gmx::anonymous_namespace{grompp.cpp} Namespace Reference

Classes
struct	ComSumContents
	Struct containing the quantities calculated by sumComForRestraints. More...

Functions
int	rm_interactions (InteractionFunction ftype, ArrayRef< MoleculeInformation > mols)
int	check_atom_names (const char *fn1, const char *fn2, gmx_mtop_t *mtop, const t_atoms *at, const MDLogger &logger)
void	check_bonds_timestep (const gmx_mtop_t *mtop, double dt, WarningHandler *wi)
void	clearSpecialParticleVelocities (const bool bGenVel, const t_inputrec &ir, const gmx_mtop_t &mtop, ArrayRef< RVec > v)
	Zeroes velocity components for special particles. More...
void	check_shells_inputrec (gmx_mtop_t *mtop, t_inputrec *ir, WarningHandler *wi)
int	nint_ftype (gmx_mtop_t *mtop, ArrayRef< const MoleculeInformation > mi, InteractionFunction ftype)
void	renumber_moltypes (gmx_mtop_t *sys, std::vector< MoleculeInformation > *molinfo)
void	molinfo2mtop (ArrayRef< const MoleculeInformation > mi, gmx_mtop_t *mtop)
void	new_status (const char *topfile, const std::optional< std::filesystem::path > &topppfile, const char *confin, t_gromppopts *opts, t_inputrec *ir, gmx_bool bZero, bool bGenVel, bool bVerbose, t_state *state, PreprocessingAtomTypes *atypes, gmx_mtop_t *sys, std::vector< MoleculeInformation > *mi, std::unique_ptr< MoleculeInformation > *intermolecular_interactions, EnumerationArray< InteractionFunction, InteractionsOfType > &interactions, CombinationRule *comb, double *reppow, real *fudgeQQ, gmx_bool bMorse, WarningHandler *wi, const MDLogger &logger)
void	copy_state (const char *slog, t_trxframe *fr, bool bReadVel, t_state *state, double *use_time)
void	cont_status (const char *slog, const std::optional< std::filesystem::path > &ener, bool bNeedVel, bool bGenVel, real fr_time, t_inputrec *ir, t_state *state, gmx_mtop_t *sys, const gmx_output_env_t *oenv, const MDLogger &logger)
void	read_posres (gmx_mtop_t *mtop, ArrayRef< const MoleculeInformation > molinfo, gmx_bool bTopB, const char *fn, RefCoordScaling rc_scaling, PbcType pbcType, WarningHandler *wi)
std::vector< ComSumContents >	sumComForRestraints (ArrayRef< const RVec > positionRestraintCoordinates, const MoleculeBlockIndices &inds, ArrayRef< const unsigned char > groupInds, const int numGroups, const t_atoms &atoms)
	Sum mass and mass*position of restrained atoms.
void	subComFromRestraints (ArrayRef< const RVec > comPerGroup, const MoleculeBlockIndices &inds, ArrayRef< const unsigned char > groupInds, const PbcType pbcType, ArrayRef< RVec > positionRestraintCoordinates)
	Subtracts COM position from position restraints.
std::vector< RVec >	calcPosresCom (gmx_mtop_t *mtop, const bool haveTopologyB, PbcType pbcType, const matrix box, const MDLogger &logger)
	Computes the center of mass of restrained atoms and subtracts it from restrain coordinates. More...
void	gen_posres (gmx_mtop_t *mtop, ArrayRef< const MoleculeInformation > mi, const char *fnA, const char *fnB, RefCoordScaling rc_scaling, PbcType pbcType, WarningHandler *wi)
void	set_wall_atomtype (PreprocessingAtomTypes *at, t_gromppopts *opts, t_inputrec *ir, WarningHandler *wi, const MDLogger &logger)
int	nrdf_internal (const t_atoms *atoms)
void	spline1d (double dx, const double *y, int n, double *u, double *y2)
void	interpolate1d (double xmin, double dx, const double *ya, const double *y2a, double x, double *y, double *y1)
CmapGrids	fillCmapGrids (ArrayRef< const CmapInteractionType > cmapTypes)
int	count_constraints (const gmx_mtop_t *mtop, ArrayRef< const MoleculeInformation > mi, WarningHandler *wi)
real	calc_temp (const gmx_mtop_t *mtop, const t_inputrec *ir, rvec *v)
real	get_max_reference_temp (const t_inputrec *ir, WarningHandler *wi)
void	checkForUnboundAtoms (const gmx_moltype_t *molt, gmx_bool bVerbose, WarningHandler *wi, const MDLogger &logger)
void	checkForUnboundAtoms (const gmx_mtop_t *mtop, gmx_bool bVerbose, WarningHandler *wi, const MDLogger &logger)
bool	haveDecoupledModeInMol (const gmx_moltype_t &molt, ArrayRef< const t_iparams > iparams, real massFactorThreshold)
	Checks if there are decoupled modes in moleculetype molt. More...
void	checkDecoupledModeAccuracy (const gmx_mtop_t *mtop, const t_inputrec *ir, WarningHandler *wi)
	Checks if the Verlet buffer and constraint accuracy is sufficient for decoupled dynamic modes. More...
void	set_verlet_buffer (const gmx_mtop_t *mtop, t_inputrec *ir, real buffer_temp, ArrayRef< const RVec > coordinates, matrix box, WarningHandler *wi, const MDLogger &logger)
std::tuple< real, int, int >	maxNonPerturbedExclusionDistance (const gmx_mtop_t &mtop, const bool useFep, const PbcType pbcType, ArrayRef< const RVec > x, const matrix box)
void	checkExclusionDistances (const gmx_mtop_t &mtop, const t_inputrec &ir, ArrayRef< const RVec > x, const matrix box, const MDLogger &logger, WarningHandler *wi)
void	deformInitFlow (t_state *state, const matrix deform)
	Add the velocity profile of deform to the velocities in state.

