Minima Hopping: a python implementation compatible with the atomic simulation environment!

The minimahopping method efficiently finds the global minimum of complex condensed matter systems. This version of the code is based on the atomic simulation environment (ASE) library. Any calculator implemented in there can be used for the calculation of the energy and forces.

Code development

The MH python code is developed through our GitLab repository:

https://gitlab.com/goedeckergroup/ase_mh.git

If you detect any bug please write an issue in this repository. If you can solve the bug yourself or you would like to add any code please fork the code and make a pull-request to the “develop” branch. Every now and then the develop branch is pushed to the “master” branch.

Current list of contributors:

• Marco Krummenacher (University of Basel)

• Moritz Gubler (University of Basel)

• Jonas A. Finkler (University of Basel)

MINIMA HOPPING DOCUMENTATION:

• Installing Minima Hopping
• Theory
  • Introduction
  • Technical details
  • Feedback
• Parameters
  • Minima Hopping Parameters
  • Fingerprint Adjustment
• Output
  • Minima folder
  • Output folder
• Example: Clusters
  • Exercice 1: Distinguishing minima
  • Exercise 2: Starting Minimahopping
  • Exercise 3: Graph construction
  • Exercice 4: MPI minima hopping
  • Exercise 5: MPI minima hopping with group communicators
• Example: Bulk
  • Exercice 1: Distinguishing minima
  • Exercise 2: Starting Minimahopping
• Example: Foundation Models
• Example: GPU accelerated Minima Hopping on the DFT level.
• Example: MD Calculator
• Example: Slab Boundary Conditions
  • Example 1: Fixed cell slab
  • Example 2: Variable cell shape slab
• Example: Constraints

Citing MinimaHopping

This implementation

13. Krummenacher, M. Gubler, J. A. Finkler, H. Huber, M. Sommer-Jörgensen, S.Goedecker, Performing highly efficient Minima Hopping strucutre predictions using the Atomic Simulation Environment, SoftwareX Volume 25, February 2024, 101632

Geometry Optimizer:

13. Gubler, M. Krummenacher, H. Huber, S. Goedecker, Efficient variable cell shape geometry optimization, Journal of Computational Physics: X Volume 17, November 2023, 100131

Minima Hopping method:

19. Goedecker, Minima hopping: An efficient search method for the global minimum of the potential energy surface of complex molecular systems,The Journal of chemical physics 120 (21) (2004) 9911-9917

Fingerprint:

1. Sadeghi, S. A. Ghasemi, B. Schaefer, S. Mohr, M. A. Lill, S. Goedecker, Metrics for measuring distances in configuration spaces, The Journal of chemical physics 139 (18) (2013) 184118

12. Zhu, M. Amsler, T. Fuhrer, B. Schaefer, S. Faraji, S. Rostami, S. A. Ghasemi, A. Sadeghi, M. Grauzinyte, C. Wolverton, et al., A fingerprint based metric for measuring similarities of crystalline structures, The Journal of chemical physics 144 (3) (2016) 034203.