Gromacs
2019-beta3
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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 | |
SimulationContext | gmx::createSimulationContext (t_commrec *simulationCommunicator) |
Get ownership of a new SimulationContext object. 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 | logging.cpp |
Implements the MD log file handling routines. | |
file | logging.h |
Declares the MD log file handling routines. | |
file | md.cpp |
Implements the integrator for normal molecular dynamics simulations. | |
file | md.h |
Declares the integrator for normal molecular dynamics simulations. | |
file | mimic.cpp |
Declares the loop for MiMiC QM/MM. | |
file | mimic.h |
Declares the loop for MiMiC QM/MM. | |
file | minimize.cpp |
This file defines integrators for energy minimization. | |
file | multisim.cpp |
Implements the multi-simulation support routines. | |
file | multisim.h |
Declares the multi-simulation support routines. | |
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 | rerun.h |
Declares 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 | tpi.cpp |
This file defines the integrator for test particle insertion. | |
file | mdrun.cpp |
This file implements mdrun. | |
SimulationContext gmx::createSimulationContext | ( | t_commrec * | simulationCommunicator | ) |
Get ownership of a new SimulationContext object.
A client must share ownership of some resources and transfer ownership of other resources to create or configure the context. The simulation may in turn consume or borrow some resources from the context. This is a new framework that will evolve in the contexts of https://redmine.gromacs.org/issues/2375 https://redmine.gromacs.org/issues/2587 https://redmine.gromacs.org/issues/2605
Ownership is returned as a smart pointer because ownership or reference may need to be transferred through higher level code or maintained as a heap object, and there is not yet a public interface, wrapper, or separate handle object.
This call signature sets all parameters processed by the command-line client code. Additional call signatures can allow implementation-specified default values or newer initialization interfaces.
simulationCommunicator | Handle to communication data structure. |