stages:
- test
testing:
stage: test
script:
- cd .. && rm -rf nomad-lab-base
- git clone --recursive git@gitlab.mpcdf.mpg.de:nomad-lab/nomad-lab-base.git
- cd nomad-lab-base
- git submodule foreach git checkout master
- git submodule foreach git pull
- sbt bigdft/test
- export PYTHONEXE=/labEnv/bin/python
- sbt bigdft/test
only:
- master
tags:
- test
- spec2
This is the main repository of the [NOMAD](https://www.nomad-coe.eu/) parser for This is a NOMAD parser for [BigDFT](http://bigdft.org/). It will read BigDFT input and
[BigDFT](http://bigdft.org/). output files and provide all information in NOMAD's unified Metainfo based Archive format.
# Example ## Preparing code input and output file for uploading to NOMAD
```python
from bigdftparser import BigDFTParser NOMAD accepts `.zip` and `.tar.gz` archives as uploads. Each upload can contain arbitrary
import matplotlib.pyplot as mpl 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.
For BigDFT please provide at least the files from this table if applicable to your
calculations (remember that you can provide more files if you want):
# 1. Initialize a parser with a set of default units.
default_units = ["eV"]
parser = BigDFTParser(default_units=default_units)
# 2. Parse a file
path = "path/to/main.file"
results = parser.parse(path)
# 3. Query the results with using the id's created specifically for NOMAD. To create an upload with all calculations in a directory structure:
scf_energies = results["energy_total_scf_iteration"]
mpl.plot(scf_energies) ```
mpl.show() zip -r <upload-file>.zip <directory>/*
``` ```
# Installation Go to the [NOMAD upload page](https://nomad-lab.eu/prod/rae/gui/uploads) to upload files
The code is python 2 and python 3 compatible. First download and install or find instructions about how to upload files from the command line.
the nomadcore package:
## Using the parser
```sh You can use NOMAD's parsers and normalizers locally on your computer. You need to install
git clone https://gitlab.mpcdf.mpg.de/nomad-lab/python-common.git NOMAD's pypi package:
cd python-common
pip install -r requirements.txt ```
pip install -e . pip install nomad-lab
``` ```
Then download the metainfo definitions to the same folder where the To parse code input/output from the command line, you can use NOMAD's command line
'python-common' repository was cloned: interface (CLI) and print the processing results output to stdout:
```sh
git clone https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-info.git
``` ```
nomad parse --show-archive <path-to-file>
```
To parse a file in Python, you can program something like this:
```python
import sys
from nomad.cli.parse import parse, normalize_all
# match and run the parser
archive = parse(sys.argv[1])
# run all normalizers
normalize_all(archive)
Finally download and install the parser: # get the 'main section' section_run as a metainfo object
section_run = archive.section_run[0]
```sh # get the same data as JSON serializable Python dict
git clone https://gitlab.mpcdf.mpg.de/nomad-lab/parser-big-dft.git python_dict = section_run.m_to_dict()
cd parser-big-dft
pip install -e .
``` ```
# Notes ## Developing the parser
The parser is based on BigDFT 1.8.
Also install NOMAD's pypi package:
```
pip install nomad-lab
```
Clone the parser project and install it in development mode:
```
git clone https://gitlab.mpcdf.mpg.de/nomad-lab/parser-bigdft parser-bigdft
pip install -e parser-bigdft
```
Running the parser now, will use the parser's Python code from the clone project.
codeLabel: BigDFT
codeLabelStyle: 'Capitals: B,D,F,T,'
codeUrl: http://bigdft.org/
parserDirName: dependencies/parsers/bigdft/
parserGitUrl: https://gitlab.mpcdf.mpg.de/nomad-lab/parser-bigdft
parserSpecific: ''
tableOfFiles: ''