Merge branch 'master' into new-ob-conformer

Signed-off-by: Geoff Hutchison <[email protected]>

.github/workflows/build_cmake.yml

@@ -15,6 +15,10 @@ env:
   CACHE: -DCMAKE_C_COMPILER_LAUNCHER=sccache -DCMAKE_CXX_COMPILER_LAUNCHER=sccache
   SCCACHE_GHA_ENABLED: "true"
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 jobs:
   build:
     name: ${{ matrix.config.name }}

.github/workflows/build_m1.yml

@@ -8,6 +8,10 @@ env:
   MACOS_TARGET: 10.12
   FEATURES: -DUSE_VTK=ON -DBUILD_GPL_PLUGINS=ON -DWITH_COORDGEN=OFF -DUSE_3DCONNEXION=ON
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 jobs:
   build:
     name: ${{ matrix.config.name }}

.github/workflows/build_wheels.yml

@@ -2,6 +2,10 @@ name: Build Wheels
 
 on: [push, pull_request]
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 env:
   # Don't build python 2.7, pypy, or 32-bit wheels or Mac arm64 on Py3.8
   CIBW_SKIP: "cp36-* cp37-* cp311-* cp38-macosx_arm64 pp* *-musllinux_* *-manylinux_i686 *-win32"

.github/workflows/codacy.yml

@@ -28,11 +28,14 @@ permissions:
 
 jobs:
   codacy-security-scan:
+    name: Codacy Security Scan
     permissions:
       contents: read # for actions/checkout to fetch code
       security-events: write # for github/codeql-action/upload-sarif to upload SARIF results
-    name: Codacy Security Scan
     runs-on: ubuntu-latest
+    concurrency:
+      group: ${{ github.workflow }}-${{ github.ref }}
+      cancel-in-progress: true
     steps:
       # Checkout the repository to the GitHub Actions runner
       - name: Checkout code

.github/workflows/codeql.yml

@@ -20,6 +20,10 @@ on:
   schedule:
     - cron: '42 6 * * 6'
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 env:
   QT_VERSION: 5.15.2
   FEATURES: -DBUILD_GPL_PLUGINS=ON -DWITH_COORDGEN=OFF

.gitignore

@@ -1,2 +1,156 @@
 docs/build
-.DS_Store
+.DS_Store
+.vscode
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/

CMakeLists.txt

@@ -22,8 +22,8 @@ include(DetermineVersion)
 
 # Set up our version.
 set(AvogadroLibs_VERSION_MAJOR   "1")
-set(AvogadroLibs_VERSION_MINOR   "97")
-set(AvogadroLibs_VERSION_PATCH   "0")
+set(AvogadroLibs_VERSION_MINOR   "98")
+set(AvogadroLibs_VERSION_PATCH   "1")
 set(AvogadroLibs_VERSION
   "${AvogadroLibs_VERSION_MAJOR}.${AvogadroLibs_VERSION_MINOR}.${AvogadroLibs_VERSION_PATCH}")
 find_package(Git)

README.md

@@ -1,6 +1,8 @@
 # ![Avogadro 2][Avogadro2Logo] Avogadro 2
 
-[![Latest Release](https://img.shields.io/github/v/release/openchemistry/avogadrolibs)](https://github.com/OpenChemistry/avogadrolibs/releases) [![BSD License](https://img.shields.io/github/license/openchemistry/avogadrolibs)](https://github.com/OpenChemistry/avogadrolibs/blob/master/LICENSE) [![Build Status](https://img.shields.io/github/actions/workflow/status/openchemistry/avogadrolibs/build_cmake.yml?branch=master)](https://github.com/OpenChemistry/avogadrolibs/actions) [![PRs Welcome](https://img.shields.io/badge/PRs-welcome-brightgreen.svg?style=flat-square)](http://makeapullrequest.com) [![GitHub contributors](https://img.shields.io/github/contributors/openchemistry/avogadrolibs.svg?style=flat)](https://github.com/OpenChemistry/avogadrolibs/graphs/contributors)  [![OpenCollective Backers](https://img.shields.io/opencollective/all/open-chemistry)](https://opencollective.com/open-chemistry)
+[![Latest Release](https://img.shields.io/github/v/release/openchemistry/avogadrolibs)](https://github.com/OpenChemistry/avogadrolibs/releases) [![BSD License](https://img.shields.io/github/license/openchemistry/avogadrolibs)](https://github.com/OpenChemistry/avogadrolibs/blob/master/LICENSE) [![Build Status](https://img.shields.io/github/actions/workflow/status/openchemistry/avogadrolibs/build_cmake.yml?branch=master)](https://github.com/OpenChemistry/avogadrolibs/actions) [![Codacy Badge](https://app.codacy.com/project/badge/Grade/44bb12662c564ed8a27ee8a7fd89ed50)](https://app.codacy.com/gh/OpenChemistry/avogadrolibs/dashboard?utm_source=gh&utm_medium=referral&utm_content=&utm_campaign=Badge_grade)  
+[![Download Count](https://avogadro.cc/downloads.svg?readme)](https://github.com/OpenChemistry/avogadrolibs/releases) [![Citation Count](https://avogadro.cc/citations.svg?readme)](http://doi.org/10.1186/1758-2946-4-17)  
+[![PRs Welcome](https://img.shields.io/badge/PRs-welcome-brightgreen.svg?style=flat)](http://makeapullrequest.com) [![GitHub contributors](https://img.shields.io/github/contributors/openchemistry/avogadrolibs.svg?style=flat&color=0bf)](https://github.com/OpenChemistry/avogadrolibs/graphs/contributors)  [![OpenCollective Backers](https://img.shields.io/opencollective/all/open-chemistry)](https://opencollective.com/open-chemistry)
 
