tinker Namespace Reference

Namespaces
namespace	d
namespace	g
	Global handles for the GPU runtime libraries.
namespace	v1

Classes
class	AnisoBaroDevice
class	BasicBarostat
class	BasicIntegrator
class	BasicPropagator
	The interface class of a Verlet or an RESPA-Verlet MD step. More...
class	BasicThermostat
class	BerendsenBarostat
struct	Box
struct	BufferTraits
struct	BufferTraits< float, Nincr >
class	BussiThermostat
struct	calc
	Bitmasks for MD. More...
class	CrdReader
class	CrdWriter
class	darray
	Device array. More...
struct	DeviceAllocator
struct	DeviceAttribute
	Device attributes. More...
struct	double2
struct	double3
struct	double4
class	dvector
struct	EnableEnumBitMask
	Direct mathematical calculation of enum class is prohibited in C++. More...
struct	EnableEnumBitMask< Nbl >
struct	EnableEnumBitMask< Platform >
struct	EnableEnumBitMask< ResourceOperation >
class	FatalError
	Errors and exceptions that we do not intend to fix or handle. More...
struct	FFTPlan
	FFT plan. More...
struct	float2
struct	float3
struct	float4
class	FortranStringView
	Reference to the non-NULL-terminated Fortran strings. Provides a few std::string-style methods to handle the fortran strings. More...
class	GenericUnit
	Resource handle. Analogous to Fortran i/o unit represented by a signed integer. More...
struct	GenericUnitAlloc
struct	GenericUnitAlloc< GenericUnitVersion::DISABLE_ON_DEVICE >
struct	GenericUnitAlloc< GenericUnitVersion::ENABLE_ON_DEVICE >
struct	Group
	Partitioning of system into atom groups. More...
struct	int2
struct	int3
struct	int4
class	IntegratorStaticData
class	IsoBaroDevice
class	LeapFrogLPIntegrator
struct	LocalFrame
	Local axis type and x,y,z-axis defining atoms for each multipole site. More...
class	LogVDevice
class	LP22Barostat
class	LP22Integrator
struct	Molecule
	Individual molecules in current system. More...
class	MonteCarloBarostat
struct	NBList
	Verlet list: pairwise neighbor list indices and storage. More...
class	Nhc06Barostat
class	Nhc06Integrator
class	Nhc06Thermostat
class	Nhc96Integrator
class	NhcDevice
	Applies a velocity correction as needed for the Nose-Hoover Chains at the half time step. More...
struct	OpLogicOr
struct	OpPlus
struct	PairMPoleGrad
	Components of the pairwise multipole electrostatic gradient between atoms i and k, where i is less than k. More...
struct	PairPolarGrad
struct	PairRepelGrad
class	PbcMono
class	PbcOct
class	PbcOrtho
class	PbcTri
class	PbcUnbound
struct	PME
	Particle mesh ewald girds and parameters. More...
struct	PtrTrait
struct	PtrTrait< T * >
struct	PtrTrait< T(*)[N]>
class	ResourceManagement
	Resource management. Allocates resources in the object constructor and deallocates resources in the object destructor. More...
class	RespaDevice
class	RespaIntegrator
class	Spatial
class	TestFile
	Writes a file to disk in its constructor and removes the file in its destructor, unless the file is set to be kept. More...
class	TestReference
	Reads reference values from a text file. More...
class	TestRemoveFileOnExit
	Removes the file in its destructor as necessary. More...
class	Text
	Plain ascii text stored by lines. More...
class	ThrustCache
	Device memory cache (allocator) for the Thrust Library. More...
class	VerletDevice
class	VerletIntegrator

Typedefs
typedef BufferTraits< int, 1 >	CountBufferTraits
typedef BufferTraits< e_prec, 1 >	EnergyBufferTraits
typedef BufferTraits< v_prec, 6 >	VirialBufferTraits
typedef CountBufferTraits::type *	CountBuffer
typedef EnergyBufferTraits::type *	EnergyBuffer
typedef VirialBufferTraits::type(*	VirialBuffer)[VirialBufferTraits::value]
typedef GenericUnit< NBList, GenericUnitVersion::ENABLE_ON_DEVICE >	NBListUnit
using	PMEUnit = GenericUnit< PME, GenericUnitVersion::ENABLE_ON_DEVICE >
typedef unsigned long long	fixed
typedef float	real
typedef double	mixed
typedef mixed	time_prec
	Floating-point type for time. More...
typedef mixed	T_prec
	Floating-point type for temperature. More...
typedef mixed	vel_prec
	Floating-point type for velocities. More...
typedef mixed	pos_prec
	Floating-point type for coordinates. More...
typedef real	e_prec
	Floating-point type for the pairwise energy components. More...
typedef real	v_prec
	Floating-point type for the pairwise virial components. More...
typedef real	g_prec
	Floating-point type for the pairwise gradient components. More...
typedef mixed	energy_prec
	Floating-point type for total energies. More...
typedef mixed	virial_prec
typedef fixed	grad_prec
typedef GenericUnit< Spatial, GenericUnitVersion::DISABLE_ON_DEVICE >	SpatialUnit
typedef std::map< std::string, int >	TimeScaleConfig
typedef GenericUnit< FFTPlan, GenericUnitVersion::DISABLE_ON_DEVICE >	FFTPlanUnit
using	FstrView = FortranStringView
	An alias of FortranStringView. More...
using	RcOp = ResourceOperation
using	RcMan = ResourceManagement
	Type alias. More...

Enumerations
enum class	BoxShape {   BoxShape::UNBOUND , BoxShape::ORTHO , BoxShape::MONO , BoxShape::TRI ,   BoxShape::OCT }
	Shapes of the periodic box. More...
enum class	Bond : int { Bond::HARMONIC , Bond::MORSE }
enum class	Angle : int { Angle::IN_PLANE , Angle::HARMONIC , Angle::LINEAR , Angle::FOURIER }
enum class	OPBend : int { OPBend::WDC , OPBend::ALLINGER }
enum class	Vdw : int {   Vdw::DECOUPLE = 0 , Vdw::ANNIHILATE = 1 , Vdw::ATOM_TYPE = 10 , Vdw::ATOM_CLASS = 11 ,   Vdw::ARITHMETIC = 20 , Vdw::GEOMETRIC = 21 , Vdw::CUBIC_MEAN = 22 , Vdw::HHG = 23 ,   Vdw::W_H = 24 , Vdw::LJ , Vdw::BUCK , Vdw::MM3HB ,   Vdw::HAL , Vdw::GAUSS }
	Constant flags for the VDW energy functions. More...
enum class	Nbl { Nbl::UNDEFINED = 0x00 , Nbl::DOUBLE_LOOP = 0x01 , Nbl::VERLET = 0x02 , Nbl::SPATIAL = 0x04 }
enum class	Potent {   Potent::BOND , Potent::ANGLE , Potent::STRBND , Potent::UREY ,   Potent::ANGANG , Potent::OPBEND , Potent::OPDIST , Potent::IMPROP ,   Potent::IMPTORS , Potent::TORSION , Potent::PITORS , Potent::STRTOR ,   Potent::ANGTOR , Potent::TORTOR , Potent::VDW , Potent::REPULS ,   Potent::DISP , Potent::CHARGE , Potent::CHGDPL , Potent::DIPOLE ,   Potent::MPOLE , Potent::POLAR , Potent::CHGTRN , Potent::RXNFLD ,   Potent::SOLV , Potent::METAL , Potent::GEOM , Potent::EXTRA ,   Potent::CHGFLX , Potent::MUTATE }
enum class	CrdFormat { NONE , TXYZ1 , TXYZ2_PBC , DCD }
enum class	Switch {   Switch::DEFAULT , Switch::VDW , Switch::REPULS , Switch::DISP ,   Switch::CHARGE , Switch::CHGDPL , Switch::DIPOLE , Switch::MPOLE ,   Switch::CHGTRN , Switch::EWALD , Switch::DEWALD , Switch::USOLVE ,   Switch::GKV , Switch::GKSA }
enum	{   MPL_PME_0 = 0 , MPL_PME_X = 1 , MPL_PME_Y = 2 , MPL_PME_Z = 3 ,   MPL_PME_XX = 4 , MPL_PME_YY = 5 , MPL_PME_ZZ = 6 , MPL_PME_XY = 7 ,   MPL_PME_XZ = 8 , MPL_PME_YZ = 9 , MPL_TOTAL = 10 , MPL_PME_YX = MPL_PME_XY ,   MPL_PME_ZX = MPL_PME_XZ , MPL_PME_ZY = MPL_PME_YZ , LFRM_NONE = 0 , LFRM_Z_ONLY = 1 ,   LFRM_Z_THEN_X = 2 , LFRM_BISECTOR = 3 , LFRM_Z_BISECT = 4 , LFRM_3_FOLD = 5 }
enum class	UPred { NONE , GEAR , ASPC , LSQR }
enum class	Chgpen { NONE , GORDON1 , GORDON2 }
enum class	Chgtrn { Chgtrn::NONE , Chgtrn::SEPARATE , Chgtrn::COMBINED }
enum class	ExpolScr { NONE , S2U , S2 , G }
enum class	PropagatorEnum { PropagatorEnum::RESPA , PropagatorEnum::VERLET , PropagatorEnum::m_LOGV }
enum class	ThermostatEnum {   ThermostatEnum::NONE , ThermostatEnum::ANDERSEN , ThermostatEnum::BERENDSEN , ThermostatEnum::BUSSI ,   ThermostatEnum::NHC , ThermostatEnum::m_LEAPFROGLP , ThermostatEnum::m_LP2022 , ThermostatEnum::m_NHC1996 ,   ThermostatEnum::m_NHC2006 }
enum class	BarostatEnum {   BarostatEnum::NONE , BarostatEnum::BERENDSEN , BarostatEnum::BUSSI , BarostatEnum::LP2022 ,   BarostatEnum::MONTECARLO , BarostatEnum::NHC2006 , BarostatEnum::m_LEAPFROGLP , BarostatEnum::m_LOGVISO ,   BarostatEnum::m_LOGVANISO , BarostatEnum::m_NHC1996 }
enum class	IntegratorEnum {   IntegratorEnum::BEEMAN , IntegratorEnum::RESPA , IntegratorEnum::VERLET , IntegratorEnum::LEAPFROGLP ,   IntegratorEnum::LP2022 , IntegratorEnum::NHC1996 , IntegratorEnum::NHC2006 }
enum class	GenericUnitVersion { DISABLE_ON_DEVICE , ENABLE_ON_DEVICE }
enum class	Platform { Platform::UNKNOWN = 0x000 , Platform::ACC = 0x001 , Platform::CUDA = 0x002 }
enum class	ResourceOperation { ResourceOperation::DEALLOC = 0x001 , ResourceOperation::ALLOC = 0x002 , ResourceOperation::INIT = 0x004 }

