Procedures

Procedure	Location	Procedure Type	Description
ActivateLogger	LoggingModule	Subroutine	Activate the logger.
AddSparseVectors	SVectorModule	Interface
AppendToTripletList	TripletListModule	Interface
AppendToVector	CholeskyModule	Interface
BroadcastVector	CholeskyModule	Interface
CGSolver	LinearSolversModule	Subroutine	Solve the matrix equation AX = B using the conjugate gradient method.
CheckAllocError	ErrorModule	Function	Routine to call if an alloc error has occurred.
CheckMemoryPoolValidity	PMatrixMemoryPoolModule	Interface
CheckMemoryPoolValidity	MatrixMemoryPoolModule	Interface
CheckMPIError	ErrorModule	Function	Routine to call to check if an MPI error has occurred.
CholeskyDecomposition	LinearSolversModule	Subroutine	Compute The Cholesky Decomposition of a Hermitian Positive Definite matrix. This is a really naive implementation, that might be worth revisiting.
Cleanup	ErrorModule	Subroutine	As a last case resort, this will print an error message and quit.
CommSplitMatrix	PSMatrixModule	Interface
CompareTriplets	TripletModule	Interface
ComposeMatrix	SMatrixModule	Interface
ComposeMatrix	DMatrixModule	Interface
ComposeMatrixColumns	SMatrixModule	Interface
Compute	ChebyshevSolversModule	Interface
Compute	HermiteSolversModule	Interface
Compute	PolynomialSolversModule	Interface
ComputeDenseExponential	ExponentialSolversModule	Subroutine
ComputeDenseFOE	FermiOperatorModule	Subroutine	Compute the density matrix using a dense routine.
ComputeDenseLogarithm	ExponentialSolversModule	Subroutine
ComputeExponential	ExponentialSolversModule	Subroutine	Compute the exponential of a matrix.
ComputeExponentialPade	ExponentialSolversModule	Subroutine	Compute the exponential of a matrix using a pade approximation. Be warned, the pade method can result in a lot of intermediate fill.
ComputeExponentialTaylor	ExponentialSolversModule	Subroutine	Compute the exponential of a matrix using a taylor series expansion. This is only really useful if you have a very small spectrum, because quite a bit of scaling is required.
ComputeGridSize	ProcessGridModule	Subroutine	Sometimes we only want to specify for a process grid the number of slices and then automatically compute the right number of rows and columns.
ComputeInverseRoot	RootSolversModule	Subroutine	Compute a general inverse matrix root.
ComputeLogarithm	ExponentialSolversModule	Subroutine	Compute the logarithm of a matrix.
ComputeLogarithmTaylor	ExponentialSolversModule	Subroutine	Compute the logarithm of a matrix using a taylor series expansion.
ComputeRoot	RootSolversModule	Subroutine	Compute a general matrix root.
ConjugateMatrix	SMatrixModule	Interface
ConjugateMatrix	PSMatrixModule	Interface
ConstructDefaultPermutation	PermutationModule	Subroutine	Constructs a permutation that preserves the original order.
ConstructDiag	CholeskyModule	Interface
ConstructEmptyMatrix	SMatrixModule	Interface
ConstructEmptyMatrix	DMatrixModule	Interface
ConstructEmptyMatrix	PSMatrixModule	Interface
ConstructError	ErrorModule	Subroutine	Default constructor for an error type.
ConstructLimitedRandomPermutation	PermutationModule	Subroutine	Constructs a permutation that has a random order, but there is no permutation from beyond the actual matrix dimension.
ConstructMatrixDFromS	DMatrixModule	Interface
ConstructMatrixFromBinary	PSMatrixModule	Interface
ConstructMatrixFromFile	SMatrixModule	Interface
ConstructMatrixFromMatrixMarket	PSMatrixModule	Interface
ConstructMatrixFromTripletList	SMatrixModule	Interface
ConstructMatrixMemoryPool	PMatrixMemoryPoolModule	Interface
ConstructMatrixMemoryPool	MatrixMemoryPoolModule	Interface
ConstructMatrixSFromD	DMatrixModule	Interface
ConstructNewProcessGrid	ProcessGridModule	Interface
ConstructPolynomial	ChebyshevSolversModule	Interface
ConstructPolynomial	HermiteSolversModule	Interface
ConstructPolynomial	PolynomialSolversModule	Interface
ConstructProcessGrid	ProcessGridModule	Interface
ConstructRandomPermutation	PermutationModule	Subroutine	Constructs a permutation that has a random order. Implements Knuth shuffle.
