doc/notebooks/demo_shallow_water_lbm.ipynb

@@ -541,7 +541,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -555,7 +555,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.2"
+   "version": "3.11.4"
   }
  },
  "nbformat": 4,

doc/sphinx/api.rst

@@ -8,13 +8,10 @@ API Reference
    enums.rst
    stencils.rst
    kernelcreation.rst
-   methods.rst
    equilibrium.rst
    moment_transforms.rst
    maxwellian_equilibrium.rst
    continuous_distribution_measures.rst
    moments.rst
    cumulants.rst
-   boundary_conditions.rst
-   forcemodels.rst
    zbibliography.rst

doc/sphinx/lbmpy.bib

@@ -110,6 +110,24 @@ issn = {0898-1221},
 doi = {10.1016/j.camwa.2015.05.001},
 }
 
+@article{geier2017,
+author = {Geier, Martin and Pasquali, Andrea and Sch{\"{o}}nherr, Martin},
+title = {Parametrization of the Cumulant Lattice Boltzmann Method for Fourth Order Accurate Diffusion Part I},
+year = {2017},
+issue_date = {November 2017},
+publisher = {Academic Press Professional, Inc.},
+address = {USA},
+volume = {348},
+number = {C},
+issn = {0021-9991},
+url = {https://doi.org/10.1016/j.jcp.2017.05.040},
+doi = {10.1016/j.jcp.2017.05.040},
+journal = {J. Comput. Phys.},
+month = {nov},
+pages = {862–888},
+numpages = {27}
+}
+
 @Article{Coreixas2019,
   title = {Comprehensive comparison of collision models in the lattice Boltzmann framework: Theoretical investigations},
   author = {Coreixas, Christophe and Chopard, Bastien and Latt, Jonas},
@@ -248,4 +266,52 @@ journal = {Communications in Computational Physics}
   publisher = {Springer Link},
 }
 
+@article{BouzidiBC,
+    author = {Bouzidi, M’hamed and Firdaouss, Mouaouia and Lallemand, Pierre},
+    title = "{Momentum transfer of a Boltzmann-lattice fluid with boundaries}",
+    journal = {Physics of Fluids},
+    year = {2001},
+    month = {11},
+    doi = {10.1063/1.1399290},
+    url = {https://doi.org/10.1063/1.1399290},
+}
+
+@Article{rozema15,
+  doi       = {10.1063/1.4928700},
+  year      = {2015},
+  month     = {aug},
+  publisher = {AIP Publishing},
+  volume    = {27},
+  number    = {8},
+  author    = {Wybe Rozema and Hyun J. Bae and Parviz Moin and Roel Verstappen},
+  title     = {Minimum-dissipation models for large-eddy simulation},
+  journal   = {Physics of Fluids}
+}
+
+@article{Han2021,
+   doi = {10.1088/1873-7005/ac1782},
+   url = {https://dx.doi.org/10.1088/1873-7005/ac1782}                    ,
+   year = {2021},
+   month = {aug},
+   publisher = {IOP Publishing},
+   volume = {53},
+   number = {4},
+   pages = {045506},
+   author = {Mengtao Han and Ryozo Ooka and Hideki Kikumoto},
+   title = {A wall function approach in lattice Boltzmann method: algorithm and validation using turbulent channel flow},
+   journal = {Fluid Dynamics Research}
+}
+
+@article{Maronga2020,
+ author = {Maronga, Bj{\"o}rn and Knigge, Christoph and Raasch, Siegfried},
+ year = {2020},
+ title = {{An Improved Surface Boundary Condition for Large-Eddy Simulations Based on Monin--Obukhov Similarity Theory: Evaluation and Consequences for Grid Convergence in Neutral and Stable Conditions}},
+ pages = {297--325},
+ volume = {174},
+ number = {2},
+ issn = {0006-8314},
+ journal = {{Boundary-layer meteorology}},
+ doi = {10.1007/s10546-019-00485-w}
+}
+
 @Comment{jabref-meta: databaseType:bibtex;}

doc/sphinx/methods.rst

-*******************************************
-Methods and Method Creation (lbmpy.methods)
-*******************************************
+********************************
+Collision models (lbmpy.methods)
+********************************
 
 This module defines the classes defining all types of lattice Boltzmann methods available in *lbmpy*,
 together with a set of factory functions used to create their instances. The factory functions are
@@ -22,21 +22,6 @@ Abstract LB Method Base Class
 .. autoclass:: lbmpy.methods.AbstractLbMethod
     :members:
 
