Classes
struct	OutputQuantities
	Output from bonded kernels. More...

struct	iListInput
	Input structure for listed forces tests. More...

Functions
void	checkOutput (TestReferenceChecker *checker, const OutputQuantities &output, const BondedKernelFlavor bondedKernelFlavor)
	Utility to check the output from bonded tests. More...

std::ostream &	operator<< (std::ostream &out, const iListInput &input)
	Prints the interaction and parameters to a stream.

void	fillIatoms (int ftype, std::vector< t_iatom > *iatoms)
	Utility to fill iatoms struct. More...

Variables
constexpr int	c_numAtoms = 4
	Number of atoms used in these tests.

std::vector< iListInput >	c_InputBonds
	Function types for testing bonds. Add new terms at the end. More...

const real	cQuarticAngles [5] = { 1.1, 2.3, 4.6, 7.8, 9.2 }
	Constants for Quartic Angles.

std::vector< iListInput >	c_InputAngles
	Function types for testing angles. Add new terms at the end. More...

const real	rbcA [NR_RBDIHS] = { -5.35, 13.6, 8.4, -16.7, 0.3, 12.4 }
	Constants for Ryckaert-Bellemans A.

const real	rbcB [NR_RBDIHS] = { -6.35, 12.6, 8.1, -10.7, 0.9, 15.4 }
	Constants for Ryckaert-Bellemans B.

const real	rbc [NR_RBDIHS] = { -7.35, 13.6, 8.4, -16.7, 1.3, 12.4 }
	Constants for Ryckaert-Bellemans without FEP.

std::vector< iListInput >	c_InputDihs
	Function types for testing dihedrals. Add new terms at the end. More...

std::vector< iListInput >	c_InputPols
	Function types for testing polarization. Add new terms at the end. More...

std::vector< iListInput >	c_InputRestraints
	Function types for testing polarization. Add new terms at the end. More...

std::vector< iListInput >	c_InputBondsZeroLength
	Function types for testing bond with zero length, has zero reference length to make physical sense. More...

std::vector< iListInput >	c_InputAnglesZeroAngle
	Function types for testing angles with zero angle, has zero reference angle to make physical sense. More...

std::vector< PaddedVector< RVec > >	c_coordinatesForTests
	Coordinates for testing. More...

std::vector< PaddedVector< RVec > >	c_coordinatesForTestsZeroBondLength
	Coordinates for testing bonds with zero length. More...

std::vector< PaddedVector< RVec > >	c_coordinatesForTestsZeroAngle
	Coordinates for testing bonds with zero length. More...

std::vector< PbcType >	c_pbcForTests = { PbcType::No, PbcType::XY, PbcType::Xyz }
	PBC values for testing.

Function Documentation

void gmx::test::anonymous_namespace{bonded.cpp}::checkOutput	(	TestReferenceChecker *	checker,
		const OutputQuantities &	output,
		const BondedKernelFlavor	bondedKernelFlavor
	)

Utility to check the output from bonded tests.

Parameters

[in]	checker	Reference checker
[in]	output	The output from the test to check
[in]	bondedKernelFlavor	Flavor for determining what output to check

void gmx::test::anonymous_namespace{bonded.cpp}::fillIatoms	(	int	ftype,
		std::vector< t_iatom > *	iatoms
	)

Utility to fill iatoms struct.

Parameters

[in]	ftype	Function type
[out]	iatoms	Pointer to iatoms struct

Variable Documentation

std::vector<PaddedVector<RVec> > gmx::test::anonymous_namespace{bonded.cpp}::c_coordinatesForTests

Initial value:

= {
    { { 1.382, 1.573, 1.482 }, { 1.281, 1.559, 1.596 }, { 1.292, 1.422, 1.663 }, { 1.189, 1.407, 1.775 } }
}

Coordinates for testing.

Taken from a butane molecule, so we have some normal-sized bonds and angles to test.

Todo:: Test also some weirder values

std::vector<PaddedVector<RVec> > gmx::test::anonymous_namespace{bonded.cpp}::c_coordinatesForTestsZeroAngle

Initial value:

= {
    { { 0.005, 0.0, 0.1 }, { 0.0, 0.0, 0.0 }, { 0.005, 0.0, 0.1 }, { 0.5, 0.18, 0.22 } }
}

Coordinates for testing bonds with zero length.

std::vector<PaddedVector<RVec> > gmx::test::anonymous_namespace{bonded.cpp}::c_coordinatesForTestsZeroBondLength

Initial value:

= {
    { { 0.0, 0.0, 0.0 }, { 0.0, 0.0, 0.0 }, { 0.005, 0.0, 0.1 }, { 0.005, 0.0, 0.1 } }
}

Coordinates for testing bonds with zero length.

std::vector<iListInput> gmx::test::anonymous_namespace{bonded.cpp}::c_InputAngles

Initial value:

