scmat.dox

大型并行量子化学软件；支持密度泛函（DFT）。可以进行各种量子化学计算。支持CHARMM并行计算。非常具有应用价值。

/** \page scmat The Matrix Library

The scientific computing matrix library (SCMAT) is designed around a set of
matrix abstractions that permit very general matrix implementations.  This
flexibility is needed to support diverse computing environments.  For
example, this library must support, at a minimum: simple matrices that
provide efficient matrix computations in a uniprocessor environment,
clusters of processors with enough memory to store all matrices connected
by a relatively slow network (workstations on an LAN), clusters of
processors with enough memory to store all matrices and a fast interconnect
network (a massively parallel machine such as the Intel Paragon), and
clusters of machines that don't have enough memory to hold entire matrices.

<ul>
  <li> \ref scmatover
  <li> \ref scmatdim
  <li> \ref scmatref
  <li> \ref scmatabstract
  <li> \ref scmatstor
  <li> \ref scmatop
  <li> \ref scmatopsp
  <li> \ref scmatlocal
  <li> \ref scmatrepl
  <li> \ref scmatdist
  <li> \ref scmatblocked
</ul>

\section scmatover Overview

The design of SCMAT differs from other object-oriented matrix packages in
two important ways.  First, the matrix classes are abstract base classes.
No storage layout is defined and virtual function calls must be used to
access individual matrix elements.  This would have a negative performance
impact if users needed to frequently access matrix elements.  The interface
to the matrix classes is hopefully rich enough to avoid individual matrix
element access for any computationally significant task.  The second major
difference is that symmetric matrices do not inherit from matrices, etc.
The SCMAT user must know whether a matrix is symmetric at all places it is
used if any performance gain, by virtue of symmetry, is expected.

Dimension information is contained objects of the SCDimension type.  In
addition to the simple integer dimension, application specific blocking
information can be provided.  For example, in a quantum chemistry
application, the dimension corresponding to the atomic orbital basis set
will have block sizes that correspond to the shells.  Dimensions are used
to create new matrix or vector objects.

The primary abstract classes are SCMatrix, SymmSCMatrix, DiagSCMatrix, and
SCVector.  These represent matrices, symmetric matrices, diagonal matrices,
and vectors, respectively.  These abstract classes are specialized into
groups of classes.  For example, the locally stored matrix implementation
specializes the abstract classes to LocalSCMatrix, LocalSymmSCMatrix,
LocalDiagSCMatrix, LocalSCVector, LocalSCDimension, and LocalSCMatrixKit.
These specializations are all designed to work with each other.  However, a
given specialization is incompatible with other matrix specializations.  An
attempt to multiply a local matrix by a distributed matrix would generate
an error at runtime.

Since the different groups of classes do not interoperate, some mechanism
of creating consistent specializations is needed.  This is done with
SCMatrixKit objects.  SCMatrixKit is an abstract base type which has
specializations that correspond to each group of the matrix
specializations.  It is used to create matrices and vectors from that
group.  For example, the DistSCMatrixKit is used to create objects of type
DistSCMatrix, DistSymmSCMatrix, DistDiagSCMatrix, and DistSCVector.

The abstract matrix classes and their derivations are usually not directly
used by SCMAT users.  The most convenient classes to use are the smart
pointer classes RefSCMatrix, RefSymmSCMatrix, RefDiagSCMatrix,
and RefSCDimension.
These classes respectively inherit from Ref<SCMatrix>, Ref<SymmSCMatrix>,
Ref<DiagSCMatrix>, and Ref<SCDimension>, providing automatic memory
management through reference counting.
The smart pointer classes also have matrix
operations such as operator *(), operator -(), and operator +() defined as
members for convenience.  These forward the operations to the contained
matrix object.  The smart pointer classes also simplify creation of
matrices by providing constructors that take as arguments one or more
RefSCDimension's and a Ref<SCMatrixKit>.  These initialize the smart pointer
to contain a new matrix with a specialization corresponding to that of the
Ref<SCMatrixKit>.  Matrix operations not provided by the smart pointer
classes but present as member in the abstract classes can be accessed with
operator->().

