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36 * \brief Implements test of 1-4 interactions
38 * This test is copied from the bonded interactions test and slightly
39 * modified since 'do_pairs' takes a different set of arguments than
40 * 'calculateSimpleBond'. To keep the test setup uncluttered this test is
41 * therefore not merged into the bonded test but implemented standalone.
43 * The test setup consists of 2 atom pairs that are tested in an fep setting
44 * (vanishing charge and lennard-jones parameters of one atom) and without
45 * fep. Placement of the atoms in the box is such that shift-forces and pbc
46 * paths in do_pairs are covered.
48 * \author Sebastian Kehl <sebastian.kehl@mpcdf.mpg.de>
49 * \ingroup module_listed_forces
53 #include "gromacs/listed_forces/bonded.h"
58 #include <unordered_map>
60 #include <gtest/gtest.h>
62 #include "gromacs/listed_forces/listed_forces.h"
63 #include "gromacs/listed_forces/pairs.h"
64 #include "gromacs/math/paddedvector.h"
65 #include "gromacs/math/units.h"
66 #include "gromacs/math/vec.h"
67 #include "gromacs/math/vectypes.h"
68 #include "gromacs/mdtypes/mdatom.h"
69 #include "gromacs/mdtypes/simulation_workload.h"
70 #include "gromacs/mdtypes/enerdata.h"
71 #include "gromacs/mdtypes/forcerec.h"
72 #include "gromacs/mdtypes/inputrec.h"
73 #include "gromacs/mdtypes/interaction_const.h"
74 #include "gromacs/mdtypes/nblist.h"
75 #include "gromacs/tables/forcetable.h"
76 #include "gromacs/pbcutil/ishift.h"
77 #include "gromacs/pbcutil/pbc.h"
78 #include "gromacs/topology/idef.h"
79 #include "gromacs/utility/enumerationhelpers.h"
80 #include "gromacs/utility/strconvert.h"
81 #include "gromacs/utility/stringstream.h"
82 #include "gromacs/utility/textwriter.h"
83 #include "gromacs/utility/fatalerror.h"
85 #include "testutils/refdata.h"
86 #include "testutils/testasserts.h"
95 //! Number of atoms used in these tests.
96 constexpr int c_numAtoms = 3;
98 /*! \brief Output from pairs kernels
101 struct OutputQuantities
103 OutputQuantities(int energyGroup) :
105 dvdLambda(static_cast<int>(FreeEnergyPerturbationCouplingType::Count), 0.0)
109 //! Energy of this interaction
110 gmx_grppairener_t energy;
111 //! Derivative with respect to lambda
112 std::vector<real> dvdLambda;
114 rvec fShift[gmx::detail::c_numIvecs] = { { 0 } };
116 alignas(GMX_REAL_MAX_SIMD_WIDTH * sizeof(real)) rvec4 f[c_numAtoms] = { { 0 } };
119 /*! \brief Utility to check the output from pairs tests
121 * \param[in] checker Reference checker
122 * \param[in] output The output from the test to check
123 * \param[in] bondedKernelFlavor Flavor for determining what output to check
124 * \param[in] functionType type of the interaction
126 void checkOutput(TestReferenceChecker* checker,
127 const OutputQuantities& output,
128 const BondedKernelFlavor bondedKernelFlavor,
129 const int functionType)
131 if (computeEnergy(bondedKernelFlavor))
133 switch (functionType)
137 checker->checkReal(output.energy.energyGroupPairTerms[NonBondedEnergyTerms::Coulomb14][0],
139 checker->checkReal(output.energy.energyGroupPairTerms[NonBondedEnergyTerms::LJ14][0],
143 checker->checkReal(output.energy.energyGroupPairTerms[NonBondedEnergyTerms::CoulombSR][0],
145 checker->checkReal(output.energy.energyGroupPairTerms[NonBondedEnergyTerms::LJSR][0],
148 default: gmx_fatal(FARGS, "Unknown function type %d in do_nonbonded14", functionType);
150 checker->checkReal(output.dvdLambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Coul)],
152 checker->checkReal(output.dvdLambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Vdw)],
155 checker->checkSequence(std::begin(output.f), std::end(output.f), "Forces");
158 /* \brief Utility class to setup forcerec and interaction parameters
160 * Data is only initialized as necessary for the 1-4 interactions to work!