Functions
double	testGetEps (double epsSingle, double epsDouble)
	Returns tolerance eps depending on the predefined floating-point precision. More...
void	testBeginWithArgs (int argc, const char **argv)
	Initializes the test. More...
void	testEnd ()
	Ends the test. More...
void	testMdInit (double t=0, double atm=0)
	Initializes MD in the test. More...
void	xAnalyze (int, char **)
	Entry point of the analyze program. More...
void	xBar (int, char **)
	Entry point of the bar program. More...
void	xDynamic (int, char **)
	Entry point of the dynamic program. More...
void	xHelp (int, char **)
	Entry point of the help program. More...
void	xInfo (int, char **)
	Entry point of the info program. More...
void	xMinimize (int, char **)
	Entry point of the minimize program. More...
void	xTestgrad (int, char **)
	Entry point of the testgrad program. More...
void	promo ()
	Writes a banner message. More...
void	initial ()
void	mechanic2 ()
	Sets up extra parameters and options in addition to the Fortran mechanic subroutine. More...
void	initialize ()
	Sets up host and device environment. More...
void	finish ()
	Cleans up host and device environment. More...
void	nData (RcOp)
void	massData (RcOp)
void	xyzData (RcOp)
void	copyPosToXyz ()
void	copyPosToXyz (bool refreshNBList)
void	bounds ()
void	boxData (RcOp)
	Sets up box data on device. More...
void	boxDataP1 (RcOp)
	Internal function used in the setup. More...
void	boxExtent (double newExtent)
void	boxSetCurrent (const Box &p)
	Sets the box by the input and updates the box on device. More...
void	boxGetCurrent (Box &p)
	Copies the current PBC box to the output variable. More...
void	boxSetCurrentRecip ()
void	boxSetTinker (const Box &p)
	Updates the related PBC modules of Tinker by p. More...
void	boxCopyin ()
void	boxLattice (Box &p, BoxShape sh, double a, double b, double c, double alphaDeg, double betaDeg, double gammaDeg)
	Sets up the internal PBC data. Similar to Tinker lattice subroutine. More...
real	boxVolume ()
__global__ void	pcgUdirV1 (int n, const real *polarity, real(*udir)[3], const real(*field)[3])
	Calculates the direct induced dipoles 2b. More...
__global__ void	pcgUdirV2 (int n, const real *polarity, real(*udir)[3], real(*udirp)[3], const real(*field)[3], const real(*fieldp)[3])
	Calculates the direct induced dipoles 2b. More...
__global__ void	pcgRsd0V1 (int n, const real *polarity_inv, real(*rsd)[3], const real(*udir)[3], const real(*uind)[3], const real(*field)[3])
	Calculates the initial residuals for the predictor 3a. More...
__global__ void	pcgRsd0V2 (int n, const real *polarity_inv, real(*rsd)[3], real(*rsp)[3], const real(*udir)[3], const real(*udip)[3], const real(*uind)[3], const real(*uinp)[3], const real(*field)[3], const real(*fielp)[3])
	Calculates the initial residuals for the predictor 3a. More...
__global__ void	pcgRsd0V3 (int n, const real *polarity_inv, real(*rsd)[3], const real(*udir)[3], const real(*uind)[3], const real(*field)[3], const real(*polscale)[3][3])
	Calculates the initial residuals for the predictor 3a using the Exchange-Polarization Model. More...
__global__ void	pcgRsd0 (int n, const real *polarity, real(*rsd)[3], real(*rsdp)[3])
	Sets the residual to zero for atoms with zero polarizability. More...
__global__ void	pcgRsd1 (int n, const real *polarity, real(*rsd)[3])
	Sets the residual to zero for atoms with zero polarizability. More...
__global__ void	pcgP1 (int n, const real *polarity_inv, real(*vec)[3], real(*vecp)[3], const real(*conj)[3], const real(*conjp)[3], const real(*field)[3], const real(*fieldp)[3])
	Calculates the vector Ap – step 5a. More...
__global__ void	pcgP2 (int n, const real *polarity, const real *ka, const real *kap, const real *ksum, const real *ksump, real(*uind)[3], real(*uinp)[3], const real(*conj)[3], const real(*conjp)[3], real(*rsd)[3], real(*rsdp)[3], const real(*vec)[3], const real(*vecp)[3])
	Updates the induced dipoles and residuals – step 5bc. More...
__global__ void	pcgP3 (int n, const real *ksum, const real *ksump, const real *ksum1, const real *ksump1, real(*conj)[3], real(*conjp)[3], const real(*zrsd)[3], const real(*zrsdp)[3])
	Calculates the scalar b from s0 and s, then updates the vector p – 5ef. More...
__global__ void	pcgP4 (int n, const real *polarity_inv, real(*vec)[3], const real(*conj)[3], const real(*field)[3])
	Calculates the vector Ap – step 5a. More...
__global__ void	pcgP5 (int n, const real *polarity, const real *ka, const real *ksum, real(*uind)[3], const real(*conj)[3], real(*rsd)[3], const real(*vec)[3])
	Updates the induced dipoles and residuals – step 5bc. More...
__global__ void	pcgP6 (int n, const real *ksum, const real *ksum1, real(*conj)[3], const real(*zrsd)[3])
	Calculates the scalar b from s0 and s, then updates the vector p – 5ef. More...
__global__ void	pcgPeek (int n, float pcgpeek, const real *polarity, real(*uind)[3], real(*uinp)[3], const real(*rsd)[3], const real(*rsdp)[3])
	Applies the peek step. More...
__global__ void	pcgPeek1 (int n, float pcgpeek, const real *polarity, real(*uind)[3], const real(*rsd)[3])
	Applies the peek step. More...
void	echargeData (RcOp)
void	echarge (int vers)
void	echargeEwaldRecipSelf (int)
void	echgljData (RcOp)
void	echglj (int vers)
void	zeroEGV (int vers=rc_flag)
	Zero out all of the counts, energies, gradients, and virials on device. More...
void	scaleGradient (double scale, grad_prec *g0x, grad_prec *g0y, grad_prec *g0z)
	g0 *= scale. More...
void	sumGradient (grad_prec *g0x, grad_prec *g0y, grad_prec *g0z, const grad_prec *g1x, const grad_prec *g1y, const grad_prec *g1z)
	g0 += g1. More...
void	sumGradient (double scale, grad_prec *g0x, grad_prec *g0y, grad_prec *g0z, const grad_prec *g1x, const grad_prec *g1y, const grad_prec *g1z)
	g0 += scale*g1. More...
void	copyGradientSync (int vers, double *grdx, double *grdy, double *grdz, const grad_prec *gx_src, const grad_prec *gy_src, const grad_prec *gz_src, int queue)
	Copies the energy gradients from device to host. More...
void	copyGradient (int vers, double *grdx, double *grdy, double *grdz, const grad_prec *gx_src, const grad_prec *gy_src, const grad_prec *gz_src)
	Copies the energy gradients from device to host. More...
void	copyGradient (int vers, double *grdx, double *grdy, double *grdz)
void	copyEnergy (int vers, energy_prec *eng)
bool	useEwald ()
void	elecData (RcOp)
void	energy_core (int vers, unsigned tsflag, const TimeScaleConfig &tsconfig)
void	energy (int vers)
void	energy (int vers, unsigned tsflag, const TimeScaleConfig &tsconfig)
void	energyData (RcOp)
	Entry point to the setup functions of all the potential energy terms. More...
bool	useEnergyVdw ()
	Logical flag for use of VDW, repulsion, dispersion, etc. terms. More...
bool	useEnergyElec ()
	Logical flag for use of electrostatic terms. More...
void	egvData (RcOp)
	Sets up data on device. More...
template<class F >
F	toFloatingPoint (fixed g)
	Converts a fixed-point value g to floating-point value on host. More...
template<class F >
F	toFloatingPoint (double g)
	Converts a double-precision g to floating-point value on host. More...
template<class F >
F	toFloatingPoint (float g)
	Converts a single-precision g to floating-point value on host. More...
size_t	bufferSize ()
void	bufferAllocate (int flag, EnergyBuffer *pe, VirialBuffer *pv, grad_prec **px, grad_prec **py, grad_prec **pz)
void	bufferDeallocate (int flag, EnergyBuffer e, VirialBuffer v, grad_prec *gx, grad_prec *gy, grad_prec *gz)
void	bufferAllocate (int flag, CountBuffer *pc)
void	bufferDeallocate (int flag, CountBuffer c)
int	countReduce (const CountBuffer b)
energy_prec	energyReduce (const EnergyBuffer b)
void	virialReduce (virial_prec(&)[VirialBufferTraits::N], const VirialBuffer b)
void	virialReduce (virial_prec(&)[9], const VirialBuffer b)
void	virialReshape (virial_prec(&output)[9], const virial_prec(&input)[VirialBufferTraits::N])
	Transforms the shape of a virial variable. More...
void	evalence (int vers)
void	ebondData (RcOp)
void	ebond (int vers)
void	eangleData (RcOp)
void	eangle (int vers)
void	eopbendData (RcOp)
void	eopbend (int vers)
void	estrbndData (RcOp)
void	estrbnd (int vers)
void	eureyData (RcOp)
void	eurey (int vers)
void	eimpropData (RcOp)
void	eimprop (int vers)
void	eimptorData (RcOp)
void	eimptor (int vers)
void	etorsData (RcOp)
void	etors (int vers)
void	epitorsData (RcOp)
void	epitors (int vers)
void	estrtorData (RcOp)
void	estrtor (int vers)
void	eangtorData (RcOp)
void	eangtor (int vers)
void	etortorData (RcOp)
void	etortor (int vers)
void	egeomData (RcOp)
void	egeom (int vers)
void	vdwSoftcoreData (RcOp)
void	evdwData (RcOp)
void	evdw (int vers)
void	elj (int vers)
	Lennard-Jones 12-6 potential. More...
void	elj14 (int vers)
void	ebuck (int vers)
void	emm3hb (int vers)
void	egauss (int vers)
void	ehal (int vers)
	Halgren buffered 14-7 potential. More...
void	ehalReduceXyz ()
void	ehalResolveGradient ()
__device__ void	imageGeneral (real &__restrict__ xr, real &__restrict__ yr, real &__restrict__ zr, BoxShape sh, real3 l1, real3 l2, real3 l3, real3 ra, real3 rb, real3 rc)
__device__ real	image2General (real &__restrict__ xr, real &__restrict__ yr, real &__restrict__ zr, BoxShape sh, real3 l1, real3 l2, real3 l3, real3 ra, real3 rb, real3 rc)
__device__ real	imagen2General (real &xr, real &yr, real &zr, BoxShape sh, real3 l1, real3 l2, real3 l3, real3 ra, real3 rb, real3 rc)
void	coupleData (RcOp)
void	moleculeData (RcOp)
void	groupData (RcOp)
Nbl	vlistVersion ()
Nbl	clistVersion ()
Nbl	mlistVersion ()
	For multipole, polarization, repulsion, etc. More...
Nbl	ulistVersion ()
	For sparse preconditioner. More...
Nbl	dsplistVersion ()
	For dispersion. More...
void	nblistData (RcOp)
	Sets up data on device. More...
void	nblistRefresh ()
	Updates the neighbor lists. More...
void	pmeData (RcOp)
void	fftData (RcOp)
void	fftfront (PMEUnit)
void	fftback (PMEUnit)
bool	use (Potent term)
int	countBondedTerm (Potent term)
void	spatialUpdate (SpatialUnit)
real	switchCut (Switch mode)
real	switchOff (Switch mode)
const TimeScaleConfig &	defaultTSConfig ()
void	emplar (int vers)
	Multipole and AMOEBA polarization energy. More...
void	echgtrnData (RcOp)
void	echgtrn (int vers)
void	empoleChgpenData (RcOp)
void	empoleChgpen (int vers)
void	empoleChgpenEwaldRecip (int vers, int useCF)
void	empoleAplusEwald (int vers, int useCF)
void	empoleAplusNonEwald (int vers, int useCF)
void	epolarChgpenData (RcOp)
void	epolarChgpen (int vers)
void	epolarChgpenEwaldRecipSelf (int vers, int use_cf)
void	epolarAplusEwald (int vers, int useCF)
void	epolarAplusNonEwald (int vers, int useCF)
void	erepelData (RcOp)
void	erepel (int vers)
void	repoleInit (int vers)
void	expolData (RcOp)
void	alterpol (real(*polscale)[3][3], real(*polinv)[3][3])
void	dexpol (int vers)
void	dfieldAplus (real(*field)[3])
void	ufieldAplus (const real(*uind)[3], real(*field)[3])
void	sparsePrecondApply3 (const real(*rsd)[3], real(*zrsd)[3])
template<int N, class T >
void	symlusolve (const T *aUpRowMajor, T *b)
	This subroutine uses the LU decomposition method to solve the linear system Ax = b, returning x in b. A is an n by n real symmetric matrix with its upper triangle (including the diagonal) stored by rows. More...
template<class T , class T2 >
T	maxOf (T a, T2 b)
template<class T , class T2 , class... Ts>
T	maxOf (T a, T2 b, Ts... cs)
template<class T , class T2 >
T	minOf (T a, T2 b)
template<class T , class T2 , class... Ts>
T	minOf (T a, T2 b, Ts... cs)
double	OUProcess (double t, double x0, double gamma, double a, double b, double R)
	Returns the value of an Ornstein-Uhlenbeck process after time t. More...
template<class T >
T	reduceSum (const T *gpu_a, size_t nelem, int queue)
	Sum over all of the elements of an 1D array. More...
template<class HT , size_t HN, class DPTR >
void	reduceSum2 (HT(&h_ans)[HN], DPTR v, size_t nelem, int queue)
	Sum over all of the elements of a 2D array. More...
template<class T >
void	reduceSumOnDevice (T *dp_ans, const T *a, size_t nelem, int queue)
	Sum over all of the elements of an 1D array. This routine will save the result on the device memory in an asynchronous/non-blocking manner. A valid device pointer is required for the result on the device. More...
template<class HT , size_t HN, class DPTR >
void	reduceSum2OnDevice (HT(&dref)[HN], DPTR v, size_t nelem, int queue)
	Sum over all of the elements of a 2D array. This routine will save the result on the device memory in an asynchronous/non-blocking manner. A valid device array is required for the result on device. More...
template<class T >
T	dotProd (const T *a, const T *b, size_t nelem, int queue)
	Dot product of two linear arrays. More...
template<class T >
void	dotProd (T *ans, const T *a, const T *b, size_t nelem, int queue)
	Dot product of two linear arrays. More...
template<class T >
void	scaleArray (T *dst, T scal, size_t nelem, int queue)
	Multiply all of the elements in an 1D array by a scalar. More...
template<class T >
T	reduceSum_acc (const T *gpu_a, size_t nelem, int queue)
template<class HT , size_t HN, class DPTR >
void	reduceSum2_acc (HT(&h_ans)[HN], DPTR v, size_t nelem, int queue)
template<class T >
void	reduceSumOnDevice_acc (T *, const T *, size_t, int)
template<class HT , size_t HN, class DPTR >
void	reduceSum2OnDevice_acc (HT(&)[HN], DPTR, size_t, int)
template<class T >
T	dotProd_acc (const T *a, const T *b, size_t nelem, int queue)
template<class T >
void	dotProd_acc (T *ans, const T *a, const T *b, size_t nelem, int queue)
template<class T >
void	scaleArray_acc (T *dst, T scal, size_t nelem, int queue)
template<class T >
T	reduceSum_cu (const T *a, size_t nelem, int queue)
template<class HT , size_t HN, class DPTR >
void	reduceSum2_cu (HT(&h_ans)[HN], DPTR v, size_t nelem, int queue)
template<class T >
void	reduceSumOnDevice_cu (T *, const T *, size_t, int)
template<class HT , size_t HN, class DPTR >
void	reduceSum2OnDevice_cu (HT(&)[HN], DPTR, size_t, int)
template<class T >
void	dotProd_cu (T *ans, const T *a, const T *b, size_t nelem, int queue)
template<class T >
void	scaleArray_cu (T *dst, T scal, size_t nelem, int queue)
constexpr bool	isPow2 (size_t val)
	Return true if and only if val is a power of 2. More...
constexpr int	pow2 (int val)
	Integer base 2 power. More...
constexpr long long	pow2ll (int val)
	Long long integer base 2 power. More...
constexpr int	floorLog2_constexpr (size_t val)
	The base-2 logarithm of val. More...
constexpr size_t	pow2Le (size_t val)
	A power of 2 that is less than or equal to val. More...
constexpr size_t	pow2Ge (size_t val)
	A power of 2 that is greater than or equal to val. More...
int	floorLog2 (int val)
	Non-constexpr floorLog2(int). More...
int	floorLog2 (long long val)
	Non-constexpr floorLog2(long long). More...
int	ceilLog2 (int val)
	Non-constexpr log base 2 ceiling. More...
int	ceilLog2 (long long val)
	Non-constexpr log base 2 ceiling. More...
template<class T >
T	random ()
	Returns a random number on [0,1] from a uniform distribution. More...
template<class T >
T	normal ()
	Returns a random number from a normal Gaussian distribution with a mean of zero and a standard deviation of one. More...
template<class T >
T	normal (T u, T s)
	Returns a random number from a normal Gaussian distribution with a mean of u and a standard deviation of s. More...
template<class T >
T	chiSquared (int k)
	Returns a random number as if the square of k independent standard normal N(0,1) random variables were aggregated. More...
void	randomData (RcOp)
template<class T >
T	sinhc (T x)
	\( \sinh(x)/x \) More...
template<int N>
__device__ void	fsinhcCheck ()
template<int N, class T >
__device__ T	fsinhcPade44 (T x2)
template<int N, class T >
__device__ T	fsinhcTaylor (T x2)
template<int N, class T >
__device__ T	fsinhcSeries (T x2)
template<class T >
__device__ T	fsinhcAnalyt7 (T d, T d13, T y, T z)
template<class T >
__device__ T	fsinhcAnalyt6 (T d, T d11, T y, T z)
template<class T >
__device__ T	fsinhcAnalyt5 (T d, T d9, T y, T z)
template<class T >
__device__ T	fsinhcAnalyt4 (T d, T d7, T y, T z)
template<class T >
__device__ T	fsinhcAnalyt3 (T d, T d5, T y, T z)
template<class T >
__device__ T	fsinhcAnalyt2 (T d, T d3, T y, T z)
template<class T >
__device__ T	fsinhcAnalyt1 (T d, T y, T z)
template<int N, class T >
__device__ void	fsinhcImpl (T d, T &__restrict__ f1d, T &__restrict__ f2d, T &__restrict__ f3d, T &__restrict__ f4d, T &__restrict__ f5d, T &__restrict__ f6d, T &__restrict__ f7d)
template<int DO_DTAPER>
__device__ void	switchTaper5 (real rik, real cut, real off, real &__restrict__ taper, real &__restrict__ dtaper)
	Smooth function F: [cut,off]->[1,0]. More...
template<class T >
void	matmul3 (T R[3][3], T A[3][3], T B[3][3])
	Matrix multiplication of two 3 by 3 matrices. \( R = A B \). Matrices are stored in the row-major order (C-style). More...
template<class T >
void	matmul3 (T R[3][3], T A[3][3])
	Matrix multiplication of two 3 by 3 matrices. \( R = A R \). Matrices are stored in the row-major order (C-style). More...
template<class T >
void	trimatExp (T ans[3][3], T m[3][3], T t)
	\( \exp(mt) \). Matrix m is 3 by 3 upper triangular. Matrices are stored in the row-major order (C-style). More...
template<class T >
void	trimatExpm1c (T ans[3][3], T m[3][3], T t)
	\( (\exp(mt)-I)/(mt) \). Matrix m is 3 by 3 upper triangular. Matrices are stored in the row-major order (C-style). More...
template<class T >
void	trimatTExpm1c (T ans[3][3], T m[3][3], T t)
	\( t \frac{\exp(mt)-I}{mt} \). Matrix m is 3 by 3 upper triangular. Matrices are stored in the row-major order (C-style). More...
void	zeroOnHost (int &v)
	Zeros variable on host. More...
void	zeroOnHost (float &v)
	Zeros variable on host. More...
void	zeroOnHost (double &v)
	Zeros variable on host. More...
void	zeroOnHost (unsigned long long &v)
	Zeros variable on host. More...
template<class T >
void	zeroOnHost (T *&ptr)
	Zeros variable on host. More...
template<class T , size_t N>
void	zeroOnHost (T(&v)[N])
	Zeros variables on host. More...
template<class T , class... Ts>
void	zeroOnHost (T &v, Ts &... vs)
	Zeros variables on host. More...
template<class T >
void	zeroOnDevice3Async_acc (int nelem, T *a1, T *a2, T *a3)
template<class T >
void	zeroOnDevice3Async_cu (int nelem, T *a1, T *a2, T *a3)
template<class T >
void	zeroOnDevice3Async (int nelem, T *a1, T *a2, T *a3)
	Zeros variables on device. More...
template<class T , int N>
void	zeroOnDevice3Async_acc (int nelem, T(*a1)[N], T(*a2)[N], T(*a3)[N])
template<class T , int N>
void	zeroOnDevice3Async_cu (int nelem, T(*a1)[N], T(*a2)[N], T(*a3)[N])
template<class T , int N>
void	zeroOnDevice3Async (int nelem, T(*a1)[N], T(*a2)[N], T(*a3)[N])
	Zeros variables on device. More...
template<class T >
void	zeroOnDevice9Async_acc (int nelem, T *a1, T *a2, T *a3, T *a4, T *a5, T *a6, T *a7, T *a8, T *a9)
template<class T >
void	zeroOnDevice9Async_cu (int nelem, T *a1, T *a2, T *a3, T *a4, T *a5, T *a6, T *a7, T *a8, T *a9)
template<class T >
void	zeroOnDevice9Async (int nelem, T *a1, T *a2, T *a3, T *a4, T *a5, T *a6, T *a7, T *a8, T *a9)
	Zeros variables on device. More...
void	lf_lpiston_npt (int istep, time_prec dt_ps)
void	kineticEnergy (energy_prec &eksum_out, energy_prec(&ekin_out)[3][3], int n, const double *mass, const vel_prec *vx, const vel_prec *vy, const vel_prec *vz)
void	kineticExplicit (T_prec &temp_out, energy_prec &eksum_out, energy_prec(&ekin_out)[3][3], const vel_prec *vx, const vel_prec *vy, const vel_prec *vz)
void	kinetic (T_prec &temp)
void	bussiThermostat (time_prec dt, T_prec temp)
void	monteCarloBarostat (energy_prec epot, T_prec temp)
	Applies a box size correction as needed for the Monte Carlo barostat at the half time step. More...
void	berendsenBarostat (time_prec dt)
	Berendsen barostat by scaling the coordinates and box dimensions via coupling to an external constant pressure bath. Code for anisotropic pressure coupling was provided by Guido Raos, Dipartimento di Chimica, Politecnico di Milano, Italy. More...
void	mdData (RcOp)
void	mdIntegrateData (RcOp)
void	mdrest (int istep)
void	mdrestPrintP1 (bool prints, double e1, double e2, double e3, double totmass)
void	mdPropagate (int nsteps, time_prec dt_ps)
const TimeScaleConfig &	respaTSConfig ()
void	mdsaveAsync (int istep, time_prec dt)
void	mdsaveSynchronize ()
void	mdsaveData (RcOp)
void	osrw_mech ()
void	osrwData (RcOp)
double	osrw_lam_expr0 (int form, double lam)
double	osrw_lam_expr1 (int form, double lam)
double	osrw_lam_expr2 (int form, double lam)
void	osrw_altele (double)
void	osrw_alttor (double)
void	osrw_altvdw (double)
void	osrw_energy (int vers, unsigned tsflag, const TimeScaleConfig &tsconfig)
void	osrw_energy (int vers)
void	mdVelData (RcOp)
void	hcVelIso (vel_prec s)
	Update velocities by \( v_{ui}(t) = v_{ui}(0) + s V_{u}(0) \). More...
void	hcVelAn (vel_prec s[3][3])
	Update velocities by \( \boldsymbol{v}_{ui}(t) = \boldsymbol{v}_{ui}(0) + \boldsymbol{S} \boldsymbol{V}_{u}(0) \). More...
void	hcPosIso (pos_prec s)
void	hcPosAn (pos_prec(*scal)[3])
template<class Ver >
__device__ void	dk_angle (real &__restrict__ e, real &__restrict__ vxx, real &__restrict__ vyx, real &__restrict__ vzx, real &__restrict__ vyy, real &__restrict__ vzy, real &__restrict__ vzz, grad_prec *__restrict__ deax, grad_prec *__restrict__ deay, grad_prec *__restrict__ deaz, const Angle *__restrict__ angtyp, real angunit, int i, const int(*__restrict__ iang)[4], const real *__restrict__ anat, const real *__restrict__ ak, const real *__restrict__ afld, real cang, real qang, real pang, real sang, const real *__restrict__ x, const real *__restrict__ y, const real *__restrict__ z)
template<class Ver >
__device__ void	dk_angtor (real &__restrict__ e, real &__restrict__ vxx, real &__restrict__ vyx, real &__restrict__ vzx, real &__restrict__ vyy, real &__restrict__ vzy, real &__restrict__ vzz, grad_prec *__restrict__ deatx, grad_prec *__restrict__ deaty, grad_prec *__restrict__ deatz, real atorunit, int iangtor, const int(*__restrict__ iat)[3], const real(*__restrict__ kant)[6], const real *__restrict__ anat, const int(*__restrict__ itors)[4], const real(*__restrict__ tors1)[4], const real(*__restrict__ tors2)[4], const real(*__restrict__ tors3)[4], const real *__restrict__ x, const real *__restrict__ y, const real *__restrict__ z)
template<class Ver >
__device__ void	dk_bond (real &__restrict__ e, real &__restrict__ vxx, real &__restrict__ vyx, real &__restrict__ vzx, real &__restrict__ vyy, real &__restrict__ vzy, real &__restrict__ vzz, grad_prec *__restrict__ debx, grad_prec *__restrict__ deby, grad_prec *__restrict__ debz, Bond bndtyp, real bndunit, int i, const int(*__restrict__ ibnd)[2], const real *__restrict__ bl, const real *__restrict__ bk, real cbnd, real qbnd, const real *__restrict__ x, const real *__restrict__ y, const real *__restrict__ z)
template<int LEVEL, int bsorder>
__device__ void	bsplgen (real w, real *__restrict__ thetai, volatile real *__restrict__ bsbuild_)
	B-spline coefficients and derivatives for a single PME atomic site along a particular direction. See also subroutine bsplgen in pmestuf.f file. More...
