Release 3.0.1

CHANGELOG.rst

@@ -1,6 +1,11 @@
 Changelog
 =========
 
+Release 3.0.1
+-------------
+
+- Various bugfixes and improvements
+
 Release 3.0.0
 -------------
 

CMakeLists.txt

@@ -4,7 +4,7 @@ cmake_minimum_required(VERSION 3.9)
 # tree must then provide a properly namespaced target with the same name as
 # your project.
 project(Sparrow
-  VERSION 3.0.0
+  VERSION 3.0.1
   DESCRIPTION "Library for fast and agile quantum chemical calculations with semiempirical methods."
 )
 

CONTRIBUTING.rst

@@ -27,4 +27,4 @@ from members of the Reiher research group.
 Further Contributors
 --------------------
 
-So far, no one else has contributed to this repository.
+- Sebastian Ehlert (`@awvwgk <https://github.com/awvwgk>`_), University of Bonn (various bug reports)

conanfile.py

@@ -1,9 +1,10 @@
+import sys
 from dev.conan.base import ScineConan
 
 
 class ScineSparrowConan(ScineConan):
     name = "scine_sparrow"
-    version = "3.0.0"
+    version = "3.0.1"
     url = "https://github.com/qcscine/sparrow"
     description = """Sparrow is a code for fast semiemprical quantum chemical calculations.
 It provides the methods such as MNDO, AM1, RM1, PM3, PM6, DFTB0, DFTB2, and DFTB3.
@@ -12,20 +13,24 @@ class ScineSparrowConan(ScineConan):
         "python": [True, False],
         "tests": [True, False],
         "coverage": [True, False],
-        "microarch": ["detect", "none"]
+        "microarch": ["detect", "none"],
+        "python_version": "ANY"
     }
+    python_version_string = str(sys.version_info.major) + \
+                    "." + str(sys.version_info.minor)
     default_options = {
         "python": False,
         "tests": False,
         "coverage": False,
-        "microarch": "none"
+        "microarch": "none",
+        "python_version": python_version_string
     }
     exports = "dev/conan/*.py"
     exports_sources = ["dev/cmake/*", "src/*", "CMakeLists.txt",
                        "README.rst", "LICENSE.txt", "dev/conan/hook.cmake",
                        "dev/conan/glue/*"]
     build_requires = "cereal/1.3.0"
-    requires = "scine_utilities/[~=4.0.0]"
+    requires = "scine_utilities/[=5.0.0]"
     cmake_name = "Sparrow"
 
     def package_info(self):

manual/sparrow_manual.tex

@@ -21,7 +21,7 @@
 %\savebox{\scineimage}{\includegraphics[height=5\baselineskip]{scine_darkblue.png}}
 
 
-\title[SCINE Sparrow manual]{User Manual \vskip 0.5em {\setlength{\parindent}{0pt} \Huge SCINE Sparrow 3.0.0}}
+\title[SCINE Sparrow manual]{User Manual \vskip 0.5em {\setlength{\parindent}{0pt} \Huge SCINE Sparrow 3.0.1}}
 \author[The SCINE Sparrow Developers]{The SCINE Sparrow Developers: \newline \noindent Francesco Bosia, Tamara Husch, Charlotte H.~M\"uller, Severin Polonius, Jan-Grimo Sobez, Miguel Steiner, Jan P.~Unsleber, Alain C.~Vaucher, Thomas Weymuth, and Markus Reiher}
 \publisher{ETH Z\"urich}
 
@@ -235,7 +235,7 @@ \chapter{Introduction}
 \textsc{Interactive}, SCINE \textsc{ReaDuct}, and SCINE \textsc{Chemoton}. However, as with all SCINE modules it is also 
 a stand-alone program which can be applied on its own or easily interfaced to other programs.
 
-SCINE \textsc{Sparrow} is a command-line tool that implements many popular semiempirical models. SCINE \textsc{Sparrow} 3.0.0 
+SCINE \textsc{Sparrow} is a command-line tool that implements many popular semiempirical models. SCINE \textsc{Sparrow} 3.0.1
 provides the \texttt{MNDO}, \texttt{AM1}, \texttt{RM1}, \texttt{PM3}, \texttt{PM6}, non-SCC DFTB (\texttt{DFTB0}), \texttt{DFTB2}, and \texttt{DFTB3} methods 
 (open- and closed-shell formalisms are implemented). 
 The application of semiempirical models usually allows for rapid calculation of electronic energies and energy gradients 
@@ -266,7 +266,7 @@ \section{System Requirements}
 
