Classes
class	tinker::darray
	Device array. More...

class	tinker::GenericUnit< T, VERSION >
	Resource handle. Analogous to Fortran i/o unit represented by a signed integer. More...

struct	tinker::v1::EnableEnumBitMask< E >
	Direct mathematical calculation of enum class is prohibited in C++. More...

class	tinker::ResourceManagement
	Resource management. Allocates resources in the object constructor and deallocates resources in the object destructor. More...

struct	tinker::calc
	Bitmasks for MD. More...

Macros
#define	TINKER_ENABLE_ENUM_BITMASK(x)
	Explicitly enables mathematical calculation by casting enum class to integer. More...

Typedefs
using	tinker::RcOp = ResourceOperation

using	tinker::RcMan = ResourceManagement
	Type alias. More...

Enumerations
enum class	tinker::ResourceOperation { tinker::ResourceOperation::DEALLOC = 0x001 , tinker::ResourceOperation::ALLOC = 0x002 , tinker::ResourceOperation::INIT = 0x004 }

Functions
void	tinker::waitFor (int queue)
	Similar to OpenACC wait and CUDA stream synchronize. More...

void	tinker::deviceMemoryCopyinBytesAsync (void dst, const void src, size_t nbytes, int queue)
	Similar to OpenACC async copyin, copies data from host to device. More...

void	tinker::deviceMemoryCopyoutBytesAsync (void dst, const void src, size_t nbytes, int queue)
	Similar to OpenACC async copyout, copies data from device to host. More...

void	tinker::deviceMemoryCopyBytesAsync (void dst, const void src, size_t nbytes, int queue)
	Copies data between two pointers on device. More...

void	tinker::deviceMemoryZeroBytesAsync (void *dst, size_t nbytes, int queue)
	Writes zero bytes on device. More...

void	tinker::deviceMemoryDeallocate (void *ptr)
	Deallocates device pointer. More...

void	tinker::deviceMemoryAllocateBytes (void **pptr, size_t nbytes)
	Allocates device pointer. More...

template<class T >
void	tinker::v1::deviceMemoryCheckType ()
	Sanity check. More...

template<class DT , class ST >
void	tinker::v1::deviceMemoryCopyin1dArray (DT dst, const ST src, size_t nelem, int q)
	Copies data to 1D array, host to device. More...

template<class DT , class ST >
void	tinker::v1::deviceMemoryCopyout1dArray (DT dst, const ST src, size_t nelem, int q)
	Copies data to 1D array, device to host. More...

template<class E >
constexpr std::enable_if< EnableEnumBitMask< E >::value, E >::type	tinker::operator\| (E lhs, E rhs)

template<class E >
constexpr bool	tinker::operator& (E lhs, E rhs)

void	tinker::deviceData (RcOp)
	Set up and clean up device environment. More...

Variables
int	tinker::rc_flag
	Global bitmask. More...

Detailed Description

Class Documentation

◆ tinker::darray

class tinker::darray

Device array.

Static Public Member Functions
template<class PTR >
static void	allocate (size_t nelem, PTR *pp)

template<class PTR , class... PTRS>
static void	allocate (size_t nelem, PTR *pp, PTRS... pps)

template<class PTR >
static void	deallocate (PTR p)

template<class PTR , class... PTRS>
static void	deallocate (PTR p, PTRS... ps)

template<class PTR >
static void	zero (int q, size_t nelem, PTR p)

template<class PTR , class... PTRS>
static void	zero (int q, size_t nelem, PTR p, PTRS... ps)

template<class PTR , class U >
static void	copyin (int q, size_t nelem, PTR dst, const U *src)

template<class U , class PTR >
static void	copyout (int q, size_t nelem, U *dst, const PTR src)

template<class PTR , class U >
static void	copy (int q, size_t nelem, PTR dst, const U *src)
	Copies data across two device memory pointers. More...

template<class PTR , class PTR2 >
static PtrTrait< PTR >::type	dotThenReturn (int q, size_t nelem, const PTR ptr, const PTR2 b)
	Calculates the dot product and returns the answer to the host. More...

