digichem database
Reference
usage: digichem database [-h] [-t] [-u] [-m] file {search,s,srh,count,c,cnt,insert,i,ins,slice,S,sli,delete,d,del,recover,r,rec} ...
Positional Arguments
- file
the Silico database file to use. If not specified the default location is used
- program
Possible choices: search, s, srh, count, c, cnt, insert, i, ins, slice, S, sli, delete, d, del, recover, r, rec
Named Arguments
- -t, --tinydb
tinydb format
Default: “auto”
- -u, --unqlite
unqlite format
- -m, --mongita
mongo on-file format
Sub-commands
search (s, srh)
Export data from a Silico database.
Data is searched for in the database according to a number of given criteria. Entries in the database that match all the given criteria are returned in the format specified. Each criterion consists of three main parts: (1) a list of fields, (2) a comparison operator and (3) a match. (1) The field list is delimited by colons, and matches some result in a result set (for example, metadata:user, energies:scf:final etc).
To search in a field that contains a list, the ‘any’ pseudo-field can be specified. For example, to compare orbital energies: orbitals:values:any:energy:value.
A comparison operator, one of the following:
== Exact match, = Case insensitive match, > Greater than, < Less than, >= Greater than or equal to, <= Less than or equal to. Each operator can optionally be prefixed with an exclamation mark (!) to negate it (ie, !== would select all entries that do not match exactly).
A match, a value to check against. Values that look like specific types (ints, floats, bools etc) will be converted appropriately.
digichem database search [-h] [-I] [-V] [--log_level {DEBUG,INFO,WARNING,ERROR,CRITICAL,OFF}] [-S [SETTING ...]] [--config_files [CONFIG_FILES ...]] [--homo [CRITERIA ...]] [--lumo [CRITERIA ...]] [--beta-homo [CRITERIA ...]]
[--beta-lumo [CRITERIA ...]] [--dest [CRITERIA ...]] [--singlet-energy [CRITERIA ...]] [--singlet-wavelength [CRITERIA ...]] [--triplet-energy [CRITERIA ...]] [--triplet-wavelength [CRITERIA ...]]
[--structure [CRITERIA ...]] [--substructure [CRITERIA ...]] [-N] [-i] [-n] [-F FLOAT] [-y | -j | -c | -t | -d | -a | -s] [-f [FILTERS ...]] [-O OUTPUT]
[criteria ...]
Positional Arguments
- criteria
a number of things to search for, consisting of a list of fields, a comparison operator, and something to match against
Default: []
Named Arguments
- --homo
- --lumo
- --beta-homo
- --beta-lumo
- --dest
- --singlet-energy
- --singlet-wavelength
- --triplet-energy
- --triplet-wavelength
- --structure
- --substructure
- -N, --no-parse
disable parsing of raw results into internal result objects, this option will increase execution speed but will disable some advanced filter options
Default: False
- -i, --ignore
ignore missing properties rather than stopping
Default: False
- -n, --none
return an empty value when a missing property is encountered rather than returning nothing at all
Default: False
- -F, --float
number format to use for floats in tabular formats (–sumary, –table and –table-property)
Default: “.2f”
- -f, --filters
a list of filters to restrict which data is parsed (SCF, MOS, atoms etc)
Default: []
- -O, --output
a filename/path to write results to. If none is give, results will be written to stdout, which can also be explicitly requested with ‘-’
Default: “-”
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: []
output format
the format to write results to. Only one option from the following may be chosen
- -y, --yaml
yaml format
Default: “yaml”
- -j, --json
json format
- -c, --csv
CSV tabular format; shows one row per result; useful for comparing many results at once
- -t, --table
text table format; shows one row per result; useful for comparing many results at once
- -d, --csv-property
text property table format; shows one property per table
- -a, --table-property
text property table format; shows one property per table
- -s, --summary
summary text format
Digichem v6.6.3. Written by Oliver S. Lee. Last updated 08/11/2024.
count (c, cnt)
Count the number of matching records in a database
digichem database count [-h] [-I] [-V] [--log_level {DEBUG,INFO,WARNING,ERROR,CRITICAL,OFF}] [-S [SETTING ...]] [--config_files [CONFIG_FILES ...]] [--homo [CRITERIA ...]] [--lumo [CRITERIA ...]] [--beta-homo [CRITERIA ...]]
