Tutorials

• 0. Unit conversions
  • 1. Introduction
  • 2. Basics
  • 3. Data model representations
  • 4. Unit debugging
• 1. Defining atomic systems
  • 1. Introduction
  • 2. Create a System
  • 3. Load a System
  • 4. System Manipulations
• 1.1. Box class
  • 1. Introduction
  • 2. Box parameters
  • 3. Initializing and setting Box parameters
  • 4. Box model
  • 5. Characterization and utility methods
• 1.2. Atoms class
  • 1. Introduction
  • 2. Basics
  • 3. Per-atom properties
  • 4. Atoms by index
  • 5. Atoms.extend()
  • 6. Atoms.prop()
  • 7. Atoms.prop_atype()
  • 8. Atoms.model()
• 1.3. System class
  • 1. Introduction
  • 2. Basics
  • 3. Built-in Attributes
  • 4. Scaling Additions
  • 5. Built-in manipulations
  • 6. Built-in analysis tools
  • 7. model() and dump()
• 1.4. Load and dump conversions
  • 1. Introduction
  • 2. Load
  • 3. Dump
  • 4. Supported styles
• 1.4.1. system_model conversions
  • 1. Introduction
  • 2. Dump
  • 3. Load
• 1.4.2. POSCAR conversions
  • 1. Introduction
  • 2. System.dump(‘poscar’)
  • 3. atomman.load(‘poscar’)
• 1.4.3. CIF conversions
  • 1. Introduction
  • 2. atomman.load(‘cif’)
• 1.4.4. table conversions
  • 1. Introduction
  • 2. System.dump(‘table’)
  • 3. atomman.load(‘table’)
• 1.4.5. LAMMPS data file conversions
  • 1. Introduction
  • 2. atomman.load(‘atom_data’)
  • 3. System.dump(‘atom_data’)
• 1.4.6. LAMMPS dump file conversions
  • 1. Introduction
  • 2. System.dump(‘atom_dump’)
  • 3. atomman.load(‘atom_dump’)
• 1.4.7. ase and phonopy conversions
  • 1. Introduction
  • 2. System.dump(‘ase_Atoms’) and System.dump(‘phonopy_Atoms’)
  • 3. atomman.load(‘ase_Atoms’) and atomman.load(‘phonopy_Atoms’)
• 1.4.8. pymatgen conversions
  • 1. Introduction
  • 2. System.dump(‘pymatgen_Structure’)
  • 3. atomman.load(‘pymatgen_Structure’)
• 1.4.9. spglib conversions
  • 1. Introduction
  • 2. System.dump(‘spglib_cell’)
  • 3. atomman.load(‘spglib_cell’)
• 1.4.10. prototype loading
  • 1. Introduction
  • 2. atomman.load(‘prototype’)
• 1.4.11. crystal loading
  • 1. Introduction
  • 2. atomman.load(‘crystal’)
• 1.4.12. DFT reference crystal loading
  • 1. Introduction
  • 2. atomman.load(‘prototype’)
• 1.4.13. primitive cell dumping
  • 1. Introduction
  • 2. Dump
• 1.4.14. Conventional and primitive cell conversion dumping
  • 1. Introduction
  • 2. Dump conventional_to_primitive
  • 3. Dump primitive_to_conventional
• 1.4.15. pdb dumping
  • 1. Introduction
  • 2. System.dump(‘pdb’)
• 1.4.16. LAMMPS NEB replica dumping-Copy1
  • 1. Introduction
  • 2. System.dump(‘neb_replica’)
• 1.4.16. LAMMPS NEB replica dumping
  • 1. Introduction
  • 2. System.dump(‘neb_replica’)
• 1.5. Settings and databases
  • 1. Introduction
  • 2. Settings
  • 3. Database interface
• 2. LAMMPS functionality
  • 1. Introduction
  • 2. Interatomic Potential Control
  • 3. Generate initial system
  • 4. Converting to/from LAMMPS units
  • 5. Composing LAMMPS Input Scripts
  • 6. Run LAMMPS
  • 7. Analyzing Thermo Results
  • 8 Reading in dump files
• 2.1. Potential class
  • 1. Introduction
