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gmx::anonymous_namespace{colvarsMDModule.cpp}::ColvarsMDModule Class Referencefinal
+ Inheritance diagram for gmx::anonymous_namespace{colvarsMDModule.cpp}::ColvarsMDModule:
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Description

Colvars module.

Class that implements the colvars MDModule

Public Member Functions

 ColvarsMDModule ()=default
 Construct the colvars module.
 
void subscribeToPreProcessingNotifications (MDModulesNotifiers *notifier) override
 Requests to be notified during pre-processing. More...
 
void subscribeToSimulationSetupNotifications (MDModulesNotifiers *notifier) override
 Request to be notified. The Colvars MDModule subscribes to these notifications: More...
 
IMdpOptionProvidermdpOptionProvider () override
 From IMDModule.
 
IMDOutputProvideroutputProvider () 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 notifier)
inlineoverridevirtual

Requests to be notified during pre-processing.

Parameters
[in]notifierallows 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 warninp for for grompp warnings output
  • Coordinates, PBC and box for setting up the proxy

Implements gmx::IMDModule.

void gmx::anonymous_namespace{colvarsMDModule.cpp}::ColvarsMDModule::subscribeToSimulationSetupNotifications ( MDModulesNotifiers notifier)
inlineoverridevirtual

Request to be notified. 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 t_commrec 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.


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