template<class ANS , class PTR , class PTR2 >
static void	dot (int q, size_t nelem, ANS ans, const PTR ptr, const PTR2 ptr2)
	Calculates the dot product and saves the answer to pointer `ans`. More...

template<class FLT , class PTR >
static void	scale (int q, size_t nelem, FLT scal, PTR ptr)

template<class FLT , class PTR , class... PTRS>
static void	scale (int q, size_t nelem, FLT scal, PTR ptr, PTRS... ptrs)

Member Function Documentation

◆ allocate() [1/2]

template<class PTR >

static void tinker::darray::allocate	(	size_t	nelem,
		PTR *	pp
	)

inlinestatic

◆ allocate() [2/2]

template<class PTR , class... PTRS>

static void tinker::darray::allocate	(	size_t	nelem,
		PTR *	pp,
		PTRS...	pps
	)

inlinestatic

◆ copy()

template<class PTR , class U >

static void tinker::darray::copy	(	int	q,
		size_t	nelem,
		PTR	dst,
		const U *	src
	)

inlinestatic

Copies data across two device memory pointers.

◆ copyin()

template<class PTR , class U >

static void tinker::darray::copyin	(	int	q,
		size_t	nelem,
		PTR	dst,
		const U *	src
	)

inlinestatic

◆ copyout()

template<class U , class PTR >

static void tinker::darray::copyout	(	int	q,
		size_t	nelem,
		U *	dst,
		const PTR	src
	)

inlinestatic

◆ deallocate() [1/2]

template<class PTR >

static void tinker::darray::deallocate ( PTR p )

inlinestatic

◆ deallocate() [2/2]

template<class PTR , class... PTRS>

static void tinker::darray::deallocate	(	PTR	p,
		PTRS...	ps
	)

inlinestatic

◆ dot()

template<class ANS , class PTR , class PTR2 >

static void tinker::darray::dot	(	int	q,
		size_t	nelem,
		ANS	ans,
		const PTR	ptr,
		const PTR2	ptr2
	)

inlinestatic

Calculates the dot product and saves the answer to pointer ans.

◆ dotThenReturn()

template<class PTR , class PTR2 >

static PtrTrait< PTR >::type tinker::darray::dotThenReturn	(	int	q,
		size_t	nelem,
		const PTR	ptr,
		const PTR2	b
	)

inlinestatic

Calculates the dot product and returns the answer to the host.

◆ scale() [1/2]

template<class FLT , class PTR >

static void tinker::darray::scale	(	int	q,
		size_t	nelem,
		FLT	scal,
		PTR	ptr
	)

inlinestatic

◆ scale() [2/2]

template<class FLT , class PTR , class... PTRS>

static void tinker::darray::scale	(	int	q,
		size_t	nelem,
		FLT	scal,
		PTR	ptr,
		PTRS...	ptrs
	)

inlinestatic

◆ zero() [1/2]

template<class PTR >

static void tinker::darray::zero	(	int	q,
		size_t	nelem,
		PTR	p
	)

inlinestatic

◆ zero() [2/2]

template<class PTR , class... PTRS>

static void tinker::darray::zero	(	int	q,
		size_t	nelem,
		PTR	p,
		PTRS...	ps
	)

inlinestatic

◆ tinker::GenericUnit

class tinker::GenericUnit

template<class T, GenericUnitVersion VERSION = GenericUnitVersion::DISABLE_ON_DEVICE>
class tinker::GenericUnit< T, VERSION >

Resource handle. Analogous to Fortran i/o unit represented by a signed integer.

Public Member Functions
	GenericUnit ()

	GenericUnit (int u)

	operator int () const

bool	valid () const
	Whether the current unit is open. More...

void	close ()
	Closes the current unit. More...

void	deviceptrUpdate (const T &hobj, int queue)
	Updates the object on device by an object on host. More...


const T &	operator* () const
	Gets the (const) reference to the object on host. More...

T &	operator* ()
	Gets the (const) reference to the object on host. More...


const T *	operator-> () const
	Gets the (const) pointer to the object on host. More...