template<int LEVEL, int bsorder>
__device__ void	bsplgen2 (real w, real *__restrict__ thetai, int k, int padded_n, volatile real *__restrict__ bsbuild_)
__device__ int	intCopysignShift (int a, int b)
	If b < 0, returns -abs(a), otherwise, returns abs(a). Similar to the 32-bit integer version of Fortran SIGN(A,B). More...
__device__ int	intCopysignIf (int a, int b)
	If b < 0, returns -abs(a), otherwise, returns abs(a). More...
__device__ void	dmpthole2_a (real r, real pgamma, real pdi, real pdk, real &__restrict__ scale3, real &__restrict__ scale5)
__device__ void	damp_thole2 (real r, real pdi, real pti, real pdk, real ptk, real &__restrict__ scale3, real &__restrict__ scale5)
__device__ void	dmpthole3_a (real r, real pgamma, real pdi, real pdk, real &__restrict__ scale3, real &__restrict__ scale5, real &__restrict__ scale7)
__device__ void	damp_thole3 (real r, real pdi, real pti, real pdk, real ptk, real &__restrict__ scale3, real &__restrict__ scale5, real &__restrict__ scale7)
__device__ void	dmpthole3g_a (real r, real rr2, real xr, real yr, real zr, real pgamma, real pdi, real pdk, real &__restrict__ scale31, real &__restrict__ scale51, real &__restrict__ scale71, real &__restrict__ rc31, real &__restrict__ rc32, real &__restrict__ rc33, real &__restrict__ rc51, real &__restrict__ rc52, real &__restrict__ rc53, real &__restrict__ rc71, real &__restrict__ rc72, real &__restrict__ rc73)
__device__ void	damp_thole3g (real r, real rr2, real xr, real yr, real zr, real pdi, real pti, real pdk, real ptk, real &__restrict__ scale31, real &__restrict__ scale51, real &__restrict__ scale71, real &__restrict__ rc31, real &__restrict__ rc32, real &__restrict__ rc33, real &__restrict__ rc51, real &__restrict__ rc52, real &__restrict__ rc53, real &__restrict__ rc71, real &__restrict__ rc72, real &__restrict__ rc73)
__device__ void	dmpthole4_a (real r, real pgamma, real pdi, real pdk, real &__restrict__ ex3, real &__restrict__ ex5, real &__restrict__ ex7, real &__restrict__ ex9)
__device__ void	damp_thole4 (real r, real pdi, real pti, real pdk, real ptk, real &__restrict__ ex3, real &__restrict__ ex5, real &__restrict__ ex7, real &__restrict__ ex9)
template<int order>
__device__ void	damp_ewald (real *__restrict__ bn, real r, real rinv, real rr2, real aewald)
template<int DirOrder, int MutOrder>
__device__ void	damp_gordon1 (real *__restrict__ dmpij, real *__restrict__ dmpi, real *__restrict__ dmpj, real r, real ai, real aj)
template<int ORDER>
__device__ void	damp_pole_deprecated (real *__restrict__ dmpik, real *__restrict__ dmpi, real *__restrict__ dmpk, real r, real alphai, real alphak)
	deprecated More...
template<int order>
__device__ void	damp_pole_v2 (real *__restrict__ dmpij, real *__restrict__ dmpi, real *__restrict__ dmpj, real r, real ai, real aj)
__device__ void	damp_dir (real *__restrict__ dmpi, real *__restrict__ dmpk, real r, real alphai, real alphak)
__device__ void	damp_mut (real *__restrict__ dmpik, real r, real alphai, real alphak)
template<int order>
__device__ void	damp_rep_deprecated (real *__restrict__ dmpik, real r, real rinv, real r2, real rr3, real rr5, real rr7, real rr9, real rr11, real dmpi, real dmpk)
template<int order>
__device__ void	damp_rep (real *__restrict__ dmpik, real r, real rr1, real r2, real rr3, real rr5, real rr7, real rr9, real rr11, real ai, real aj)
template<int DO_G>
__device__ void	damp_hippodisp (real *__restrict__ dmpij, real r, real rr1, real ai, real aj)
template<int ORDER>
__device__ void	damp_gordon2 (real *__restrict__ dmpik, real *__restrict__ dmpi, real *__restrict__ dmpk, real r, real alphai, real alphak)
__device__ void	damp_aplus3 (real r, real pdi, real ddi, real pdk, real ddk, real &__restrict__ scale3, real &__restrict__ scale5, real &__restrict__ scale7)
__device__ void	damp_aplus3g (real r, real rr2, real xr, real yr, real zr, real pdi, real ddi, real pdk, real ddk, real &__restrict__ scale31, real &__restrict__ scale51, real &__restrict__ scale71, real &__restrict__ rc31, real &__restrict__ rc32, real &__restrict__ rc33, real &__restrict__ rc51, real &__restrict__ rc52, real &__restrict__ rc53, real &__restrict__ rc71, real &__restrict__ rc72, real &__restrict__ rc73)
template<bool do_a>
__global__ void	empoleSelf_cu (CountBuffer __restrict__ nem, EnergyBuffer __restrict__ em, const real(*__restrict__ rpole)[10], int n, real f, real aewald)
template<bool do_a, bool do_e, int CFLX>
__global__ void	empoleChgpenSelf_cu (CountBuffer __restrict__ nem, EnergyBuffer __restrict__ em, const real(*__restrict__ rpole)[10], real *__restrict__ pot, int n, real f, real aewald)
__device__ int	ffsnShift (int c1, int n)
	Find the position of the n-th least significant bit set in a 32-bit integer. Returns a value from 0 to 32. More...
__device__ int	ffsnLoop (int c1, int n)
	An alternative implementation of ffsn using loop. More...
template<class Ver >
__device__ void	dk_geom_group (real &__restrict__ e, real &__restrict__ vxx, real &__restrict__ vyx, real &__restrict__ vzx, real &__restrict__ vyy, real &__restrict__ vzy, real &__restrict__ vzz, grad_prec *__restrict__ degx, grad_prec *__restrict__ degy, grad_prec *__restrict__ degz, int i, const int(*__restrict__ igfix)[2], const real(*__restrict__ gfix)[3], const real *__restrict__ x, const real *__restrict__ y, const real *__restrict__ z, const double *__restrict__ mass, const int *__restrict__ molec, const int(*__restrict__ igrp)[2], const int *__restrict__ kgrp, const double *__restrict__ grpmass, BoxShape box_shape, real3 lvec1, real3 lvec2, real3 lvec3, real3 recipa, real3 recipb, real3 recipc)
template<class Ver >
__device__ void	dk_geom_distance (real &__restrict__ e, real &__restrict__ vxx, real &__restrict__ vyx, real &__restrict__ vzx, real &__restrict__ vyy, real &__restrict__ vzy, real &__restrict__ vzz, grad_prec *__restrict__ degx, grad_prec *__restrict__ degy, grad_prec *__restrict__ degz, int i, const int(*__restrict__ idfix)[2], const real(*__restrict__ dfix)[3], const real *__restrict__ x, const real *__restrict__ y, const real *__restrict__ z, const int *__restrict__ molec, BoxShape box_shape, real3 lvec1, real3 lvec2, real3 lvec3, real3 recipa, real3 recipb, real3 recipc)
template<class Ver >
__device__ void	dk_geom_angle (real &__restrict__ e, real &__restrict__ vxx, real &__restrict__ vyx, real &__restrict__ vzx, real &__restrict__ vyy, real &__restrict__ vzy, real &__restrict__ vzz, grad_prec *__restrict__ degx, grad_prec *__restrict__ degy, grad_prec *__restrict__ degz, int i, const int(*__restrict__ iafix)[3], const real(*__restrict__ afix)[3], const real *__restrict__ x, const real *__restrict__ y, const real *__restrict__ z)
template<class Ver >
__device__ void	dk_geom_torsion (real &__restrict__ e, real &__restrict__ vxx, real &__restrict__ vyx, real &__restrict__ vzx, real &__restrict__ vyy, real &__restrict__ vzy, real &__restrict__ vzz, grad_prec *__restrict__ degx, grad_prec *__restrict__ degy, grad_prec *__restrict__ degz, int i, const int(*__restrict__ itfix)[4], const real(*__restrict__ tfix)[3], const real *__restrict__ x, const real *__restrict__ y, const real *__restrict__ z)
template<class Ver >
__device__ void	dk_geom_position (real &__restrict__ e, real &__restrict__ vxx, real &__restrict__ vyx, real &__restrict__ vzx, real &__restrict__ vyy, real &__restrict__ vzy, real &__restrict__ vzz, grad_prec *__restrict__ degx, grad_prec *__restrict__ degy, grad_prec *__restrict__ degz, int i, const int *__restrict__ ipfix, const int(*__restrict__ kpfix)[3], const real *__restrict__ xpfix, const real *__restrict__ ypfix, const real *__restrict__ zpfix, const real(*__restrict__ pfix)[2], const real *__restrict__ x, const real *__restrict__ y, const real *__restrict__ z, BoxShape box_shape, real3 lvec1, real3 lvec2, real3 lvec3, real3 recipa, real3 recipb, real3 recipc)
__device__ real3	ftoc_triclinic (real3 f, real3 l1, real3 l2, real3 l3)
	Fractional to cartesian: triclinic. More...
__device__ real3	ftoc_monoclinic (real3 f, real3 l1, real3 l2, real3 l3)
	Fractional to cartesian: monoclinic. More...
__device__ real3	ftoc_orthogonal (real3 f, real3 l1, real3 l2, real3 l3)
	Fractional to cartesian: orthogonal. More...
__device__ real3	ftoc_general (real3 f, real3 l1, real3 l2, real3 l3)
	Fractional to cartesian. More...
__device__ real3	imageFrac (real3 f)
	PBC image of the fractional coordinates. More...
__device__ real3	ctof_triclinic (real xr, real yr, real zr, real3 ra, real3 rb, real3 rc)
	Cartesian to fractional: triclinic. More...
__device__ real3	ctof_monoclinic (real xr, real yr, real zr, real3 ra, real3 rb, real3 rc)
	Cartesian to fractional: monoclinic. More...
__device__ real3	ctof_orthogonal (real xr, real yr, real zr, real3 ra, real3 rb, real3 rc)
	Cartesian to fractional: orthogonal. More...
__device__ real3	imagectof_general (real xr, real yr, real zr, real3 ra, real3 rb, real3 rc)
	Cartesian to fractional. More...
template<class Ver >
__device__ void	dk_improp (real &__restrict__ e, real &__restrict__ vxx, real &__restrict__ vyx, real &__restrict__ vzx, real &__restrict__ vyy, real &__restrict__ vzy, real &__restrict__ vzz, grad_prec *__restrict__ deidx, grad_prec *__restrict__ deidy, grad_prec *__restrict__ deidz, real idihunit, int i, const int(*__restrict__ iiprop)[4], const real *__restrict__ kprop, const real *__restrict__ vprop, const real *__restrict__ x, const real *__restrict__ y, const real *__restrict__ z)
template<class Ver >
__device__ void	dk_imptor (real &__restrict__ e, real &__restrict__ vxx, real &__restrict__ vyx, real &__restrict__ vzx, real &__restrict__ vyy, real &__restrict__ vzy, real &__restrict__ vzz, grad_prec *__restrict__ deitx, grad_prec *__restrict__ deity, grad_prec *__restrict__ deitz, real itorunit, int i, const int(*__restrict__ iitors)[4], const real(*__restrict__ itors1)[4], const real(*__restrict__ itors2)[4], const real(*__restrict__ itors3)[4], const real *__restrict__ x, const real *__restrict__ y, const real *__restrict__ z)
template<class K , class... Ts>
void	launch_k3s (cudaStream_t st, size_t sh, int bs, int np, K k, Ts &&... a)
template<class K , class... Ts>
void	launch_k3b (cudaStream_t st, size_t sh, int bs, int np, K k, Ts &&... a)
template<class K , class... Ts>
void	launch_k2s (cudaStream_t st, int bs, int np, K k, Ts &&... a)
template<class K , class... Ts>
void	launch_k2b (cudaStream_t st, int bs, int np, K k, Ts &&... a)
template<class K , class... Ts>
void	launch_k1s (cudaStream_t st, int np, K k, Ts &&... a)
template<class K , class... Ts>
void	launch_k1b (cudaStream_t st, int np, K k, Ts &&... a)
template<class Ver >
__device__ void	dk_opbend (real &__restrict__ e, real &__restrict__ vxx, real &__restrict__ vyx, real &__restrict__ vzx, real &__restrict__ vyy, real &__restrict__ vzy, real &__restrict__ vzz, grad_prec *__restrict__ deopbx, grad_prec *__restrict__ deopby, grad_prec *__restrict__ deopbz, OPBend opbtyp, real opbunit, int iopbend, const int *__restrict__ iopb, const real *__restrict__ opbk, const int(*__restrict__ iang)[4], real copb, real qopb, real popb, real sopb, const real *__restrict__ x, const real *__restrict__ y, const real *__restrict__ z)
template<bool DO_G>
__device__ void	damp_expl (ExpolScr scrtyp, real &__restrict__ s2, real &__restrict__ ds2, real r, real sizik, real alphai, real alphak)
__device__ void	pair_alterpol (ExpolScr scrtyp, real r, real pscale, real cut, real off, real xr, real yr, real zr, real springi, real sizi, real alphai, real springk, real sizk, real alphak, real ks2i[3][3], real ks2k[3][3])
__device__ void	pair_dexpol (ExpolScr scrtyp, real r, real pscale, real cut, real off, real xr, real yr, real zr, real uix, real uiy, real uiz, real ukx, real uky, real ukz, real springi, real sizi, real alphai, real springk, real sizk, real alphak, const real f, real frc[3])
template<class Ver , class ETYP >
__device__ void	pair_charge (real r, real xr, real yr, real zr, real cscale, real chgi, real chgk, real ebuffer, real f, real aewald, real cut, real off, real &__restrict__ grdx, real &__restrict__ grdy, real &__restrict__ grdz, int &__restrict__ ctl, real &__restrict__ etl, real &__restrict__ vtlxx, real &__restrict__ vtlxy, real &__restrict__ vtlxz, real &__restrict__ vtlyy, real &__restrict__ vtlyz, real &__restrict__ vtlzz)
template<bool DO_G, class ETYP , int SCALE>
__device__ void	pair_chg_v2 (real r, real invr, real cscale, real chgi, real chgk, real f, real aewald, real eccut, real ecoff, real &__restrict__ ec, real &__restrict__ dec)
template<bool DO_G, class ETYP , int SCALE>
__device__ void	pair_chg_v3 (real r, real cscale, real chgi, real chgk, real ebuffer, real f, real aewald, real eccut, real ecoff, real &__restrict__ ec, real &__restrict__ dec)
template<bool DO_G>
__device__ void	pair_chgtrn (real r, real cut, real off, real mscale, real f, real alphai, real chgi, real alphak, real chgk, real elambda, e_prec &__restrict__ e, e_prec &__restrict__ de)
template<bool DO_G, class DTYP , int SCALE>
__device__ void	pair_disp_obsolete (real r, real r2, real rr1, real dspscale, real aewald, real ci, real ai, real ck, real ak, real edcut, real edoff, real &__restrict__ e, real &__restrict__ de)
template<bool DO_G, class DTYP , int SCALE, int SOFTCORE>
__device__ void	pair_disp (real r, real r2, real rr1, real dspscale, real aewald, real ci, real ai, real ck, real ak, real vlambda, real edcut, real edoff, real &__restrict__ e, real &__restrict__ de)
template<class ETYP >
__device__ void	pair_dfield (real r2, real xr, real yr, real zr, real dscale, real pscale, real ci, real dix, real diy, real diz, real qixx, real qixy, real qixz, real qiyy, real qiyz, real qizz, real pdi, real pti, real ck, real dkx, real dky, real dkz, real qkxx, real qkxy, real qkxz, real qkyy, real qkyz, real qkzz, real pdk, real ptk, real aewald, real3 &__restrict__ fid, real3 &__restrict__ fip, real3 &__restrict__ fkd, real3 &__restrict__ fkp)
template<class ETYP >
__device__ void	pair_dfield_v2 (real r2, real xr, real yr, real zr, real dscale, real pscale, real aewald, real ci, real dix, real diy, real diz, real qixx, real qixy, real qixz, real qiyy, real qiyz, real qizz, real pdi, real pti, real ck, real dkx, real dky, real dkz, real qkxx, real qkxy, real qkxz, real qkyy, real qkyz, real qkzz, real pdk, real ptk, real &__restrict__ fidx, real &__restrict__ fidy, real &__restrict__ fidz, real &__restrict__ fipx, real &__restrict__ fipy, real &__restrict__ fipz, real &__restrict__ fkdx, real &__restrict__ fkdy, real &__restrict__ fkdz, real &__restrict__ fkpx, real &__restrict__ fkpy, real &__restrict__ fkpz)
template<class ETYP >
__device__ void	pair_ufield (real r2, real xr, real yr, real zr, real uscale, real uindi0, real uindi1, real uindi2, real uinpi0, real uinpi1, real uinpi2, real pdi, real pti, real uindk0, real uindk1, real uindk2, real uinpk0, real uinpk1, real uinpk2, real pdk, real ptk, real aewald, real3 &__restrict__ fid, real3 &__restrict__ fip, real3 &__restrict__ fkd, real3 &__restrict__ fkp)
template<class ETYP >
__device__ void	pair_ufield_v2 (real r2, real xr, real yr, real zr, real uscale, real aewald, real uindi0, real uindi1, real uindi2, real uinpi0, real uinpi1, real uinpi2, real pdi, real pti, real uindk0, real uindk1, real uindk2, real uinpk0, real uinpk1, real uinpk2, real pdk, real ptk, real &__restrict__ fidx, real &__restrict__ fidy, real &__restrict__ fidz, real &__restrict__ fipx, real &__restrict__ fipy, real &__restrict__ fipz, real &__restrict__ fkdx, real &__restrict__ fkdy, real &__restrict__ fkdz, real &__restrict__ fkpx, real &__restrict__ fkpy, real &__restrict__ fkpz)
template<class ETYP >
__device__ void	pair_dfield_chgpen (real r2, real xr, real yr, real zr, real dscale, real ci, real dix, real diy, real diz, real corei, real vali, real alphai, real qixx, real qixy, real qixz, real qiyy, real qiyz, real qizz, real ck, real dkx, real dky, real dkz, real corek, real valk, real alphak, real qkxx, real qkxy, real qkxz, real qkyy, real qkyz, real qkzz, real aewald, real &__restrict__ fidx, real &__restrict__ fidy, real &__restrict__ fidz, real &__restrict__ fkdx, real &__restrict__ fkdy, real &__restrict__ fkdz)
template<class ETYP >
__device__ void	pair_ufield_chgpen (real r2, real xr, real yr, real zr, real wscale, real uindi0, real uindi1, real uindi2, real corei, real vali, real alphai, real uindk0, real uindk1, real uindk2, real corek, real valk, real alphak, real aewald, real &__restrict__ fidx, real &__restrict__ fidy, real &__restrict__ fidz, real &__restrict__ fkdx, real &__restrict__ fkdy, real &__restrict__ fkdz)
template<bool DO_G>
__device__ void	pair_hal (real rik, real rv, real eps, real vscalek, real vlambda, real ghal, real dhal, real scexp, real scalpha, real &__restrict__ e, real &__restrict__ de)
template<bool DO_G, int SCALE>
__device__ void	pair_hal_v2 (real r, real vscale, real rv, real eps, real evcut, real evoff, real vlambda, real ghal, real dhal, real scexp, real scalpha, real &__restrict__ e, real &__restrict__ de)
template<bool DO_G, bool SOFTCORE>
__device__ void	pair_lj_v0 (real r, real invr, real vlambda, real rad, real eps, real &__restrict__ ev, real &__restrict__ dev)
template<bool DO_G, bool SOFTCORE>
__device__ void	pair_lj_v1 (real rik, real vlambda, real rv, real eps, real vscalek, real &__restrict__ e, real &__restrict__ de)
template<bool DO_G, bool SOFTCORE, class RADRULE , class EPSRULE , int SCALE>
__device__ void	pair_lj_v2 (real r, real invr, real vlambda, real vscale, real radi, real epsi, real radk, real epsk, real evcut, real evoff, real &__restrict__ ev, real &__restrict__ dev)
template<bool DO_G, bool SOFTCORE, int SCALE>
__device__ void	pair_lj_v3 (real r, real invr, real vlambda, real vscale, real rad, real eps, real evcut, real evoff, real &__restrict__ ev, real &__restrict__ dev)
__device__ void	zero (PairMPoleGrad &pgrad)
template<bool do_e, bool do_g, class ETYP >
__device__ void	pair_mpole (real r2, real xr, real yr, real zr, real mscale, real ci, real dix, real diy, real diz, real qixx, real qixy, real qixz, real qiyy, real qiyz, real qizz, real ck, real dkx, real dky, real dkz, real qkxx, real qkxy, real qkxz, real qkyy, real qkyz, real qkzz, real f, real aewald, real &__restrict__ e, PairMPoleGrad &__restrict__ pgrad)
	OpenACC pairwise multipole electrostatic energy. More...
template<class Ver , class ETYP >
__device__ void	pair_mpole_v2 (real r2, real xr, real yr, real zr, real mscale, real ci, real dix, real diy, real diz, real qixx, real qixy, real qixz, real qiyy, real qiyz, real qizz, real ck, real dkx, real dky, real dkz, real qkxx, real qkxy, real qkxz, real qkyy, real qkyz, real qkzz, real f, real aewald, real &__restrict__ frcxi, real &__restrict__ frcyi, real &__restrict__ frczi, real &__restrict__ frcxk, real &__restrict__ frcyk, real &__restrict__ frczk, real &__restrict__ trqxi, real &__restrict__ trqyi, real &__restrict__ trqzi, real &__restrict__ trqxk, real &__restrict__ trqyk, real &__restrict__ trqzk, real &__restrict__ e, real &__restrict__ vxx, real &__restrict__ vxy, real &__restrict__ vxz, real &__restrict__ vyy, real &__restrict__ vyz, real &__restrict__ vzz)
template<bool do_e, bool do_g, class ETYP , int CFLX>
__device__ void	pair_mpole_chgpen (real r2, real xr, real yr, real zr, real mscale, real ci, real dix, real diy, real diz, real corei, real vali, real alphai, real qixx, real qixy, real qixz, real qiyy, real qiyz, real qizz, real ck, real dkx, real dky, real dkz, real corek, real valk, real alphak, real qkxx, real qkxy, real qkxz, real qkyy, real qkyz, real qkzz, real f, real aewald, real &__restrict__ e, real &__restrict__ poti, real &__restrict__ potk, PairMPoleGrad &__restrict__ pgrad)
__device__ void	zero (PairPolarGrad &pgrad)
template<bool do_e, bool do_g, class ETYP >
__device__ void	pair_polar (real r2, real xr, real yr, real zr, real dscale, real pscale, real uscale, real ci, real dix, real diy, real diz, real qixx, real qixy, real qixz, real qiyy, real qiyz, real qizz, real uix, real uiy, real uiz, real uixp, real uiyp, real uizp, real pdi, real pti, real ck, real dkx, real dky, real dkz, real qkxx, real qkxy, real qkxz, real qkyy, real qkyz, real qkzz, real ukx, real uky, real ukz, real ukxp, real ukyp, real ukzp, real pdk, real ptk, real f, real aewald, real &__restrict__ e, PairPolarGrad &__restrict__ pgrad)
template<class Ver , class ETYP >
__device__ void	pair_polar_v2 (real r2, real xr, real yr, real zr, real dscale, real pscale, real uscale, real ci, real dix, real diy, real diz, real qixx, real qixy, real qixz, real qiyy, real qiyz, real qizz, real uix, real uiy, real uiz, real uixp, real uiyp, real uizp, real pdi, real pti, real ck, real dkx, real dky, real dkz, real qkxx, real qkxy, real qkxz, real qkyy, real qkyz, real qkzz, real ukx, real uky, real ukz, real ukxp, real ukyp, real ukzp, real pdk, real ptk, real f, real aewald, real &__restrict__ frcxi, real &__restrict__ frcyi, real &__restrict__ frczi, real &__restrict__ frcxk, real &__restrict__ frcyk, real &__restrict__ frczk, real &__restrict__ uf0i, real &__restrict__ uf1i, real &__restrict__ uf2i, real &__restrict__ uf0k, real &__restrict__ uf1k, real &__restrict__ uf2k, real &__restrict__ duf0i, real &__restrict__ duf1i, real &__restrict__ duf2i, real &__restrict__ duf3i, real &__restrict__ duf4i, real &__restrict__ duf5i, real &__restrict__ duf0k, real &__restrict__ duf1k, real &__restrict__ duf2k, real &__restrict__ duf3k, real &__restrict__ duf4k, real &__restrict__ duf5k, real &__restrict__ e, real &__restrict__ vxx, real &__restrict__ vxy, real &__restrict__ vxz, real &__restrict__ vyy, real &__restrict__ vyz, real &__restrict__ vzz)
template<bool do_e, bool do_g, class ETYP , int CFLX>
__device__ void	pair_polar_chgpen (real r2, real xr, real yr, real zr, real dscale, real wscale, real ci, real dix, real diy, real diz, real corei, real vali, real alphai, real qixx, real qixy, real qixz, real qiyy, real qiyz, real qizz, real uix, real uiy, real uiz, real ck, real dkx, real dky, real dkz, real corek, real valk, real alphak, real qkxx, real qkxy, real qkxz, real qkyy, real qkyz, real qkzz, real ukx, real uky, real ukz, real f, real aewald, real &__restrict__ e, real &__restrict__ poti, real &__restrict__ potk, PairPolarGrad &__restrict__ pgrad)
__device__ void	zero (PairRepelGrad &pgrad)
template<bool do_g, int SOFTCORE>
__device__ void	pair_repel (real r2, real rscale, real vlambda, real cut, real off, real xr, real yr, real zr, real sizi, real dmpi, real vali, real ci, real dix, real diy, real diz, real qixx, real qixy, real qixz, real qiyy, real qiyz, real qizz, real sizk, real dmpk, real valk, real ck, real dkx, real dky, real dkz, real qkxx, real qkxy, real qkxz, real qkyy, real qkyz, real qkzz, real &__restrict__ e, PairRepelGrad &__restrict__ pgrad)
__device__ real	pair_vlambda (real vlam, Vdw vcouple, int imut, int kmut)
template<bool DO_G>
