Release 3.0.0

.clang-format

@@ -0,0 +1,103 @@
+---
+Language:        Cpp
+# BasedOnStyle:  Google
+# Reiher Group, SCINE subgroup
+AccessModifierOffset: -1
+AlignAfterOpenBracket: Align
+AlignConsecutiveAssignments: false
+AlignConsecutiveDeclarations: false
+AlignEscapedNewlinesLeft: true
+AlignOperands:   true
+AlignTrailingComments: true
+AllowAllParametersOfDeclarationOnNextLine: true
+AllowShortBlocksOnASingleLine: false
+AllowShortCaseLabelsOnASingleLine: false
+AllowShortFunctionsOnASingleLine: None
+AllowShortIfStatementsOnASingleLine: false
+AllowShortLoopsOnASingleLine: false
+AlwaysBreakAfterDefinitionReturnType: None
+AlwaysBreakAfterReturnType: None
+AlwaysBreakBeforeMultilineStrings: false
+AlwaysBreakTemplateDeclarations: true
+BinPackArguments: true
+BinPackParameters: true
+BraceWrapping:   
+  AfterClass:      false
+  AfterControlStatement: false
+  AfterEnum:       false
+  AfterFunction:   false
+  AfterNamespace:  false
+  AfterObjCDeclaration: false
+  AfterStruct:     false
+  AfterUnion:      false
+  BeforeCatch:     true
+  BeforeElse:      true
+  IndentBraces:    false
+  SplitEmptyFunction: true
+  SplitEmptyRecord: true
+  SplitEmptyNamespace: true
+BreakBeforeBinaryOperators: None
+BreakBeforeBraces: Custom
+BreakBeforeTernaryOperators: true
+BreakConstructorInitializers: BeforeColon
+BreakAfterJavaFieldAnnotations: false
+BreakStringLiterals: true
+ColumnLimit:     120
+CommentPragmas:  '^ IWYU pragma:'
+ConstructorInitializerAllOnOneLineOrOnePerLine: true
+ConstructorInitializerIndentWidth: 2
+ContinuationIndentWidth: 4
+Cpp11BracedListStyle: true
+DerivePointerAlignment: false
+DisableFormat:   false
+FixNamespaceComments: true
+ForEachMacros:   [ foreach, Q_FOREACH, BOOST_FOREACH ]
+IncludeBlocks: Merge
+IncludeCategories: 
+  - Regex:           '^".*\.h"'
+    Priority:        1
+  - Regex:           '^".*'
+    Priority:        2
+  - Regex:           '^<.*\.h>'
+    Priority:        3
+  - Regex:           '^<.*'
+    Priority:        4
+  - Regex:           '.*'
+    Priority:        5
+IncludeIsMainRegex: '([-_](test|unittest))?$'
+IndentCaseLabels: true
+IndentPPDirectives: AfterHash
+IndentWidth:     2
+IndentWrappedFunctionNames: false
+JavaScriptQuotes: Leave
+JavaScriptWrapImports: true
+KeepEmptyLinesAtTheStartOfBlocks: false
+MacroBlockBegin: ''
+MacroBlockEnd:   ''
+MaxEmptyLinesToKeep: 1
+NamespaceIndentation: None
+PenaltyBreakBeforeFirstCallParameter: 20
+PenaltyBreakComment: 5
+PenaltyBreakFirstLessLess: 3
+PenaltyBreakString: 100
+PenaltyExcessCharacter: 2
+PenaltyReturnTypeOnItsOwnLine: 40
+PointerAlignment: Left
+ReflowComments:  true
+SortIncludes:    true
+SpaceAfterCStyleCast: false
+SpaceAfterTemplateKeyword: false
+SpaceBeforeAssignmentOperators: true
+SpaceBeforeParens: ControlStatements
+SpaceInEmptyParentheses: false
+SpacesBeforeTrailingComments: 1
+SpacesInAngles:  false
+SpacesInContainerLiterals: true
+SpacesInCStyleCastParentheses: false
+SpacesInParentheses: false
+SpacesInSquareBrackets: false
+Standard:        Cpp11
+TabWidth:        8
+UseTab:          Never
+...
+

