Updates to nblib test infra and tests

diff --git a/api/nblib/box.cpp b/api/nblib/box.cpp
index a48a138c8fb89edc4e69cb545bf6d494b5595273..51995a9932552a5673f4e434c6c432376cafa41d 100644 (file)
--- a/api/nblib/box.cpp
+++ b/api/nblib/box.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2020, by the GROMACS development team, led by
+ * Copyright (c) 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.
@@ -63,4 +63,12 @@ Box::Box(real x, real y, real z) : legacyMatrix_{ { 0 } }
     legacyMatrix_[dimZ][dimZ] = z;
 }
 
+bool operator==(const Box& rhs, const Box& lhs)
+{
+    using real_ptr = const real*;
+    return std::equal(real_ptr(rhs.legacyMatrix()),
+                      real_ptr(rhs.legacyMatrix()) + dimSize * dimSize,
+                      real_ptr(lhs.legacyMatrix()));
+}
+
 } // namespace nblib

diff --git a/api/nblib/box.h b/api/nblib/box.h
index ea729f0d2e807aa96fdb407d237efdbdc008167d..aa7c6836989dc9ee974218280ef6f31474c9e2b4 100644 (file)
--- a/api/nblib/box.h
+++ b/api/nblib/box.h
@@ -72,6 +72,10 @@ public:
     [[nodiscard]] LegacyMatrix const& legacyMatrix() const { return legacyMatrix_; }
 
 private:
+    //! \brief check two boxes for equality
+    friend bool operator==(const Box& rhs, const Box& lhs);
+
+    //! Stores data in the GROMACS legacy data type
     LegacyMatrix legacyMatrix_;
 };
 

diff --git a/api/nblib/listed_forces/tests/calculator.cpp b/api/nblib/listed_forces/tests/calculator.cpp
index fe0c107cd5ff3b372ad6aef7ce783df312f13487..4d94a33c2d33d655320c9a04f1c2a4b23bdd4c65 100644 (file)
--- a/api/nblib/listed_forces/tests/calculator.cpp
+++ b/api/nblib/listed_forces/tests/calculator.cpp
@@ -137,8 +137,8 @@ TEST_F(ListedExampleData, ComputeHarmonicBondForces)
     auto bonds   = pickType<HarmonicBondType>(interactions).parameters;
     computeForces(indices, bonds, x, &forces, *pbc);
 
-    Vector3DTest vector3DTest(1e-3);
-    vector3DTest.testVectors(forces, "Bond forces");
+    RefDataChecker vector3DTest(1e-3);
+    vector3DTest.testArrays<Vec3>(forces, "Bond forces");
 }
 
 TEST_F(ListedExampleData, ComputeHarmonicBondEnergies)
@@ -147,7 +147,7 @@ TEST_F(ListedExampleData, ComputeHarmonicBondEnergies)
     auto bonds   = pickType<HarmonicBondType>(interactions).parameters;
     real energy  = computeForces(indices, bonds, x, &forces, *pbc);
 
-    Vector3DTest vector3DTest(1e-4);
+    RefDataChecker vector3DTest(1e-4);
     vector3DTest.testReal(energy, "Bond energy");
 }
 
@@ -157,16 +157,16 @@ TEST_F(ListedExampleData, ComputeHarmonicAngleForces)
     auto angles  = pickType<HarmonicAngleType>(interactions).parameters;
     computeForces(indices, angles, x, &forces, *pbc);
 
-    Vector3DTest vector3DTest(1e-4);
-    vector3DTest.testVectors(forces, "Angle forces");
+    RefDataChecker vector3DTest(1e-4);
+    vector3DTest.testArrays<Vec3>(forces, "Angle forces");
 }
 
 TEST_F(ListedExampleData, CanReduceForces)
 {
     reduceListedForces(interactions, x, &forces, *pbc);
 
-    Vector3DTest vector3DTest(1e-2);
-    vector3DTest.testVectors(forces, "Reduced forces");
+    RefDataChecker vector3DTest(1e-2);
+    vector3DTest.testArrays<Vec3>(forces, "Reduced forces");
 }
 
 TEST_F(ListedExampleData, CanReduceEnergies)
@@ -174,7 +174,7 @@ TEST_F(ListedExampleData, CanReduceEnergies)
     auto energies    = reduceListedForces(interactions, x, &forces, *pbc);
     real totalEnergy = std::accumulate(begin(energies), end(energies), 0.0);
 
-    Vector3DTest vector3DTest(1e-4);
+    RefDataChecker vector3DTest(1e-4);
     vector3DTest.testReal(totalEnergy, "Reduced energy");
 }
 

diff --git a/api/nblib/tests/CMakeLists.txt b/api/nblib/tests/CMakeLists.txt
index 33d34e58c7b65a87539f2bc5f79c607ddd35c4a2..d224dbe7eb7841178de2d7fd86604fc3ee18b7c3 100644 (file)
--- a/api/nblib/tests/CMakeLists.txt
+++ b/api/nblib/tests/CMakeLists.txt
@@ -31,7 +31,7 @@
 #
 # To help us fund GROMACS development, we humbly ask that you cite
 # the research papers on the package. Check out http://www.gromacs.org.
-#
+
 # \author Victor Holanda <victor.holanda@cscs.ch>
 # \author Joe Jordan <ejjordan@kth.se>
 # \author Prashanth Kanduri <kanduri@cscs.ch>
@@ -41,14 +41,11 @@
 # Make a static library for test infrastructure code that we re-use
 # in multiple test executables across the repository.
 gmx_add_unit_test_library(nblib_test_infrastructure
-        testhelpers.cpp
         testsystems.cpp
     )
 target_include_directories(nblib_test_infrastructure PRIVATE ${PROJECT_SOURCE_DIR}/api)
 target_include_directories(nblib_test_infrastructure SYSTEM PRIVATE ${PROJECT_SOURCE_DIR}/src/external)
-target_link_libraries(nblib_test_infrastructure PRIVATE legacy_api)
-# TODO: Explicitly link specific modules: math,
-target_link_libraries(nblib_test_infrastructure PRIVATE legacy_modules)
+target_link_libraries(nblib_test_infrastructure PUBLIC legacy_api)
 
