Unit test 150 (SimVascular#198)

--------- Co-authored-by: Yuecheng Yu <[email protected]> Co-authored-by: Yuecheng Yu <[email protected]> Co-authored-by: Yuecheng Yu <[email protected]> Co-authored-by: Yuecheng Yu <[email protected]> Co-authored-by: Yuecheng Yu <[email protected]> Co-authored-by: Yuecheng Yu <[email protected]>
mrp089 · Mar 14, 2024 · b28958c · b28958c
1 parent 29a94c3
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diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -29,7 +29,7 @@ jobs:
         run: |
           mkdir build
           cd build
-          cmake -DENABLE_COVERAGE=ON -DENABLE_ARRAY_INDEX_CHECKING=ON ..
+          cmake -DENABLE_COVERAGE=ON -DENABLE_ARRAY_INDEX_CHECKING=ON -DENABLE_UNIT_TEST=ON ..
           make -j2
       - name: Install test dependencies
         run: |
@@ -40,6 +40,10 @@ jobs:
           git lfs pull
           cd tests
           conda run -n svfsiplus pytest -rPv --durations=0
+      - name: Run unit tests
+        run: |
+          cd build/svFSI-build/Source/svFSI
+          ctest --verbose
       - name: Generate code coverage
         if: startsWith(matrix.os, 'ubuntu-22.04')
         run: |

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -88,6 +88,7 @@ set(SV_PETSC_DIR "" CACHE STRING "Path to a local install of the PETSc linear al
 set(ENABLE_COVERAGE OFF CACHE BOOL "Enable code coverage")
 set(ENABLE_ARRAY_INDEX_CHECKING OFF CACHE BOOL "Enable Array index checking")
 set(SV_LOCAL_VTK_PATH "" CACHE STRING "Path to a local build of VTK.")
+set(ENABLE_UNIT_TEST OFF CACHE BOOL "Enable Unit Test by Google Test")
 
 #-----------------------------------------------------------------------------
 # RPATH handling
@@ -147,6 +148,7 @@ ExternalProject_Add(svFSI
     #-DSV_USE_PETSC:BOOL=${SV_USE_PETSC}
     -DSV_PETSC_DIR:STRING=${SV_PETSC_DIR}
     -DENABLE_COVERAGE:BOOL=${ENABLE_COVERAGE}
+    -DENABLE_UNIT_TEST:BOOL=${ENABLE_UNIT_TEST}
     -DENABLE_ARRAY_INDEX_CHECKING:BOOL=${ENABLE_ARRAY_INDEX_CHECKING}
     -DSV_LOCAL_VTK_PATH:STRING=${SV_LOCAL_VTK_PATH}
     ${SV_APPLE_CMAKE_ARGS}

diff --git a/Code/Source/svFSI/CMakeLists.txt b/Code/Source/svFSI/CMakeLists.txt
@@ -260,4 +260,56 @@ if(ENABLE_COVERAGE)
     WORKING_DIRECTORY ${CMAKE_BINARY_DIR})
 endif()
 
