Enumerations
enum	SDUpdate : int { ForcesOnly, FrictionAndNoiseOnly, Combined, Count }
	Sets the SD update type.

Functions
void	simdLoadRvecs (const RVec r, int index, UpdateSimdReal r0, UpdateSimdReal r1, UpdateSimdReal r2)
	Load (aligned) the contents of GMX_SIMD_REAL_WIDTH RVec elements sequentially into 3 SIMD registers. More...

void	simdStoreRvecs (RVec *r, int index, UpdateSimdReal r0, UpdateSimdReal r1, UpdateSimdReal r2)
	Store (aligned) 3 SIMD registers sequentially to GMX_SIMD_REAL_WIDTH RVec elements. More...

template<StoreUpdatedVelocities storeUpdatedVelocities, NumTempScaleValues numTempScaleValues, typename VelocityType >
std::enable_if_t < std::is_same_v< VelocityType, RVec >\|\|std::is_same_v < VelocityType, const RVec > , void >	updateMDLeapfrogSimpleSimd (int start, int nrend, real dt, ArrayRef< const real > invMass, ArrayRef< const t_grp_tcstat > tcstat, const RVec gmx_restrict x, RVec gmx_restrict xprime, VelocityType gmx_restrict v, const RVec gmx_restrict f)
	Integrate using leap-frog with single group T-scaling and SIMD. More...

template<AccelerationType accelerationType>
void	updateMDLeapfrogGeneral (int start, int nrend, bool doNoseHoover, real dt, real dtPressureCouple, ArrayRef< const unsigned short > cTC, ArrayRef< const unsigned short > cAcceleration, const RVec gmx_restrict acceleration, const matrix boxDeformation, ArrayRef< const RVec > invMassPerDim, const gmx_ekindata_t ekind, const matrix box, const RVec gmx_restrict x, RVec gmx_restrict xprime, RVec gmx_restrict v, const RVec gmx_restrict f, const double *gmx_restrict nh_vxi, const int nsttcouple, const Matrix3x3 &parrinelloRahmanM)
	Integrate using leap-frog with support for everything. More...

void	do_update_md (int start, int nrend, real dt, int64_t step, const RVec gmx_restrict x, RVec gmx_restrict xprime, RVec gmx_restrict v, const RVec gmx_restrict f, const TemperatureCoupling etc, const PressureCoupling epc, const int nsttcouple, const int nstpcouple, ArrayRef< const unsigned short > cTC, const AccelerationType simulationAccelerationType, ArrayRef< const unsigned short > cAcceleration, ArrayRef< const RVec > acceleration, const matrix boxDeformation, ArrayRef< const real > gmx_unused invmass, ArrayRef< const RVec > invMassPerDim, const gmx_ekindata_t ekind, const matrix box, const double gmx_restrict nh_vxi, const Matrix3x3 &parrinelloRahmanM, bool gmx_unused havePartiallyFrozenAtoms)
	Handles the Leap-frog MD x and v integration.

void	doUpdateMDDoNotUpdateVelocities (int start, int nrend, real dt, const RVec gmx_restrict x, RVec gmx_restrict xprime, const RVec gmx_restrict v, const RVec gmx_restrict f, bool gmx_unused havePartiallyFrozenAtoms, ArrayRef< const real > gmx_unused invmass, ArrayRef< const RVec > invMassPerDim, const gmx_ekindata_t &ekind)
	Handles the Leap-frog MD x and v integration.

void	do_update_vv_vel (int start, int nrend, real dt, ArrayRef< const ivec > nFreeze, ArrayRef< const unsigned short > cAcceleration, const RVec gmx_restrict acceleration, ArrayRef< const real > invmass, ArrayRef< const ParticleType > ptype, ArrayRef< const unsigned short > cFREEZE, RVec gmx_restrict v, const RVec *gmx_restrict f, gmx_bool bExtended, real veta, real alpha)

void	do_update_vv_pos (int start, int nrend, real dt, ArrayRef< const ivec > nFreeze, ArrayRef< const ParticleType > ptype, ArrayRef< const unsigned short > cFREEZE, const RVec gmx_restrict x, RVec gmx_restrict xprime, const RVec *gmx_restrict v, gmx_bool bExtended, real veta)

