Simulations (`relentless.simulate`)#

relentless.simulate implements a generalizable and human-readable interface for performing molecular simulations. The simulations are used to evolve a system described by interactions in relentless.potential to generate statistical ensembles. This module implements code to translate one common simulation “recipe” into a running simulation in a variety of popular packages. This gives you the freedom to choose simulation software this is most compatible with your environment and resources using a single common code! It also helps document workflows that can be shared and reproduced by others.

Example

init = relentless.simulate.InitializeRandomly(seed=1)
avg = relentless.simulate.EnsembleAverage(
        check_thermo_every=5,
        check_rdf_every=5,
        rdf_dr=0.1)
ops = [relentless.simulate.RunLangevinDynamics(
            steps=1e3,
            timestep=0.001,
            friction=0.8,
            seed=2),
        relentless.simulate.RunLangevinDynamics(
            steps=1e4,
            timestep=0.001,
            friction=0.8,
            seed=3,
            analyzers=avg)
        ]

# perform simulation using LAMMPS and save ensemble
lmp = relentless.simulate.LAMMPS(init, ops)
sim = lmp.run(potentials)
sim[avg].ensemble.save('ensemble.json')

Major versions of simulation engines are officially supported for two years after their last patch or stable release.

Engines#

`Dilute`(initializer[, operations])	Simulation of a dilute system.
`HOOMD`(initializer[, operations, device])	Simulation using HOOMD-blue.
`LAMMPS`(initializer[, operations, quiet, ...])	Simulation using LAMMPS.

Initializers#

`InitializeFromFile`(filename[, format, dimension])	Initialize a simulation from a file.
`InitializeRandomly`(seed, N, V[, T, masses, ...])	Initialize a randomly generated simulation box.

Molecular dynamics#

RunMolecularDynamics(steps, timestep[, ...])

Perform a molecular dynamics simulation.

Thermostats#

`BerendsenThermostat`(T, tau)	Berendsen thermostat.
`NoseHooverThermostat`(T, tau)	Nosé-Hoover thermostat.

Barostats#

`BerendsenBarostat`(P, tau)	Berendsen barostat.
`MTKBarostat`(P, tau)	MTK barostat.

Other dynamics#

`MinimizeEnergy`(energy_tolerance, ...[, options])	Perform energy minimization on a configuration.
`RunBrownianDynamics`(steps, timestep, T, ...)	Perform a Brownian dynamics simulation.
`RunLangevinDynamics`(steps, timestep, T, ...)	Perform a Langevin dynamics simulation.

Analyzers#

`EnsembleAverage`(filename, every[, rdf, ...])	Compute average properties.
`Record`(filename, every, quantities)	Record quantities during a simulation.
`WriteTrajectory`(filename, every[, format, ...])	Write a simulation trajectory to file.

Running a simulation#

Results#

SimulationInstance(backend, initializer, ...)

Specific instance of a simulation and its data.

Defining interactions#

`Potentials`([kB])	Set of interaction potentials.
`PotentialTabulator`(potentials, start, stop, num)	Tabulator for an interaction potential.
`AnglePotentialTabulator`(potentials, num)	Tabulate one or more angle potentials.
`BondPotentialTabulator`(potentials, start, ...)	Tabulate one or more bond potentials.
`DihedralPotentialTabulator`(potentials, num)	Tabulate one or more dihedral potentials.
`PairPotentialTabulator`(potentials, start, ...)	Tabulate one or more pair potentials.

Developer classes#

`Simulation`(initializer[, operations])	Simulation engine.
`SimulationOperation`(analyzers)	Operation to be performed by a `Simulation`.
`AnalysisOperation`()	Analysis operation to be performed by a `Simulation`.
`Barostat`(P)	Barostat.
`Thermostat`(T)	Thermostat.

Simulations (relentless.simulate)#