 \textsc{Sparrow} is distributed as an open source code. In order to compile \textsc{Sparrow} from this source code, you need
 \begin{itemize}
- \item A C++ compiler supporting the C++14 standard,
+ \item A C++ compiler supporting the C++17 standard,
  \item cmake (at least version 3.9),
  \item the Boost library (at least version 1.65.0), and
  \item the Eigen3 library (at least version 3.3.2).
@@ -356,7 +356,7 @@ \section{Command Line Arguments}
 modes and the vibrational frequencies. This option has no effect if the Hessian is not calculated (see above).
 \item \texttt{-{}-bond\_orders}, \texttt{-B}: If given, the bond order matrix will be calculated.
 \item \texttt{-{}-method}, \texttt{-M}: With this option, the desired calculation method can be set. Options in
-\textsc{Sparrow} 3.0.0 are \texttt{MNDO}, \texttt{AM1}, \texttt{RM1}, \texttt{PM3}, \texttt{PM6}, \texttt{DFTB0}, \texttt{DFTB2}, and
+\textsc{Sparrow} 3.0.1 are \texttt{MNDO}, \texttt{AM1}, \texttt{RM1}, \texttt{PM3}, \texttt{PM6}, \texttt{DFTB0}, \texttt{DFTB2}, and
 \texttt{DFTB3}. By default, \texttt{PM6} is selected.
 \item \texttt{-{}-output\_to\_file}, \texttt{-o}: If this option is given, the output will not only be printed to the screen, 
 but also to files. By default, the energy is stored in a file named ``energy.dat'', the nuclear gradients in a file named
@@ -705,8 +705,8 @@ \chapter{References}
 \vspace{1.0cm}
 
 \begin{itemize}
-\item Primary reference for Sparrow 3.0.0:
-F.~Bosia, T.~Husch, C.~H.~M\"uller, S.~Polonius, J.-G.~Sobez, M.~Steiner, J.~P.~Unsleber, A.~C.~Vaucher, T.~Weymuth, M.~Reiher, \href{https://doi.org/10.5281/zenodo.3244105}{"qcscine/sparrow: Release 3.0.0 (Version 3.0.0)"}, Zenodo, 2021.
+\item Primary reference for Sparrow 3.0.1:
+F.~Bosia, T.~Husch, C.~H.~M\"uller, S.~Polonius, J.-G.~Sobez, M.~Steiner, J.~P.~Unsleber, A.~C.~Vaucher, T.~Weymuth, M.~Reiher, \href{https://doi.org/10.5281/zenodo.3244105}{"qcscine/sparrow: Release 3.0.1 (Version 3.0.1)"}, Zenodo, 2022.
 \item Presentation of the formalism of MNDO-type and OMx models: \newline
 T.~Husch, A.~C.~Vaucher, M.~Reiher \href{https://doi.org/10.1002/qua.25799}{"Semiempirical Molecular Orbital Models Based on the Neglect of Diatomic Differential Overlap Approximation"}, \textit{Int.~J.~Quantum Chem.}, \textbf{2018}, \textit{118}, e25799.
 \item Presentation of DFTB approaches: \newline

src/Sparrow/App/main.cpp

@@ -28,8 +28,9 @@ int main(int argc, char* argv[]) {
     CalculationHandler calculationHandler(commandLineParser);
     calculationHandler.calculate(std::cout);
   }
-  catch (MethodNotAvailableException& e) {
+  catch (const std::exception& e) {
     std::cout << e.what() << std::endl;
+    return 1;
   }
 
   return 0;

src/Sparrow/CMakeLists.txt

@@ -73,6 +73,10 @@ scine_install_component_cmake_files(
   EXPORT_NAME sparrowTargets
 )
 
+if(SCINE_BUILD_TESTS OR SCINE_BUILD_PYTHON_BINDINGS)
+  find_package(PythonInterp REQUIRED)
+endif()
+
 # Tests
 if(SCINE_BUILD_TESTS)
   include(ImportGTest)
@@ -87,7 +91,6 @@ if(SCINE_BUILD_TESTS)
     ${CMAKE_DL_LIBS}
   )
   add_test(NAME Sparrow COMMAND Sparrow_tests)
-  find_package(PythonInterp REQUIRED)
   if ("${CMAKE_BUILD_TYPE}" STREQUAL "Debug")
     set(TEST_SELECTION "::TestSparrowFast")
   else()
@@ -103,7 +106,7 @@ if(SCINE_BUILD_TESTS)
   set_tests_properties(Sparrow_App PROPERTIES
     ENVIRONMENT SCINE_MODULE_PATH=${CMAKE_CURRENT_BINARY_DIR}:$ENV{SCINE_MODULE_PATH}
     ENVIRONMENT PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}:$ENV{PYTHONPATH}
-    ENVIRONMENT PATH=${CMAKE_CURRENT_BINARY_DIR}:$ENV{PATH}
+    ENVIRONMENT PATH=${CMAKE_CURRENT_BINARY_DIR}:${PROJECT_BINARY_DIR}:$ENV{PATH}
   )
 endif()
 
