Code cleanup (using namespace std)

.github/workflows/ls1_staticCodeAnalysis.yml

@@ -0,0 +1,21 @@
+name: Static-Code-Analysis
+
+on:
+  push:
+    # pushes to master
+    branches: [ master ]
+  pull_request:
+    # PRs to master
+    branches: [ master ]
+
+jobs:
+  static_analysis:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Setup
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y cpplint
+      - name: Run static code analysis script
+        run: ./checks/run-staticAnalysis.sh $PWD

checks/check-buildOptions.sh

@@ -0,0 +1,52 @@
+#!/bin/bash
+# Script to test the building process by altering through different build options
+# It uses the default settings and sets the specified options one by one
+
+numJobs=20
+
+checkFolder=$PWD
+buildFolder=$PWD/../build_test_$(date '+%Y-%m-%d')
+
+declare -A optionsList
+
+optionsList[ENABLE_MPI]=ON
+optionsList[VECTOR_INSTRUCTIONS]=SSE
+optionsList[VECTOR_INSTRUCTIONS]=AVX2
+optionsList[CMAKE_BUILD_TYPE]=Debug
+optionsList[OPENMP]=ON
+optionsList[ENABLE_AUTOPAS]=ON
+optionsList[ENABLE_UNIT_TESTS]=ON
+optionsList[QUICKSCHED]=ON
+optionsList[FMM_FFT]=ON
+optionsList[WITH_PAPI]=ON
+optionsList[ENABLE_ALLLBL]=ON
+optionsList[ENABLE_VTK]=ON
+optionsList[REDUCED_MEMORY_MODE]=ON
+
+
+# CMAKE
+mkdir -p $buildFolder
+cd $buildFolder
+
+echo "Running CMAKE in folder: $buildFolder"
+
+for option in "${!optionsList[@]}"
+do
+	echo "   Running option: ${option}=${optionsList[${option}]}"
+	rm $buildFolder/* -rf
+	( CC=mpicc CXX=mpicxx cmake -D${option}=${optionsList[${option}]} .. && make -j${numJobs} ; echo "$?" ) &> $checkFolder/build_test_cmake_${option}.log
+done
+
+
+# MAKE
+cd $checkFolder/../src
+
+echo "Running make in src"
+
+for option in "${!optionsList[@]}"
+do
+	echo "   Running option: ${option}=${optionsList[${option}]}"
+	make clean &> /dev/null
+	( make -j${numJobs} -f Makefile ${option}=${optionsList[${option}]} ; echo "$?" ) &> $checkFolder/build_test_make_${option}.log
+done
+

checks/run-staticAnalysis.sh

@@ -0,0 +1,82 @@
+#!/bin/bash
+# Script to run static code analysis
+
+#set strict pipefail option
+#set -eo pipefail
+
+# A path to the root folder of ls1 mardyn can be set via an argument; if not, the parent folder of "checks" is used
+if [ $# -eq 1 ]
+then
+  rootFolder=$1
+else
+  rootFolder=$PWD/..
+fi
+
+echo "Running in $rootFolder"
+
+warnings=""
+
+codeFiles=$( find $rootFolder/src -name "*.h" -or -name "*.cpp" -printf "%p " )
+
+# Similar to check_format of MegaMol repo
+for file in $codeFiles; do
+
+  # Check if using namespace std is used
+  if grep -q "using namespace std;" "$file"; then
+    echo "\"using namespace std;\" was used in $file"
+    warnings+="Do not use \"using namespace std;\"\n"
+  fi
+
+  # Check if using Log::global_log is used
+  if grep -q "using Log::global_log;" "$file"; then
+    echo "\"using Log::global_log;\" was used in $file"
+    warnings+="Do not use \"using Log::global_log;\"\n"
+  fi
+
+  # Check if file is UTF-8 (or ASCII)
+  encoding=$(file -b --mime-encoding "$file")
+  if [[ $encoding != "us-ascii" && $encoding != "utf-8" ]]; then
+    echo "The following file is not ASCII/UTF-8 encoded: $file ($encoding)"
+    echo "  Fix with:"
+    echo "    tmp_file=\$(mktemp)"
+    echo "    iconv -f \"\$(file -b --mime-encoding \"$file\")\" -t utf-8 -o \"\$tmp_file\" \"\$file\""
+    echo "    mv -f \"\$tmp_file\" \"\$file\""
+    warnings+="At least one file is not ASCII/UTF-8 encoded\n"
+  fi
+
+  # Check if file contains CRLF line endings
+  fileinfo=$(file -k "$file")
+  if [[ $fileinfo == *"CRLF"* ]]; then
+    echo "The following file contains CRLF line endings: $file"
+    echo "  Fix with:"
+    echo "    sed -i 's/\r$//' \"$file\""
+              sed -i 's/\r$//' "$file"
+    warnings+="At least one file contains CRLF line endings\n"
+  fi
+
+  # Check if file starts with BOM
+  if [[ $fileinfo == *"BOM"* ]]; then
+    echo "The following file starts with BOM: $file"
+    echo "  Fix with:"
+    echo "    sed -i '1s/^\xEF\xBB\xBF//' \"$file\""
+    warnings+="At least one file starts with BOM\n"
+  fi
+
+  # Check if file ends with newline
+  if [[ -n "$(tail -c 1 "$file")" ]]; then
+    echo "The following file does not end with newline: $file"
+    echo "  Fix with:"
+    echo "    sed -i -e '\$a\' \"$file\""
+    warnings+="At least one file does not end with newline\n"
+  fi
+
+done
+
+printf "\n\n\n"  # Some space to make output clearer
+
+# Only print warnings once to job summary
+warnings=$(printf "$warnings" | sort | uniq)
+warnings="# Warnings\n"$warnings"\n\n"
+
+printf "\n$warnings\n"  # Print to job output
+printf "\n$warnings\n" >> $GITHUB_STEP_SUMMARY  # Print to job summary

