Release 5.0.0

qcscine · Nov 20, 2023 · 79378ed · 79378ed
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diff --git a/.conan_test_package/conanfile.py b/.conan_test_package/conanfile.py
@@ -1,6 +1,6 @@
-__copyright__ = """This file is part of SCINE Utilities.
+__copyright__ = """This file is part of SCINE Sparrow.
 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.
 """
 

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -1,6 +1,12 @@
 Changelog
 =========
 
+Release 5.0.0
+-------------
+
+- Improve support for compilation on Windows (MSVC)
+- Update address in license
+
 Release 4.0.0
 -------------
 

diff --git a/CMakeLists.txt b/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 4.0.0
+  VERSION 5.0.0
   DESCRIPTION "Library for fast and agile quantum chemical calculations with semiempirical methods."
 )
 

diff --git a/CONTRIBUTING.rst b/CONTRIBUTING.rst
@@ -28,3 +28,4 @@ Further Contributors
 --------------------
 
 - Sebastian Ehlert (`@awvwgk <https://github.com/awvwgk>`_), University of Bonn (various bug reports)
+- Juuso Lehtivarjo, NMR Solutions Ltd.
diff --git a/LICENSE.txt b/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:

diff --git a/conanfile.py b/conanfile.py
@@ -4,7 +4,7 @@
 
 class ScineSparrowConan(ScineConan):
     name = "scine_sparrow"
-    version = "4.0.0"
+    version = "5.0.0"
     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.
@@ -30,7 +30,7 @@ class ScineSparrowConan(ScineConan):
                        "README.rst", "LICENSE.txt", "dev/conan/hook.cmake",
                        "dev/conan/glue/*"]
     build_requires = "cereal/1.3.0"
-    requires = "scine_utilities/8.0.0"
+    requires = "scine_utilities/9.0.0"
     cmake_name = "Sparrow"
 
     def package_info(self):

diff --git a/dev b/dev
diff --git a/manual/sparrow_manual.tex b/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 4.0.0}}
+\title[SCINE Sparrow manual]{User Manual \vskip 0.5em {\setlength{\parindent}{0pt} \Huge SCINE Sparrow 5.0.0}}
 \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} 4.0.0
+SCINE \textsc{Sparrow} is a command-line tool that implements many popular semiempirical models. SCINE \textsc{Sparrow} 5.0.0
 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 
@@ -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} 4.0.0 are \texttt{MNDO}, \texttt{AM1}, \texttt{RM1}, \texttt{PM3}, \texttt{PM6}, \texttt{DFTB0}, \texttt{DFTB2}, and
+\textsc{Sparrow} 5.0.0 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
@@ -531,7 +531,7 @@ \chapter{Using the Python Bindings}
 structure.positions = [[-0.7, 0, 0], [0.7, 0, 0]]
 
 # Get calculator
-manager = su.core.ModuleManager()
+manager = su.core.ModuleManager.get_instance()
 calculator = manager.get('calculator', 'AM1')
 
 # Configure Calculator
@@ -564,7 +564,7 @@ \chapter{Using the Python Bindings}
 import scine_sparrow
 
 # Load xyz into calculator
-manager = su.core.ModuleManager()
+manager = su.core.ModuleManager.get_instance()
 calculator = manager.get('calculator', 'AM1')
 calculator.structure = su.io.read('h2.xyz')[0]
 
@@ -600,7 +600,7 @@ \chapter{Using the Python Bindings}
 structure.positions = structure.positions * su.BOHR_PER_ANGSTROM
 
 # Get excited-state calculator
-manager = su.core.ModuleManager()
+manager = su.core.ModuleManager.get_instance()
 excited_states_calculator = manager.get('calculator_with_reference', 'TD-DFTB')
 # Generate a suitable ground-state reference calculator
 excited_states_calculator.reference_calculator = manager.get('calculator', 'DFTB2')
@@ -650,7 +650,7 @@ \chapter{Using the Python Bindings}
 structure.positions = structure.positions * su.BOHR_PER_ANGSTROM
 