__device__ void	pair_chgtrn_aplus (real r, real cut, real off, real mscale, real f, real alphai, real chgi, real alphak, real chgk, real elambda, e_prec &__restrict__ e, e_prec &__restrict__ de)
template<class ETYP >
__device__ void	pair_dfield_aplus (real r2, real xr, real yr, real zr, real dscale, real ci, real dix, real diy, real diz, real pdi, real ddi, real qixx, real qixy, real qixz, real qiyy, real qiyz, real qizz, real ck, real dkx, real dky, real dkz, real pdk, real ddk, real qkxx, real qkxy, real qkxz, real qkyy, real qkyz, real qkzz, real aewald, real &__restrict__ fidx, real &__restrict__ fidy, real &__restrict__ fidz, real &__restrict__ fkdx, real &__restrict__ fkdy, real &__restrict__ fkdz)
template<class ETYP >
__device__ void	pair_dfield_aplus_v2 (real r2, real xr, real yr, real zr, real dscale, real ci, real dix, real diy, real diz, real pdi, real ddi, real qixx, real qixy, real qixz, real qiyy, real qiyz, real qizz, real ck, real dkx, real dky, real dkz, real pdk, real ddk, real qkxx, real qkxy, real qkxz, real qkyy, real qkyz, real qkzz, real aewald, real &__restrict__ fidx, real &__restrict__ fidy, real &__restrict__ fidz, real &__restrict__ fkdx, real &__restrict__ fkdy, real &__restrict__ fkdz)
template<class ETYP >
__device__ void	pair_ufield_aplus (real r2, real xr, real yr, real zr, real uscale, real uindi0, real uindi1, real uindi2, real pdi, real pti, real uindk0, real uindk1, real uindk2, real pdk, real ptk, real aewald, real &__restrict__ fidx, real &__restrict__ fidy, real &__restrict__ fidz, real &__restrict__ fkdx, real &__restrict__ fkdy, real &__restrict__ fkdz)
template<class ETYP >
__device__ void	pair_ufield_aplus_v2 (real r2, real xr, real yr, real zr, real uscale, real uindi0, real uindi1, real uindi2, real pdi, real pti, real uindk0, real uindk1, real uindk2, real pdk, real ptk, real aewald, real &__restrict__ fidx, real &__restrict__ fidy, real &__restrict__ fidz, real &__restrict__ fkdx, real &__restrict__ fkdy, real &__restrict__ fkdz)
template<bool do_e, bool do_g, class ETYP , int CFLX>
__device__ void	pair_mpole_chgpen_aplus (real r2, real xr, real yr, real zr, real mscale, real ci, real dix, real diy, real diz, real corei, real vali, real alphai, real qixx, real qixy, real qixz, real qiyy, real qiyz, real qizz, real ck, real dkx, real dky, real dkz, real corek, real valk, real alphak, real qkxx, real qkxy, real qkxz, real qkyy, real qkyz, real qkzz, real f, real aewald, real &__restrict__ e, real &__restrict__ poti, real &__restrict__ potk, PairMPoleGrad &__restrict__ pgrad)
template<bool do_e, bool do_g, class ETYP , int CFLX>
__device__ void	pair_polar_aplus (real r2, real xr, real yr, real zr, real dscale, real uscale, real ci, real dix, real diy, real diz, real pdi, real pti, real ddi, real qixx, real qixy, real qixz, real qiyy, real qiyz, real qizz, real uix, real uiy, real uiz, real ck, real dkx, real dky, real dkz, real pdk, real ptk, real ddk, real qkxx, real qkxy, real qkxz, real qkyy, real qkyz, real qkzz, real ukx, real uky, real ukz, real f, real aewald, real &__restrict__ e, real &__restrict__ poti, real &__restrict__ potk, PairPolarGrad &__restrict__ pgrad)
template<class Ver , class ETYP , int CFLX>
__device__ void	pair_polar_aplus_v2 (real r2, real xr, real yr, real zr, real dscale, real uscale, real ci, real dix, real diy, real diz, real qixx, real qixy, real qixz, real qiyy, real qiyz, real qizz, real uix, real uiy, real uiz, real pdi, real pti, real ddi, real ck, real dkx, real dky, real dkz, real qkxx, real qkxy, real qkxz, real qkyy, real qkyz, real qkzz, real ukx, real uky, real ukz, real pdk, real ptk, real ddk, real f, real aewald, real &__restrict__ frcxi, real &__restrict__ frcyi, real &__restrict__ frczi, real &__restrict__ frcxk, real &__restrict__ frcyk, real &__restrict__ frczk, real &__restrict__ uf0i, real &__restrict__ uf1i, real &__restrict__ uf2i, real &__restrict__ uf0k, real &__restrict__ uf1k, real &__restrict__ uf2k, real &__restrict__ duf0i, real &__restrict__ duf1i, real &__restrict__ duf2i, real &__restrict__ duf3i, real &__restrict__ duf4i, real &__restrict__ duf5i, real &__restrict__ duf0k, real &__restrict__ duf1k, real &__restrict__ duf2k, real &__restrict__ duf3k, real &__restrict__ duf4k, real &__restrict__ duf5k, real &__restrict__ e, real &__restrict__ vxx, real &__restrict__ vxy, real &__restrict__ vxz, real &__restrict__ vyy, real &__restrict__ vyz, real &__restrict__ vzz, real &__restrict__ poti, real &__restrict__ potk)
template<class Ver >
__device__ void	dk_pitors (real &__restrict__ e, real &__restrict__ vxx, real &__restrict__ vyx, real &__restrict__ vzx, real &__restrict__ vyy, real &__restrict__ vzy, real &__restrict__ vzz, grad_prec *__restrict__ deptx, grad_prec *__restrict__ depty, grad_prec *__restrict__ deptz, real ptorunit, int i, const int(*__restrict__ ipit)[6], const real *__restrict__ kpit, const real *__restrict__ x, const real *__restrict__ y, const real *__restrict__ z)
template<class T , unsigned int B, class Op >
__device__ void	warp_reduce (volatile T *sd, unsigned int t, Op op)
template<class T , unsigned int HN, unsigned int B, class Op >
__device__ void	warp_reduce2 (volatile T(*sd)[B], unsigned int t, Op op)
template<class T , unsigned int B, class Op >
__global__ void	reduce (T *g_odata, const T *g_idata, size_t n, Op op=Op())
template<class T , unsigned int B, unsigned int HN, size_t N, class Op >
__global__ void	reduce2 (T(*g_odata)[HN], const T(*g_idata)[N], size_t n, Op op=Op())
__device__ void	chkpoleAtomI (int i, real(*__restrict__ pole)[MPL_TOTAL], LocalFrame *zaxis, const real *__restrict__ x, const real *__restrict__ y, const real *__restrict__ z)
__device__ void	rotpoleNorm (real *a)
__device__ void	rotpoleAddBy (real *__restrict__ a, const real *__restrict__ b)
__device__ void	rotpoleAddBy2 (real *__restrict__ a, const real *__restrict__ b, const real *__restrict__ c)
__device__ void	rotsite (int isite, const real(*__restrict__ a)[3], real(*__restrict__ rpole)[10], const real(*__restrict__ pole)[10])
__device__ void	rotpoleAtomI (int i, real(*__restrict__ rpole)[MPL_TOTAL], const real(*__restrict__ pole)[MPL_TOTAL], const LocalFrame *__restrict__ zaxis, const real *__restrict__ x, const real *__restrict__ y, const real *__restrict__ z)
template<class HTYPE >
__device__ void	dk_settle1 (time_prec dt, int iw, const pos_prec *__restrict__ xold, const pos_prec *__restrict__ yold, const pos_prec *__restrict__ zold, pos_prec *__restrict__ xnew, pos_prec *__restrict__ ynew, pos_prec *__restrict__ znew, vel_prec *__restrict__ vx, vel_prec *__restrict__ vy, vel_prec *__restrict__ vz, const double *__restrict__ mass, const int(*__restrict__ iratwt)[3], const pos_prec(*__restrict__ kratwt)[3])
template<bool DO_V>
__device__ void	dk_settle2 (time_prec dt, int iw, vel_prec *__restrict__ vx, vel_prec *__restrict__ vy, vel_prec *__restrict__ vz, const pos_prec *__restrict__ xpos, const pos_prec *__restrict__ ypos, const pos_prec *__restrict__ zpos, const double *__restrict__ mass, const int(*__restrict__ iratwt)[3], double &__restrict__ vxx, double &__restrict__ vyx, double &__restrict__ vzx, double &__restrict__ vyy, double &__restrict__ vzy, double &__restrict__ vzz)
template<class Ver >
__device__ void	dk_strbnd (real &__restrict__ e, real &__restrict__ vxx, real &__restrict__ vyx, real &__restrict__ vzx, real &__restrict__ vyy, real &__restrict__ vzy, real &__restrict__ vzz, grad_prec *__restrict__ debax, grad_prec *__restrict__ debay, grad_prec *__restrict__ debaz, real stbnunit, int istrbnd, const int(*__restrict__ isb)[3], const real(*__restrict__ sbk)[2], const real *__restrict__ bl, const int(*__restrict__ iang)[4], const real *__restrict__ anat, const real *__restrict__ x, const real *__restrict__ y, const real *__restrict__ z)
template<class Ver >
__device__ void	dk_strtor (real &__restrict__ e, real &__restrict__ vxx, real &__restrict__ vyx, real &__restrict__ vzx, real &__restrict__ vyy, real &__restrict__ vzy, real &__restrict__ vzz, grad_prec *__restrict__ debtx, grad_prec *__restrict__ debty, grad_prec *__restrict__ debtz, real storunit, int istrtor, const int(*__restrict__ ist)[4], const real(*__restrict__ kst)[9], const real *__restrict__ bl, const int(*__restrict__ itors)[4], const real(*__restrict__ tors1)[4], const real(*__restrict__ tors2)[4], const real(*__restrict__ tors3)[4], const real *__restrict__ x, const real *__restrict__ y, const real *__restrict__ z)
__device__ real	torqueDot (const real *__restrict__ a, const real *__restrict__ b)
__device__ void	torqueCross (real *__restrict__ ans, const real *__restrict__ u, const real *__restrict__ v)
__device__ void	torqueNormal (real *__restrict__ a, real _1_na)
template<class Ver >
__device__ void	dk_tors (real &__restrict__ e, real &__restrict__ vxx, real &__restrict__ vyx, real &__restrict__ vzx, real &__restrict__ vyy, real &__restrict__ vzy, real &__restrict__ vzz, grad_prec *__restrict__ detx, grad_prec *__restrict__ dety, grad_prec *__restrict__ detz, real torsunit, int i, const int(*__restrict__ itors)[4], const real(*__restrict__ tors1)[4], const real(*__restrict__ tors2)[4], const real(*__restrict__ tors3)[4], const real(*__restrict__ tors4)[4], const real(*__restrict__ tors5)[4], const real(*__restrict__ tors6)[4], const real *__restrict__ x, const real *__restrict__ y, const real *__restrict__ z)
template<class Ver >
__device__ void	dk_tortor (real &__restrict__ e, real &__restrict__ vxx, real &__restrict__ vyx, real &__restrict__ vzx, real &__restrict__ vyy, real &__restrict__ vzy, real &__restrict__ vzz, grad_prec *__restrict__ dettx, grad_prec *__restrict__ detty, grad_prec *__restrict__ dettz, real ttorunit, int itortor, const int(*__restrict__ itt)[3], const int(*__restrict__ ibitor)[5], const int *__restrict__ chkttor_ia_, const int *__restrict__ tnx, const int *__restrict__ tny, const real(*__restrict__ ttx)[ktrtor::maxtgrd], const real(*__restrict__ tty)[ktrtor::maxtgrd], const real(*__restrict__ tbf)[ktrtor::maxtgrd2], const real(*__restrict__ tbx)[ktrtor::maxtgrd2], const real(*__restrict__ tby)[ktrtor::maxtgrd2], const real(*__restrict__ tbxy)[ktrtor::maxtgrd2], const real *__restrict__ x, const real *__restrict__ y, const real *__restrict__ z)
__device__ int	xy_to_tri (int x, int y)
__device__ void	tri_to_xy (int f, int &x, int &y)
template<class Ver >
__device__ void	dk_urey (real &__restrict__ e, real &__restrict__ vxx, real &__restrict__ vyx, real &__restrict__ vzx, real &__restrict__ vyy, real &__restrict__ vzy, real &__restrict__ vzz, grad_prec *__restrict__ deubx, grad_prec *__restrict__ deuby, grad_prec *__restrict__ deubz, real ureyunit, int i, const int(*__restrict__ iury)[3], const real *__restrict__ uk, const real *__restrict__ ul, real cury, real qury, const real *__restrict__ x, const real *__restrict__ y, const real *__restrict__ z)
template<class T >
void	atomic_add (T value, T *buffer, size_t offset=0)
template<class T , class = typename std::enable_if<std::is_same<T, float>::value || std::is_same<T, double>::value>::type>
void	atomic_add (T value, fixed *buffer, size_t offset=0)
template<class T >
void	atomic_add (T vxx, T vyx, T vzx, T vyy, T vzy, T vzz, T(*buffer)[8], size_t offset=0)
	Adds virial {xx,yx,zx,yy,zy,zz} to buffer[offset][0 to 7]. More...
template<class T , class = typename std::enable_if<std::is_same<T, float>::value || std::is_same<T, double>::value>::type>
void	atomic_add (T vxx, T vyx, T vzx, T vyy, T vzy, T vzz, fixed(*buffer)[8], size_t offset=0)
template<class G , class T >
G	floatTo (T val)
	Converts val of floating-point to type G. More...
template<class T >
T	fixedTo (fixed val)
	Converts val of fixed-point to floating-point. More...
template<class T >
T	toFloatGrad (fixed g)
	Converts a fixed-point value g to floating-point value. More...
template<class T >
T	toFloatGrad (double g)
	Converts a double-precision value g to floating-point value. More...
template<class T >
T	toFloatGrad (float g)
	Converts a single-precision value g to floating-point value. More...
template<class T , class U >
constexpr bool	eq ()
	Used as eq<T1,T2>() for two type identifiers. More...
int2	make_int2 (int x, int y)
int3	make_int3 (int x, int y, int z)
int4	make_int4 (int x, int y, int z, int w)
float2	make_float2 (float x, float y)
float3	make_float3 (float x, float y, float z)
float4	make_float4 (float x, float y, float z, float w)
double2	make_double2 (double x, double y)
double3	make_double3 (double x, double y, double z)
double4	make_double4 (double x, double y, double z, double w)
template<class T >
__device__ void	atomic_add (T value, T *buffer, size_t offset=0)
template<class T , class = typename std::enable_if<std::is_same<T, float>::value || std::is_same<T, double>::value>::type>
__device__ void	atomic_add (T value, fixed *buffer, size_t offset=0)
	Adds value to buffer[offset] via fixed-point arithmetic. More...
template<class T >
__device__ void	atomic_add (T vxx, T vyx, T vzx, T vyy, T vzy, T vzz, T(*buffer)[8], size_t offset=0)
	Adds virial {xx,yx,zx,yy,zy,zz} to buffer[offset][0 to 7]. More...
template<class T , class = typename std::enable_if<std::is_same<T, float>::value || std::is_same<T, double>::value>::type>
__device__ void	atomic_add (T vxx, T vyx, T vzx, T vyy, T vzy, T vzz, fixed(*buffer)[8], size_t offset=0)
template<class G , class T >
__device__ G	floatTo (T val)
	Converts val of floating-point to type G. More...
template<class T >
__device__ T	fixedTo (fixed val)
	Converts val of fixed-point to floating-point. More...
template<class T >
__device__ T	toFloatGrad (fixed g)
	Converts a fixed-point value g to floating-point value. More...
template<class T >
__device__ T	toFloatGrad (double g)
	Converts a double-precision value g to floating-point value. More...
template<class T >
__device__ T	toFloatGrad (float g)
	Converts a single-precision value g to floating-point value. More...
template<class T , class U >
__device__ __host__ constexpr bool	eq ()
	Used as eq<T1,T2>() for two type identifiers. More...
void	nextarg (size_t len, char *str, bool &exist)
template<size_t Len>
void	nextarg (char(&str)[Len], bool &exist)
template<class T1 , class T2 >
void	getKV (std::string k, T1 &v, T2 vIfKNotFound)
template<class T >
void	getKV (std::string k, std::vector< T > &v)
std::string	cxxCompilerName ()
	Returns the name of the C++ compiler. More...
std::string	accCompilerName ()
	Returns the name of the OpenACC compiler. More...
std::string	cudaCompilerName ()
	Returns the name of the CUDA compiler. More...
void	cudalibData (RcOp)
	Sets up the CUDA variables including but not limited to CUDA streams, CUDA library handles, CUDA memory buffers, and integer units for the OpenACC queues. More...
void	waitFor (int queue)
	Similar to OpenACC wait and CUDA stream synchronize. More...
void	deviceMemoryCopyinBytesAsync (void *dst, const void *src, size_t nbytes, int queue)
	Similar to OpenACC async copyin, copies data from host to device. More...
void	deviceMemoryCopyoutBytesAsync (void *dst, const void *src, size_t nbytes, int queue)
	Similar to OpenACC async copyout, copies data from device to host. More...
void	deviceMemoryCopyBytesAsync (void *dst, const void *src, size_t nbytes, int queue)
	Copies data between two pointers on device. More...
void	deviceMemoryZeroBytesAsync (void *dst, size_t nbytes, int queue)
	Writes zero bytes on device. More...
void	deviceMemoryDeallocate (void *ptr)
	Deallocates device pointer. More...
void	deviceMemoryAllocateBytes (void **pptr, size_t nbytes)
	Allocates device pointer. More...
template<class T >
void	deviceMemoryCheckType ()
	Sanity check. More...
template<class DT , class ST >
void	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	deviceMemoryCopyout1dArray (DT *dst, const ST *src, size_t nelem, int q)
	Copies data to 1D array, device to host. More...
template<class T >
std::string	translateErrorCode (T errcode)
	Translates the error code to text. More...
void	printError ()
	Writes the current coordinates to a disk file prior to aborting on a serious error. More...
void	printBacktrace (std::FILE *out=stderr)
	Prints the call stack to a FILE pointer. More...
std::string	exec (const std::string &cmd)
	Executes a command in shell and returns the output in a string. More...
void	throwExceptionMissingFunction (const char *functionName, const char *file, int lineNum)
std::string	gpuCudaRuntimeVersion ()
std::string	gpuCudaDriverVersion ()
std::string	gpuThrustVersion ()
std::vector< DeviceAttribute > &	gpuDeviceAttributes ()
void	gpuData (RcOp)
	Sets up the GPU card. More...
int	gpuGridSize (int nthreadsPerBlock)
int	gpuMaxNParallel (int idev)
template<class T >
const T &	formatForward (const T &t)
const char *	formatForward (const std::string &s)
template<class F , class... Ts>
void	print (std::FILE *out, const F &f, Ts &&... args)
	Formatted output. More...
template<class F >
void	print (std::FILE *out, const F &f)
	Formatted output. More...
template<class F , class... Ts>
std::string	format (const F &f, Ts &&... args)
	Writes the formatted output to an std::string object. More...
std::string	operator* (size_t k, std::string str)
	Duplicates then concatenates multiple copies of string. More...
std::string	operator* (std::string str, size_t k)
	Duplicates then concatenate multiple copies of string. More...
std::string	operator""_s (const char *s, size_t len)
	Uses _s suffix to convert a const char* to std::string. More...
template<class Arg , class Invalid >
void	ioReadStream (Arg &arg, std::string prompt, Arg auto_fill, Invalid &&invalid, std::istream &istream=std::cin)
	Tests the validity of arg. If invalid, read ONE value from an std::istream object. arg will not change until the reading successfully exits. More...
template<class T >
void	ioRewindStream (T &stream)
	Rewind a stream object. More...
void	platformData (RcOp)
template<class E >
constexpr std::enable_if< EnableEnumBitMask< E >::value, E >::type	operator| (E lhs, E rhs)
template<class E >
constexpr bool	operator& (E lhs, E rhs)
void	deviceData (RcOp)
	Set up and clean up device environment. More...
void	bsplineFill (PMEUnit, int level)
void	gridPchg (PMEUnit, real *pchg)
void	gridDisp (PMEUnit, real *csix)
void	gridMpole (PMEUnit, real(*fmp)[10])
void	gridUind (PMEUnit, real(*find)[3], real(*finp)[3])
void	pmeConv (PMEUnit)
void	pmeConv (PMEUnit, VirialBuffer v)
void	pmeConv (PMEUnit, EnergyBuffer e)
void	pmeConv (PMEUnit, EnergyBuffer e, VirialBuffer v)
void	fphiMpole (PMEUnit)
void	fphiUind (PMEUnit, real(*fdip_phi1)[10], real(*fdip_phi2)[10], real(*fdip_sum_phi)[20])
void	fphiUind2 (PMEUnit, real(*fdip_phi1)[10], real(*fdip_phi2)[10])
void	rpoleToCmp ()
void	cmpToFmp (PMEUnit, const real(*cmp)[10], real(*fmp)[10])
void	cuindToFuind (PMEUnit, const real(*cind)[3], const real(*cinp)[3], real(*fuind)[3], real(*fuinp)[3])
void	fphiToCphi (PMEUnit, const real(*fphi)[20], real(*cphi)[10])
void	pmeStreamStartRecord (bool usePmeStream)
void	pmeStreamStartWait (bool usePmeStream)
void	pmeStreamFinishRecord (bool usePmeStream)
void	pmeStreamFinishWait (bool usePmeStream)
void	empoleData (RcOp)
void	empole (int vers)
void	empoleEwaldRecip (int vers)
void	torque (int vers, grad_prec *dx, grad_prec *dy, grad_prec *dz)
void	mpoleInit (int vers)
void	epolarData (RcOp)
void	epolar (int vers)
void	epolarEwaldRecipSelf (int vers)
void	epolar0DotProd (const real(*uind)[3], const real(*udirp)[3])
void	dfield (real(*field)[3], real(*fieldp)[3])
void	dfieldNonEwald (real(*field)[3], real(*fieldp)[3])
void	dfieldEwald (real(*field)[3], real(*fieldp)[3])
void	dfieldEwaldRecipSelfP1 (real(*field)[3])
void	ufield (const real(*uind)[3], const real(*uinp)[3], real(*field)[3], real(*fieldp)[3])
void	ufieldNonEwald (const real(*uind)[3], const real(*uinp)[3], real(*field)[3], real(*fieldp)[3])
void	ufieldEwald (const real(*uind)[3], const real(*uinp)[3], real(*field)[3], real(*fieldp)[3])
void	diagPrecond (const real(*rsd)[3], const real(*rsdp)[3], real(*zrsd)[3], real(*zrsdp)[3])
void	sparsePrecondBuild ()
void	sparsePrecondApply (const real(*rsd)[3], const real(*rsdp)[3], real(*zrsd)[3], real(*zrsdp)[3])
void	ulspredSave (const real(*uind)[3], const real(*uinp)[3])
void	ulspredSum (real(*uind)[3], real(*uinp)[3])
void	inducePrint (const real(*ud)[3])
void	induce (real(*uind)[3], real(*uinp)[3])
void	cfluxData (RcOp)
void	alterchg ()
void	cfluxZeroPot ()
void	dcflux (int vers, grad_prec *gx, grad_prec *gy, grad_prec *gz, VirialBuffer vir)
bool	useDEwald ()
void	edispData (RcOp)
void	edisp (int vers)
void	dfieldChgpen (real(*field)[3])
void	ufieldChgpen (const real(*uind)[3], real(*field)[3])
void	ufieldChgpenEwaldRecipSelf (const real(*uind)[3], real(*field)[3])
void	diagPrecond2 (const real(*rsd)[3], real(*zrsd)[3])
void	sparsePrecondBuild2 ()
void	sparsePrecondApply2 (const real(*rsd)[3], real(*zrsd)[3])
void	induce2 (real(*uind)[3])
template<class T >
__device__ void	fsinhc1 (T d, T &__restrict__ f1d)
template<class T >
__device__ void	fsinhc2 (T d, T &__restrict__ f1d, T &__restrict__ f2d)
template<class T >
__device__ void	fsinhc3 (T d, T &__restrict__ f1d, T &__restrict__ f2d, T &__restrict__ f3d)
template<class T >
__device__ void	fsinhc4 (T d, T &__restrict__ f1d, T &__restrict__ f2d, T &__restrict__ f3d, T &__restrict__ f4d)
template<class T >
__device__ void	fsinhc5 (T d, T &__restrict__ f1d, T &__restrict__ f2d, T &__restrict__ f3d, T &__restrict__ f4d, T &__restrict__ f5d)
template<class T >
__device__ void	fsinhc6 (T d, T &__restrict__ f1d, T &__restrict__ f2d, T &__restrict__ f3d, T &__restrict__ f4d, T &__restrict__ f5d, T &__restrict__ f6d)
template<class T >
__device__ void	fsinhc7 (T d, T &__restrict__ f1d, T &__restrict__ f2d, T &__restrict__ f3d, T &__restrict__ f4d, T &__restrict__ f5d, T &__restrict__ f6d, T &__restrict__ f7d)
bool	useRattle ()
void	rattleData (RcOp)
void	rattle (time_prec dt, const pos_prec *xold, const pos_prec *yold, const pos_prec *zold)
void	rattle2 (time_prec dt, bool do_v)
void	shake (time_prec dt, pos_prec *xnew, pos_prec *ynew, pos_prec *znew, const pos_prec *xold, const pos_prec *yold, const pos_prec *zold)
void	hcKinetic ()
void	hcVirial ()
void	hcCenterOfMass (const pos_prec *atomx, const pos_prec *atomy, const pos_prec *atomz, pos_prec *molx, pos_prec *moly, pos_prec *molz)
template<class Arg >
int	ioReadString (Arg &arg, const char *str, size_t len)
	Reads ONE value from a string and save to arg. arg will not change until the reading successfully exits. More...
int	ioReadString (std::string &arg, const char *str, size_t len)
	Reads ONE value from a string and save to arg. arg will not change until the reading successfully exits. More...
template<class Arg , size_t Len>
int	ioReadString (Arg &arg, const char(&src)[Len])
	Reads ONE value from a string and save to arg. arg will not change until the reading successfully exits. More...