-
-Conserved Quantity Computation
-==============================
-
-The classes of the conserved quantity computation (CQC) submodule define an LB Method's conserved quantities and
-the equations to compute them. For hydrodynamic methods, :class:`lbmpy.methods.DensityVelocityComputation` is
-the typical choice. For custom methods, however, a custom CQC class might have to be created.
-
-.. autoclass:: lbmpy.methods.AbstractConservedQuantityComputation
-    :members:
-
-.. autoclass:: lbmpy.methods.DensityVelocityComputation
-    :members:
-
-
 .. _methods_rawmomentbased:
 
 Raw Moment-based methods
@@ -163,3 +148,17 @@ Low-Level Creation Functions
 .. autofunction:: lbmpy.methods.creationfunctions.create_with_continuous_maxwellian_equilibrium
 
 .. autofunction:: lbmpy.methods.creationfunctions.create_from_equilibrium
+
+
+Conserved Quantity Computation
+==============================
+
+The classes of the conserved quantity computation (CQC) submodule define an LB Method's conserved quantities and
+the equations to compute them. For hydrodynamic methods, :class:`lbmpy.methods.DensityVelocityComputation` is
+the typical choice. For custom methods, however, a custom CQC class might have to be created.
+
+.. autoclass:: lbmpy.methods.AbstractConservedQuantityComputation
+    :members:
+
+.. autoclass:: lbmpy.methods.DensityVelocityComputation
+    :members:
\ No newline at end of file

doc/sphinx/tutorials.rst

@@ -4,6 +4,10 @@ Tutorials
 All tutorials are automatically created by Jupyter Notebooks.
 You can open the notebooks directly to play around with the code examples.
 
+=================
+Basics
+=================
+
 .. toctree::
     :maxdepth: 1
 
@@ -13,17 +17,68 @@ You can open the notebooks directly to play around with the code examples.
     /notebooks/03_tutorial_lbm_formulation.ipynb
     /notebooks/04_tutorial_cumulant_LBM.ipynb
     /notebooks/05_tutorial_nondimensionalization_and_scaling.ipynb
+
+===================
+Turbulence modeling
+===================
+
+.. toctree::
+    :maxdepth: 1
+
     /notebooks/06_tutorial_modifying_method_smagorinsky.ipynb
+
+=================
+Thermal flows
+=================
+
+.. toctree::
+    :maxdepth: 1
+
     /notebooks/07_tutorial_thermal_lbm.ipynb
+    /notebooks/demo_thermalized_lbm.ipynb
+
+=================
+Multiphase flows
+=================
+
+.. toctree::
+    :maxdepth: 1
+
     /notebooks/08_tutorial_shanchen_twophase.ipynb
     /notebooks/09_tutorial_shanchen_twocomponent.ipynb
     /notebooks/10_tutorial_conservative_allen_cahn_two_phase.ipynb
+
+========================
+Thermocapillary flows
+========================
+
+.. toctree::
+    :maxdepth: 1
+
+    /notebooks/12_Thermocapillary_flows_heated_channel.ipynb
+    /notebooks/13_Thermocapillary_flows_droplet_motion.ipynb
+
+===================
+Non Newtonian flow
+===================
+
+.. toctree::
+    :maxdepth: 1
+
     /notebooks/11_tutorial_Non_Newtonian_Flow.ipynb
+
+=================
+Diverse
+=================
+
+.. toctree::
+    :maxdepth: 1
+
     /notebooks/demo_stencils.ipynb
     /notebooks/demo_streaming_patterns.ipynb
     /notebooks/demo_create_method_from_scratch.ipynb
     /notebooks/demo_moments_cumulants_and_maxwellian_equilibrium.ipynb
     /notebooks/demo_automatic_chapman_enskog_analysis.ipynb
-    /notebooks/demo_thermalized_lbm.ipynb
+    /notebooks/demo_interpolation_boundary_conditions.ipynb
     /notebooks/demo_shallow_water_lbm.ipynb
     /notebooks/demo_theoretical_background_generic_equilibrium_construction.ipynb

