Expanding test suite

.github/workflows/build.yml

@@ -20,7 +20,7 @@ jobs:
     - name: Build
       run: cd build && make -j
     - name: Perform unit tests
-      run: cd build && OMP_NUM_THREADS=1 make test # suppress parallel sections for tests
+      run: cd build && make test
     - name: Perform code coverage
       run: |
         cd build

src/CMakeLists.txt

@@ -91,6 +91,7 @@ find_package(BZip2 REQUIRED)
 find_package(CPPUNIT REQUIRED) # for unit tests
 pkg_check_modules(TCLAP tclap REQUIRED)
 pkg_check_modules(EIGEN eigen3 REQUIRED)
+pkg_check_modules(CRYPTO libcrypto REQUIRED) # for unit tests
 
 # Set include folders
 include_directories(${CMAKE_CURRENT_SOURCE_DIR}
@@ -137,4 +138,4 @@ endif()
 ###
 # Installing
 ##
-install (TARGETS den2obj DESTINATION bin)
+install (TARGETS den2obj DESTINATION bin)

src/isosurface_mesh.cpp

@@ -148,10 +148,10 @@ void IsoSurfaceMesh::write_to_file(const std::string& filename, const std::strin
 
     if(filename.substr(filename.size()-4) == ".obj") {
         std::cout << "Writing mesh as Wavefront file (.obj)." << std::endl;
-        this->write_obj(filename, path.filename().string(), path.filename().string());
+        this->write_obj(filename, header, name);
     } else if(filename.substr(filename.size()-4) == ".ply") {
         std::cout << "Writing mesh as Standford Triangle Format file (.ply)." << std::endl;
-        this->write_ply(filename, path.filename().string(), path.filename().string());
+        this->write_ply(filename, header, name);
     } else if(filename.substr(filename.size()-4) == ".stl") {
         std::cout << "Writing mesh as Stereolithography file (.stl)." << std::endl;
         this->write_stl(filename);

src/test/CMakeLists.txt

@@ -23,23 +23,33 @@ add_library(unittest STATIC unittest.cpp)
 # set executables
 SET(EXECUTABLES TestIsosurface TestScalarField TestD2OFileFormat)
 
-# remove this test from the list as it takes too long
+# only add this test when not using GCOV
 if(NOT USE_GCOV)
     list(APPEND EXECUTABLES TestGenerator)
 endif()
 
+# only add this test when not using GCOV
+if(USE_GCOV)
+    list(APPEND EXECUTABLES TestFileCreation)
+endif()
+
 #######################################################
 # Add executables
 #######################################################
 add_executable(TestIsosurface test_isosurface.cpp)
 add_executable(TestScalarField test_scalarfield.cpp)
 add_executable(TestD2OFileFormat test_d2o_fileformat.cpp)
 
-# remove this test from the list as it takes too long
+# only add this test when not using GCOV
 if(NOT USE_GCOV)
     add_executable(TestGenerator test_generator.cpp)
 endif()
 
+# only add this test when not using OpenVDB
+if(USE_GCOV)
+    add_executable(TestFileCreation test_file_creation.cpp)
+endif()
+
 #######################################################
 # Link mkmsources and other dependencies
 #######################################################
@@ -51,7 +61,7 @@ endif()
 
 # add unpacking of dataset to the test suite
 add_test(NAME DatasetSetup COMMAND tar -xvjf dataset.tar.bz2)
-add_test(NAME DatasetCleanup COMMAND rm -rvf CHGCAR_* PARCHG_*)
+add_test(NAME DatasetCleanup COMMAND rm -rvf CHGCAR_* PARCHG_* *.d2o *.cub)
 set_tests_properties(DatasetSetup PROPERTIES FIXTURES_SETUP Dataset)
 set_tests_properties(DatasetCleanup PROPERTIES FIXTURES_CLEANUP Dataset)
 