Variables
int	padded_n
int	n
	Number of atoms padded by WARP_SIZE. More...
int	trajn
	Number of atoms. More...
real *	x
	Number of the trajectory frames. More...
real *	y
	Current coordinates used in energy evaluation and neighbor lists. More...
real *	z
	Current coordinates used in energy evaluation and neighbor lists. More...
real *	trajx
	Coordinates of all the trajectory frames. More...
real *	trajy
	Coordinates of all the trajectory frames. More...
real *	trajz
	Coordinates of all the trajectory frames. More...
pos_prec *	xpos
pos_prec *	ypos
pos_prec *	zpos
double *	mass
	Atomic mass. More...
double *	massinv
	Inversed atomic mass. More...
BoxShape	box_shape
real3	lvec1
real3	lvec2
real3	lvec3
real3	recipa
real3	recipb
real3	recipc
Box *	trajbox
	Host pointer to the PBC boxes of a trajectory. More...
real *	pchg
	Magnitude of the partial charges (e-) of each atom. More...
CountBuffer	nec
EnergyBuffer	ec
VirialBuffer	vir_ec
grad_prec *	decx
grad_prec *	decy
grad_prec *	decz
energy_prec	energy_ec
virial_prec	virial_ec [9]
real	ebuffer
real	c2scale
real	c3scale
real	c4scale
real	c5scale
int	ncexclude
int(*	cexclude )[2]
real *	cexclude_scale
int	ncvexclude
int(*	cvexclude )[2]
real(*	cvexclude_scale )[2]
bool	vdwpr_in_use
int *	mut_coalesced
real *	chg_coalesced
real *	radeps_coalesced
real	electric
real	dielec
real	elam
grad_prec *	gx
	Gradient of valence terms; also works as total gradient array. More...
grad_prec *	gy
	Gradient of valence terms; also works as total gradient array. More...
grad_prec *	gz
	Gradient of valence terms; also works as total gradient array. More...
grad_prec *	gx_vdw
	Gradient of VDW, repulsion, dispersion, etc. terms. More...
grad_prec *	gy_vdw
	Gradient of VDW, repulsion, dispersion, etc. terms. More...
grad_prec *	gz_vdw
	Gradient of VDW, repulsion, dispersion, etc. terms. More...
grad_prec *	gx_elec
	Gradient of electrostatic terms. More...
grad_prec *	gy_elec
	Gradient of electrostatic terms. More...
grad_prec *	gz_elec
	Gradient of electrostatic terms. More...
EnergyBuffer	eng_buf
	Energy buffer for the valence terms. More...
EnergyBuffer	eng_buf_vdw
	Energy buffer for the vdw terms. More...
EnergyBuffer	eng_buf_elec
	Energy buffer for the electrostatic terms. More...
VirialBuffer	vir_buf
	Virial buffer for the valence terms. More...
VirialBuffer	vir_buf_vdw
	Virial buffer for the vdw terms. More...
VirialBuffer	vir_buf_elec
	Virial buffer for the electrostatic terms. More...
energy_prec	esum
	Total potential energy. More...
energy_prec	energy_valence
	Total valence energy. More...
energy_prec	energy_vdw
	Total vdw energy. More...
energy_prec	energy_elec
	Total electrostatic energy. More...
virial_prec	vir [9]
	Total potential virial tensor. More...
virial_prec	virial_valence [9]
	Total valence virial tensor. More...
virial_prec	virial_vdw [9]
	Total vdw virial tensor. More...
virial_prec	virial_elec [9]
	Total electrostatic virial tensor. More...
int	nelem_buffer
Bond	bndtyp
real	bndunit
real	cbnd
real	qbnd
int	nbond
int(*	ibnd )[2]
real *	bk
real *	bl
EnergyBuffer	eb
VirialBuffer	vir_eb
grad_prec *	debx
grad_prec *	deby
grad_prec *	debz
energy_prec	energy_eb
virial_prec	virial_eb [9]
real	angunit
real	stbnunit
real	opbunit
real	cang
real	qang
real	pang
real	sang
real	copb
real	qopb
real	popb
real	sopb
OPBend	opbtyp
Angle *	angtyp
int	nangle
int(*	iang )[4]
real *	ak
real *	anat
real *	afld
EnergyBuffer	ea
VirialBuffer	vir_ea
grad_prec *	deax
grad_prec *	deay
grad_prec *	deaz
energy_prec	energy_ea
virial_prec	virial_ea [9]
int	nopbend
int *	iopb
real *	opbk
EnergyBuffer	eopb
VirialBuffer	vir_eopb
grad_prec *	deopbx
grad_prec *	deopby
grad_prec *	deopbz
energy_prec	energy_eopb
virial_prec	virial_eopb [9]
int	nstrbnd
int(*	isb )[3]
real(*	sbk )[2]
EnergyBuffer	eba
VirialBuffer	vir_eba
grad_prec *	debax
grad_prec *	debay
grad_prec *	debaz
energy_prec	energy_eba
virial_prec	virial_eba [9]
real	ureyunit
real	cury
real	qury
int	nurey
int(*	iury )[3]
real *	uk
real *	ul
EnergyBuffer	eub
VirialBuffer	vir_eub
grad_prec *	deubx
grad_prec *	deuby
grad_prec *	deubz
energy_prec	energy_eub
virial_prec	virial_eub [9]
real	idihunit
real	itorunit
real	torsunit
real	ptorunit
real	storunit
real	atorunit
real	ttorunit
int(*	iiprop )[4]
real *	kprop
real *	vprop
int	niprop
EnergyBuffer	eid
VirialBuffer	vir_eid
grad_prec *	deidx
grad_prec *	deidy
grad_prec *	deidz
energy_prec	energy_eid
virial_prec	virial_eid [9]
int(*	iitors )[4]
real(*	itors1 )[4]
real(*	itors2 )[4]
real(*	itors3 )[4]
int	nitors
EnergyBuffer	eit
VirialBuffer	vir_eit
grad_prec *	deitx
grad_prec *	deity
grad_prec *	deitz
energy_prec	energy_eit
virial_prec	virial_eit [9]
int	ntors
int(*	itors )[4]
real(*	tors1 )[4]
real(*	tors2 )[4]
real(*	tors3 )[4]
real(*	tors4 )[4]
real(*	tors5 )[4]
real(*	tors6 )[4]
EnergyBuffer	et
VirialBuffer	vir_et
grad_prec *	detx
grad_prec *	dety
grad_prec *	detz
energy_prec	energy_et
virial_prec	virial_et [9]
int	npitors
int(*	ipit )[6]
real *	kpit
EnergyBuffer	ept
VirialBuffer	vir_ept
grad_prec *	deptx
grad_prec *	depty
grad_prec *	deptz
energy_prec	energy_ept
virial_prec	virial_ept [9]
int	nstrtor
int(*	ist )[4]
real(*	kst )[9]
EnergyBuffer	ebt
VirialBuffer	vir_ebt
grad_prec *	debtx
grad_prec *	debty
grad_prec *	debtz
energy_prec	energy_ebt
virial_prec	virial_ebt [9]
int	nangtor
int(*	iat )[3]
real(*	kant )[6]
EnergyBuffer	eat
VirialBuffer	vir_eat
grad_prec *	deatx
grad_prec *	deaty
grad_prec *	deatz
energy_prec	energy_eat
virial_prec	virial_eat [9]
int	nbitor
int(*	ibitor )[5]
int *	tnx
int *	tny
real(*	ttx )[ktrtor::maxtgrd]
real(*	tty )[ktrtor::maxtgrd]
real(*	tbf )[ktrtor::maxtgrd2]
real(*	tbx )[ktrtor::maxtgrd2]
real(*	tby )[ktrtor::maxtgrd2]
real(*	tbxy )[ktrtor::maxtgrd2]
int *	chkttor_ia_
int	ntortor
int(*	itt )[3]
EnergyBuffer	ett
VirialBuffer	vir_ett
grad_prec *	dettx
grad_prec *	detty
grad_prec *	dettz
energy_prec	energy_ett
virial_prec	virial_ett [9]
int	npfix
int *	ipfix
int(*	kpfix )[3]
real *	xpfix
real *	ypfix
real *	zpfix
real(*	pfix )[2]
int	ngfix
	Number of group distance restraints to be applied. More...
int(*	igfix )[2]
	Group numbers defining each group distance restraint. More...
real(*	gfix )[3]
	Force constant and target range for each group distance. More...
int	ndfix
int(*	idfix )[2]
real(*	dfix )[3]
int	nafix
int(*	iafix )[3]
real(*	afix )[3]
int	ntfix
int(*	itfix )[4]
real(*	tfix )[3]
EnergyBuffer	eg
VirialBuffer	vir_eg
grad_prec *	degx
grad_prec *	degy
grad_prec *	degz
energy_prec	energy_eg
virial_prec	virial_eg [9]
real	ghal
	Value of \( \gamma \) in buffered 14-7 vdw potential. More...
real	dhal
	Value of \( \delta \) in buffered 14-7 vdw potential. More...
real	v2scale
real	v3scale
real	v4scale
real	v5scale
Vdw	vdwtyp
Vdw	vdwindex
Vdw	radrule
Vdw	epsrule
energy_prec	elrc_vol
	Long-range energy correction (lrc), used as e += lrc/volume. More...
virial_prec	vlrc_vol
	Long-range virial correction (lrc), used as v(i,i) += lrc/volume. More...
int *	jvdw
	Type or class index into vdw parameters for each atom. The indices have been sorted and start from 0. More...
int *	ired
real *	kred
real *	xred
	Halgren buffered 14-7 reduced x, y, z coordinates for each atom. More...
real *	yred
real *	zred
real *	radmin
	Minimum energy distance (radmin) or well depth parameter (epsilon) for each jvdw pair. Element [j1][j2] is accessed by [njvdw*j1 + j2]. More...
real *	epsilon
real *	radmin4
	VDW 1-4 parameters: minimum energy distance and well depth. More...
real *	epsilon4
real *	atom_rad
real *	atom_eps
CountBuffer	nev
EnergyBuffer	ev
VirialBuffer	vir_ev
grad_prec *	devx
grad_prec *	devy
grad_prec *	devz
energy_prec	energy_ev
virial_prec	virial_ev [9]
int	njvdw
	Number of unique values in the jvdw array. More...
grad_prec *	gxred
	Halgren buffered 14-7 reduced vdw gradients for each atom. More...
grad_prec *	gyred
grad_prec *	gzred
int	nvdw14
int(*	vdw14ik )[2]
int	nvexclude
int(*	vexclude )[2]
real *	vexclude_scale
Vdw	vcouple
real	scexp
	Exponential factor for soft core buffered 14-7 potential. More...
real	scalpha
	Scale factor \( \alpha \) for soft core buffered 14-7 potential. More...
real	vlam
int *	mut
	State weighting values (lambda) of all atoms for van der Waals potentials. More...
LocalFrame *	zaxis
real(*	pole )[MPL_TOTAL]
real(*	rpole )[MPL_TOTAL]
real *	trqx
real *	trqy
real *	trqz
VirialBuffer	vir_trq
CountBuffer	nem
EnergyBuffer	em
VirialBuffer	vir_em
grad_prec *	demx
grad_prec *	demy
grad_prec *	demz
energy_prec	energy_em
virial_prec	virial_em [9]
real	m2scale
real	m3scale
real	m4scale
real	m5scale
int	nmexclude
int(*	mexclude )[2]
real *	mexclude_scale
int	njpolar
int *	jpolar
real *	thlval
real *	polarity
real *	thole
real *	pdamp
real(*	udir )[3]
real(*	udirp )[3]
real(*	uind )[3]
real(*	uinp )[3]
CountBuffer	nep
EnergyBuffer	ep
VirialBuffer	vir_ep
grad_prec *	depx
grad_prec *	depy
grad_prec *	depz
energy_prec	energy_ep
virial_prec	virial_ep [9]
real *	polarity_inv
real(*	ufld )[3]
real(*	dufld )[6]
real(*	work01_ )[3]
real(*	work02_ )[3]
real(*	work03_ )[3]
real(*	work04_ )[3]
real(*	work05_ )[3]
real(*	work06_ )[3]
real(*	work07_ )[3]
real(*	work08_ )[3]
real(*	work09_ )[3]
real(*	work10_ )[3]
real	u1scale
real	u2scale
real	u3scale
real	u4scale
real	d1scale
real	d2scale
real	d3scale
real	d4scale
real	p2scale
real	p3scale
real	p4scale
real	p5scale
real	p2iscale
real	p3iscale
real	p4iscale
real	p5iscale
real	udiag
int	nuexclude
int(*	uexclude )[2]
real *	uexclude_scale
int	ndpexclude
int(*	dpexclude )[2]
real(*	dpexclude_scale )[2]
int	ndpuexclude
int(*	dpuexclude )[2]
real(*	dpuexclude_scale )[3]
int	nmdpuexclude
int(*	mdpuexclude )[2]
real(*	mdpuexclude_scale )[4]
UPred	polpred
int	maxualt
int	nualt
real(*	udalt_00 )[3]
real(*	udalt_01 )[3]
real(*	udalt_02 )[3]
real(*	udalt_03 )[3]
real(*	udalt_04 )[3]
real(*	udalt_05 )[3]
real(*	udalt_06 )[3]
real(*	udalt_07 )[3]
real(*	udalt_08 )[3]
real(*	udalt_09 )[3]
real(*	udalt_10 )[3]
real(*	udalt_11 )[3]
real(*	udalt_12 )[3]
real(*	udalt_13 )[3]
real(*	udalt_14 )[3]
real(*	udalt_15 )[3]
real(*	upalt_00 )[3]
real(*	upalt_01 )[3]
real(*	upalt_02 )[3]
real(*	upalt_03 )[3]
real(*	upalt_04 )[3]
real(*	upalt_05 )[3]
real(*	upalt_06 )[3]
real(*	upalt_07 )[3]
real(*	upalt_08 )[3]
real(*	upalt_09 )[3]
real(*	upalt_10 )[3]
real(*	upalt_11 )[3]
real(*	upalt_12 )[3]
real(*	upalt_13 )[3]
real(*	upalt_14 )[3]
real(*	upalt_15 )[3]
real *	udalt_lsqr_a
real *	upalt_lsqr_a
real *	udalt_lsqr_b
real *	upalt_lsqr_b
real *	dirdamp
Chgpen	pentyp
real *	bflx
real(*	aflx )[2]
real(*	abflx )[2]
int *	atomic
int(*	balist )[2]
real *	mono0
real *	pdelta
real *	pot
real *	decfx
real *	decfy
real *	decfz
real *	pcore
real *	pval
real *	pval0
real *	palpha
real	w2scale
real	w3scale
real	w4scale
real	w5scale
int	nmdwexclude
int(*	mdwexclude )[2]
real(*	mdwexclude_scale )[3]
int	nwexclude
int(*	wexclude )[2]
real *	wexclude_scale
real *	chgct
real *	dmpct
CountBuffer	nct
EnergyBuffer	ect
VirialBuffer	vir_ect
grad_prec *	dectx
grad_prec *	decty
grad_prec *	dectz
energy_prec	energy_ect
virial_prec	virial_ect [9]
Chgtrn	ctrntyp
real *	kpep
real *	prepep
real *	dmppep
int *	lpep
real(*	polscale )[3][3]
real(*	polinv )[3][3]
ExpolScr	scrtyp
const int	couple_maxn12 = 8
int(*	couple_i12 )[couple_maxn12]
int *	couple_n12
Molecule	molecule
Group	grp
NBListUnit	vlist_unit
NBListUnit	clist_unit
NBListUnit	mlist_unit
NBListUnit	ulist_unit
NBListUnit	dsplist_unit
SpatialUnit	cspatial_v2_unit
SpatialUnit	vspatial_v2_unit
SpatialUnit	uspatial_v2_unit
SpatialUnit	mspatial_v2_unit
SpatialUnit	dspspatial_v2_unit
constexpr int	cspatial_fresh_mask_echglj = 0x00000001
real	csixpr
real *	csix
real *	adisp
int	ndspexclude
int(*	dspexclude )[2]
real *	dspexclude_scale
CountBuffer	ndisp
EnergyBuffer	edsp
VirialBuffer	vir_edsp
grad_prec *	dedspx
grad_prec *	dedspy
grad_prec *	dedspz
energy_prec	energy_edsp
virial_prec	virial_edsp [9]
real	dsp2scale
real	dsp3scale
real	dsp4scale
real	dsp5scale
real	elrc_vol_dsp
real	vlrc_vol_dsp
real(*	repole )[MPL_TOTAL]
real(*	rrepole )[MPL_TOTAL]
real *	sizpr
real *	dmppr
real *	elepr
int	nrepexclude
int(*	repexclude )[2]
real *	repexclude_scale
CountBuffer	nrep
EnergyBuffer	er
VirialBuffer	vir_er
grad_prec *	derx
grad_prec *	dery
grad_prec *	derz
energy_prec	energy_er
virial_prec	virial_er [9]
real	r2scale
real	r3scale
real	r4scale
real	r5scale
constexpr real	pi = M_PI
	\( \pi \) More...
constexpr real	sqrtpi = 1.77245385090551602730
	\( \sqrt{\pi} \) More...
constexpr real	radian = 57.2957795130823208768
	\( 180/\pi \) More...
constexpr real	_1radian = 0.01745329251994329576924
	\( \pi/180 \) More...
constexpr int	maxnose = bath::maxnose
	Maximum length of the NH chain. More...
energy_prec	eksum_old
energy_prec	eksum_mid
pos_prec *	leapfrog_x
pos_prec *	leapfrog_y
pos_prec *	leapfrog_z
vel_prec *	leapfrog_vx
vel_prec *	leapfrog_vy
vel_prec *	leapfrog_vz
vel_prec *	leapfrog_vxold
vel_prec *	leapfrog_vyold
vel_prec *	leapfrog_vzold
double	hdot_lp
double	hmass_lp
double	pnhv_lp
double	pnhv_pre_lp
double	pnhm_lp
double	pnhf_lp
double	pnh_lp
constexpr unsigned	RESPA_FAST = 1
constexpr unsigned	RESPA_SLOW = 2
energy_prec	eksum
	Kinetic energy. More...
energy_prec	ekin [3][3]
	Kinetic energy tensor. More...
constexpr int	OSRW_LAM_LINEAR = 0
constexpr int	OSRW_LAM_QUADRATIC = 1
bool	use_osrw
double	osrw_lambda
int	osrw_vdw
int	osrw_ele
int	osrw_tor
energy_prec	osrw_du1
virial_prec	osrw_dv1 [9]
grad_prec *	osrw_dgx
grad_prec *	osrw_dgy
grad_prec *	osrw_dgz
real *	osrw_pchg
real(*	osrw_pole )[MPL_TOTAL]
real *	osrw_polarity
int	osrw_ntbnd
int(*	osrw_itbnd )[2]
real(*	osrw_tors1 )[4]
real(*	osrw_tors2 )[4]
real(*	osrw_tors3 )[4]
real(*	osrw_tors4 )[4]
real(*	osrw_tors5 )[4]
real(*	osrw_tors6 )[4]
bool	use_pme_stream
	Logical flag for use of a separate CUDA stream for PME. More...
void *	pinned_buf
	Preallocated pinned host memory. More...
void *	dptr_buf
	Preallocated device memory. More...
cudaEvent_t	pme_event_start
cudaEvent_t	pme_event_finish
constexpr unsigned	WARP_SIZE = 32
constexpr unsigned	ALL_LANES = 0xFFFFFFFF
	Mask for all of the lanes in a warp. More...
constexpr unsigned	BLOCK_DIM = 128
	Default dimension of thread blocks. More...
constexpr int	PME_BLOCKDIM = 64
	Dimension of the thread blocks for some PME kernels. More...
int	ndevice
	Total number of visible devices. More...
int	idevice
	Device ID number in use. More...
Platform	pltfm_config
int	rc_flag
	Global bitmask. More...
PMEUnit	epme_unit
PMEUnit	ppme_unit
PMEUnit	pvpme_unit
PMEUnit	dpme_unit
real(*	cmp )[10]
real(*	fmp )[10]
real(*	cphi )[10]
real(*	fphi )[20]
real(*	fuind )[3]
real(*	fuinp )[3]
real(*	fdip_phi1 )[10]
real(*	fdip_phi2 )[10]
real(*	cphidp )[10]
real(*	fphidp )[20]
VirialBuffer	vir_m
constexpr int	TINKER_CU_THETA_ON_THE_FLY_GRID_MPOLE = 1
constexpr int	TINKER_CU_THETA_ON_THE_FLY_GRID_UIND = 0
pos_prec *	x_pmonte
	Temporary coordinates created for the Monte Carlo barostat. More...
pos_prec *	y_pmonte
	Temporary coordinates created for the Monte Carlo barostat. More...
pos_prec *	z_pmonte
	Temporary coordinates created for the Monte Carlo barostat. More...
double	qbar
	Mass of the piston. More...
double	vbar
	Velocity of the isotropic piston. More...
double	vbar_matrix [3][3]
	Velocity matrix of the anisotropic piston. More...
grad_prec *	gx1
	Gradient for the fast RESPA energy terms. More...
grad_prec *	gy1
	Gradient for the fast RESPA energy terms. More...
grad_prec *	gz1
	Gradient for the fast RESPA energy terms. More...
grad_prec *	gx2
	Gradient for the slow RESPA energy terms. More...
grad_prec *	gy2
	Gradient for the slow RESPA energy terms. More...
grad_prec *	gz2
	Gradient for the slow RESPA energy terms. More...
vel_prec *	vx
	Velocities. More...
vel_prec *	vy
	Velocities. More...
vel_prec *	vz
	Velocities. More...
pos_prec	rateps
int	nratwt
int(*	iratwt )[3]
pos_prec(*	kratwt )[3]
int	nratch
int(*	iratch )[2]
pos_prec *	kratch
int	nratch2
int(*	iratch2 )[3]
pos_prec(*	kratch2 )[2]
int	nratch3
int(*	iratch3 )[4]
pos_prec(*	kratch3 )[3]
int	nrat
int(*	irat )[2]
pos_prec *	krat
int	nratmol
int(*	iratmol )[2]
pos_prec *	rattle_xold
pos_prec *	rattle_yold
pos_prec *	rattle_zold
Molecule	rattle_dmol
pos_prec *	ratcom_x
pos_prec *	ratcom_y
pos_prec *	ratcom_z
vel_prec *	ratcom_vx
vel_prec *	ratcom_vy
vel_prec *	ratcom_vz
double *	ratcom_massfrac
energy_prec	hc_eksum
energy_prec	hc_ekin [3][3]
virial_prec	hc_vir [9]
VirialBuffer	hc_vir_buf
using	real2 = float2
using	real3 = float3
using	real4 = float4
__device__ real3	operator- (real3 a)
__device__ real3	operator+ (real3 a, real3 b)
__device__ real3	operator- (real3 a, real3 b)
__device__ real3	operator* (real a, real3 b)
__device__ real3	operator* (real3 b, real a)
__device__ void	operator+= (real3 &a, real3 b)
__device__ void	operator-= (real3 &a, real3 b)
__device__ void	operator*= (real3 &a, real b)
__device__ real	dot3 (real3 a, real3 b)
__device__ real	dot3 (real3 a, real bx, real by, real bz)
__device__ real	dot3 (real ax, real ay, real az, real3 b)
__device__ real	dot3 (real ax, real ay, real az, real bx, real by, real bz)
__device__ real3	matvec (real xx, real xy, real xz, real yy, real yz, real zz, real3 v)
__device__ real3	cross (real ax, real ay, real az, real bx, real by, real bz)
__device__ real3	cross (real ax, real ay, real az, real3 b)
__device__ real3	cross (real3 a, real bx, real by, real bz)
__device__ real3	cross (real3 a, real3 b)
constexpr int	BOUNDS_EVERY_X_STEPS = 500
	Calls bounds() at least every x steps in MD. More...
void	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	mdPos (time_prec dt)
	Calls bounds() at least every x steps in MD. More...
void	mdPosAxbv (pos_prec a, pos_prec b)
	Updates x, y, z via \( r = a r + b v \). More...
void	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	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	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	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	mdVelScale (vel_prec scal, int nelem, vel_prec *vx0, vel_prec *vy0, vel_prec *vz0)
	Updates velocities via \( v = s v \). More...
void	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	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...