  • 2. Loading LAMMPS Potentials
  • 3. Potential Classes
  • 4. Building a new potential
  • 5. potential_LAMMPS Data Model
• 2.2. Running LAMMPS and the Log class
  • 1. Introduction
  • 2. Running LAMMPS
  • 3. Accessing results with Log class
  • 4. Restarting and flattening
  • 5. Error messages
• 3. Basic support and analysis tools
  • 1. Introduction
  • 2. Elastic constants
  • 3. Relative distances between atoms
  • 4. Region selectors
  • 5. Basic tools
• 3.1. ElasticConstants class
  • 1. Introduction
  • 2. Elastic constants representations
  • 3. Setting values
  • 4. ElasticConstants.tranform()
  • 5. Shear and bulk modulus estimates
  • 6. Crystal system normalized values
  • 7. ElasticConstants.model()
• 3.2. NeighborList class
  • 1. Introduction
  • 2. Identifying neighbors
  • 3. build()
  • 4. dump() and load()
• 3.3. Region selectors
  • 1. Introduction
  • 2. Plane slicing
  • 3. Volume selection
• 3.4. Minimum energy paths
  • 1. Introduction
  • 2. Theory and Methodology
  • 3. BasePath class and common setup
  • 4. ISMPath
• 3.5. Cluster generators
  • 1. BondAngleMap
• 4. Defect creation and analysis
  • 1. Introduction
  • 2. Point defects
  • 3. Free surfaces
  • 4. Stacking faults
  • 5. Dislocations
  • 6. Strain class
• 4.1. Point defect generation
  • 1. Introduction
  • 2. atomman.defect.vacancy()
  • 3. atomman.defect.interstitial()
  • 4. atomman.defect.substitutional()
  • 5. atomman.defect.dumbbell()
  • 6. atomman.defect.point()
• 4.2. Free surface generator
  • 1. Introduction
  • 2. Theory
  • 3. Class basics
  • 4. Examples
• 4.3. Stacking fault generator
  • 1. Introduction
  • 2. Theory
  • 3. Class basics
  • 4. Examples
• 4.4. Volterra dislocation solutions
  • 1. Introduction
  • 2. Theory
  • 3. Volterra dislocation methods and objects
  • 4. Direct check of strain energy
• 4.5. Gamma surface plotting
  • 1. Introduction
  • 2. Underlying theory
  • 3. Defining gamma surface data
  • 4. Plotting methods
  • 5. Minimum energy slip path
  • 6. Utility methods
• 4.6. Dislocation analysis tools
  • 1. Introduction
  • 1.1. Load atomic systems
  • 2. Slip vector
  • 3. Disregistry
  • 4. Nye tensor
  • 5. Differential displacement maps
• 4.7. Semidiscrete variational Peierls-Nabarro model
  • 1. Introduction
  • 2. Theory
  • 3. Methodology overview
  • 4. Initialize SDVPN using GammaSurface and VolterraDislocation
  • 5. Generate initial disregistry
  • 6. Solve SDVPN model
  • 7. Save and load results
  • 8. Peierls stress estimates
• 4.8. Strain class
  • 1. Introduction
  • 2. Theory
  • 3. Calculation parameter options
  • 4. Strain class
  • 5. Plotting
• 4.9. Dislocation configurations generator
  • 1. Introduction
  • 2. Theory
  • 3. Dislocation initialization
  • 4. Dislocation Monopole Configuration
  • 5. Periodic Array of Dislocations Configuration
  • 6. Dislocation dipole configuration
• 4.10 Differential Displacement Maps
  • 1. Introduction
  • 2. Theory
  • 3. Generating dd maps with the DifferentialDisplacement class
  • 3.3. Combined DD map and Nye tensor plots