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 castep/full:test
- export PYTHONEXE=/labEnv/bin/python
- sbt castep/full:test
only:
- master
tags:
- test
- spec2
\ No newline at end of file
# CASTEP Parser
This is a NOMAD parser for [CASTEP](http://www.castep.org/). It will read CASTEP input and
output files and provide all information in NOMAD's unified Metainfo based Archive format.
This is the parser for [CASTEP](http://www.castep.org/).
It is part of the [NOMAD Laboratory](http://nomad-lab.eu).
The official version lives at
## Preparing code input and output file for uploading to NOMAD
git@gitlab.mpcdf.mpg.de:nomad-lab/parser-castep.git
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 CASTEP please provide at least the files from this table if applicable to your
calculations (remember that you can provide more files if you want):
https://gitlab.mpcdf.mpg.de/nomad-lab/parser-castep
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 git@gitlab.mpcdf.mpg.de:nomad-lab/nomad-lab-base.git
To create an upload with all calculations in a directory structure:
then this will be in parsers/castep.
```
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.
# TEST OUTPUT FILES
## Using the parser
Few output files where to test the parser are provided in the directory test examples.
You can use NOMAD's parsers and normalizers locally on your computer. You need to install
NOMAD's pypi package:
```
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:
```
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)
# 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()
```
## 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 https://gitlab.mpcdf.mpg.de/nomad-lab/parser-castep parser-castep
pip install -e parser-castep
```
Running the parser now, will use the parser's Python code from the clone project.
---
## Parser Specific
### CASTEP output examples
[Note: The list below is much shorter than the existing examples]
A few output files to test the parser are provided in the directory `castep/test/examples/*/`.
FILE NAME | FILE DESCRIPTION
__________________|___________________________________________________
"Si2.castep_v_1" --> Single Point Calculation (minimum verbosity)
"Si2.castep_v_2" --> Single Point Calculation (medium verbosity)
"Si2.castep_v_3" --> Single Point Calculation (maximum verbosity)
"Si2.castep_b_v_1" --> Band Structure Calculation (minimum verbosity)
"Si2.castep_b_v_2" --> Band Structure Calculation (medium verbosity)
"Si2.castep_b_v_3" --> Band Structure Calculation (maximum verbosity)
\ No newline at end of file
"Si2.castep_b_v_3" --> Band Structure Calculation (maximum verbosity)
codeLabel: CASTEP
codeLabelStyle: all in capitals
codeUrl: http://www.castep.org/
parserDirName: dependencies/parsers/castep/
parserGitUrl: https://gitlab.mpcdf.mpg.de/nomad-lab/parser-castep
parserSpecific: |
### CASTEP output examples
[Note: The list below is much shorter than the existing examples]
A few output files to test the parser are provided in the directory `castep/test/examples/*/`.
FILE NAME | FILE DESCRIPTION
__________________|___________________________________________________
"Si2.castep_v_1" --> Single Point Calculation (minimum verbosity)
"Si2.castep_v_2" --> Single Point Calculation (medium verbosity)
"Si2.castep_v_3" --> Single Point Calculation (maximum verbosity)
"Si2.castep_b_v_1" --> Band Structure Calculation (minimum verbosity)
"Si2.castep_b_v_2" --> Band Structure Calculation (medium verbosity)
"Si2.castep_b_v_3" --> Band Structure Calculation (maximum verbosity)
tableOfFiles: ''