nb_free_energy.cpp File Reference

#include "gmxpre.h"
#include "gromacs/gmxlib/nonbonded/nb_free_energy.h"
#include "config.h"
#include <cmath>
#include <iterator>
#include <memory>
#include <string>
#include <tuple>
#include <utility>
#include <vector>
#include <gtest/gtest.h>
#include "gromacs/ewald/ewald_utils.h"
#include "gromacs/gmxlib/nonbonded/nonbonded.h"
#include "gromacs/gmxlib/nrnb.h"
#include "gromacs/math/arrayrefwithpadding.h"
#include "gromacs/math/paddedvector.h"
#include "gromacs/math/units.h"
#include "gromacs/math/vec.h"
#include "gromacs/math/vectypes.h"
#include "gromacs/mdlib/forcerec.h"
#include "gromacs/mdtypes/enerdata.h"
#include "gromacs/mdtypes/forceoutput.h"
#include "gromacs/mdtypes/forcerec.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/interaction_const.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/mdtypes/mdatom.h"
#include "gromacs/mdtypes/nblist.h"
#include "gromacs/pbcutil/ishift.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/tables/forcetable.h"
#include "gromacs/topology/forcefieldparameters.h"
#include "gromacs/topology/idef.h"
#include "gromacs/topology/ifunc.h"
#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/enumerationhelpers.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/real.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/strconvert.h"
#include "gromacs/utility/stringstream.h"
#include "gromacs/utility/textwriter.h"
#include "testutils/refdata.h"
#include "testutils/testasserts.h"

Include dependency graph for nb_free_energy.cpp:

Description

Implements test of nonbonded fep kernel.

Implements the test logic from the bonded interactions also for the nonbonded fep kernel. This requires setting up some more input structures that in the bonded case.

The test setup consists of an atom pair that is evaluated in an fep setting (vanishing charge and lennard-jones parameters of atom #2) with and without softcore Potentials.

Author

Sebastian Kehl sebas.nosp@m.tian.nosp@m..kehl.nosp@m.@mpc.nosp@m.df.mp.nosp@m.g.de

Classes
struct	gmx::test::anonymous_namespace{nb_free_energy.cpp}::OutputQuantities
	Output from nonbonded fep kernel. More...
struct	gmx::test::anonymous_namespace{nb_free_energy.cpp}::AtomData
	Utility structure to hold atoms data. More...
struct	gmx::test::anonymous_namespace{nb_free_energy.cpp}::ListInput
	Input structure for nonbonded fep kernel. More...

Functions
void	gmx::test::anonymous_namespace{nb_free_energy.cpp}::checkOutput (TestReferenceChecker *checker, const OutputQuantities &output)
	Utility to check the output from nonbonded test. More...

Variables
constexpr int	gmx::test::anonymous_namespace{nb_free_energy.cpp}::c_numAtoms = 4
	Number of atoms used in these tests.
constexpr int	gmx::test::anonymous_namespace{nb_free_energy.cpp}::c_numAtomTypes = 3
std::vector< ListInput >	gmx::test::anonymous_namespace{nb_free_energy.cpp}::c_interaction
	configurations to test More...
std::vector< real >	gmx::test::anonymous_namespace{nb_free_energy.cpp}::c_fepLambdas = { 0.0, 0.5, 1.0 }
	test parameters
std::vector< real >	gmx::test::anonymous_namespace{nb_free_energy.cpp}::c_softcoreBeutlerAlphaOrGapsysLinpointScaling = { 0.0, 0.3 }
std::vector< bool >	gmx::test::anonymous_namespace{nb_free_energy.cpp}::c_softcoreCoulomb = { true, false }
std::vector< SoftcoreType >	gmx::test::anonymous_namespace{nb_free_energy.cpp}::c_softcoreType = { SoftcoreType::Beutler, SoftcoreType::Gapsys }
std::vector< PaddedVector< RVec > >	gmx::test::anonymous_namespace{nb_free_energy.cpp}::c_coordinates
	Coordinates for testing. More...
std::vector< PaddedVector< RVec > >	gmx::test::anonymous_namespace{nb_free_energy.cpp}::c_coordinatesShortDistance
	Coordinates for testing with near atomic overlap. More...