 # Get orbital steering calculator
-manager = su.core.ModuleManager()
+manager = su.core.ModuleManager.get_instance()
 orbital_steering_calculator = manager.get('calculator_with_reference',
 'orbital_steering')
 # Generate a suitable reference calculator
@@ -706,8 +706,8 @@ \chapter{References}
 \vspace{1.0cm}
 
 \begin{itemize}
-\item Primary reference for Sparrow 4.0.0:
-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 4.0.0 (Version 4.0.0)"}, Zenodo, 2023.
+\item Primary reference for Sparrow 5.0.0:
+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 5.0.0 (Version 5.0.0)"}, Zenodo, 2023.
 \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

diff --git a/src/Sparrow/App/CalculationHandler.cpp b/src/Sparrow/App/CalculationHandler.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.
  */
 /* Internal Includes */

diff --git a/src/Sparrow/App/CalculationHandler.h b/src/Sparrow/App/CalculationHandler.h
@@ -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.
  */
 #ifndef SPARROW_CALCULATIONHANDLER_H

diff --git a/src/Sparrow/App/CommandLineOptions.cpp b/src/Sparrow/App/CommandLineOptions.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.
  */
 #include "CommandLineOptions.h"

diff --git a/src/Sparrow/App/CommandLineOptions.h b/src/Sparrow/App/CommandLineOptions.h
@@ -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.
  */
 #ifndef SPARROW_COMMANDLINEOPTIONS_H

diff --git a/src/Sparrow/App/IRSpectroscopy.cpp b/src/Sparrow/App/IRSpectroscopy.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.
  */
 

diff --git a/src/Sparrow/App/RTSpectroscopyDriver.cpp b/src/Sparrow/App/RTSpectroscopyDriver.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.
  */
 

diff --git a/src/Sparrow/App/SparrowInitializer.cpp b/src/Sparrow/App/SparrowInitializer.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.
  */
 #include "SparrowInitializer.h"

diff --git a/src/Sparrow/App/SparrowInitializer.h b/src/Sparrow/App/SparrowInitializer.h
@@ -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.
  */
 #ifndef SPARROW_SPARROWINITIALIZER_H

diff --git a/src/Sparrow/App/main.cpp b/src/Sparrow/App/main.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.
  */
 

diff --git a/src/Sparrow/CMakeLists.txt b/src/Sparrow/CMakeLists.txt
@@ -32,13 +32,19 @@ set_target_properties(Sparrow PROPERTIES
   WINDOWS_EXPORT_ALL_SYMBOLS ON
 )
 
+if(MSVC)
+  target_compile_definitions(Sparrow PUBLIC BOOST_ALL_NO_LIB)
+endif()
+
 # Add an option to repropduce the standard PM6 errors
 # This is needed until a new reparametrization of PM6 is done with the right method.
 option(REPRODUCE_PM6_ERRORS "Reproduce the errors of standard PM6 implementations" ON)
 
-target_compile_options(Sparrow PRIVATE
-  $<$<BOOL:${OpenMP_CXX_FOUND}>:${OpenMP_CXX_FLAGS}>
-)
+if(SCINE_PARALLELIZE)
+  target_compile_options(Sparrow PRIVATE
+    $<$<BOOL:${OpenMP_CXX_FOUND}>:${OpenMP_CXX_FLAGS}>
+  )
+endif()
 target_compile_definitions(Sparrow
  PRIVATE
   $<$<CONFIG:Debug>:EIGEN_INITIALIZE_MATRICES_BY_NAN>
@@ -55,6 +61,10 @@ target_link_libraries(Sparrow
     $<$<BOOL:${OpenMP_CXX_FOUND}>:OpenMP::OpenMP_CXX>
 )
 
