refactor: remove engine dependency from FilesInputFileParser and upda…

changes/developer/internal.input-file-parser.md

@@ -1,2 +1,3 @@
 - prepare celllist input file parser to remove engine dependency
 - prepare constraints input file parser to remove engine dependency
+- prepare files input file parser to remove engine dependency

include/engine/engine.hpp

@@ -105,14 +105,16 @@ namespace engine
         const std::shared_ptr<simulationBox::CellList> &getCellList() const;
         [[nodiscard]]
         const std::shared_ptr<constraints::Constraints> &getConstraints() const;
+        [[nodiscard]]
+        const std::shared_ptr<
+            intraNonBonded::IntraNonBonded> &getIntraNonBonded() const;
 
-        [[nodiscard]] simulationBox::SimulationBox   &getSimulationBox();
-        [[nodiscard]] physicalData::PhysicalData     &getPhysicalData();
-        [[nodiscard]] physicalData::PhysicalData     &getAveragePhysicalData();
-        [[nodiscard]] forceField::ForceField         &getForceField();
-        [[nodiscard]] intraNonBonded::IntraNonBonded &getIntraNonBonded();
-        [[nodiscard]] virial::Virial                 &getVirial();
-        [[nodiscard]] potential::Potential           &getPotential();
+        [[nodiscard]] simulationBox::SimulationBox &getSimulationBox();
+        [[nodiscard]] physicalData::PhysicalData   &getPhysicalData();
+        [[nodiscard]] physicalData::PhysicalData   &getAveragePhysicalData();
+        [[nodiscard]] forceField::ForceField       &getForceField();
+        [[nodiscard]] virial::Virial               &getVirial();
+        [[nodiscard]] potential::Potential         &getPotential();
 
         /*************************
          * output getter methods *
@@ -133,12 +135,11 @@ namespace engine
          * get pointer methods *
          ***********************/
 
-        [[nodiscard]] forceField::ForceField         *getForceFieldPtr();
-        [[nodiscard]] potential::Potential           *getPotentialPtr();
-        [[nodiscard]] virial::Virial                 *getVirialPtr();
-        [[nodiscard]] simulationBox::SimulationBox   *getSimulationBoxPtr();
-        [[nodiscard]] physicalData::PhysicalData     *getPhysicalDataPtr();
-        [[nodiscard]] intraNonBonded::IntraNonBonded *getIntraNonBondedPtr();
+        [[nodiscard]] forceField::ForceField       *getForceFieldPtr();
+        [[nodiscard]] potential::Potential         *getPotentialPtr();
+        [[nodiscard]] virial::Virial               *getVirialPtr();
+        [[nodiscard]] simulationBox::SimulationBox *getSimulationBoxPtr();
+        [[nodiscard]] physicalData::PhysicalData   *getPhysicalDataPtr();
 
         /******************************
          * get shared pointer methods *
@@ -151,9 +152,6 @@ namespace engine
         [[nodiscard]]
         std::shared_ptr<physicalData::PhysicalData> getSharedPhysicalData(
         ) const;
-        [[nodiscard]]
-        std::shared_ptr<intraNonBonded::IntraNonBonded> getSharedIntraNonBonded(
-        ) const;
         [[nodiscard]] std::shared_ptr<virial::Virial> getSharedVirial() const;
         [[nodiscard]] std::shared_ptr<potential::Potential> getSharedPotential(
         ) const;

include/input/inputFileParser/filesInputParser.hpp

@@ -39,11 +39,14 @@ namespace input
     class FilesInputParser : public InputFileParser
     {
        private:
+        std::shared_ptr<intraNonBonded::IntraNonBonded> _intraNonBonded;
+
         bool _validateFilePaths;
 
        public:
         explicit FilesInputParser(
             engine::Engine &,
+            std::shared_ptr<intraNonBonded::IntraNonBonded> intraNonBonded,
             bool validateFilePaths = true
         );
 

src/engine/engine.cpp

@@ -184,9 +184,12 @@ ForceField &Engine::getForceField() { return *_forceField; }
 /**
  * @brief get the reference to the intra non bonded interactions
  *
- * @return IntraNonBonded&
+ * @return const std::shared_ptr<IntraNonBonded>&
  */
-IntraNonBonded &Engine::getIntraNonBonded() { return *_intraNonBonded; }
+const std::shared_ptr<IntraNonBonded> &Engine::getIntraNonBonded() const
+{
+    return _intraNonBonded;
+}
 