167 fepVals_.sc_alpha = 0.3;
168 fepVals_.sc_power = 1;
169 fepVals_.sc_r_power = 6.0;
170 fepVals_.sc_sigma = 0.3;
171 fepVals_.sc_sigma_min = 0.3;
172 fepVals_.bScCoul = true;
174 fr_.ic = std::make_unique<interaction_const_t>();
176 fr_.ic->softCoreParameters = std::make_unique<interaction_const_t::SoftCoreParameters>(fepVals_);
179 real tableRange = 2.9;
180 fr_.pairsTable = make_tables(nullptr, fr_.ic.get(), nullptr, tableRange, GMX_MAKETABLES_14ONLY);
183 fr_.use_simd_kernels = useSimd_;
184 fr_.bMolPBC = haveMolPBC_;
187 t_forcerec* get() { return &fr_; }
190 FreeEnergyPerturbationType haveFep_ = FreeEnergyPerturbationType::No;
191 bool useSimd_ = false;
192 bool haveMolPBC_ = false;
198 ForcerecHelper frHelper;
201 /*! \brief Input structure for listed forces tests
210 //! Tolerance for float evaluation
211 float floatToler = 1e-6;
212 //! Tolerance for double evaluation
213 double doubleToler = 1e-8;
214 //! Interaction parameters
215 t_iparams iparams = { { 0 } };
220 /*! \brief Constructor with tolerance
222 * \param[in] ftol Single precision tolerance
223 * \param[in] dtol Double precision tolerance
225 ListInput(float ftol, double dtol)
231 /*! \brief Set parameters for lj14 interaction
233 * Fep is used if either c6A != c6B or c12A != c12B.
235 * \param[in] c6A lj-c6 of state A
236 * \param[in] c12A lj-c12 of state A
237 * \param[in] c6B lj-c6 of state B
238 * \param[in] c12B lj-c12 of state B
240 ListInput setLj14Interaction(real c6A, real c12A, real c6B, real c12B)
243 fep = (c6A != c6B || c12A != c12B);
244 iparams.lj14.c6A = c6A;
245 iparams.lj14.c12A = c12A;
246 iparams.lj14.c6B = c6B;
247 iparams.lj14.c12B = c12B;
252 /*! \brief Set parameters for ljc14 interaction
254 * \param[in] qi charge i
255 * \param[in] qj charge j
256 * \param[in] c6 lj-c6
257 * \param[in] c12 lj-c12
258 * \param[in] fudgeQ fudge factor
260 ListInput setLjc14Interaction(real qi, real qj, real c6, real c12, real fudgeQ)
263 iparams.ljc14.qi = qi;
264 iparams.ljc14.qj = qj;
265 iparams.ljc14.c6 = c6;
266 iparams.ljc14.c12 = c12;
267 iparams.ljc14.fqq = fudgeQ;
272 /*! \brief Set parameters for ljcnb interaction
274 * \param[in] qi charge i
275 * \param[in] qj charge j
276 * \param[in] c6 lj-c6
277 * \param[in] c12 lj-c12
279 ListInput setLjcnbInteraction(real qi, real qj, real c6, real c12)
281 fType = F_LJC_PAIRS_NB;
282 iparams.ljcnb.qi = qi;
283 iparams.ljcnb.qj = qj;
284 iparams.ljcnb.c6 = c6;
285 iparams.ljcnb.c12 = c12;
291 class ListedForcesPairsTest :
292 public ::testing::TestWithParam<std::tuple<ListInput, PaddedVector<RVec>, PbcType>>
297 PaddedVector<RVec> x_;
300 TestReferenceData refData_;
301 TestReferenceChecker checker_;
303 ListedForcesPairsTest() : checker_(refData_.rootChecker())
305 input_ = std::get<0>(GetParam());
306 x_ = std::get<1>(GetParam());
307 pbcType_ = std::get<2>(GetParam());
309 box_[0][0] = box_[1][1] = box_[2][2] = 1.0;
310 set_pbc(&pbc_, pbcType_, box_);
312 FloatingPointTolerance tolerance = relativeToleranceAsPrecisionDependentFloatingPoint(
313 1.0, input_.floatToler, input_.doubleToler);
315 checker_.setDefaultTolerance(tolerance);
318 void testOneIfunc(TestReferenceChecker* checker, const real lambda)
320 SCOPED_TRACE(std::string("Testing PBC type: ") + c_pbcTypeNames[pbcType_]);
322 // 'definition of pairs' is a concatenation of #npairs (here 2)
323 // 'nAtomsPerPair+1'-tuples (fType a_0 a_i ... a_nAtomsPerPair)
324 std::vector<t_iatom> iatoms = { 0, 1, 2, 0, 0, 2 };
326 std::vector<int> ddgatindex = { 0, 1, 2 };
327 std::vector<real> chargeA = { 1.0, -0.5, -0.5 };
328 std::vector<real> chargeB = { 0.0, 0.0, 0.0 };
329 std::vector<unsigned short> egrp = { 0, 0, 0 };
330 t_mdatoms mdatoms = { 0 };