+if(MSVC)
+  target_compile_options(Sparrow PRIVATE /openmp- /bigobj /MP)
+endif()
+
 # Add namespaced aliases
 add_library(Scine::Sparrow ALIAS Sparrow)
 add_library(Scine::SparrowModule ALIAS Sparrow)
@@ -97,6 +107,10 @@ if(SCINE_BUILD_TESTS)
     set(TEST_SELECTION "")
   endif()
 
+  if(MSVC)
+    target_compile_options(Sparrow_tests PRIVATE /bigobj /MP /openmp-)
+  endif()
+
   # App tests
   add_test(
     NAME Sparrow_App
@@ -122,11 +136,19 @@ endif()
 add_executable(SparrowApp ${SPARROW_APP_FILES})
 add_executable(Scine::SparrowApp ALIAS SparrowApp)
 
+if(MSVC)
+  target_compile_definitions(SparrowApp PUBLIC BOOST_ALL_DYN_LINK)
+endif()
+
 set_target_properties(SparrowApp PROPERTIES OUTPUT_NAME sparrow)
 if(APPLE)
   set_target_properties(SparrowApp PROPERTIES RUNTIME_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR})
 endif()
 
+if(MSVC)
+  target_compile_options(SparrowApp PRIVATE /bigobj /MP /openmp-)
+endif()
+
 target_link_libraries(SparrowApp PRIVATE
   Boost::program_options
   Scine::UtilsOS
@@ -146,6 +168,10 @@ target_link_libraries(RTSpectroscopyDriver
     ${CMAKE_DL_LIBS}
 )
 
+if(MSVC)
+  target_compile_options(RTSpectroscopyDriver PRIVATE /bigobj /MP /openmp-)
+endif()
+
 # Add link library specific to MinGW
 if(WIN32 AND MINGW)
   target_link_libraries(SparrowApp PRIVATE ws2_32)

diff --git a/src/Sparrow/Embed/Basisfile.cpp b/src/Sparrow/Embed/Basisfile.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.
  */
 #include "Basisfile.h"

diff --git a/src/Sparrow/Embed/Basisfile.h b/src/Sparrow/Embed/Basisfile.h
@@ -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.
  */
 #ifndef INCLUDE_SPARROW_EMBED_BASISFILE_H

diff --git a/src/Sparrow/Embed/Common.h b/src/Sparrow/Embed/Common.h
@@ -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.
  */
 #ifndef INCLUDE_SPARROW_EMBED_COMMON_H
 #define INCLUDE_SPARROW_EMBED_COMMON_H
 
 #include "boost/optional.hpp"
+#include <iso646.h>
 #include <algorithm>
 #include <fstream>
 #include <iostream>
@@ -40,7 +41,7 @@ struct CppFileStructure {
  * @file
  * @copy)delim"
        << R"delim(right 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.
  *
  * @note This file was generated by the Embed binary from runtime values.

diff --git a/src/Sparrow/Embed/DftbParameterSet.cpp b/src/Sparrow/Embed/DftbParameterSet.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.
  */
 #include "DftbParameterSet.h"

diff --git a/src/Sparrow/Embed/DftbParameterSet.h b/src/Sparrow/Embed/DftbParameterSet.h
@@ -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.
  */
 #ifndef INCLUDE_SPARROW_EMBED_DFTB_PARAMETER_SET_H

diff --git a/src/Sparrow/Embed/Indent.h b/src/Sparrow/Embed/Indent.h
@@ -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.
  */
 #ifndef INCLUDE_SPARROW_EMBED_INDENT_H

diff --git a/src/Sparrow/Embed/NddoParameters.cpp b/src/Sparrow/Embed/NddoParameters.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.
  */
 #include "NddoParameters.h"

diff --git a/src/Sparrow/Embed/NddoParameters.h b/src/Sparrow/Embed/NddoParameters.h
@@ -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.
  */
 #ifndef INCLUDE_SPARROW_EMBED_NDDO_PARAMETERS_H

diff --git a/src/Sparrow/Embed/embed.cpp b/src/Sparrow/Embed/embed.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.
  */
 #include "Basisfile.h"