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
Docs
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Simulations
»
Propagator
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Propagator
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Versions
latest
dev
v0.1.0
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