vsite.h File Reference

#include <array>
#include <memory>
#include <vector>
#include "gromacs/topology/idef.h"
#include "gromacs/topology/ifunc.h"
#include "gromacs/utility/real.h"
#include "gromacs/utility/vectypes.h"

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Description

Declares the VirtualSitesHandler class and vsite standalone functions.

Author

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

Classes
class	gmx::ArrayRef< typename >
	STL-like interface to a C array of T (or part of a std container of T). More...
class	gmx::VirtualSitesHandler
	Class that handles construction of vsites and spreading of vsite forces. More...

Typedefs
typedef std::array < std::vector< int > , numFtypes >	gmx::VsitePbc
	Type for storing PBC atom information for all vsite types in the system.

Enumerations
enum	gmx::VSiteOperation { gmx::VSiteOperation::Positions, gmx::VSiteOperation::Velocities, gmx::VSiteOperation::PositionsAndVelocities, gmx::VSiteOperation::Count }
	Whether we calculate vsite positions, velocities, or both. More...
enum	gmx::VirtualSiteVirialHandling : int { gmx::VirtualSiteVirialHandling::None, gmx::VirtualSiteVirialHandling::Pbc, gmx::VirtualSiteVirialHandling::NonLinear }
	Tells how to handle virial contributions due to virtual sites. More...

Functions
void	gmx::constructVirtualSites (ArrayRef< RVec > x, ArrayRef< const t_iparams > ip, const gmx::EnumerationArray< InteractionFunction, InteractionList > *ilist)
	Create positions of vsite atoms based for the local system. More...
void	gmx::constructVirtualSitesGlobal (const gmx_mtop_t &mtop, ArrayRef< RVec > x)
	Create positions of vsite atoms for the whole system assuming all molecules are wholex. 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, gmx_domdec_t *domdec, PbcType pbcType, ArrayRef< const RangePartitioning > updateGroupingPerMoleculeType)
	Create the virtual site handler. More...

Variables
static constexpr InteractionFunction	gmx::c_ftypeVsiteStart = InteractionFunction::VirtualSite1
	The start value of the vsite indices in the ftype enum. More...
static constexpr InteractionFunction	gmx::c_ftypeVsiteEnd
	The start and end value of the vsite indices in the ftype enum. More...
static constexpr int	gmx::numFtypes = static_cast<int>(c_ftypeVsiteEnd) - static_cast<int>(c_ftypeVsiteStart)
const std::array < InteractionFunction, numFtypes >	gmx::vSiteFunctionTypes
const std::array < InteractionFunction, numFtypes >	gmx::vSiteFunctionTypesReversed