Jumos
Simulations
Usage example
Lennard-Jones fluid
Usual simulation steps
Setting the simulation
Get topology
Setup interaction
Initial positions
Initial velocities
Setup simulation
Running the simulation
Integrate
Get forces
Control
Check
Compute
Output
Creating simulations
The Simulation type
Default algorithms
Potentials
Potential functions
Short-range pair potential
Bonded potential
Adding interactions to a simulation
Defining a new potential
User potential
Subtyping PotentialFunction
Potential computation
Which computation for which potential ?
Using non-default computation
Exporting values of interest
Existing outputs
Trajectory output
Energy output
Defining a new output
Custom output
Computing values of interest
Energy related values
Volume
Pressure
Selecting the algorithms
Integrator: running the simulation
Verlet integrators
Checking the simulation consistency
Existing checks
Controlling the simulation
Controlling the temperature: Thermostats
Controlling the pressure: Barostats
Other controls
Functions for algorithms selection
Trajectories
Reading and writing trajectories
Base types
Usage
Reading frames from a file
Writing frames in a file
Supported formats
Readind and writing topologies
Supported formats for topology
Analysis
Base Histogram type
Radial distribution function
Density profile
Internal units
Developer documentation
Atoms
Atom type
Topology
Topology functions
Periodic table information
Universe
Array3D
Simulation Cell
Creating simulation cell
Indexing simulation cell
Boundary conditions and cells
Distances and cells
Frame
Creating frames
Reading and writing frames from files
Periodic boundary conditions and distances computations
Minimal images
Distances
Within one Frame
Between two Frames
Interaction with others units systems
Developping new algorithms
Writing a new
integrator
Computing the forces
Naive force computation
New algorithm for forces computations
Adding a new
check
Adding new
controls
Computing values
Outputing values
Jumos
Docs
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Developer documentation
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Developer documentation
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Atoms
Atom type
Topology
Periodic table information
Universe
Array3D
Simulation Cell
Frame
Periodic boundary conditions and distances computations
Minimal images
Distances
Interaction with others units systems
Developping new algorithms
Writing a new
integrator
Computing the forces
Adding a new
check
Adding new
controls
Computing values
Outputing values
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