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/plams -h in a terminal: this should print PLAMS’ 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¶
- Geometry optimization of water
- Initial imports
- Initial structure
- Calculation settings
- Create an AMSJob
- Run the job
- Main results files: ams.rkf and dftb.rkf
- Optimized coordinates
- Optimized bond lengths and angle
- Calculation timing
- Energy
- Vibrational frequencies
- Dipole moment
- HOMO, LUMO, and HOMO-LUMO gap
- Read results directly from binary .rkf files
- Finish PLAMS
- AMS Settings: Chemical System (Molecule)
- Helium dimer dissociation curve
- Many jobs in parallel
Molecule analysis¶
Benchmarks¶
Workflows¶
COSMO-RS and property prediction¶
For more examples, see the COSMO-RS documentation.
Packmol and AMS-ASE interfaces¶
- Packmol example
- Engine ASE: AMS geometry optimizer with forces from any ASE calculator
- AMSCalculator: ASE geometry optimizer with AMS forces
- AMSCalculator: Access results files & Charged systems
- i-PI path integral MD with AMS
- Sella transition state search with AMS
ParAMS and pyZacros¶
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.