Release 2.0.1

qcscine · Jun 25, 2020 · 1d798e5 · 1d798e5
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,10 @@
 # Changelog
 
+## Release 2.0.1
+
+- Corrected bug in setting the element collection in Python bindings
+- Added missing include statement that prevented compilation on GCC 10.0.1.
+
 ## Release 2.0.0
 
 - Calculate thermochemical properties

diff --git a/manual/sparrow_manual.tex b/manual/sparrow_manual.tex
@@ -20,7 +20,7 @@
 %\savebox{\scineimage}{\includegraphics[height=5\baselineskip]{scine_darkblue.png}}
 
 
-\title[SCINE Sparrow manual]{User Manual \vskip 0.5em {\setlength{\parindent}{0pt} \Huge SCINE Sparrow 2.0.0}}
+\title[SCINE Sparrow manual]{User Manual \vskip 0.5em {\setlength{\parindent}{0pt} \Huge SCINE Sparrow 2.0.1}}
 \author[The SCINE Sparrow Developers]{The SCINE Sparrow Developers: \newline \noindent Francesco Bosia, Tamara Husch, Alain Vaucher, and Markus Reiher}
 \publisher{ETH Z\"urich}
 
@@ -234,7 +234,7 @@ \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} 2.0.0 
+SCINE \textsc{Sparrow} is a command-line tool that implements many popular semiempirical models. SCINE \textsc{Sparrow} 2.0.1 
 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 
@@ -352,7 +352,7 @@ \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} 2.0.0 are \texttt{MNDO}, \texttt{AM1}, \texttt{RM1}, \texttt{PM3}, \texttt{PM6}, \texttt{DFTB0}, \texttt{DFTB2}, and
+\textsc{Sparrow} 2.0.1 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
@@ -463,8 +463,8 @@ \chapter{References}
 \vspace{1.0cm}
 
 \begin{itemize}
-\item Primary reference for Sparrow 2.0.0:
-F.~Bosia, T.~Husch, A.~C.~Vaucher, M.~Reiher, \href{https://zenodo.org/record/3244106}{"qcscine/sparrow: Release 2.0.0 (Version 2.0.0)"}, Zenodo, 2020.
+\item Primary reference for Sparrow 2.0.1:
+F.~Bosia, T.~Husch, A.~C.~Vaucher, M.~Reiher, \href{https://doi.org/10.5281/zenodo.3244105}{"qcscine/sparrow: Release 2.0.1 (Version 2.0.1)"}, Zenodo, 2020.
 \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/Python/Calculation.cpp b/src/Sparrow/Python/Calculation.cpp
@@ -88,6 +88,7 @@ void Calculation::setStructure(const std::string& structureFile) {
 }
 
 void Calculation::setElements(pybind11::list elements) {
+  elementTypeCollection_.clear();
   std::string elementString;
   Utils::ElementType elementType;
   for (auto element : elements) {

diff --git a/src/Sparrow/Python/setup.py b/src/Sparrow/Python/setup.py
@@ -7,7 +7,7 @@
 # Define the setup
 setuptools.setup(
   name="scine_sparrow",
-  version="2.0.0",
+  version="2.0.1",
   author="ETH Zurich, Laboratory for Physical Chemistry, Reiher Group",
   author_email="scine@phys.chem.ethz.ch",
   description="Open source semi-empirical quantum chemistry implementations.",

diff --git a/src/Sparrow/Sparrow/Implementations/Nddo/Utils/ParameterUtils/RawParametersContainer.h b/src/Sparrow/Sparrow/Implementations/Nddo/Utils/ParameterUtils/RawParametersContainer.h
@@ -12,6 +12,7 @@
 #include <array>
 #include <map>
 #include <memory>
+#include <string>
 
 namespace Scine {
 namespace Sparrow {