nblib/tests/molecules.cpp

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/*! \internal \file
 * \brief
 * This implements molecule setup tests
 *
 * \author Victor Holanda <victor.holanda@cscs.ch>
 * \author Joe Jordan <ejjordan@kth.se>
 * \author Prashanth Kanduri <kanduri@cscs.ch>
 * \author Sebastian Keller <keller@cscs.ch>
 * \author Artem Zhmurov <zhmurov@gmail.com>
 */
#include "nblib/molecules.h"
#include "nblib/exception.h"
#include "nblib/particletype.h"
#include "nblib/tests/testsystems.h"

#include "testutils/testasserts.h"

namespace nblib
{
namespace test
{
namespace
{

TEST(NBlibTest, CanConstructMoleculeWithoutChargeOrResidueName)
{
    ArAtom       arAtom;
    ParticleType Ar(arAtom.particleTypeName, arAtom.mass);
    Molecule     argon(arAtom.moleculeName);
    EXPECT_NO_THROW(argon.addParticle(arAtom.particleName, Ar));
}

TEST(NBlibTest, CanConstructMoleculeWithChargeWithoutResidueName)
{
    ArAtom       arAtom;
    ParticleType Ar(arAtom.particleTypeName, arAtom.mass);
    Molecule     argon(arAtom.moleculeName);
    EXPECT_NO_THROW(argon.addParticle(arAtom.particleName, Charge(0), Ar));
}

TEST(NBlibTest, CanConstructMoleculeWithoutChargeWithResidueName)
{
    ArAtom       arAtom;
    ParticleType Ar(arAtom.particleTypeName, arAtom.mass);
    Molecule     argon(arAtom.moleculeName);
    EXPECT_NO_THROW(argon.addParticle(arAtom.particleName, ResidueName("ar2"), Ar));
}

TEST(NBlibTest, CanConstructMoleculeWithChargeWithResidueName)
{
    ArAtom       arAtom;
    ParticleType Ar(arAtom.particleTypeName, arAtom.mass);
    Molecule     argon(arAtom.moleculeName);
    EXPECT_NO_THROW(argon.addParticle(arAtom.particleName, ResidueName("ar2"), Charge(0), Ar));
}

TEST(NBlibTest, CanGetNumParticlesInMolecule)
{
    WaterMoleculeBuilder waterMolecule;
    Molecule             water        = waterMolecule.waterMolecule();
    auto                 numParticles = water.numParticlesInMolecule();

    EXPECT_EQ(3, numParticles);
}

TEST(NBlibTest, CanConstructExclusionListFromNames)
{
    WaterMoleculeBuilder waterMolecule;
    Molecule             water = waterMolecule.waterMolecule();

    std::vector<std::tuple<int, int>> exclusions = water.getExclusions();

    std::vector<std::tuple<int, int>> reference{ { 0, 0 }, { 0, 1 }, { 0, 2 }, { 1, 0 }, { 1, 1 },
                                                 { 1, 2 }, { 2, 0 }, { 2, 1 }, { 2, 2 } };

    ASSERT_EQ(exclusions.size(), 9);
    for (std::size_t i = 0; i < exclusions.size(); ++i)
    {
        EXPECT_EQ(exclusions[i], reference[i]);
    }
}

TEST(NBlibTest, CanConstructExclusionListFromNamesAndIndicesMixed)
{
    WaterMoleculeBuilder waterMolecule;
    Molecule             water = waterMolecule.waterMoleculeWithoutExclusions();

    //! Add the exclusions
    water.addExclusion(ParticleName("H1"), ParticleName("Oxygen"));
    water.addExclusion(ParticleName("H2"), ParticleName("Oxygen"));
    water.addExclusion(ParticleName("H1"), ParticleName("H2"));

    std::vector<std::tuple<int, int>> exclusions = water.getExclusions();

    std::vector<std::tuple<int, int>> reference{ { 0, 0 }, { 0, 1 }, { 0, 2 }, { 1, 0 }, { 1, 1 },
                                                 { 1, 2 }, { 2, 0 }, { 2, 1 }, { 2, 2 } };