If a needed matrix operation is missing, mechanisms exist to add more
general operations.  Operations which only depend on individual elements of
matrices can be provided by specializations of the SCElementOp class.
Sometimes we need operations on matrices with identical dimensions that
examine each element in one matrix along with the corresponding element
from the other matrix.  This is accomplished with SCElementOp2 for two
matrices and with SCElementOp3 for three.

Other features of SCMAT include run-time type facilities and persistence.
Castdown operations (type conversions from less to more derived objects)
and other run-time type information are provided by the DescribedClass base
class.  Persistence is not provided by inheriting from SavableState base
clase as is the case with many other classes in the SC class hierarchies,
because it is necessary to save objects in an implementation independent
manner.  If a calculation checkpoints a matrix on a single processor
machine and later is restarted on a multiprocessor machine the matrix would
need to be restored as a different matrix specialization.  This is handled
by saving and restoring matrices' and vectors' data without reference to
the specialization.

The following include files are provided by the matrix library:

<dl>
<dt><tt>matrix.h</tt><dd>
Usually, this is the only include file needed by users of matrices.  It
declares reference counting pointers to abstract matrices.

If kit for a matrix must be created, or a member specific to an
implementation is needed, then that implementation's header file must be
included.

<dt><tt>elemop.h</tt><dd>
This is the next most useful include file.  It defines useful
SCElementOp, SCElementOp2, and SCElementOp3
specializations.

<dt><tt>abstract.h</tt><dd>
This include file contains the declarations for abstract classes that
users do not usually need to see.  These include SCDimension,
SCMatrix, SymmSCMatrix, DiagSCMatrix,
SCMatrixKit.  This file is currently included by
matrix.h.

<dt><tt>block.h</tt><dd>
This file declares SCMatrixBlock and specializations.  It
only need be include by users implementing new SCElementOp
specializations.

<dt><tt>blkiter.h</tt><dd>
This include file declares the implementations of
SCMatrixBlockIter.  It only need be include by users implementing
new SCElementOp specializations.

<dt><tt>vector3.h</tt><dd>
This declares SCVector3, a lightweight vector of length three.

<dt><tt>matrix3.h</tt><dd>
This declares SCMatrix3, a lightweight matrix of dimension three by
three.  It includes vector3.h.

<dt><tt>local.h</tt><dd>
This include file is the matrix implementation for locally stored
matrices.  These are suitable for use in a uniprocessor environment.  The
LocalSCMatrixKit is the default matrix implementation returned
by the static member SCMatrixKit::default_matrixkit.
This file usually doesn't need to be included.

<dt><tt>dist.h</tt><dd>
This include file is the matrix implementation for distributed matrices.
These are suitable for use in a distributed memory multiprocessor which
does not have enough memory to hold all of the matrix elements on each
processor.  This file usually doesn't need to be included.

<dt><tt>repl.h</tt><dd>
This include file is the matrix implementation for replicated matrices.
These are suitable for use in a distributed memory multiprocessor which
does have enough memory to hold all of the matrix elements on each
processor.  This file usually doesn't need to be included.

<dt><tt>blocked.h</tt><dd>
This include file is the matrix implementation for blocked matrices.
Blocked matrices store a matrix as subblocks that are matrices from another
matrix specialization.  These are used to save storage and computation time
in quantum chemistry applications for molecules with other than \f$C_1\f$ point
group symmetry.

</dl>

\section scmatdim Matrix Dimensions

In addition to the simple integer dimension, objects of the SCDimension
class contain application specific blocking information.  This information
is held in an object of class SCBlockInfo.

