Release 9.0.0

.conan_test_package/conanfile.py

@@ -1,6 +1,6 @@
 __copyright__ = """This file is part of SCINE Utilities.
 This code is licensed under the 3-clause BSD license.
-Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.
+Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.
 See LICENSE.txt for details.
 """
 

CHANGELOG.rst

@@ -8,12 +8,32 @@ It is intended that only the first two groups (``New Features and Feature Update
 ``Important Technical Changes``) are important for the average user, while
 the last one is mainly aimed at developers and users that link deeply into the code.
 
-Release 8.0.0
+Release 9.0.0
 -------------
 
 New Features and Feature Updates
 ................................
+- Enable calculation of 57-Fe Mössbauer parameters with Orca.
+- Enable DLPNO-CCSD(T)-F12 calculations with Orca.
+- Added a MRCC calculator (requires MRCC executables at the `MRCC_BINARY_PATH` path
+  environment variable).
+  -  Supported methods: DFT, HF, MP2 [LNO-MP2], CC [LNO-CCSD, LNO-CCSD(T)]
+- Added transition state optimizer for QM/MM
+- Molecular trajectories in the PDB file format can now be read.
+
+Important Technical Changes
+...........................
+- Improve support for compilation on Windows (MSVC)
+
+Other
+.....
+- Update address in license
 
+Release 8.0.0
+-------------
+
+New Features and Feature Updates
+................................
 - Turbomole calculator can now calculate Hessians numerically.
 - The DFT grid for the Turbomole calculator can now be varied.
 - The cavity construction for implicit solvation with the Turbomole calculator can now be modified by setting the points and segments per atom.

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(UtilsOS
-  VERSION 8.0.0
+  VERSION 9.0.0
   DESCRIPTION "Utilities to be used (statically linked) in all other SCINE modules."
 )
 

CONTRIBUTING.rst

@@ -31,3 +31,4 @@ Further Contributors
   (https://github.com/qcscine/utilities/pull/1)
 - Sebastian Ehlert (`@awvwgk <https://github.com/awvwgk>`_), University of Bonn
   (https://github.com/qcscine/utilities/issues/4)
+- Juuso Lehtivarjo, NMR Solutions Ltd.

LICENSE.txt

@@ -1,4 +1,4 @@
-Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group
+Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group
 
 Redistribution and use in source and binary forms, with or without modification,
 are permitted provided that the following conditions are met:

README.rst

@@ -44,7 +44,7 @@ commands::
     git submodule update
     mkdir build
     cd build
-    cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=../inst ..
+    cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=../inst -DSCINE_BUILD_PYTHON_BINDINGS=ON ..
     make -j 4
     make UtilsOSDocumentation
     make test

conanfile.py

@@ -1,6 +1,6 @@
 __copyright__ = """This file is part of SCINE Utilities.
 This code is licensed under the 3-clause BSD license.
-Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.
+Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.
 See LICENSE.txt for details.
 """
 
@@ -12,7 +12,7 @@
 
 class ScineUtilsConan(ScineConan):
     name = "scine_utilities"
-    version = "8.0.0"
+    version = "9.0.0"
     url = "https://github.com/qcscine/utilities"
     description = """
 Functionality which is used in most SCINE modules. It is vital for the correct

src/Utils/CMakeLists.txt

@@ -44,6 +44,10 @@ set_target_properties(UtilsOS PROPERTIES
   WINDOWS_EXPORT_ALL_SYMBOLS ON
 )
 
+if(MSVC)
+  target_compile_options(UtilsOS PRIVATE /bigobj /MP /openmp-)
+endif()
+
 target_link_libraries(UtilsOS
   PUBLIC
     Boost::boost
@@ -58,6 +62,10 @@ target_link_libraries(UtilsOS
     symspg_objects
 )
 
+if(MSVC)
+  target_compile_definitions(UtilsOS PUBLIC BOOST_ALL_NO_LIB)
+endif()
+
 target_include_directories(UtilsOS
   PUBLIC
     $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}>
@@ -77,6 +85,10 @@ set_target_properties(UtilsOSModule PROPERTIES
   PREFIX ""
 )
 
+if(MSVC)
+  target_compile_options(UtilsOSModule PRIVATE /bigobj /MP /openmp-)
+endif()
+
 # -- Define Install
 # Headers
 install(
@@ -125,6 +137,10 @@ if(SCINE_BUILD_TESTS)
     COPY ${CMAKE_CURRENT_SOURCE_DIR}/Tests/Resources
     DESTINATION ${CMAKE_CURRENT_BINARY_DIR}
   )
+
+  if(MSVC)
+    target_compile_options(UtilsOS_tests PRIVATE /bigobj /MP /openmp-)
+  endif()
 endif()
 
