Implementation of mdrun

Collaboration diagram for Implementation of mdrun:

Description

This module contains code that implements mdrun.

Namespaces
	gmx
	Generic GROMACS namespace.

Classes
class	gmx::Mdrunner
	Runner object for supporting setup and execution of mdrun. More...
class	gmx::MdrunnerBuilder
	Build a gmx::Mdrunner. More...
class	gmx::SimulationContext
	Simulation environment and configuration. More...

Functions
SimulationInputHandle	gmx::makeSimulationInput (const LegacyMdrunOptions &options)
	Direct the construction of a SimulationInput. More...

Files
file	legacymdrunoptions.cpp
	This file declares helper functionality for legacy option handling for mdrun.
file	legacymdrunoptions.h
	This file declares helper functionality for legacy option handling for mdrun.
file	md.cpp
	Implements the integrator for normal molecular dynamics simulations.
file	mdmodules.h
	Declares gmx::MDModules.
file	mimic.cpp
	Declares the loop for MiMiC QM/MM.
file	minimize.cpp
	This file defines integrators for energy minimization.
file	replicaexchange.cpp
	Implements the replica exchange routines.
file	replicaexchange.h
	Declares the routines for replica exchange.
file	rerun.cpp
	Implements the loop for simulation reruns.
file	runner.cpp
	Implements the MD runner routine calling all integrators.
file	runner.h
	Declares the routine running the inetgrators.
file	simulationcontext.h
	Provide ways for client code to own simulation resources.
file	simulationinput.h
	Utilities for interacting with SimulationInput.
file	simulationinputhandle.h
	Public interface for SimulationInput facilities.
file	simulatorbuilder.cpp
	Defines the simulator builder for mdrun.
file	tpi.cpp
	This file defines the integrator for test particle insertion.
file	mdrun.cpp
	This file implements mdrun.
file	mdrun_main.h
	This file declares C-style entrypoints for mdrun.

Function Documentation

SimulationInputHandle gmx::makeSimulationInput

(

const LegacyMdrunOptions &

options

)

Direct the construction of a SimulationInput.

Warning

Creation methods for SimulationInput resources are under rapid development. Reference https://gitlab.com/gromacs/gromacs/-/issues/3652

Parameters

options

library-internal container holding partially processed user input.

This isn't really a public API function until its arguments are obtainable through the public API.

Design notes: SimulationInput creation will warrant a builder protocol, and this helper can evolve into a director to apply the contents of LegacyMdrunOptions, while such an operation is still relevant.

Example: // After preparing a LegacyMdrunOptions and calling handleRestart()... SimulationInputBuilder builder; auto simulationInputHandle = makeSimulationInput(options, &builder);

// In addition to MdrunnerBuilder::addFiles(), mdrunnerBuilder.addInput(simulationInputHandle.get());