 /**
  * @brief get the reference to the virial
@@ -237,13 +240,6 @@ SimulationBox *Engine::getSimulationBoxPtr() { return _simulationBox.get(); }
  */
 PhysicalData *Engine::getPhysicalDataPtr() { return _physicalData.get(); }
 
-/**
- * @brief get the pointer to the intra non bonded interactions
- *
- * @return IntraNonBonded*
- */
-IntraNonBonded *Engine::getIntraNonBondedPtr() { return _intraNonBonded.get(); }
-
 /**
  * @brief set the inter-water interactions handler
  *
@@ -391,16 +387,6 @@ const std::shared_ptr<Constraints> &Engine::getConstraints() const
     return _constraints;
 }
 
-/**
- * @brief get the shared pointer to the intra non bonded interactions
- *
- * @return std::shared_ptr<IntraNonBonded>
- */
-std::shared_ptr<IntraNonBonded> Engine::getSharedIntraNonBonded() const
-{
-    return _intraNonBonded;
-}
-
 /**
  * @brief get the shared pointer to the virial
  *

src/engine/hessianEngine.cpp

@@ -105,7 +105,7 @@ std::shared_ptr<Evaluator> HessianEngine::setupEvaluator()
     evaluator->setPotential(getSharedPotential());
     evaluator->setForceField(getSharedForceField());
     evaluator->setConstraints(getConstraints());
-    evaluator->setIntraNonBonded(getSharedIntraNonBonded());
+    evaluator->setIntraNonBonded(getIntraNonBonded());
     evaluator->setVirial(getSharedVirial());
     evaluator->setPhysicalData(getSharedPhysicalData());
     evaluator->setPhysicalDataOld(getSharedPhysicalDataOld());

src/input/inputFileParser/filesInputParser.cpp

@@ -50,8 +50,14 @@ using namespace utilities;
  *
  * @param engine
  */
-FilesInputParser::FilesInputParser(Engine &engine, const bool validateFilePaths)
-    : InputFileParser(engine), _validateFilePaths(validateFilePaths)
+FilesInputParser::FilesInputParser(
+    Engine                                         &engine,
+    std::shared_ptr<intraNonBonded::IntraNonBonded> intraNonBonded,
+    const bool                                      validateFilePaths
+)
+    : InputFileParser(engine),
+      _intraNonBonded(intraNonBonded),
+      _validateFilePaths(validateFilePaths)
 {
     addKeyword(
         std::string("intra-nonBonded_file"),
@@ -144,7 +150,7 @@ void FilesInputParser::parseIntraNonBondedFile(
             std::format("Intra non bonded file \"{}\" File not found", fileName)
         );
 
-    _engine.getIntraNonBonded().activate();
+    _intraNonBonded->activate();
 
     FileSettings::setIntraNonBondedFileName(fileName);
     FileSettings::setIsIntraNonBondedFileNameSet();

src/input/inputFileReader.cpp

@@ -88,7 +88,11 @@ InputFileReader::InputFileReader(
     );
     _parsers.push_back(make_unique<CoulombLongRangeInputParser>(_engine));
     _parsers.push_back(
-        make_unique<FilesInputParser>(_engine, validateFilePaths)
+        make_unique<FilesInputParser>(
+            _engine,
+            _engine.getIntraNonBonded(),
+            validateFilePaths
+        )
     );
     _parsers.push_back(make_unique<MMInputParser>(_engine));
     _parsers.push_back(make_unique<GeneralInputParser>(_engine));

src/input/intraNonBondedReader.cpp

@@ -33,7 +33,6 @@
 #include "engine.hpp"                    // for Engine
 #include "exceptions.hpp"                // for IntraNonBondedException
 #include "fileSettings.hpp"              // for FileSettings
-#include "intraNonBonded.hpp"            // for IntraNonBonded
 #include "intraNonBondedContainer.hpp"   // for IntraNonBondedContainer
 #include "mathUtilities.hpp"             // for sign, utilities
 #include "simulationBox.hpp"             // for SimulationBox
@@ -92,7 +91,9 @@ IntraNonBondedReader::IntraNonBondedReader(
     const std::string &fileName,
     Engine            &engine
 )
-    : _fileName(fileName), _fp(fileName), _engine(engine){};
+    : _fileName(fileName), _fp(fileName), _engine(engine)
+{
+}
 
 /**
  * @brief reads the intra non bonded interactions from the intraNonBonded file
@@ -285,7 +286,7 @@ void IntraNonBondedReader::processMolecule(const size_t moleculeType)
 
     const auto container = IntraNonBondedContainer(moleculeType, atomIndices);
 
