pyscal- A python module for structural analysis of atomic environments
pyscal is a python module for the calculation of local atomic structural environments including Steinhardt’s bond orientational order parameters during post-processing of atomistic simulation data. The core functionality of pyscal is written in C++ with python wrappers using pybind11 which allows for fast calculations with possibilities for easy expansion in python.
Steinhardt’s order parameters are widely used for identification of crystal structures. They are also used to identify if an atom is solid or liquid. pyscal is inspired by BondOrderAnalysis code, but has since incorporated many additions and modifications. pyscal module includes the following functionality-
Highlights
fast and efficient calculations using C++ and expansion using python.
calculation of Steinhardt’s order parameters and their averaged version and disorder parameters.
links with Voro++ code, for calculation of Steinhardt parameters weighted using face area of Voronoi polyhedra.
classification of atoms as solid or liquid.
clustering of particles based on a user defined property.
methods for calculating radial distribution function, voronoi volume of particles, number of vertices and face area of voronoi polyhedra and coordination number.
calculation of angular parameters such as for identification of diamond structure and Ackland-Jones angular parameters.
Centrosymmetry parameter for identification of defects.
Adaptive common neighbor analysis for identification of crystal structures.
Documentation
- Download and Install
- News and updates
- Methods and examples
- Methods
- Examples
- Getting started with pyscal
- Calculating coordination numbers
- Calculating bond orientational order parameters
- Analyzing a lammps trajectory
- Disorder variable
- Distinction of solid liquid atoms and clustering
- Voronoi parameters
- Angular parameter
- \(\chi\) parameters
- Centrosymmetry parameter
- Cowley short range order parameter
- Entropy parameters
- Calculating energy
- Entropy and enthalpy parameters
- Visualizing System objects
- pyscal
Trajectory
- pyscal reference
- pyscal Reference
- pyscal.core module
SystemSystem.boxSystem.atomsSystem.__init__()System.add_atoms()System.atomsSystem.boxSystem.calculate_angularcriteria()System.calculate_centrosymmetry()System.calculate_chiparams()System.calculate_cna()System.calculate_disorder()System.calculate_energy()System.calculate_entropy()System.calculate_pmsro()System.calculate_q()System.calculate_rdf()System.calculate_solidneighbors()System.calculate_sro()System.calculate_vorovector()System.cluster_atoms()System.embed_in_cubic_box()System.extract_cubic_box()System.find_diamond_neighbors()System.find_largestcluster()System.find_neighbors()System.find_solids()System.get_atom()System.get_concentration()System.get_custom()System.get_distance()System.get_qvals()System.identify_diamond()System.iter_atoms()System.read_inputfile()System.remap_atoms()System.repeat()System.reset_neighbors()System.set_atom()System.set_atom_cutoff()System.show()System.to_ase()System.to_file()
test()AtomAtom.__init__()Atom.allaqAtom.allqAtom.angularAtom.avg_angularAtom.avg_disorderAtom.avg_energyAtom.avg_entropyAtom.avg_sijAtom.avg_volumeAtom.bondsAtom.centrosymmetryAtom.chiparamsAtom.clusterAtom.cnaAtom.commonAtom.conditionAtom.coordinationAtom.customAtom.cutoffAtom.disorderAtom.edge_lengthsAtom.energyAtom.entropyAtom.face_perimetersAtom.face_verticesAtom.get_q()Atom.get_qlm()Atom.ghostAtom.idAtom.largest_clusterAtom.locAtom.local_anglesAtom.maskAtom.neighbor_distanceAtom.neighbor_vectorAtom.neighbor_weightsAtom.neighborsAtom.next_neighbor_distancesAtom.next_neighborsAtom.posAtom.set_q()Atom.sijAtom.solidAtom.sroAtom.structureAtom.surfaceAtom.typeAtom.vertex_numbersAtom.vertex_positionsAtom.vertex_vectorsAtom.volumeAtom.vorovector
- pyscal.crystal_structures module
- pyscal.trajectory module
- pyscal.traj_process module
- pyscal.misc module
- pyscal.core module
- pyscal Reference
- Publications and Projects
- Support, contributing and extending
- Help and support
- Citing the code
- Acknowledgements
- License