# This file is part of the GROMACS molecular simulation package.
#
# Copyright (c) 2009,2010,2012,2014,2015 by the GROMACS development team.
-# Copyright (c) 2016,2020, by the GROMACS development team, led by
+# Copyright (c) 2016,2020,2021, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
# TODO: Explicitly link specific modules.
#target_link_libraries(gmxlib PRIVATE legacy_modules)
-# if(BUILD_TESTING)
-# add_subdirectory(tests)
-# endif()
+if(BUILD_TESTING)
+ add_subdirectory(nonbonded/tests)
+endif()
--- /dev/null
+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright (c) 2021, by the GROMACS development team, led by
+# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+# and including many others, as listed in the AUTHORS file in the
+# top-level source directory and at http://www.gromacs.org.
+#
+# GROMACS is free software; you can redistribute it and/or
+# modify it under the terms of the GNU Lesser General Public License
+# as published by the Free Software Foundation; either version 2.1
+# of the License, or (at your option) any later version.
+#
+# GROMACS is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+# Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with GROMACS; if not, see
+# http://www.gnu.org/licenses, or write to the Free Software Foundation,
+# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+#
+# If you want to redistribute modifications to GROMACS, please
+# consider that scientific software is very special. Version
+# control is crucial - bugs must be traceable. We will be happy to
+# consider code for inclusion in the official distribution, but
+# derived work must not be called official GROMACS. Details are found
+# in the README & COPYING files - if they are missing, get the
+# official version at http://www.gromacs.org.
+#
+# To help us fund GROMACS development, we humbly ask that you cite
+# the research papers on the package. Check out http://www.gromacs.org.
+
+gmx_add_unit_test(GmxlibTests nonbonded-fep-test
+ CPP_SOURCE_FILES
+ nb_free_energy.cpp
+ )
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2021, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+
+/*! \internal \file
+ * \brief 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 <sebastian.kehl@mpcdf.mpg.de>
+ * \ingroup module_gmxlib_nonbonded
+ */
+#include "gmxpre.h"
+
+#include "gromacs/gmxlib/nonbonded/nb_free_energy.h"
+#include "gromacs/gmxlib/nonbonded/nonbonded.h"
+
+#include <cmath>
+
+#include <gtest/gtest.h>
+
+#include "gromacs/math/paddedvector.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/math/arrayrefwithpadding.h"
+#include "gromacs/mdtypes/mdatom.h"
+#include "gromacs/mdtypes/enerdata.h"
+#include "gromacs/mdtypes/forcerec.h"
+#include "gromacs/mdtypes/inputrec.h"
+#include "gromacs/mdtypes/interaction_const.h"
+#include "gromacs/mdtypes/nblist.h"
+#include "gromacs/mdtypes/forceoutput.h"
+#include "gromacs/mdlib/forcerec.h"
+#include "gromacs/tables/forcetable.h"
+#include "gromacs/pbcutil/ishift.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/idef.h"
+#include "gromacs/topology/forcefieldparameters.h"
+#include "gromacs/utility/enumerationhelpers.h"
+#include "gromacs/utility/strconvert.h"
+#include "gromacs/utility/stringstream.h"
+#include "gromacs/utility/textwriter.h"
+#include "gromacs/utility/arrayref.h"
+#include "gromacs/utility/smalloc.h"
+#include "gromacs/ewald/ewald_utils.h"
+#include "gromacs/gmxlib/nrnb.h"
+
+#include "testutils/refdata.h"
+#include "testutils/testasserts.h"
+
+namespace gmx
+{
+namespace test
+{
+namespace
+{
+
+//! Number of atoms used in these tests.