+# unit tests and Google Test
+if(ENABLE_UNIT_TEST)
+
+  # link pthread on ubuntu20
+  find_package(Threads REQUIRED)
+
+  # install Google Test
+  include(FetchContent)
+  FetchContent_Declare(
+    googletest
+    URL https://github.com/google/googletest/archive/03597a01ee50ed33e9dfd640b249b4be3799d395.zip
+  )
+  FetchContent_MakeAvailable(googletest)
+  enable_testing()
+  include(GoogleTest)
+
+  # add test.cpp for unit test
+
+  # remove the main.cpp and add test.cpp
+  list(APPEND CSRCS "../../../tests/unitTests/test.cpp")
+  list(REMOVE_ITEM CSRCS "main.cpp")
+
+  # include source files (same as what svFSI does except for main.cpp)
+  add_executable(run_all_unit_tests ${CSRCS})
+
+  # libraries
+  target_link_libraries(run_all_unit_tests
+    ${GLOBAL_LIBRARIES}
+    ${INTELRUNTIME_LIBRARIES}
+    ${ZLIB_LIBRARY}
+    ${BLAS_LIBRARIES}
+    ${LAPACK_LIBRARIES}
+    ${METIS_SVFSI_LIBRARY_NAME}
+    ${PARMETIS_SVFSI_LIBRARY_NAME}
+    ${TETGEN_LIBRARY_NAME}
+    ${TINYXML_LIBRARY_NAME}
+    ${SV_LIB_SVFSILS_NAME}${SV_MPI_NAME_EXT}
+    ${VTK_LIBRARIES}
+  )
+
+  # link Google Test
+  target_link_libraries(
+    run_all_unit_tests
+    gtest
+    GTest::gtest_main 
+    pthread   # link pthread on ubuntu20
+  )
+
+  # gtest_discover_tests(runUnitTest)
+  add_test(NAME all_unit_tests COMMAND run_all_unit_tests)
+
+endif()
 