 set(testname "NbLibSetupTests")
 set(exename "nblib-setup-test")
@@ -64,6 +61,7 @@ gmx_add_gtest_executable(
         molecules.cpp
         topology.cpp
     )
+target_link_libraries(${exename} PRIVATE mdrun_test_infrastructure)
 target_link_libraries(${exename} PRIVATE nblib_test_infrastructure nblib)
 target_include_directories(${exename} PRIVATE ${PROJECT_SOURCE_DIR}/api)
 gmx_register_gtest_test(${testname} ${exename} INTEGRATION_TEST)
@@ -78,7 +76,6 @@ gmx_add_gtest_executable(
     # files with code for tests
         gmxcalculator.cpp
         nbkernelsystem.cpp
-        nbnxnsetup.cpp
         simstate.cpp
     )
 target_link_libraries(${exename} PRIVATE nblib_test_infrastructure nblib)

diff --git a/api/nblib/tests/box.cpp b/api/nblib/tests/box.cpp
index 45900e7af84dfd2cb48ef0ff7e283c762178fbae..338220376aca375f0a86a5776668b6e5bc6321f4 100644 (file)
--- a/api/nblib/tests/box.cpp
+++ b/api/nblib/tests/box.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2020, by the GROMACS development team, led by
+ * Copyright (c) 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.
@@ -93,4 +93,24 @@ TEST(NBlibTest, CubicBoxWorks)
     }
 }
 
+TEST(NBlibTest, BoxEqual)
+{
+    {
+        Box a(0), b(0);
+        EXPECT_TRUE(a == b);
+    }
+    {
+        Box a(1), b(1);
+        EXPECT_TRUE(a == b);
+    }
+    {
+        Box a(1, 2, 3), b(1, 2, 3);
+        EXPECT_TRUE(a == b);
+    }
+    {
+        Box a(0, 2, 3), b(1, 2, 3);
+        EXPECT_FALSE(a == b);
+    }
+}
+
 } // namespace nblib

diff --git a/api/nblib/tests/gmxcalculator.cpp b/api/nblib/tests/gmxcalculator.cpp
index 164e5e784e1a4bada92458df61991a42c8ec15ac..ae10568258c8303a0698e284ece35e39cc3241d6 100644 (file)
--- a/api/nblib/tests/gmxcalculator.cpp
+++ b/api/nblib/tests/gmxcalculator.cpp
@@ -57,7 +57,7 @@ namespace
 {
 TEST(NBlibTest, GmxForceCalculatorCanCompute)
 {
-    ArgonSimulationStateBuilder argonSystemBuilder;
+    ArgonSimulationStateBuilder argonSystemBuilder(fftypes::GROMOS43A1);
     SimulationState             simState = argonSystemBuilder.setupSimulationState();
     NBKernelOptions             options  = NBKernelOptions();
     options.nbnxmSimd                    = SimdKernels::SimdNo;

diff --git a/api/nblib/tests/integrator.cpp b/api/nblib/tests/integrator.cpp
index fb484557d3200d4b49daf3fff24640a95fbde3da..687d45ac3d4b912a82af635cb6f28b97bbe29845 100644 (file)
--- a/api/nblib/tests/integrator.cpp
+++ b/api/nblib/tests/integrator.cpp
@@ -42,13 +42,14 @@
  * \author Sebastian Keller <keller@cscs.ch>
  * \author Artem Zhmurov <zhmurov@gmail.com>
  */
-#include "nblib/integrator.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/utility/arrayref.h"
+#include "nblib/integrator.h"
 #include "nblib/molecules.h"
 #include "nblib/particletype.h"
 #include "nblib/simulationstate.h"
 #include "nblib/topology.h"
+#include "nblib/vector.h"
 
 #include "testutils/testasserts.h"
 

diff --git a/api/nblib/tests/interactions.cpp b/api/nblib/tests/interactions.cpp
index ca6a950d039fc88abab32b0a191fbe8dbad915d4..651fa80a907cdbd0c56cd5b51ea43b13f21ce5d1 100644 (file)
--- a/api/nblib/tests/interactions.cpp
+++ b/api/nblib/tests/interactions.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2020, by the GROMACS development team, led by
+ * Copyright (c) 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.

diff --git a/api/nblib/tests/molecules.cpp b/api/nblib/tests/molecules.cpp
index a63cadcd16a532e612d10f16d7783310acf07cbe..ae277248f4abbca845f383d942524082d1bdb8c3 100644 (file)
--- a/api/nblib/tests/molecules.cpp
+++ b/api/nblib/tests/molecules.cpp
@@ -193,9 +193,9 @@ TEST(NBlibTest, CanAddInteractions)
     molecule.addParticle(ParticleName("H1"), H);
     molecule.addParticle(ParticleName("H2"), H);
 
-    HarmonicBondType  hb(1, 2);
-    CubicBondType     cub(1, 2, 3);
-    HarmonicAngleType ang(Degrees(1), 1);
+    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);

diff --git a/api/nblib/tests/nbkernelsystem.cpp b/api/nblib/tests/nbkernelsystem.cpp
index ca1524675ec330d8454a8a95ac6fcea4b2a8d345..cedaf185b9ca582f2923603f79d8aa66198cafd5 100644 (file)
--- a/api/nblib/tests/nbkernelsystem.cpp
+++ b/api/nblib/tests/nbkernelsystem.cpp
@@ -81,8 +81,8 @@ TEST(NBlibTest, SpcMethanolForcesAreCorrect)
     gmx::ArrayRef<Vec3> forces(simState.forces());
     ASSERT_NO_THROW(forceCalculator.compute(simState.coordinates(), forces));
 
