The SQL database consists of two tables, model and contrib. The column wrapId is used to link them.
A wrapId uniquely identifies a single invocation of wrapUpload.py to upload a group of directories. A typical wrapId is:
@2013.08.13@12.58.22.735311@someUser@home.someUser.redmesa.old.td.testlada.2013.04.06.Fe.O@
The wrapId is broken into fields separated by “@”:
- Date, yyyy.mm.dd
- Time, hh.mm.ss.uuuuuu where uuuuuu is microseconds padded to 6 characters
- User name.
- Top directory specified to wrapUpload, with “/” replaced by ”.”.
The model table has an auto-increment key, mident. The mident value is used as a unique indentifier for entries in the MatDB. The model table has about 60 columns, and the columns fall into a few main categories:
Some example general metadata columns are:
Column SQL type Description mident serial Unique auto-increment ID wrapid text Upload identifier, link with contrib table abspath text Absolute path to dir relpath text Relative path below topDir
The ICSD info is present only on runs adhering to the ICSD file naming conventions. To extract ICSD info from the file names, file names must be like:
.../icsd_083665/icsd_083665.cif/ls-anti-ferro-7/relax_cellshape/1
^^^^^^ ^^^^^^^^ ^ ^^^^^^^^^^^^^^^ ^
icsdNum magType magNum relaxType relaxNum
Some example ICSD information columns are:
Column SQL type Description icsdNum int ICSD number in CIF file magType text type of magnetic moment hs-ferro, etc. magNum int number of hs-anti-ferro or ls-anti-ferro relaxType text Type of run: relax-cellshape, etc. relaxNum int Folder num for relax runs
Some example VASP input columns are:
Column SQL type Description encut_ev double VASP ENCUT parameter from INCAR ibrion int VASP IBRION parameter from INCAR isif int VASP ISIF parameter from INCAR
The majority of the columns in the model table are VASP output values. Some example VASP output columns are:
Column SQL type Description typeNames text[] [‘Mo’, ‘S’] typeNums int[] [2, 4] finalBasisMat double precision[][] finalRecipBasisMat double precision[][] finalForceMat_ev_ang double precision[][] eV/angstrom finalStressMat_kbar double precision[][] kbar finalPressure_kbar double precision kbar eigenMat double precision[][] energyNoEntrp double precision eV energyPerAtom double precision eV
The author metadata columns derive from the metadata files specified by the researcher. Some example author metadata columns are:
Column SQL type Description hashstring text sha512 of our vasprun.xml meta_parents text[] sha512 of parent vasprun.xml, or null meta_firstName text metadata: first name meta_lastName text metadata: last name meta_publications text[] metadata: publication DOI or placeholder meta_standards text[] metadata: controlled vocab keywords meta_keywords text[] metadata: uncontrolled vocab keywords meta_notes text metadata: notes
The contrib table is brief, consisting of ...
Column SQL type Description wrapid text wrapId for this upload, link with model table curdate timestamp date, time of this wrapId userid text user id doing the upload hostname text hostname of the upload topDir text top level dir of the upload numkeptdir int num of subdirs uploaded reldirs text[] list of relative subdirs