.clang-tidy

@@ -0,0 +1,66 @@
+---
+# Remarks about the checks:
+# * modernize-use-equals-delete: removed to avoid warnings generated in TEST_F macro from google-test
+# * clang-analyzer-cplusplus.NewDelete: removed to avoid warnings generated in TEST_F macro from google-test
+# * clang-analyzer-cplusplus.NewDeleteLeaks: removed to avoid warnings generated in TEST_F macro from google-test
+# * clang-analyzer-optin.cplusplus.VirtualCall: removed to avoid warnings generated in google-test
+# * cppcoreguidelines-slicing: removed because of PropertyData in Delib
+# * clang-analyzer-core.NullDereference: removed because of warning in clang's headers
+Checks:          '-*,
+                  bugprone-*,
+                  clang-analyzer-*,
+                  -clang-analyzer-cplusplus.NewDelete,
+                  -clang-analyzer-cplusplus.NewDeleteLeaks,
+                  -clang-analyzer-optin.cplusplus.VirtualCall,
+                  -clang-analyzer-core.NullDereference,
+                  cppcoreguidelines-*,
+                  -cppcoreguidelines-avoid-magic-numbers,
+                  -cppcoreguidelines-owning-memory,
+                  -cppcoreguidelines-pro-bounds-array-to-pointer-decay,
+                  -cppcoreguidelines-pro-bounds-constant-array-index,
+                  -cppcoreguidelines-pro-bounds-pointer-arithmetic,
+                  -cppcoreguidelines-pro-type-const-cast,
+                  -cppcoreguidelines-pro-type-member-init,
+                  -cppcoreguidelines-pro-type-vararg,
+                  -cppcoreguidelines-special-member-functions,
+                  -cppcoreguidelines-slicing,
+                  -cppcoreguidelines-non-private-member-variables-in-classes,
+                  misc-*,
+                  -misc-non-private-member-variables-in-classes,
+                  modernize-*,
+                  -modernize-use-equals-delete,
+                  -modernize-use-trailing-return-type,
+                  performance-*,
+                  portability-*,
+                  readability-*,
+                  -readability-magic-numbers'
+#HeaderFilterRegex: './src/*'
+AnalyzeTemporaryDtors: false
+FormatStyle:     none
+CheckOptions:
+  - key:             google-readability-braces-around-statements.ShortStatementLines
+    value:           '1'
+  - key:             google-readability-function-size.StatementThreshold
+    value:           '800'
+  - key:             google-readability-namespace-comments.ShortNamespaceLines
+    value:           '10'
+  - key:             google-readability-namespace-comments.SpacesBeforeComments
+    value:           '2'
+  - key:             modernize-loop-convert.MaxCopySize
+    value:           '16'
+  - key:             modernize-loop-convert.MinConfidence
+    value:           reasonable
+  - key:             modernize-loop-convert.NamingStyle
+    value:           CamelCase
+  - key:             modernize-pass-by-value.IncludeStyle
+    value:           llvm
+  - key:             modernize-replace-auto-ptr.IncludeStyle
+    value:           llvm
+  - key:             modernize-use-nullptr.NullMacros
+    value:           'NULL'
+  - key:             readability-implicit-bool-conversion.AllowPointerConditions # Do not complain for "if (x)" when x is a pointer
+    value:           1
+  - key:             performance-move-const-arg.CheckTriviallyCopyableMove # Do not complain on "std::move(x)" if x is trivially copyable
+    value:           0
+...
+

.conan_test_package/conanfile.py

@@ -0,0 +1,18 @@
+__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.
+See LICENSE.txt for details.
+"""
+
+from conans import ConanFile
+
+
+class TestPackageConan(ConanFile):
+    def build(self):
+        pass
+
+    def test(self):
+        if self.options["scine_sparrow"].python:
+            self.output.info("Trying to import 'scine_sparrow'")
+            import scine_sparrow
+            self.output.info("Import worked")

.gitmodules

@@ -1,3 +1,3 @@
-[submodule "cmake"]
-	path = cmake
-	url = https://github.com/qcscine/cmake.git
+[submodule "dev"]
+	path = dev
+	url = https://github.com/qcscine/development-utils.git

