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 --output-on-failure
  - 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 +260,72 @@ 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 hello_test, a sample test file to check the installation of Google Test
+ add_executable(
+ hello_test
+ ../../../tests/unitTests/hello_test.cpp
+ )
+ target_link_libraries(
+ hello_test
+ gtest
+ GTest::gtest_main
+ pthread # link pthread on ubuntu20
+ )
+ # gtest_discover_tests(hello_test)
+ add_test(NAME GTestSample COMMAND hello_test)
+
+
+ # 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(runUnitTest ${CSRCS})
+
+ # libraries
+ target_link_libraries(runUnitTest
+ ${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(
+ runUnitTest
+ gtest
+ GTest::gtest_main 
+ pthread # link pthread on ubuntu20
+ )
+ target_compile_definitions(runUnitTest PRIVATE GTEST_HAS_PTHREAD=1)
+
+ # gtest_discover_tests(runUnitTest)
+ add_test(NAME UnitTest COMMAND runUnitTest)
+
+endif()
 

tests/unitTests/hello_test.cpp

@@ -0,0 +1,53 @@
+/* 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.
+ */
+
+/**
+ * This function is adapted from Google Test's Quickstart Guide.
+ * Source: Google Test Quickstart for Google Test and CMake
+ * URL: https://google.github.io/googletest/quickstart-cmake.html
+ */
+
+#include <gtest/gtest.h>
+
+// Demonstrate some basic assertions.
+TEST(HelloTest, BasicAssertions) {
+ // Expect two strings not to be equal.
+ EXPECT_STRNE("hello", "world");
+ // Expect equality.
+ EXPECT_EQ(7 * 6, 42);
+}
+
+// Main function running the tests
+int main(int argc, char **argv) {
+
+ ::testing::InitGoogleTest(&argc, argv);
+ return RUN_ALL_TESTS();
+
+}

tests/unitTests/test.cpp

@@ -0,0 +1,186 @@
+/* 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.
+ */
+
+/* unit test for get_pk2cc
+* this program generates a simple svFSI simulation to test function get_pk2cc.
+* it allows you to create input deformation gradients to check the output 
+* stress and tangent modulus. it usese Google Test for test cases.
+*/
+
+#include <stdlib.h>
+#include <iomanip>
+#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"
+#include "Simulation.h"
+#include "sv_struct.h"
+#include "distribute.h"
+#include "initialize.h"
+#include "read_files.h"
+
+
+// Using global variables: 
+// for the output: stress tensor and tangent tensor
+
+Array<double> S_0(3,3), Dm_0(6,6); // for identity test
+Array<double> S_1(3,3), Dm_1(6,6); // for non-identity test
+
+
+// Google Test test cases
+
+TEST(ExampleTest, OneEqualsToOne) {
+ EXPECT_EQ(1, 1);
+}
+
+TEST(GetPK2ccTest, Identity) {
+ // input: 
+ // 1 0 0
+ // 0 1 0
+ // 0 0 1
+ for (short i = 0; i < 3; i++){
+ for (short j = 0; j < 3; j++){
+ EXPECT_EQ(S_0(i,j), 0); 
+ }
+ }
+}
+
+TEST(GetPK2ccTest, Non_Identity) {
+ // input: 
+ // 2 0 0
+ // 0 1 0
+ // 0 0 1
+ for (short i = 0; i < 3; i++){
+ for (short j = 0; j < 3; j++){
+ if (i == j) {
+ EXPECT_NE(S_1(i,j), 0); 
+ } else {
+ EXPECT_EQ(S_1(i,j), 0); 
+ } 
+ }
+ }
+}
+
+
+void read_files(Simulation* simulation, const std::string& file_name)
+{
+ simulation->com_mod.timer.set_time();
+
+ if (simulation->com_mod.cm.slv(simulation->cm_mod)) {
+ return;
+ }
+
+ read_files_ns::read_files(simulation, file_name);
+}
+
+
+// Main function running the tests
+int main(int argc, char **argv) {
+ // define deformation gradient as input for get_pk2cc
+ Array<double> F_0 = mat_fun::mat_id(3);
+ Array<double> F_1 = mat_fun::mat_id(3);
+ F_1(0,0) = 2;
+
+ // Initialize MPI.
+ //
+ int mpi_rank, mpi_size;
+ MPI_Init(&argc, &argv);
+ MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank);
+ MPI_Comm_size(MPI_COMM_WORLD, &mpi_size);
+
+ auto simulation = new Simulation();
+
+ std::string file_name = "../../../../tests/unitTests/unitTest.xml";
+ // std::string file_name = "";
+
+ read_files(simulation, file_name);
+
+ std::cout << "Finish reading files" << std::endl;
+
+ distribute(simulation);
+ Vector<double> init_time(3);
+ initialize(simulation, init_time);
+
+ // preparing input arguments for get_pk2cc
+ auto com_mod = simulation->com_mod;
+ auto cm_mod_ = simulation->cm_mod;
+ auto cm = com_mod.cm;
+ auto cep_mod = simulation->get_cep_mod();
+ const int nsd = com_mod.nsd;
+ auto iM = com_mod.nMsh; // nMsh = 1 from unit mesh 
+ auto& lM = com_mod.msh[iM-1]; 
+ auto e = lM.gnEl; // global number of elements
+ int eNoN = lM.eNoN;
+ int nFn = lM.nFn;
+ if (nFn == 0) {nFn = 1;}
+ Array<double> fN(nsd,nFn);
+ fN = 0.0;
+
+ if (lM.fN.size() != 0) {
+ for (int iFn = 0; iFn < nFn; iFn++) {
+ for (int i = 0; i < nsd; i++) {
+ fN(i,iFn) = lM.fN(i+nsd*iFn,e);
+ }
+ }
+ }
+
+ int cEq = com_mod.cEq;
+ auto& eq = com_mod.eq[cEq];
+ int cDmn = com_mod.cDmn;
+ auto& dmn = eq.dmn[cDmn];
+ double ya_g = 0.0; // ya_g or ya: a constant related to electromechanics ?
+
+ // Call get_pk2cc, which is originally called from sv_struct.cpp
+ mat_models::get_pk2cc(com_mod, cep_mod, dmn, F_0, nFn, fN, ya_g, S_0, Dm_0);
+ mat_models::get_pk2cc(com_mod, cep_mod, dmn, F_1, nFn, fN, ya_g, S_1, Dm_1);
+
+ // results printing
+ // std::cout <<"==================== INPUT ===================" << std::endl;
+ // F.print("Input Deformation ");
+ // std::cout <<"=================== OUTPUT ===================" << std::endl;
+ // S.print("Output stress tensor:");
+ // Dm.print("Output stiffness matrix:");
+
+ // the following is where each argument of get_pk2cc from: 
+ // mat_models_carray::get_pk2cc<3>(com_mod, cep_mod, dmn, F, nFn, fN, ya_g, S, Dm);
+ // from struct_3d(...): com_mod, cep_mod, dmn <- eq <- com_mod, nFn, fN 
+ // from construct_dsolid(...): com_mod, cep_mod, nFn <- lM, fN <- lM
+ // from global_eq_assem(...): com_mod, cep_mod, lM
+ // from iterate_simulation(simulation): com_mod <- simulation, cep_mod <- simulation, 
+ // lM <- com_mod.msh[iM] (iM < com_mod.nMsh)
+ // iterate_simulation(simulation) <- run_simulation(simulation) <- main(...)
+
+ // run Google Test
+ ::testing::InitGoogleTest(&argc, argv);
+ return RUN_ALL_TESTS();
+
+}