digichem report

usage: digichem report [options] file.log [file2.log] [-O report.pdf]

Positional Arguments

log_files

a (number of) calculation result file(s) (.log) to extract results from

Default: []

Named Arguments

-C, --calc, --calculation

specify a number of log files that all correspond to the same calculation

Default: []

-m, --merge

a (number of) calculation result file(s) (.log) from which individual results should be merged together, presenting a summary of the merged data rather than each calculation separately

Default: []

-N, --num_cpu

the number of CPUs to use in parallel to parse given log_files, defaults to the number of CPUs on the system

Default: 12

--format

Possible choices: auto, log, yaml, json

the format of the log files to parse, the default is to intelligently guess for each file

Default: “auto”

-O, --output

a filename to write the report to; this option can only be specified if writing a single report

-r, --relative

a filename/path to write each report to, relative to each input file

-d, --dir

an absolute path to write each report to (each report will be created in a subdirectory of this directory)

--name

name of the molecule/system to use in the report

--style

Possible choices: journal, traditional

the style of report to make

Default: “journal”

-M, --memory

the maximum amount of memory to use for cubegen

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: []