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CrystOD v0.4.6

  • CrystOD

Getting started

  • Installation
  • Quick start
  • Your first analysis
  • CrystOD for phonopy users

Tutorials

  • Tutorials

Commands

  • crystod (main command)
    • 1. Theoretical background
    • 2. Irreps of SALC
    • 3. Crystal-orbital diagrams
    • 4. Dipole selection rules (--diagram)
    • 5. Star of k
    • 6. SALC basis visualization (--visualize)
  • crystod-group
    • 8. Direct products (--product)
    • 9. Symmetrized squares and Jahn-Teller modes (--symmetric, --antisymmetric, --jahn-teller)
    • 10. Representation decomposition (--decompose)
    • 11. Ligand-field splitting (--ligand-field)
    • 12. Basis functions (--basis)
    • 13. Property tensors (--tensor)
    • 14. Basis-function generation (--generate-basis)
    • 15. Coset decomposition (--coset)
    • 16. Correlation and compatibility (--correlate)
    • 17. Isotropy subgroups (--parent)
    • 18. Invariant polynomials (--invariants)
    • 19. Reverse lookup (--child)
    • 20. Group-subgroup graph (--graph)
    • 21. Multi-electron terms (--multiplet)
    • 22. POSCAR <-> CIF (--poscar2cif / --cif2poscar)
    • 23. Symmetry-mode analysis (--supergroup-cif)
  • crystod-bz
    • 25. Brillouin zone plot
    • 26. Supercell Brillouin zone (--trans-mat)
  • crystod-phonon
    • 28. Phonon irreps (--irreps)
    • 29. Phonon activity (IR, Raman, mode charges)
    • 30. Phonon fatbands (--fatband)
    • 31. Longitudinal/transverse bands (--lt)
    • 32. Phonon eigenvectors (--vector)
    • 33. Phonon modulation (--modulation)
    • 34. Vibration bases (--vibration)
    • 35. Subgroups from imaginary modes (--subgroup)
    • 51. Phonon band unfolding (--unfold)
    • 52. Phonon mode viewer (--visualize)
  • crystod-mag
    • 36. Symmetry-adapted spin bases
    • 37. Magnetic space groups and collinear classes (--classify-only)
  • crystod-md
    • 39. ADPs from an MD trajectory (--adp)
    • 39.1 Trajectory summary (--summary)
    • 40. Mode projection of an MD trajectory (--project)
  • crystod-mol
    • 42. Molecular point groups and SALCs
    • 43. Molecular-orbital diagrams (--diagram)
  • crystod-xrd
    • 46. Powder X-ray diffraction patterns
    • 47. Superlattice reflections and neutron patterns (--parent, --radiation neutron)
  • crystod-search
    • 48. Searching the Materials Project
  • crystod-slab
    • 53. Surface slabs
  • crystod-example
    • 50. Packaged example directories

Theory

  • Theoretical background
    • What is a representation matrix?
    • How CrystOD computes D for any l
    • From matrices to irreps: characters and the reduction formula
    • From irreps to basis functions: the projection operator
    • Irrep labels and the frame of a structure
    • Multi-electron terms: symmetrized products and the Pauli principle
  • How the orbital diagrams are computed
    • How the molecular-orbital diagram is built (extended-Hückel engine)
    • Why ghost atoms? The basis-set superposition error (BSSE)
    • Two conventions that keep the molecular fragment columns honest
    • How the crystal-orbital diagram is built (extended-Hückel engine)
    • Ghost atoms, cell neutrality and the deep-level alignment (crystal --pyscf)
    • Why --onsite takes the fragment columns from the crystal Fock
    • What the composition percentages mean (Löwdin vs Mulliken)
    • Why a valence level can look antibonding (--valence-only)
    • What the crystal-orbital regression test asserts
    • References for the extended-Hückel construction
  • Order parameters and isotropy subgroups
    • Complex- and pseudoreal-type irreps (doubled real form)
    • Symmetry-mode analysis: algorithm internals and AMPLIMODES validation
    • Validation of crystod-group --parent against ISOSUBGROUP

Python API

  • Python API
    • Isotropy subgroups of an irrep
    • Phonon modes and their irreps
    • From imaginary phonons to subgroups
    • Group theory and spectroscopy entry points
    • Magnetic groups, MD projection and superlattice reflections
    • Band irreps of a VASP run
    • The packaged examples
    • The other domains
    • Library use: keywords and input checks
  • API reference
    • crystod.salc
    • crystod.group
    • crystod.phonon
    • crystod.bz
    • crystod.mag
    • crystod.md
    • crystod.mol
    • crystod.xrd
    • crystod.search
    • crystod.slab

Integrations

  • MCP server (crystod-mcp)

Reference

  • Citation
  • Changelog
  • Contributing

Python Module Index

c
 
c
- crystod
    crystod.bz
    crystod.group
    crystod.mag
    crystod.md
    crystod.mol
    crystod.phonon
    crystod.salc
    crystod.search
    crystod.slab
    crystod.xrd

By Yasuhide Mochizuki and Hiroki Koiso

© Copyright 2024-2026, Yasuhide Mochizuki and Hiroki Koiso.