+constexpr int c_numAtoms = 4;
+constexpr int c_numAtomTypes = 3;
+
+/*! \brief Output from nonbonded fep kernel
+ *
+ */
+struct OutputQuantities
+{
+ OutputQuantities() :
+ energy(static_cast<int>(NonBondedEnergyTerms::Count)),
+ dvdLambda(static_cast<int>(FreeEnergyPerturbationCouplingType::Count), 0.0),
+ fShift(1, { 0.0, 0.0, 0.0 }),
+ f(c_numAtoms, { 0.0, 0.0, 0.0 })
+ {
+ }
+
+ //! Energies of this interaction (size EgNR)
+ gmx_grppairener_t energy;
+ //! Derivative with respect to lambda (size efptNR)
+ std::vector<real> dvdLambda;
+ //! Shift force vectors (size N_IVEC but in this test only 1)
+ std::vector<RVec> fShift;
+ //! Forces (size c_numAtoms)
+ PaddedVector<RVec> f;
+};
+
+/*! \brief Utility to check the output from nonbonded test
+ *
+ * \param[in] checker Reference checker
+ * \param[in] output The output from the test to check
+ */
+void checkOutput(TestReferenceChecker* checker, const OutputQuantities& output)
+{
+ checker->checkReal(output.energy.energyGroupPairTerms[NonBondedEnergyTerms::LJSR][0], "EVdw ");
+ checker->checkReal(output.energy.energyGroupPairTerms[NonBondedEnergyTerms::CoulombSR][0],
+ "ECoul ");
+ checker->checkReal(output.dvdLambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Coul)],
+ "dVdlCoul ");
+ checker->checkReal(output.dvdLambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Vdw)],
+ "dVdlVdw ");
+
+ checker->checkSequence(std::begin(output.f), std::end(output.f), "Forces");
+
+ auto shiftForcesChecker = checker->checkCompound("Shift-Forces", "Shift-forces");
+ shiftForcesChecker.checkVector(output.fShift[0], "Central");
+}
+
+class InteractionConstHelper
+{
+public:
+ InteractionConstHelper() {}
+
+ //! init data to construct interaction_const
+ void initInteractionConst(CoulombInteractionType coulType, VanDerWaalsType vdwType, InteractionModifiers vdwMod)
+ {
+ coulType_ = coulType;
+ vdwType_ = vdwType;
+ vdwMod_ = vdwMod;
+
+ // initialize correction tables
+ interaction_const_t tmp;
+ tmp.ewaldcoeff_q = calc_ewaldcoeff_q(1.0, 1.0e-5);
+ tmp.ewaldcoeff_lj = calc_ewaldcoeff_lj(1.0, 1.0e-5);
+ tmp.eeltype = coulType;
+ tmp.vdwtype = vdwType;
+ tmp.coulombEwaldTables = std::make_unique<EwaldCorrectionTables>();
+ tmp.vdwEwaldTables = std::make_unique<EwaldCorrectionTables>();
+
+ init_interaction_const_tables(nullptr, &tmp, 1.0, 0.0);
+ coulombTables_ = *tmp.coulombEwaldTables;
+ vdwTables_ = *tmp.vdwEwaldTables;
+ }
+
+ /*! \brief Setup interaction_const_t
+ *
+ * \param[in] fepVals t_lambda struct of fep values
+ * \param[out] ic interaction_const_t pointer with data
+ */
+ void getInteractionConst(const t_lambda& fepVals, interaction_const_t* ic)
+ {
+ ic->softCoreParameters = std::unique_ptr<interaction_const_t::SoftCoreParameters>(
+ new interaction_const_t::SoftCoreParameters(fepVals));
+
+ ic->coulombEwaldTables = std::unique_ptr<EwaldCorrectionTables>(new EwaldCorrectionTables);
+ *ic->coulombEwaldTables = coulombTables_;
+
+ ic->vdwEwaldTables = std::unique_ptr<EwaldCorrectionTables>(new EwaldCorrectionTables);
+ *ic->vdwEwaldTables = vdwTables_;
+
+ // set coulomb and vdw types
+ ic->eeltype = coulType_;
+ ic->vdwtype = vdwType_;
+ ic->vdw_modifier = vdwMod_;
+
+ // some non default parameters used in this testcase
+ ic->epsfac = gmx::c_one4PiEps0 * 0.25;
+ ic->reactionFieldCoefficient = 0.0; // former k_rf
+ ic->reactionFieldShift = 1.0; // former c_rf
+ ic->sh_ewald = 1.0e-5;
+ ic->sh_lj_ewald = -1.0;
+ ic->dispersion_shift.cpot = -1.0;
+ ic->repulsion_shift.cpot = -1.0;
+ }
+
+private:
+ //! correction tables
+ EwaldCorrectionTables coulombTables_;
+ EwaldCorrectionTables vdwTables_;
+
+ //! coulomb and vdw type specifiers
+ CoulombInteractionType coulType_;
+ VanDerWaalsType vdwType_;
+ InteractionModifiers vdwMod_;
+};
+
+
+/* \brief Utility class to setup forcerec
+ *
+ * This helper takes care of handling the neccessary data that are kept
+ * at various places and in various forms in the forcerec hierarchy such
+ * that this class can safely be used.
+ *
+ * Data is only initialized as necessary for the nonbonded kernel to work!
