digichem submit

usage: digichem submit [options] coord1.file [coord2.file] -c d1/p1/c1 [d2/p2/c2] [-I]
       digichem submit [options] coord1.file [coord2.file] -m method1.file [method2.file] [-I]

Positional Arguments

coordinate_files

Coordinate input files to submit

Named Arguments

-O, --output

Base directory to perform calculations in. Defaults to the current directory

Default: .

-m, --method-files

Methods to perform, identified by file name

Default: []

-c, --method-codes

Methods to perform, identified either by name or by ID (such, as 1/1/1)

Default: []

-C, --charge

Set the molecular charge of all input files

-M, --multiplicity, --mult

Set the multiplicity of all input files

-o, --options

Set a calculation option to a value. The given option will be set for all calculations.

Default: []

--gen3D

Whether to generate 3D coordinates from any given 2D input coordinate files using a rapid pre-optimisation step (which will scramble existing atom coordinates). The default is True, but only if it can be safely determined that the loaded coordinates are not already in 3D). Set to False to disable all pre-optimisation

-p, --prepare-only

Whether to only perform setup for the calculation without actually performing it

Default: False

--exit-status

If given and the submission is successful, the exit status set by digichem will be a positive integer equal to the number of files successfully submitted. If not given (the default), the exit status will be zero if all given files were submitted successfully, and a negative integer otherwise.

Default: False

General Options

General options that control various aspects of silico

-I, --interactive

Run this command interactively

Default: False

-V, --verbose

Increase verbosity, stack with itself to further increase verbosity (each time this option is given, log_level is increased by one stage)

--log_level

Possible choices: DEBUG, INFO, WARNING, ERROR, CRITICAL, OFF

The level of messages to print

-S, --setting

Set a config option to a value. Options of this type are parsed as if they were a config file (in yaml format) and are then used to set corresponding options, eg -S “absorption_graph: {fwhm: 100}”

Default: []

--config_files

An additional config file to read from. See the master config file for possible config options. Note that the master config file (at silico/data/config/silico.yaml) and user config file (at ~/.config/silico/silico.yaml) are always read automatically and do not need to be specified here. Multiple files may be given and will be processed in the order specified (the last having highest priority)

Default: []