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  2. Structure generation
  • Table of contents

Structure generation

CrySPY currently has three random structure generation modes: crystal (default), mol, and mol_bs. PyXtal (or find_wy) is used for the structure generation.

Table of contents

  • struc_mode = crystal
    • struc_mode = mol
      • struc_mode = mol_bs
        CrySPY
        • Home
        • Version information
          • Version 1.4.0
          • Version 1.3.0
          • Version 1.2.5
          • Version 1.2.4
          • Version 1.2.3
          • Version 1.2.2
          • Version 1.2.1
          • Version 1.2.0
          • Version 1.1.1
          • Version 1.1.0
          • Version 1.0.0
          • Version 0.10.3 or earlier
        • Installation
          • System requirements
            • Python
            • Structure optimizer
            • find_wy (optional)
          • CrySPY
            • CrySPY 1.3.0 or later
            • CrySPY 1.0.0 -- 1.2.5
            • CrySPY 0.10.3 or earlier
          • CrySPY utility (optional)
        • Tutorial
          • Random Search (RS)
            • ASE on your local PC
            • soiap on your local PC
            • VASP
            • QE
            • OpenMX
            • LAMMPS
            • Check cryspy.in
            • Script to run
            • Firsrt run
            • Submit job
            • Check results
            • Append structures
            • Analysis and visualization
          • Evolutionary Algorithm (EA)
            • ASE on your local PC
            • Create next generation
            • Check results
            • Analysis and visualization
          • Variable-composition evolutionary algorithm (EA-vc)
            • ASE on your local PC (Cu-Ag-Au)
            • ASE-CHGNet（Cu-Au）
            • Create next generation
            • Check results
            • Analysis and visualization
          • Bayesian Optimization (BO)
          • LAQA
          • Molecular crystal structure prediction
          • Random structure generation with MPI
          • Interactive mode (Jupyter Notebook)
        • Interface
        • Search algorithms
          • Random search (RS)
          • Evolutionary algorithm (EA)
            • Crossover
            • Permutation
            • Strain
            • Tournament selection
            • Roulette selection
          • Variable-composition evolutionary algorithm (EA-vc)
            • Crossover (vc)
            • Addition
            • Elimination
            • Substitution
          • Bayesian optimizaion (BO)
          • LAQA
        • Structure generation
          • struc_mode = crystal
          • struc_mode = mol
          • struc_mode = mol_bs
        • Features
          • Logging
          • Backup
          • Clean
          • Restriction on interatomic distances
          • CrySPY_ID in job files
          • Structure generation with MPI parallelization
          • Enthalpy
          • As library
          • Interactive mode
        • Input file
          • File format
          • [basic] section
          • [structure] section
          • [VASP] section
          • [QE] section
          • [OMX] section
          • [soaip] section
          • [LAMMPS] section
          • [ASE] section
          • [EA] section
          • [BO] section
          • [LAQA] section
          • [option] section
          • Kpoint
        • Data format
          • Common data
            • Initial and optimized structure data
            • Result data
          • Random Search (RS)
          • Evolutionary algorithm (EA)
          • Bayesian Optimization (BO)
          • LAQA
          • Optional data
            • Energy step data
            • Structure step data
            • Force step data
            • Stress step data
        • CrySPY utility
          • repeat_cryspy
          • extract_struc.py
          • print_pkl.py
          • pos2pkl.py
          • kpt_check.py
        • FAQ
          • Can I change njob in the middle of the simulation?
        • Logo
        Link
        • GitHub repo
        • GitHub discussions
        • CrySPY utility
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