1. CrySPY>
  2. Tutorial
  • Table of contents

Tutorial

Info
  • Beginners are encouraged to start with a random search.
  • Additional example files not included in the tutorials are also available in CrySPY utility.
.

Table of contents

  • Random Search (RS)
  • Evolutionary Algorithm (EA)
  • Variable-composition evolutionary algorithm (EA-vc)
  • Bayesian Optimization (BO)
  • LAQA
  • Molecular crystal structure prediction
  • Random structure generation with MPI
  • Interactive mode (Jupyter Notebook)
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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