The wrapper of AMS and Zacros drivers for SimPhoNy
Project description
ReaxPro wrappers:
This repository is a collection of wrappers used in the ReaxPro project. It holds wrappers for the Amsterdam Modeling Suite (AMS) and Zacros.
Authors
- Pablo Lopez-Tarifa (Main author). The Netherlands eScience Center.
- Matthias Büschelberger (Contributor). Fraunhofer Instituet for Mechanics of Materials (IWM)
- Joana Francisco Morgado (Contributor). Fraunhofer Institute for Mechanics of Materials (IWM)
Index
Requiremnts
If you want to use this wrapper set, make sure you have installed:
- The Simphony OSP-core version > 3.8.0.
- The ReaxPro ontology.
- For AMS users, a licensed copy of AMS installed.
- For Zacros users, both a licensed copy of Zacros code and pyZacros library installed.
Structure
A wrapper is a piece of code that slightly modifies the behavior of a function.
The ReaxPro wrappers are built around the running functions of the above-mentioned software. Their main task is to translate (map) the semantic script provided by the user to the terms that are understood by the engines.
For a given engine XXX, there is a folder reaxpro-wrappers/osp/wrappers/simXXX/simXXX_session.py containing the Simphony wrapper session that will trigger the job execution.
In the folder reaxpro-wrappers/osp/tools is placed all the tooling for the semantic to syntactic mapping.
Installation
First of all, you will need to install OSP-core and pyZacros
(env) user@computer:~/reaxpro-wrappers$ pip install osp-core https://github.com/SCM-NV/pyZacros/archive/refs/tags/v.1.2.zip
Then, make sure that the wrapper can access the ontology from the Fraunhofer Gitlab and download it with a given access token (with read_api
and read_repository
scopes).
If you are using Windows, please type:
(env) C:\Users\user> set GITLAB_ACCESS_TOKEN=<your-access-token>
If you are using Linux, please type:
(env) user@computer:~/reaxpro-wrappers$ export GITLAB_ACCESS_TOKEN=<your-access-token>
Then, finally install the wrapper. Simply type:
(env) user@computer:~/reaxpro-wrappers$ python setup.py install
... or:
(env) user@computer:~/reaxpro-wrappers$ pip install .
Example
The script ams_wrapper.py provides a simple semantic workflow to run a geometry optimization of a water molecule.
To run the script:
(env) user@computer:~/reaxpro-wrappers$ python ams_wrapper.py
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