Commit 4e2b218c authored by temok-mx's avatar temok-mx

Updated README.md; added metadata.yml; the lead branch is now master, inactive branches became tags

parent cc6c9545
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 charmm/full:test
only:
- master
tags:
- test
- spec2
# CHARMM Parser
[NOMAD Laboratory CoE](http://nomad-coe.eu) parser for [CHARMM](https://www.charmm.org/charmm/)
## Version 0.0.2
This is a NOMAD parser for [CHARMM](https://www.charmm.org/charmm/). It will read CHARMM input and
output files and provide all information in NOMAD's unified Metainfo based Archive format.
This is the parser for CHARMM (Chemistry at HARvard Macromolecular Mechanics) code in [CHARMM](https://www.charmm.org/charmm/).
## Preparing code input and output file for uploading to NOMAD
## Features
- All input and output files are expected to be in the supplied directory and its subdirectories.
- The parser searches for the main input file for extraction more information of the order of the commands and
input CARDS. The main input file is assumed to hold at least 80% of the commands given to charmm main process.
- `MINI`, `DYNA`, `ENER`, `GETE`, `PRINT`, `OPEN`, `READ`, and `WRITE` commands can be prossesed with this parser.
- Any new `MINI`, `DYNA`, `ENER`, `GETE` commands are assumed to be a new simulation and each simulation is given in a new [section\_run](https://metainfo.nomad-coe.eu/nomadmetainfo_public/index.html#/public/section_run) in standardized meta information of NOMAD.
- Parser can extract topology information from **PSF**, **RTF**, **PAR** files and CARDS through MDDataAccess package.
- **SEQ** CARDS can be read only for additional information if topology information is not complete.
- Additional topology information can also be extracted from **COOR**, **CRD** files(ascii) and CARDS.
- Input and output coordinates are mainly extracted from both ascii and binary **COOR** and **CRD** files/CARDS and
`PRINT COOR` commands.
...The coordinate information of the most recent command before any given command in the second item of this list is assumed to be the input coordinates of the simulation. Similarly, the next `PRINT`, `WRITE` command after each simulation is also assumed to be the output coordinates if trajectory data (`IUNCRD` or `IUNWRI` units) are missing.
- Trajectory of the simulations are also accessed through MDDataAccess package of [python-common](https://gitlab.rzg.mpg.de/nomad-lab/python-common).
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.
## Download and Installation
The official version lives at:
For charmm please provide at least the files from this table if applicable to your
calculations (remember that you can provide more files if you want):
git@gitlab.mpcdf.mpg.de:nomad-lab/parser-charmm.git
You can browse it at:
https://gitlab.rzg.mpg.de/nomad-lab/parser-charmm
To create an upload with all calculations in a directory structure:
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:
```
zip -r <upload-file>.zip <directory>/*
```
git clone --recursive git@gitlab.mpcdf.mpg.de:nomad-lab/nomad-lab-base.git
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.
This parser will be in the directory parsers/charmm of this repository.
## Using the parser
## Running and Testing the Parser
### Requirements
The required python packages can be installed with (see [python-common](https://gitlab.rzg.mpg.de/nomad-lab/python-common)):
You can use NOMAD's parsers and normalizers locally on your computer. You need to install
NOMAD's pypi package:
pip install -r nomad-lab-base/python-common/requirements.txt
```
pip install nomad-lab
```
### Usage
CHARMM MD log output files can be parsed with:
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:
python CHARMMParser.py [path/toFile]
```
nomad parse --show-archive <path-to-file>
```
### Test Files
Example log output files of CHARMM can be found in the directory test/examples.
More details about the calculations and files are explained in the README file under examples directory.
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
backend = parse(sys.argv[1])
# run all normalizers
normalize_all(backend)
# get the 'main section' section_run as a metainfo object
section_run = backend.resource.contents[0].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-charmm parser-charmm
pip install -e parser-charmm
```
Running the parser now, will use the parser's Python code from the clone project.
code-label: CHARMM
code-label-style: all in capitals
code-url: https://www.charmm.org/charmm/
parser-dir-name: dependencies/parsers/charmm/
parser-git-url: https://gitlab.mpcdf.mpg.de/nomad-lab/parser-charmm
table-of-files: ''
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