T *	operator-> ()
	Gets the (const) pointer to the object on host. More...


const T *	deviceptr () const
	Gets (const) device pointer to the object. More...

T *	deviceptr ()
	Gets (const) device pointer to the object. More...

Static Public Member Functions
static int	size ()
	Gets the number of open units. More...

static void	clear ()
	Releases all of the resources and reset `size()` to 0. More...

template<class DT = T>
static void	resize (int s)
	Resizes the capacity for the objects on host. More...

static GenericUnit	open ()
	Returns a new unit, similar to opening a new Fortran i/o unit. More...

Constructor & Destructor Documentation

◆ GenericUnit() [1/2]

template<class T , GenericUnitVersion VERSION = GenericUnitVersion::DISABLE_ON_DEVICE>

tinker::GenericUnit< T, VERSION >::GenericUnit ( )

inline

◆ GenericUnit() [2/2]

template<class T , GenericUnitVersion VERSION = GenericUnitVersion::DISABLE_ON_DEVICE>

tinker::GenericUnit< T, VERSION >::GenericUnit ( int u )

inline

Member Function Documentation

◆ clear()

template<class T , GenericUnitVersion VERSION = GenericUnitVersion::DISABLE_ON_DEVICE>

static void tinker::GenericUnit< T, VERSION >::clear ( )

inlinestatic

Releases all of the resources and reset size() to 0.

◆ close()

template<class T , GenericUnitVersion VERSION = GenericUnitVersion::DISABLE_ON_DEVICE>

void tinker::GenericUnit< T, VERSION >::close ( )

inline

Closes the current unit.

Note: The resource will not be released until clear() is called.

◆ deviceptr() [1/2]

template<class T , GenericUnitVersion VERSION = GenericUnitVersion::DISABLE_ON_DEVICE>

T * tinker::GenericUnit< T, VERSION >::deviceptr ( )

inline

Gets (const) device pointer to the object.

◆ deviceptr() [2/2]

template<class T , GenericUnitVersion VERSION = GenericUnitVersion::DISABLE_ON_DEVICE>

const T * tinker::GenericUnit< T, VERSION >::deviceptr ( ) const

inline

Gets (const) device pointer to the object.

◆ deviceptrUpdate()

template<class T , GenericUnitVersion VERSION = GenericUnitVersion::DISABLE_ON_DEVICE>

void tinker::GenericUnit< T, VERSION >::deviceptrUpdate	(	const T &	hobj,
		int	queue
	)

inline

Updates the object on device by an object on host.

Parameters

hobj	Reference to the object on host that can be accessed by the same unit number.
queue	Device queue for the update.

◆ open()

template<class T , GenericUnitVersion VERSION = GenericUnitVersion::DISABLE_ON_DEVICE>

static GenericUnit tinker::GenericUnit< T, VERSION >::open ( )

inlinestatic

Returns a new unit, similar to opening a new Fortran i/o unit.

◆ operator int()

template<class T , GenericUnitVersion VERSION = GenericUnitVersion::DISABLE_ON_DEVICE>

tinker::GenericUnit< T, VERSION >::operator int ( ) const

inline

◆ operator*() [1/2]

template<class T , GenericUnitVersion VERSION = GenericUnitVersion::DISABLE_ON_DEVICE>

T & tinker::GenericUnit< T, VERSION >::operator* ( )

inline

Gets the (const) reference to the object on host.

◆ operator*() [2/2]

template<class T , GenericUnitVersion VERSION = GenericUnitVersion::DISABLE_ON_DEVICE>

const T & tinker::GenericUnit< T, VERSION >::operator* ( ) const

inline

Gets the (const) reference to the object on host.

◆ operator->() [1/2]

template<class T , GenericUnitVersion VERSION = GenericUnitVersion::DISABLE_ON_DEVICE>

T * tinker::GenericUnit< T, VERSION >::operator-> ( )

inline

Gets the (const) pointer to the object on host.

◆ operator->() [2/2]

template<class T , GenericUnitVersion VERSION = GenericUnitVersion::DISABLE_ON_DEVICE>

const T * tinker::GenericUnit< T, VERSION >::operator-> ( ) const

inline

Gets the (const) pointer to the object on host.