template<SDUpdate updateType>
void	doSDUpdateGeneral (const gmx_stochd_t &sd, int start, int nrend, real dt, ArrayRef< const ivec > nFreeze, ArrayRef< const real > invmass, ArrayRef< const ParticleType > ptype, ArrayRef< const unsigned short > cFREEZE, ArrayRef< const unsigned short > cTC, ArrayRef< const unsigned short > cAcceleration, const RVec gmx_restrict acceleration, const RVec gmx_restrict x, RVec gmx_restrict xprime, RVec gmx_restrict v, const RVec gmx_restrict f, int64_t step, int seed, const int gatindex, real dtPressureCouple, const Matrix3x3 &parrinelloRahmanM)
	SD integrator update. More...

void	do_update_sd (int start, int nrend, real dt, int64_t step, const RVec gmx_restrict x, RVec gmx_restrict xprime, RVec gmx_restrict v, const RVec gmx_restrict f, ArrayRef< const ivec > nFreeze, ArrayRef< const real > invmass, ArrayRef< const ParticleType > ptype, ArrayRef< const unsigned short > cFREEZE, ArrayRef< const unsigned short > cTC, ArrayRef< const unsigned short > cAcceleration, ArrayRef< const RVec > acceleration, int seed, const gmx_domdec_t *dd, const gmx_stochd_t &sd, bool haveConstraints, const PressureCoupling pressureCoupling, const int nstpcouple, const Matrix3x3 &parrinelloRahmanM)

void	do_update_bd (int start, int nrend, real dt, int64_t step, const RVec gmx_restrict x, RVec gmx_restrict xprime, RVec gmx_restrict v, const RVec gmx_restrict f, ArrayRef< const ivec > nFreeze, ArrayRef< const real > invmass, ArrayRef< const ParticleType > ptype, ArrayRef< const unsigned short > cFREEZE, ArrayRef< const unsigned short > cTC, real friction_coefficient, const real rf, int seed, const int gatindex)

Function Documentation

template<SDUpdate updateType>

void gmx::anonymous_namespace{update.cpp}::doSDUpdateGeneral	(	const gmx_stochd_t &	sd,
		int	start,
		int	nrend,
		real	dt,
		ArrayRef< const ivec >	nFreeze,
		ArrayRef< const real >	invmass,
		ArrayRef< const ParticleType >	ptype,
		ArrayRef< const unsigned short >	cFREEZE,
		ArrayRef< const unsigned short >	cTC,
		ArrayRef< const unsigned short >	cAcceleration,
		const RVec *gmx_restrict	acceleration,
		const RVec *gmx_restrict	x,
		RVec *gmx_restrict	xprime,
		RVec *gmx_restrict	v,
		const RVec *gmx_restrict	f,
		int64_t	step,
		int	seed,
		const int *	gatindex,
		real	dtPressureCouple,
		const Matrix3x3 &	parrinelloRahmanM
	)

SD integrator update.

Two phases are required in the general case of a constrained update, the first phase from the contribution of forces, before applying constraints, and then a second phase applying the friction and noise, and then further constraining. For details, see Goga2012.

Without constraints, the two phases can be combined, for efficiency.

Thus three instantiations of this templated function will be made, two with only one contribution, and one with both contributions.

To maximize the ability of the compiler to optimize, all the arrays of RVec should be annotated with gmx_restrict, so the compiler knows there is no aliasing, and for the same reason we do not use ArrayRef<RVec> for them.

void gmx::anonymous_namespace{update.cpp}::simdLoadRvecs	(	const RVec *	r,
		int	index,
		UpdateSimdReal *	r0,
		UpdateSimdReal *	r1,
		UpdateSimdReal *	r2
	)

inline

Load (aligned) the contents of GMX_SIMD_REAL_WIDTH RVec elements sequentially into 3 SIMD registers.

The loaded output is: r0: { r[index][XX], r[index][YY], ... } r1: { ... } r2: { ..., r[index+GMX_SIMD_REAL_WIDTH-1][YY], r[index+GMX_SIMD_REAL_WIDTH-1][ZZ] }

Parameters

[in]	r	Real to an RVec array, has to be aligned to SIMD register width
[in]	index	Index of the first RVec triplet of reals to load
[out]	r0	Pointer to first SIMD register
[out]	r1	Pointer to second SIMD register
[out]	r2	Pointer to third SIMD register

void gmx::anonymous_namespace{update.cpp}::simdStoreRvecs	(	RVec *	r,
		int	index,
		UpdateSimdReal	r0,
		UpdateSimdReal	r1,
		UpdateSimdReal	r2
	)

inline

Store (aligned) 3 SIMD registers sequentially to GMX_SIMD_REAL_WIDTH RVec elements.

