reaxpro-wrappers 1.3.1

The wrapper of AMS and Zacros drivers for SimPhoNy

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

• Requirements
• Wrapper generals
• Installation
• Example

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