ConstructRankLookup	CholeskyModule	Subroutine	Construct a lookup for columns
ConstructReversePermutation	PermutationModule	Subroutine	Constructs a permutation that reverses the original order.
ConstructSolverParameters	SolverParametersModule	Subroutine	Construct a data type which stores iterative solver parameters.
ConstructTripletList	TripletListModule	Interface
ConvertMatrixToComplex	PSMatrixModule	Subroutine	Converts the current matrix to a complex type matrix.
ConvertMatrixToReal	PSMatrixModule	Subroutine	Converts the current matrix to a real type matrix.
ConvertMatrixType	SMatrixModule	Interface
ConvertTripletListType	TripletListModule	Interface
ConvertTripletType	TripletModule	Interface
CopyMatrix	SMatrixModule	Interface
CopyMatrix	DMatrixModule	Interface
CopyMatrix	PSMatrixModule	Interface
CopyPermutation	PermutationModule	Subroutine	Copy one permutation to another in a safe way.
CopyProcessGrid	ProcessGridModule	Subroutine	Copy a process grid. Note that this makes a complete and independent copy of the process grid. Which of course means that whatever is currently stored in new_grid will be destroyed, so do not leave any matrices pointing to it.
CopySolverParameters	SolverParametersModule	Subroutine
CopyTripletList	TripletListModule	Interface
Cosine	TrigonometrySolversModule	Subroutine	Compute the cosine of a matrix.
DeactivateLogger	LoggingModule	Subroutine	Deactivate the logger.
DenseCosine	TrigonometrySolversModule	Subroutine	Compute the cosine of a matrix. (dense version).
DenseDensity	DensityMatrixSolversModule	Subroutine	Compute the density matrix using a dense routine.
DenseInverseSquareRoot	SquareRootSolversModule	Subroutine	Computes the matrix inverse square root function (dense version).
DenseInvert	InverseSolversModule	Subroutine	Compute the inverse of a matrix using the eigendecomposition.
DenseMatrixFunction	EigenSolversModule	Subroutine	Apply an arbitrary matrix function defined by a matrix map as a
DenseSignFunction	SignSolversModule	Subroutine	Computes the matrix sign function (dense version).
DenseSine	TrigonometrySolversModule	Subroutine	Compute the sine of a matrix. (dense version).
DenseSquareRoot	SquareRootSolversModule	Subroutine	Computes the matrix square root function (dense version).
DestructMatrix	SMatrixModule	Interface
DestructMatrix	DMatrixModule	Interface
DestructMatrix	PSMatrixModule	Interface
DestructMatrixMemoryPool	PMatrixMemoryPoolModule	Interface
DestructMatrixMemoryPool	MatrixMemoryPoolModule	Interface
DestructPermutation	PermutationModule	Subroutine	Destruct a permutation object.
DestructPolynomial	ChebyshevSolversModule	Interface
DestructPolynomial	HermiteSolversModule	Interface
DestructPolynomial	PolynomialSolversModule	Interface
DestructProcessGrid	ProcessGridModule	Subroutine	Destruct a process grid. Be careful about doing this. Matrices have pointers to process grids. If you destruct a process grid without destructing the matrices pointing to it, they will become unusable.
DestructSolverParameters	SolverParametersModule	Subroutine	Cleanup the solver parameters datastructure.
DestructTripletList	TripletListModule	Interface
DotAllHelper	CholeskyModule	Interface
DotAllPivoted	CholeskyModule	Interface
DotMatrix	SMatrixAlgebraModule	Interface
DotMatrix	PSMatrixAlgebraModule	Interface
DotSparseVectors	SVectorModule	Interface
EigenDecomposition	EigenSolversModule	Subroutine	Compute the eigendecomposition of a matrix.
EigenDecomposition	DMatrixModule	Interface
EnergyDensityMatrix	DensityMatrixSolversModule	Subroutine	Compute the energy-weighted density matrix.
EnterSubLog	LoggingModule	Subroutine	Call this subroutine when you enter into a section with verbose output
ErrorOccurred	ErrorModule	Function	Check if an error has occurred or not.