-    Vector3DTest forcesOutputTest(5e-5);
-    forcesOutputTest.testVectors(forces, "SPC-methanol forces");
+    RefDataChecker forcesOutputTest(5e-5);
+    forcesOutputTest.testArrays<Vec3>(forces, "SPC-methanol forces");
 }
 
 TEST(NBlibTest, ExpectedNumberOfForces)
@@ -192,13 +192,13 @@ TEST(NBlibTest, UpdateChangesForces)
     }
 }
 
-TEST(NBlibTest, ArgonForcesAreCorrect)
+TEST(NBlibTest, ArgonOplsaForcesAreCorrect)
 {
     auto options        = NBKernelOptions();
     options.nbnxmSimd   = SimdKernels::SimdNo;
     options.coulombType = CoulombType::Cutoff;
 
-    ArgonSimulationStateBuilder argonSystemBuilder;
+    ArgonSimulationStateBuilder argonSystemBuilder(fftypes::OPLSA);
 
     auto simState        = argonSystemBuilder.setupSimulationState();
     auto forceCalculator = ForceCalculator(simState, options);
@@ -206,8 +206,26 @@ TEST(NBlibTest, ArgonForcesAreCorrect)
     gmx::ArrayRef<Vec3> testForces(simState.forces());
     forceCalculator.compute(simState.coordinates(), simState.forces());
 
-    Vector3DTest forcesOutputTest;
-    forcesOutputTest.testVectors(testForces, "Argon forces");
+    RefDataChecker forcesOutputTest(1e-7);
+    forcesOutputTest.testArrays<Vec3>(testForces, "Argon forces");
+}
+
+TEST(NBlibTest, ArgonGromos43A1ForcesAreCorrect)
+{
+    auto options        = NBKernelOptions();
+    options.nbnxmSimd   = SimdKernels::SimdNo;
+    options.coulombType = CoulombType::Cutoff;
+
+    ArgonSimulationStateBuilder argonSystemBuilder(fftypes::GROMOS43A1);
+
+    auto simState        = argonSystemBuilder.setupSimulationState();
+    auto forceCalculator = ForceCalculator(simState, options);
+
+    gmx::ArrayRef<Vec3> testForces(simState.forces());
+    forceCalculator.compute(simState.coordinates(), simState.forces());
+
+    RefDataChecker forcesOutputTest(1e-7);
+    forcesOutputTest.testArrays<Vec3>(testForces, "Argon forces");
 }
 
 } // namespace

diff --git a/api/nblib/tests/refdata/NBlibTest_ArgonGromos43A1ForcesAreCorrect.xml b/api/nblib/tests/refdata/NBlibTest_ArgonGromos43A1ForcesAreCorrect.xml
new file mode 100644 (file)
index 0000000..ddaa587
--- /dev/null
+++ b/api/nblib/tests/refdata/NBlibTest_ArgonGromos43A1ForcesAreCorrect.xml
@@ -0,0 +1,67 @@
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+  <Sequence Name="Argon forces">
+    <Int Name="Length">12</Int>
+    <Vector>
+      <Real Name="X">-0.41298821868424429</Real>
+      <Real Name="Y">-1.0982427445010643</Real>
+      <Real Name="Z">-0.11318936363938557</Real>
+    </Vector>
+    <Vector>
+      <Real Name="X">0</Real>
+      <Real Name="Y">0</Real>
+      <Real Name="Z">0</Real>
+    </Vector>
+    <Vector>
+      <Real Name="X">0.41298821868424429</Real>
+      <Real Name="Y">1.0982427445010643</Real>
+      <Real Name="Z">0.11318936363938557</Real>
+    </Vector>
+    <Vector>
+      <Real Name="X">0</Real>
+      <Real Name="Y">0</Real>
+      <Real Name="Z">0</Real>
+    </Vector>
+    <Vector>
+      <Real Name="X">0</Real>
+      <Real Name="Y">0</Real>
+      <Real Name="Z">0</Real>
+    </Vector>
+    <Vector>
+      <Real Name="X">0</Real>
+      <Real Name="Y">0</Real>
+      <Real Name="Z">0</Real>
+    </Vector>
+    <Vector>
+      <Real Name="X">0</Real>
+      <Real Name="Y">0</Real>
+      <Real Name="Z">0</Real>
+    </Vector>
+    <Vector>
+      <Real Name="X">0</Real>
+      <Real Name="Y">0</Real>
+      <Real Name="Z">0</Real>
+    </Vector>
+    <Vector>
+      <Real Name="X">0</Real>
+      <Real Name="Y">0</Real>
+      <Real Name="Z">0</Real>
+    </Vector>
+    <Vector>
+      <Real Name="X">0</Real>
+      <Real Name="Y">0</Real>
+      <Real Name="Z">0</Real>
+    </Vector>
+    <Vector>
+      <Real Name="X">0</Real>
+      <Real Name="Y">0</Real>
+      <Real Name="Z">0</Real>
+    </Vector>
+    <Vector>
+      <Real Name="X">0</Real>
+      <Real Name="Y">0</Real>
+      <Real Name="Z">0</Real>
+    </Vector>
+  </Sequence>
+</ReferenceData>