lbmpy/__init__.py

-from .creationfunctions import create_lb_ast, create_lb_collision_rule, create_lb_function,\
-    create_lb_method, create_lb_update_rule, LBMConfig, LBMOptimisation
-from .enums import Stencil, Method, ForceModel, CollisionSpace
-from .lbstep import LatticeBoltzmannStep
-from .macroscopic_value_kernels import pdf_initialization_assignments, macroscopic_values_getter,\
-    compile_macroscopic_values_getter, compile_macroscopic_values_setter, create_advanced_velocity_setter_collision_rule
-from .maxwellian_equilibrium import get_weights
-from .relaxationrates import relaxation_rate_from_lattice_viscosity, lattice_viscosity_from_relaxation_rate,\
-    relaxation_rate_from_magic_number
-from .scenarios import create_lid_driven_cavity, create_fully_periodic_flow
-from .stencils import LBStencil
-
-
-__all__ = ['create_lb_ast', 'create_lb_collision_rule', 'create_lb_function', 'create_lb_method',
-           'create_lb_method_from_existing', 'create_lb_update_rule', 'LBMConfig', 'LBMOptimisation',
-           'Stencil', 'Method', 'ForceModel', 'CollisionSpace',
-           'LatticeBoltzmannStep',
-           'pdf_initialization_assignments', 'macroscopic_values_getter', 'compile_macroscopic_values_getter',
-           'compile_macroscopic_values_setter', 'create_advanced_velocity_setter_collision_rule',
-           'get_weights',
-           'relaxation_rate_from_lattice_viscosity', 'lattice_viscosity_from_relaxation_rate',
-           'relaxation_rate_from_magic_number',
-           'create_lid_driven_cavity', 'create_fully_periodic_flow',
-           'LBStencil']
-
-
-from ._version import get_versions
-__version__ = get_versions()['version']
-del get_versions

lbmpy/boundaries/__init__.py

-from lbmpy.boundaries.boundaryconditions import (
-    UBB, FixedDensity, DiffusionDirichlet, SimpleExtrapolationOutflow,
-    ExtrapolationOutflow, NeumannByCopy, NoSlip, StreamInConstant, FreeSlip)
-from lbmpy.boundaries.boundaryhandling import LatticeBoltzmannBoundaryHandling
-
-__all__ = ['NoSlip', 'FreeSlip', 'UBB', 'SimpleExtrapolationOutflow', 'ExtrapolationOutflow',
-           'FixedDensity', 'DiffusionDirichlet', 'NeumannByCopy',
-           'LatticeBoltzmannBoundaryHandling', 'StreamInConstant']

lbmpy/phasefield_allen_cahn/analytical.py

-
-def analytic_rising_speed(gravitational_acceleration, bubble_diameter, viscosity_gas):
-    r"""
-    Calculated the analytical rising speed of a bubble. This is the expected end rising speed.
-    Args:
-        gravitational_acceleration: the gravitational acceleration acting in the simulation scenario. Usually it gets
-                                    calculated based on dimensionless parameters which describe the scenario
-        bubble_diameter: the diameter of the bubble at the beginning of the simulation
-        viscosity_gas: the viscosity of the fluid inside the bubble
-    """
-    result = -(gravitational_acceleration * bubble_diameter * bubble_diameter) / (12.0 * viscosity_gas)
-    return result

lbmpy/phasefield_allen_cahn/phasefield_simplifications.py

-import sympy as sp
-
-from pystencils.simp import (
-    SimplificationStrategy, apply_to_all_assignments,
-    insert_aliases, insert_zeros, insert_constants)
-
-
-def create_phasefield_simplification_strategy(lb_method):
-    s = SimplificationStrategy()
-    expand = apply_to_all_assignments(sp.expand)
-
-    s.add(expand)
-
-    s.add(insert_zeros)
-    s.add(insert_aliases)
-    s.add(insert_constants)
-    s.add(lambda ac: ac.new_without_unused_subexpressions())
-
-    return s

