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 crystal/test
- export PYTHONEXE=/labEnv/bin/python
- sbt crystal/test
only:
- master
tags:
- test
- spec2
\ No newline at end of file
This is the main repository of the [NOMAD](https://www.nomad-coe.eu/) parser for
[Crystal](http://www.crystal.unito.it).
This is a NOMAD parser for [CRYSTAL](https://www.crystal.unito.it/). It will read CRYSTAL input and
output files and provide all information in NOMAD's unified Metainfo based Archive format.
# Example
```python
from crystalparser import CrystalParser
import matplotlib.pyplot as mpl
## Preparing code input and output file for uploading to NOMAD
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.
For CRYSTAL please provide at least the files from this table if applicable to your
calculations (remember that you can provide more files if you want):
To create an upload with all calculations in a directory structure:
```
zip -r <upload-file>.zip <directory>/*
```
Go to the [NOMAD upload page](https://nomad-lab.eu/prod/rae/gui/uploads) to upload files
or find instructions about how to upload files from the command line.
## Using the parser
# 1. Initialize a parser with a set of default units.
default_units = ["eV"]
parser = CrystalParser(default_units=default_units)
You can use NOMAD's parsers and normalizers locally on your computer. You need to install
NOMAD's pypi package:
# 2. Parse a file
path = "path/to/main.file"
results = parser.parse(path)
```
pip install nomad-lab
```
To parse code input/output from the command line, you can use NOMAD's command line
interface (CLI) and print the processing results output to stdout:
# 3. Query the results with using the id's created specifically for NOMAD.
scf_energies = results["energy_total_scf_iteration"]
mpl.plot(scf_energies)
mpl.show()
```
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
# Installation
The code is python 2 and python 3 compatible. First download and install
the nomadcore package:
# match and run the parser
archive = parse(sys.argv[1])
# run all normalizers
normalize_all(archive)
```sh
git clone https://gitlab.mpcdf.mpg.de/nomad-lab/python-common.git
cd python-common
pip install -r requirements.txt
pip install -e .
# get the 'main section' section_run as a metainfo object
section_run = archive.section_run[0]
# get the same data as JSON serializable Python dict
python_dict = section_run.m_to_dict()
```
Then download the metainfo definitions to the same folder where the
'python-common' repository was cloned:
## Developing the parser
Also install NOMAD's pypi package:
```sh
git clone https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-info.git
```
pip install nomad-lab
```
Finally download and install the parser:
Clone the parser project and install it in development mode:
```sh
git clone https://gitlab.mpcdf.mpg.de/nomad-lab/parser-crystal.git
cd parser-crystal
pip install -e .
```
git clone https://gitlab.mpcdf.mpg.de/nomad-lab/parser-crystal parser-crystal
pip install -e parser-crystal
```
Running the parser now, will use the parser's Python code from the clone project.
# Notes
The parser is based on Crystal 14.
codeLabel: CRYSTAL
codeLabelStyle: all in capitals
codeUrl: https://www.crystal.unito.it/
parserDirName: dependencies/parsers/crystal/
parserGitUrl: https://gitlab.mpcdf.mpg.de/nomad-lab/parser-crystal
parserSpecific: ''
tableOfFiles: ''