Release 4.0.0

.clang-tidy

@@ -14,6 +14,7 @@ Checks:          '-*,
                   -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,
@@ -23,14 +24,16 @@ Checks:          '-*,
                   -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-braces-around-statements,
-                  -readability-else-after-return'
+                  -readability-magic-numbers'
 #HeaderFilterRegex: './src/*'
 AnalyzeTemporaryDtors: false
 FormatStyle:     none

.conan_test_package/conanfile.py

@@ -4,24 +4,20 @@
 See LICENSE.txt for details.
 """
 
-import os
 from conans import ConanFile, CMake
 
 
-def conan_paths_str(build_folder):
-    return os.path.join(build_folder, "conan_paths.cmake")
-
-
 class TestPackageConan(ConanFile):
     settings = "os", "compiler", "build_type", "arch"
-    generators = "cmake_paths"
-    build_requires = [("cmake/[>3.13.4]@scine/stable")]
+    generators = "cmake_find_package"
+    # CMake 3.20.0 has a bug when finding/linking openmp
+    #  so it is exluded from the allowed versions, the version
+    #  gap can be increased if 3.20.1 does not fix the error
+    build_requires = "cmake/[>=3.18.0 <3.20.0 || >3.20.0]"
     exports_sources = "CMakeLists.txt", "test.cpp"
 
     def _configure(self):
         cmake = CMake(self)
-        cmake.definitions["CMAKE_PROJECT_UtilsTestPackage_INCLUDE"] = conan_paths_str(
-            self.build_folder)
         cmake.configure()
         return cmake
 
@@ -32,3 +28,8 @@ def build(self):
     def test(self):
         cmake = self._configure()
         cmake.test()
+
+        if self.options["scine_utilities"].python:
+            self.output.info("Trying to import 'scine_utilities'")
+            import scine_utilities
+            self.output.info("Import worked!")

.gitignore

@@ -1,15 +1,17 @@
 # build files
 build/*
+build-*
 cmake-build-*
 compile_commands.json
 install/*
+.conan_test_package/build
 
 # hidden files
+.cache
 *.swp
 .idea/*
 .lvimrc
 .vscode
-.conan_test_package/build
 
 # python files
 *__pycache__*

CHANGELOG.rst

@@ -1,29 +1,97 @@
-=========
 Changelog
 =========
 
+All changes are grouped into one of three categories: those changes that are considered
+being related to features, meaning that they add or update new functionalities,
+those that are considered important technical updates, and all other notable updates.
+It is intended that only the first two groups (``New Features and Feature Updates`` and
+``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 4.0.0
+-------------
+
+New Features and Feature Updates
+................................
+- Improve GDIIS: numerical stability
+- Improve BFGS: add automatic damping
+- Improve EVF and Bofill: allows to select mode and follows mode independent of order
+- Add periodic boundary conditions
+- Add support for CP2K
+- Improve Gaussian interface: allows to reuse SCF results as guesses in subsequent calculations and
+  to retrieve molecular orbital coefficients
+- Add support for Turbomole
+- Improve MD: Fix a bug regarding the time step size, check gradient
+  calculations for SCF convergence, add the option to use bias potentials and
+  add a stochastic dynamics integrator
+
+Important Technical Changes
+...........................
+- Add Python bindings for CalculatorWithReference
+- Add Log accessor to Python bindings of Calculator and CalculatorWithReference
+- Add Python bindings for Davidson diagonalizer with possibility of having
+  custom sigma vector evaluators/preconditioners
+- Add functions to get all closest atoms within a certain distance and to
+  build an atom pair-list
+- Distinguish now between true internal, true Cartesian, and Cartesian with removed
+  translation and rotation coordinate systems
+- Add Python bindings for ThermochemistryCalculator to calculate thermodynamic properties from a Hessian in Python
+- Add Python bindings for SettingsNames
+- Add support for the SMD solvation model in ORCA
+- Add the option to obtain gradients from a CalculatorWithReference in MD simulations
+
+Development Changes
+...................
+- Refactoring of GeometryUtilities into sub-namespaces
+- Add data structures needed for downstream methods that are general to linear response methods
+- Remove Logger option for downstream LcaoMethods as it can be accessed through the calculator interface
+- Refactor Davidson diagonalizers:
+
+  - Create IterativeDiagonalizer interface
+  - Create KrylovDiagonalizer interface, inheriting from IterativeDiagonalizer
+  - Create the 2 versions, NonOrthogonalDavidson and OrthogonalDavidson
+  - Add Python bindings for OrthogonalDavidson and NonOrthogonalDavidson,
+    tested in Python and added an example on how to extend the SigmaVectorEvaluator
+    to customize the Davidson directly in Python
+
 Release 3.0.1
-=============
+-------------
+
+Important Technical Changes
+...........................
 