 # Python bindings

src/Utils/Module/Cp2kModule.cpp

@@ -1,7 +1,7 @@
 /**
  * @file
  * @copyright This code is licensed under the 3-clause BSD license.\n
- *            Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.\n
+ *            Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.\n
  *            See LICENSE.txt for details.
  */
 

src/Utils/Module/Cp2kModule.h

@@ -2,7 +2,7 @@
  * @file
  * @brief Default module that is always loaded by Core
  * @copyright This code is licensed under the 3-clause BSD license.\n
- *            Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.\n
+ *            Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.\n
  *            See LICENSE.txt for details.
  */
 #ifndef SCINE_CP2K_MODULE_H
@@ -41,4 +41,4 @@ std::vector<std::shared_ptr<Core::Module>> moduleFactory();
 } // namespace Utils
 } // namespace Scine
 
-#endif // SCINE_CP2K_MODULE_H
+#endif // SCINE_CP2K_MODULE_H

src/Utils/Module/GaussianModule.cpp

@@ -1,7 +1,7 @@
 /**
  * @file
  * @copyright This code is licensed under the 3-clause BSD license.\n
- *            Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.\n
+ *            Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.\n
  *            See LICENSE.txt for details.
  */
 

src/Utils/Module/GaussianModule.h

@@ -2,7 +2,7 @@
  * @file
  * @brief Default module that is always loaded by Core
  * @copyright This code is licensed under the 3-clause BSD license.\n
- *            Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.\n
+ *            Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.\n
  *            See LICENSE.txt for details.
  */
 #ifndef SCINE_GAUSSIAN_MODULE_H

src/Utils/Module/LennardJonesModule.cpp

@@ -1,7 +1,7 @@
 /**
  * @file
  * @copyright This code is licensed under the 3-clause BSD license.\n
- *            Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.\n
+ *            Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.\n
  *            See LICENSE.txt for details.
  */
 

src/Utils/Module/LennardJonesModule.h

@@ -2,7 +2,7 @@
  * @file
  * @brief Default module that is always loaded by Core
  * @copyright This code is licensed under the 3-clause BSD license.\n
- *            Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.\n
+ *            Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.\n
  *            See LICENSE.txt for details.
  */
 #ifndef SCINE_LENNARDJONES_MODULE_H

src/Utils/Module/ModuleFactory.cpp

@@ -1,13 +1,14 @@
 /**
  * @file
  * @copyright This code is licensed under the 3-clause BSD license.\n
- *            Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.\n
+ *            Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.\n
  *            See LICENSE.txt for details.
  */
 
 #include "Cp2kModule.h"
 #include "GaussianModule.h"
 #include "LennardJonesModule.h"
+#include "MrccModule.h"
 #include "OrcaModule.h"
 #include "TestModule.h"
 #include "TurbomoleModule.h"
@@ -16,8 +17,8 @@ namespace Scine {
 namespace Utils {
 
 std::vector<std::shared_ptr<Scine::Core::Module>> moduleFactory() {
-  return {Cp2kModule::make(),      OrcaModule::make(), GaussianModule::make(),
-          TurbomoleModule::make(), TestModule::make(), LennardJonesModule::make()};
+  return {Cp2kModule::make(), OrcaModule::make(),         GaussianModule::make(), TurbomoleModule::make(),
+          TestModule::make(), LennardJonesModule::make(), MrccModule::make()};
 }
 