diff --git a/api/nblib/tests/refdata/NBlibTest_ArgonOplsaForcesAreCorrect.xml b/api/nblib/tests/refdata/NBlibTest_ArgonOplsaForcesAreCorrect.xml
new file mode 100644 (file)
index 0000000..8020088
--- /dev/null
+++ b/api/nblib/tests/refdata/NBlibTest_ArgonOplsaForcesAreCorrect.xml
@@ -0,0 +1,67 @@
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+  <Sequence Name="Argon forces">
+    <Int Name="Length">12</Int>
+    <Vector>
+      <Real Name="X">-1.4060510037205805</Real>
+      <Real Name="Y">-3.7390541506347286</Real>
+      <Real Name="Z">-0.38536212694564093</Real>
+    </Vector>
+    <Vector>
+      <Real Name="X">0</Real>
+      <Real Name="Y">0</Real>
+      <Real Name="Z">0</Real>
+    </Vector>
+    <Vector>
+      <Real Name="X">1.4060510037205805</Real>
+      <Real Name="Y">3.7390541506347286</Real>
+      <Real Name="Z">0.38536212694564093</Real>
+    </Vector>
+    <Vector>
+      <Real Name="X">0</Real>
+      <Real Name="Y">0</Real>
+      <Real Name="Z">0</Real>
+    </Vector>
+    <Vector>
+      <Real Name="X">0</Real>
+      <Real Name="Y">0</Real>
+      <Real Name="Z">0</Real>
+    </Vector>
+    <Vector>
+      <Real Name="X">0</Real>
+      <Real Name="Y">0</Real>
+      <Real Name="Z">0</Real>
+    </Vector>
+    <Vector>
+      <Real Name="X">0</Real>
+      <Real Name="Y">0</Real>
+      <Real Name="Z">0</Real>
+    </Vector>
+    <Vector>
+      <Real Name="X">0</Real>
+      <Real Name="Y">0</Real>
+      <Real Name="Z">0</Real>
+    </Vector>
+    <Vector>
+      <Real Name="X">0</Real>
+      <Real Name="Y">0</Real>
+      <Real Name="Z">0</Real>
+    </Vector>
+    <Vector>
+      <Real Name="X">0</Real>
+      <Real Name="Y">0</Real>
+      <Real Name="Z">0</Real>
+    </Vector>
+    <Vector>
+      <Real Name="X">0</Real>
+      <Real Name="Y">0</Real>
+      <Real Name="Z">0</Real>
+    </Vector>
+    <Vector>
+      <Real Name="X">0</Real>
+      <Real Name="Y">0</Real>
+      <Real Name="Z">0</Real>
+    </Vector>
+  </Sequence>
+</ReferenceData>

diff --git a/api/nblib/tests/refdata/NBlibTest_SpcMethanolEnergiesAreCorrect.xml b/api/nblib/tests/refdata/NBlibTest_SpcMethanolEnergiesAreCorrect.xml
new file mode 100644 (file)
index 0000000..a39890c
--- /dev/null
+++ b/api/nblib/tests/refdata/NBlibTest_SpcMethanolEnergiesAreCorrect.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+  <Sequence Name="SPC-methanol energies">
+    <Int Name="Length">5</Int>
+    <Real>-7.1674767</Real>
+    <Real>-0.11698186</Real>
+    <Real>0</Real>
+    <Real>0</Real>
+    <Real>0</Real>
+  </Sequence>
+</ReferenceData>

diff --git a/api/nblib/tests/refdata/NBlibTest_SpcMethanolForcesAreCorrectOnGpu.xml b/api/nblib/tests/refdata/NBlibTest_SpcMethanolForcesAreCorrectOnGpu.xml
new file mode 100644 (file)
index 0000000..a73cebd
--- /dev/null
+++ b/api/nblib/tests/refdata/NBlibTest_SpcMethanolForcesAreCorrectOnGpu.xml
@@ -0,0 +1,37 @@
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+  <Sequence Name="SPC-methanol forces on GPU">
+    <Int Name="Length">6</Int>
+    <Vector>
+      <Real Name="X">-0.38183594</Real>
+      <Real Name="Y">0.87922907</Real>
+      <Real Name="Z">-6.1406441</Real>
+    </Vector>
+    <Vector>
+      <Real Name="X">8.3033295</Real>
+      <Real Name="Y">-7.338829</Real>
+      <Real Name="Z">27.783722</Real>
+    </Vector>
+    <Vector>
+      <Real Name="X">-9.4221649</Real>
+      <Real Name="Y">6.2920837</Real>
+      <Real Name="Z">-33.986099</Real>
+    </Vector>
+    <Vector>
+      <Real Name="X">27.494339</Real>
+      <Real Name="Y">8.3915062</Real>
+      <Real Name="Z">39.693787</Real>
+    </Vector>
+    <Vector>
+      <Real Name="X">-19.009857</Real>
+      <Real Name="Y">-5.3975139</Real>
+      <Real Name="Z">-15.545643</Real>
+    </Vector>
+    <Vector>
+      <Real Name="X">-6.9838257</Real>
+      <Real Name="Y">-2.8264766</Real>
+      <Real Name="Z">-11.805126</Real>
+    </Vector>
+  </Sequence>
+</ReferenceData>

