- 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 amber/full:test
- master
- test
- spec2
# AMBER Parser
## Version 0.0.5
Fixed bugs on test issues
This is a NOMAD parser for [Amber]( It will read Amber input and
output files and provide all information in NOMAD's unified Metainfo based Archive format.
This is the parser for SANDER and PMEMD Molecular Dynamics codes in [AMBER](
The official version lives at:
## 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.
You can browse it at:
For Amber 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/amber of this repository.
zip -r <upload-file>.zip <directory>/*
# Running and Testing the Parser
## Requirements
The required python packages can be installed with (see [python-common](
Go to the [NOMAD upload page]( to upload files
or find instructions about how to upload files from the command line.
pip install -r nomad-lab-base/python-common/requirements.txt
## Using the parser
## Usage
AMBER (SANDER/PMEMD) output files can be parsed with:
You can use NOMAD's parsers and normalizers locally on your computer. You need to install
NOMAD's pypi package:
python [path/toFile]
pip install nomad-lab
## Test Files
Example output files of AMBER (SANDER/PMEMD) can be found in the directory test/examples.
More details about the calculations and files will be explained in this README file.
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:
# Documentation
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
# 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 parser-amber
pip install -e parser-amber
Running the parser now, will use the parser's Python code from the clone project.
## Parser Specific
The Amber parser supports the SANDER and PMEMD Molecular Dynamics codes.
## Installation of NOMAD Infrastructure
More information on the installation of NOMAD infrastructure can be found [here](
codeLabel: Amber
codeLabelStyle: only first character in capitals
parserDirName: dependencies/parsers/amber/
parserSpecific: |
The Amber parser supports the SANDER and PMEMD Molecular Dynamics codes.
tableOfFiles: ''