checks/run-validation.sh

@@ -0,0 +1,31 @@
+#!/bin/bash
+# Testscript running validation tests according to GitHub Actions but without comparison to master
+#
+# Copyright (c) 2023 Simon Homes
+#
+
+repoPath="$PWD/.."  # Path to root directory
+
+export OMP_NUM_THREADS=2
+
+logfileName="${repoPath}/examples/run-validation.log"
+rm -f ${logfileName}
+
+IFS=$'\n'
+for i in $(cat "${repoPath}/examples/example-list.txt" )
+do
+	# skip if comment or empty line
+	if [[ $i == \#* || -z "$i" ]]
+	then
+		continue
+	fi
+	cd ${repoPath}/examples/$(dirname $i)
+
+	# run the examples
+	printf "Running example: ${i} ... " | tee -a ${logfileName}
+	EXE=${repoPath}/build/src/MarDyn
+
+	mpirun --oversubscribe -np 4 ${EXE} $(basename $i) --steps=20 | tee -a ${logfileName}
+	printf "done\n"
+done
+

dependencies-external/cppunit-1.12.1/examples/cppunittest/BaseTestCase.cpp

@@ -12,26 +12,26 @@ BaseTestCase::~BaseTestCase()
 }
 
 
-void 
+void
 BaseTestCase::setUp()
 {
 }
 
 
-void 
+void
 BaseTestCase::tearDown()
 {
 }
 
 
-void 
+void
 BaseTestCase::testUsingCheckIt()
 {
   checkIt();
 }
 
 
-void 
+void
 BaseTestCase::checkIt()
 {
 }

dependencies-external/cppunit-1.12.1/examples/cppunittest/ExceptionTest.cpp

@@ -18,32 +18,32 @@ ExceptionTest::~ExceptionTest()
 }
 
 
-void 
+void
 ExceptionTest::setUp()
 {
 }
 
 
-void 
+void
 ExceptionTest::tearDown()
 {
 }
 
 
-void 
+void
 ExceptionTest::testConstructor()
 {
   const CPPUNIT_NS::Message message( "a message" );
   const CPPUNIT_NS::SourceLine sourceLine( "dir/afile.cpp", 17 );
-  
+
   CPPUNIT_NS::Exception e( message, sourceLine );
 
   CPPUNIT_ASSERT_EQUAL( message.shortDescription(), e.message().shortDescription() );
   CPPUNIT_ASSERT( sourceLine == e.sourceLine() );
 }
 
 
-void 
+void
 ExceptionTest::testDefaultConstructor()
 {
   CPPUNIT_NS::Exception e;
@@ -53,7 +53,7 @@ ExceptionTest::testDefaultConstructor()
 }
 
 
-void 
+void
 ExceptionTest::testCopyConstructor()
 {
   CPPUNIT_NS::SourceLine sourceLine( "fileName.cpp", 123 );
@@ -63,7 +63,7 @@ ExceptionTest::testCopyConstructor()
 }
 
 
-void 
+void
 ExceptionTest::testAssignment()
 {
   CPPUNIT_NS::SourceLine sourceLine( "fileName.cpp", 123 );
@@ -74,7 +74,7 @@ ExceptionTest::testAssignment()
 }
 
 
-void 
+void
 ExceptionTest::testClone()
 {
   CPPUNIT_NS::SourceLine sourceLine( "fileName.cpp", 123 );
@@ -84,8 +84,8 @@ ExceptionTest::testClone()
 }
 
 
-void 
-ExceptionTest::checkIsSame( CPPUNIT_NS::Exception &e, 
+void
+ExceptionTest::checkIsSame( CPPUNIT_NS::Exception &e,
                             CPPUNIT_NS::Exception &other )
 {
   std::string eWhat( e.what() );

dependencies-external/cppunit-1.12.1/examples/cppunittest/ExceptionTest.h

@@ -30,7 +30,7 @@ class ExceptionTest : public CPPUNIT_NS::TestFixture
 private:
   ExceptionTest( const ExceptionTest &copy );
   void operator =( const ExceptionTest &copy );
-  void checkIsSame( CPPUNIT_NS::Exception &e, 
+  void checkIsSame( CPPUNIT_NS::Exception &e,
                     CPPUNIT_NS::Exception &other );
 
 private:

dependencies-external/cppunit-1.12.1/examples/cppunittest/ExceptionTestCaseDecoratorTest.cpp

@@ -21,7 +21,7 @@ ExceptionTestCaseDecoratorTest::~ExceptionTestCaseDecoratorTest()
 }
 
 
-void 
+void
 ExceptionTestCaseDecoratorTest::setUp()
 {
   m_testListener = new MockTestListener( "mock-testlistener" );
@@ -33,7 +33,7 @@ ExceptionTestCaseDecoratorTest::setUp()
 }
 
 
-void 
+void
 ExceptionTestCaseDecoratorTest::tearDown()
 {
   delete m_decorator;
@@ -42,7 +42,7 @@ ExceptionTestCaseDecoratorTest::tearDown()
 }
 
 
-void 
+void
 ExceptionTestCaseDecoratorTest::testNoExceptionThrownFailed()
 {
   m_testListener->setExpectedAddFailureCall(1);
@@ -56,7 +56,7 @@ ExceptionTestCaseDecoratorTest::testNoExceptionThrownFailed()
 }
 
 
-void 
+void
 ExceptionTestCaseDecoratorTest::testExceptionThrownPass()
 {
   m_testListener->setExpectNoFailure();