◆ resize()

template<class T , GenericUnitVersion VERSION = GenericUnitVersion::DISABLE_ON_DEVICE>

template<class DT = T>

static void tinker::GenericUnit< T, VERSION >::resize ( int s )

inlinestatic

Resizes the capacity for the objects on host.

Note: Cannot be called if device pointers are used.

◆ size()

template<class T , GenericUnitVersion VERSION = GenericUnitVersion::DISABLE_ON_DEVICE>

static int tinker::GenericUnit< T, VERSION >::size ( )

inlinestatic

Gets the number of open units.

◆ valid()

template<class T , GenericUnitVersion VERSION = GenericUnitVersion::DISABLE_ON_DEVICE>

bool tinker::GenericUnit< T, VERSION >::valid ( ) const

inline

Whether the current unit is open.

◆ tinker::v1::EnableEnumBitMask

struct tinker::v1::EnableEnumBitMask

template<class E>
struct tinker::v1::EnableEnumBitMask< E >

Direct mathematical calculation of enum class is prohibited in C++.

Static Public Attributes
static constexpr bool	value = false

Member Data Documentation

◆ value

template<class E >

constexpr bool tinker::v1::EnableEnumBitMask< E >::value = false

staticconstexpr

◆ tinker::ResourceManagement

class tinker::ResourceManagement

Resource management. Allocates resources in the object constructor and deallocates resources in the object destructor.

To deallocate resource in reverse order of allocation, use named objects.

RcMan foo42{fooData, op};

RcMan bar42{barData, op};

tinker::ResourceManagement

Resource management. Allocates resources in the object constructor and deallocates resources in the o...

Definition: rcman.h:72

To deallocate resource in the same order of allocation, use unnamed objects.

RcMan {fooData, op};

RcMan {barData, op};

Public Member Functions
	ResourceManagement (void(*f)(RcOp), RcOp op)

	~ResourceManagement ()

Constructor & Destructor Documentation

◆ ResourceManagement()

tinker::ResourceManagement::ResourceManagement	(	void(*)(RcOp)	f,
		RcOp	op
	)

Parameters

f	Function to (de)allocate and/or initialize resource.
op	Resource operation flag.

◆ ~ResourceManagement()

tinker::ResourceManagement::~ResourceManagement ( )

◆ tinker::calc

struct tinker::calc

Bitmasks for MD.

Public Types
using	V0 = Eng

using	V1 = EngGradVir

using	V3 = EngAlyz

using	V4 = EngGrad

using	V5 = Grad

using	V6 = GradVir

Static Public Attributes
static constexpr int	xyz = 0x001
	Use coordinates. More...

static constexpr int	vel = 0x002
	Use velocities. More...

static constexpr int	mass = 0x004
	Use mass. More...

static constexpr int	traj = 0x008
	Use multi-frame trajectory. More...

static constexpr int	energy = 0x010
	Evaluate energy. More...

static constexpr int	grad = 0x020
	Evaluate energy gradient. More...

static constexpr int	virial = 0x040
	Evaluate virial tensor. More...

static constexpr int	analyz = 0x080
	Evaluate number of interactions. More...

static constexpr int	md = 0x100
	Run MD simulation. More...

static constexpr int	vmask = energy + grad + virial + analyz
	Bits mask to clear energy-irrelevant flags. More...

static constexpr int	v0 = energy
	Similar to Tinker energy routines. Energy only. More...

static constexpr int	v1 = energy + grad + virial

static constexpr int	v3 = energy + analyz

static constexpr int	v4 = energy + grad
	Energy and gradient. More...

static constexpr int	v5 = grad
	Gradient only. More...

static constexpr int	v6 = grad + virial
	Gradient and virial. More...

Member Typedef Documentation

◆ V0

using tinker::calc::V0 = Eng

◆ V1

using tinker::calc::V1 = EngGradVir

◆ V3

using tinker::calc::V3 = EngAlyz

◆ V4

using tinker::calc::V4 = EngGrad

◆ V5

using tinker::calc::V5 = Grad

◆ V6

using tinker::calc::V6 = GradVir

Member Data Documentation

◆ analyz

constexpr int tinker::calc::analyz = 0x080

staticconstexpr

Evaluate number of interactions.

