vsite.cpp File Reference

#include "gmxpre.h"
#include "vsite.h"
#include <cstdio>
#include <algorithm>
#include <filesystem>
#include <memory>
#include <vector>
#include "gromacs/domdec/domdec.h"
#include "gromacs/domdec/domdec_struct.h"
#include "gromacs/gmxlib/network.h"
#include "gromacs/gmxlib/nrnb.h"
#include "gromacs/math/functions.h"
#include "gromacs/math/vec.h"
#include "gromacs/mdlib/gmx_omp_nthreads.h"
#include "gromacs/mdtypes/commrec.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/pbcutil/ishift.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/timing/wallcycle.h"
#include "gromacs/topology/block.h"
#include "gromacs/topology/forcefieldparameters.h"
#include "gromacs/topology/ifunc.h"
#include "gromacs/topology/mtop_util.h"
#include "gromacs/topology/topology.h"
#include "gromacs/topology/topology_enums.h"
#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/gmxomp.h"

Include dependency graph for vsite.cpp:

Description

Implements the VirtualSitesHandler class and vsite standalone functions.

Author

Berk Hess hess@.nosp@m.kth..nosp@m.se

Classes
struct	gmx::DomainInfo
	Information on PBC and domain decomposition for virtual sites. More...
struct	gmx::AtomIndex
	List of atom indices belonging to a task. More...
struct	gmx::InterdependentTask
	Data structure for thread tasks that use constructing atoms outside their own atom range. More...
struct	gmx::VsiteThread
	Vsite thread task data structure. More...
class	gmx::ThreadingInfo
	Information on how the virtual site work is divided over thread tasks. More...
class	gmx::VirtualSitesHandler::Impl
	Impl class for VirtualSitesHandler. More...

Typedefs
using	gmx::VirialHandling = VirtualSitesHandler::VirialHandling
	VirialHandling is often used outside VirtualSitesHandler class members.

Enumerations
enum	gmx::VSiteCalculatePosition { Yes, No }
	Whether we're calculating the virtual site position.
enum	gmx::VSiteCalculateVelocity { Yes, No }
	Whether we're calculating the virtual site velocity.
enum	gmx::PbcMode { gmx::PbcMode::all, gmx::PbcMode::none }
	PBC modes for vsite construction and spreading. More...

Functions
static int	gmx::vsiteIlistNrCount (ArrayRef< const InteractionList > ilist)
	Returns the sum of the vsite ilist sizes over all vsite types. More...
static int	gmx::pbc_rvec_sub (const t_pbc *pbc, const rvec xi, const rvec xj, rvec dx)
	Computes the distance between xi and xj, pbc is used when pbc!=nullptr.
static real	gmx::inverseNorm (const rvec x)
	Returns the 1/norm(x)
static PbcMode	gmx::getPbcMode (const t_pbc *pbcPtr)
	Returns the PBC mode based on the system PBC and vsite properties. More...
template<VSiteCalculatePosition calculatePosition, VSiteCalculateVelocity calculateVelocity>
static void	gmx::construct_vsites_thread (ArrayRef< RVec > x, ArrayRef< RVec > v, ArrayRef< const t_iparams > ip, ArrayRef< const InteractionList > ilist, const t_pbc *pbc_null)
	Executes the vsite construction task for a single thread. More...
template<VSiteCalculatePosition calculatePosition, VSiteCalculateVelocity calculateVelocity>
static void	gmx::construct_vsites (const ThreadingInfo *threadingInfo, ArrayRef< RVec > x, ArrayRef< RVec > v, ArrayRef< const t_iparams > ip, ArrayRef< const InteractionList > ilist, const DomainInfo &domainInfo, const matrix box)
	Dispatch the vsite construction tasks for all threads. More...
void	gmx::constructVirtualSites (ArrayRef< RVec > x, ArrayRef< const t_iparams > ip, ArrayRef< const InteractionList > ilist)
	Create positions of vsite atoms based for the local system. More...
static int	gmx::vsite_count (ArrayRef< const InteractionList > ilist, int ftype)
	Returns the number of virtual sites in the interaction list, for VSITEN the number of atoms.
template<VirialHandling virialHandling>
static void	gmx::spreadForceForThread (ArrayRef< const RVec > x, ArrayRef< RVec > f, ArrayRef< RVec > fshift, matrix dxdf, ArrayRef< const t_iparams > ip, ArrayRef< const InteractionList > ilist, const t_pbc *pbc_null)
	Executes the force spreading task for a single thread.
static void	gmx::spreadForceWrapper (ArrayRef< const RVec > x, ArrayRef< RVec > f, const VirialHandling virialHandling, ArrayRef< RVec > fshift, matrix dxdf, const bool clearDxdf, ArrayRef< const t_iparams > ip, ArrayRef< const InteractionList > ilist, const t_pbc *pbc_null)
	Wrapper function for calling the templated thread-local spread function.
static void	gmx::clearTaskForceBufferUsedElements (InterdependentTask *idTask)
	Clears the task force buffer elements that are written by task idTask.
static std::vector< int >	gmx::makeAtomToGroupMapping (const gmx::RangePartitioning &grouping)
	Returns the an array with group indices for each atom. More...
int	gmx::countNonlinearVsites (const gmx_mtop_t &mtop)
	Return the number of non-linear virtual site constructions in the system.
int	gmx::countInterUpdategroupVsites (const gmx_mtop_t &mtop, ArrayRef< const RangePartitioning > updateGroupingsPerMoleculeType)
	Return the number of virtual sites that cross update groups. More...
std::unique_ptr < VirtualSitesHandler >	gmx::makeVirtualSitesHandler (const gmx_mtop_t &mtop, const t_commrec *cr, PbcType pbcType, ArrayRef< const RangePartitioning > updateGroupingPerMoleculeType)
	Create the virtual site handler. More...
	gmx::iparams_ (mtop.ffparams.iparams)
static void	gmx::flagAtom (InterdependentTask *idTask, const int atom, const int numThreads, const int numAtomsPerThread)
	Flag that atom atom which is home in another task, if it has not already been added before.
static void	gmx::assignVsitesToThread (VsiteThread *tData, int thread, int nthread, int natperthread, gmx::ArrayRef< int > taskIndex, ArrayRef< const InteractionList > ilist, ArrayRef< const t_iparams > ip, ArrayRef< const ParticleType > ptype)
	Here we try to assign all vsites that are in our local range. More...
static void	gmx::assignVsitesToSingleTask (VsiteThread *tData, int task, gmx::ArrayRef< const int > taskIndex, ArrayRef< const InteractionList > ilist, ArrayRef< const t_iparams > ip)
	Assign all vsites with taskIndex[]==task to task tData.