TCOD database exporter¶
TCOD database exporter is used to export computation results of
StructureData
,
CifData
and
TrajectoryData
(or any other data type, which can be converted to them) to the
Theoretical Crystallography Open Database (TCOD).
Setup¶
To be able to export data to TCOD, one has to
install dependencies for CIF manipulation
as well as cod-tools package, and set up an
AiiDA Code
for cif_cod_deposit
script
from cod-tools.
How to deposit a structure¶
Best way to deposit data is to use the command line interface:
verdi DATATYPE structure deposit tcod [--type {published,prepublication,personal}]
[--username USERNAME] [--password]
[--user-email USER_EMAIL] [--title TITLE]
[--author-name AUTHOR_NAME]
[--author-email AUTHOR_EMAIL] [--url URL]
[--code CODE_LABEL]
[--computer COMPUTER_NAME]
[--replace REPLACE] [-m MESSAGE]
[--reduce-symmetry] [--no-reduce-symmetry]
[--parameter-data PARAMETER_DATA]
[--dump-aiida-database]
[--no-dump-aiida-database]
[--exclude-external-contents]
[--no-exclude-external-contents] [--gzip]
[--no-gzip]
[--gzip-threshold GZIP_THRESHOLD]
PK
Where:
DATATYPE
– one of AiiDA structural data types (at the moment of writing, they wereStructureData
,CifData
andTrajectoryData
);TITLE
– the title of the publication, where the exported data is/will be published; in case of personal communication, the title should be chosen so as to reflect the exported dataset the best;CODE_LABEL
– label of AiiDACode
, associated with cif_cod_deposit;COMPUTER_NAME
– name of AiiDAComputer
, where cif_cod_deposit script is to be launched;REPLACE
– TCOD ID of the replaced entry in the event of redeposition;MESSAGE
– string to describe changes for redeposited structures;--reduce-symmetry
,--no-reduce-symmetry
– turn on/off symmetry reduction of the exported structure (on by default);--parameter-data
– specify the PK ofParameterData
object, describing the result of the final (or single) calculation step of the workflow;--dump-aiida-database
,--no-dump-aiida-database
– turn on/off addition of relevant AiiDA database dump (on by default).Warning
be aware that TCOD is an open database, thus no copyright-protected data should be deposited unless permission is given by the owner of the rights.
Note
data, which is deposited as pre-publication material, will be kept private on TCOD server and will not be disclosed to anyone without depositor’s permission.
--exclude-external-contents
,--no-exclude-external-contents
– exclude contents of initial input files, that containsource
property with definitions on how to obtain the contents from external resources (on by default);--gzip
, –no-gzip` – turn on/off gzip compression for large files (off by default);--gzip-threshold
sets the minimum file size to be compressed.
Other command line options correspond to the options of cif_cod_deposit of the same name. To ease the use of TCOD exporter, one can define persistent parameters in AiiDA properties. Corresponding command line parameters and AiiDA properties are presented in the table:
Command line parameter | AiiDA property |
---|---|
--author-email |
tcod.depositor_author_email |
--author-name |
tcod.depositor_author_name |
--user-email |
tcod.depositor_email |
--username |
tcod.depositor_password |
--password |
tcod.depositor_username |
Note
--password
does not accept any value; instead, the option
will prompt the user to enter one’s password in the terminal.
Note
command line parameters can be used to override AiiDA properties even if properties are set.
Return values¶
The deposition process, which is of
JobCalculation
type, returns the output of cif_cod_deposit
, wrapped in
ParameterData
.