Unit test 150

.github/workflows/test.yml

@@ -28,7 +28,7 @@ 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: |
@@ -39,6 +39,10 @@ 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: |

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}

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()
 

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);
+
+}
+

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); 
+ }
+ }
+ }
+};