 } // namespace Utils

src/Utils/Module/MrccModule.cpp

@@ -0,0 +1,65 @@
+/**
+ * @file
+ * @brief Default module that is always loaded by Core
+ * @copyright This code is licensed under the 3-clause BSD license.\n
+ *            Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.\n
+ *            See LICENSE.txt for details.
+ */
+#include "MrccModule.h"
+#include <Core/DerivedModule.h>
+#include <Utils/ExternalQC/MRCC/MrccCCCalculator.h>
+#include <Utils/ExternalQC/MRCC/MrccDFTCalculator.h>
+#include <Utils/ExternalQC/MRCC/MrccHFCalculator.h>
+#include <Utils/ExternalQC/MRCC/MrccMP2Calculator.h>
+
+namespace Scine {
+namespace Utils {
+
+using MrccInterfaceModelMap =
+    boost::mpl::map<boost::mpl::pair<Scine::Core::Calculator, boost::mpl::vector<ExternalQC::MrccHFCalculator, ExternalQC::MrccDFTCalculator,
+                                                                                 ExternalQC::MrccMP2Calculator, ExternalQC::MrccCCCalculator>>>;
+
+std::string MrccModule::name() const noexcept {
+  return "MRCC";
+}
+
+bool MrccModule::mrccFound() {
+  return std::getenv(ExternalQC::MrccCalculator::binaryEnvVariable) != nullptr;
+}
+
+boost::any MrccModule::get(const std::string& interface, const std::string& model) const {
+  boost::any resolved = Scine::Core::DerivedModule::resolve<MrccInterfaceModelMap>(interface, model);
+  // Throw an exception if we could not match an interface or model
+  if (resolved.empty()) {
+    throw Scine::Core::ClassNotImplementedError();
+  }
+  return resolved;
+}
+
+bool MrccModule::has(const std::string& interface, const std::string& model) const noexcept {
+  return Scine::Core::DerivedModule::has<MrccInterfaceModelMap>(interface, model) && mrccFound();
+}
+
+std::vector<std::string> MrccModule::announceInterfaces() const noexcept {
+  return Scine::Core::DerivedModule::announceInterfaces<MrccInterfaceModelMap>();
+}
+
+std::vector<std::string> MrccModule::announceModels(const std::string& interface) const noexcept {
+  auto models = Scine::Core::DerivedModule::announceModels<MrccInterfaceModelMap>(interface);
+
+  if (interface == Scine::Core::Calculator::interface && !mrccFound()) {
+    auto mrccModels = {ExternalQC::MrccHFCalculator::model, ExternalQC::MrccDFTCalculator::model,
+                       ExternalQC::MrccMP2Calculator::model, ExternalQC::MrccCCCalculator::model};
+    for (const auto& mrccModel : mrccModels) {
+      models.erase(std::remove(std::begin(models), std::end(models), mrccModel), std::end(models));
+    }
+  }
+  return models;
+}
+
+std::shared_ptr<Scine::Core::Module> MrccModule::make() {
+  return std::make_shared<MrccModule>();
+}
+
+} // namespace Utils
+} // namespace Scine

src/Utils/Module/MrccModule.h

@@ -0,0 +1,43 @@
+/**
+ * @file
+ * @brief Default module that is always loaded by Core
+ * @copyright This code is licensed under the 3-clause BSD license.\n
+ *            Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.\n
+ *            See LICENSE.txt for details.
+ */
+
+#ifndef UTILS_MRCCMODULE_H
+#define UTILS_MRCCMODULE_H
+
+#include "Core/Module.h"
+
+namespace Scine {
+namespace Utils {
+/**
+ * @class
+ * @brief MRCC module provided by OSUtils.
+ */
+class MrccModule : public Core::Module {
+ public:
+  std::string name() const noexcept final;
+
+  boost::any get(const std::string& interface, const std::string& model) const final;
+
+  bool has(const std::string& interface, const std::string& model) const noexcept final;
+
+  std::vector<std::string> announceInterfaces() const noexcept final;
+
+  std::vector<std::string> announceModels(const std::string& interface) const noexcept final;
+
+  static std::shared_ptr<Core::Module> make();
+
+  static bool mrccFound();
+};
+
+// Shared library entry point creating pointers to all contained modules
+std::vector<std::shared_ptr<Core::Module>> moduleFactory();
+
+} // namespace Utils
+} // namespace Scine
+
+#endif // UTILS_MRCCMODULE_H

src/Utils/Module/OrcaModule.cpp

@@ -1,7 +1,7 @@
 /**
  * @file
  * @copyright This code is licensed under the 3-clause BSD license.\n
- *            Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.\n
+ *            Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.\n
  *            See LICENSE.txt for details.
  */
 

src/Utils/Module/OrcaModule.h

@@ -2,7 +2,7 @@
  * @file
  * @brief Default module that is always loaded by Core
  * @copyright This code is licensed under the 3-clause BSD license.\n
- *            Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.\n
+ *            Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.\n
  *            See LICENSE.txt for details.
  */
 #ifndef SCINE_ORCA_MODULE_H
@@ -41,4 +41,4 @@ std::vector<std::shared_ptr<Core::Module>> moduleFactory();
 } // namespace Utils
 } // namespace Scine
 
-#endif // SCINE_ORCA_MODULE_H
+#endif // SCINE_ORCA_MODULE_H

src/Utils/Module/TestModule.cpp

@@ -1,7 +1,7 @@
 /**
  * @file
  * @copyright This code is licensed under the 3-clause BSD license.\n
- *            Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.\n
+ *            Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.\n
  *            See LICENSE.txt for details.
  */
 

src/Utils/Module/TestModule.h

@@ -2,7 +2,7 @@
  * @file
  * @brief Default module that is always loaded by Core
  * @copyright This code is licensed under the 3-clause BSD license.\n
- *            Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.\n
+ *            Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.\n
  *            See LICENSE.txt for details.
  */
 #ifndef SCINE_TEST_MODULE_H

src/Utils/Module/TurbomoleModule.cpp

@@ -1,7 +1,7 @@
 /**
  * @file
  * @copyright This code is licensed under the 3-clause BSD license.\n
- *            Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.\n
+ *            Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.\n
  *            See LICENSE.txt for details.
  */