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37 * Tests COM handling code.
39 * \author Paul Bauer <paul.bauer.q@gmail.com>
40 * \ingroup module_pbcutil
44 #include "gromacs/pbcutil/com.h"
48 #include <gtest/gtest.h>
50 #include "gromacs/math/vectypes.h"
51 #include "gromacs/pbcutil/pbc.h"
52 #include "gromacs/topology/mtop_util.h"
53 #include "gromacs/topology/topology.h"
55 #include "testutils/refdata.h"
56 #include "testutils/testasserts.h"
67 /*! \brief Populates a molectype for generate a graph
69 * This moleculetype has the first and last atom not connected to the other atoms
70 * so we test optimizations in the shift code that generates the actual graph only
71 * for the atom range from the first to the last connected atoms.
73 * Defines three residues to test residue and molecule COM handling.
75 * \todo Return moltype once t_atoms is a proper class.
77 void populateMoleculeType(gmx_moltype_t* moltype)
79 constexpr int atomNumber = 5;
80 constexpr int residueNumber = 3;
81 moltype->atoms.nr = atomNumber;
82 moltype->ilist[F_CONSTR].iatoms = { 0, 1, 2 };
83 moltype->ilist[F_ANGLES].iatoms = { 1, 2, 1, 3 };
85 snew(moltype->atoms.atom, atomNumber);
86 snew(moltype->atoms.resinfo, residueNumber);
87 moltype->atoms.atom[0].resind = 0;
88 moltype->atoms.atom[1].resind = 1;
89 moltype->atoms.atom[2].resind = 1;
90 moltype->atoms.atom[3].resind = 1;
91 moltype->atoms.atom[4].resind = 2;
93 moltype->atoms.atom[0].m = 42;
94 moltype->atoms.atom[1].m = 13;
95 moltype->atoms.atom[2].m = 7;
96 moltype->atoms.atom[3].m = 23;
97 moltype->atoms.atom[4].m = 2;
100 //! Set up initial coordinates.
101 std::vector<RVec> initialCoordinates()
103 std::vector<RVec> coordinates;
104 coordinates.emplace_back(-1, 0, 3);
105 coordinates.emplace_back(1.5, 1.5, 4.5);
106 coordinates.emplace_back(1.6, 1.5, 4.5);
107 coordinates.emplace_back(1.6, 1.7, 4.5);
108 coordinates.emplace_back(1, 4, 2);
110 coordinates.emplace_back(1, 0, -3);
111 coordinates.emplace_back(-1.5, -1.5, -4.5);
112 coordinates.emplace_back(-1.6, -1.5, -4.5);
113 coordinates.emplace_back(-1.6, -1.7, -4.5);
114 coordinates.emplace_back(-1, -4, -2);
119 using COMInPlaceTestParams = std::tuple<UnitCellType, CenteringType, PbcType>;
120 using test::FloatingPointTolerance;
123 * Test fixture for checking correct molecule COM treatment.
125 class COMInPlaceTest : public ::testing::Test, public ::testing::WithParamInterface<COMInPlaceTestParams>
130 //! Run the test with the given input for molecule COM.
131 void runTestMolecule(const matrix box);
132 //! Run the test with the given input for residue COM.
133 void runTestResidue(const matrix box);
136 //! Coordinates to use.
137 std::vector<RVec> testCoordinates_;
138 //! Dummy topology to use.
139 gmx_mtop_t testTopology_;
140 //! Reference data holder.
141 TestReferenceData data_;
142 //! Checker for data.
143 TestReferenceChecker checker_;
146 COMInPlaceTest::COMInPlaceTest() :
147 testCoordinates_(initialCoordinates()), checker_(data_.rootChecker())
149 auto& moltype = testTopology_.moltype.emplace_back();
150 populateMoleculeType(&moltype);
151 auto& molblock = testTopology_.molblock.emplace_back();
154 testTopology_.natoms = moltype.atoms.nr * molblock.nmol;
155 testTopology_.finalize();
156 FloatingPointTolerance tolerance(
157 FloatingPointTolerance(1.0e-6, 1.0e-6, 1.0e-8, 1.0e-12, 10000, 100, false));
158 checker_.setDefaultTolerance(tolerance);
161 void COMInPlaceTest::runTestMolecule(const matrix box)
163 auto params = GetParam();
164 auto unitcell = std::get<0>(params);
165 auto center = std::get<1>(params);
166 auto pbcType = std::get<2>(params);
167 placeCoordinatesWithCOMInBox(
168 pbcType, unitcell, center, box, testCoordinates_, testTopology_, COMShiftType::Molecule);
169 std::string testString = "Molecule " + std::string(unitCellTypeNames(unitcell))
170 + std::string(centerTypeNames(center)) + c_pbcTypeNames[pbcType]
171 + c_pbcTypeNames[guessPbcType(box)];
172 checker_.checkSequence(std::begin(testCoordinates_), std::end(testCoordinates_), testString.c_str());
175 void COMInPlaceTest::runTestResidue(const matrix box)
177 auto params = GetParam();
178 auto unitcell = std::get<0>(params);
179 auto center = std::get<1>(params);
180 auto pbcType = std::get<2>(params);
181 placeCoordinatesWithCOMInBox(
182 pbcType, unitcell, center, box, testCoordinates_, testTopology_, COMShiftType::Residue);
183 std::string testString = "Residue " + std::string(unitCellTypeNames(unitcell))
184 + std::string(centerTypeNames(center)) + c_pbcTypeNames[pbcType]
185 + c_pbcTypeNames[guessPbcType(box)];
186 checker_.checkSequence(std::begin(testCoordinates_), std::end(testCoordinates_), testString.c_str());
189 TEST(ShiftTest, CoordinateShiftWorks)
191 auto coords = initialCoordinates();
192 const RVec shift(1.5, -2.2, 0);
194 shiftAtoms(shift, coords);
195 EXPECT_FLOAT_EQ(coords[4][0], 2.5);
196 EXPECT_FLOAT_EQ(coords[3][1], -0.5);
197 EXPECT_FLOAT_EQ(coords[9][2], -2);
201 TEST_P(COMInPlaceTest, MatrixDefault)
203 const matrix box = { { 3, 0, 0 }, { 0, 3, 0 }, { 0, 0, 3 } };
205 runTestMolecule(box);
209 INSTANTIATE_TEST_SUITE_P(CorrectCoordinates,
211 testing::Combine(::testing::Values(UnitCellType::Compact,
212 UnitCellType::Rectangular,
213 UnitCellType::Triclinic),
214 ::testing::Values(CenteringType::Rectangular,
215 CenteringType::Triclinic,
216 CenteringType::Zero),
217 ::testing::Values(PbcType::No, PbcType::Xyz, PbcType::XY)));
219 // TODO add PbcType::Screw once it is fully supported.