◆ energy

constexpr int tinker::calc::energy = 0x010

staticconstexpr

Evaluate energy.

◆ grad

constexpr int tinker::calc::grad = 0x020

staticconstexpr

Evaluate energy gradient.

◆ mass

constexpr int tinker::calc::mass = 0x004

staticconstexpr

Use mass.

◆ md

constexpr int tinker::calc::md = 0x100

staticconstexpr

Run MD simulation.

◆ traj

constexpr int tinker::calc::traj = 0x008

staticconstexpr

Use multi-frame trajectory.

◆ v0

constexpr int tinker::calc::v0 = energy

staticconstexpr

Similar to Tinker energy routines. Energy only.

◆ v1

constexpr int tinker::calc::v1 = energy + grad + virial

staticconstexpr

Similar to version 1 Tinker energy routines. Energy, gradient, and virial.

◆ v3

constexpr int tinker::calc::v3 = energy + analyz

staticconstexpr

Similar to version 3 Tinker energy routines. Energy and number of interactions.

◆ v4

constexpr int tinker::calc::v4 = energy + grad

staticconstexpr

Energy and gradient.

◆ v5

constexpr int tinker::calc::v5 = grad

staticconstexpr

Gradient only.

◆ v6

constexpr int tinker::calc::v6 = grad + virial

staticconstexpr

Gradient and virial.

◆ vel

constexpr int tinker::calc::vel = 0x002

staticconstexpr

Use velocities.

◆ virial

constexpr int tinker::calc::virial = 0x040

staticconstexpr

Evaluate virial tensor.

◆ vmask

constexpr int tinker::calc::vmask = energy + grad + virial + analyz

staticconstexpr

Bits mask to clear energy-irrelevant flags.

◆ xyz

constexpr int tinker::calc::xyz = 0x001

staticconstexpr

Use coordinates.

Macro Definition Documentation

◆ TINKER_ENABLE_ENUM_BITMASK

#define TINKER_ENABLE_ENUM_BITMASK ( x )

Value:

   template <>                            \
   struct EnableEnumBitMask<x>            \
   {                                      \
      static constexpr bool value = true; \
   }

Explicitly enables mathematical calculation by casting enum class to integer.

Typedef Documentation

◆ RcMan

using tinker::RcMan = typedef ResourceManagement

Type alias.

◆ RcOp

using tinker::RcOp = typedef ResourceOperation

Type alias.

Enumeration Type Documentation

◆ ResourceOperation

enum class tinker::ResourceOperation

strong

Enumerator
DEALLOC	Deallocates resource.
ALLOC	Allocates resource.
INIT	Initializes resource.

Function Documentation

◆ deviceData()

void tinker::deviceData ( RcOp )

Set up and clean up device environment.

◆ deviceMemoryAllocateBytes()

void tinker::deviceMemoryAllocateBytes	(	void **	pptr,
		size_t	nbytes
	)

Allocates device pointer.

Parameters

pptr	Pointer to the device pointer.
nbytes	Number of bytes.

◆ deviceMemoryCheckType()

template<class T >

void tinker::v1::deviceMemoryCheckType ( )

Sanity check.

◆ deviceMemoryCopyBytesAsync()

void tinker::deviceMemoryCopyBytesAsync	(	void *	dst,
		const void *	src,
		size_t	nbytes,
		int	queue
	)

Copies data between two pointers on device.

Note: Different from OpenACC copy.

Parameters

dst	Destination device pointer.
src	Source device pointer.
nbytes	Number of bytes.
queue	OpenACC queue.

◆ deviceMemoryCopyin1dArray()

template<class DT , class ST >

void tinker::v1::deviceMemoryCopyin1dArray	(	DT *	dst,
		const ST *	src,
		size_t	nelem,
		int	q
	)

Copies data to 1D array, host to device.

Parameters

dst	Destination address.
src	Source address.
nelem	Number of elements to copy to the 1D device array.
q	OpenACC queue.