Enumeration Type Documentation

anonymous enum

anonymous enum

Enumerator
MPL_PME_0
MPL_PME_X
MPL_PME_Y
MPL_PME_Z
MPL_PME_XX
MPL_PME_YY
MPL_PME_ZZ
MPL_PME_XY
MPL_PME_XZ
MPL_PME_YZ
MPL_TOTAL
MPL_PME_YX
MPL_PME_ZX
MPL_PME_ZY
LFRM_NONE
LFRM_Z_ONLY
LFRM_Z_THEN_X
LFRM_BISECTOR
LFRM_Z_BISECT
LFRM_3_FOLD

Chgpen

enum class tinker::Chgpen

strong

Enumerator
NONE
GORDON1	HIPPO.
GORDON2	AMOEBA Plus.

CrdFormat

enum class tinker::CrdFormat

strong

Enumerator
NONE
TXYZ1
TXYZ2_PBC
DCD

ExpolScr

enum class tinker::ExpolScr

strong

Enumerator
NONE
S2U
S2
G

UPred

enum class tinker::UPred

strong

Enumerator
NONE
GEAR
ASPC
LSQR

Function Documentation

alterpol()

void tinker::alterpol	(	real(*)	polscale[3][3],
		real(*)	polinv[3][3]
	)

bsplgen2()

template<int LEVEL, int bsorder>

__device__ void tinker::bsplgen2	(	real	w,
		real *__restrict__	thetai,
		int	k,
		int	padded_n,
		volatile real *__restrict__	bsbuild_
	)

chkpoleAtomI()

__device__ void tinker::chkpoleAtomI ( int  i, real(*)  pole[MPL_TOTAL], LocalFrame *  zaxis, const real *__restrict__  x, const real *__restrict__  y, const real *__restrict__  z  )

inline

damp_aplus3()

__device__ void tinker::damp_aplus3 ( real  r, real  pdi, real  ddi, real  pdk, real  ddk, real &__restrict__  scale3, real &__restrict__  scale5, real &__restrict__  scale7  )

inline

damp_aplus3g()

__device__ void tinker::damp_aplus3g ( real  r, real  rr2, real  xr, real  yr, real  zr, real  pdi, real  ddi, real  pdk, real  ddk, real &__restrict__  scale31, real &__restrict__  scale51, real &__restrict__  scale71, real &__restrict__  rc31, real &__restrict__  rc32, real &__restrict__  rc33, real &__restrict__  rc51, real &__restrict__  rc52, real &__restrict__  rc53, real &__restrict__  rc71, real &__restrict__  rc72, real &__restrict__  rc73  )

inline

damp_dir()

__device__ void tinker::damp_dir ( real *__restrict__  dmpi, real *__restrict__  dmpk, real  r, real  alphai, real  alphak  )

inline

damp_ewald()

template<int order>

__device__ void tinker::damp_ewald ( real *__restrict__  bn, real  r, real  rinv, real  rr2, real  aewald  )

inline

damp_expl()

template<bool DO_G>

__device__ void tinker::damp_expl ( ExpolScr  scrtyp, real &__restrict__  s2, real &__restrict__  ds2, real  r, real  sizik, real  alphai, real  alphak  )

inline

damp_gordon1()

template<int DirOrder, int MutOrder>

__device__ void tinker::damp_gordon1 ( real *__restrict__  dmpij, real *__restrict__  dmpi, real *__restrict__  dmpj, real  r, real  ai, real  aj  )

inline

damp_gordon2()

template<int ORDER>

__device__ void tinker::damp_gordon2 ( real *__restrict__  dmpik, real *__restrict__  dmpi, real *__restrict__  dmpk, real  r, real  alphai, real  alphak  )

inline

damp_hippodisp()

template<int DO_G>

__device__ void tinker::damp_hippodisp ( real *__restrict__  dmpij, real  r, real  rr1, real  ai, real  aj  )

inline

damp_mut()

__device__ void tinker::damp_mut ( real *__restrict__  dmpik, real  r, real  alphai, real  alphak  )

inline

damp_pole_deprecated()

template<int ORDER>

__device__ void tinker::damp_pole_deprecated ( real *__restrict__  dmpik, real *__restrict__  dmpi, real *__restrict__  dmpk, real  r, real  alphai, real  alphak  )

inline

deprecated

damp_pole_v2()

template<int order>

__device__ void tinker::damp_pole_v2 ( real *__restrict__  dmpij, real *__restrict__  dmpi, real *__restrict__  dmpj, real  r, real  ai, real  aj  )

inline

damp_rep()

template<int order>

__device__ void tinker::damp_rep ( real *__restrict__  dmpik, real  r, real  rr1, real  r2, real  rr3, real  rr5, real  rr7, real  rr9, real  rr11, real  ai, real  aj  )

inline

rr1: 1/r ai: dmpi aj: dmpk

damp_rep_deprecated()

template<int order>

__device__ void tinker::damp_rep_deprecated ( real *__restrict__  dmpik, real  r, real  rinv, real  r2, real  rr3, real  rr5, real  rr7, real  rr9, real  rr11, real  dmpi, real  dmpk  )

inline

deprecated

damp_thole2()

__device__ void tinker::damp_thole2 ( real  r, real  pdi, real  pti, real  pdk, real  ptk, real &__restrict__  scale3, real &__restrict__  scale5  )

inline

damp_thole3()

__device__ void tinker::damp_thole3 ( real  r, real  pdi, real  pti, real  pdk, real  ptk, real &__restrict__  scale3, real &__restrict__  scale5, real &__restrict__  scale7  )

inline

damp_thole3g()

__device__ void tinker::damp_thole3g ( real  r, real  rr2, real  xr, real  yr, real  zr, real  pdi, real  pti, real  pdk, real  ptk, real &__restrict__  scale31, real &__restrict__  scale51, real &__restrict__  scale71, real &__restrict__  rc31, real &__restrict__  rc32, real &__restrict__  rc33, real &__restrict__  rc51, real &__restrict__  rc52, real &__restrict__  rc53, real &__restrict__  rc71, real &__restrict__  rc72, real &__restrict__  rc73  )

inline

damp_thole4()

__device__ void tinker::damp_thole4 ( real  r, real  pdi, real  pti, real  pdk, real  ptk, real &__restrict__  ex3, real &__restrict__  ex5, real &__restrict__  ex7, real &__restrict__  ex9  )

inline

dexpol()

void tinker::dexpol

(

int

vers

)

dfieldAplus()

void tinker::dfieldAplus

(

real(*)

field[3]

)

dk_angle()

template<class Ver >

__device__ void tinker::dk_angle	(	real &__restrict__	e,
		real &__restrict__	vxx,
		real &__restrict__	vyx,
		real &__restrict__	vzx,
		real &__restrict__	vyy,
		real &__restrict__	vzy,
		real &__restrict__	vzz,
		grad_prec *__restrict__	deax,
		grad_prec *__restrict__	deay,
		grad_prec *__restrict__	deaz,
		const Angle *__restrict__	angtyp,
		real	angunit,
		int	i,
		const int(*)	iang[4],
		const real *__restrict__	anat,
		const real *__restrict__	ak,
		const real *__restrict__	afld,
		real	cang,
		real	qang,
		real	pang,
		real	sang,
		const real *__restrict__	x,
		const real *__restrict__	y,
		const real *__restrict__	z
	)

Comment Zhi Wang, July 1, 2019

The original Tinker implementation has following expressions xip = xib + xt * delta xap = xia - xip

And they were reorganized to xap = xia - xib - xt * delta for higher accuracy in the single precision mode.

Consider an example where xia = 33.553368, xib = 34.768604 xt = 0.33142909, delta = 0.0044494048, the later expression gives a better numerical result.

dk_angtor()

template<class Ver >

__device__ void tinker::dk_angtor	(	real &__restrict__	e,
		real &__restrict__	vxx,
		real &__restrict__	vyx,
		real &__restrict__	vzx,
		real &__restrict__	vyy,
		real &__restrict__	vzy,
		real &__restrict__	vzz,
		grad_prec *__restrict__	deatx,
		grad_prec *__restrict__	deaty,
		grad_prec *__restrict__	deatz,
		real	atorunit,
		int	iangtor,
		const int(*)	iat[3],
		const real(*)	kant[6],
		const real *__restrict__	anat,
		const int(*)	itors[4],
		const real(*)	tors1[4],
		const real(*)	tors2[4],
		const real(*)	tors3[4],
		const real *__restrict__	x,
		const real *__restrict__	y,
		const real *__restrict__	z
	)

dk_bond()

template<class Ver >

__device__ void tinker::dk_bond	(	real &__restrict__	e,
		real &__restrict__	vxx,
		real &__restrict__	vyx,
		real &__restrict__	vzx,
		real &__restrict__	vyy,
		real &__restrict__	vzy,
		real &__restrict__	vzz,
		grad_prec *__restrict__	debx,
		grad_prec *__restrict__	deby,
		grad_prec *__restrict__	debz,
		Bond	bndtyp,
		real	bndunit,
		int	i,
		const int(*)	ibnd[2],
		const real *__restrict__	bl,
		const real *__restrict__	bk,
		real	cbnd,
		real	qbnd,
		const real *__restrict__	x,
		const real *__restrict__	y,
		const real *__restrict__	z
	)

dk_geom_angle()

template<class Ver >

__device__ void tinker::dk_geom_angle	(	real &__restrict__	e,
		real &__restrict__	vxx,
		real &__restrict__	vyx,
		real &__restrict__	vzx,
		real &__restrict__	vyy,
		real &__restrict__	vzy,
		real &__restrict__	vzz,
		grad_prec *__restrict__	degx,
		grad_prec *__restrict__	degy,
		grad_prec *__restrict__	degz,
		int	i,
		const int(*)	iafix[3],
		const real(*)	afix[3],
		const real *__restrict__	x,
		const real *__restrict__	y,
		const real *__restrict__	z
	)

dk_geom_distance()

template<class Ver >

__device__ void tinker::dk_geom_distance	(	real &__restrict__	e,
		real &__restrict__	vxx,
		real &__restrict__	vyx,
		real &__restrict__	vzx,
		real &__restrict__	vyy,
		real &__restrict__	vzy,
		real &__restrict__	vzz,
		grad_prec *__restrict__	degx,
		grad_prec *__restrict__	degy,
		grad_prec *__restrict__	degz,
		int	i,
		const int(*)	idfix[2],
		const real(*)	dfix[3],
		const real *__restrict__	x,
		const real *__restrict__	y,
		const real *__restrict__	z,
		const int *__restrict__	molec,
		BoxShape	box_shape,
		real3	lvec1,
		real3	lvec2,
		real3	lvec3,
		real3	recipa,
		real3	recipb,
		real3	recipc
	)

dk_geom_group()

template<class Ver >

__device__ void tinker::dk_geom_group	(	real &__restrict__	e,
		real &__restrict__	vxx,
		real &__restrict__	vyx,
		real &__restrict__	vzx,
		real &__restrict__	vyy,
		real &__restrict__	vzy,
		real &__restrict__	vzz,
		grad_prec *__restrict__	degx,
		grad_prec *__restrict__	degy,
		grad_prec *__restrict__	degz,
		int	i,
		const int(*)	igfix[2],
		const real(*)	gfix[3],
		const real *__restrict__	x,
		const real *__restrict__	y,
		const real *__restrict__	z,
		const double *__restrict__	mass,
		const int *__restrict__	molec,
		const int(*)	igrp[2],
		const int *__restrict__	kgrp,
		const double *__restrict__	grpmass,
		BoxShape	box_shape,
		real3	lvec1,
		real3	lvec2,
		real3	lvec3,
		real3	recipa,
		real3	recipb,
		real3	recipc
	)

dk_geom_position()

template<class Ver >

__device__ void tinker::dk_geom_position	(	real &__restrict__	e,
		real &__restrict__	vxx,
		real &__restrict__	vyx,
		real &__restrict__	vzx,
		real &__restrict__	vyy,
		real &__restrict__	vzy,
		real &__restrict__	vzz,
		grad_prec *__restrict__	degx,
		grad_prec *__restrict__	degy,
		grad_prec *__restrict__	degz,
		int	i,
		const int *__restrict__	ipfix,
		const int(*)	kpfix[3],
		const real *__restrict__	xpfix,
		const real *__restrict__	ypfix,
		const real *__restrict__	zpfix,
		const real(*)	pfix[2],
		const real *__restrict__	x,
		const real *__restrict__	y,
		const real *__restrict__	z,
		BoxShape	box_shape,
		real3	lvec1,
		real3	lvec2,
		real3	lvec3,
		real3	recipa,
		real3	recipb,
		real3	recipc
	)

dk_geom_torsion()

template<class Ver >

__device__ void tinker::dk_geom_torsion	(	real &__restrict__	e,
		real &__restrict__	vxx,
		real &__restrict__	vyx,
		real &__restrict__	vzx,
		real &__restrict__	vyy,
		real &__restrict__	vzy,
		real &__restrict__	vzz,
		grad_prec *__restrict__	degx,
		grad_prec *__restrict__	degy,
		grad_prec *__restrict__	degz,
		int	i,
		const int(*)	itfix[4],
		const real(*)	tfix[3],
		const real *__restrict__	x,
		const real *__restrict__	y,
		const real *__restrict__	z
	)

dk_improp()

template<class Ver >

__device__ void tinker::dk_improp	(	real &__restrict__	e,
		real &__restrict__	vxx,
		real &__restrict__	vyx,
		real &__restrict__	vzx,
		real &__restrict__	vyy,
		real &__restrict__	vzy,
		real &__restrict__	vzz,
		grad_prec *__restrict__	deidx,
		grad_prec *__restrict__	deidy,
		grad_prec *__restrict__	deidz,
		real	idihunit,
		int	i,
		const int(*)	iiprop[4],
		const real *__restrict__	kprop,
		const real *__restrict__	vprop,
		const real *__restrict__	x,
		const real *__restrict__	y,
		const real *__restrict__	z
	)

dk_imptor()

template<class Ver >

__device__ void tinker::dk_imptor	(	real &__restrict__	e,
		real &__restrict__	vxx,
		real &__restrict__	vyx,
		real &__restrict__	vzx,
		real &__restrict__	vyy,
		real &__restrict__	vzy,
		real &__restrict__	vzz,
		grad_prec *__restrict__	deitx,
		grad_prec *__restrict__	deity,
		grad_prec *__restrict__	deitz,
		real	itorunit,
		int	i,
		const int(*)	iitors[4],
		const real(*)	itors1[4],
		const real(*)	itors2[4],
		const real(*)	itors3[4],
		const real *__restrict__	x,
		const real *__restrict__	y,
		const real *__restrict__	z
	)

dk_opbend()

template<class Ver >

__device__ void tinker::dk_opbend	(	real &__restrict__	e,
		real &__restrict__	vxx,
		real &__restrict__	vyx,
		real &__restrict__	vzx,
		real &__restrict__	vyy,
		real &__restrict__	vzy,
		real &__restrict__	vzz,
		grad_prec *__restrict__	deopbx,
		grad_prec *__restrict__	deopby,
		grad_prec *__restrict__	deopbz,
		OPBend	opbtyp,
		real	opbunit,
		int	iopbend,
		const int *__restrict__	iopb,
		const real *__restrict__	opbk,
		const int(*)	iang[4],
		real	copb,
		real	qopb,
		real	popb,
		real	sopb,
		const real *__restrict__	x,
		const real *__restrict__	y,
		const real *__restrict__	z
	)

Comments Zhi Wang, Jun 25, 2019

The original implementation in Tinker uses ACOS(cosine) to calculate the out-of-plane angle, which is the major source of error in the single precision mode.

These angles (theta) are usually very small (e.g. 0.001 rad), so the value of variable cosine is very close to 1 (cosine = SQRT(1 - eps**2)). As a result, it is much more accurate to use theta = ASIN(eps) instead of theta = ACOS(cosine) to calculate the angles.

dk_pitors()

template<class Ver >

__device__ void tinker::dk_pitors	(	real &__restrict__	e,
		real &__restrict__	vxx,
		real &__restrict__	vyx,
		real &__restrict__	vzx,
		real &__restrict__	vyy,
		real &__restrict__	vzy,
		real &__restrict__	vzz,
		grad_prec *__restrict__	deptx,
		grad_prec *__restrict__	depty,
		grad_prec *__restrict__	deptz,
		real	ptorunit,
		int	i,
		const int(*)	ipit[6],
		const real *__restrict__	kpit,
		const real *__restrict__	x,
		const real *__restrict__	y,
		const real *__restrict__	z
	)

dk_settle1()

template<class HTYPE >

__device__ void tinker::dk_settle1	(	time_prec	dt,
		int	iw,
		const pos_prec *__restrict__	xold,
		const pos_prec *__restrict__	yold,
		const pos_prec *__restrict__	zold,
		pos_prec *__restrict__	xnew,
		pos_prec *__restrict__	ynew,
		pos_prec *__restrict__	znew,
		vel_prec *__restrict__	vx,
		vel_prec *__restrict__	vy,
		vel_prec *__restrict__	vz,
		const double *__restrict__	mass,
		const int(*)	iratwt[3],
		const pos_prec(*)	kratwt[3]
	)

dk_settle2()

template<bool DO_V>

__device__ void tinker::dk_settle2	(	time_prec	dt,
		int	iw,
		vel_prec *__restrict__	vx,
		vel_prec *__restrict__	vy,
		vel_prec *__restrict__	vz,
		const pos_prec *__restrict__	xpos,
		const pos_prec *__restrict__	ypos,
		const pos_prec *__restrict__	zpos,
		const double *__restrict__	mass,
		const int(*)	iratwt[3],
		double &__restrict__	vxx,
		double &__restrict__	vyx,
		double &__restrict__	vzx,
		double &__restrict__	vyy,
		double &__restrict__	vzy,
		double &__restrict__	vzz
	)

dk_strbnd()

template<class Ver >

__device__ void tinker::dk_strbnd	(	real &__restrict__	e,
		real &__restrict__	vxx,
		real &__restrict__	vyx,
		real &__restrict__	vzx,
		real &__restrict__	vyy,
		real &__restrict__	vzy,
		real &__restrict__	vzz,
		grad_prec *__restrict__	debax,
		grad_prec *__restrict__	debay,
		grad_prec *__restrict__	debaz,
		real	stbnunit,
		int	istrbnd,
		const int(*)	isb[3],
		const real(*)	sbk[2],
		const real *__restrict__	bl,
		const int(*)	iang[4],
		const real *__restrict__	anat,
		const real *__restrict__	x,
		const real *__restrict__	y,
		const real *__restrict__	z
	)

dk_strtor()

template<class Ver >

__device__ void tinker::dk_strtor	(	real &__restrict__	e,
		real &__restrict__	vxx,
		real &__restrict__	vyx,
		real &__restrict__	vzx,
		real &__restrict__	vyy,
		real &__restrict__	vzy,
		real &__restrict__	vzz,
		grad_prec *__restrict__	debtx,
		grad_prec *__restrict__	debty,
		grad_prec *__restrict__	debtz,
		real	storunit,
		int	istrtor,
		const int(*)	ist[4],
		const real(*)	kst[9],
		const real *__restrict__	bl,
		const int(*)	itors[4],
		const real(*)	tors1[4],
		const real(*)	tors2[4],
		const real(*)	tors3[4],
		const real *__restrict__	x,
		const real *__restrict__	y,
		const real *__restrict__	z
	)

dk_tors()

template<class Ver >

__device__ void tinker::dk_tors	(	real &__restrict__	e,
		real &__restrict__	vxx,
		real &__restrict__	vyx,
		real &__restrict__	vzx,
		real &__restrict__	vyy,
		real &__restrict__	vzy,
		real &__restrict__	vzz,
		grad_prec *__restrict__	detx,
		grad_prec *__restrict__	dety,
		grad_prec *__restrict__	detz,
		real	torsunit,
		int	i,
		const int(*)	itors[4],
		const real(*)	tors1[4],
		const real(*)	tors2[4],
		const real(*)	tors3[4],
		const real(*)	tors4[4],
		const real(*)	tors5[4],
		const real(*)	tors6[4],
		const real *__restrict__	x,
		const real *__restrict__	y,
		const real *__restrict__	z
	)

dk_tortor()

template<class Ver >

__device__ void tinker::dk_tortor	(	real &__restrict__	e,
		real &__restrict__	vxx,
		real &__restrict__	vyx,
		real &__restrict__	vzx,
		real &__restrict__	vyy,
		real &__restrict__	vzy,
		real &__restrict__	vzz,
		grad_prec *__restrict__	dettx,
		grad_prec *__restrict__	detty,
		grad_prec *__restrict__	dettz,
		real	ttorunit,
		int	itortor,
		const int(*)	itt[3],
		const int(*)	ibitor[5],
		const int *__restrict__	chkttor_ia_,
		const int *__restrict__	tnx,
		const int *__restrict__	tny,
		const real(*)	ttx[ktrtor::maxtgrd],
		const real(*)	tty[ktrtor::maxtgrd],
		const real(*)	tbf[ktrtor::maxtgrd2],
		const real(*)	tbx[ktrtor::maxtgrd2],
		const real(*)	tby[ktrtor::maxtgrd2],
		const real(*)	tbxy[ktrtor::maxtgrd2],
		const real *__restrict__	x,
		const real *__restrict__	y,
		const real *__restrict__	z
	)

dk_urey()

template<class Ver >

__device__ void tinker::dk_urey	(	real &__restrict__	e,
		real &__restrict__	vxx,
		real &__restrict__	vyx,
		real &__restrict__	vzx,
		real &__restrict__	vyy,
		real &__restrict__	vzy,
		real &__restrict__	vzz,
		grad_prec *__restrict__	deubx,
		grad_prec *__restrict__	deuby,
		grad_prec *__restrict__	deubz,
		real	ureyunit,
		int	i,
		const int(*)	iury[3],
		const real *__restrict__	uk,
		const real *__restrict__	ul,
		real	cury,
		real	qury,
		const real *__restrict__	x,
		const real *__restrict__	y,
		const real *__restrict__	z
	)

dmpthole2_a()

__device__ void tinker::dmpthole2_a ( real  r, real  pgamma, real  pdi, real  pdk, real &__restrict__  scale3, real &__restrict__  scale5  )

inline

dmpthole3_a()

__device__ void tinker::dmpthole3_a ( real  r, real  pgamma, real  pdi, real  pdk, real &__restrict__  scale3, real &__restrict__  scale5, real &__restrict__  scale7  )

inline

dmpthole3g_a()

__device__ void tinker::dmpthole3g_a ( real  r, real  rr2, real  xr, real  yr, real  zr, real  pgamma, real  pdi, real  pdk, real &__restrict__  scale31, real &__restrict__  scale51, real &__restrict__  scale71, real &__restrict__  rc31, real &__restrict__  rc32, real &__restrict__  rc33, real &__restrict__  rc51, real &__restrict__  rc52, real &__restrict__  rc53, real &__restrict__  rc71, real &__restrict__  rc72, real &__restrict__  rc73  )

inline

dmpthole4_a()

__device__ void tinker::dmpthole4_a ( real  r, real  pgamma, real  pdi, real  pdk, real &__restrict__  ex3, real &__restrict__  ex5, real &__restrict__  ex7, real &__restrict__  ex9  )

inline

dotProd_acc() [1/2]

template<class T >

T tinker::dotProd_acc	(	const T *	a,
		const T *	b,
		size_t	nelem,
		int	queue
	)

dotProd_acc() [2/2]

template<class T >

void tinker::dotProd_acc	(	T *	ans,
		const T *	a,
		const T *	b,
		size_t	nelem,
		int	queue
	)

dotProd_cu()

template<class T >

void tinker::dotProd_cu	(	T *	ans,
		const T *	a,
		const T *	b,
		size_t	nelem,
		int	queue
	)

empoleAplusEwald()

void tinker::empoleAplusEwald	(	int	vers,
		int	useCF
	)

empoleAplusNonEwald()

void tinker::empoleAplusNonEwald	(	int	vers,
		int	useCF
	)

empoleChgpenSelf_cu()

template<bool do_a, bool do_e, int CFLX>

__global__ void tinker::empoleChgpenSelf_cu	(	CountBuffer __restrict__	nem,
		EnergyBuffer __restrict__	em,
		const real(*)	rpole[10],
		real *__restrict__	pot,
		int	n,
		real	f,
		real	aewald
	)

empoleSelf_cu()

template<bool do_a>

__global__ void tinker::empoleSelf_cu	(	CountBuffer __restrict__	nem,
		EnergyBuffer __restrict__	em,
		const real(*)	rpole[10],
		int	n,
		real	f,
		real	aewald
	)

epolarAplusEwald()

void tinker::epolarAplusEwald	(	int	vers,
		int	useCF
	)

epolarAplusNonEwald()

void tinker::epolarAplusNonEwald	(	int	vers,
		int	useCF
	)

expolData()

void tinker::expolData

(

RcOp

)

getKV() [1/2]

template<class T >

void tinker::getKV	(	std::string	k,
		std::vector< T > &	v
	)

getKV() [2/2]

template<class T1 , class T2 >

void tinker::getKV	(	std::string	k,
		T1 &	v,
		T2	vIfKNotFound
	)

lf_lpiston_npt()

void tinker::lf_lpiston_npt	(	int	istep,
		time_prec	dt_ps
	)

nextarg() [1/2]

template<size_t Len>

void tinker::nextarg	(	char(&)	str[Len],
		bool &	exist
	)

nextarg() [2/2]

void tinker::nextarg	(	size_t	len,
		char *	str,
		bool &	exist
	)

osrw_altele()

void tinker::osrw_altele

(

double

)

osrw_alttor()

void tinker::osrw_alttor

(

double

)

osrw_altvdw()

void tinker::osrw_altvdw

(

double

)

osrw_energy() [1/2]

void tinker::osrw_energy

(

int

vers

)

osrw_energy() [2/2]

void tinker::osrw_energy	(	int	vers,
		unsigned	tsflag,
		const TimeScaleConfig &	tsconfig
	)

osrw_lam_expr0()

double tinker::osrw_lam_expr0	(	int	form,
		double	lam
	)

osrw_lam_expr1()

double tinker::osrw_lam_expr1	(	int	form,
		double	lam
	)

osrw_lam_expr2()

double tinker::osrw_lam_expr2	(	int	form,
		double	lam
	)

osrw_mech()

void tinker::osrw_mech

(

)

osrwData()

void tinker::osrwData

(

RcOp

)

pair_alterpol()

