From 9ec7699c7c574353fb18424db9a3bd602c2d880d Mon Sep 17 00:00:00 2001 From: David van der Spoel Date: Sun, 3 Feb 2019 08:49:19 +0100 Subject: [PATCH] Tests for polarization functions. Part of #2795 Change-Id: I30d0c67bac3e16412ca2afaa12ea7e28e8c01f6e --- src/gromacs/listed_forces/tests/bonded.cpp | 103 +++++++++++++++++- .../Polarize_ListedForcesTest_Ifunc_0.xml | 38 +++++++ .../Polarize_ListedForcesTest_Ifunc_1.xml | 38 +++++++ .../Polarize_ListedForcesTest_Ifunc_10.xml | 38 +++++++ .../Polarize_ListedForcesTest_Ifunc_11.xml | 38 +++++++ .../Polarize_ListedForcesTest_Ifunc_12.xml | 38 +++++++ .../Polarize_ListedForcesTest_Ifunc_13.xml | 38 +++++++ .../Polarize_ListedForcesTest_Ifunc_14.xml | 38 +++++++ .../Polarize_ListedForcesTest_Ifunc_15.xml | 38 +++++++ .../Polarize_ListedForcesTest_Ifunc_16.xml | 38 +++++++ .../Polarize_ListedForcesTest_Ifunc_17.xml | 38 +++++++ .../Polarize_ListedForcesTest_Ifunc_18.xml | 38 +++++++ .../Polarize_ListedForcesTest_Ifunc_19.xml | 38 +++++++ .../Polarize_ListedForcesTest_Ifunc_2.xml | 38 +++++++ .../Polarize_ListedForcesTest_Ifunc_20.xml | 38 +++++++ .../Polarize_ListedForcesTest_Ifunc_21.xml | 38 +++++++ .../Polarize_ListedForcesTest_Ifunc_22.xml | 38 +++++++ .../Polarize_ListedForcesTest_Ifunc_23.xml | 38 +++++++ .../Polarize_ListedForcesTest_Ifunc_24.xml | 38 +++++++ .../Polarize_ListedForcesTest_Ifunc_25.xml | 38 +++++++ .../Polarize_ListedForcesTest_Ifunc_26.xml | 38 +++++++ .../Polarize_ListedForcesTest_Ifunc_27.xml | 38 +++++++ .../Polarize_ListedForcesTest_Ifunc_28.xml | 38 +++++++ .../Polarize_ListedForcesTest_Ifunc_29.xml | 38 +++++++ .../Polarize_ListedForcesTest_Ifunc_3.xml | 38 +++++++ .../Polarize_ListedForcesTest_Ifunc_30.xml | 38 +++++++ .../Polarize_ListedForcesTest_Ifunc_31.xml | 38 +++++++ .../Polarize_ListedForcesTest_Ifunc_32.xml | 38 +++++++ .../Polarize_ListedForcesTest_Ifunc_33.xml | 38 +++++++ .../Polarize_ListedForcesTest_Ifunc_34.xml | 38 +++++++ .../Polarize_ListedForcesTest_Ifunc_35.xml | 38 +++++++ .../Polarize_ListedForcesTest_Ifunc_4.xml | 38 +++++++ .../Polarize_ListedForcesTest_Ifunc_5.xml | 38 +++++++ .../Polarize_ListedForcesTest_Ifunc_6.xml | 38 +++++++ .../Polarize_ListedForcesTest_Ifunc_7.xml | 38 +++++++ .../Polarize_ListedForcesTest_Ifunc_8.xml | 38 +++++++ .../Polarize_ListedForcesTest_Ifunc_9.xml | 38 +++++++ 37 files changed, 1467 insertions(+), 4 deletions(-) create mode 100644 src/gromacs/listed_forces/tests/refdata/Polarize_ListedForcesTest_Ifunc_0.xml create mode 100644 src/gromacs/listed_forces/tests/refdata/Polarize_ListedForcesTest_Ifunc_1.xml create mode 100644 src/gromacs/listed_forces/tests/refdata/Polarize_ListedForcesTest_Ifunc_10.xml create mode 100644 src/gromacs/listed_forces/tests/refdata/Polarize_ListedForcesTest_Ifunc_11.xml create mode 100644 src/gromacs/listed_forces/tests/refdata/Polarize_ListedForcesTest_Ifunc_12.xml