diff --git a/api/nblib/tests/refdata/TprReaderTest_ArgonImportedDataIsCorrect.xml b/api/nblib/tests/refdata/TprReaderTest_ArgonImportedDataIsCorrect.xml
new file mode 100644 (file)
index 0000000..35ae227
--- /dev/null
+++ b/api/nblib/tests/refdata/TprReaderTest_ArgonImportedDataIsCorrect.xml
@@ -0,0 +1,170 @@
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+    <Sequence Name="coordinates">
+        <Int Name="Length">12</Int>
+        <Vector>
+            <Real Name="X">0.794</Real>
+            <Real Name="Y">1.439</Real>
+            <Real Name="Z">0.61</Real>
+        </Vector>
+        <Vector>
+            <Real Name="X">1.397</Real>
+            <Real Name="Y">0.673</Real>
+            <Real Name="Z">1.916</Real>
+        </Vector>
+        <Vector>
+            <Real Name="X">0.659</Real>
+            <Real Name="Y">1.08</Real>
+            <Real Name="Z">0.573</Real>
+        </Vector>
+        <Vector>
+            <Real Name="X">1.105</Real>
+            <Real Name="Y">0.09</Real>
+            <Real Name="Z">3.431</Real>
+        </Vector>
+        <Vector>
+            <Real Name="X">1.741</Real>
+            <Real Name="Y">1.291</Real>
+            <Real Name="Z">3.432</Real>
+        </Vector>
+        <Vector>
+            <Real Name="X">1.936</Real>
+            <Real Name="Y">1.441</Real>
+            <Real Name="Z">5.873</Real>
+        </Vector>
+        <Vector>
+            <Real Name="X">0.96</Real>
+            <Real Name="Y">2.246</Real>
+            <Real Name="Z">1.659</Real>
+        </Vector>
+        <Vector>
+            <Real Name="X">0.382</Real>
+            <Real Name="Y">3.023</Real>
+            <Real Name="Z">2.793</Real>
+        </Vector>
+        <Vector>
+            <Real Name="X">0.053</Real>
+            <Real Name="Y">4.857</Real>
+            <Real Name="Z">4.242</Real>
+        </Vector>
+        <Vector>
+            <Real Name="X">2.655</Real>
+            <Real Name="Y">5.057</Real>
+            <Real Name="Z">2.211</Real>
+        </Vector>
+        <Vector>
+            <Real Name="X">4.114</Real>
+            <Real Name="Y">0.737</Real>
+            <Real Name="Z">0.614</Real>
+        </Vector>
+        <Vector>
+            <Real Name="X">5.977</Real>
+            <Real Name="Y">5.104</Real>
+            <Real Name="Z">5.217</Real>
+        </Vector>
+    </Sequence>
+
+    <Sequence Name="velocities">
+        <Int Name="Length">12</Int>
+        <Vector>
+            <Real Name="X">0.0055</Real>
+            <Real Name="Y">-0.14</Real>
+            <Real Name="Z">0.2127</Real>
+        </Vector>
+        <Vector>
+            <Real Name="X">0.093</Real>
+            <Real Name="Y">-0.016</Real>
+            <Real Name="Z">-0.0086</Real>
+        </Vector>
+        <Vector>
+            <Real Name="X">0.1678</Real>
+            <Real Name="Y">0.2476</Real>
+            <Real Name="Z">-0.066</Real>
+        </Vector>
+        <Vector>
+            <Real Name="X">0.1591</Real>
+            <Real Name="Y">-0.0934</Real>
+            <Real Name="Z">-0.0835</Real>
+        </Vector>
+        <Vector>
+            <Real Name="X">-0.0317</Real>
+            <Real Name="Y">0.0573</Real>
+            <Real Name="Z">0.1453</Real>
+        </Vector>
+        <Vector>
+            <Real Name="X">0.0597</Real>
+            <Real Name="Y">0.0013</Real>
+            <Real Name="Z">-0.0462</Real>
+        </Vector>
+        <Vector>
+            <Real Name="X">0.0484</Real>
+            <Real Name="Y">-0.0357</Real>
+            <Real Name="Z">0.0168</Real>
+        </Vector>
+        <Vector>
+            <Real Name="X">0.053</Real>
+            <Real Name="Y">0.0295</Real>
+            <Real Name="Z">-0.2694</Real>
+        </Vector>
+        <Vector>
+            <Real Name="X">-0.055</Real>
+            <Real Name="Y">-0.0896</Real>
+            <Real Name="Z">0.0494</Real>
+        </Vector>
+        <Vector>
+            <Real Name="X">-0.0799</Real>
+            <Real Name="Y">-0.2534</Real>
+            <Real Name="Z">-0.0079</Real>
+        </Vector>
+        <Vector>
+            <Real Name="X">0.0436</Real>
+            <Real Name="Y">-0.1557</Real>
+            <Real Name="Z">0.1849</Real>
+        </Vector>
+        <Vector>
+            <Real Name="X">-0.0214</Real>
+            <Real Name="Y">0.0446</Real>
+            <Real Name="Z">0.0758</Real>
+        </Vector>
+    </Sequence>
+
+    <Sequence Name="nbparams">
+        <Int Name="Length">2</Int>
+        <Real>0.0351364166</Real>
+        <Real>9.8438366e-05</Real>
+    </Sequence>
+
+    <Sequence Name="exclusion elements">
+        <Int Name="Length">12</Int>
+        <Int>0</Int>
+        <Int>1</Int>
+        <Int>2</Int>
+        <Int>3</Int>
+        <Int>4</Int>
+        <Int>5</Int>
+        <Int>6</Int>
+        <Int>7</Int>
+        <Int>8</Int>
+        <Int>9</Int>
+        <Int>10</Int>
+        <Int>11</Int>
+    </Sequence>
+
+    <Sequence Name="exclusion ranges">
+        <Int Name="Length">13</Int>
+        <Int>0</Int>
+        <Int>1</Int>
+        <Int>2</Int>
+        <Int>3</Int>
+        <Int>4</Int>
+        <Int>5</Int>
+        <Int>6</Int>
+        <Int>7</Int>
+        <Int>8</Int>
+        <Int>9</Int>
+        <Int>10</Int>
+        <Int>11</Int>
+        <Int>12</Int>
+    </Sequence>
+</ReferenceData>