+ */
+class ForcerecHelper
+{
+public:
+ ForcerecHelper()
+ {
+ fepVals_.sc_alpha = 0.3;
+ fepVals_.sc_power = 1;
+ fepVals_.sc_r_power = 6.0;
+ fepVals_.sc_sigma = 0.3;
+ fepVals_.sc_sigma_min = 0.3;
+ fepVals_.bScCoul = true;
+ }
+
+ //! initialize data structure to construct forcerec
+ void initForcerec(const gmx_ffparams_t& idef,
+ CoulombInteractionType coulType,
+ VanDerWaalsType vdwType,
+ InteractionModifiers vdwMod)
+ {
+ icHelper_.initInteractionConst(coulType, vdwType, vdwMod);
+ nbfp_ = makeNonBondedParameterLists(idef, false);
+ t_forcerec frTmp;
+ ljPmeC6Grid_ = makeLJPmeC6GridCorrectionParameters(idef, frTmp);
+ }
+
+ void setSoftcoreAlpha(const real scAlpha) { fepVals_.sc_alpha = scAlpha; }
+ void setSoftcoreCoulomb(const real scCoulomb) { fepVals_.bScCoul = scCoulomb; }
+
+ //! get forcerec data as wanted by the nonbonded kernel
+ void getForcerec(t_forcerec* fr)
+ {
+ fr->ic = std::make_unique<interaction_const_t>();
+
+ // set data in ic
+ icHelper_.getInteractionConst(fepVals_, fr->ic.get());
+
+ // set data in fr
+ fr->ljpme_c6grid = ljPmeC6Grid_;
+ fr->nbfp = nbfp_;
+ fr->shift_vec = { { 0.0, 0.0, 0.0 } };
+ fr->rlist = rlist_;
+ fr->ntype = c_numAtomTypes;
+
+ // simd
+ fr->use_simd_kernels = GMX_USE_SIMD_KERNELS;
+ }
+
+private:
+ InteractionConstHelper icHelper_;
+ std::vector<real> ljPmeC6Grid_;
+ std::vector<real> nbfp_;
+ t_lambda fepVals_;
+ real rlist_ = 1.0;
+};
+
+/*! \brief Utility structure to hold atoms data
+ *
+ * A system having 4 interactions with the following perturbation pattern:
+ * - no perturbation
+ * - vdw- and coulomb-perturbation
+ * - coulomb-perturbation only
+ * - vdw-perturbation only
+ *
+ * This is realized by defining 3 different atom types that control
+ * the vdw-perturbation. The coulomb-perturbation is controlled by directly
+ * setting the charge of the atoms at the lambda states A/B.
+ */
+struct AtomData
+{
+ AtomData()
+ {
+ idef.atnr = c_numAtomTypes;
+ idef.iparams.resize(2 * c_numAtomTypes * c_numAtomTypes);
+
+ // set interaction parameters for different combinations of types
+ idef.iparams[0].lj = { 0.001458, 1.0062882e-6 }; // 0-0
+ idef.iparams[1].lj = { 0.0, 0.0 }; // 0-1
+ idef.iparams[2].lj = { 0.001458, 1.0062882e-6 }; // 0-2
+ idef.iparams[3].lj = { 0.0, 0.0 }; // 1-0
+ idef.iparams[4].lj = { 0.0, 0.0 }; // 1-1
+ idef.iparams[5].lj = { 0.0, 0.0 }; // 1-2
+ idef.iparams[6].lj = { 0.001458, 1.0062882e-6 }; // 2-0
+ idef.iparams[7].lj = { 0.0, 0.0 }; // 2-1
+ idef.iparams[8].lj = { 0.001458, 1.0062882e-6 }; // 2-2
+
+ GMX_ASSERT(chargeA.size() == c_numAtoms, "This test wants 4 atoms");
+ GMX_ASSERT(chargeB.size() == c_numAtoms, "This test wants 4 atoms");
+ GMX_ASSERT(typeA.size() == c_numAtoms, "This test wants 4 atoms");
+ GMX_ASSERT(typeB.size() == c_numAtoms, "This test wants 4 atoms");
+ }
+
+ // forcefield parameters
+ gmx_ffparams_t idef;
+
+ // atom data
+ std::vector<real> chargeA = { 1.0, -1.0, -1.0, 1.0 };
+ std::vector<real> chargeB = { 1.0, 0.0, 0.0, 1.0 };
+ std::vector<int> typeA = { 0, 0, 0, 0 };
+ std::vector<int> typeB = { 0, 1, 2, 1 };
+ // perturbation pattern: {no-pert, vdw- and coul-pert, coul-pert, vdw-pert}
+
+ // neighbourhood information
+ std::vector<int> iAtoms = { 0 };
+ std::vector<int> jAtoms = { 0, 1, 2, 3 };
+ std::vector<int> jIndex = { 0, 4 };
+ std::vector<int> shift = { 0 };
