digichem image
usage: digichem image [-h] [-I] [-V] [--log_level {DEBUG,INFO,WARNING,ERROR,CRITICAL,OFF}] [-S [SETTING ...]] [--config_files [CONFIG_FILES ...]] [-i [IMAGE ...]] [-c [CUBE ...]] [--no-overwrite] [-O OUTPUT | -r RELATIVE]
[-d DIR | -R RELATIVE_DIR | -D COMMON_DIR] [-l] [-M MEMORY] [-C [CALC ...]] [-m [MERGE ...]] [-N [NUM_CPU]] [--format {auto,log,yaml,json}]
[log_files ...]
Positional Arguments
- log_files
a (number of) calculation result file(s) (.log) to extract results from
Default: []
Named Arguments
- -i, --image
a list of the images to generate
Default: []
- -c, --cube
a list of cube files to generate
Default: []
- --no-overwrite
don’t overwrite existing image files
Default: False
- -O, --output
an absolute path to write the image to
- -r, --relative
a path to write the image to, relative to each input file
- -l, --list
show a list of available images for each result file
Default: False
- -M, --memory
the maximum amount of memory to use for cubegen
- -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”
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: []
Working directory options
These options control the working directory for report/image generation. The working directory is where Digichem initially writes the files for each report. Files may be copied from this location if a different output location has been specified. The default working directory is the Report folder.
- -d, --dir
the working directory, specified as an absolute path (each image will be created in the image subdirectory of this directory)
- -R, --relative-dir
the working directory, relative to each input file (each image will be created in the image subdirectory of this directory)
- -D, --common-dir
use a common working directory, with a separate sub-folder for each molecule (each image will be created in the image subdirectory of this directory)