Release 5.1.0

qcscine · Aug 26, 2024 · 95645ba · 95645ba
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diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -1,6 +1,11 @@
 Changelog
 =========
 
+Release 5.1.0
+-------------
+
+- Make compatible with Unity builds
+
 Release 5.0.0
 -------------
 

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 5.0.0
+  VERSION 5.1.0
   DESCRIPTION "Library for fast and agile quantum chemical calculations with semiempirical methods."
 )
 

diff --git a/README.rst b/README.rst
@@ -49,6 +49,13 @@ T. Husch, A. C. Vaucher, M. Reiher, "Semiempirical molecular orbital models
 based on the neglect of diatomic differential overlap approximation", *Int.
 J. Quantum Chem.*, **2018**, *118*, e25799.
 
+Furthermore, when publishing results obtained with any SCINE module, please cite the following paper:
+
+T. Weymuth, J. P. Unsleber, P. L. Türtscher, M. Steiner, J.-G. Sobez, C. H. Müller, M. Mörchen,
+V. Klasovita, S. A. Grimmel, M. Eckhoff, K.-S. Csizi, F. Bosia, M. Bensberg, M. Reiher,
+"SCINE—Software for chemical interaction networks", *J. Chem. Phys.*, **2024**, *160*, 222501
+(DOI `10.1063/5.0206974 <https://doi.org/10.1063/5.0206974>`_).
+
 Support and Contact
 -------------------
 

diff --git a/conanfile.py b/conanfile.py
@@ -4,7 +4,7 @@
 
 class ScineSparrowConan(ScineConan):
     name = "scine_sparrow"
-    version = "5.0.0"
+    version = "5.1.0"
     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/9.0.0"
+    requires = "scine_utilities/[=10.0.0]"
     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 5.0.0}}
+\title[SCINE Sparrow manual]{User Manual \vskip 0.5em {\setlength{\parindent}{0pt} \Huge SCINE Sparrow 5.1.0}}
 \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} 5.0.0
+SCINE \textsc{Sparrow} is a command-line tool that implements many popular semiempirical models. SCINE \textsc{Sparrow} 5.1.0
 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} 5.0.0 are \texttt{MNDO}, \texttt{AM1}, \texttt{RM1}, \texttt{PM3}, \texttt{PM6}, \texttt{DFTB0}, \texttt{DFTB2}, and
+\textsc{Sparrow} 5.1.0 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
@@ -706,8 +706,8 @@ \chapter{References}
 \vspace{1.0cm}
 
 \begin{itemize}
-\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 Primary reference for Sparrow 5.1.0:
+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 5.1.0 (Version 5.1.0)"}, Zenodo, 2024.
 \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/CMakeLists.txt b/src/Sparrow/CMakeLists.txt
@@ -17,6 +17,10 @@ if(NOT TARGET Boost::filesystem OR NOT TARGET Boost::program_options)
   find_package(Boost REQUIRED COMPONENTS program_options filesystem)
 endif()
 
+set_source_files_properties(
+    ${SPARROW_UNITY_DISABLE} PROPERTIES SKIP_UNITY_BUILD_INCLUSION ON
+)
+
 # Sparrow is a Scine module and is always shared, never linked against
 add_library(Sparrow SHARED ${SPARROW_MODULE_FILES})
 

diff --git a/src/Sparrow/Files.cmake b/src/Sparrow/Files.cmake
@@ -14,6 +14,10 @@ set(SPARROW_MODULE_FILES ${SPARROW_MODULE_HEADERS} ${SPARROW_MODULE_CPPS})
 
 list(FILTER SPARROW_MODULE_FILES EXCLUDE REGEX ".*RealTimeSpectroscopy.*")
 
+# specify files that are not Unity build compatible
+file(GLOB_RECURSE SPARROW_DFTB_PARAMETER_CPPS ${CMAKE_CURRENT_SOURCE_DIR}/Sparrow/Resources/Dftb/*/Parameters.cpp)
+set(SPARROW_UNITY_DISABLE ${SPARROW_DFTB_PARAMETER_CPPS})
+
 file(GLOB_RECURSE SPARROW_TEST_HEADERS ${CMAKE_CURRENT_SOURCE_DIR}/Tests/*.h)
 file(GLOB_RECURSE SPARROW_TEST_CPPS ${CMAKE_CURRENT_SOURCE_DIR}/Tests/*.cpp)
 list(FILTER SPARROW_TEST_CPPS EXCLUDE REGEX ".*Slow.*Test.cpp")

diff --git a/src/Sparrow/Python/setup.py b/src/Sparrow/Python/setup.py
@@ -6,7 +6,7 @@
 import setuptools
 
 # Read README.rst for the long description
-with open("README.rst", "r") as fh:
+with open("README.rst", "r", encoding="utf-8") as fh:
     long_description = fh.read()
 
 

diff --git a/src/Sparrow/Python/sphinx/index.rst b/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/v5.0.0/sparrow_manual.pdf>`
+- :download:`Download Latest User Manual PDF <https://scine.ethz.ch/static/download/manuals/v5.1.0/sparrow_manual.pdf>`
+- :download:`Download User Manual PDF v5.1.0 <https://scine.ethz.ch/static/download/manuals/v5.1.0/sparrow_manual.pdf>`
 - :download:`Download User Manual PDF v5.0.0 <https://scine.ethz.ch/static/download/manuals/v5.0.0/sparrow_manual.pdf>`
 - :download:`Download User Manual PDF v4.0.0 <https://scine.ethz.ch/static/download/manuals/v4.0.0/sparrow_manual.pdf>`
 - :download:`Download User Manual PDF v3.1.0 <https://scine.ethz.ch/static/download/manuals/v3.1.0/sparrow_manual.pdf>`

diff --git a/src/Sparrow/Sparrow/Implementations/RealTimeSpectroscopy/IR/IntensitiesCalculator.cpp b/src/Sparrow/Sparrow/Implementations/RealTimeSpectroscopy/IR/IntensitiesCalculator.cpp
@@ -9,7 +9,6 @@
 #include "IntensitiesCalculator.h"
 #include "../Utils/LineWidthGenerator.h"
 #include <cmath>
-#include <iostream>
 
 namespace Scine {
 namespace Sparrow {

diff --git a/src/Sparrow/Sparrow/Implementations/RealTimeSpectroscopy/UvVis/UvVisCalculator.cpp b/src/Sparrow/Sparrow/Implementations/RealTimeSpectroscopy/UvVis/UvVisCalculator.cpp
@@ -20,14 +20,6 @@ namespace Scine {
 namespace Sparrow {
 namespace RealTimeSpectroscopy {
 
-constexpr double unitaryChargeSquared = 1.6021765e-19 * 1.6021765e-19;
-constexpr double coulombForceConstant = 8.9875517873681e9;
-constexpr double avogadrosNumber = 6.02214199e23;
-constexpr double c = 299792458.;
-constexpr double atomicMassUnit = 1.6605387280149467e-27;
-constexpr double conversionFactor =
-    unitaryChargeSquared * M_PI * coulombForceConstant * avogadrosNumber / (3. * c * c) / atomicMassUnit / 1000.;
-
 UvVisCalculator::UvVisCalculator() : settings_(std::make_shared<UvVisSettings>()) {
 }