@@ -66,6 +76,7 @@ foreach(testexec ${EXECUTABLES})
                           ${LIBLZMA_LIBRARIES}
                           ${ZLIB_LIBRARIES}
                           ${BZIP2_LIBRARIES}
+                          ${CRYPTO_LIBRARIES}
                           -lgcov)
     set_target_properties(${testexec} PROPERTIES COMPILE_FLAGS "--coverage")
     add_test(NAME ${testexec} COMMAND ${testexec})

src/test/test_file_creation.cpp

@@ -0,0 +1,134 @@
+/**************************************************************************
+ *                                                                        *
+ *   Author: Ivo Filot <i.a.w.filot@tue.nl>                               *
+ *                                                                        *
+ *   DEN2OBJ is free software:                                            *
+ *   you can redistribute it and/or modify it under the terms of the      *
+ *   GNU General Public License as published by the Free Software         *
+ *   Foundation, either version 3 of the License, or (at your option)     *
+ *   any later version.                                                   *
+ *                                                                        *
+ *   DEN2OBJ is distributed in the hope that it will be useful,           *
+ *   but WITHOUT ANY WARRANTY; without even the implied warranty          *
+ *   of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.              *
+ *   See the GNU General Public License for more details.                 *
+ *                                                                        *
+ *   You should have received a copy of the GNU General Public License    *
+ *   along with this program.  If not, see http://www.gnu.org/licenses/.  *
+ *                                                                        *
+ **************************************************************************/
+
+#include "test_file_creation.h"
+
+CPPUNIT_TEST_SUITE_REGISTRATION( TestFileCreation );
+
+void TestFileCreation::setUp() {
+}
+
+void TestFileCreation::tearDown() {
+}
+
+void TestFileCreation::test_ply_file() {
+    // set number of threads to 1
+    omp_set_num_threads(1);
+
+    // read scalar field
+    ScalarField sf("co_2pi_x.cub", ScalarFieldInputFileType::SFF_CUB);
+    sf.read();
+
+    // perform marching cubes algorithm
+    IsoSurface is(&sf);
+    is.marching_cubes(0.01);
+
+    // construct mesh
+    IsoSurfaceMesh ism(&sf, &is);
+    ism.construct_mesh(true);
+
+    // create file
+    ism.write_to_file("test.ply", "co molecule 2pi_x orbital test", "molecule");
+
+    // test md5sum
+    CPPUNIT_ASSERT_EQUAL(this->md5("test.ply"), std::string("ec143f6ebf9b72761803c3b091f54bf3"));
+}
+
+void TestFileCreation::test_stl_file() {
+    // set number of threads to 1
+    omp_set_num_threads(1);
+
+    // read scalar field
+    ScalarField sf("co_2pi_x.cub", ScalarFieldInputFileType::SFF_CUB);
+    sf.read();
+
+    // perform marching cubes algorithm
+    IsoSurface is(&sf);
+    is.marching_cubes(0.01);
+
+    // construct mesh
+    IsoSurfaceMesh ism(&sf, &is);
+    ism.construct_mesh(true);
+
+    // create file
+    ism.write_to_file("test.stl", "co molecule 2pi_x orbital test", "molecule");
+
+    // test md5sum
+    CPPUNIT_ASSERT_EQUAL(this->md5("test.stl"), std::string("c2194ba639caf5092654862bb9f93298"));
+}
+
+void TestFileCreation::test_obj_file() {
+    // set number of threads to 1
+    omp_set_num_threads(1);
+
+    // read scalar field
+    ScalarField sf("co_2pi_x.cub", ScalarFieldInputFileType::SFF_CUB);
+    sf.read();
+
+    // perform marching cubes algorithm
+    IsoSurface is(&sf);
+    is.marching_cubes(0.01);
+
+    // construct mesh
+    IsoSurfaceMesh ism(&sf, &is);
+    ism.construct_mesh(true);
+
+    // create file
+    ism.write_to_file("test.obj", "co molecule 2pi_x orbital test", "molecule");
+
+    // test md5sum
+    CPPUNIT_ASSERT_EQUAL(this->md5("test.obj"), std::string("e2b3e09f9c010dac99a7bc0137c187ec"));
+}
+
+/**
+ * @brief      Calculate MD5 checksum of a file
+ *
+ * @param[in]  name      Path to the file
+ * 
+ * @return     32 byte string containing md5 checksum
+ */
+std::string TestFileCreation::md5(const std::string& filename) {
+    // read the file
+    std::ifstream mfile(filename, std::ios::binary | std::ios::ate);
+    std::streamsize size = mfile.tellg();
+    mfile.seekg(0, std::ios::beg);
+    char buffer[size];
+    mfile.read(buffer, size);
+    mfile.close();
+
+    // output variable for hash
+    unsigned char hash[MD5_DIGEST_LENGTH];
+
+    // calculate the md5 hash
+    EVP_MD_CTX *ctx = EVP_MD_CTX_create();
+    EVP_MD_CTX_init(ctx);
+    const EVP_MD *md_type = EVP_md5();
+    EVP_DigestInit_ex(ctx, md_type, NULL);
+    EVP_DigestUpdate(ctx, buffer, size);
+    EVP_DigestFinal_ex(ctx, hash, NULL);
+    EVP_MD_CTX_destroy(ctx);
+
+    // output as a 32-byte hex-string
+    std::stringstream ss;
+    for(int i = 0; i < MD5_DIGEST_LENGTH; i++){
+        ss << std::hex << std::setw(2) << std::setfill('0') << static_cast<int>( hash[i] );
+    }
+    return ss.str();
+}