+ std::vector<int> gid = { 0 };
+ std::vector<int> exclFep = { 0, 1, 1, 1 };
+
+ // construct t_nblist
+ t_nblist getNbList()
+ {
+ t_nblist nbl;
+ nbl.nri = 1;
+ nbl.nrj = 4;
+ nbl.iinr = iAtoms;
+ nbl.jindex = jIndex;
+ nbl.jjnr = jAtoms;
+ nbl.shift = shift;
+ nbl.gid = gid;
+ nbl.excl_fep = exclFep;
+ return nbl;
+ }
+};
+
+/*! \brief Input structure for nonbonded fep kernel
+ */
+struct ListInput
+{
+public:
+ //! Function type
+ int fType = F_LJ;
+ //! Tolerance for float evaluation
+ float floatToler = 1e-6;
+ //! Tolerance for double evaluation
+ double doubleToler = 1e-8;
+ //! atom parameters
+ AtomData atoms;
+ //! forcerec helper
+ ForcerecHelper frHelper;
+
+ //! Constructor
+ ListInput() {}
+
+ /*! \brief Constructor with tolerance
+ *
+ * \param[in] ftol Single precision tolerance
+ * \param[in] dtol Double precision tolerance
+ */
+ ListInput(float ftol, double dtol)
+ {
+ floatToler = ftol;
+ doubleToler = dtol;
+ }
+
+ /*! \brief Set parameters for nonbonded interaction
+ *
+ * \param[in] coulType coulomb type
+ * \param[in] vdwType vdw type
+ * \param[in] vdwMod vdw potential modifier
+ */
+ ListInput setInteraction(CoulombInteractionType coulType, VanDerWaalsType vdwType, InteractionModifiers vdwMod)
+ {
+ frHelper.initForcerec(atoms.idef, coulType, vdwType, vdwMod);
+ return *this;
+ }
+};
+
+class NonbondedFepTest :
+ public ::testing::TestWithParam<std::tuple<ListInput, PaddedVector<RVec>, real, real, bool>>
+{
+protected:
+ PaddedVector<RVec> x_;
+ ListInput input_;
+ real lambda_;
+ real softcoreAlpha_;
+ bool softcoreCoulomb_;
+ TestReferenceData refData_;
+ TestReferenceChecker checker_;
+
+ NonbondedFepTest() : checker_(refData_.rootChecker())
+ {
+ input_ = std::get<0>(GetParam());
+ x_ = std::get<1>(GetParam());
+ lambda_ = std::get<2>(GetParam());
+ softcoreAlpha_ = std::get<3>(GetParam());
+ softcoreCoulomb_ = std::get<4>(GetParam());
+
+ test::FloatingPointTolerance tolerance(
+ input_.floatToler, input_.doubleToler, 1.0e-6, 1.0e-12, 10000, 100, false);
+ checker_.setDefaultTolerance(tolerance);
+ }
+
+ void testKernel()
+ {
+ input_.frHelper.setSoftcoreAlpha(softcoreAlpha_);
+ input_.frHelper.setSoftcoreCoulomb(softcoreCoulomb_);
+
+ // get forcerec and interaction_const
+ t_forcerec fr;
+ input_.frHelper.getForcerec(&fr);
+
+ // t_nblist
+ t_nblist nbl = input_.atoms.getNbList();
+
+ // output buffers
+ OutputQuantities output;
+
+ // lambda vector
+ int numFepCouplingTerms = static_cast<int>(FreeEnergyPerturbationCouplingType::Count);
+ std::vector<real> lambdas(numFepCouplingTerms, lambda_);
+
+ // fep kernel data
+ int doNBFlags = 0;
+ doNBFlags |= GMX_NONBONDED_DO_FORCE;
+ doNBFlags |= GMX_NONBONDED_DO_SHIFTFORCE;
+ doNBFlags |= GMX_NONBONDED_DO_POTENTIAL;
+
+ // force buffers
+ bool unusedBool = true; // this bool has no effect in the kernel
+ gmx::ForceWithShiftForces forces(output.f.arrayRefWithPadding(), unusedBool, output.fShift);
+
+ // dummy counter
+ t_nrnb nrnb;
+
+ // run fep kernel
+ gmx_nb_free_energy_kernel(nbl,
+ x_.arrayRefWithPadding().unpaddedArrayRef(),
+ &forces,
+ fr,
+ input_.atoms.chargeA,
+ input_.atoms.chargeB,
+ input_.atoms.typeA,
+ input_.atoms.typeB,
+ doNBFlags,
+ lambdas,
+ output.dvdLambda,
+ output.energy.energyGroupPairTerms[NonBondedEnergyTerms::CoulombSR],
+ output.energy.energyGroupPairTerms[NonBondedEnergyTerms::LJSR],
