Positions and Velocities

Functions
void	tinker::mdVelData (RcOp)
constexpr int	tinker::BOUNDS_EVERY_X_STEPS = 500
	Calls bounds() at least every x steps in MD. More...
void	tinker::mdPos (time_prec, pos_prec *, pos_prec *, pos_prec *, const vel_prec *, const vel_prec *, const vel_prec *)
	Updates x, y, z via \( x(t) = x(0) + v(0) t \). More...
void	tinker::mdPos (time_prec dt)
	Calls bounds() at least every x steps in MD. More...
void	tinker::mdPosAxbv (pos_prec a, pos_prec b)
	Updates x, y, z via \( r = a r + b v \). More...
void	tinker::mdPosAxbvAn (pos_prec(*a)[3], pos_prec(*b)[3])
	Updates x, y, z via \( \boldsymbol{r} = \boldsymbol{A}\boldsymbol{r} + \boldsymbol{B}\boldsymbol{v} \). More...
void	tinker::mdDebugPosNorm (pos_prec poseps, time_prec dt, const vel_prec *vx, const vel_prec *vy, const vel_prec *vz)
	Throws an error if one of the atoms moves too far in one position update, and saves the last good coordinates in an external file. More...
void	tinker::mdVel (time_prec dt, const grad_prec *grx, const grad_prec *gry, const grad_prec *grz)
	Updates velocities via \( v(t) = v(0) - (g/m)t \). More...
void	tinker::mdVel2 (time_prec dt, const grad_prec *grx, const grad_prec *gry, const grad_prec *grz, time_prec dt2, const grad_prec *grx2, const grad_prec *gry2, const grad_prec *grz2)
	Updates velocities via \( v = v - (g_1/m) t_1 - (g_2/m) t_2 \). More...
void	tinker::mdVelScale (vel_prec scal, int nelem, vel_prec *vx0, vel_prec *vy0, vel_prec *vz0)
	Updates velocities via \( v = s v \). More...
void	tinker::mdVelAvbf (int nrespa, vel_prec a, vel_prec b, const grad_prec *gx1, const grad_prec *gy1, const grad_prec *gz1, const grad_prec *gx2, const grad_prec *gy2, const grad_prec *gz2)
	Updates velocities via \( v = a v + b (g_1/n + g_2)/m \) (isotropic). If n equals 1, the 2nd set of gradients are ignored. More...
void	tinker::mdVelAvbfAn (int nrespa, vel_prec a[3][3], vel_prec b[3][3], const grad_prec *gx1, const grad_prec *gy1, const grad_prec *gz1, const grad_prec *gx2, const grad_prec *gy2, const grad_prec *gz2)
	Updates velocities via \( \boldsymbol{v} = \boldsymbol{Av} + \boldsymbol{B} (\boldsymbol{g}_1/n + \boldsymbol{g}_2)/m \) (anisotropic). If n equals 1, the 2nd set of gradients are ignored. More...
vel_prec *	tinker::vx
	Velocities. More...
vel_prec *	tinker::vy
	Velocities. More...
vel_prec *	tinker::vz
	Velocities. More...

Detailed Description

Function Documentation

mdDebugPosNorm()

void tinker::mdDebugPosNorm	(	pos_prec	poseps,
		time_prec	dt,
		const vel_prec *	vx,
		const vel_prec *	vy,
		const vel_prec *	vz
	)

Throws an error if one of the atoms moves too far in one position update, and saves the last good coordinates in an external file.

mdPos() [1/2]

void tinker::mdPos

(

time_prec

dt

)

Calls bounds() at least every x steps in MD.

mdPos() [2/2]

void tinker::mdPos	(	time_prec	,
		pos_prec *	,
		pos_prec *	,
		pos_prec *	,
		const vel_prec *	,
		const vel_prec *	,
		const vel_prec *
	)

Updates x, y, z via \( x(t) = x(0) + v(0) t \).

Currently xpos, ypos, and zpos are integrated first, then they are copied to x, y, z by copyPosToXyz().

mdPosAxbv()

void tinker::mdPosAxbv	(	pos_prec	a,
		pos_prec	b
	)

Updates x, y, z via \( r = a r + b v \).

mdPosAxbvAn()

void tinker::mdPosAxbvAn	(	pos_prec(*)	a[3],
		pos_prec(*)	b[3]
	)

Updates x, y, z via \( \boldsymbol{r} = \boldsymbol{A}\boldsymbol{r} + \boldsymbol{B}\boldsymbol{v} \).

mdVel()

void tinker::mdVel	(	time_prec	dt,
		const grad_prec *	grx,
		const grad_prec *	gry,
		const grad_prec *	grz
	)

Updates velocities via \( v(t) = v(0) - (g/m)t \).

mdVel2()

void tinker::mdVel2	(	time_prec	dt,
		const grad_prec *	grx,
		const grad_prec *	gry,
		const grad_prec *	grz,
		time_prec	dt2,
		const grad_prec *	grx2,
		const grad_prec *	gry2,
		const grad_prec *	grz2
	)

Updates velocities via \( v = v - (g_1/m) t_1 - (g_2/m) t_2 \).

mdVelAvbf()

void tinker::mdVelAvbf	(	int	nrespa,
		vel_prec	a,
		vel_prec	b,
		const grad_prec *	gx1,
		const grad_prec *	gy1,
		const grad_prec *	gz1,
		const grad_prec *	gx2,
		const grad_prec *	gy2,
		const grad_prec *	gz2
	)

Updates velocities via \( v = a v + b (g_1/n + g_2)/m \) (isotropic). If n equals 1, the 2nd set of gradients are ignored.

mdVelAvbfAn()

void tinker::mdVelAvbfAn	(	int	nrespa,
		vel_prec	a[3][3],
		vel_prec	b[3][3],
		const grad_prec *	gx1,
		const grad_prec *	gy1,
		const grad_prec *	gz1,
		const grad_prec *	gx2,
		const grad_prec *	gy2,
		const grad_prec *	gz2
	)

Updates velocities via \( \boldsymbol{v} = \boldsymbol{Av} + \boldsymbol{B} (\boldsymbol{g}_1/n + \boldsymbol{g}_2)/m \) (anisotropic). If n equals 1, the 2nd set of gradients are ignored.

mdVelData()

void tinker::mdVelData

(

RcOp

)

mdVelScale()

void tinker::mdVelScale	(	vel_prec	scal,
		int	nelem,
		vel_prec *	vx0,
		vel_prec *	vy0,
		vel_prec *	vz0
	)

Updates velocities via \( v = s v \).

Variable Documentation

BOUNDS_EVERY_X_STEPS

constexpr int tinker::BOUNDS_EVERY_X_STEPS = 500

constexpr

Calls bounds() at least every x steps in MD.

vx

tinker::vx

extern

Velocities.

vy

tinker::vy

Velocities.

vz

tinker::vz

Velocities.