pyproject.toml

+[project]
+name = "lbmpy"
+description = "Code Generation for Lattice Boltzmann Methods"
+dynamic = ["version"]
+readme = "README.md"
+authors = [
+    { name = "Martin Bauer" },
+    { name = "Markus Holzer" },
+    { name = "Frederik Hennig" },
+    { email = "cs10-codegen@fau.de" },
+]
+license = { file = "COPYING.txt" }
+requires-python = ">=3.10"
+dependencies = ["pystencils>=1.3", "sympy>=1.9,<=1.12.1", "numpy>=1.8.0", "appdirs", "joblib"]
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Framework :: Jupyter",
+    "Topic :: Software Development :: Code Generators",
+    "Topic :: Scientific/Engineering :: Physics",
+    "Intended Audience :: Developers",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: GNU Affero General Public License v3 or later (AGPLv3+)",
+]
+
+[project.urls]
+"Bug Tracker" = "https://i10git.cs.fau.de/pycodegen/lbmpy/-/issues"
+"Documentation" = "https://pycodegen.pages.i10git.cs.fau.de/lbmpy/"
+"Source Code" = "https://i10git.cs.fau.de/pycodegen/lbmpy"
+
+[project.optional-dependencies]
+gpu = ['cupy']
+alltrafos = ['islpy', 'py-cpuinfo']
+bench_db = ['blitzdb', 'pymongo', 'pandas']
+interactive = [
+    'matplotlib',
+    'ipy_table',
+    'imageio',
+    'jupyter',
+    'pyevtk',
+    'rich',
+    'graphviz',
+    'scipy',
+    'scikit-image'
+]
+use_cython = [
+    'Cython'
+]
+doc = [
+    'sphinx',
+    'sphinx_rtd_theme',
+    'nbsphinx',
+    'sphinxcontrib-bibtex',
+    'sphinx_autodoc_typehints',
+    'pandoc',
+]
+tests = [
+    'pytest',
+    'pytest-cov',
+    'pytest-html',
+    'ansi2html',
+    'pytest-xdist',
+    'flake8',
+    'nbformat',
+    'nbconvert',
+    'ipython',
+    'randomgen>=1.18',
+]
+
+[build-system]
+requires = [
+    "setuptools>=69",
+    "versioneer[toml]>=0.29",
+]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools.package-data]
+
+[tool.setuptools.packages.find]
+where = ["src"]
+include = ["lbmpy", "lbmpy.*"]
+namespaces = false
+
+[tool.versioneer]
+# See the docstring in versioneer.py for instructions. Note that you must
+# re-run 'versioneer.py setup' after changing this section, and commit the
+# resulting files.
+VCS = "git"
+style = "pep440"
+versionfile_source = "src/lbmpy/_version.py"
+versionfile_build = "lbmpy/_version.py"
+tag_prefix = "release/"
+parentdir_prefix = "lbmpy-"

pytest.ini

 [pytest]
+testpaths = src tests doc/notebooks
+pythonpath = src
 python_files = test_*.py *_test.py scenario_*.py
 norecursedirs = *.egg-info .git .cache .ipynb_checkpoints htmlcov
 addopts = --doctest-modules --durations=20  --cov-config pytest.ini
 markers =
        longrun: tests only run at night since they have large execution time
-       notebook: jupyter notebooks
+       notebook: mark for notebooks
 # these warnings all come from third party libraries.
 filterwarnings =
        ignore:the imp module is deprecated in favour of importlib:DeprecationWarning
@@ -14,15 +16,16 @@ filterwarnings =
 
 [run]
 branch = True
-source = lbmpy
-         lbmpy_tests
+source = src/lbmpy
+         tests
 
 omit = doc/*
-       lbmpy_tests/*
+       tests/*
        setup.py
        conftest.py
        versioneer.py
-       lbmpy/_version.py
+       src/lbmpy/_version.py
+       venv/
 
 [report]
 exclude_lines =
@@ -35,6 +38,7 @@ exclude_lines =
        # Don't complain if tests don't hit defensive assertion code:
        raise AssertionError
        raise NotImplementedError
+       NotImplementedError()
        #raise ValueError
 
        # Don't complain if non-runnable code isn't run:
@@ -43,7 +47,7 @@ exclude_lines =
        if __name__ == .__main__.:
 
 skip_covered = True
-fail_under = 88
+fail_under = 87
 
 [html]
 directory = coverage_report

quicktest.py

+#!/usr/bin/env python3
+
+from contextlib import redirect_stdout
+import io
+from tests.test_quicktests import (
+    test_poiseuille_channel_quicktest,
+    test_entropic_methods,
+    test_cumulant_ldc
+)
+
+quick_tests = [
+    test_poiseuille_channel_quicktest,
+    test_entropic_methods,
+    test_cumulant_ldc,
+]
+
+if __name__ == "__main__":
+    print("Running lbmpy quicktests")
+    for qt in quick_tests:
+        print(f"   -> {qt.__name__}")
+        with redirect_stdout(io.StringIO()):
+            qt()

setup.cfg

-# See the docstring in versioneer.py for instructions. Note that you must
-# re-run 'versioneer.py setup' after changing this section, and commit the
-# resulting files.
-
-[versioneer]
-VCS = git
-style = pep440
-versionfile_source = lbmpy/_version.py
-versionfile_build = lbmpy/_version.py
-tag_prefix = release/
-parentdir_prefix = lbmpy-
\ No newline at end of file

setup.py

-import os
-import io
-from setuptools import setup, find_packages
-import distutils
-from contextlib import redirect_stdout
-from importlib import import_module
+from setuptools import setup, __version__ as setuptools_version
 
