Commit e85232d7 authored by temok-mx's avatar temok-mx

Further update of README.md; mv metadata.yml -> metadata.yaml

parent a9ea7db5
......@@ -13,7 +13,7 @@ in the same directory as files that also belong to that entry. Parsers
might also read information from these auxillary files. This way you can add more files
to an entry, even if the respective parser/code might not directly support it.
For cp2k please provide at least the files from this table if applicable to your
For CP2K please provide at least the files from this table if applicable to your
calculations (remember that you can provide more files if you want):
......@@ -49,12 +49,12 @@ import sys
from nomad.cli.parse import parse, normalize_all
# match and run the parser
backend = parse(sys.argv[1])
archive = parse(sys.argv[1])
# run all normalizers
normalize_all(backend)
normalize_all(archive)
# get the 'main section' section_run as a metainfo object
section_run = backend.resource.contents[0].section_run[0]
section_run = archive.section_run[0]
# get the same data as JSON serializable Python dict
python_dict = section_run.m_to_dict()
......@@ -76,3 +76,31 @@ pip install -e parser-cp2k
```
Running the parser now, will use the parser's Python code from the clone project.
---
## Parser Specific
## Usage notes
The parser is based on CP2K 2.6.2.
The CP2K input setting
[PRINT_LEVEL](https://manual.cp2k.org/trunk/CP2K_INPUT/GLOBAL.html#PRINT_LEVEL)
controls the amount of details that are outputted during the calculation. The
higher this setting is, the more can be parsed from the upload.
The parser will try to find the paths to all the input and output files, but if
they are located very deep inside some folder structure or outside the folder
where the output file is, the parser will not be able to locate them. For this
reason it is recommended to keep the upload structure as flat as possible.
Here is a list of features/fixes that would make the parsing of CP2K results
easier:
- The pdb trajectory output doesn't seem to conform to the actual standard as
the different configurations are separated by the END keyword which is
supposed to be written only once in the file. The [format
specification](http://www.wwpdb.org/documentation/file-format) states that
different configurations should start with MODEL and end with ENDMDL tags.
- The output file should contain the paths/filenames of different input and
output files that are accessed during the program run. This data is already
available for some files (input file, most files produced by MD), but many
are not mentioned.
code-label: CP2K
code-label-style: all in capitals
code-url: https://www.cp2k.org/
parser-dir-name: dependencies/parsers/cp2k/
parser-git-url: https://gitlab.mpcdf.mpg.de/nomad-lab/parser-cp2k
parser-specific: |
codeLabel: CP2K
codeLabelStyle: all in capitals
codeUrl: https://www.cp2k.org/
parserDirName: dependencies/parsers/cp2k/
parserGitUrl: https://gitlab.mpcdf.mpg.de/nomad-lab/parser-cp2k
parserSpecific: |
## Usage notes
The parser is based on CP2K 2.6.2.
......@@ -29,4 +29,4 @@ parser-specific: |
available for some files (input file, most files produced by MD), but many
are not mentioned.
table-of-files: ''
tableOfFiles: ''
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