ExitSubLog	LoggingModule	Subroutine	Call this subroutine when you exit a section with verbose output
ExtractMatrixColumn	SMatrixModule	Interface
ExtractMatrixRow	SMatrixModule	Interface
FactorizedCompute	ChebyshevSolversModule	Interface
FactorizedCompute	PolynomialSolversModule	Interface
FillMatrixDense	PSMatrixModule	Interface
FillMatrixFromTripletList	PSMatrixModule	Interface
FillMatrixIdentity	PSMatrixModule	Interface
FillMatrixPermutation	PSMatrixModule	Interface
FilterMatrix	PSMatrixModule	Interface
GatherMatrixColumn	CholeskyModule	Interface
GatherMatrixToProcess	PSMatrixModule	Interface
GershgorinBounds	EigenBoundsModule	Subroutine	Compute a bounds on the minimum and maximum eigenvalue of a matrix. Uses the Gershgorin theorem.
GetLoggerLevel	LoggingModule	Function	Get the current logging level
GetMatrixActualDimension	PSMatrixModule	Interface
GetMatrixBlock	PSMatrixModule	Interface
GetMatrixColumns	SMatrixModule	Interface
GetMatrixLoadBalance	PSMatrixModule	Interface
GetMatrixLogicalDimension	PSMatrixModule	Interface
GetMatrixRows	SMatrixModule	Interface
GetMatrixSize	PSMatrixModule	Interface
GetMatrixSlice	PSMatrixModule	Subroutine	Copy an arbitrary slice from a matrix into a new smaller matrix. NTPoly only works with square matrices, so if the number of rows and columns is different the matrix is resized to the maximum size.
GetMatrixTripletList	PSMatrixModule	Interface
GetMPITripletType_c	TripletModule	Function	Returns an MPI derived data type for a triplet (complex). We statically store this derived type so that we do not have to recreate it every time this function is called. Thus this functional call should add very little overhead.
GetMPITripletType_r	TripletModule	Function	Returns an MPI derived data type for a triplet (Real). We statically store this derived type so that we do not have to recreate it every time this function is called. Thus this functional call should add very little overhead.
GetMyColumn	ProcessGridModule	Function	Get the column of the current process.
GetMyRow	ProcessGridModule	Function	Get the row of the current process.
GetMySlice	ProcessGridModule	Function	Get the slice of the current process.
GetPivot	CholeskyModule	Interface
GetTripletAt	TripletListModule	Interface
GetTripletListSize	TripletListModule	Interface
GetTripletValues	TripletModule	Interface
HPCP	DensityMatrixSolversModule	Subroutine	Compute the density matrix from a Hamiltonian using the HPCP method. Based on the algorithm presented in \cite truflandier2016communication.
IncrementMatrix	SMatrixAlgebraModule	Interface
IncrementMatrix	DMatrixModule	Interface
IncrementMatrix	PSMatrixAlgebraModule	Interface
InverseSquareRoot	SquareRootSolversModule	Subroutine	Compute the inverse square root of a matrix.
Invert	InverseSolversModule	Subroutine	Compute the inverse of a matrix. An implementation of the method of Hotelling \cite palser1998canonical.
IsIdentity	PSMatrixModule	Function	Determine if this is the identity matrix.
IsLoggerActive	LoggingModule	Function	Check if the logger is currently active
IsRoot	ProcessGridModule	Function	Check if the current process is the root process.
LowdinExtrapolate	GeometryOptimizationModule	Subroutine	Create a new guess at the Density Matrix after updating the geometry. Based on the lowdin algorithm in \cite exner2002comparison .
MapMatrix_psc	MatrixMapsModule	Subroutine	Given a distributed matrix, apply this procedure to each element (complex).
MapMatrix_psr	MatrixMapsModule	Subroutine	Given a distributed matrix, apply this procedure to each element (real).
MapTripletList	MatrixMapsModule	Interface
MatrixColumnNorm	SMatrixAlgebraModule	Interface
MatrixGrandSum	SMatrixAlgebraModule	Interface
MatrixGrandSum	PSMatrixAlgebraModule	Interface
MatrixMultiply	SMatrixAlgebraModule	Interface
MatrixMultiply	PSMatrixAlgebraModule	Interface
MatrixNorm	SMatrixAlgebraModule	Interface
MatrixNorm	DMatrixModule	Interface
MatrixNorm	PSMatrixAlgebraModule	Interface
MatrixSigma	PSMatrixAlgebraModule	Interface
MatrixToTripletList	SMatrixModule	Interface
MatrixTrace	PSMatrixAlgebraModule	Interface
McWeenyStep	DensityMatrixSolversModule	Subroutine	Take one McWeeny Step DOut = 3DSD - 2DSDSD
MergeMatrixLocalBlocks	PSMatrixModule	Interface
MultiplyMatrix	DMatrixModule	Interface
PairwiseMultiplyMatrix	SMatrixAlgebraModule	Interface
PairwiseMultiplyMatrix	PSMatrixAlgebraModule	Interface
PairwiseMultiplyVectors	SVectorModule	Interface
ParseMMHeader	MatrixMarketModule	Function	Parse a matrix market header.
