Examples

In this chapter we present example PLAMS scripts covering various applications, from very simple tasks (like running the same calculation for multiple molecules) to more advanced dynamic workflows.

The example scripts use computational engines from the Amsterdam Modeling Suite, and you will need a license to run them. Contact license@scm.com for further questions.

In order to run the examples, the AMSBIN environment variable should be properly set. You can test this by typing $AMSBIN/amspython -h in a terminal: this should print the help message. If this is not the case (e.g. you get ‘No such file or directory’), you need to set up the environmental variable $AMSBIN (see the Linux Quickstart guide for details).

Getting Started

Molecule analysis

MD trajectory analysis

Benchmarks

Workflows

COSMO-RS and property prediction

For more examples, see the COSMO-RS documentation.

Packmol and AMS-ASE interfaces

ParAMS, Simple Active Learning, and pyZacros

See the respective documentation pages:

Other AMS calculations

Pymatgen

Pre-made recipes

The examples presented in here are simple job types built using basic PLAMS elements. They are shipped with PLAMS in the recipes subpackage and can be directly used in your scripts. In other words, the code presented there is already included in PLAMS and (unlike examples from two other sections) does not need to be copied to your script. The source code of recipes modules is presented here to demonstrate how easy it is to build on top of existing PLAMS elements and create your own fully customized job types.