 - Update development-utils
 
 Release 3.0.0
-=============
+-------------
 
-- Enable ``conan`` builds and PyPI releases
-- Add Newton-Trajectory type optimizer
+New Features and Feature Updates
+................................
+- Add Newton-Trajectory reaction search optimizer
+- Improve Dimer transition state search algorithm
+- Improve BFGS/GDIIS geometry optimization algorithm
 - Add statistics and machine learning tools (PCA, k-fold cross-validation, kernel ridge regression)
 - Add chemical representations for machine-learned force fields
-- Charge Model 5 corrections for Hirshfeld atomic partial charges
+- Add possibility to generate Charge Model 5 (CM5) corrections for Hirshfeld atomic partial charges
 - Add various conceptual DFT quantities
+- Add implicit solvation options to ORCA and Gaussian interfaces
+
+Important Technical Changes
+...........................
+- Enable ``conan`` builds and PyPI releases
+- Add Python bindings sphinx documentation
+
+Development Changes
+...................
 - Enable access to the density matrix and GTOs in Python
-- Improve Dimer transition state search algorithm
-- Add implicit solvation option to ORCA and Gaussian interfaces
-- Add python bindings sphinx documentation
-- Separate ``Settings`` from its base ``ValueCollection`` in python bindings
+- Separate ``Settings`` from its base ``ValueCollection`` in Python bindings
+- Add Python bindings for molecular dynamics simulations
+- Rework the Python wrapper for ``Settings``, ``ValueCollection`` and ``DescriptorCollection``
+- Add a ``TestCalculator`` and module that implements the ``Test`` method to allow mocked calls
+  to QC programs. (Uses a modified Lennard-Jones potential)
 
 Release 2.0.0
-=============
+-------------
 
 - Add support for internal coordinates
 - Add interface to Gaussian
@@ -33,12 +101,12 @@ Release 2.0.0
 - Various bugfixes and improvements
 
 Release 1.0.1
-=============
+-------------
 
 Hotfix to allow compilation on OSX using Clang.
 
 Release 1.0.0
-=============
+-------------
 
 Initial release with all necessary functionality to support Sparrow and ReaDuct.
 Among other things, this includes:

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 3.0.0
+  VERSION 4.0.0
   DESCRIPTION "Utilities to be used (statically linked) in all other SCINE modules."
 )
 

CONTRIBUTING.rst

@@ -1,9 +1,8 @@
-===========================================
 Contributing to SCINE Open Source Utilities
 ===========================================
 
 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.
@@ -19,16 +18,14 @@ 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
-====================
+--------------------
 
 - Eric Hermes, Sandia National Laboratories
   (https://github.com/qcscine/utilities/pull/1)

README.rst

@@ -1,23 +1,22 @@
-=============================
 SCINE - Open Source Utilities
 =============================
 
 Introduction
-============
+------------
 
 This repository contains functionality which is used in most SCINE modules.
 It is vital for the correct functioning of all SCINE modules, but it does not
 directly provide any functionality for end users. Therefore, only developers
 of SCINE need to directly interact with this repository.
 
 License and Copyright Information
-=================================
+---------------------------------
 
-For license and copyright information, see the file `LICENSE.txt` in this
+For license and copyright information, see the file ``LICENSE.txt`` in this
 directory.
 