CHANGELOG.rst

@@ -0,0 +1,71 @@
+Changelog
+=========
+
+Release 3.0.0
+-------------
+
+- Excited-state calculations with NDDO-CIS and TD-DFTB
+- Added a binary for the calculation of IR and UV/Vis spectra of trajectories
+- Orbital steering calculations possible with binary (using a single system, single
+  point) and Python bindings (can handle an individual system and systems along a
+  trajectory)
+- Can now set symmetry number for thermodynamics calculation
+- Added density matrix RMSD SCF convergence check
+- Calculate atomic second derivatives
+- Removed Sparrow-specific Python bindings in favour of the more general ``Core::Calculator`` Python bindings
+- Added Python bindings for excited-state calculators; see Utilities for more 
+  infos on them
+- Added patching functionality in DFTB embedded parameters, i.e. if the znorg-0-1 
+  parameter set is chosen, then parameters are automatically sorted out between
+  znorg-0-1 and mio-0-1 (patch parameters available: znorg-0-1, hyb-0-2)
+- Fixed bug causing an instability in the calculation of the gradients (and Hessian matrix) in DFTBx
+- Added ``conanfile.py`` for easier compilation and dependency-handling by Conan
+- Made Sparrow relocatable by embedding the parameters in the compiled program;
+  it is still possible to give parameter files externally
+- Multiple bug fixes and stability fixes
+- Improved testing
+
+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
+- Explicitly symmetrized Hessians
+- Generation of molden input files for molecular orbital visualization
+- General stability/performance improvements
+- Access to the calculations and molden file generations also through SCINE Core::Calculator Python bindings
+- Addition of 3ob-3-1 parameters sets for DFTB. Spin constants are extracted from
+  Christof Köhler, Berücksichtigung von Spinpolarisationseffekten in einem dichtefunktionalbasierten Ansatz,
+  PhD thesis, Departement Physik der Fakultät für Naturwissenschaften an der Universität Paderborn, 2004
+- Addition of automatic linking to MKL/LAPACK/BLAS through Eigen
+- Various bugfixes and improvements
+
+Release 1.0.1
+-------------
+
+- Hotfix to allow compilation on OSX using Clang
+
+Release 1.0.0
+-------------
+
+Initial release with the following features:
+
+- Calculate electronic energies, nuclear gradients, and Hessians
+- Calculate bond orders
+- Restricted and unrestricted formalisms are implemented
+- The following methods are available:
+  - MNDO
+  - AM1
+  - RM1
+  - PM3
+  - PM6
+  - non-SCC DFTB (DFTB0)
+  - DFTB2
+  - DFTB3
+- All functionality can be accessed through a standalone binary
+- Parallelized with OpenMP

CMakeLists.txt

@@ -4,12 +4,12 @@ cmake_minimum_required(VERSION 3.9)
 # tree must then provide a properly namespaced target with the same name as
 # your project.
 project(Sparrow
-  VERSION 2.0.0
+  VERSION 3.0.0
   DESCRIPTION "Library for fast and agile quantum chemical calculations with semiempirical methods."
 )
 
 # Set the module path for universal cmake files inclusion
-set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${CMAKE_CURRENT_SOURCE_DIR}/cmake)
+set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${CMAKE_CURRENT_SOURCE_DIR}/dev/cmake)
 
 # Component setup
 include(ComponentSetup)
@@ -23,3 +23,6 @@ endif()
 
 # Subdirectories
 add_subdirectory(src)
+
+# Documentation
+scine_component_documentation(UtilsOSDocumentation)

CONTRIBUTING.md → CONTRIBUTING.rst

@@ -7,7 +7,7 @@ Contribution Process
 The development for this code is done in a private repository maintained by the 
 Reiher Research Group. GitHub is only used for the official releases.
 
-If you would like to contribute a larger change, please write to <scine@phys.chem.ethz.ch>.
+If you would like to contribute a larger change, please write to scine@phys.chem.ethz.ch.
 For smaller changes, you can create a pull request on GitHub. If we agree with
 the changes, a member of the Reiher Research Group will include them in our
 development code. Of course, we will give proper acknowledgment for any external
@@ -18,14 +18,12 @@ and/or issues on GitHub.
 Please note that contributing a small change does in no way mean that you will
 be added to the author list of a future paper and/or Zenodo entry!
 
-
 Main Contributors
 -----------------
 
 Almost all contributions to SCINE in general and this repository in specific come 
 from members of the Reiher research group.
 
-
 Further Contributors
 --------------------
 

LICENSE.txt

@@ -1,26 +1,26 @@
-Copyright ETH Zurich, Laboratory for Physical Chemistry, Reiher Group
+Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group
 
-Redistribution and use in source and binary forms, with or without modification, 
+Redistribution and use in source and binary forms, with or without modification,
 are permitted provided that the following conditions are met:
 
-1. Redistributions of source code must retain the above copyright notice, this 
+1. Redistributions of source code must retain the above copyright notice, this
 list of conditions and the following disclaimer.
 
-2. Redistributions in binary form must reproduce the above copyright notice, 
-this list of conditions and the following disclaimer in the documentation and/or 
+2. Redistributions in binary form must reproduce the above copyright notice,
+this list of conditions and the following disclaimer in the documentation and/or
 other materials provided with the distribution.
 
-3. Neither the name of the copyright holder nor the names of its contributors 
-may be used to endorse or promote products derived from this software without 
+3. Neither the name of the copyright holder nor the names of its contributors
+may be used to endorse or promote products derived from this software without
 specific prior written permission.
 
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 
-ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
-WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. 
-IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, 
-INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, 
-BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, 
-DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF 
-LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE 
-OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED 
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
+IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
+INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
+BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED
 OF THE POSSIBILITY OF SUCH DAMAGE.