This is the Linux app named piv_clustering whose latest release can be downloaded as piv_clustering_1.3.tar.gz. It can be run online in the free hosting provider OnWorks for workstations.
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This program allows to perform a structural cluster analysis of atomic trajectories obtained, e.g., from molecular dynamics simulations.
At variance with other approaches, it is possible to analyse also processes in solution, e.g., chemical reactions in liquid water, since the distance metric is based on a Permutation Invariant Vector (PIV) that is symmetric under exchange of identical atoms or molecules, including on the same footing both solute and solvent degrees of freedom. The approach is general and the definition of PIV only requires to specify the range of interatomic distances that is relevant for the process under study. Alternatively, also the SPRINT topological coordinates can be employed, that are particularly suited for nanostructures.
The output is a partitioning of the trajectory into a few structural clusters (i.e., sets of frames), allowing for simpler analysis and visualization.
Please read and cite Gallet & Pietrucci, J. Chem. Phys. 139, 074101 (2013)
- Structural clustering of atomistic trajectories
- Permutation invariance: crystals, amorphous solids, liquids, nanostructures
- All simulation cells are supported (from orthorombic to triclininc)
- Parallel MPI implementation
This is an application that can also be fetched from https://sourceforge.net/projects/pivclustering/. It has been hosted in OnWorks in order to be run online in an easiest way from one of our free Operative Systems.