[--beta-lumo [CRITERIA ...]] [--dest [CRITERIA ...]] [--singlet-energy [CRITERIA ...]] [--singlet-wavelength [CRITERIA ...]] [--triplet-energy [CRITERIA ...]] [--triplet-wavelength [CRITERIA ...]]
[--structure [CRITERIA ...]] [--substructure [CRITERIA ...]] [-N]
[criteria ...]
Positional Arguments
- criteria
a number of things to search for, consisting of a list of fields, a comparison operator, and something to match against
Default: []
Named Arguments
- --homo
- --lumo
- --beta-homo
- --beta-lumo
- --dest
- --singlet-energy
- --singlet-wavelength
- --triplet-energy
- --triplet-wavelength
- --structure
- --substructure
- -N, --no-parse
disable parsing of raw results into internal result objects, this option will increase execution speed but will disable some advanced filter options
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: []
Digichem v6.6.3. Written by Oliver S. Lee. Last updated 08/11/2024.
insert (i, ins)
Insert data into a Silico database.
digichem database insert [-h] [-I] [-V] [--log_level {DEBUG,INFO,WARNING,ERROR,CRITICAL,OFF}] [-S [SETTING ...]] [--config_files [CONFIG_FILES ...]] [--force] [-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
- --force
Force writing to an internal Silico database file.
Default: False
- -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: []
Digichem v6.6.3. Written by Oliver S. Lee. Last updated 08/11/2024.
slice (S, sli)
Take a slice (a sub-section) of a DB and insert into another DB
digichem database slice [-h] [-I] [-V] [--log_level {DEBUG,INFO,WARNING,ERROR,CRITICAL,OFF}] [-S [SETTING ...]] [--config_files [CONFIG_FILES ...]] [-t] [-u] [-m] [--force] [--homo [CRITERIA ...]] [--lumo [CRITERIA ...]]
[--beta-homo [CRITERIA ...]] [--beta-lumo [CRITERIA ...]] [--dest [CRITERIA ...]] [--singlet-energy [CRITERIA ...]] [--singlet-wavelength [CRITERIA ...]] [--triplet-energy [CRITERIA ...]]
[--triplet-wavelength [CRITERIA ...]] [--structure [CRITERIA ...]] [--substructure [CRITERIA ...]] [-N]
out_file [criteria ...]
Positional Arguments
- out_file
the database file to insert into
- criteria
a number of things to search for, consisting of a list of fields, a comparison operator, and something to match against
Default: []
Named Arguments
- -t, --tinydb
tinydb format
Default: “auto”
- -u, --unqlite
unqlite format
- -m, --mongita
mongo on-file format
- --force
Force writing to an internal Silico database file.
Default: False
- --homo
- --lumo
- --beta-homo
- --beta-lumo
- --dest
- --singlet-energy
- --singlet-wavelength
- --triplet-energy
- --triplet-wavelength
- --structure
- --substructure
- -N, --no-parse
disable parsing of raw results into internal result objects, this option will increase execution speed but will disable some advanced filter options
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: []
Digichem v6.6.3. Written by Oliver S. Lee. Last updated 08/11/2024.
delete (d, del)
Delete data from a Silico database.
digichem database delete [-h] [-I] [-V] [--log_level {DEBUG,INFO,WARNING,ERROR,CRITICAL,OFF}] [-S [SETTING ...]] [--config_files [CONFIG_FILES ...]] [-s [SEARCH ...]] [--force] [ids ...]
Positional Arguments
- ids
a number of IDs to delete from the DB
Named Arguments
- -s, --search
a number of things to search for, consisting of a list of fields, a comparison operator, and something to match against
Default: []
- --force
Force writing to an internal Silico database file.
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: []
Digichem v6.6.3. Written by Oliver S. Lee. Last updated 08/11/2024.
recover (r, rec)
Insert data from a temporary cache into a Silico database.
digichem database recover [-h] [-I] [-V] [--log_level {DEBUG,INFO,WARNING,ERROR,CRITICAL,OFF}] [-S [SETTING ...]] [--config_files [CONFIG_FILES ...]] [--force] [-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
- --force
Force writing to an internal Silico database file.
Default: False
- -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: []
Digichem v6.6.3. Written by Oliver S. Lee. Last updated 08/11/2024.