332 mdatoms.chargeA = chargeA.data();
333 mdatoms.chargeB = chargeB.data();
334 mdatoms.cENER = egrp.data();
335 // nPerturbed is not decisive for fep to be used; it is overruled by
336 // other conditions in do_pairs_general; just here to not segfault
338 mdatoms.nPerturbed = 0;
340 t_forcerec* fr = frHelper.get();
341 fr->efep = input_.fep ? FreeEnergyPerturbationType::Yes : FreeEnergyPerturbationType::No;
342 if (pbcType_ != PbcType::No)
347 std::vector<BondedKernelFlavor> flavors = { BondedKernelFlavor::ForcesAndVirialAndEnergy };
349 if (!input_.fep || lambda == 0)
351 fr->use_simd_kernels = true;
352 flavors.push_back(BondedKernelFlavor::ForcesSimdWhenAvailable);
355 for (const auto flavor : flavors)
357 SCOPED_TRACE("Testing bonded kernel flavor: " + c_bondedKernelFlavorStrings[flavor]);
359 StepWorkload stepWork;
360 stepWork.computeVirial = computeVirial(flavor);
361 stepWork.computeEnergy = computeEnergy(flavor);
363 bool havePerturbedInteractions = input_.fep;
364 if (flavor == BondedKernelFlavor::ForcesSimdWhenAvailable)
366 havePerturbedInteractions = false;
369 int numEnergyTerms = static_cast<int>(NonBondedEnergyTerms::Count);
370 int numFepCouplingTerms = static_cast<int>(FreeEnergyPerturbationCouplingType::Count);
371 OutputQuantities output(numEnergyTerms);
372 std::vector<real> lambdas(numFepCouplingTerms, lambda);
374 do_pairs(input_.fType,
378 as_rvec_array(x_.data()),
383 output.dvdLambda.data(),
384 gmx::arrayRefFromArray(mdatoms.chargeA, mdatoms.nr),
385 gmx::arrayRefFromArray(mdatoms.chargeB, mdatoms.nr),
386 gmx::arrayRefFromArray(mdatoms.bPerturbed, mdatoms.nr),
387 gmx::arrayRefFromArray(mdatoms.cENER, mdatoms.nr),
390 havePerturbedInteractions,
395 checkOutput(checker, output, flavor, input_.fType);
396 auto shiftForcesChecker = checker->checkCompound("Shift-Forces", "Shift-forces");
398 if (computeVirial(flavor))
400 shiftForcesChecker.checkVector(output.fShift[gmx::c_centralShiftIndex], "Central");
404 // Permit omitting to compare shift forces with
405 // reference data when that is useless.
406 shiftForcesChecker.disableUnusedEntriesCheck();
413 TestReferenceChecker thisChecker =
414 checker_.checkCompound("FunctionType", interaction_function[input_.fType].name)
415 .checkCompound("FEP", (input_.fep ? "Yes" : "No"));
419 const int numLambdas = 3;
420 for (int i = 0; i < numLambdas; ++i)
422 const real lambda = i / (numLambdas - 1.0);
423 auto lambdaChecker = thisChecker.checkCompound("Lambda", toString(lambda));
424 testOneIfunc(&lambdaChecker, lambda);
429 testOneIfunc(&thisChecker, 0.0);
434 TEST_P(ListedForcesPairsTest, Ifunc)
439 //! Function types for testing 1-4 interaction. Add new terms at the end.
440 std::vector<ListInput> c_14Interaction = {
441 { ListInput(1e-5, 1e-7).setLj14Interaction(0.001458, 1.0062882e-6, 0.0, 0.0) },
442 { ListInput(1e-5, 1e-7).setLj14Interaction(0.001458, 1.0062882e-6, 0.001458, 1.0062882e-6) },
443 { ListInput(1e-5, 1e-7).setLjc14Interaction(1.0, -1.0, 0.001458, 1.0062882e-6, 0.5) },
444 { ListInput(1e-5, 1e-7).setLjcnbInteraction(1.0, -1.0, 0.001458, 1.0062882e-6) }
447 //! PBC values for testing
448 std::vector<PbcType> c_pbcForTests = { PbcType::No, PbcType::XY, PbcType::Xyz };
450 /*! \brief Coordinates for testing 1-4 interaction
452 * Define coordinates for 3 atoms here, which will be used in 2 interactions.
454 std::vector<PaddedVector<RVec>> c_coordinatesFor14Interaction = {
455 { { 0.0, 0.0, 0.0 }, { 1.0, 1.0, 1.0 }, { 1.1, 1.2, 1.3 } }
458 INSTANTIATE_TEST_CASE_P(14Interaction,
459 ListedForcesPairsTest,
460 ::testing::Combine(::testing::ValuesIn(c_14Interaction),
461 ::testing::ValuesIn(c_coordinatesFor14Interaction),
462 ::testing::ValuesIn(c_pbcForTests)));