-    _engine.getIntraNonBonded().addIntraNonBondedContainer(container);
+    _engine.getIntraNonBonded()->addIntraNonBondedContainer(container);
 }
 
 /**
@@ -297,8 +298,8 @@ void IntraNonBondedReader::processMolecule(const size_t moleculeType)
  */
 void IntraNonBondedReader::checkDuplicates() const
 {
-    auto      &intraNonBonded = _engine.getIntraNonBonded();
-    const auto nonBondedCont  = intraNonBonded.getIntraNonBondedContainers();
+    const auto &intraNonBonded = _engine.getIntraNonBonded();
+    const auto  nonBondedCont  = intraNonBonded->getIntraNonBondedContainers();
 
     auto transform = [](const auto &container)
     { return container.getMolType(); };
@@ -333,4 +334,4 @@ void IntraNonBondedReader::setFileName(const std::string_view &fileName)
 /**
  * @brief reinitializes the file pointer
  */
-void IntraNonBondedReader::reInitializeFp() { _fp = std::ifstream(_fileName); }
+void IntraNonBondedReader::reInitializeFp() { _fp = std::ifstream(_fileName); }

src/setup/intraNonBondedSetup.cpp

@@ -22,9 +22,8 @@
 
 #include "intraNonBondedSetup.hpp"
 
-#include "engine.hpp"           // for Engine
-#include "intraNonBonded.hpp"   // for IntraNonBonded
-#include "potential.hpp"        // for Potential
+#include "engine.hpp"      // for Engine
+#include "potential.hpp"   // for Potential
 
 using namespace setup;
 using namespace engine;
@@ -52,7 +51,7 @@ void setup::setupIntraNonBonded(engine::Engine &engine)
  *
  * @param engine
  */
-IntraNonBondedSetup::IntraNonBondedSetup(Engine &engine) : _engine(engine){};
+IntraNonBondedSetup::IntraNonBondedSetup(Engine &engine) : _engine(engine) {}
 
 /**
  * @brief Setup intra non bonded interactions
@@ -71,8 +70,8 @@ void IntraNonBondedSetup::setup()
     const auto &nonCoulombPot  = potential.getNonCoulombPotSharedPtr();
     const auto &coulombPot     = potential.getCoulombPotSharedPtr();
 
-    intraNonBonded.setNonCoulombPotential(nonCoulombPot);
-    intraNonBonded.setCoulombPotential(coulombPot);
+    intraNonBonded->setNonCoulombPotential(nonCoulombPot);
+    intraNonBonded->setCoulombPotential(coulombPot);
 
-    intraNonBonded.fillIntraNonBondedMaps(_engine.getSimulationBox());
-}
+    intraNonBonded->fillIntraNonBondedMaps(_engine.getSimulationBox());
+}

src/setup/optimizerSetup.cpp

@@ -240,7 +240,7 @@ std::shared_ptr<Evaluator> OptimizerSetup::setupEvaluator()
     evaluator->setPotential(_optEngine.getSharedPotential());
     evaluator->setForceField(_optEngine.getSharedForceField());
     evaluator->setConstraints(_optEngine.getConstraints());
-    evaluator->setIntraNonBonded(_optEngine.getSharedIntraNonBonded());
+    evaluator->setIntraNonBonded(_optEngine.getIntraNonBonded());
     evaluator->setVirial(_optEngine.getSharedVirial());
     evaluator->setSimulationBox(_optEngine.getSharedSimulationBox());
     evaluator->setPhysicalData(_optEngine.getSharedPhysicalData());

tests/include/input/testIntraNonBondedReader.hpp

@@ -58,7 +58,7 @@ class TestIntraNonBondedReader : public ::testing::Test
         _engine = new engine::MMMDEngine();
 
         _engine->getSimulationBox().addMoleculeType(molecule1);
-        _engine->getIntraNonBonded().activate();
+        _engine->getIntraNonBonded()->activate();
 
         _intraNonBondedReader =
             new input::intraNonBondedReader::IntraNonBondedReader(
@@ -75,4 +75,4 @@ class TestIntraNonBondedReader : public ::testing::Test
     }
 };
 
