Porting to AMatrix

This page provides a list of common changes for migration from ublas to AMatrix

Compiling

In order to compile AMatrix with Kratos add the following to your configure.sh:

-DAMATRIX_DIR="/your_kratos_location/Kratos/external_libraries/a_matrix/" \

Using Kratos vector and matrix aliases

It is recommended to use Kratos vector and matrix aliases instead of ones define by ublas:

• Using Vector for a dynamic size vector of double
• Using Matrix for a dynamic size matrix of double
• Replacing the boost::numeric::ublas::vector with DenseVector
• Replacing the boost::numeric::ublas::matrix with DenseMatrix
• Replacing the boost::numeric::ublas::bounded_vector with BoundedVector
• Replacing the boost::numeric::ublas::bounded_matrix with BoundedMatrix
• Replacing the bounded_vector with BoundedVector
• Replacing the bounded_matrix with BoundedMatrix
• Relplacing the matrix< with DenseMatrix< NOTE: the < character should be included in this step to avoid unnecessary changes
• Replacing the boost::numeric::ublas::prod with prod
• Replacing the boost::numeric::ublas::trans with trans

Other common changes

There are differences in interface and also behavior of these to libraries. The most important ones are the resize which does not preserve the values and there is no operator() for vector. Here is the list of common changes:

• Passing false to vector resize: vector.resize(new_sizse) to vector.resize(new_size, false)
• Passing false to matrix resize: matrix.resize(size1,size2) to matrix.resize(size1,size2, false)
• There is no constructor with value for matrix and vector. Please use ScalarMatrix for that: Matrix m(size1,size2, value) to Matrix m = ScalarMatrix(size1,size2, value)
• IdentityMatrix is only square and accept one size: IdentityMatrix(size,size) to IdentityMatrix(size)
• The array_1d does not have constructor with size: array_1d<double,3> a(3) to array_1d<double,3> a
• Changing the ublas vector<double> to Vector
• Changing the ublas vector<other_type> to DenseVector<other_type>
• Amatrix classes does not have oprator() and please use the [] instead: v(i) to v[i]
• data() method returns a raw pointer to the first member and not an iterator
• when dealing with spaces please take care of using correctly the SparseSpace::DenseVector and LocalSpace::DenseVector as they are different types now.
• There is no project function in amatrix. Instead there is a SubMatrix expression: AMatrix::SubMatrix<MatrixType>a_sub_matrix(original_matrix, sub_index1, sub_index2, sub_size1, sub_size2); The arguments are different so it might be used with KRATOS_USE_AMATRIX macro in order to maintain the compatibility to ublas
• Replacing the matrix_row(rVariables.Strain.Eigen.Vectors,i) with row((rVariables.Strain.Eigen.Vectors,i)

In order to maintain the backward compatibility until all applications are migrated a A new KRATOS_USE_AMATRIX macro is added which is used when the AMatrix interface is different than Ublas. The idea is to remove KRATOS_USE_AMATRIX macro after the migration, so please use it wisely and as less as possible.

Tips and tricks

Using Matrix and Vector from within an Internals namespace

Sometimes you may want to use Matrix and Vector types within an Internals namespace for your class, but the names Kratos::Internals::Matrix and Kratos::Internals::Vectors are already taken when you compile Kratos with AMatrix. The name clash may manifest with an error like:

error: invalid use of template-name ‘Kratos::Internals::Matrix’ without an argument list
     typedef Matrix MatrixType;
             ^~~~~~
/home/jcotela/Kratos/kratos/utilities/helper_classes_for_constraint_builder.h:431:13: note: class template argument deduction is only available with -std=c++17 or -std=gnu++17
In file included from /home/jcotela/Kratos/kratos/includes/ublas_interface.h:35,
                 from /home/jcotela/Kratos/kratos/includes/serializer.h:31,
                 from /home/jcotela/Kratos/kratos/includes/model_part.h:33,
                 from /home/jcotela/Kratos/kratos/python/add_strategies_to_python.cpp:25:
/home/jcotela/Kratos/kratos/includes/amatrix_interface.h:39:7: note: ‘template<class TDataType, long unsigned int TSize1, long unsigned int TSize2> class Kratos::Internals::Matrix’ declared here
 class Matrix : public AMatrix::MatrixExpression<Matrix<TDataType, TSize1, TSize2>,
       ^~~~~~

If this happens, declare your local MatrixType using the complete type name:

namespace Kratos
{
    namespace Internals
    {
        //...
        typedef Kratos::Matrix MatrixType;
        typedef Kratos::Vector VectorType;
        //...
    }
}

Runtime errors when importing application strategies, builder and solvers or processes

Keep in mind that the SparseSpace type used as template argument to define strategies and builder and solvers still uses ublas types. This means that you will probably need to update the add_whatever_to_python.cpp files in your application.

If you have a type definition that looks like

typedef UblasSpace<double, CompressedMatrix, Vector > SparseSpaceType;

keep in mind that the Vector type has been redefined in AMatrix, so you need to point back to the ublas type:

typedef UblasSpace<double, CompressedMatrix, boost::numeric::ublas::vector<double>> SparseSpaceType;

Note that this may require adding an include for "boost/numeric/ublas/matrix.hpp".