diff --git a/api/nblib/tests/refdata/TprReaderTest_FCfromTprDataWorks.xml b/api/nblib/tests/refdata/TprReaderTest_FCfromTprDataWorks.xml
new file mode 100644 (file)
index 0000000..8020088
--- /dev/null
+++ b/api/nblib/tests/refdata/TprReaderTest_FCfromTprDataWorks.xml
@@ -0,0 +1,67 @@
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+  <Sequence Name="Argon forces">
+    <Int Name="Length">12</Int>
+    <Vector>
+      <Real Name="X">-1.4060510037205805</Real>
+      <Real Name="Y">-3.7390541506347286</Real>
+      <Real Name="Z">-0.38536212694564093</Real>
+    </Vector>
+    <Vector>
+      <Real Name="X">0</Real>
+      <Real Name="Y">0</Real>
+      <Real Name="Z">0</Real>
+    </Vector>
+    <Vector>
+      <Real Name="X">1.4060510037205805</Real>
+      <Real Name="Y">3.7390541506347286</Real>
+      <Real Name="Z">0.38536212694564093</Real>
+    </Vector>
+    <Vector>
+      <Real Name="X">0</Real>
+      <Real Name="Y">0</Real>
+      <Real Name="Z">0</Real>
+    </Vector>
+    <Vector>
+      <Real Name="X">0</Real>
+      <Real Name="Y">0</Real>
+      <Real Name="Z">0</Real>
+    </Vector>
+    <Vector>
+      <Real Name="X">0</Real>
+      <Real Name="Y">0</Real>
+      <Real Name="Z">0</Real>
+    </Vector>
+    <Vector>
+      <Real Name="X">0</Real>
+      <Real Name="Y">0</Real>
+      <Real Name="Z">0</Real>
+    </Vector>
+    <Vector>
+      <Real Name="X">0</Real>
+      <Real Name="Y">0</Real>
+      <Real Name="Z">0</Real>
+    </Vector>
+    <Vector>
+      <Real Name="X">0</Real>
+      <Real Name="Y">0</Real>
+      <Real Name="Z">0</Real>
+    </Vector>
+    <Vector>
+      <Real Name="X">0</Real>
+      <Real Name="Y">0</Real>
+      <Real Name="Z">0</Real>
+    </Vector>
+    <Vector>
+      <Real Name="X">0</Real>
+      <Real Name="Y">0</Real>
+      <Real Name="Z">0</Real>
+    </Vector>
+    <Vector>
+      <Real Name="X">0</Real>
+      <Real Name="Y">0</Real>
+      <Real Name="Z">0</Real>
+    </Vector>
+  </Sequence>
+</ReferenceData>

diff --git a/api/nblib/tests/simstate.cpp b/api/nblib/tests/simstate.cpp
index 01a0bf54323e5fd1a37e0bd50581432e719eee39..4081a59dcf7f3628b20b206e99ebf740a8395df1 100644 (file)
--- a/api/nblib/tests/simstate.cpp
+++ b/api/nblib/tests/simstate.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2020, by the GROMACS development team, led by
+ * Copyright (c) 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.
@@ -74,55 +74,55 @@ void compareValues(const std::vector<Vec3>& ref, const std::vector<Vec3>& test)
 
 TEST(NBlibTest, CanConstructSimulationState)
 {
-    ArgonSimulationStateBuilder argonSimulationStateBuilder;
+    ArgonSimulationStateBuilder argonSimulationStateBuilder(fftypes::GROMOS43A1);
     EXPECT_NO_THROW(argonSimulationStateBuilder.setupSimulationState());
 }
 
 TEST(NBlibTest, SimulationStateThrowsCoordinateNAN)
 {
-    ArgonSimulationStateBuilder argonSimulationStateBuilder;
+    ArgonSimulationStateBuilder argonSimulationStateBuilder(fftypes::GROMOS43A1);
     argonSimulationStateBuilder.setCoordinate(2, 0, NAN);
     EXPECT_THROW(argonSimulationStateBuilder.setupSimulationState(), InputException);
 }
 
 TEST(NBlibTest, SimulationStateThrowsCoordinateINF)
 {
-    ArgonSimulationStateBuilder argonSimulationStateBuilder;
+    ArgonSimulationStateBuilder argonSimulationStateBuilder(fftypes::GROMOS43A1);
     argonSimulationStateBuilder.setCoordinate(2, 0, INFINITY);
     EXPECT_THROW(argonSimulationStateBuilder.setupSimulationState(), InputException);
 }
 
 TEST(NBlibTest, SimulationStateThrowsVelocityNAN)
 {
-    ArgonSimulationStateBuilder argonSimulationStateBuilder;
+    ArgonSimulationStateBuilder argonSimulationStateBuilder(fftypes::GROMOS43A1);
     argonSimulationStateBuilder.setVelocity(2, 0, NAN);
     EXPECT_THROW(argonSimulationStateBuilder.setupSimulationState(), InputException);
 }
 
 TEST(NBlibTest, SimulationStateThrowsVelocityINF)
 {
-    ArgonSimulationStateBuilder argonSimulationStateBuilder;
+    ArgonSimulationStateBuilder argonSimulationStateBuilder(fftypes::GROMOS43A1);
     argonSimulationStateBuilder.setVelocity(2, 0, INFINITY);
     EXPECT_THROW(argonSimulationStateBuilder.setupSimulationState(), InputException);
 }
 
 TEST(NBlibTest, SimulationStateCanMove)
 {
-    ArgonSimulationStateBuilder argonSimulationStateBuilder;
+    ArgonSimulationStateBuilder argonSimulationStateBuilder(fftypes::GROMOS43A1);
     SimulationState             simState = argonSimulationStateBuilder.setupSimulationState();
     EXPECT_NO_THROW(SimulationState movedSimState = std::move(simState));
 }
 
 TEST(NBlibTest, SimulationStateCanAssign)
 {
-    ArgonSimulationStateBuilder argonSimulationStateBuilder;
+    ArgonSimulationStateBuilder argonSimulationStateBuilder(fftypes::GROMOS43A1);
     SimulationState             simState = argonSimulationStateBuilder.setupSimulationState();
     EXPECT_NO_THROW(const SimulationState& gmx_unused AssignedSimState = simState);
 }
 
 TEST(NBlibTest, SimulationStateHasBox)
 {
-    ArgonSimulationStateBuilder argonSimulationStateBuilder;
+    ArgonSimulationStateBuilder argonSimulationStateBuilder(fftypes::GROMOS43A1);
     SimulationState             simState = argonSimulationStateBuilder.setupSimulationState();
     const Box&                  testBox  = simState.box();
     const Box&                  refBox   = argonSimulationStateBuilder.box();
@@ -133,7 +133,7 @@ TEST(NBlibTest, SimulationStateHasBox)
 