PermuteMatrix	LoadBalancerModule	Subroutine	Apply a permutation to a matrix.
PivotedCholeskyDecomposition	AnalysisModule	Subroutine	Compute The Pivoted Cholesky Decomposition of a Hermitian Semi-Definite matrix. This is one way to generate localized orbitals.
PM	DensityMatrixSolversModule	Subroutine	Compute the density matrix from a Hamiltonian using the PM method. Based on the PM algorithm presented in \cite palser1998canonical
PolarDecomposition	SignSolversModule	Subroutine	Computes the polar decomposition of a matrix Mat = U*H.
PowerBounds	EigenBoundsModule	Subroutine	Compute a bounds on the maximum eigenvalue of a matrix. Uses The Power Method.
PrintAllTimers	TimerModule	Subroutine	Print out the elapsed time for each timer on this process.
PrintAllTimersDistributed	TimerModule	Subroutine	Print out the elapsed time for each timer based on the max value across processes.
PrintError	ErrorModule	Subroutine	Print out that an error has occurred.
PrintMatrix	SMatrixModule	Interface
PrintMatrix	PSMatrixModule	Interface
PrintMatrixInformation	PSMatrixModule	Interface
PrintParameters	SolverParametersModule	Subroutine	Print out the iterative solver parameter values.
PrintTimer	TimerModule	Subroutine	Print out the elapsed time for a given timer.
PseudoInverse	InverseSolversModule	Subroutine	Compute the pseudoinverse of a matrix. An implementation of the method of Hotelling \cite palser1998canonical.
PurificationExtrapolate	GeometryOptimizationModule	Subroutine	Create a new guess at the Density Matrix after updating the geometry. Based on the purification algorithm in \cite niklasson2010trace .
RedistributeTripletLists	TripletListModule	Interface
ReduceAndComposeMatrix	MatrixReduceModule	Interface
ReduceAndComposeMatrixCleanup	MatrixReduceModule	Interface
ReduceAndComposeMatrixData	MatrixReduceModule	Interface
ReduceAndComposeMatrixSizes	MatrixReduceModule	Interface
ReduceAndSumMatrix	MatrixReduceModule	Interface
ReduceAndSumMatrixCleanup	MatrixReduceModule	Interface
ReduceAndSumMatrixData	MatrixReduceModule	Interface
ReduceAndSumMatrixSizes	MatrixReduceModule	Interface
ReduceDimension	AnalysisModule	Subroutine	When we want to only compute the first n eigenvalues of a matrix, this routine will project out the higher eigenvalues.
RegisterTimer	TimerModule	Subroutine	Register a timer with the timer module. Call this before using that timer.
ResizeMatrix	PSMatrixModule	Subroutine	Change the size of a matrix. If the new size is smaller, then values outside that range are deleted. IF the new size is bigger, zero padding is applied. Warning: this requires a full data redistribution.
ResizeTripletList	TripletListModule	Interface
ScaleAndFold	DensityMatrixSolversModule	Subroutine	Compute the density matrix from a Hamiltonian using the Scale and Fold method. Based on the method of \cite rubensson2011nonmonotonic . Note that for this method, you must provide the value of the homo and lumo gap. It is not necessary for these to be accurate, but give a conservative value.
ScaleMatrix	SMatrixAlgebraModule	Interface
ScaleMatrix	PSMatrixAlgebraModule	Interface
ScaleSquareTrigonometryTaylor	TrigonometrySolversModule	Subroutine	Compute trigonometric functions of a matrix using a taylor series.
SetCoefficient	ChebyshevSolversModule	Interface
SetCoefficient	HermiteSolversModule	Interface
SetCoefficient	PolynomialSolversModule	Interface
SetCustomError	ErrorModule	Subroutine
SetGenericError	ErrorModule	Subroutine	Routine to call if a generic error has occurred.
SetInitialOffset	LoggingModule	Subroutine	Set a manual initial offset spacing.
SetLoggerLevel	LoggingModule	Subroutine	Set the logging level manually
SetMatrixProcessGrid	PSMatrixModule	Subroutine	When you want to change the process grid of a matrix, you can call this routine with the new process grid value. Data will be automatically redistributed.
SetParametersBeVerbose	SolverParametersModule	Subroutine	Set the value of the verbosity.