diff --git a/tests/unitTests/test.cpp b/tests/unitTests/test.cpp
@@ -0,0 +1,86 @@
+/* Copyright (c) Stanford University, The Regents of the University of California, and others.
+ *
+ * All Rights Reserved.
+ *
+ * See Copyright-SimVascular.txt for additional details.
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining
+ * a copy of this software and associated documentation files (the
+ * "Software"), to deal in the Software without restriction, including
+ * without limitation the rights to use, copy, modify, merge, publish,
+ * distribute, sublicense, and/or sell copies of the Software, and to
+ * permit persons to whom the Software is furnished to do so, subject
+ * to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included
+ * in all copies or substantial portions of the Software.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS
+ * IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
+ * TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+ * PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER
+ * OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+ * EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+ * PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+ * PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+ * LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+ * NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+ * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+#include "test.h"
+
+using namespace mat_fun;
+using namespace std;
+
+
+TEST(UnitTestIso_1, nHK) {
+    // Step 1: define parameters
+    auto matType = consts::ConstitutiveModelType::stIso_nHook;   // Material_model: options refer to consts.h 
+    auto volType = consts::ConstitutiveModelType::stVol_ST91;   // Dilational_penalty_model
+    double E = 1e6;   // Elasticity_modulus
+    double nu = 0.5;   // Poisson_ratio
+    double pen = 4e9;   // Penalty_parameter
+    double C01;   // additional parameter to C10 (optional)
+
+    // Step 2: construct test object
+    UnitTestIso nHK(matType, E, nu, volType, pen, C01);
+
+    // Step 3: define the input 
+    double F[3][3] = {};
+    F[0][0] = 1.0; F[1][1] = 1.0; F[2][2] = 1.0;   // set to Identity
+
+    // Step 4: define the reference output 
+    double S_ref[3][3] = {};
+    double Dm_ref[6][6] = {};
+
+    // Step 5: run unit test
+    nHK.runUnitTest(F, S_ref, Dm_ref);
+
+}
+
+TEST(UnitTestIso_2, MR) {
+    // Step 1: define parameters
+    auto matType = consts::ConstitutiveModelType::stIso_MR;   // Material_model: options refer to consts.h 
+    auto volType = consts::ConstitutiveModelType::stVol_ST91;   // Dilational_penalty_model
+    double E = 1e6;   // Elasticity_modulus
+    double nu = 0.495;   // Poisson_ratio
+    double pen = 4e9;   // Penalty_parameter
+    double C01 = 0.1;   // additional parameter to C10 (optional)
+
+    // Step 2: construct test object
+    UnitTestIso MR(matType, E, nu, volType, pen, C01);
+
+    // Step 3: define the input 
+    double F[3][3] = {};
+    F[0][0] = 1.0; F[1][1] = 1.0; F[2][2] = 1.0;   // set to Identity
+
+    // Step 4: define the reference output 
+    double S_ref[3][3] = {};
+    double Dm_ref[6][6] = {};
+
+    // Step 5: run unit test
+    MR.runUnitTest(F, S_ref, Dm_ref);
+
+}
+
diff --git a/tests/unitTests/test.h b/tests/unitTests/test.h
@@ -0,0 +1,119 @@
+/* Copyright (c) Stanford University, The Regents of the University of California, and others.
+ *
+ * All Rights Reserved.
+ *
+ * See Copyright-SimVascular.txt for additional details.
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining
+ * a copy of this software and associated documentation files (the
+ * "Software"), to deal in the Software without restriction, including
+ * without limitation the rights to use, copy, modify, merge, publish,
+ * distribute, sublicense, and/or sell copies of the Software, and to
+ * permit persons to whom the Software is furnished to do so, subject
+ * to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included
+ * in all copies or substantial portions of the Software.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS
+ * IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
+ * TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+ * PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER
+ * OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+ * EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+ * PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+ * PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+ * LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+ * NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+ * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+#include <stdlib.h>
+#include <iostream>
+#include "gtest/gtest.h"   // include GoogleTest
+#include "mat_fun.h"
+#include "mat_fun_carray.h"
+#include "mat_models.h"
+#include "mat_models_carray.h"
+
+class MockCepMod : public CepMod {
+public:
+    MockCepMod() {
+        // initialize if needed 
+    }
+    // Mock methods if needed
+};
+class MockdmnType : public dmnType {
+public:
+    MockdmnType() {
+        // initialize if needed 
+    }
+    // MockstModelType mockStM;
+    // Mock methods if needed
+};
+class MockmshType : public mshType {
+public:
+    MockmshType() {
+        // initialize if needed 
+    }
+    // Mock methods if needed
+};
+class MockeqType : public eqType {
+public:
+    MockeqType() {
+        // initialize if needed 
+    }
+    MockdmnType mockDmn;
+    // Mock methods if needed
+};
+class MockComMod : public ComMod {
+public:
+    MockComMod() {
+        // initialize if needed 
+        nsd = 3;
+    }
+    MockeqType mockEq;
+    MockmshType mockMsh;
+    // Mock methods if needed
+};
+
+// Class for unit test of isotropic material model (currently only introduced two 
+// parameters C10 and C01)
+class UnitTestIso {
+public:
+    MockComMod com_mod;
+    MockCepMod cep_mod;
+
+    UnitTestIso(consts::ConstitutiveModelType matType, double E, double nu, 
+                consts::ConstitutiveModelType penType, double pen, double C01 = 0.0) {
+        int nsd = com_mod.nsd;
+        auto &dmn = com_mod.mockEq.mockDmn;
+        mat_fun_carray::ten_init(nsd);                        // initialize tensor index pointer
+        dmn.stM.isoType = matType;                            // Mat_model
+        double mu  = 0.5 * E / (1.0 + nu);                    // Shear_modulus
+        dmn.stM.C10 = 0.5 * mu - C01;                         // set_material_props.h 
+        dmn.stM.C01 = C01;
+        dmn.stM.volType = penType;                            // Dilational_penalty_model
+        dmn.stM.Kpen = pen;                                   // Penalty_parameter
+    }
+
+    void runUnitTest(double F[3][3], double S_ref[3][3], double Dm_ref[6][6]) {
+        int nsd = com_mod.nsd;
+        auto &dmn = com_mod.mockEq.mockDmn;
+        // hard code for nHK
+        int nFn = 1; 
+        Array<double> fN(nsd, nFn);
+        double ya_g = 0.0;   
+        double S[3][3], Dm[6][6];
+
+        mat_models_carray::get_pk2cc(com_mod, cep_mod, dmn, F, nFn, fN, ya_g, S, Dm);
+        double tol = 1e-12;   // tolerance
+
+        // Compare with reference solution
+        for (int i = 0; i < 3; i++){
+            for (int j = 0; j < 3; j++){
+                EXPECT_NEAR(S[i][j], S_ref[i][j], tol);   
+            }
+        }
+    }
+};