mdlib Directory Reference

Directory dependency graph for mdlib:

Directories
directory	tests

Files
file	boxdeformation.cpp
	Defines the box deformation code.
file	boxdeformation.h
	Declares interface to box deformation code.
file	broadcaststructs.cpp
file	broadcaststructs.h
	Convenience wrappers for broadcasting structs.
file	calc_verletbuf.cpp
file	calc_verletbuf.h
file	calcmu.cpp
file	calcmu.h
file	calcvir.cpp
file	calcvir.h
file	checkpointhandler.cpp
	Defines the checkpoint handler class.
file	checkpointhandler.h
	Declares the checkpoint handler class.
file	compute_io.cpp
file	compute_io.h
file	constr.cpp
	Defines the high-level constraint code.
file	constr.h
	Declares interface to constraint code.
file	constraintrange.cpp
file	constraintrange.h
file	coupling.cpp
file	coupling.h
file	dispersioncorrection.cpp
file	dispersioncorrection.h
file	ebin.cpp
file	ebin.h
file	enerdata_utils.cpp
file	enerdata_utils.h
file	energydrifttracker.cpp
	Implements functions from the EnergyDriftTracker class.
file	energydrifttracker.h
	Declares and defines the EnergyDriftTracker class.
file	energyoutput.cpp
	Defines code that writes energy-like quantities.
file	energyoutput.h
	Header for the code that writes energy-like quantities.
file	expanded.cpp
file	expanded.h
file	expanded_internal.cpp
	Implements internal functionality for expanded ensemble.
file	expanded_internal.h
	Declares internal functionality for expanded ensemble.
file	force.cpp
file	force.h
file	force_flags.h
file	forcerec.cpp
file	forcerec.h
file	freeenergyparameters.cpp
	Implements routines in freeenergyparameters.h .
file	freeenergyparameters.h
	Handling of free energy parameters.
file	gmx_omp_nthreads.cpp
file	gmx_omp_nthreads.h
file	gpuforcereduction.h
	Declares the GPU Force Reduction.
file	gpuforcereduction_impl.cpp
	Implements backend-agnostic GPU Force Reduction functions.
file	gpuforcereduction_impl.h
	Declares the GPU Force Reduction.
file	gpuforcereduction_impl_internal.h
	Declares vendor-specific function to launch force reduction kernel.
file	gpuforcereduction_impl_internal_sycl.cpp
	Implements GPU Force Reduction using SYCL.
file	gpuforcereduction_impl_stubs.cpp
	May be used to implement force reduction interfaces for non-GPU builds.
file	groupcoord.cpp
file	groupcoord.h
	Assemble atomic positions of a (small) subset of atoms and distribute to all nodes.
file	leapfrog_gpu.cpp
	Implements Leap-Frog using CUDA.
file	leapfrog_gpu.h
	Declarations for GPU implementation of Leap-Frog.
file	leapfrog_gpu_internal.h
	Declarations for backend specific GPU functions for Leap-Frog.
file	leapfrog_gpu_internal_sycl.cpp
	Implements Leap-Frog using SYCL.
file	lincs.cpp
	Defines LINCS code.
file	lincs.h
	Declares interface to LINCS code.
file	lincs_gpu.cpp
	Implementations of LINCS GPU class.
file	lincs_gpu.h
	Declares the class for GPU implementation of LINCS.
file	lincs_gpu_internal.h
	Declare backend-specific LINCS GPU functions.
file	lincs_gpu_internal_sycl.cpp
	Implements LINCS kernels using SYCL.
file	makeconstraints.h
	Declares and implements factory function for Constraints.
file	md_support.cpp
file	md_support.h
file	mdatoms.cpp
file	mdatoms.h
file	mdebin_bar.cpp
file	mdebin_bar.h
file	mdoutf.cpp
file	mdoutf.h
file	membed.cpp
file	membed.h
file	perf_est.cpp
file	perf_est.h
file	rbin.cpp
file	rbin.h
file	resethandler.cpp
	Defines the reset handler class.
file	resethandler.h
	Declares the reset handler class.
file	rf_util.cpp
file	rf_util.h
file	settle.cpp
	Defines SETTLE code.
file	settle.h
	Declares interface to SETTLE code.
file	settle_gpu.cpp
	Implements SETTLE using GPU.
file	settle_gpu.h
	Declares class for GPU implementation of SETTLE.
file	settle_gpu_internal.h
	Declares backend-specific functions for GPU implementation of SETTLE.
file	settle_gpu_internal_sycl.cpp
	SYCL-specific routines for the GPU implementation of SETTLE constraints algorithm.
file	shake.cpp
	Defines SHAKE code.
file	shake.h
	Declares interface to SHAKE code.
file	sighandler.cpp
file	sighandler.h
file	sim_util.cpp
file	simulationsignal.cpp
	This file defines functions for inter- and intra-simulation signalling by mdrun.
file	simulationsignal.h
	This file declares functions for inter-rank signalling by mdrun.
file	splitter.cpp
file	splitter.h
file	stat.cpp
file	stat.h
file	stophandler.cpp
	Defines StopHandler, a helper class and two stop conditions.
file	stophandler.h
	Declares StopHandler, a helper class and two stop conditions.
file	tgroup.cpp
file	tgroup.h
file	trajectory_writing.cpp
file	trajectory_writing.h
file	update.cpp
file	update.h
file	update_constrain_gpu.h
	Declaration of high-level functions of GPU implementation of update and constrain class.
file	update_constrain_gpu_impl.cpp
	Implements update and constraints class.
file	update_constrain_gpu_impl.h
	Declares GPU implementation class for update and constraints.
file	update_constrain_gpu_impl_stubs.cpp
	Stub for update and constraints class CPU implementation.
file	update_constrain_gpu_internal.h
	Declares GPU implementations of backend-specific update-constraints functions.
file	update_constrain_gpu_internal_sycl.cpp
	Implements backend-specific functions of the update-constraints in SYCL.
file	update_vv.cpp
file	update_vv.h
file	updategroups.cpp
file	updategroups.h
	Declares the functions for generating update groups.
file	updategroupscog.cpp
file	updategroupscog.h
	Declares the UpdateGroupsCog class for managing centers of mass of update groups.
file	vcm.cpp
file	vcm.h
file	vsite.cpp
	Implements the VirtualSitesHandler class and vsite standalone functions.
file	vsite.h
	Declares the VirtualSitesHandler class and vsite standalone functions.
file	wall.cpp
file	wall.h
file	wholemoleculetransform.cpp
file	wholemoleculetransform.h
	Declares the WholeMolecules class for generating whole molecules.