__device__ void tinker::pair_alterpol ( ExpolScr  scrtyp, real  r, real  pscale, real  cut, real  off, real  xr, real  yr, real  zr, real  springi, real  sizi, real  alphai, real  springk, real  sizk, real  alphak, real  ks2i[3][3], real  ks2k[3][3]  )

inline

pair_charge()

template<class Ver , class ETYP >

__device__ void tinker::pair_charge	(	real	r,
		real	xr,
		real	yr,
		real	zr,
		real	cscale,
		real	chgi,
		real	chgk,
		real	ebuffer,
		real	f,
		real	aewald,
		real	cut,
		real	off,
		real &__restrict__	grdx,
		real &__restrict__	grdy,
		real &__restrict__	grdz,
		int &__restrict__	ctl,
		real &__restrict__	etl,
		real &__restrict__	vtlxx,
		real &__restrict__	vtlxy,
		real &__restrict__	vtlxz,
		real &__restrict__	vtlyy,
		real &__restrict__	vtlyz,
		real &__restrict__	vtlzz
	)

pair_chg_v2()

template<bool DO_G, class ETYP , int SCALE>

__device__ void tinker::pair_chg_v2	(	real	r,
		real	invr,
		real	cscale,
		real	chgi,
		real	chgk,
		real	f,
		real	aewald,
		real	eccut,
		real	ecoff,
		real &__restrict__	ec,
		real &__restrict__	dec
	)

pair_chg_v3()

template<bool DO_G, class ETYP , int SCALE>

__device__ void tinker::pair_chg_v3	(	real	r,
		real	cscale,
		real	chgi,
		real	chgk,
		real	ebuffer,
		real	f,
		real	aewald,
		real	eccut,
		real	ecoff,
		real &__restrict__	ec,
		real &__restrict__	dec
	)

pair_chgtrn()

template<bool DO_G>

__device__ void tinker::pair_chgtrn	(	real	r,
		real	cut,
		real	off,
		real	mscale,
		real	f,
		real	alphai,
		real	chgi,
		real	alphak,
		real	chgk,
		real	elambda,
		e_prec &__restrict__	e,
		e_prec &__restrict__	de
	)

pair_chgtrn_aplus()

template<bool DO_G>

__device__ void tinker::pair_chgtrn_aplus	(	real	r,
		real	cut,
		real	off,
		real	mscale,
		real	f,
		real	alphai,
		real	chgi,
		real	alphak,
		real	chgk,
		real	elambda,
		e_prec &__restrict__	e,
		e_prec &__restrict__	de
	)

pair_dexpol()

__device__ void tinker::pair_dexpol ( ExpolScr  scrtyp, real  r, real  pscale, real  cut, real  off, real  xr, real  yr, real  zr, real  uix, real  uiy, real  uiz, real  ukx, real  uky, real  ukz, real  springi, real  sizi, real  alphai, real  springk, real  sizk, real  alphak, const real  f, real  frc[3]  )

inline

pair_dfield()

template<class ETYP >

__device__ void tinker::pair_dfield	(	real	r2,
		real	xr,
		real	yr,
		real	zr,
		real	dscale,
		real	pscale,
		real	ci,
		real	dix,
		real	diy,
		real	diz,
		real	qixx,
		real	qixy,
		real	qixz,
		real	qiyy,
		real	qiyz,
		real	qizz,
		real	pdi,
		real	pti,
		real	ck,
		real	dkx,
		real	dky,
		real	dkz,
		real	qkxx,
		real	qkxy,
		real	qkxz,
		real	qkyy,
		real	qkyz,
		real	qkzz,
		real	pdk,
		real	ptk,
		real	aewald,
		real3 &__restrict__	fid,
		real3 &__restrict__	fip,
		real3 &__restrict__	fkd,
		real3 &__restrict__	fkp
	)

pair_dfield_aplus()

template<class ETYP >

__device__ void tinker::pair_dfield_aplus	(	real	r2,
		real	xr,
		real	yr,
		real	zr,
		real	dscale,
		real	ci,
		real	dix,
		real	diy,
		real	diz,
		real	pdi,
		real	ddi,
		real	qixx,
		real	qixy,
		real	qixz,
		real	qiyy,
		real	qiyz,
		real	qizz,
		real	ck,
		real	dkx,
		real	dky,
		real	dkz,
		real	pdk,
		real	ddk,
		real	qkxx,
		real	qkxy,
		real	qkxz,
		real	qkyy,
		real	qkyz,
		real	qkzz,
		real	aewald,
		real &__restrict__	fidx,
		real &__restrict__	fidy,
		real &__restrict__	fidz,
		real &__restrict__	fkdx,
		real &__restrict__	fkdy,
		real &__restrict__	fkdz
	)

pair_dfield_aplus_v2()

template<class ETYP >

__device__ void tinker::pair_dfield_aplus_v2	(	real	r2,
		real	xr,
		real	yr,
		real	zr,
		real	dscale,
		real	ci,
		real	dix,
		real	diy,
		real	diz,
		real	pdi,
		real	ddi,
		real	qixx,
		real	qixy,
		real	qixz,
		real	qiyy,
		real	qiyz,
		real	qizz,
		real	ck,
		real	dkx,
		real	dky,
		real	dkz,
		real	pdk,
		real	ddk,
		real	qkxx,
		real	qkxy,
		real	qkxz,
		real	qkyy,
		real	qkyz,
		real	qkzz,
		real	aewald,
		real &__restrict__	fidx,
		real &__restrict__	fidy,
		real &__restrict__	fidz,
		real &__restrict__	fkdx,
		real &__restrict__	fkdy,
		real &__restrict__	fkdz
	)

pair_dfield_chgpen()

template<class ETYP >

__device__ void tinker::pair_dfield_chgpen	(	real	r2,
		real	xr,
		real	yr,
		real	zr,
		real	dscale,
		real	ci,
		real	dix,
		real	diy,
		real	diz,
		real	corei,
		real	vali,
		real	alphai,
		real	qixx,
		real	qixy,
		real	qixz,
		real	qiyy,
		real	qiyz,
		real	qizz,
		real	ck,
		real	dkx,
		real	dky,
		real	dkz,
		real	corek,
		real	valk,
		real	alphak,
		real	qkxx,
		real	qkxy,
		real	qkxz,
		real	qkyy,
		real	qkyz,
		real	qkzz,
		real	aewald,
		real &__restrict__	fidx,
		real &__restrict__	fidy,
		real &__restrict__	fidz,
		real &__restrict__	fkdx,
		real &__restrict__	fkdy,
		real &__restrict__	fkdz
	)

pair_dfield_v2()

template<class ETYP >

__device__ void tinker::pair_dfield_v2	(	real	r2,
		real	xr,
		real	yr,
		real	zr,
		real	dscale,
		real	pscale,
		real	aewald,
		real	ci,
		real	dix,
		real	diy,
		real	diz,
		real	qixx,
		real	qixy,
		real	qixz,
		real	qiyy,
		real	qiyz,
		real	qizz,
		real	pdi,
		real	pti,
		real	ck,
		real	dkx,
		real	dky,
		real	dkz,
		real	qkxx,
		real	qkxy,
		real	qkxz,
		real	qkyy,
		real	qkyz,
		real	qkzz,
		real	pdk,
		real	ptk,
		real &__restrict__	fidx,
		real &__restrict__	fidy,
		real &__restrict__	fidz,
		real &__restrict__	fipx,
		real &__restrict__	fipy,
		real &__restrict__	fipz,
		real &__restrict__	fkdx,
		real &__restrict__	fkdy,
		real &__restrict__	fkdz,
		real &__restrict__	fkpx,
		real &__restrict__	fkpy,
		real &__restrict__	fkpz
	)

pair_disp()

template<bool DO_G, class DTYP , int SCALE, int SOFTCORE>

__device__ void tinker::pair_disp	(	real	r,
		real	r2,
		real	rr1,
		real	dspscale,
		real	aewald,
		real	ci,
		real	ai,
		real	ck,
		real	ak,
		real	vlambda,
		real	edcut,
		real	edoff,
		real &__restrict__	e,
		real &__restrict__	de
	)

pair_disp_obsolete()

template<bool DO_G, class DTYP , int SCALE>

__device__ void tinker::pair_disp_obsolete	(	real	r,
		real	r2,
		real	rr1,
		real	dspscale,
		real	aewald,
		real	ci,
		real	ai,
		real	ck,
		real	ak,
		real	edcut,
		real	edoff,
		real &__restrict__	e,
		real &__restrict__	de
	)

pair_mpole_chgpen()

template<bool do_e, bool do_g, class ETYP , int CFLX>

__device__ void tinker::pair_mpole_chgpen	(	real	r2,
		real	xr,
		real	yr,
		real	zr,
		real	mscale,
		real	ci,
		real	dix,
		real	diy,
		real	diz,
		real	corei,
		real	vali,
		real	alphai,
		real	qixx,
		real	qixy,
		real	qixz,
		real	qiyy,
		real	qiyz,
		real	qizz,
		real	ck,
		real	dkx,
		real	dky,
		real	dkz,
		real	corek,
		real	valk,
		real	alphak,
		real	qkxx,
		real	qkxy,
		real	qkxz,
		real	qkyy,
		real	qkyz,
		real	qkzz,
		real	f,
		real	aewald,
		real &__restrict__	e,
		real &__restrict__	poti,
		real &__restrict__	potk,
		PairMPoleGrad &__restrict__	pgrad
	)

pair_mpole_chgpen_aplus()

template<bool do_e, bool do_g, class ETYP , int CFLX>

__device__ void tinker::pair_mpole_chgpen_aplus	(	real	r2,
		real	xr,
		real	yr,
		real	zr,
		real	mscale,
		real	ci,
		real	dix,
		real	diy,
		real	diz,
		real	corei,
		real	vali,
		real	alphai,
		real	qixx,
		real	qixy,
		real	qixz,
		real	qiyy,
		real	qiyz,
		real	qizz,
		real	ck,
		real	dkx,
		real	dky,
		real	dkz,
		real	corek,
		real	valk,
		real	alphak,
		real	qkxx,
		real	qkxy,
		real	qkxz,
		real	qkyy,
		real	qkyz,
		real	qkzz,
		real	f,
		real	aewald,
		real &__restrict__	e,
		real &__restrict__	poti,
		real &__restrict__	potk,
		PairMPoleGrad &__restrict__	pgrad
	)

pair_mpole_v2()

template<class Ver , class ETYP >

__device__ void tinker::pair_mpole_v2	(	real	r2,
		real	xr,
		real	yr,
		real	zr,
		real	mscale,
		real	ci,
		real	dix,
		real	diy,
		real	diz,
		real	qixx,
		real	qixy,
		real	qixz,
		real	qiyy,
		real	qiyz,
		real	qizz,
		real	ck,
		real	dkx,
		real	dky,
		real	dkz,
		real	qkxx,
		real	qkxy,
		real	qkxz,
		real	qkyy,
		real	qkyz,
		real	qkzz,
		real	f,
		real	aewald,
		real &__restrict__	frcxi,
		real &__restrict__	frcyi,
		real &__restrict__	frczi,
		real &__restrict__	frcxk,
		real &__restrict__	frcyk,
		real &__restrict__	frczk,
		real &__restrict__	trqxi,
		real &__restrict__	trqyi,
		real &__restrict__	trqzi,
		real &__restrict__	trqxk,
		real &__restrict__	trqyk,
		real &__restrict__	trqzk,
		real &__restrict__	e,
		real &__restrict__	vxx,
		real &__restrict__	vxy,
		real &__restrict__	vxz,
		real &__restrict__	vyy,
		real &__restrict__	vyz,
		real &__restrict__	vzz
	)

pair_polar()

template<bool do_e, bool do_g, class ETYP >

__device__ void tinker::pair_polar	(	real	r2,
		real	xr,
		real	yr,
		real	zr,
		real	dscale,
		real	pscale,
		real	uscale,
		real	ci,
		real	dix,
		real	diy,
		real	diz,
		real	qixx,
		real	qixy,
		real	qixz,
		real	qiyy,
		real	qiyz,
		real	qizz,
		real	uix,
		real	uiy,
		real	uiz,
		real	uixp,
		real	uiyp,
		real	uizp,
		real	pdi,
		real	pti,
		real	ck,
		real	dkx,
		real	dky,
		real	dkz,
		real	qkxx,
		real	qkxy,
		real	qkxz,
		real	qkyy,
		real	qkyz,
		real	qkzz,
		real	ukx,
		real	uky,
		real	ukz,
		real	ukxp,
		real	ukyp,
		real	ukzp,
		real	pdk,
		real	ptk,
		real	f,
		real	aewald,
		real &__restrict__	e,
		PairPolarGrad &__restrict__	pgrad
	)

pair_polar_aplus()

template<bool do_e, bool do_g, class ETYP , int CFLX>

__device__ void tinker::pair_polar_aplus	(	real	r2,
		real	xr,
		real	yr,
		real	zr,
		real	dscale,
		real	uscale,
		real	ci,
		real	dix,
		real	diy,
		real	diz,
		real	pdi,
		real	pti,
		real	ddi,
		real	qixx,
		real	qixy,
		real	qixz,
		real	qiyy,
		real	qiyz,
		real	qizz,
		real	uix,
		real	uiy,
		real	uiz,
		real	ck,
		real	dkx,
		real	dky,
		real	dkz,
		real	pdk,
		real	ptk,
		real	ddk,
		real	qkxx,
		real	qkxy,
		real	qkxz,
		real	qkyy,
		real	qkyz,
		real	qkzz,
		real	ukx,
		real	uky,
		real	ukz,
		real	f,
		real	aewald,
		real &__restrict__	e,
		real &__restrict__	poti,
		real &__restrict__	potk,
		PairPolarGrad &__restrict__	pgrad
	)

pair_polar_aplus_v2()

template<class Ver , class ETYP , int CFLX>

__device__ void tinker::pair_polar_aplus_v2	(	real	r2,
		real	xr,
		real	yr,
		real	zr,
		real	dscale,
		real	uscale,
		real	ci,
		real	dix,
		real	diy,
		real	diz,
		real	qixx,
		real	qixy,
		real	qixz,
		real	qiyy,
		real	qiyz,
		real	qizz,
		real	uix,
		real	uiy,
		real	uiz,
		real	pdi,
		real	pti,
		real	ddi,
		real	ck,
		real	dkx,
		real	dky,
		real	dkz,
		real	qkxx,
		real	qkxy,
		real	qkxz,
		real	qkyy,
		real	qkyz,
		real	qkzz,
		real	ukx,
		real	uky,
		real	ukz,
		real	pdk,
		real	ptk,
		real	ddk,
		real	f,
		real	aewald,
		real &__restrict__	frcxi,
		real &__restrict__	frcyi,
		real &__restrict__	frczi,
		real &__restrict__	frcxk,
		real &__restrict__	frcyk,
		real &__restrict__	frczk,
		real &__restrict__	uf0i,
		real &__restrict__	uf1i,
		real &__restrict__	uf2i,
		real &__restrict__	uf0k,
		real &__restrict__	uf1k,
		real &__restrict__	uf2k,
		real &__restrict__	duf0i,
		real &__restrict__	duf1i,
		real &__restrict__	duf2i,
		real &__restrict__	duf3i,
		real &__restrict__	duf4i,
		real &__restrict__	duf5i,
		real &__restrict__	duf0k,
		real &__restrict__	duf1k,
		real &__restrict__	duf2k,
		real &__restrict__	duf3k,
		real &__restrict__	duf4k,
		real &__restrict__	duf5k,
		real &__restrict__	e,
		real &__restrict__	vxx,
		real &__restrict__	vxy,
		real &__restrict__	vxz,
		real &__restrict__	vyy,
		real &__restrict__	vyz,
		real &__restrict__	vzz,
		real &__restrict__	poti,
		real &__restrict__	potk
	)

pair_polar_chgpen()

template<bool do_e, bool do_g, class ETYP , int CFLX>

__device__ void tinker::pair_polar_chgpen	(	real	r2,
		real	xr,
		real	yr,
		real	zr,
		real	dscale,
		real	wscale,
		real	ci,
		real	dix,
		real	diy,
		real	diz,
		real	corei,
		real	vali,
		real	alphai,
		real	qixx,
		real	qixy,
		real	qixz,
		real	qiyy,
		real	qiyz,
		real	qizz,
		real	uix,
		real	uiy,
		real	uiz,
		real	ck,
		real	dkx,
		real	dky,
		real	dkz,
		real	corek,
		real	valk,
		real	alphak,
		real	qkxx,
		real	qkxy,
		real	qkxz,
		real	qkyy,
		real	qkyz,
		real	qkzz,
		real	ukx,
		real	uky,
		real	ukz,
		real	f,
		real	aewald,
		real &__restrict__	e,
		real &__restrict__	poti,
		real &__restrict__	potk,
		PairPolarGrad &__restrict__	pgrad
	)

pair_polar_v2()

template<class Ver , class ETYP >

__device__ void tinker::pair_polar_v2	(	real	r2,
		real	xr,
		real	yr,
		real	zr,
		real	dscale,
		real	pscale,
		real	uscale,
		real	ci,
		real	dix,
		real	diy,
		real	diz,
		real	qixx,
		real	qixy,
		real	qixz,
		real	qiyy,
		real	qiyz,
		real	qizz,
		real	uix,
		real	uiy,
		real	uiz,
		real	uixp,
		real	uiyp,
		real	uizp,
		real	pdi,
		real	pti,
		real	ck,
		real	dkx,
		real	dky,
		real	dkz,
		real	qkxx,
		real	qkxy,
		real	qkxz,
		real	qkyy,
		real	qkyz,
		real	qkzz,
		real	ukx,
		real	uky,
		real	ukz,
		real	ukxp,
		real	ukyp,
		real	ukzp,
		real	pdk,
		real	ptk,
		real	f,
		real	aewald,
		real &__restrict__	frcxi,
		real &__restrict__	frcyi,
		real &__restrict__	frczi,
		real &__restrict__	frcxk,
		real &__restrict__	frcyk,
		real &__restrict__	frczk,
		real &__restrict__	uf0i,
		real &__restrict__	uf1i,
		real &__restrict__	uf2i,
		real &__restrict__	uf0k,
		real &__restrict__	uf1k,
		real &__restrict__	uf2k,
		real &__restrict__	duf0i,
		real &__restrict__	duf1i,
		real &__restrict__	duf2i,
		real &__restrict__	duf3i,
		real &__restrict__	duf4i,
		real &__restrict__	duf5i,
		real &__restrict__	duf0k,
		real &__restrict__	duf1k,
		real &__restrict__	duf2k,
		real &__restrict__	duf3k,
		real &__restrict__	duf4k,
		real &__restrict__	duf5k,
		real &__restrict__	e,
		real &__restrict__	vxx,
		real &__restrict__	vxy,
		real &__restrict__	vxz,
		real &__restrict__	vyy,
		real &__restrict__	vyz,
		real &__restrict__	vzz
	)

pair_repel()

template<bool do_g, int SOFTCORE>

__device__ void tinker::pair_repel	(	real	r2,
		real	rscale,
		real	vlambda,
		real	cut,
		real	off,
		real	xr,
		real	yr,
		real	zr,
		real	sizi,
		real	dmpi,
		real	vali,
		real	ci,
		real	dix,
		real	diy,
		real	diz,
		real	qixx,
		real	qixy,
		real	qixz,
		real	qiyy,
		real	qiyz,
		real	qizz,
		real	sizk,
		real	dmpk,
		real	valk,
		real	ck,
		real	dkx,
		real	dky,
		real	dkz,
		real	qkxx,
		real	qkxy,
		real	qkxz,
		real	qkyy,
		real	qkyz,
		real	qkzz,
		real &__restrict__	e,
		PairRepelGrad &__restrict__	pgrad
	)

pair_ufield()

template<class ETYP >

__device__ void tinker::pair_ufield	(	real	r2,
		real	xr,
		real	yr,
		real	zr,
		real	uscale,
		real	uindi0,
		real	uindi1,
		real	uindi2,
		real	uinpi0,
		real	uinpi1,
		real	uinpi2,
		real	pdi,
		real	pti,
		real	uindk0,
		real	uindk1,
		real	uindk2,
		real	uinpk0,
		real	uinpk1,
		real	uinpk2,
		real	pdk,
		real	ptk,
		real	aewald,
		real3 &__restrict__	fid,
		real3 &__restrict__	fip,
		real3 &__restrict__	fkd,
		real3 &__restrict__	fkp
	)

pair_ufield_aplus()

template<class ETYP >

__device__ void tinker::pair_ufield_aplus	(	real	r2,
		real	xr,
		real	yr,
		real	zr,
		real	uscale,
		real	uindi0,
		real	uindi1,
		real	uindi2,
		real	pdi,
		real	pti,
		real	uindk0,
		real	uindk1,
		real	uindk2,
		real	pdk,
		real	ptk,
		real	aewald,
		real &__restrict__	fidx,
		real &__restrict__	fidy,
		real &__restrict__	fidz,
		real &__restrict__	fkdx,
		real &__restrict__	fkdy,
		real &__restrict__	fkdz
	)

pair_ufield_aplus_v2()

template<class ETYP >

__device__ void tinker::pair_ufield_aplus_v2	(	real	r2,
		real	xr,
		real	yr,
		real	zr,
		real	uscale,
		real	uindi0,
		real	uindi1,
		real	uindi2,
		real	pdi,
		real	pti,
		real	uindk0,
		real	uindk1,
		real	uindk2,
		real	pdk,
		real	ptk,
		real	aewald,
		real &__restrict__	fidx,
		real &__restrict__	fidy,
		real &__restrict__	fidz,
		real &__restrict__	fkdx,
		real &__restrict__	fkdy,
		real &__restrict__	fkdz
	)

pair_ufield_chgpen()

template<class ETYP >

__device__ void tinker::pair_ufield_chgpen	(	real	r2,
		real	xr,
		real	yr,
		real	zr,
		real	wscale,
		real	uindi0,
		real	uindi1,
		real	uindi2,
		real	corei,
		real	vali,
		real	alphai,
		real	uindk0,
		real	uindk1,
		real	uindk2,
		real	corek,
		real	valk,
		real	alphak,
		real	aewald,
		real &__restrict__	fidx,
		real &__restrict__	fidy,
		real &__restrict__	fidz,
		real &__restrict__	fkdx,
		real &__restrict__	fkdy,
		real &__restrict__	fkdz
	)

pair_ufield_v2()

template<class ETYP >

__device__ void tinker::pair_ufield_v2	(	real	r2,
		real	xr,
		real	yr,
		real	zr,
		real	uscale,
		real	aewald,
		real	uindi0,
		real	uindi1,
		real	uindi2,
		real	uinpi0,
		real	uinpi1,
		real	uinpi2,
		real	pdi,
		real	pti,
		real	uindk0,
		real	uindk1,
		real	uindk2,
		real	uinpk0,
		real	uinpk1,
		real	uinpk2,
		real	pdk,
		real	ptk,
		real &__restrict__	fidx,
		real &__restrict__	fidy,
		real &__restrict__	fidz,
		real &__restrict__	fipx,
		real &__restrict__	fipy,
		real &__restrict__	fipz,
		real &__restrict__	fkdx,
		real &__restrict__	fkdy,
		real &__restrict__	fkdz,
		real &__restrict__	fkpx,
		real &__restrict__	fkpy,
		real &__restrict__	fkpz
	)

reduce()

template<class T , unsigned int B, class Op >

__global__ void tinker::reduce	(	T *	g_odata,
		const T *	g_idata,
		size_t	n,
		Op	op = Op()
	)

reduce2()

template<class T , unsigned int B, unsigned int HN, size_t N, class Op >

__global__ void tinker::reduce2	(	T(*)	g_odata[HN],
		const T(*)	g_idata[N],
		size_t	n,
		Op	op = Op()
	)

reduceSum2_acc()

template<class HT , size_t HN, class DPTR >

void tinker::reduceSum2_acc	(	HT(&)	h_ans[HN],
		DPTR	v,
		size_t	nelem,
		int	queue
	)

reduceSum2_cu()

template<class HT , size_t HN, class DPTR >

void tinker::reduceSum2_cu	(	HT(&)	h_ans[HN],
		DPTR	v,
		size_t	nelem,
		int	queue
	)

reduceSum2OnDevice_acc()

template<class HT , size_t HN, class DPTR >

void tinker::reduceSum2OnDevice_acc	(	HT(&)	[HN],
		DPTR	,
		size_t	,
		int
	)

reduceSum2OnDevice_cu()

template<class HT , size_t HN, class DPTR >

void tinker::reduceSum2OnDevice_cu	(	HT(&)	[HN],
		DPTR	,
		size_t	,
		int
	)

reduceSum_acc()

template<class T >

T tinker::reduceSum_acc	(	const T *	gpu_a,
		size_t	nelem,
		int	queue
	)

reduceSum_cu()

template<class T >

T tinker::reduceSum_cu	(	const T *	a,
		size_t	nelem,
		int	queue
	)

reduceSumOnDevice_acc()

template<class T >

void tinker::reduceSumOnDevice_acc	(	T *	,
		const T *	,
		size_t	,
		int
	)

reduceSumOnDevice_cu()

template<class T >

void tinker::reduceSumOnDevice_cu	(	T *	,
		const T *	,
		size_t	,
		int
	)

rotpoleAddBy()