@@ -120,6 +123,9 @@ add_executable(SparrowApp ${SPARROW_APP_FILES})
 add_executable(Scine::SparrowApp ALIAS SparrowApp)
 
 set_target_properties(SparrowApp PROPERTIES OUTPUT_NAME sparrow)
+if(APPLE)
+  set_target_properties(SparrowApp PROPERTIES RUNTIME_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR})
+endif()
 
 target_link_libraries(SparrowApp PRIVATE
   Boost::program_options
@@ -240,8 +246,6 @@ if(SCINE_BUILD_PYTHON_BINDINGS)
     SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/Python/sphinx
     OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/doc-py
     LINK UtilsPythonDoc
-    DOCTEST
-    DOCTEST_REQUIRES scine_utilities
   )
 endif()
 

src/Sparrow/Python/sphinx/index.rst

@@ -6,7 +6,8 @@ User Manual
 
 The user manuals are available for download as PDF files:
 
-- :download:`Download Latest User Manual PDF <https://scine.ethz.ch/static/download/manuals/v3.0.0/sparrow_manual.pdf>`
+- :download:`Download Latest User Manual PDF <https://scine.ethz.ch/static/download/manuals/v3.0.1/sparrow_manual.pdf>`
+- :download:`Download User Manual PDF v3.0.1 <https://scine.ethz.ch/static/download/manuals/v3.0.1/sparrow_manual.pdf>`
 - :download:`Download User Manual PDF v3.0.0 <https://scine.ethz.ch/static/download/manuals/v3.0.0/sparrow_manual.pdf>`
 - :download:`Download User Manual PDF v2.0.1 <https://scine.ethz.ch/static/download/manuals/v2.0.1/sparrow_manual.pdf>`
 - :download:`Download User Manual PDF v2.0.0 <https://scine.ethz.ch/static/download/manuals/v2.0.0/sparrow_manual.pdf>`

src/Sparrow/Sparrow/Implementations/Dftb/Dftb0/Wrapper/DFTB0Settings.h

@@ -26,6 +26,11 @@ class DFTB0Settings : public Scine::Utils::Settings {
     Utils::UniversalSettings::SettingPopulator::populateLcaoSettings(_fields);
     Utils::UniversalSettings::SettingPopulator::populateSemiEmpiricalSettings(_fields, "3ob-3-1");
 
+    // Method
+    Utils::UniversalSettings::StringDescriptor method("The method to be used.");
+    method.setDefaultValue("dftb0");
+    _fields.push_back(Utils::SettingsNames::method, method);
+
     resetToDefaults();
   };
 };

src/Sparrow/Sparrow/Implementations/Dftb/Dftb2/Wrapper/DFTB2Settings.h

@@ -25,6 +25,11 @@ class DFTB2Settings : public Scine::Utils::Settings {
     Utils::UniversalSettings::SettingPopulator::populateScfSettings(_fields);
     Utils::UniversalSettings::SettingPopulator::populateSemiEmpiricalSettings(_fields, "mio-1-1");
 
+    // Method
+    Utils::UniversalSettings::StringDescriptor method("The method to be used.");
+    method.setDefaultValue("dftb2");
+    _fields.push_back(Utils::SettingsNames::method, method);
+
     resetToDefaults();
   };
 };

src/Sparrow/Sparrow/Implementations/Dftb/Dftb3/Wrapper/DFTB3Settings.h

@@ -25,6 +25,11 @@ class DFTB3Settings : public Scine::Utils::Settings {
     Utils::UniversalSettings::SettingPopulator::populateScfSettings(_fields);
     Utils::UniversalSettings::SettingPopulator::populateSemiEmpiricalSettings(_fields, "3ob-3-1");
 
+    // Method
+    Utils::UniversalSettings::StringDescriptor method("The method to be used.");
+    method.setDefaultValue("dftb3");
+    _fields.push_back(Utils::SettingsNames::method, method);
+
     resetToDefaults();
   }
 };

src/Sparrow/Sparrow/Implementations/Dftb/TimeDependent/LinearResponse/TDDFTBData.h

@@ -24,7 +24,8 @@ namespace Sparrow {
  * Right now the data needed to perform TD-SCC-DFTB are present. In order to implement
  * TD-DFTB3 other data might be needed.
  */
-struct TDDFTBData : public LinearResponseData {
+class TDDFTBData : public LinearResponseData {
+ public:
   /// @brief Gamma parameters size: nAtoms x nAtoms
   std::shared_ptr<Eigen::MatrixXd> gammaMatrix;
   /// @brief Magnetic Hubbard parameters (spin constants) size: nAtoms

src/Sparrow/Sparrow/Implementations/GenericMethodWrapper.cpp

@@ -66,6 +66,8 @@ const Utils::Results& GenericMethodWrapper::calculate(std::string description) {
   if (dipoleMatrixCalculator_)
     dipoleMatrixCalculator_->invalidate();
   applySettings();
+  // Check method and basis set fields
+  checkBasicSettings();
   calculateImpl(requiredDerivative);
 