= {
    { iListInput(2e-3, 1e-8).setHarmonic(F_ANGLES, 100.0, 50.0) },
    { iListInput(2e-3, 1e-8).setHarmonic(F_ANGLES, 100.15, 50.0, 95.0, 30.0) },
    { iListInput(8e-3, 1e-8).setHarmonic(F_G96ANGLES, 100.0, 50.0) },
    { iListInput(8e-3, 1e-8).setHarmonic(F_G96ANGLES, 100.0, 50.0, 95.0, 30.0) },
    { iListInput().setLinearAngle(50.0, 0.4) },
    { iListInput().setLinearAngle(50.0, 0.4, 40.0, 0.6) },
    { iListInput(2e-6, 1e-8).setCrossBondBonds(0.8, 0.7, 45.0) },
    { iListInput(3e-6, 1e-8).setCrossBondAngles(0.8, 0.7, 0.3, 45.0) },
    { iListInput(2e-2, 1e-8).setUreyBradley(950.0, 46.0, 0.3, 5.0) },
    { iListInput(2e-2, 1e-8).setUreyBradley(100.0, 45.0, 0.3, 5.0, 90.0, 47.0, 0.32, 7.0) },
    { iListInput(2e-3, 1e-8).setQuarticAngles(87.0, cQuarticAngles) }
}

Function types for testing angles. Add new terms at the end.

std::vector<iListInput> gmx::test::anonymous_namespace{bonded.cpp}::c_InputAnglesZeroAngle

Initial value:

= {
    { iListInput(2e-3, 1e-8).setHarmonic(F_ANGLES, 0.0, 50.0) },
}

Function types for testing angles with zero angle, has zero reference angle to make physical sense.

std::vector<iListInput> gmx::test::anonymous_namespace{bonded.cpp}::c_InputBonds

Initial value:

= {
    { iListInput(2e-6F, 1e-8).setHarmonic(F_BONDS, 0.15, 500.0) },
    { iListInput(2e-6F, 1e-8).setHarmonic(F_BONDS, 0.15, 500.0, 0.17, 400.0) },
    { iListInput(1e-4F, 1e-8).setHarmonic(F_G96BONDS, 0.15, 50.0) },
    { iListInput().setHarmonic(F_G96BONDS, 0.15, 50.0, 0.17, 40.0) },
    { iListInput().setCubic(0.16, 50.0, 2.0) },
    { iListInput(2e-6F, 1e-8).setMorse(0.15, 50.0, 2.0, 0.17, 40.0, 1.6) },
    { iListInput(2e-6F, 1e-8).setMorse(0.15, 30.0, 2.7) },
    { iListInput().setFene(0.4, 5.0) }
}

Function types for testing bonds. Add new terms at the end.

std::vector<iListInput> gmx::test::anonymous_namespace{bonded.cpp}::c_InputBondsZeroLength

Initial value:

= {
    { iListInput().setHarmonic(F_BONDS, 0.0, 500.0) },
}

Function types for testing bond with zero length, has zero reference length to make physical sense.

std::vector<iListInput> gmx::test::anonymous_namespace{bonded.cpp}::c_InputDihs

Initial value:

= {
    { iListInput(5e-4, 1e-8).setPDihedrals(F_PDIHS, -100.0, 10.0, 2, -80.0, 20.0) },
    { iListInput(1e-4, 1e-8).setPDihedrals(F_PDIHS, -105.0, 15.0, 2) },
    { iListInput(2e-4, 1e-8).setHarmonic(F_IDIHS, 100.0, 50.0) },
    { iListInput(2e-4, 1e-8).setHarmonic(F_IDIHS, 100.15, 50.0, 95.0, 30.0) },
    { iListInput(4e-4, 1e-8).setRbDihedrals(rbcA, rbcB) },
    { iListInput(4e-4, 1e-8).setRbDihedrals(rbc) }
}

Function types for testing dihedrals. Add new terms at the end.

std::vector<iListInput> gmx::test::anonymous_namespace{bonded.cpp}::c_InputPols

Initial value:

= {
    { iListInput(2e-5, 1e-8).setPolarization(0.12) },
    { iListInput(2e-3, 1e-8).setAnharmPolarization(0.0013, 0.02, 1235.6) },
    { iListInput(1.4e-3, 1e-8).setTholePolarization(0.26, 0.07, 0.09) },
    { iListInput(2e-3, 1e-8).setWaterPolarization(0.001, 0.0012, 0.0016, 0.095, 0.15, 0.02) },
}

Function types for testing polarization. Add new terms at the end.

std::vector<iListInput> gmx::test::anonymous_namespace{bonded.cpp}::c_InputRestraints

Initial value:

= {
    { iListInput(1e-4, 1e-8).setPDihedrals(F_ANGRES, -100.0, 10.0, 2, -80.0, 20.0) },
    { iListInput(1e-4, 1e-8).setPDihedrals(F_ANGRES, -105.0, 15.0, 2) },
    { iListInput(1e-4, 1e-8).setPDihedrals(F_ANGRESZ, -100.0, 10.0, 2, -80.0, 20.0) },
    { iListInput(1e-4, 1e-8).setPDihedrals(F_ANGRESZ, -105.0, 15.0, 2) },
    { iListInput(2e-3, 1e-8).setHarmonic(F_RESTRANGLES, 100.0, 50.0) },
    { iListInput(2e-3, 1e-8).setHarmonic(F_RESTRANGLES, 100.0, 50.0, 110.0, 45.0) }
}

Function types for testing polarization. Add new terms at the end.

Classes

Functions

Variables

Function Documentation

Variable Documentation