The stored output is: r[index] = { { r0[0], r0[1], ... } ... r[index+GMX_SIMD_REAL_WIDTH-1] = { ... , r2[GMX_SIMD_REAL_WIDTH-2], r2[GMX_SIMD_REAL_WIDTH-1] }

Parameters

[out]	r	Pointer to an RVec array, has to be aligned to SIMD register width
[in]	index	Index of the first RVec triplet of reals to store to
[in]	r0	First SIMD register
[in]	r1	Second SIMD register
[in]	r2	Third SIMD register

template<AccelerationType accelerationType>

void gmx::anonymous_namespace{update.cpp}::updateMDLeapfrogGeneral	(	int	start,
		int	nrend,
		bool	doNoseHoover,
		real	dt,
		real	dtPressureCouple,
		ArrayRef< const unsigned short >	cTC,
		ArrayRef< const unsigned short >	cAcceleration,
		const RVec *gmx_restrict	acceleration,
		const matrix	boxDeformation,
		ArrayRef< const RVec >	invMassPerDim,
		const gmx_ekindata_t *	ekind,
		const matrix	box,
		const RVec *gmx_restrict	x,
		RVec *gmx_restrict	xprime,
		RVec *gmx_restrict	v,
		const RVec *gmx_restrict	f,
		const double *gmx_restrict	nh_vxi,
		const int	nsttcouple,
		const Matrix3x3 &	parrinelloRahmanM
	)

Integrate using leap-frog with support for everything.

Template Parameters

accelerationType Type of NEMD acceleration.

Parameters

[in]	start	Index of first atom to update.
[in]	nrend	Last atom to update: `nrend` - 1.
[in]	doNoseHoover	If to apply Nose-Hoover T-coupling.
[in]	dt	The time step.
[in]	dtPressureCouple	Time step for pressure coupling, is 0 when no pressure coupling should be applied at this step.
[in]	cTC	Temperature coupling group indices
[in]	cAcceleration	Acceleration group indices
[in]	acceleration	Acceleration per group.
[in]	boxDeformation	Velocity of box components in units of nm/ps
[in]	invMassPerDim	Inverse mass per dimension
[in]	ekind	Kinetic energy data.
[in]	box	The box dimensions.
[in]	x	Input coordinates.
[out]	xprime	Updated coordinates.
[in,out]	v	Velocities.
[in]	f	Forces.
[in]	nh_vxi	Nose-Hoover velocity scaling factors.
[in]	nsttcouple	Frequency of the temperature coupling steps.
[in]	parrinelloRahmanM	Parrinello-Rahman scaling matrix.

template<StoreUpdatedVelocities storeUpdatedVelocities, NumTempScaleValues numTempScaleValues, typename VelocityType >

std::enable_if_t<std::is_same_v<VelocityType, RVec> \|\| std::is_same_v<VelocityType, const RVec>, void> gmx::anonymous_namespace{update.cpp}::updateMDLeapfrogSimpleSimd	(	int	start,
		int	nrend,
		real	dt,
		ArrayRef< const real >	invMass,
		ArrayRef< const t_grp_tcstat >	tcstat,
		const RVec *gmx_restrict	x,
		RVec *gmx_restrict	xprime,
		VelocityType *gmx_restrict	v,
		const RVec *gmx_restrict	f
	)

Integrate using leap-frog with single group T-scaling and SIMD.

Template Parameters

storeUpdatedVelocities	Tells whether we should store the updated velocities
numTempScaleValues	The number of different T-couple values
VelocityType	Either RVec or const RVec according to whether we store velocities

Parameters

[in]	start	Index of first atom to update
[in]	nrend	Last atom to update: `nrend` - 1
[in]	dt	The time step
[in]	invMass	1/mass per atom
[in]	tcstat	Temperature coupling information
[in]	x	Input coordinates
[out]	xprime	Updated coordinates
[in,out]	v	Velocities, type either RVec* or const RVec*
[in]	f	Forces

Enumerations

Functions

Function Documentation