gmx::test::anonymous_namespace{parrinellorahman.cpp} Namespace Reference

Classes
struct	Matrix3x3ToString
	Helper functor for naming tests. More...

Typedefs
using	ParrinelloRahmanTestParameters = std::tuple< PressureCouplingOptions, PressureMatrixType, BoxShape, Matrix3x3, Matrix3x3 >
	Convenience typedef of the test input parameters. More...
using	ParrRahmTest = ::testing::TestWithParam< ParrinelloRahmanTestParameters >
	Test fixture - abbreviated ParrinelloRahman to ParrRahm for shorter refdata filenames.

Enumerations
enum	PressureMatrixType {   UniformDiagonal, PressureMatrixType::PartlyUniformDiagonal, PressureMatrixType::Diagonal, PressureMatrixType::General,   PressureMatrixType::Extreme, PressureMatrixType::Count }
	Some kinds of matrices of simulation box pressure. More...
enum	BoxShape : int {   Cubic, Rectilinear, RhombicDodecahedronXYSquare, RhombicDodecahedronXYHexagon,   TruncatedOctahedron, Other, Count }
	Simulation box types.

Functions
void	isAlmostDiagonalMatrix (const char *name, const Matrix3x3 &m)
	GoogleTest expectations about whether matrices are diagonal or not.
std::string	pressureCouplingOptionsToString (const PressureCouplingOptions options)
	Helper function for naming tests.
template<BoxShape boxShape>
Matrix3x3	makeBox (real spacing)
	Template for box-making function.
template<>
Matrix3x3	makeBox< BoxShape::Cubic > (real spacing)
	Template specialization to make a cubic box.
template<>
Matrix3x3	makeBox< BoxShape::Rectilinear > (real spacing)
	Template specialization to make a rectilinear box.
template<>
Matrix3x3	makeBox< BoxShape::RhombicDodecahedronXYSquare > (real spacing)
	Template specialization to make a rhombic dodecahedral box where the XY face is a square.
template<>
Matrix3x3	makeBox< BoxShape::RhombicDodecahedronXYHexagon > (real spacing)
	Template specialization to make a rhombic dodecahedral box where the XY face is a hexagon.
template<>
Matrix3x3	makeBox< BoxShape::TruncatedOctahedron > (real spacing)
	Template specialization to make a truncated octahedral box.
template<>
Matrix3x3	makeBox< BoxShape::Other > (real spacing)
	Template specialization to make an arbitrary conformant box.
template<BoxShape boxShape>
std::vector< Matrix3x3 >	makeBoxes (std::initializer_list< real > boxSizes)
	Make a vector of boxes whose type is boxShape and leading dimension one of the boxSizes.

Variables
constexpr gmx::EnumerationArray < PressureMatrixType, const char * >	sc_pressureMatrixTypeNames
	Helper array for describing tests. More...
const EnumerationArray < PressureMatrixType, Matrix3x3 >	c_pressureMatrices
	Some matrices of simulation box pressure. More...
constexpr gmx::EnumerationArray < BoxShape, const char * >	sc_boxShapeNames
const NameOfTestFromTuple < ParrinelloRahmanTestParameters >	sc_testNamer
	Tuple of formatters to name the parameterized test cases. More...
const EnumerationArray < BoxShape, std::vector < Matrix3x3 > >	c_boxVectors
	Sets of box vectors to use in tests. More...
const EnumerationArray < BoxShape, std::vector < Matrix3x3 > >	c_boxVelocities
	Sets of box velocity vectors to use in tests. More...
const std::vector < PressureCouplingOptions >	c_options
	Sets of pressure-coupling MDP options to use in tests. More...

Typedef Documentation

using gmx::test::anonymous_namespace{parrinellorahman.cpp}::ParrinelloRahmanTestParameters = typedef std::tuple<PressureCouplingOptions, PressureMatrixType, BoxShape, Matrix3x3, Matrix3x3>

Convenience typedef of the test input parameters.

Parameters:

• pressure-coupling MDP options
• the matrix properties of the input pressure
• the shape of the box
• the box matrix
• the box velocity matrix

Enumeration Type Documentation

enum gmx::test::anonymous_namespace{parrinellorahman.cpp}::PressureMatrixType

strong

Some kinds of matrices of simulation box pressure.

The symmetric ones are useful for testing e.g. that anisotropic coupling preserves symmetry if the inputs are symmetric.

Enumerator
PartlyUniformDiagonal	all three diagonal entries are equal
Diagonal	two diagonal entries are equal
General	diagonal with unequal entries
Extreme	All elements non-zero.
Count	All elements non-zero and of large magnitude.