◆ deviceMemoryCopyinBytesAsync()

void tinker::deviceMemoryCopyinBytesAsync	(	void *	dst,
		const void *	src,
		size_t	nbytes,
		int	queue
	)

Similar to OpenACC async copyin, copies data from host to device.

Parameters

dst	Device pointer.
src	Host pointer.
nbytes	Number of bytes.
queue	OpenACC queue.

◆ deviceMemoryCopyout1dArray()

template<class DT , class ST >

void tinker::v1::deviceMemoryCopyout1dArray	(	DT *	dst,
		const ST *	src,
		size_t	nelem,
		int	q
	)

Copies data to 1D array, device to host.

Parameters

dst	Destination address.
src	Source address.
nelem	Number of elements to copy to the 1D host array.
q	OpenACC queue.

◆ deviceMemoryCopyoutBytesAsync()

void tinker::deviceMemoryCopyoutBytesAsync	(	void *	dst,
		const void *	src,
		size_t	nbytes,
		int	queue
	)

Similar to OpenACC async copyout, copies data from device to host.

Parameters

dst	Host pointer.
src	Device pointer.
nbytes	Number of bytes.
queue	OpenACC queue.

◆ deviceMemoryDeallocate()

void tinker::deviceMemoryDeallocate ( void * ptr )

Deallocates device pointer.

Parameters

ptr	Device pointer.

◆ deviceMemoryZeroBytesAsync()

void tinker::deviceMemoryZeroBytesAsync	(	void *	dst,
		size_t	nbytes,
		int	queue
	)

Writes zero bytes on device.

Parameters

dst	Device pointer.
nbytes	Number of bytes.
queue	OpenACC queue.

◆ operator&()

template<class E >

constexpr bool tinker::operator&	(	E	lhs,
		E	rhs
	)

constexpr

◆ operator|()

template<class E >

constexpr std::enable_if< EnableEnumBitMask< E >::value, E >::type tinker::operator\|	(	E	lhs,
		E	rhs
	)

constexpr

◆ waitFor()

void tinker::waitFor ( int queue )

Similar to OpenACC wait and CUDA stream synchronize.

Parameters

queue OpenACC queue.

Variable Documentation

◆ rc_flag

int tinker::rc_flag

extern

Global bitmask.

Classes

Macros

Typedefs

Enumerations

Functions

Variables

Detailed Description

Class Documentation

◆ tinker::darray

Static Public Member Functions

Member Function Documentation

◆ allocate() [1/2]

◆ allocate() [2/2]

◆ copy()

◆ copyin()

◆ copyout()

◆ deallocate() [1/2]

◆ deallocate() [2/2]

◆ dot()

◆ dotThenReturn()

◆ scale() [1/2]

◆ scale() [2/2]

◆ zero() [1/2]

◆ zero() [2/2]

◆ tinker::GenericUnit

Public Member Functions

Static Public Member Functions

Constructor & Destructor Documentation

◆ GenericUnit() [1/2]

◆ GenericUnit() [2/2]

Member Function Documentation

◆ clear()

◆ close()

◆ deviceptr() [1/2]

◆ deviceptr() [2/2]

◆ deviceptrUpdate()

◆ open()

◆ operator int()

◆ operator*() [1/2]

◆ operator*() [2/2]

◆ operator->() [1/2]

◆ operator->() [2/2]

◆ resize()

◆ size()

◆ valid()

◆ tinker::v1::EnableEnumBitMask

Static Public Attributes

Member Data Documentation

◆ value

◆ tinker::ResourceManagement

Public Member Functions

Constructor & Destructor Documentation

◆ ResourceManagement()

◆ ~ResourceManagement()

◆ tinker::calc

Public Types

Static Public Attributes

Member Typedef Documentation

◆ V0

◆ V1

◆ V3

◆ V4

◆ V5

◆ V6

Member Data Documentation

◆ analyz

◆ energy

◆ grad

◆ mass

◆ md

◆ traj

◆ v0

◆ v1

◆ v3

◆ v4

◆ v5

◆ v6

◆ vel

◆ virial

◆ vmask