SetParametersConvergeDiff	SolverParametersModule	Subroutine	Set the value of the convergence difference.
SetParametersLoadBalance	SolverParametersModule	Subroutine	Set the value of the load balance.
SetParametersMaxIterations	SolverParametersModule	Subroutine	Set the value of the max iterations.
SetParametersStepThreshold	SolverParametersModule	Subroutine	Set the value of the step threshold.
SetParametersThreshold	SolverParametersModule	Subroutine	Set the value of the threshold.
SetPoolSparsity	MatrixMemoryPoolModule	Interface
SetTriplet	TripletModule	Interface
SetTripletAt	TripletListModule	Interface
ShiftTripletList	TripletListModule	Interface
SignFunction	SignSolversModule	Subroutine	Computes the matrix sign function.
SimilarityTransform	PSMatrixAlgebraModule	Subroutine	Transform a matrix B = P * A * P^-1
Sine	TrigonometrySolversModule	Subroutine	Compute the sine of a matrix.
SingularValueDecomposition	SingularValueSolversModule	Subroutine	Compute the singular values and singular vectors of a matrix.
SnapMatrixToSparsityPattern	MatrixConversionModule	Subroutine	Some codes use a fixed sparsity pattern for a matrix instead of filtering small values. Using this routine, the matrix is filled to have the same pattern as the second matrix argument. Zeros of the sparsity pattern are left in, whereas values outside the sparsity are removed. This can faciliate conversion between formats.
SortTripletList	TripletListModule	Interface
SplitMatrix	SMatrixModule	Interface
SplitMatrix	DMatrixModule	Interface
SplitMatrixColumns	SMatrixModule	Interface
SplitMatrixToLocalBlocks	PSMatrixModule	Interface
SplitProcessGrid	ProcessGridModule	Subroutine	Given a process grid, this splits it into two grids of even size
SquareRoot	SquareRootSolversModule	Subroutine	Compute the square root of a matrix.
StartTimer	TimerModule	Subroutine	Start the clock running for a given timer.
StopTimer	TimerModule	Subroutine	Stop the clock for a given timer.
SymmetrizeTripletList	TripletListModule	Interface
TestReduceDataRequest	MatrixReduceModule	Function	Test if a request for the data of the matrices is complete.
TestReduceInnerRequest	MatrixReduceModule	Function	Test if a request for the inner indices of the matrices is complete.
TestReduceSizeRequest	MatrixReduceModule	Function	Test if a request for the size of the matrices is complete.
TransposeMatrix	SMatrixModule	Interface
TransposeMatrix	DMatrixModule	Interface
TransposeMatrix	PSMatrixModule	Interface
TRS2	DensityMatrixSolversModule	Subroutine	Compute the density matrix from a Hamiltonian using the TRS2 method. Based on the TRS2 algorithm presented in \cite niklasson2002.
TRS4	DensityMatrixSolversModule	Subroutine	Compute the density matrix from a Hamiltonian using the TRS4 method. Based on the TRS4 algorithm presented in \cite niklasson2002
UndoPermuteMatrix	LoadBalancerModule	Subroutine	Undo a permutation applied to a matrix.
UnpackCholesky	CholeskyModule	Interface
WOM_C	FermiOperatorModule	Subroutine	Compute the density matrix according to the wave operator minization
WOM_GC	FermiOperatorModule	Subroutine	Compute the density matrix according to the wave operator minization
WriteElement	LoggingModule	Interface
WriteHeader	LoggingModule	Subroutine	Write out a header to the log.
WriteListElement	LoggingModule	Interface
WriteMatrixToBinary	PSMatrixModule	Interface
WriteMatrixToMatrixMarket	PSMatrixModule	Interface
WriteMMLine	MatrixMarketModule	Interface
WriteMMLine_f	MatrixMarketModule	Subroutine	Write a single line that would correspond to a matrix market entry.
WriteMMLine_ff	MatrixMarketModule	Subroutine	Write a single line that would correspond to a matrix market entry.
WriteMMLine_ii	MatrixMarketModule	Subroutine	Write a single line that would correspond to a matrix market entry.
WriteMMLine_iif	MatrixMarketModule	Subroutine	Write a single line that would correspond to a matrix market entry.
WriteMMLine_iiff	MatrixMarketModule	Subroutine	Write a single line that would correspond to a matrix market entry.
WriteMMSize	MatrixMarketModule	Subroutine	Write the line describing the size of the matrix
WriteProcessGridInfo	ProcessGridModule	Subroutine	Write out some basic information about this process grid to the log.