 ## Introduction
 

SECURITY.md

@@ -9,6 +9,7 @@ patches for widely used long-term-support OS.
 
 | Version | Supported          | 
 | ------- | ------------------ | 
+| 1.98.x  | :white_check_mark: |
 | 1.97.x  | :white_check_mark: |
 | < 1.97  | :x:                |
 

avogadro/calc/CMakeLists.txt

@@ -4,15 +4,21 @@ avogadro_headers(Calc
   chargemodel.h
   chargemanager.h
   defaultmodel.h
+  energycalculator.h
+  energymanager.h
+  lennardjones.h
 )
 
 target_sources(Calc PRIVATE
   chargemodel.cpp
   chargemanager.cpp
   defaultmodel.cpp
+  energycalculator.cpp
+  energymanager.cpp
+  lennardjones.cpp
 )
 
 avogadro_add_library(Calc)
 
 target_link_libraries(Calc
-  PUBLIC Avogadro::Core)
+  PUBLIC Avogadro::Core cppoptlib)

avogadro/calc/chargemanager.cpp

@@ -10,7 +10,6 @@
 #include <algorithm>
 #include <memory>
 
-
 namespace Avogadro::Calc {
 
 ChargeManager& ChargeManager::instance()
@@ -88,7 +87,7 @@ ChargeManager::ChargeManager()
 ChargeManager::~ChargeManager()
 {
   // Delete the models that were loaded.
-  for (auto & m_model : m_models) {
+  for (auto& m_model : m_models) {
     delete m_model;
   }
   m_models.clear();
@@ -102,7 +101,6 @@ std::set<std::string> ChargeManager::identifiersForMolecule(
 
   // check our models for compatibility
   for (auto m_model : m_models) {
-
     // We check that every element in the molecule
     // is handled by the model
     auto mask = m_model->elements() & molecule.elements();
@@ -113,8 +111,8 @@ std::set<std::string> ChargeManager::identifiersForMolecule(
   return identifiers;
 }
 
-MatrixX ChargeManager::partialCharges(
-  const std::string& identifier, Core::Molecule& molecule) const
+MatrixX ChargeManager::partialCharges(const std::string& identifier,
+                                      Core::Molecule& molecule) const
 {
   // first check if the type is found in the molecule
   // (i.e., read from a file not computed dynamically)
@@ -181,4 +179,4 @@ Core::Array<double> ChargeManager::potentials(
   return model->potentials(molecule, points);
 }
 
-} // namespace Avogadro
+} // namespace Avogadro::Calc

avogadro/calc/chargemanager.h

@@ -53,7 +53,7 @@ class AVOGADROCALC_EXPORT ChargeManager
 
   /**
    * @brief Register a new charge model with the manager.
-   * @param format An instance of the format to manage, the manager assumes
+   * @param model An instance of the model to manage, the manager assumes
    * ownership of the object passed in.
    * @return True on success, false on failure.
    */
@@ -80,16 +80,6 @@ class AVOGADROCALC_EXPORT ChargeManager
    */
   bool removeModel(const std::string& identifier);
 
-  /**
-   * New instance of the model for the specified @p identifier. Ownership
-   * is passed to the caller.
-   * @param identifier The unique identifier of the format.
-   * @return Instance of the format, nullptr if not found. Ownership passes to
-   * the
-   * caller.
-   */
-  ChargeModel* newModelFromIdentifier(const std::string& identifier) const;
-
   /**
    * Get a list of all loaded identifiers
    */
@@ -111,7 +101,7 @@ class AVOGADROCALC_EXPORT ChargeManager
    * @return atomic partial charges for the molecule, or 0.0 if undefined
    */
   MatrixX partialCharges(const std::string& identifier,
-                               Core::Molecule& mol) const;
+                         Core::Molecule& mol) const;
 
   /**
    * @return the potential at the point for the molecule, or 0.0 if the model is

avogadro/calc/chargemodel.cpp

@@ -16,7 +16,7 @@ using Core::Molecule;
 namespace Calc {
 
 #ifndef M_PI
-#define M_PI 3.14159265358979323846
+constexpr double M_PI = 3.14159265358979323846;
 #endif
 
 ChargeModel::ChargeModel() : m_dielectric(1.0) {}
@@ -39,7 +39,7 @@ double ChargeModel::potential(Molecule& mol, const Vector3& point) const
     double distance = (positions[i] - point).norm();
     if (distance > 0.01) {
       // drop small distances to avoid overflow
-      potential += charges(i,0) / distance;
+      potential += charges(i, 0) / distance;
     }
   }
 
@@ -52,12 +52,13 @@ Array<double> ChargeModel::potentials(Core::Molecule& mol,
   // This is naive and slow, but can be re-implemented by methods
   // for batching
   Array<double> potentials(points.size(), 0.0);
-  for(unsigned int i = 0; i < points.size(); ++i)
+  for (unsigned int i = 0; i < points.size(); ++i)
     potentials[i] = potential(mol, points[i]);
   return potentials;
 }
 
-void ChargeModel::appendError(const std::string& errorString, bool newLine) const
+void ChargeModel::appendError(const std::string& errorString,
+                              bool newLine) const
 {
   m_error += errorString;
   if (newLine)