create mode 100644 src/gromacs/listed_forces/tests/refdata/Polarize_ListedForcesTest_Ifunc_13.xml create mode 100644 src/gromacs/listed_forces/tests/refdata/Polarize_ListedForcesTest_Ifunc_14.xml create mode 100644 src/gromacs/listed_forces/tests/refdata/Polarize_ListedForcesTest_Ifunc_15.xml create mode 100644 src/gromacs/listed_forces/tests/refdata/Polarize_ListedForcesTest_Ifunc_16.xml create mode 100644 src/gromacs/listed_forces/tests/refdata/Polarize_ListedForcesTest_Ifunc_17.xml create mode 100644 src/gromacs/listed_forces/tests/refdata/Polarize_ListedForcesTest_Ifunc_18.xml create mode 100644 src/gromacs/listed_forces/tests/refdata/Polarize_ListedForcesTest_Ifunc_19.xml create mode 100644 src/gromacs/listed_forces/tests/refdata/Polarize_ListedForcesTest_Ifunc_2.xml create mode 100644 src/gromacs/listed_forces/tests/refdata/Polarize_ListedForcesTest_Ifunc_20.xml create mode 100644 src/gromacs/listed_forces/tests/refdata/Polarize_ListedForcesTest_Ifunc_21.xml create mode 100644 src/gromacs/listed_forces/tests/refdata/Polarize_ListedForcesTest_Ifunc_22.xml create mode 100644 src/gromacs/listed_forces/tests/refdata/Polarize_ListedForcesTest_Ifunc_23.xml create mode 100644 src/gromacs/listed_forces/tests/refdata/Polarize_ListedForcesTest_Ifunc_24.xml create mode 100644 src/gromacs/listed_forces/tests/refdata/Polarize_ListedForcesTest_Ifunc_25.xml create mode 100644 src/gromacs/listed_forces/tests/refdata/Polarize_ListedForcesTest_Ifunc_26.xml create mode 100644 src/gromacs/listed_forces/tests/refdata/Polarize_ListedForcesTest_Ifunc_27.xml create mode 100644 src/gromacs/listed_forces/tests/refdata/Polarize_ListedForcesTest_Ifunc_28.xml create mode 100644 src/gromacs/listed_forces/tests/refdata/Polarize_ListedForcesTest_Ifunc_29.xml create mode 100644 src/gromacs/listed_forces/tests/refdata/Polarize_ListedForcesTest_Ifunc_3.xml create mode 100644 src/gromacs/listed_forces/tests/refdata/Polarize_ListedForcesTest_Ifunc_30.xml create mode 100644 src/gromacs/listed_forces/tests/refdata/Polarize_ListedForcesTest_Ifunc_31.xml create mode 100644 src/gromacs/listed_forces/tests/refdata/Polarize_ListedForcesTest_Ifunc_32.xml create mode 100644 src/gromacs/listed_forces/tests/refdata/Polarize_ListedForcesTest_Ifunc_33.xml create mode 100644 src/gromacs/listed_forces/tests/refdata/Polarize_ListedForcesTest_Ifunc_34.xml create mode 100644 src/gromacs/listed_forces/tests/refdata/Polarize_ListedForcesTest_Ifunc_35.xml create mode 100644 src/gromacs/listed_forces/tests/refdata/Polarize_ListedForcesTest_Ifunc_4.xml create mode 100644 src/gromacs/listed_forces/tests/refdata/Polarize_ListedForcesTest_Ifunc_5.xml create mode 100644 src/gromacs/listed_forces/tests/refdata/Polarize_ListedForcesTest_Ifunc_6.xml create mode 100644 src/gromacs/listed_forces/tests/refdata/Polarize_ListedForcesTest_Ifunc_7.xml