    ASSERT_EQ(exclusions.size(), 9);
    for (std::size_t i = 0; i < exclusions.size(); ++i)
    {
        EXPECT_EQ(exclusions[i], reference[i]);
    }
}

TEST(NBlibTest, AtWorks)
{
    WaterMoleculeBuilder waterMolecule;
    Molecule             water = waterMolecule.waterMolecule();
    EXPECT_NO_THROW(water.at("Ow"));
    EXPECT_NO_THROW(water.at("H"));
}

TEST(NBlibTest, AtThrows)
{
    WaterMoleculeBuilder waterMolecule;
    Molecule             water = waterMolecule.waterMolecule();
    EXPECT_THROW_GMX(water.at("Hw"), std::out_of_range);
}

TEST(NBlibTest, MoleculeThrowsSameParticleTypeNameDifferentMass)
{
    //! User error: Two different ParticleTypes with the same name
    ParticleType atom1(ParticleTypeName("Atom"), Mass(1));
    ParticleType atom2(ParticleTypeName("Atom"), Mass(2));

    Molecule molecule(MoleculeName("UraniumDimer"));
    EXPECT_NO_THROW(molecule.addParticle(ParticleName("U1"), atom1));
    EXPECT_THROW(molecule.addParticle(ParticleName("U2"), atom2), InputException);
}

TEST(NBlibTest, MoleculeDontThrowsSameParticleTypeNameDifferentMass)
{
    //! User error: Two different ParticleTypes with the same name
    ParticleType atom1(ParticleTypeName("Atom"), Mass(1));
    ParticleType atom2(ParticleTypeName("Atom"), Mass(1));

    Molecule molecule(MoleculeName("UraniumDimer"));
    EXPECT_NO_THROW(molecule.addParticle(ParticleName("U1"), atom1));
    EXPECT_NO_THROW(molecule.addParticle(ParticleName("U2"), atom2));
}

TEST(NBlibTest, MoleculeNoThrowsSameParticleTypeName)
{
    //! User error: Two different ParticleTypes with the same name
    ParticleType atom1(ParticleTypeName("Atom"), Mass(1));
    ParticleType atom2(ParticleTypeName("Atom"), Mass(1));

    Molecule molecule(MoleculeName("UraniumDimer"));
    EXPECT_NO_THROW(molecule.addParticle(ParticleName("U1"), atom1));
    EXPECT_NO_THROW(molecule.addParticle(ParticleName("U2"), atom2));
}

TEST(NBlibTest, CanAddInteractions)
{
    Molecule     molecule(MoleculeName("BondTest"));
    ParticleType O(ParticleTypeName("Ow"), Mass(1));
    ParticleType H(ParticleTypeName("Hw"), Mass(1));
    molecule.addParticle(ParticleName("O"), O);
    molecule.addParticle(ParticleName("H1"), H);
    molecule.addParticle(ParticleName("H2"), H);

    HarmonicBondType  hb(1, 2);
    CubicBondType     cub(1, 2, 3);
    HarmonicAngleType ang(Degrees(1), 1);

    molecule.addInteraction(ParticleName("O"), ParticleName("H1"), hb);
    molecule.addInteraction(ParticleName("O"), ParticleName("H2"), hb);
    molecule.addInteraction(ParticleName("H1"), ParticleName("H2"), cub);
    molecule.addInteraction(ParticleName("H1"), ParticleName("O"), ParticleName("H2"), ang);

    const auto& interactionData = molecule.interactionData();

    //! harmonic bonds
    EXPECT_EQ(pickType<HarmonicBondType>(interactionData).interactions_.size(), 2);
    //! cubic bonds
    EXPECT_EQ(pickType<CubicBondType>(interactionData).interactions_.size(), 1);
    //! angular interactions
    EXPECT_EQ(pickType<HarmonicAngleType>(interactionData).interactions_.size(), 1);
}

} // namespace
} // namespace test
} // namespace nblib