   // If you want the Hessian, but cannot calculate it analytically,
@@ -152,6 +154,21 @@ Utils::Derivative GenericMethodWrapper::highestDerivativeRequired() const {
   return requiredDerivative;
 }
 
+void GenericMethodWrapper::checkBasicSettings() {
+  Utils::Settings settingsCopy(*(this->settings_));
+  settingsCopy.resetToDefaults();
+  auto methodDefault = settingsCopy.getString(Utils::SettingsNames::method);
+  auto currentMethod = this->settings_->getString(Utils::SettingsNames::method);
+
+  // Check selected method
+  std::transform(currentMethod.begin(), currentMethod.end(), currentMethod.begin(),
+                 [](unsigned char c) { return std::tolower(c); });
+  if (currentMethod != methodDefault && currentMethod != "any") {
+    throw std::runtime_error("This calculator does not provide the requested method.");
+  }
+  settings_->modifyString(Utils::SettingsNames::method, methodDefault);
+}
+
 void GenericMethodWrapper::assembleResults(const std::string& description) {
   results_.set<Utils::Property::Description>(description);
   results_.set<Utils::Property::Energy>(getLcaoMethod().getEnergy());

src/Sparrow/Sparrow/Implementations/GenericMethodWrapper.h

@@ -143,6 +143,8 @@ class GenericMethodWrapper : public Utils::CloneInterface<Utils::Abstract<Generi
   virtual bool successfulCalculation() const = 0;
   virtual bool canCalculateAnalyticalHessian() const;
 
+  void checkBasicSettings();
+
   /**
    * @brief Function to apply the settings to the actual calculation method.
    * This method is needed in every calculator as the modification of the

src/Sparrow/Sparrow/Implementations/Nddo/Am1/Wrapper/AM1Settings.h

@@ -40,20 +40,38 @@ class AM1Settings : public AM1TypeSettings {
  public:
   static constexpr const char* settingsDescription = "AM1Settings";
   AM1Settings() : AM1TypeSettings(settingsDescription) {
+    // Method
+    Utils::UniversalSettings::StringDescriptor method("The method to be used.");
+    method.setDefaultValue("am1");
+    _fields.push_back(Utils::SettingsNames::method, method);
+
+    resetToDefaults();
   }
 };
 
 class RM1Settings : public AM1TypeSettings {
  public:
   static constexpr const char* settingsDescription = "RM1Settings";
   RM1Settings() : AM1TypeSettings(settingsDescription) {
+    // Method
+    Utils::UniversalSettings::StringDescriptor method("The method to be used.");
+    method.setDefaultValue("rm1");
+    _fields.push_back(Utils::SettingsNames::method, method);
+
+    resetToDefaults();
   }
 };
 
 class PM3Settings : public AM1TypeSettings {
  public:
   static constexpr const char* settingsDescription = "PM3Settings";
   PM3Settings() : AM1TypeSettings(settingsDescription) {
+    // Method
+    Utils::UniversalSettings::StringDescriptor method("The method to be used.");
+    method.setDefaultValue("pm3");
+    _fields.push_back(Utils::SettingsNames::method, method);
+
+    resetToDefaults();
   }
 };
 

src/Sparrow/Sparrow/Implementations/Nddo/Mndo/Wrapper/MNDOSettings.h

@@ -29,6 +29,11 @@ class MNDOSettings : public Scine::Utils::Settings {
     useNDDODipoleApprox.setDefaultValue(true);
     _fields.push_back(Utils::SettingsNames::NDDODipoleApproximation, std::move(useNDDODipoleApprox));
 
+    // Method
+    Utils::UniversalSettings::StringDescriptor method("The method to be used.");
+    method.setDefaultValue("mndo");
+    _fields.push_back(Utils::SettingsNames::method, method);
+
     resetToDefaults();
   }
 };

src/Sparrow/Sparrow/Implementations/Nddo/Pm6/Wrapper/PM6Settings.h

@@ -29,6 +29,11 @@ class PM6Settings : public Scine::Utils::Settings {
     useNDDODipoleApprox.setDefaultValue(true);
     _fields.push_back(Utils::SettingsNames::NDDODipoleApproximation, std::move(useNDDODipoleApprox));
 
+    // Method
+    Utils::UniversalSettings::StringDescriptor method("The method to be used.");
+    method.setDefaultValue("pm6");
+    _fields.push_back(Utils::SettingsNames::method, method);
+
     resetToDefaults();
   };
 };