feat!: improve integrator stability and reliability (#416)

This commit improves parameter choices for the integrators overall. In particular, we now make more similar choices to scipy.integrate.solve_ivp, which should lead to fewer surprises.

BREAKING: It was found out that the currently calculated analytical Jacobian leads to problems when implicit integrators are employed. This affects LSODA, Radau and BDF. **The usage of analytical Jacobians is then disabled for this version until we find a fix for the bug**. Even though it is a breaking chance per se, it is mild, as most of the change happened in places the user had previously no access.

.gitignore

@@ -1,6 +1,7 @@
-# Vim files
-*~
+# Created by https://www.toptal.com/developers/gitignore/api/python
+# Edit at https://www.toptal.com/developers/gitignore?templates=python
 
+### Python ###
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
@@ -23,6 +24,7 @@ parts/
 sdist/
 var/
 wheels/
+share/python-wheels/
 *.egg-info/
 .installed.cfg
 *.egg
@@ -41,14 +43,17 @@ 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
@@ -58,6 +63,7 @@ coverage.xml
 *.log
 local_settings.py
 db.sqlite3
+db.sqlite3-journal
 
 # Flask stuff:
 instance/
@@ -67,21 +73,52 @@ instance/
 .scrapy
 
 # Sphinx documentation
-docsrc/_build/
-docs/.buildinfo
-docs/.doctrees
+docs/_build/
 
 # PyBuilder
+.pybuilder/
 target/
 
 # Jupyter Notebook
 .ipynb_checkpoints
 
-# pyenv
-.python-version
+# IPython
+profile_default/
+ipython_config.py
 
-# celery beat schedule file
+# 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
@@ -107,3 +144,33 @@ venv.bak/
 
 # mypy
 .mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+### Python Patch ###
+# Poetry local configuration file - https://python-poetry.org/docs/configuration/#local-configuration
+poetry.toml
+
+# ruff
+.ruff_cache/
+
+# LSP config files
+pyrightconfig.json
+
+# End of https://www.toptal.com/developers/gitignore/api/python

.python-version

@@ -0,0 +1 @@
+3.10.9

overreact/_cli.py

@@ -143,7 +143,7 @@ def __init__(  # noqa: PLR0913
         pressure=constants.atm,
         bias=0.0,
         tunneling="eckart",
-        method="LSODA",
+        method="RK23",
         max_time=1 * 60 * 60,
         rtol=1e-3,
         atol=1e-6,
@@ -873,8 +873,8 @@ def main(arguments=None):
         "--method",
         help="integrator used in solving the ODE system of the microkinetic "
         "simulation",
-        choices=["BDF", "Radau", "LSODA"],
-        default="LSODA",
+        choices=["RK23", "DOP853", "RK45", "LSODA", "BDF", "Radau"],
+        default="RK23",
     )
     parser.add_argument(
         "--max-time",

overreact/api.py

@@ -780,7 +780,7 @@ def get_drc(  # noqa: PLR0913
     compounds,
     y0,
     t_span=None,
-    method="LSODA",
+    method="RK23",
     qrrho=True,  # noqa: FBT002
     scale="l mol-1 s-1",
     temperature=298.15,

overreact/coords.py

@@ -1486,9 +1486,10 @@ def _operation(name, order=2, axis=None):
 
     if name == "i":
         return -np.eye(3)
-    elif name == "e":  # noqa: RET505
+    if name == "e":
         return np.eye(3)
-    elif name in {"c", "σ", "sigma", "s"}:  # noqa: RUF001
+
+    if name in {"c", "σ", "sigma", "s"}:  # noqa: RUF001
         # normalize axis
         axis = np.asarray(axis)
         axis = axis / np.linalg.norm(axis)
@@ -1497,12 +1498,14 @@ def _operation(name, order=2, axis=None):
             rotation = Rotation.from_rotvec(2.0 * np.pi * axis / order).as_matrix()
         if name in {"σ", "sigma", "s"}:  # noqa: RUF001
             reflection = np.eye(3) - 2.0 * np.outer(axis, axis)
+
         if name == "c":
             return rotation
-        elif name in {"σ", "sigma"}:  # noqa: RUF001
+        if name in {"σ", "sigma"}:  # noqa: RUF001
             return reflection
-        elif name == "s":
+        if name == "s":
             return rotation @ reflection
+
     raise ValueError(f"unknown operation: '{name}'")  # noqa: EM102, TRY003