-#endif   // _TEST_INTRA_NON_BONDED_READER_HPP_
+#endif   // _TEST_INTRA_NON_BONDED_READER_HPP_

tests/src/input/inputFileParsing/testFilesParser.cpp

@@ -43,7 +43,7 @@ using namespace input;
  */
 TEST_F(TestInputFileReader, testParseTopologyFilename)
 {
-    FilesInputParser parser(*_engine);
+    FilesInputParser parser(*_engine, _engine->getIntraNonBonded());
 
     std::vector<std::string> lineElements = {
         "topology_file",
@@ -73,7 +73,7 @@ TEST_F(TestInputFileReader, testParseTopologyFilename)
  */
 TEST_F(TestInputFileReader, testParseParameterFilename)
 {
-    FilesInputParser parser(*_engine);
+    FilesInputParser parser(*_engine, _engine->getIntraNonBonded());
 
     std::vector<std::string> lineElements = {
         "parameter_file",
@@ -104,7 +104,7 @@ TEST_F(TestInputFileReader, testParseParameterFilename)
  */
 TEST_F(TestInputFileReader, parseIntraNonBondedFile)
 {
-    FilesInputParser         parser(*_engine);
+    FilesInputParser         parser(*_engine, _engine->getIntraNonBonded());
     std::vector<std::string> lineElements = {
         "intra-nonBonded_file",
         "=",
@@ -134,7 +134,7 @@ TEST_F(TestInputFileReader, parseIntraNonBondedFile)
  */
 TEST_F(TestInputFileReader, testStartFileName)
 {
-    FilesInputParser         parser(*_engine);
+    FilesInputParser         parser(*_engine, _engine->getIntraNonBonded());
     std::vector<std::string> lineElements = {
         "startFile_name",
         "=",
@@ -160,7 +160,7 @@ TEST_F(TestInputFileReader, testStartFileName)
  */
 TEST_F(TestInputFileReader, testMoldescriptorFileName)
 {
-    FilesInputParser         parser(*_engine);
+    FilesInputParser         parser(*_engine, _engine->getIntraNonBonded());
     std::vector<std::string> lineElements = {
         "moldescriptorFile_name",
         "=",
@@ -191,7 +191,7 @@ TEST_F(TestInputFileReader, testMoldescriptorFileName)
  */
 TEST_F(TestInputFileReader, testGuffPath)
 {
-    FilesInputParser               parser(*_engine);
+    FilesInputParser parser(*_engine, _engine->getIntraNonBonded());
     const std::vector<std::string> lineElements = {"guff_path", "=", "guff"};
     EXPECT_THROW_MSG(
         parser.parseGuffPath(lineElements, 0),
@@ -206,7 +206,7 @@ TEST_F(TestInputFileReader, testGuffPath)
  */
 TEST_F(TestInputFileReader, guffDatFilename)
 {
-    FilesInputParser         parser(*_engine);
+    FilesInputParser         parser(*_engine, _engine->getIntraNonBonded());
     std::vector<std::string> lineElements = {"guffdat_file", "=", "guff.dat"};
     EXPECT_THROW_MSG(
         parser.parseGuffDatFilename(lineElements, 0),
@@ -227,7 +227,7 @@ TEST_F(TestInputFileReader, guffDatFilename)
  */
 TEST_F(TestInputFileReader, testRpmdStartFileName)
 {
-    FilesInputParser         parser(*_engine);
+    FilesInputParser         parser(*_engine, _engine->getIntraNonBonded());
     std::vector<std::string> lineElements = {
         "rpmd_start_file",
         "=",
@@ -256,7 +256,7 @@ TEST_F(TestInputFileReader, testRpmdStartFileName)
  */
 TEST_F(TestInputFileReader, testMShakeFileName)
 {
-    FilesInputParser         parser(*_engine);
+    FilesInputParser         parser(*_engine, _engine->getIntraNonBonded());
     std::vector<std::string> lineElements = {"mshake_file", "=", "mshake.dat"};
 
     EXPECT_THROW_MSG(
@@ -278,7 +278,7 @@ TEST_F(TestInputFileReader, testMShakeFileName)
  */
 TEST_F(TestInputFileReader, testDFTBFileName)
 {
-    FilesInputParser         parser(*_engine);
+    FilesInputParser         parser(*_engine, _engine->getIntraNonBonded());
     std::vector<std::string> lineElements = {
         "dftb_file",
         "=",
@@ -304,7 +304,7 @@ TEST_F(TestInputFileReader, testDFTBFileName)
  */
 TEST_F(TestInputFileReader, testTMFileName)
 {
-    FilesInputParser         parser(*_engine);
+    FilesInputParser         parser(*_engine, _engine->getIntraNonBonded());
     std::vector<std::string> lineElements = {
         "turbomole_file",
         "=",
@@ -327,4 +327,4 @@ TEST_F(TestInputFileReader, testTMFileName)
         settings::FileSettings::getTMFileName(),
         "data/turbomoleReader/tm_define.template"
     );
-}
+}