__device__ void tinker::rotpoleAddBy ( real *__restrict__  a, const real *__restrict__  b  )

inline

rotpoleAddBy2()

__device__ void tinker::rotpoleAddBy2 ( real *__restrict__  a, const real *__restrict__  b, const real *__restrict__  c  )

inline

rotpoleAtomI()

__device__ void tinker::rotpoleAtomI ( int  i, real(*)  rpole[MPL_TOTAL], const real(*)  pole[MPL_TOTAL], const LocalFrame *__restrict__  zaxis, const real *__restrict__  x, const real *__restrict__  y, const real *__restrict__  z  )

inline

rotpoleNorm()

__device__ void tinker::rotpoleNorm ( real *  a )

inline

rotsite()

__device__ void tinker::rotsite ( int  isite, const real(*)  a[3], real(*)  rpole[10], const real(*)  pole[10]  )

inline

scaleArray_acc()

template<class T >

void tinker::scaleArray_acc	(	T *	dst,
		T	scal,
		size_t	nelem,
		int	queue
	)

scaleArray_cu()

template<class T >

void tinker::scaleArray_cu	(	T *	dst,
		T	scal,
		size_t	nelem,
		int	queue
	)

sparsePrecondApply3()

void tinker::sparsePrecondApply3	(	const real(*)	rsd[3],
		real(*)	zrsd[3]
	)

torqueCross()

__device__ void tinker::torqueCross ( real *__restrict__  ans, const real *__restrict__  u, const real *__restrict__  v  )

inline

torqueDot()

__device__ real tinker::torqueDot ( const real *__restrict__  a, const real *__restrict__  b  )

inline

torqueNormal()

__device__ void tinker::torqueNormal ( real *__restrict__  a, real  _1_na  )

inline

tri_to_xy()

__device__ void tinker::tri_to_xy ( int  f, int &  x, int &  y  )

inline

ufieldAplus()

void tinker::ufieldAplus	(	const real(*)	uind[3],
		real(*)	field[3]
	)

warp_reduce()

template<class T , unsigned int B, class Op >

__device__ void tinker::warp_reduce ( volatile T *  sd, unsigned int  t, Op  op  )

inline

warp_reduce2()

template<class T , unsigned int HN, unsigned int B, class Op >

__device__ void tinker::warp_reduce2 ( volatile T(*)  sd[B], unsigned int  t, Op  op  )

inline

xy_to_tri()

__device__ int tinker::xy_to_tri ( int  x, int  y  )

inline

zero() [1/3]

__device__ void tinker::zero ( PairMPoleGrad &  pgrad )

inline

zero() [2/3]

__device__ void tinker::zero ( PairPolarGrad &  pgrad )

inline

zero() [3/3]

__device__ void tinker::zero ( PairRepelGrad &  pgrad )

inline

zeroOnDevice3Async_acc() [1/2]

template<class T >

void tinker::zeroOnDevice3Async_acc	(	int	nelem,
		T *	a1,
		T *	a2,
		T *	a3
	)

zeroOnDevice3Async_acc() [2/2]

template<class T , int N>

void tinker::zeroOnDevice3Async_acc	(	int	nelem,
		T(*)	a1[N],
		T(*)	a2[N],
		T(*)	a3[N]
	)

zeroOnDevice3Async_cu() [1/2]

template<class T >

void tinker::zeroOnDevice3Async_cu	(	int	nelem,
		T *	a1,
		T *	a2,
		T *	a3
	)

zeroOnDevice3Async_cu() [2/2]

template<class T , int N>

void tinker::zeroOnDevice3Async_cu	(	int	nelem,
		T(*)	a1[N],
		T(*)	a2[N],
		T(*)	a3[N]
	)

zeroOnDevice9Async_acc()

template<class T >

void tinker::zeroOnDevice9Async_acc	(	int	nelem,
		T *	a1,
		T *	a2,
		T *	a3,
		T *	a4,
		T *	a5,
		T *	a6,
		T *	a7,
		T *	a8,
		T *	a9
	)

zeroOnDevice9Async_cu()

template<class T >

void tinker::zeroOnDevice9Async_cu	(	int	nelem,
		T *	a1,
		T *	a2,
		T *	a3,
		T *	a4,
		T *	a5,
		T *	a6,
		T *	a7,
		T *	a8,
		T *	a9
	)

Variable Documentation

abflx

real(* tinker::abflx)[2]

extern

adisp

real* tinker::adisp

extern

aflx

real(* tinker::aflx)[2]

extern

atom_eps

real* tinker::atom_eps

extern

atom_rad

real* tinker::atom_rad

extern

atomic

int* tinker::atomic

extern

balist

int(* tinker::balist)[2]

extern

bflx

real* tinker::bflx

extern

c2scale

real tinker::c2scale

extern

c3scale

real tinker::c3scale

c4scale

real tinker::c4scale

c5scale

real tinker::c5scale

cexclude

int(* tinker::cexclude)[2]

extern

cexclude_scale

real* tinker::cexclude_scale

extern

chg_coalesced

real* tinker::chg_coalesced

extern

chgct

real* tinker::chgct

extern

csix

real* tinker::csix

extern

csixpr

real tinker::csixpr

extern

ctrntyp

Chgtrn tinker::ctrntyp

extern

cvexclude

int(* tinker::cvexclude)[2]

extern

cvexclude_scale

real(* tinker::cvexclude_scale)[2]

extern

d1scale

real tinker::d1scale

extern

d2scale

real tinker::d2scale

extern

d3scale

real tinker::d3scale

extern

d4scale

real tinker::d4scale

extern

decfx

real* tinker::decfx

extern

decfy

real* tinker::decfy

extern

decfz

real* tinker::decfz

extern

dectx

grad_prec* tinker::dectx

extern

decty

grad_prec* tinker::decty

extern

dectz

grad_prec* tinker::dectz

extern

decx

grad_prec* tinker::decx

extern

decy

grad_prec* tinker::decy

extern

decz

grad_prec* tinker::decz

extern

dedspx

grad_prec* tinker::dedspx

extern

dedspy

grad_prec* tinker::dedspy

extern

dedspz

grad_prec* tinker::dedspz

extern

demx

grad_prec* tinker::demx

extern

demy

grad_prec* tinker::demy

extern

demz

grad_prec* tinker::demz

extern

depx

grad_prec* tinker::depx

extern

depy

grad_prec* tinker::depy

extern

depz

grad_prec* tinker::depz

extern

derx

grad_prec* tinker::derx

extern

dery

grad_prec* tinker::dery

extern

derz

grad_prec* tinker::derz

extern

devx

grad_prec* tinker::devx

extern

devy

grad_prec* tinker::devy

extern

devz

grad_prec* tinker::devz

extern

dirdamp

real* tinker::dirdamp

extern

dmpct

real* tinker::dmpct

extern

dmppep

real* tinker::dmppep

extern

dmppr

real* tinker::dmppr

extern

dpexclude

int(* tinker::dpexclude)[2]

extern

dpexclude_scale

real(* tinker::dpexclude_scale)[2]

extern

dpuexclude

int(* tinker::dpuexclude)[2]

extern

dpuexclude_scale

real(* tinker::dpuexclude_scale)[3]

extern

dsp2scale

real tinker::dsp2scale

extern

dsp3scale

real tinker::dsp3scale

extern

dsp4scale

real tinker::dsp4scale

extern

dsp5scale

real tinker::dsp5scale

extern

dspexclude

int(* tinker::dspexclude)[2]

extern

dspexclude_scale

real* tinker::dspexclude_scale

extern

dufld

real(* tinker::dufld)[6]

extern

ebuffer

real tinker::ebuffer

extern

ec

EnergyBuffer tinker::ec

extern

ect

EnergyBuffer tinker::ect

extern

edsp

EnergyBuffer tinker::edsp

extern

eksum_mid

energy_prec tinker::eksum_mid

extern

eksum_old

energy_prec tinker::eksum_old

extern

elepr

real* tinker::elepr

extern

elrc_vol_dsp

real tinker::elrc_vol_dsp

extern

em

EnergyBuffer tinker::em

extern

energy_ec

energy_prec tinker::energy_ec

extern

energy_ect

energy_prec tinker::energy_ect

extern

energy_edsp

energy_prec tinker::energy_edsp

extern

energy_em

energy_prec tinker::energy_em

extern

energy_ep

energy_prec tinker::energy_ep

extern

energy_er

energy_prec tinker::energy_er

extern

energy_ev

energy_prec tinker::energy_ev

extern

ep

EnergyBuffer tinker::ep

extern

epsilon

real* tinker::epsilon

extern

epsilon4

real* tinker::epsilon4

extern

epsrule

Vdw tinker::epsrule

extern

er

EnergyBuffer tinker::er

extern

ev

EnergyBuffer tinker::ev

extern

gyred

grad_prec* tinker::gyred

extern

gzred

grad_prec* tinker::gzred

extern

hdot_lp

double tinker::hdot_lp

extern

hmass_lp

double tinker::hmass_lp

extern

ired

int* tinker::ired

extern

jpolar

int* tinker::jpolar

extern

kpep

real* tinker::kpep

extern

kred

real* tinker::kred

extern

leapfrog_vx

vel_prec* tinker::leapfrog_vx

extern

leapfrog_vxold

vel_prec* tinker::leapfrog_vxold

extern

leapfrog_vy

vel_prec* tinker::leapfrog_vy

extern

leapfrog_vyold

vel_prec* tinker::leapfrog_vyold

extern

leapfrog_vz

vel_prec* tinker::leapfrog_vz

extern

leapfrog_vzold

vel_prec* tinker::leapfrog_vzold

extern

leapfrog_x

pos_prec* tinker::leapfrog_x

extern

leapfrog_y

pos_prec* tinker::leapfrog_y

extern

leapfrog_z

pos_prec* tinker::leapfrog_z

extern

lpep

int* tinker::lpep

extern

m2scale

real tinker::m2scale

extern

m3scale

real tinker::m3scale

extern

m4scale

real tinker::m4scale

extern

m5scale

real tinker::m5scale

extern

maxualt

int tinker::maxualt

extern

mdpuexclude

int(* tinker::mdpuexclude)[2]

extern

mdpuexclude_scale

real(* tinker::mdpuexclude_scale)[4]

extern

mdwexclude

int(* tinker::mdwexclude)[2]

extern

mdwexclude_scale

real(* tinker::mdwexclude_scale)[3]

extern

mexclude

int(* tinker::mexclude)[2]

extern

mexclude_scale

real* tinker::mexclude_scale

extern

mono0

real* tinker::mono0

extern

mut_coalesced

int* tinker::mut_coalesced

extern

ncexclude

int tinker::ncexclude

extern

nct

CountBuffer tinker::nct

extern

ncvexclude

int tinker::ncvexclude

extern

ndisp

CountBuffer tinker::ndisp

extern

ndpexclude

int tinker::ndpexclude

extern

ndpuexclude

int tinker::ndpuexclude

extern

ndspexclude

int tinker::ndspexclude

extern

nec

CountBuffer tinker::nec

extern

nem

CountBuffer tinker::nem

extern

nep

CountBuffer tinker::nep

extern

nev

CountBuffer tinker::nev

extern

njpolar

int tinker::njpolar

extern

nmdpuexclude

int tinker::nmdpuexclude

extern

nmdwexclude

int tinker::nmdwexclude

extern

nmexclude

int tinker::nmexclude

extern

nrep

CountBuffer tinker::nrep

extern

nrepexclude

int tinker::nrepexclude

extern

nualt

int tinker::nualt

extern

nuexclude

int tinker::nuexclude

extern

nvdw14

int tinker::nvdw14

extern

nvexclude

int tinker::nvexclude

extern

nwexclude

int tinker::nwexclude

extern

osrw_dgx

grad_prec* tinker::osrw_dgx

extern

osrw_dgy

grad_prec * tinker::osrw_dgy

osrw_dgz

grad_prec * tinker::osrw_dgz

osrw_du1

energy_prec tinker::osrw_du1

extern

osrw_dv1

virial_prec tinker::osrw_dv1[9]

extern

osrw_ele

int tinker::osrw_ele

extern

osrw_itbnd

int(* tinker::osrw_itbnd)[2]

extern

OSRW_LAM_LINEAR

constexpr int tinker::OSRW_LAM_LINEAR = 0

constexpr

OSRW_LAM_QUADRATIC

constexpr int tinker::OSRW_LAM_QUADRATIC = 1

constexpr

osrw_lambda

double tinker::osrw_lambda

extern

osrw_ntbnd

int tinker::osrw_ntbnd

extern

osrw_pchg

real* tinker::osrw_pchg

extern

osrw_polarity

real* tinker::osrw_polarity

extern

osrw_pole

real(* tinker::osrw_pole)[MPL_TOTAL]

extern

osrw_tor

int tinker::osrw_tor

extern

osrw_tors1

real(* tinker::osrw_tors1)[4]

extern

osrw_tors2

real(* tinker::osrw_tors2)[4]

extern

osrw_tors3

real(* tinker::osrw_tors3)[4]

extern

osrw_tors4

real(* tinker::osrw_tors4)[4]

extern

osrw_tors5

real(* tinker::osrw_tors5)[4]

extern

osrw_tors6

real(* tinker::osrw_tors6)[4]

extern

osrw_vdw

int tinker::osrw_vdw

extern

p2iscale

real tinker::p2iscale

extern

p2scale

real tinker::p2scale

extern

p3iscale

real tinker::p3iscale

extern

p3scale

real tinker::p3scale

extern

p4iscale

real tinker::p4iscale

extern

p4scale

real tinker::p4scale

extern

p5iscale

real tinker::p5iscale

extern

p5scale

real tinker::p5scale

extern

palpha

real* tinker::palpha

extern

pcore

real* tinker::pcore

extern

pdamp

real* tinker::pdamp

extern

pdelta

real* tinker::pdelta

extern

pentyp

Chgpen tinker::pentyp

extern

pnh_lp

double tinker::pnh_lp

extern

pnhf_lp

double tinker::pnhf_lp

extern

pnhm_lp

double tinker::pnhm_lp

extern

pnhv_lp

double tinker::pnhv_lp

extern

pnhv_pre_lp

double tinker::pnhv_pre_lp

extern

polarity

real* tinker::polarity

extern

polarity_inv

real* tinker::polarity_inv

extern

pole

real(* tinker::pole)[MPL_TOTAL]

extern

polinv

real(* tinker::polinv)[3][3]

extern

polpred

UPred tinker::polpred

extern

polscale

real(* tinker::polscale)[3][3]

extern

pot

real* tinker::pot

extern

prepep

real* tinker::prepep

extern

pval

real* tinker::pval

extern

pval0

real* tinker::pval0

extern

r2scale

real tinker::r2scale

extern

r3scale

real tinker::r3scale

extern

r4scale

real tinker::r4scale

extern

r5scale

real tinker::r5scale

extern

radeps_coalesced

real* tinker::radeps_coalesced

extern

radrule

Vdw tinker::radrule

extern

repexclude

int(* tinker::repexclude)[2]

extern

repexclude_scale

real* tinker::repexclude_scale

extern

repole

real(* tinker::repole)[MPL_TOTAL]

extern

rpole

real(* tinker::rpole)[MPL_TOTAL]

extern

rrepole

real(* tinker::rrepole)[MPL_TOTAL]

extern

scrtyp

ExpolScr tinker::scrtyp

extern

sizpr

real* tinker::sizpr

extern

thlval

real* tinker::thlval

extern

thole

real* tinker::thole

extern

trqx

real* tinker::trqx

extern

trqy

real* tinker::trqy

extern

trqz

real* tinker::trqz

extern

u1scale

real tinker::u1scale

extern

u2scale

real tinker::u2scale

extern

u3scale

real tinker::u3scale

extern

u4scale

real tinker::u4scale

extern

udalt_00

real(* tinker::udalt_00)[3]

extern

udalt_01

real(* tinker::udalt_01)[3]

extern

udalt_02

real(* tinker::udalt_02)[3]

extern

udalt_03

real(* tinker::udalt_03)[3]

extern

udalt_04

real(* tinker::udalt_04)[3]

extern

udalt_05

real(* tinker::udalt_05)[3]

extern

udalt_06

real(* tinker::udalt_06)[3]

extern

udalt_07

real(* tinker::udalt_07)[3]

extern

udalt_08

real(* tinker::udalt_08)[3]

extern

udalt_09

real(* tinker::udalt_09)[3]

extern

udalt_10

real(* tinker::udalt_10)[3]

extern

udalt_11

real(* tinker::udalt_11)[3]

extern

udalt_12

real(* tinker::udalt_12)[3]

extern

udalt_13

real(* tinker::udalt_13)[3]

extern

udalt_14

real(* tinker::udalt_14)[3]

extern

udalt_15

real(* tinker::udalt_15)[3]

extern

udalt_lsqr_a

real* tinker::udalt_lsqr_a

extern

udalt_lsqr_b

real* tinker::udalt_lsqr_b

extern

udiag

real tinker::udiag

extern

udir

real(* tinker::udir)[3]

extern

udirp

real(* tinker::udirp)[3]

extern

uexclude

int(* tinker::uexclude)[2]

extern

uexclude_scale

real* tinker::uexclude_scale

extern

ufld

real(* tinker::ufld)[3]

extern

uind

real(* tinker::uind)[3]

extern

uinp

real(* tinker::uinp)[3]

extern

upalt_00

real(* tinker::upalt_00)[3]

extern

upalt_01

real(* tinker::upalt_01)[3]

extern

upalt_02

real(* tinker::upalt_02)[3]

extern

upalt_03

real(* tinker::upalt_03)[3]

extern

upalt_04

real(* tinker::upalt_04)[3]

extern

upalt_05

real(* tinker::upalt_05)[3]

extern

upalt_06

real(* tinker::upalt_06)[3]

extern

upalt_07

real(* tinker::upalt_07)[3]

extern

upalt_08

real(* tinker::upalt_08)[3]

extern

upalt_09

real(* tinker::upalt_09)[3]

extern

upalt_10

real(* tinker::upalt_10)[3]

extern

upalt_11

real(* tinker::upalt_11)[3]

extern

upalt_12

real(* tinker::upalt_12)[3]

extern

upalt_13

real(* tinker::upalt_13)[3]

extern

upalt_14

real(* tinker::upalt_14)[3]

extern

upalt_15

real(* tinker::upalt_15)[3]

extern

upalt_lsqr_a

real* tinker::upalt_lsqr_a

extern

upalt_lsqr_b

real* tinker::upalt_lsqr_b

extern

use_osrw

bool tinker::use_osrw

extern

v2scale

real tinker::v2scale

extern

v3scale

real tinker::v3scale

extern

v4scale

real tinker::v4scale

extern

v5scale

real tinker::v5scale

extern

vcouple

Vdw tinker::vcouple

extern

vdw14ik

int(* tinker::vdw14ik)[2]

extern

vdwindex

Vdw tinker::vdwindex

extern

vdwpr_in_use

bool tinker::vdwpr_in_use

extern

vdwtyp

Vdw tinker::vdwtyp

extern

vexclude

int(* tinker::vexclude)[2]

extern

vexclude_scale

real* tinker::vexclude_scale

extern

vir_ec

VirialBuffer tinker::vir_ec

extern

vir_ect

VirialBuffer tinker::vir_ect

extern

vir_edsp

VirialBuffer tinker::vir_edsp

extern

vir_em

VirialBuffer tinker::vir_em

extern

vir_ep

VirialBuffer tinker::vir_ep

extern

vir_er

VirialBuffer tinker::vir_er

extern

vir_ev

VirialBuffer tinker::vir_ev

extern

vir_trq

VirialBuffer tinker::vir_trq

extern

virial_ec

virial_prec tinker::virial_ec[9]

extern

virial_ect

virial_prec tinker::virial_ect[9]

extern

virial_edsp

virial_prec tinker::virial_edsp[9]

extern

virial_em

virial_prec tinker::virial_em[9]

extern

virial_ep

virial_prec tinker::virial_ep[9]

extern

virial_er

virial_prec tinker::virial_er[9]

extern

virial_ev

virial_prec tinker::virial_ev[9]

extern

vlam

real tinker::vlam

extern

vlrc_vol_dsp

real tinker::vlrc_vol_dsp

extern

w2scale

real tinker::w2scale

extern

w3scale

real tinker::w3scale

extern

w4scale

real tinker::w4scale

extern

w5scale

real tinker::w5scale

extern

wexclude

int(* tinker::wexclude)[2]

extern

wexclude_scale

real* tinker::wexclude_scale

extern

work01_

real(* tinker::work01_)[3]

extern

work02_

real(* tinker::work02_)[3]

extern

work03_

real(* tinker::work03_)[3]

extern

work04_

real(* tinker::work04_)[3]

extern

work05_

real(* tinker::work05_)[3]

extern

work06_

real(* tinker::work06_)[3]

extern

work07_

real(* tinker::work07_)[3]

extern

work08_

real(* tinker::work08_)[3]

extern

work09_

real(* tinker::work09_)[3]

extern

work10_

real(* tinker::work10_)[3]

extern

yred

real* tinker::yred

extern

zaxis

LocalFrame* tinker::zaxis

extern

zred

real* tinker::zred

extern