src/test/test_file_creation.h

@@ -0,0 +1,62 @@
+/**************************************************************************
+ *                                                                        *
+ *   Author: Ivo Filot <i.a.w.filot@tue.nl>                               *
+ *                                                                        *
+ *   DEN2OBJ is free software:                                            *
+ *   you can redistribute it and/or modify it under the terms of the      *
+ *   GNU General Public License as published by the Free Software         *
+ *   Foundation, either version 3 of the License, or (at your option)     *
+ *   any later version.                                                   *
+ *                                                                        *
+ *   DEN2OBJ is distributed in the hope that it will be useful,           *
+ *   but WITHOUT ANY WARRANTY; without even the implied warranty          *
+ *   of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.              *
+ *   See the GNU General Public License for more details.                 *
+ *                                                                        *
+ *   You should have received a copy of the GNU General Public License    *
+ *   along with this program.  If not, see http://www.gnu.org/licenses/.  *
+ *                                                                        *
+ **************************************************************************/
+
+#ifndef _TEST_FILE_CREATION
+#define _TEST_FILE_CREATION
+
+#include <cppunit/extensions/HelperMacros.h>
+
+// we need these for the MD5 checksums
+#include <iomanip>
+#include <openssl/md5.h>
+#include <openssl/evp.h>
+
+#include "scalar_field.h"
+#include "isosurface.h"
+#include "isosurface_mesh.h"
+
+/**
+ * Test that verifies file creation (obj, stl and ply)
+ * 
+ * Because the marching cubes algorithm uses OpenMP parallellization, we need
+ * to set the number of threads to 1 to obtain consistent results. With
+ * higher number of cores, the results are subject to race conditions, leading
+ * to different (although not incorrect) results preventing the use of a simple
+ * MD5 checksum for file validation.
+*/
+class TestFileCreation : public CppUnit::TestFixture {
+    CPPUNIT_TEST_SUITE( TestFileCreation );
+    CPPUNIT_TEST( test_ply_file );
+    CPPUNIT_TEST( test_stl_file );
+    CPPUNIT_TEST( test_obj_file );
+    CPPUNIT_TEST_SUITE_END();
+
+public:
+    void setUp();
+    void test_ply_file();
+    void test_stl_file();
+    void test_obj_file();
+    void tearDown();
+
+private:
+    std::string md5(const std::string &str);
+};
+
+#endif

src/test/test_scalarfield.cpp

@@ -28,7 +28,7 @@ void TestScalarField::setUp() {
 void TestScalarField::tearDown() {
 }
 
-void TestScalarField::testReading() {
+void TestScalarField::testReadingCHGCAR() {
     // create scalar field
     ScalarField sf("CHGCAR_CH4", ScalarFieldInputFileType::SFF_CHGCAR);
     CPPUNIT_ASSERT_EQUAL( (uint)0, sf.get_size() );
@@ -90,3 +90,8 @@ void TestScalarField::testReading() {
                                   sf.get_value_interp(0.0,0.0,10.0),
                                   1e-12);
 }
+
+void TestScalarField::testReadingCUB() {
+    // test reading sf file
+    ScalarField sf("co_2pi_x.cub", ScalarFieldInputFileType::SFF_CUB);
+}

src/test/test_scalarfield.h

@@ -28,15 +28,16 @@
 class TestScalarField : public CppUnit::TestFixture
 {
   CPPUNIT_TEST_SUITE( TestScalarField );
-  CPPUNIT_TEST( testReading );
+  CPPUNIT_TEST( testReadingCHGCAR );
+  CPPUNIT_TEST( testReadingCUB );
   CPPUNIT_TEST_SUITE_END();
 
 public:
   void setUp();
   void tearDown();
 
-  void testReading();
-  void testD2OFileFormat();
+  void testReadingCHGCAR();
+  void testReadingCUB();
 
 private:
 };

src/test/testinput/.gitignore

@@ -0,0 +1,5 @@
+CHGCAR*
+PARCHG*
+LOCPOT*
+*.d2o
+*.cub