create mode 100644 src/gromacs/listed_forces/tests/refdata/Polarize_ListedForcesTest_Ifunc_8.xml create mode 100644 src/gromacs/listed_forces/tests/refdata/Polarize_ListedForcesTest_Ifunc_9.xml diff --git a/src/gromacs/listed_forces/tests/bonded.cpp b/src/gromacs/listed_forces/tests/bonded.cpp index 24723bd574..fc8a0528d7 100644 --- a/src/gromacs/listed_forces/tests/bonded.cpp +++ b/src/gromacs/listed_forces/tests/bonded.cpp @@ -54,6 +54,7 @@ #include "gromacs/math/units.h" #include "gromacs/math/vec.h" #include "gromacs/math/vectypes.h" +#include "gromacs/mdtypes/mdatom.h" #include "gromacs/pbcutil/ishift.h" #include "gromacs/pbcutil/pbc.h" #include "gromacs/topology/idef.h" @@ -407,6 +408,85 @@ struct iListInput { return setRbDihedrals(rbc, rbc); } + /*! \brief Set parameters for Polarization + * + * \param[in] alpha Polarizability + * \return The structure itself. + */ + iListInput setPolarization(real alpha) + { + ftype = F_POLARIZATION; + fep = false; + iparams.polarize.alpha = alpha; + return *this; + } + /*! \brief Set parameters for Anharmonic Polarization + * + * \param[in] alpha Polarizability (nm^3) + * \param[in] drcut The cut-off distance (nm) after which the + * fourth power kicks in + * \param[in] khyp The force constant for the fourth power + * \return The structure itself. + */ + iListInput setAnharmPolarization(real alpha, + real drcut, + real khyp) + { + ftype = F_ANHARM_POL; + fep = false; + iparams.anharm_polarize.alpha = alpha; + iparams.anharm_polarize.drcut = drcut; + iparams.anharm_polarize.khyp = khyp; + return *this; + } + /*! \brief Set parameters for Thole Polarization + * + * \param[in] a Thole factor + * \param[in] alpha1 Polarizability 1 (nm^3) + * \param[in] alpha2 Polarizability 2 (nm^3) + * \param[in] rfac Distance factor + * \return The structure itself. + */ + iListInput setTholePolarization(real a, + real alpha1, + real alpha2, + real rfac) + { + ftype = F_THOLE_POL; + fep = false; + iparams.thole.a = a; + iparams.thole.alpha1 = alpha1; + iparams.thole.alpha2 = alpha2; + iparams.thole.rfac = rfac; + return *this; + } + /*! \brief Set parameters for Water Polarization + * + * \param[in] alpha_x Polarizability X (nm^3) + * \param[in] alpha_y Polarizability Y (nm^3) + * \param[in] alpha_z Polarizability Z (nm^3) + * \param[in] rOH Oxygen-Hydrogen distance + * \param[in] rHH Hydrogen-Hydrogen distance + * \param[in] rOD Oxygen-Dummy distance + * \return The structure itself. + */ + iListInput setWaterPolarization(real alpha_x, + real alpha_y, + real alpha_z, + real rOH, + real rHH, + real rOD) + { + ftype = F_WATER_POL; + fep = false; + iparams.wpol.al_x = alpha_x; + iparams.wpol.al_y = alpha_y; + iparams.wpol.al_z = alpha_z; + iparams.wpol.rOH = rOH; + iparams.wpol.rHH = rHH; + iparams.wpol.rOD = rOD; + return *this; + } }; /*! \brief