Commit 8a2cfdb2 authored by temok-mx's avatar temok-mx
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Updated; added metadata.yml; the lead branch is now master, inactive branches became tags

parent 7f5fc6a3
- test
stage: test
- cd .. && rm -rf nomad-lab-base
- git clone --recursive
- cd nomad-lab-base
- git submodule foreach git checkout master
- git submodule foreach git pull
- sbt tinker/full:test
- master
- test
- spec2
# Tinker Parser This is a NOMAD parser for [Tinker]( It will read Tinker input and
[NOMAD Laboratory CoE]( parser for [TINKER]( output files and provide all information in NOMAD's unified Metainfo based Archive format.
## Version 0.0.3
This is the parser for Tinker in [TINKER]( ## Preparing code input and output file for uploading to NOMAD
The official version lives at: NOMAD accepts `.zip` and `.tar.gz` archives as uploads. Each upload can contain arbitrary
files and directories. NOMAD will automatically try to choose the right parser for you files.
For each parser (i.e. for each supported code) there is one type of file that the respective
parser can recognize. We call these files `mainfiles` as they typically are the main
output file a code. For each `mainfile` that NOMAD discovers it will create an entry
in the database that users can search, view, and download. NOMAD will associate all files
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.
You can browse it at: For tinker please provide at least the files from this table if applicable to your
calculations (remember that you can provide more files if you want):
It relies on having the nomad-meta-info and the python-common repositories one level higher.
The simplest way to have this is to check out nomad-lab-base recursively:
git clone --recursive To create an upload with all calculations in a directory structure:
This parser will be in the directory parsers/tinker of this repository. ```
zip -r <upload-file>.zip <directory>/*
## Running and Testing the Parser Go to the [NOMAD upload page]( to upload files
### Requirements or find instructions about how to upload files from the command line.
The required python packages can be installed with (see [python-common](
pip install -r nomad-lab-base/python-common/requirements.txt ## Using the parser
### Usage You can use NOMAD's parsers and normalizers locally on your computer. You need to install
Tinker MD log output files can be parsed with: NOMAD's pypi package:
python [path/toFile] ```
pip install nomad-lab
### Test Files To parse code input/output from the command line, you can use NOMAD's command line
Example log output files of Tinker can be found in the directory test/examples. interface (CLI) and print the processing results output to stdout:
More details about the calculations and files are explained in README file of test/examples.
nomad parse --show-archive <path-to-file>
To parse a file in Python, you can program something like this:
import sys
from nomad.cli.parse import parse, normalize_all
# match and run the parser
backend = parse(sys.argv[1])
# run all normalizers
# get the 'main section' section_run as a metainfo object
section_run = backend.resource.contents[0].section_run[0]
# get the same data as JSON serializable Python dict
python_dict = section_run.m_to_dict()
## Developing the parser
Also install NOMAD's pypi package:
pip install nomad-lab
Clone the parser project and install it in development mode:
git clone parser-tinker
pip install -e parser-tinker
Running the parser now, will use the parser's Python code from the clone project.
code-label: Tinker
code-label-style: 'Capitals: T'
parser-dir-name: dependencies/parsers/tinker/
parser-specific: ''
table-of-files: ''
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