 TEST(NBlibTest, SimulationStateHasCorrectCoordinates)
 {
-    ArgonSimulationStateBuilder argonSimulationStateBuilder;
+    ArgonSimulationStateBuilder argonSimulationStateBuilder(fftypes::GROMOS43A1);
     SimulationState             simState = argonSimulationStateBuilder.setupSimulationState();
     std::vector<Vec3>           test     = simState.coordinates();
     std::vector<Vec3>           ref      = argonSimulationStateBuilder.coordinates();
@@ -142,7 +142,7 @@ TEST(NBlibTest, SimulationStateHasCorrectCoordinates)
 
 TEST(NBlibTest, SimulationStateHasCorrectVelocities)
 {
-    ArgonSimulationStateBuilder argonSimulationStateBuilder;
+    ArgonSimulationStateBuilder argonSimulationStateBuilder(fftypes::GROMOS43A1);
     SimulationState             simState = argonSimulationStateBuilder.setupSimulationState();
     std::vector<Vec3>           test     = simState.velocities();
     std::vector<Vec3>           ref      = argonSimulationStateBuilder.velocities();

diff --git a/api/nblib/tests/testhelpers.h b/api/nblib/tests/testhelpers.h
index 6c323571c51692e46ebd23adb5f9875beff90931..b98357056d5c70ebe22f997587f79c9b180dad6d 100644 (file)
--- a/api/nblib/tests/testhelpers.h
+++ b/api/nblib/tests/testhelpers.h
@@ -46,11 +46,12 @@
 
 #include "gromacs/math/vectypes.h"
 #include "gromacs/utility/arrayref.h"
+
 #include "nblib/box.h"
 #include "nblib/vector.h"
 
+#include "testutils/conftest.h"
 #include "testutils/refdata.h"
-#include "testutils/testasserts.h"
 
 namespace nblib
 {
@@ -58,35 +59,33 @@ namespace nblib
 namespace test
 {
 
-//! Compare between two instances of the Box object
-bool operator==(const Box& a, const Box& b);
-
 /*! \internal \brief
  *  Simple test harness for checking 3D vectors like coordinates, velocities,
  *  forces against reference data
  *
  */
-class Vector3DTest
+class RefDataChecker
 {
 public:
-    Vector3DTest() : checker_(refData_.rootChecker())
+    RefDataChecker() : checker_(refData_.rootChecker())
     {
         gmx::test::FloatingPointTolerance tolerance(
                 gmx::test::FloatingPointTolerance(1e-8, 1.0e-12, 1e-8, 1.0e-12, 200, 100, true));
         checker_.setDefaultTolerance(tolerance);
     }
 
-    Vector3DTest(real relativeFloatingPointTolerance) : checker_(refData_.rootChecker())
+    RefDataChecker(real relativeFloatingPointTolerance) : checker_(refData_.rootChecker())
     {
         gmx::test::FloatingPointTolerance tolerance(gmx::test::FloatingPointTolerance(
-                1e-8, 1.0e-12, relativeFloatingPointTolerance, 1.0e-12, 200, 100, true));
+                1e-6, 1.0e-9, relativeFloatingPointTolerance, relativeFloatingPointTolerance, 200, 100, true));
         checker_.setDefaultTolerance(tolerance);
     }
 
-    //! Compare a given input vector of cartesians with the reference data
-    void testVectors(gmx::ArrayRef<Vec3> forces, const std::string& testName)
+    //! Compare a given input array of cartesians, reals, integers, etc with the reference data
+    template<class T>
+    void testArrays(gmx::ArrayRef<T> tArray, const std::string& testString)
     {
-        checker_.checkSequence(forces.begin(), forces.end(), testName.c_str());
+        checker_.checkSequence(tArray.begin(), tArray.end(), testString.c_str());
     }
 
     void testReal(real value, const std::string& testName)

diff --git a/api/nblib/tests/testsystems.cpp b/api/nblib/tests/testsystems.cpp
index b9d438e4fe1f233d78a387259df54e76968c9975..1559f73293b9b14685b7792e64f8f3c2be8bb40f 100644 (file)
--- a/api/nblib/tests/testsystems.cpp
+++ b/api/nblib/tests/testsystems.cpp
@@ -59,25 +59,29 @@ public:
         ParticleType H(ParticleTypeName("H"), Mass(1.008));
         ParticleType OMet(ParticleTypeName("OMet"), Mass(15.999));
         ParticleType CMet(ParticleTypeName("CMet"), Mass(15.035));
-        ParticleType Ar(ParticleTypeName("Ar"), Mass(39.94800));
+        ParticleType Ar_gromos(ParticleTypeName("Ar_gromos"), Mass(39.94800));
+        ParticleType Ar_opls(ParticleTypeName("Ar_opls"), Mass(39.94800));
 
         particles_.insert(std::make_pair(Ow.name(), Ow));
         particles_.insert(std::make_pair(H.name(), H));
         particles_.insert(std::make_pair(OMet.name(), OMet));
         particles_.insert(std::make_pair(CMet.name(), CMet));
-        particles_.insert(std::make_pair(Ar.name(), Ar));
-
-        c6_[Ow.name()]   = 0.0026173456;
-        c6_[H.name()]    = 0;
-        c6_[OMet.name()] = 0.0022619536;
-        c6_[CMet.name()] = 0.0088755241;
-        c6_[Ar.name()]   = 0.0062647225;
-
-        c12_[Ow.name()]   = 2.634129e-06;
-        c12_[H.name()]    = 0;
-        c12_[OMet.name()] = 1.505529e-06;
-        c12_[CMet.name()] = 2.0852922e-05;
-        c12_[Ar.name()]   = 9.847044e-06;
+        particles_.insert(std::make_pair(Ar_gromos.name(), Ar_gromos));
+        particles_.insert(std::make_pair(Ar_opls.name(), Ar_opls));
+
+        c6_[Ow.name()]        = 0.0026173456;
+        c6_[H.name()]         = 0;
+        c6_[OMet.name()]      = 0.0022619536;
+        c6_[CMet.name()]      = 0.0088755241;
+        c6_[Ar_gromos.name()] = 0.0062647225;
+        c6_[Ar_opls.name()]   = 0.0058560692;
+
+        c12_[Ow.name()]        = 2.634129e-06;
+        c12_[H.name()]         = 0;
+        c12_[OMet.name()]      = 1.505529e-06;
+        c12_[CMet.name()]      = 2.0852922e-05;
+        c12_[Ar_gromos.name()] = 9.847044e-06;
+        c12_[Ar_opls.name()]   = 8.203193e-06;
     }
 