Variable Documentation

const EnumerationArray<BoxShape, std::vector<Matrix3x3> > gmx::test::anonymous_namespace{parrinellorahman.cpp}::c_boxVectors

Initial value:

= {
    makeBoxes<BoxShape::Cubic>({ 2.5, 1e4 }),
    makeBoxes<BoxShape::Rectilinear>({ 2.5, 1e4 }),
    makeBoxes<BoxShape::RhombicDodecahedronXYSquare>({ 2.5, 1e4 }),
    makeBoxes<BoxShape::RhombicDodecahedronXYHexagon>({ 2.5, 1e4 }),
    makeBoxes<BoxShape::TruncatedOctahedron>({ 2.5, 1e4 }),
    makeBoxes<BoxShape::Other>({ 2.5, 1e4 }),
}

Sets of box vectors to use in tests.

const EnumerationArray<BoxShape, std::vector<Matrix3x3> > gmx::test::anonymous_namespace{parrinellorahman.cpp}::c_boxVelocities

Initial value:

= {
    makeBoxes<BoxShape::Cubic>({ -1e2, -1., -1e-7, 0., 1e-7, 1., 1e2 }),
    makeBoxes<BoxShape::Rectilinear>({ -1e2, -1., -1e-7, 0., 1e-7, 1., 1e2 }),
    makeBoxes<BoxShape::RhombicDodecahedronXYSquare>({ -1e2, -1., -1e-7, 0., 1e-7, 1., 1e2 }),
    makeBoxes<BoxShape::RhombicDodecahedronXYHexagon>({ -1e2, -1., -1e-7, 0., 1e-7, 1., 1e2 }),
    makeBoxes<BoxShape::TruncatedOctahedron>({ -1e2, -1., -1e-7, 0., 1e-7, 1., 1e2 }),
    makeBoxes<BoxShape::Other>({ -1e2, -1., -1e-7, 0., 1e-7, 1., 1e2 }),
}

Sets of box velocity vectors to use in tests.

const std::vector<PressureCouplingOptions> gmx::test::anonymous_namespace{parrinellorahman.cpp}::c_options

Initial value:

= []() {
    PressureCouplingOptions options;
    options.epc               = PressureCoupling::ParrinelloRahman;
    options.tau_p             = 1.;
    Matrix3x3 compressibility = diagonalMatrix<real, 3, 3>(4.5e-5);
    fillLegacyMatrix(compressibility, options.compress);

    Matrix3x3 referencePressure = identityMatrix<real, 3, 3>();
    fillLegacyMatrix(referencePressure, options.ref_p);

    std::vector<PressureCouplingOptions> optionsVector;
    for (const PressureCouplingType pressureCouplingType : { PressureCouplingType::Isotropic,
                                                             
                                                             PressureCouplingType::Anisotropic })
    {
        options.epct = pressureCouplingType;
        optionsVector.push_back(options);
    }

    return optionsVector;
}()

Sets of pressure-coupling MDP options to use in tests.

const EnumerationArray<PressureMatrixType, Matrix3x3> gmx::test::anonymous_namespace{parrinellorahman.cpp}::c_pressureMatrices

Initial value:

= {
    
     Matrix3x3{{ -2.1,    0,    0,
                    0, -2.1,    0,
                    0,    0, -2.1 }},
     Matrix3x3{{ -2.1,    0,    0,
                    0, -2.1,    0,
                    0,    0,  3.4 }},
     Matrix3x3{{ -2.1,    0,    0,
                    0, -1.7,    0,
                    0,    0,  3.4 }},
     Matrix3x3{{ -2.1,  1.3, -1.1,
                  1.4, -1.7,  2.3,
                 -1.0,  2.2,  3.4}},
     
     Matrix3x3{{  2e5,  1e5,  3e5,
                  3e5,  1e5,  2e5,
                  1e5,  2e5,  3e5}}
    
}

Some matrices of simulation box pressure.

constexpr gmx::EnumerationArray<BoxShape, const char*> gmx::test::anonymous_namespace{parrinellorahman.cpp}::sc_boxShapeNames

Initial value:

= {
    "shape_cubic",
    "shape_rect", 
    "shape_rds",  
    "shape_rdh",  
    "shape_to",   
    "shape_other"
}

constexpr gmx::EnumerationArray<PressureMatrixType, const char*> gmx::test::anonymous_namespace{parrinellorahman.cpp}::sc_pressureMatrixTypeNames

Initial value:

= {
    "pmt_unif diag",
    "pmt_part unif diag",
    "pmt_diagonal",
    "pmt_general",
    "pmt_extreme"
}

Helper array for describing tests.

These are used in naming test reference data files, and we have hard limits on file lengths, so we must abbreviate.

const NameOfTestFromTuple<ParrinelloRahmanTestParameters> gmx::test::anonymous_namespace{parrinellorahman.cpp}::sc_testNamer

Initial value:

{ std::make_tuple(
        pressureCouplingOptionsToString,
        sc_pressureMatrixTypeNames,
        sc_boxShapeNames,
        Matrix3x3ToString{ "box" },
        Matrix3x3ToString{ "boxv" }) }

Tuple of formatters to name the parameterized test cases.