Function Documentation

std::vector<RVec> gmx::anonymous_namespace{grompp.cpp}::calcPosresCom	(	gmx_mtop_t *	mtop,
		const bool	haveTopologyB,
		PbcType	pbcType,
		const matrix	box,
		const MDLogger &	logger
	)

Computes the center of mass of restrained atoms and subtracts it from restrain coordinates.

mtop contains the restraint reference coordinates which are shifted by the COM.

Number of specified groups for independent COM scaling.

Subtract COM from posres positions

void gmx::anonymous_namespace{grompp.cpp}::checkDecoupledModeAccuracy	(	const gmx_mtop_t *	mtop,
		const t_inputrec *	ir,
		WarningHandler *	wi
	)

Checks if the Verlet buffer and constraint accuracy is sufficient for decoupled dynamic modes.

When decoupled modes are present and the accuracy in insufficient, this routine issues a warning if the accuracy is insufficient.

void gmx::anonymous_namespace{grompp.cpp}::clearSpecialParticleVelocities	(	const bool	bGenVel,
		const t_inputrec &	ir,
		const gmx_mtop_t &	mtop,
		ArrayRef< RVec >	v
	)

Zeroes velocity components for special particles.

Shells and virtual sites have their degrees of freedom constructed from other particles and thus do not have velocity. Particles with frozen dimensions likewise do not have velocities. These should be zeroed during grompp, so users cannot be concerned over observing a non-zero velocity, and if they see one it's a bug.

The implementation is fairly efficient even for an enormous system, but many simulations have none of these special atom types and would waste time here. If we need to optimize, then we can make the previous code count the numbers of such particles and then we would know in advance whether we need to do such clearing.

bool gmx::anonymous_namespace{grompp.cpp}::haveDecoupledModeInMol	(	const gmx_moltype_t &	molt,
		ArrayRef< const t_iparams >	iparams,
		real	massFactorThreshold
	)

Checks if there are decoupled modes in moleculetype molt.

The specific decoupled modes this routine check for are angle modes where the two bonds are constrained and the atoms a both ends are only involved in a single constraint; the mass of the two atoms needs to differ by more than massFactorThreshold.