\section scmatref Matrix Reference Classes

The easiest way to use SCMAT is through the smart pointer classes
RefSCMatrix, RefSymmSCMatrix, RefDiagSCMatrix, RefSCVector, RefSCDimension,
and Ref<SCMatrixKit>.  These are based on the Ref reference counting package
and automatically delete matrix objects when they are no longer needed.
These reference classes also have common operations defined as members for
convenience.  This makes it unnecessary to also use the sometimes awkward
syntax of operator->() to manipulate the contained objects.

\section scmatabstract Abstract Matrix Classes

This section documents the primary abstract classes: SCMatrix,
SymmSCMatrix, DiagSCMatrix, and SCVector, as well as the SCMatrixKit class
which allows the programmer to generate consistent specializations of
matrices.  These represent matrices, symmetric matrices, diagonal matrices,
and vectors, respectively.

This section is primarily for implementers of new specializations
of matrices.  Users of existing matrices will be most interested
in the matrix reference classes.

\section scmatstor Matrix Storage

All elements of matrices and vectors are kept in blocks.  The
choice of blocks and where they are keep is left up to each
matrix specialization.

\section scmatop Manipulating Matrix Elements with Element Operations

The SCElementOp, SCElementOp2, and SCElementOp3 classes can
be used to maniupulate matrix elements.

\section scmatopsp SCElementOp Specializations

Several commonly needed element operations are already coded up and
available by including math/scmat/elemop.h.  Below are descriptions
of these classes:

<dl>
<dt>SCElementScalarProduct<dd> This SCElementOp2 computes
the scalar product of two matrices or vectors.  The result is available
after the operation from the return value of the result() member.
<dt>SCDestructiveElementProduct<dd> This SCElementOp2
replaces the elements of the matrix or vector whose element_op
member is called.  The resulting values are the element by element products
of the two matrices or vectors.
<dt>SCElementScale<dd> This scales each element by an amount given
in the constructor.
<dt>SCElementRandomize<dd> This generates random elements.
<dt>SCElementAssign<dd> Assign to each element the value passed to
the constructor.
<dt>SCElementSquareRoot<dd> Replace each element with its square
root.
<dt>SCElementInvert<dd> Replace each element by its reciprocal.
<dt>SCElementScaleDiagonal<dd> Scales the diagonal elements of a
matrix by the argument passed to the constructor.  Use of this on a vector
is undefined.
<dt>SCElementShiftDiagonal<dd> Add the value passed to the
constructor to the diagonal elements of the matrix.  Use of this on a
vector is undefined.
<dt>SCElementMaxAbs<dd> Find the maximum absolute value element in a
matrix or vector.  The result is available as the return value of the
<tt>result()</tt> member.
<dt>SCElementDot<dd> The constructor for this class takes three
arguments: SCElementDot(double**a,
double**b, int length).  The length of each vector given by
a and b is given by length.  The number of vectors in
a is the number of rows in the matrix and the number in b is
the number of columns.  To each element in the matrix \f$m_{ij}\f$ the dot
product of the \f$a_i\f$ and \f$b_j\f$ is added.
<dt>SCElementAccumulateSCMatrix<dd>  This is obsolete---do not use it.
<dt>SCElementAccumulateSymmSCMatrix<dd> This is obsolete---do not
use it.
<dt>SCElementAccumulateDiagSCMatrix<dd> This is obsolete---do not
use it.
<dt>SCElementAccumulateSCVector<dd> This is obsolete---do not use
it.
</dl>

\section scmatlocal Local Matrices

Local matrices do no communication.  All elements reside on each node
and all computations are duplicated on each node.

\section scmatrepl Replicated Matrices

Replicated matrices hold all of the elements on each node, however
do some communications in order to reduce computation time.

\section scmatdist Distributed Matrices

Distributed matrices spread the elements across all the nodes and
thus require less storage than local matrices however these use
more communications than replicated matrices.

\section scmatblocked Blocked Matrices

Blocked matrices are used to implement point group symmetry.  Another
matrix specialization is used to hold the diagonal subblocks of a
matrix.  The offdiagonal subblocks are known to be zero and not stored.
This results in considerable savings in storage and computation for
those cases where it applies.

*/