 Installation and Usage
-======================
+----------------------
 
 As a user of one of the SCINE modules (such as Sparrow), you do not need
 to set up Open Source Utilities yourself. Instead, this is done as part of the
@@ -26,7 +25,7 @@ instructions are only necessary for developers of SCINE, or those interfacing
 this library directly.
 
 Dependencies
-------------
+............
 
 Required software, minimum required versions in brackets, for this SCINE project are:
 
@@ -36,7 +35,7 @@ Required software, minimum required versions in brackets, for this SCINE project
 - Eigen3 (3.3.2)
 
 Installation
-------------
+............
 
 In order to compile this as a SCINE developer, execute the following
 commands::
@@ -51,14 +50,21 @@ commands::
     make test
     make install
 
+Known Issues
+------------
+
+Due to a `bug <https://github.com/boostorg/process/issues/62>`_ in boost 
+version 1.69.0, linkage against this version will result in a leakage
+of file handles if the ORCA and Gaussian Calculators are called repeatedly.
+
 Support and Contact
-===================
+-------------------
 
 In case you should encounter problems or bugs, please write a short message
 to [email protected].
 
 Third-Party Libraries Used
-==========================
+--------------------------
 
 SCINE Utilities makes use of the following third-party libraries:
 

conanfile.py

@@ -9,7 +9,7 @@
 
 class ScineUtilsConan(ScineConan):
     name = "scine_utilities"
-    version = "3.0.0"
+    version = "4.0.0"
     url = "https://github.com/qcscine/utilities"
     description = """
 Functionality which is used in most SCINE modules. It is vital for the correct
@@ -28,13 +28,31 @@ class ScineUtilsConan(ScineConan):
                        "microarch": "none"}
     exports = "dev/conan/*.py"
     exports_sources = ["dev/cmake/*", "src/*", "CMakeLists.txt", "README.rst",
-                       "LICENSE.txt", "dev/conan/hook.cmake"]
-    requires = ["eigen/[~=3.3.7]@conan/stable",
-                "boost/[>1.65.0]@conan/stable",
-                "yaml-cpp/0.6.3@scine/stable"]
+                       "LICENSE.txt", "dev/conan/hook.cmake",
+                       "dev/conan/glue/*"]
+    requires = ["eigen/[~=3.3.7]", "boost/[>1.65.0]", "yaml-cpp/0.6.3"]
+    cmake_name = "UtilsOS"
+    cmake_definitions = {
+        "CMAKE_UNITY_BUILD": "ON",
+        "CMAKE_UNITY_BUILD_BATCH_SIZE": 16
+    }
 
     def requirements(self):
-        self.requires("irc/6d5c7c37@scine/stable", private=self.options.shared)
+        # Cannot mark irc as private until #7585 gets merged and a new conan
+        # was released. Replace with:
+        # >>>  self.requires("irc/6d5c7c37", private=self.options.shared)
+        self.requires("irc/6d5c7c37")
+
+    def package_info(self):
+        super().package_info()
 
-    def _configure_cmake(self):
-        return super()._configure_cmake_base("UtilsOS", None)
+        # Add Core's targets as components and model dependency chain
+        self.cpp_info.components["CoreHeaders"].includedirs = ["include/Scine"]
+        self.cpp_info.components["CoreHeaders"].requires = ["boost::boost"]
+        self.cpp_info.components["Core"].libs = ["core"]
+        self.cpp_info.components["Core"].requires = ["CoreHeaders"]
+        self.cpp_info.components["UtilsOS"].libs.remove("core")
+        self.cpp_info.components["UtilsOS"].requires.append("CoreHeaders")
+        self.cpp_info.components["UtilsOS"].cxxflags = ["-fopenmp"]
+        self.cpp_info.components["UtilsOS"].sharedlinkflags = ["-fopenmp"]
+        self.cpp_info.components["UtilsOS"].exelinkflags = ["-fopenmp"]