This is a NOMAD parser for ABACUS. It will read ABACUS input and output files and provide all information in NOMAD's unified Metainfo based Archive format.
For ABACUS please provide at least the files from this table if applicable to your calculations (remember that you can provide more files if you want):
| Input Filename | Description |
|---|---|
<file name>.xml |
Mainfile, output in XML format |
<file name>.out |
Fallback mainfile, output in text format |
<file name>.inp |
input file |
To create an upload with all calculations in a directory structure:
zip -r <upload-file>.zip <directory>/*
Go to the NOMAD upload page to upload files or find instructions about how to upload files from the command line.
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:
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()Create a virtual environment to install the parser in development mode:
pip install virtualenv
virtualenv -p `which python3` .pyenv
source .pyenv/bin/activate
Install NOMAD's pypi package:
pip install nomad-lab
Clone the parser project and install it in development mode:
git clone https://github.com/nomad-coe/nomad-parser-abacus.git nomad-parser-abacus
pip install -e nomad-parser-abacus
Running the parser now, will use the parser's Python code from the clone project.