:

0 - []: (no files)
1 - [method, basis, orb_type]: files: - info - input - energy

Parameters: prefix (str) – sets the path where this filesystem will sit

autofile.fs.high_spin(prefix)¶

construct the high-spin, single-point filesystem (2 layers)

locators:

0 - []: (no files)
1 - [method, basis, orb_type]: files: - info - input - energy

Parameters: prefix (str) – sets the path where this filesystem will sit

autofile.fs.symmetry(prefix)¶

Create a symmetry-conformer file system manager for a given path.

Layers:

[0] The “trunk” layer.

Specifiers: []

Files:

trajectory

Generated by autofile.schema.data_series.symmetry_trunk()

[1] The “leaf” layer.

Specifiers: [Conformer ID]

Files:

geometry

Generated by autofile.schema.data_series.conformer_leaf()

Parameters: prefix (str) – Path to where the file system will be created
Returns: A tuple of DataSeries objects. Each item in this tuple manages a different layer in the file system, as described above.

autofile.fs.zmatrix(prefix)¶

Create a z-matrix file system manager for a given path.

Layers:

[0] The zmatrix “trunk” layer.

Specifiers: []

(no files)

Generated by autofile.schema.data_series.zmatrix_trunk()

[1] The zmatrix “leaf” layer.

Specifiers: [Z-Matrix Number]

Files:

Generated by autofile.schema.data_series.zmatrix_leaf()

Parameters: prefix (str) – Path to where the file system will be created
Returns: A tuple of DataSeries objects. Each item in this tuple manages a different layer in the file system, as described above.

autofile.fs.scan(prefix)¶

construct the scan filesystem (3 layers)

three layers with the following locators:

0 - []: files: - vmatrix
1 - [coo_names]: files: - info - trajectory
2 - [coo_names, coo_vals]: files: - geometry_info - gradient_info - hessian_info - irc_info - geometry_input - gradient_input - hessian_input - irc_input - energy - geometry - zmatrix - gradient - hessian - harmonic_frequencies

Parameters: prefix (str) – sets the path where this filesystem will sit

autofile.fs.cscan(prefix)¶

Create a constrained scan (c-scan) file system manager for a given path.

Layers:

[0] The c-scan “trunk” layer.

Specifiers: []

(no files)

Generated by autofile.schema.data_series.cscan_trunk()

[1] The first c-scan “branch” layer.

Specifiers: [Constraints]

Files:

info
trajectory

Generated by autofile.schema.data_series.cscan_branch1()

[2] The second c-scan “branch” layer.

Specifiers: [Constraints, Scan Coordinate Names]

(no files)

Generated by autofile.schema.data_series.cscan_branch2()

[3] The c-scan “leaf” layer.

Specifiers: [Constraints, Scan Coordinate Names, Scan Coordinate Values]

Files:

geometry_info
gradient_info
hessian_info
geometry_input
gradient_input
hessian_input
energy
geometry
zmatrix
gradient
hessian
harmonic_frequencies

Generated by autofile.schema.data_series.cscan_leaf()

Parameters: prefix (str) – Path to where the file system will be created
Returns: A tuple of DataSeries objects. Each item in this tuple manages a different layer in the file system, as described above.

autofile.fs.tau(prefix)¶

construct the tau filesystem (2 layers)

locators:

0 - []: files: - vmatrix - info - trajectory
0 - [tid]: files: - geometry_info - gradient_info - hessian_info - geometry_input - gradient_input - hessian_input - energy - geometry - zmatrix - gradient - hessian - harmonic_frequencies

Parameters: prefix (str) – sets the path where this filesystem will sit

autofile.fs.energy_transfer(prefix)¶

construct the energy transfer filesystem (3 layers)

locators:

0 - []: files: - info
1 - [ich, chg, mul]: (no files)
2 - [ich, chg, mul, method, basis, orb_type]: files: - lennard_jones_epsilon - lennard_jones_sigma - trajectory

Parameters: prefix (str) – sets the path where this filesystem will sit

autofile.fs.vrctst(prefix)¶

Create a VRC-TST file system manager for a given path.

Layers:

[0] The VRC-TST “trunk” layer.

Specifiers: []

(no files)

Generated by autofile.schema.data_series.vrctst_trunk()

[1] The VRC-TST “leaf” layer.

Specifiers: [VRC-TST Number]

Files:

tst.inp (VaReCoF Input)
divsur.inp (VaReCoF Input)
els.tml (VaReCoF Input)
structure.inp (VaReCoF Input)
corr_pot.f (VaReCoF Input)
flux file

Generated by autofile.schema.data_series.vrctst_leaf()

Parameters: prefix (str) – Path to where the file system will be created
Returns: A tuple of DataSeries objects. Each item in this tuple manages a different layer in the file system, as described above.

autofile.fs.run(prefix)¶

construct the run filesystem (2 layers)

locators:

0 - []: files: - info
1 - [job]: files: - info - input - output - geometry - zmatrix

Parameters: prefix (str) – sets the path where this filesystem will sit

autofile.fs.subrun(prefix)¶

construct the subrun filesystem (1 layer)

locators:

0 - [macro_idx, micro_idx]: files: - info - input - output

Parameters: prefix (str) – sets the path where this filesystem will sit

autofile.fs.build(prefix)¶

construct the build filesystem (2 layers)

locators:

0 - [job]: (no files)
2 - [job, formula]: (no files)
2 - [job, formula, num]: files: - input - output

Parameters: prefix (str) – sets the path where this filesystem will sit

autofile.fs.path(pfx, key_locs_lst)¶: Get the path through a file system hierarchy

autofile.fs.manager(pfx, key_locs_lst, key)¶: Get the manager for a specific part of the file system

autofile.fs.iterate_locators(pfx, keys)¶: Iterate over locators for all existing paths

autofile.fs.iterate_paths(pfx, keys)¶: Iterate over all existing paths

autofile.fs.iterate_managers(pfx, keys, key)¶: Iterate over managers at a specific level in the file system hierarchy

autofile.fs.path_prefix(pth, keys)¶

Given a path and some layer keys, find the prefix

Parameters

pth – The path to some point in the file system
keys – Keys to layers on top of the desired prefix

Returns

The prefix path (the original path, without the layers specified by keys)

autofile.fs¶

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