mrmd::data Namespace Reference

Namespaces
namespace	impl

Classes
struct	ArrayT
struct	Bond
struct	EnergyAndVirialReducer
struct	Histogram
struct	MPIInfo
struct	MultiHistogram
struct	Subdomain
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Typedefs
using	HostAtoms = impl::GeneralAtoms< HostType, false >
	atoms with memory allocated on host
using	DeviceAtoms = impl::GeneralAtoms< DeviceType, true >
	atoms with memory allocated on device
using	Atoms = DeviceAtoms
using	BondView = Kokkos::View< Bond * >
using	HostMolecules = impl::GeneralMolecules< HostType, false >
using	DeviceMolecules = impl::GeneralMolecules< DeviceType, true >
using	Molecules = DeviceMolecules

Functions
template<class DEVICE_TYPE_A , bool DEVICE_A, class DEVICE_TYPE_B , bool DEVICE_B>
void	deep_copy (impl::GeneralAtoms< DEVICE_TYPE_A, DEVICE_A > &dst, const impl::GeneralAtoms< DEVICE_TYPE_B, DEVICE_B > &src)
data::Histogram	gradient (const data::Histogram &input)
std::ostream &	operator<< (std::ostream &os, const data::Histogram &hist)
	Overload for writing to console/files.
template<class DEVICE_TYPE_A , bool DEVICE_A, class DEVICE_TYPE_B , bool DEVICE_B>
void	deep_copy (impl::GeneralMolecules< DEVICE_TYPE_A, DEVICE_A > &dst, const impl::GeneralMolecules< DEVICE_TYPE_B, DEVICE_B > &src)
data::Molecules	createMoleculeForEachAtom (data::Atoms &atoms)
void	cumulativeMovingAverage (data::MultiHistogram &average, const data::MultiHistogram &current, const real_t movingAverageFactor=10_r)
	Add new item to the comulative moving average.
data::MultiHistogram	gradient (const data::MultiHistogram &input, const bool periodic=false)
	Calculates the gradient of the histogram.
data::MultiHistogram	smoothen (data::MultiHistogram &input, const real_t &sigma, const real_t &range, const bool periodic=false)
	Smoothen a histogram using gaussian convolution.
ScalarView	createGrid (const MultiHistogram &input)
template<class BinaryOp >
void	transform (const MultiHistogram &input1, const MultiHistogram &input2, MultiHistogram &output, const BinaryOp &binary_op)
	Applies a binary operation to corresponding elements of two input MultiHistograms and stores the result in an output MultiHistogram.
template<OneCoordinatePredicate Pred>
void	replace_if_bin_position (MultiHistogram &hist, const Pred &pred, real_t newValue)
	Replaces histogram values with a new value if the bin position satisfies a predicate.
void	checkInvariants (const Subdomain &subdomain)

Typedef Documentation

Atoms

using mrmd::data::Atoms = typedef DeviceAtoms

BondView

using mrmd::data::BondView = typedef Kokkos::View<Bond*>

DeviceAtoms

using mrmd::data::DeviceAtoms = typedef impl::GeneralAtoms<DeviceType, true>

atoms with memory allocated on device

DeviceMolecules

using mrmd::data::DeviceMolecules = typedef impl::GeneralMolecules<DeviceType, true>

HostAtoms

using mrmd::data::HostAtoms = typedef impl::GeneralAtoms<HostType, false>

atoms with memory allocated on host

HostMolecules

using mrmd::data::HostMolecules = typedef impl::GeneralMolecules<HostType, false>

Molecules

using mrmd::data::Molecules = typedef DeviceMolecules

Function Documentation

checkInvariants()

void mrmd::data::checkInvariants

(

const Subdomain &

subdomain

)

createGrid()

ScalarView mrmd::data::createGrid

(

const MultiHistogram &

input

)

createMoleculeForEachAtom()

data::Molecules mrmd::data::createMoleculeForEachAtom

(

data::Atoms &

atoms

)

cumulativeMovingAverage()

void mrmd::data::cumulativeMovingAverage	(	data::MultiHistogram &	average,
		const data::MultiHistogram &	current,
		const real_t	movingAverageFactor = 10_r
	)

Add new item to the comulative moving average.

Parameters

average	averaged histogram (output)
current	current value
movingAverageFactor	new value = (n * average + current) / (n + 1)

deep_copy() [1/2]

template<class DEVICE_TYPE_A , bool DEVICE_A, class DEVICE_TYPE_B , bool DEVICE_B>

void mrmd::data::deep_copy	(	impl::GeneralAtoms< DEVICE_TYPE_A, DEVICE_A > &	dst,
		const impl::GeneralAtoms< DEVICE_TYPE_B, DEVICE_B > &	src
	)

deep_copy() [2/2]

template<class DEVICE_TYPE_A , bool DEVICE_A, class DEVICE_TYPE_B , bool DEVICE_B>

void mrmd::data::deep_copy	(	impl::GeneralMolecules< DEVICE_TYPE_A, DEVICE_A > &	dst,
		const impl::GeneralMolecules< DEVICE_TYPE_B, DEVICE_B > &	src
	)

gradient() [1/2]

data::Histogram mrmd::data::gradient

(

const data::Histogram &

input

)

gradient() [2/2]

data::MultiHistogram mrmd::data::gradient	(	const data::MultiHistogram &	input,
		const bool	periodic = false
	)

Calculates the gradient of the histogram.

Uses central difference for all inner values and one-sided/central difference for boundary values depending on periodicity.

Parameters

input	input histogram
periodic	treat boundaries as periodic

Returns

gradient of the histogram

operator<<()

std::ostream & mrmd::data::operator<<	(	std::ostream &	os,
		const data::Histogram &	hist
	)

Overload for writing to console/files.

Attention

If the data is located in device memory the data will be copied into host memory.

replace_if_bin_position()

template<OneCoordinatePredicate Pred>

void mrmd::data::replace_if_bin_position	(	MultiHistogram &	hist,
		const Pred &	pred,
		real_t	newValue
	)

Replaces histogram values with a new value if the bin position satisfies a predicate.

Parameters

hist	The MultiHistogram object whose values will be conditionally replaced.
pred	A unary predicate function that is evaluated for each bin position. If it returns true for a bin position, all histogram values at that bin are replaced with newValue.
newValue	The value to assign to histogram entries whose bin position satisfies the predicate.

smoothen()

data::MultiHistogram mrmd::data::smoothen	(	data::MultiHistogram &	input,
		const real_t &	sigma,
		const real_t &	range,
		const bool	periodic = false
	)

Smoothen a histogram using gaussian convolution.

Parameters

input	input histogram
sigma	sigma of the gaussian convolution
range	calculation range in multiples of sigma
periodic	treat boundaries as periodic

Returns

smoothened histogram

how many neighboring bins are affected

transform()

template<class BinaryOp >

void mrmd::data::transform	(	const MultiHistogram &	input1,
		const MultiHistogram &	input2,
		MultiHistogram &	output,
		const BinaryOp &	binary_op
	)

Applies a binary operation to corresponding elements of two input MultiHistograms and stores the result in an output MultiHistogram.

Template Parameters

BinaryOp

The type of the binary operation to be applied.

Parameters

input1	The first input MultiHistogram.
input2	The second input MultiHistogram.
output	The MultiHistogram where the result of the binary operation will be stored.
binary_op	The binary operation to apply to the elements of input1 and input2.

Precondition

The dimensions (numBins and numHistograms) of input1, input2, and output must match.