     //! Get particle type using the string identifier
@@ -234,16 +238,29 @@ Molecule SpcMethanolTopologyBuilder::water()
     return waterMolecule_.waterMolecule();
 }
 
-ArgonTopologyBuilder::ArgonTopologyBuilder(const int& numParticles)
+ArgonTopologyBuilder::ArgonTopologyBuilder(const int& numParticles, const fftypes forceField)
 {
     ParticleLibrary library;
 
     ParticleTypesInteractions nbinteractions;
-    nbinteractions.add(
-            ParticleTypeName("Ar"), library.c6(ParticleName("Ar")), library.c12(ParticleName("Ar")));
 
     Molecule argonMolecule(MoleculeName("AR"));
-    argonMolecule.addParticle(ParticleName("AR"), library.type("Ar"));
+
+    std::string particleName;
+
+    if (forceField == fftypes::GROMOS43A1)
+    {
+        particleName = "Ar_gromos";
+    }
+    else if (forceField == fftypes::OPLSA)
+    {
+        particleName = "Ar_opls";
+    }
+
+    nbinteractions.add(ParticleTypeName(particleName),
+                       library.c6(ParticleName(particleName)),
+                       library.c12(ParticleName(particleName)));
+    argonMolecule.addParticle(ParticleName("AR"), library.type(particleName));
 
     topologyBuilder_.addMolecule(argonMolecule, numParticles);
     topologyBuilder_.addParticleTypesInteractions((nbinteractions));
@@ -254,8 +271,8 @@ Topology ArgonTopologyBuilder::argonTopology()
     return topologyBuilder_.buildTopology();
 }
 
-ArgonSimulationStateBuilder::ArgonSimulationStateBuilder() :
-    box_(6.05449), topology_(ArgonTopologyBuilder(12).argonTopology())
+ArgonSimulationStateBuilder::ArgonSimulationStateBuilder(const fftypes forceField) :
+    box_(6.05449), topology_(ArgonTopologyBuilder(12, forceField).argonTopology())
 {
 
     coordinates_ = {

diff --git a/api/nblib/tests/testsystems.h b/api/nblib/tests/testsystems.h
index f4d4dace63793ba93cbabe707bb41e9355d51bf4..25cde120e2783ce1b2054a85cc2cba1764b5209a 100644 (file)
--- a/api/nblib/tests/testsystems.h
+++ b/api/nblib/tests/testsystems.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2020, by the GROMACS development team, led by
+ * Copyright (c) 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.
@@ -56,6 +56,13 @@
 namespace nblib
 {
 
+//! \internal \brief Force field types to select parameter sets
+enum class fftypes : int
+{
+    GROMOS43A1,
+    OPLSA
+};
+
 //! \internal \brief Parameters from gromos43A1
 struct ArAtom
 {
@@ -149,7 +156,7 @@ class ArgonTopologyBuilder
 {
 public:
     //! Build a topology with specified argon molecules
-    ArgonTopologyBuilder(const int& numParticles);
+    ArgonTopologyBuilder(const int& numParticles, const fftypes forceField);
 
     //! Get the topology with specified argon molecules
     Topology argonTopology();
@@ -162,7 +169,7 @@ private:
 class ArgonSimulationStateBuilder
 {
 public:
-    ArgonSimulationStateBuilder();
+    ArgonSimulationStateBuilder(const fftypes forceField);
 
     //! Set coordinates of particles in the defined system
     void setCoordinate(int particleNum, int dimension, real value);

diff --git a/api/nblib/tests/topology.cpp b/api/nblib/tests/topology.cpp
index ff4d0336d929edc9eaa0e3c2af468a7d70628dfa..218eb614444fcb1db93fa644519551472bf3fb75 100644 (file)
--- a/api/nblib/tests/topology.cpp
+++ b/api/nblib/tests/topology.cpp
@@ -366,7 +366,7 @@ TEST(NBlibTest, TopologyListedInteractionsMultipleTypes)
     Molecule water    = WaterMoleculeBuilder{}.waterMolecule();
     Molecule methanol = MethanolMoleculeBuilder{}.methanolMolecule();
 
-    CubicBondType     testBond(1., 1., 1.);
+    CubicBondType testBond(1., 1., 1.);
     HarmonicAngleType testAngle(Degrees(1), 1);
 
     water.addInteraction(ParticleName("H1"), ParticleName("H2"), testBond);

diff --git a/api/nblib/util/tests/setup.cpp b/api/nblib/util/tests/setup.cpp
index fb59d06e4d4517175971a29084ecdf5a97d70478..aa2a05b1c674aae0b727c37aa06d3324410fa433 100644 (file)
--- a/api/nblib/util/tests/setup.cpp
+++ b/api/nblib/util/tests/setup.cpp
@@ -98,8 +98,8 @@ TEST(NBlibTest, GeneratedVelocitiesAreCorrect)
     std::vector<Vec3> velocities;
     velocities = generateVelocity(300.0, 1, masses);
 
-    Vector3DTest velocitiesTest;
-    velocitiesTest.testVectors(velocities, "generated-velocities");
+    RefDataChecker velocitiesTest;
+    velocitiesTest.testArrays<Vec3>(velocities, "generated-velocities");
 }
 TEST(NBlibTest, generateVelocitySize)
 {