+ &nrnb);
+
+ checkOutput(&checker_, output);
+ }
+};
+
+TEST_P(NonbondedFepTest, testKernel)
+{
+ testKernel();
+}
+
+//! configurations to test
+std::vector<ListInput> c_interaction = {
+ { ListInput(1e-6, 1e-8).setInteraction(CoulombInteractionType::Cut, VanDerWaalsType::Cut, InteractionModifiers::None) },
+ { ListInput(1e-6, 1e-8).setInteraction(CoulombInteractionType::Cut, VanDerWaalsType::Cut, InteractionModifiers::PotSwitch) },
+ { ListInput(1e-6, 1e-8).setInteraction(CoulombInteractionType::Pme, VanDerWaalsType::Pme, InteractionModifiers::None) }
+};
+
+//! test parameters
+std::vector<real> c_fepLambdas = { 0.0, 0.5, 1.0 };
+std::vector<real> c_softcoreAlphas = { 0.0, 0.3 };
+std::vector<bool> c_softcoreCoulomb = { true, false };
+
+//! Coordinates for testing
+std::vector<PaddedVector<RVec>> c_coordinates = {
+ { { 1.0, 1.0, 1.0 }, { 1.1, 1.15, 1.2 }, { 0.9, 0.85, 0.8 }, { 1.1, 1.15, 0.8 } }
+};
+
+INSTANTIATE_TEST_CASE_P(NBInteraction,
+ NonbondedFepTest,
+ ::testing::Combine(::testing::ValuesIn(c_interaction),
+ ::testing::ValuesIn(c_coordinates),
+ ::testing::ValuesIn(c_fepLambdas),
+ ::testing::ValuesIn(c_softcoreAlphas),
+ ::testing::ValuesIn(c_softcoreCoulomb)));
+
+} // namespace
+
+} // namespace test
+
+} // namespace gmx
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Real Name="EVdw ">9.3145478052213058</Real>
+ <Real Name="ECoul ">-111.63140175473714</Real>
+ <Real Name="dVdlCoul ">188.52893909837877</Real>
+ <Real Name="dVdlVdw ">-6.2096985368142033</Real>
+ <Sequence Name="Forces">
+ <Int Name="Length">4</Int>
+ <Vector>
+ <Real Name="X">-260.95857104646757</Real>
+ <Real Name="Y">-391.43785656970101</Real>
+ <Real Name="Z">521.9171420929348</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-94.898901947422004</Real>
+ <Real Name="Y">-142.3483529211328</Real>
+ <Real Name="Z">-189.79780389484378</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">94.898901947421891</Real>
+ <Real Name="Y">142.34835292113289</Real>
+ <Real Name="Z">189.79780389484378</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">260.95857104646768</Real>
+ <Real Name="Y">391.4378565697009</Real>
+ <Real Name="Z">-521.9171420929348</Real>
+ </Vector>
+ </Sequence>
+ <Shift-Forces Name="Shift-forces">
+ <Vector Name="Central">
+ <Real Name="X">-260.95857104646757</Real>
+ <Real Name="Y">-391.43785656970101</Real>
+ <Real Name="Z">521.9171420929348</Real>
+ </Vector>
+ </Shift-Forces>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Real Name="EVdw ">9.3145478052213058</Real>
+ <Real Name="ECoul ">-111.63140175473714</Real>
+ <Real Name="dVdlCoul ">188.52893909837877</Real>
+ <Real Name="dVdlVdw ">-6.2096985368142033</Real>
+ <Sequence Name="Forces">
+ <Int Name="Length">4</Int>
+ <Vector>
+ <Real Name="X">-260.95857104646757</Real>
+ <Real Name="Y">-391.43785656970101</Real>
+ <Real Name="Z">521.9171420929348</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-94.898901947422004</Real>
+ <Real Name="Y">-142.3483529211328</Real>
+ <Real Name="Z">-189.79780389484378</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">94.898901947421891</Real>
+ <Real Name="Y">142.34835292113289</Real>
+ <Real Name="Z">189.79780389484378</Real>
+ </Vector>
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biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff