Jumos
  • Package overview
    • Simulation flow
      • System setup
      • Simulation setup
      • Running the simulation
    • Simulation example
      • Lennard-Jones fluid
      • Other example
    • Main types
      • Universe
      • Simulation
  • Universes
    • UnitCell
      • Creating simulation cell
      • Indexing simulation cell
      • Boundary conditions and cells
      • Distances and cells
    • Topology
      • Atom type
      • Topology
        • Topology functions
      • Periodic table information
    • Frame
    • Interactions
      • Using non-default computation
    • Potentials
      • Potential functions
        • Short-range pair potential
        • Bonded potential
      • Potential computation
        • Which computation for which potential ?
    • Universe type
    • Loading initial configurations from files
  • Simulations
    • Propagator
    • Molecular Dynamics
      • Time integration
        • Verlet integrators
      • Force computation
      • Controlling the simulation
        • Controlling the temperature: Thermostats
        • Controlling the pressure: Barostats
        • Other controls
      • Checking the simulation consistency
        • Existing checks
      • Default algorithms
      • Functions for algorithms selection
    • Computing values of interest
      • Energy related values
      • Volume
      • Pressure
    • Exporting values of interest
      • Existing outputs
        • Trajectory output
        • Energy output
      • Defining a new output
        • Custom output
    • Simulation type
  • Utilities
    • Internal units
    • Interaction with others units systems
    • Periodic boundary conditions and distances computations
      • Minimal images
      • Distances
        • Within one Frame
        • Between two Frames
    • Trajectories
      • Reading and writing trajectories
        • Base types
        • Usage
        • Supported formats
      • Readind and writing topologies
        • Supported formats for topology
    • Array3D
  • Extending Jumos
    • Defining a new potential
      • User potential
      • Subtyping PotentialFunction
    • Algorithms for all simulations
      • Computing values
      • Outputing values
    • Algorithms for molecular dynamics
      • Writing a new integrator
      • Computing the forces
      • Adding new checks
      • Adding new controls
 
Jumos
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Extending JumosΒΆ

In this section, you will find and how to extend Jumos base types to add more fucntionalities to your simulations.

  • Defining a new potential
    • User potential
    • Subtyping PotentialFunction
  • Algorithms for all simulations
    • Computing values
    • Outputing values
  • Algorithms for molecular dynamics
    • Writing a new integrator
    • Computing the forces
    • Adding new checks
    • Adding new controls
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