Utility to fill iatoms struct @@ -419,7 +499,8 @@ void fillIatoms(int ftype, std::vector *iatoms) std::unordered_map > ia = { { 2, { 0, 0, 1, 0, 1, 2, 0, 2, 3 } }, { 3, { 0, 0, 1, 2, 0, 1, 2, 3 } }, - { 4, { 0, 0, 1, 2, 3 } }}; + { 4, { 0, 0, 1, 2, 3 } }, + { 5, { 0, 0, 1, 2, 3, 0 } } }; EXPECT_TRUE(ftype >= 0 && ftype < F_NRE); int nral = interaction_function[ftype].nratoms; for (auto &i : ia[nral]) @@ -460,8 +541,11 @@ class ListedForcesTest : public ::testing::TestWithParam ddgatindex = { 0, 1, 2, 3 }; - OutputQuantities output; + std::vector ddgatindex = { 0, 1, 2, 3 }; + std::vector chargeA = { 1.5, -2.0, 1.5, -1.0 }; + t_mdatoms mdatoms = {0}; + mdatoms.chargeA = chargeA.data(); + OutputQuantities output; output.energy = bondedFunction(input_.ftype) (iatoms.size(), iatoms.data(), &input_.iparams, @@ -470,7 +554,7 @@ class ListedForcesTest : public ::testing::TestWithParam c_InputDihs = { iListInput(3e-4, 1e-8).setRbDihedrals(rbc) } }; +//! Function types for testing polarization. Add new terms at the end. +std::vector c_InputPols = +{ + { iListInput(2e-5, 1e-8).setPolarization(0.12) }, + { iListInput(1.7e-3, 1e-8).setAnharmPolarization(0.0013, 0.02, 1235.6) }, + { iListInput(1.4e-3, 1e-8).setTholePolarization(0.26, 0.07, 0.09, 1.6) }, + { iListInput().setWaterPolarization(0.001, 0.0012, 0.0016, 0.095, 0.15, 0.02) }, +}; + //! Coordinates for testing std::vector > c_coordinatesForTests = { @@ -576,6 +669,8 @@ INSTANTIATE_TEST_CASE_P(Angle, ListedForcesTest, ::testing::Combine(::testing::V INSTANTIATE_TEST_CASE_P(Dihedral, ListedForcesTest, ::testing::Combine(::testing::ValuesIn(c_InputDihs), ::testing::ValuesIn(c_coordinatesForTests), ::testing::ValuesIn(c_pbcForTests))); +INSTANTIATE_TEST_CASE_P(Polarize, ListedForcesTest, ::testing::Combine(::testing::ValuesIn(c_InputPols), ::testing::ValuesIn(c_coordinatesForTests), ::testing::ValuesIn(c_pbcForTests))); + } // namespace } // namespace gmx diff --git a/src/gromacs/listed_forces/tests/refdata/Polarize_ListedForcesTest_Ifunc_0.xml b/src/gromacs/listed_forces/tests/refdata/Polarize_ListedForcesTest_Ifunc_0.xml new file mode 100644 index 0000000000..1a412cb492 --- /dev/null +++ b/src/gromacs/listed_forces/tests/refdata/Polarize_ListedForcesTest_Ifunc_0.xml @@ -0,0 +1,38 @@ + + + + + + 117.28019586833446 + 0 + + 0 + 0 + 0 + + + 4 + + 0 + 0 + 926.23638559389656 + + + 13.025199172414171 + 0 + -1186.74036904218 + + + -19.971972064368394 + 115.77954819923707 + 144.72443524904634 + + + 6.9467728919542244 + -115.77954819923707 + 115.77954819923707 + + + + + diff --git a/src/gromacs/listed_forces/tests/refdata/Polarize_ListedForcesTest_Ifunc_1.xml b/src/gromacs/listed_forces/tests/refdata/Polarize_ListedForcesTest_Ifunc_1.xml new file mode 100644 index 0000000000..1a412cb492 --- /dev/null +++ b/src/gromacs/listed_forces/tests/refdata/Polarize_ListedForcesTest_Ifunc_1.xml @@ -0,0 +1,38 @@ + + + + + + 117.28019586833446 + 0 + + 0 + 0 + 0 + + + 4 + + 0 + 0 + 926.23638559389656 + + + 13.025199172414171 + 0 + -1186.74036904218 + + + -19.971972064368394 + 115.77954819923707 + 144.72443524904634 + + + 6.9467728919542244 + -115.77954819923707 + 115.77954819923707 + + + + + diff --git a/src/gromacs/listed_forces/tests/refdata/Polarize_ListedForcesTest_Ifunc_10.xml b/src/gromacs/listed_forces/tests/refdata/Polarize_ListedForcesTest_Ifunc_10.xml new file mode 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641.61678719235988 + -10693.613119872665 + 10693.613119872665 + + + + + diff --git a/src/gromacs/listed_forces/tests/refdata/Polarize_ListedForcesTest_Ifunc_12.xml b/src/gromacs/listed_forces/tests/refdata/Polarize_ListedForcesTest_Ifunc_12.xml new file mode 100644 index 0000000000..f9e3c86747 --- /dev/null +++ b/src/gromacs/listed_forces/tests/refdata/Polarize_ListedForcesTest_Ifunc_12.xml @@ -0,0 +1,38 @@ + + + + + + 6634.6501936621835 + 0 + + 0 + 0 + 0 + + + 4 + + 0 + 0 + 64134.915916992832 + + + 0 + 16834.287828835641 + -47300.628088157187 + + + 0 + -5074.6076174669543 + -16834.287828835641 + + + 0 + -11759.680211368686 + 0 + + + + + diff --git a/src/gromacs/listed_forces/tests/refdata/Polarize_ListedForcesTest_Ifunc_13.xml b/src/gromacs/listed_forces/tests/refdata/Polarize_ListedForcesTest_Ifunc_13.xml new file mode 100644 index 0000000000..f9e3c86747 --- /dev/null +++ b/src/gromacs/listed_forces/tests/refdata/Polarize_ListedForcesTest_Ifunc_13.xml @@ -0,0 +1,38 @@ + + + + + + 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a/src/gromacs/listed_forces/tests/refdata/Polarize_ListedForcesTest_Ifunc_8.xml b/src/gromacs/listed_forces/tests/refdata/Polarize_ListedForcesTest_Ifunc_8.xml new file mode 100644 index 0000000000..22bc607ac6 --- /dev/null +++ b/src/gromacs/listed_forces/tests/refdata/Polarize_ListedForcesTest_Ifunc_8.xml @@ -0,0 +1,38 @@ + + + + + + 91.193681540689695 + 0 + + 0 + 0 + 0 + + + 4 + + 529.34409436691192 + 331.59262604261494 + 0 + + + -220.64687398069611 + -480.60090457503304 + 0 + + + -468.4729969011629 + 338.42361938636998 + 0 + + + 159.77577651494713 + -189.41534085395185 + 0 + + + + + diff --git a/src/gromacs/listed_forces/tests/refdata/Polarize_ListedForcesTest_Ifunc_9.xml b/src/gromacs/listed_forces/tests/refdata/Polarize_ListedForcesTest_Ifunc_9.xml new file mode 100644 index 0000000000..1a52d5b7da --- /dev/null +++ b/src/gromacs/listed_forces/tests/refdata/Polarize_ListedForcesTest_Ifunc_9.xml @@ -0,0 +1,38 @@ + + + + + + 10827.481942307291 + 0 + + 0 + 0 + 0 + + + 4 + + 0 + 0 + 85527.567362390473 + + + 1202.4530379358848 + 0 + -109576.62812110817 + + + -1844.0698251282447 + 10693.613119872665 + 13355.447638845031 + + + 641.61678719235988 + -10693.613119872665 + 10693.613119872665 + + + + + -- 2.22.0