-import versioneer
-
-try:
-    import cython  # noqa
-
-    USE_CYTHON = True
-except ImportError:
-    USE_CYTHON = False
-
-quick_tests = [
-    'test_quicktests.test_poiseuille_channel_quicktest',
-    'test_quicktests.test_entropic_methods',
-    'test_quicktests.test_cumulant_ldc',
-]
-
-
-class SimpleTestRunner(distutils.cmd.Command):
-    """A custom command to run selected tests"""
-
-    description = 'run some quick tests'
-    user_options = []
-
-    @staticmethod
-    def _run_tests_in_module(test):
-        """Short test runner function - to work also if py.test is not installed."""
-        test = 'lbmpy_tests.' + test
-        mod, function_name = test.rsplit('.', 1)
-        if isinstance(mod, str):
-            mod = import_module(mod)
+if int(setuptools_version.split('.')[0]) < 61:
+    raise Exception(
+        "[ERROR] lbmpy requires at least setuptools version 61 to install.\n"
+        "If this error occurs during an installation via pip, it is likely that there is a conflict between "
+        "versions of setuptools installed by pip and the system package manager. "
+        "In this case, it is recommended to install lbmpy into a virtual environment instead."
+    )
 
-        func = getattr(mod, function_name)
-        with redirect_stdout(io.StringIO()):
-            func()
-
-    def initialize_options(self):
-        pass
-
-    def finalize_options(self):
-        pass
-
-    def run(self):
-        """Run command."""
-        for test in quick_tests:
-            self._run_tests_in_module(test)
-
-
-def readme():
-    with open('README.md') as f:
-        return f.read()
-
-
-def cython_extensions(*extensions):
-    from distutils.extension import Extension
-    if USE_CYTHON:
-        ext = '.pyx'
-        result = [Extension(e, [os.path.join(*e.split(".")) + ext]) for e in extensions]
-        from Cython.Build import cythonize
-        result = cythonize(result, language_level=3)
-        return result
-    elif all([os.path.exists(os.path.join(*e.split(".")) + '.c') for e in extensions]):
-        ext = '.c'
-        result = [Extension(e, [os.path.join(*e.split(".")) + ext]) for e in extensions]
-        return result
-    else:
-        return None
+import versioneer
 
 
 def get_cmdclass():
-    cmdclass = {"quicktest": SimpleTestRunner}
-    cmdclass.update(versioneer.get_cmdclass())
-    return cmdclass
+    return versioneer.get_cmdclass()
 
 
-major_version = versioneer.get_version().split("+")[0]
-setup(name='lbmpy',
-      version=versioneer.get_version(),
-      description='Code Generation for Lattice Boltzmann Methods',
-      long_description=readme(),
-      long_description_content_type="text/markdown",
-      author='Martin Bauer, Markus Holzer, Frederik Hennig',
-      license='AGPLv3',
-      author_email='cs10-codegen@fau.de',
-      url='https://i10git.cs.fau.de/pycodegen/lbmpy/',
-      packages=['lbmpy'] + ['lbmpy.' + s for s in find_packages('lbmpy')],
-      install_requires=[f'pystencils>=0.4.0,<={major_version}', 'sympy>=1.5.1,<=1.11.1', 'numpy>=1.11.0'],
-      package_data={'lbmpy': ['phasefield/simplex_projection.pyx', 'phasefield/simplex_projection.c']},
-      ext_modules=cython_extensions("lbmpy.phasefield.simplex_projection"),
-      classifiers=[
-          'Development Status :: 4 - Beta',
-          'Framework :: Jupyter',
-          'Topic :: Software Development :: Code Generators',
-          'Topic :: Scientific/Engineering :: Physics',
-          'Intended Audience :: Developers',
-          'Intended Audience :: Science/Research',
-          'License :: OSI Approved :: GNU Affero General Public License v3 or later (AGPLv3+)',
-      ],
-      python_requires=">=3.8",
-      extras_require={
-          'gpu': ['pycuda'],
-          'opencl': ['pyopencl'],
-          'alltrafos': ['islpy', 'py-cpuinfo'],
-          'interactive': ['scipy', 'scikit-image', 'cython', 'matplotlib',
-                          'ipy_table', 'imageio', 'jupyter', 'pyevtk'],
-          'doc': ['sphinx', 'sphinx_rtd_theme', 'nbsphinx',
-                  'sphinxcontrib-bibtex', 'sphinx_autodoc_typehints', 'pandoc'],
-          'phasefield': ['Cython']
-      },
-      cmdclass=get_cmdclass()
-      )
+setup(
+    version=versioneer.get_version(),
+    cmdclass=get_cmdclass(),
+)