gmx::anonymous_namespace{colvarsMDModule.cpp}::ColvarsMDModule Class Reference

Inheritance diagram for gmx::anonymous_namespace{colvarsMDModule.cpp}::ColvarsMDModule:

Collaboration diagram for gmx::anonymous_namespace{colvarsMDModule.cpp}::ColvarsMDModule:

Description

Colvars module.

Class that implements the colvars MDModule

Public Member Functions
	ColvarsMDModule ()=default
	Construct the colvars module.
void	subscribeToPreProcessingNotifications (MDModulesNotifiers *notifiers) override
	Requests to be notified during pre-processing. More...
void	subscribeToSimulationSetupNotifications (MDModulesNotifiers *notifiers) override
	Request to be notified. More...
void	subscribeToSimulationRunNotifications (MDModulesNotifiers *notifiers) override
	Request to be notified. More...
IMdpOptionProvider *	mdpOptionProvider () override
	From IMDModule.
IMDOutputProvider *	outputProvider () override
	From IMDModule Colvars provide its own output.
void	initForceProviders (ForceProviders *forceProviders) override
	From IMDModule Add this module to the force providers if active.

Member Function Documentation

void gmx::anonymous_namespace{colvarsMDModule.cpp}::ColvarsMDModule::subscribeToPreProcessingNotifications ( MDModulesNotifiers *  notifiers )

inlineoverridevirtual

Requests to be notified during pre-processing.

Parameters

[in]

notifiers

allows the module to subscribe to notifications from MdModules.

The Colvars MDModule subscribes to these notifications:

• storing its internal parameters in a tpr file by writing to a key-value-tree during pre-processing by a function taking a KeyValueTreeObjectBuilder as parameter
• Acess topology using gmx_mtop_t notification
• Access MDLogger for notifications output
• Access warning for for grompp warnings output
• Coordinates, PBC and box for setting up the proxy

Implements gmx::IMDModule.

void gmx::anonymous_namespace{colvarsMDModule.cpp}::ColvarsMDModule::subscribeToSimulationRunNotifications ( MDModulesNotifiers *  notifiers )

inlineoverridevirtual

Request to be notified.

Parameters

[in]

notifiers

allows the module to subscribe to notifications from MdModules.

The Colvars MDModule subscribes to this notification:

• the atom redistributed signal

Implements gmx::IMDModule.

void gmx::anonymous_namespace{colvarsMDModule.cpp}::ColvarsMDModule::subscribeToSimulationSetupNotifications ( MDModulesNotifiers *  notifiers )

inlineoverridevirtual

Request to be notified.

Parameters

[in]

notifiers

allows the module to subscribe to notifications from MdModules.

The Colvars MDModule subscribes to these notifications:

• the LocalAtomSetManager sets in the simulation parameter setup by taking a LocalAtomSetManager * as parameter
• the type of periodic boundary conditions that are used by taking a PeriodicBoundaryConditionType as parameter
• the topology of the system by taking a gmx_mtop_t * as parameter
• the communicator by taking a MpiComm as parameter
• the simulation time step by taking a SimulationTimeStep as a parameter
• MDLogger for notifications output
• the .edr filename to provide a user-defined output prefix for Colvars output files

Implements gmx::IMDModule.

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The documentation for this class was generated from the following file:

• src/gromacs/applied_forces/colvars/colvarsMDModule.cpp