doc/sphinx/api.rst

@@ -5,14 +5,13 @@ API Reference
    :maxdepth: 1
 
    scenarios.rst
-   kernelcreation.rst
-   methodcreation.rst
+   enums.rst
    stencils.rst
-   methods.rst
+   kernelcreation.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/enums.rst

+************
+Enumerations
+************
+
+.. automodule:: lbmpy.enums
+   :members:

doc/sphinx/equilibrium.rst

+*********************************************
+Equilibrium Distributions (lbmpy.equilibrium)
+*********************************************
+
+.. automodule:: lbmpy.equilibrium
+
+
+Abstract Base Class
+===================
+
+.. autoclass:: lbmpy.equilibrium.AbstractEquilibrium
+    :members:
+    :private-members: _monomial_raw_moment, _monomial_central_moment, _monomial_cumulant
+
+Generic Discrete Equilibria
+===========================
+
+Use the following class for custom discrete equilibria.
+
+.. autoclass:: lbmpy.equilibrium.GenericDiscreteEquilibrium
+    :members:
+
+Maxwellian Equilibria for Hydrodynamics
+=======================================
+
+The following classes represent the continuous and the discrete variant of the Maxwellian equilibrium for
+hydrodynamics.
+
+.. autoclass:: lbmpy.equilibrium.ContinuousHydrodynamicMaxwellian
+    :members:
+
+.. autoclass:: lbmpy.equilibrium.DiscreteHydrodynamicMaxwellian
+    :members:

doc/sphinx/lbmpy.bib

@@ -6,7 +6,8 @@
   number={4},
   pages={043309},
   year={2015},
-  publisher={APS}
+  publisher={APS},
+  doi={10.1103/PhysRevE.92.043309},
 }
 
 @PHDTHESIS{luo1993lattice,
@@ -16,7 +17,7 @@
    school = {GEORGIA INSTITUTE OF TECHNOLOGY.},
      year = 1993,
    adsurl = {http://adsabs.harvard.edu/abs/1993PhDT.......233L},
-  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+  adsnote = {Provided by the SAO/NASA Astrophysics Data System},
 }
 
 @Article{guo2002discrete,
@@ -28,8 +29,24 @@
   number    = {4},
   pages     = {046308},
   publisher = {APS},
+  doi = {10.1103/PhysRevE.65.046308},
 }
 
+@article{HeForce,
+  title = {Discrete Boltzmann equation model for nonideal gases},
+  author = {He, Xiaoyi and Shan, Xiaowen and Doolen, Gary D.},
+  journal = {Physical Review E},
+  volume = {57},
+  issue = {1},
+  pages = {R13--R16},
+  numpages = {0},
+  year = {1998},
+  month = {1},
+  publisher = {APS},
+  doi = {10.1103/PhysRevE.57.R13}
+}
+
+
 @article{buick2000gravity,
   title={Gravity in a lattice Boltzmann model},
   author={Buick, JM and Greated, CA},
@@ -38,7 +55,8 @@
   number={5},
   pages={5307},
   year={2000},
-  publisher={APS}
+  publisher={APS},
+  doi = {10.1103/PhysRevE.61.5307},
 }
 
 @phdthesis{schiller2008thermal,
@@ -67,35 +85,62 @@ year = {2018}
 
 
 @article{Semprebon2016,
-author = {Semprebon, Ciro and Kusumaatmaja, Halim},
-doi = {10.1103/PhysRevE.93.033305},
-keywords = {lbm,multiphase,phasefield},
-mendeley-tags = {lbm,multiphase,phasefield},
-pages = {1--11},
-title = {{Ternary free-energy lattice Boltzmann model with tunable surface tensions and contact angles}},
-volume = {033305},
-year = {2016}
+  title = {Ternary free-energy lattice Boltzmann model with tunable surface tensions and contact angles},
+  author = {Semprebon, Ciro and Kr\"uger, Timm and Kusumaatmaja, Halim},
+  journal = {Phys. Rev. E},
+  volume = {93},
+  issue = {3},
+  pages = {033305},
+  numpages = {11},
+  year = {2016},
+  month = {Mar},
+  publisher = {American Physical Society},
+  doi = {10.1103/PhysRevE.93.033305},
 }
 
 @article{geier2015,
 author = {Geier, Martin and Sch{\"{o}}nherr, Martin and Pasquali, Andrea and Krafczyk, Manfred},
 title = {{The cumulant lattice Boltzmann equation in three dimensions: Theory and validation}},
 journal = {Computers \& Mathematics with Applications},
+volume = {70},
+number = {4},
+pages = {507-547},
 year = {2015},
-doi = {10.1016/j.camwa.2015.05.001}
+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,
-  author    = {Christophe Coreixas and Bastien Chopard and Jonas Latt},
-  journal   = {Physical Review E},
-  title     = {Comprehensive comparison of collision models in the lattice Boltzmann framework: Theoretical investigations},
-  year      = {2019},
-  month     = {sep},
-  number    = {3},
-  pages     = {033305},
-  volume    = {100},
-  doi       = {10.1103/physreve.100.033305},
-  publisher = {American Physical Society ({APS})},
+  title = {Comprehensive comparison of collision models in the lattice Boltzmann framework: Theoretical investigations},
+  author = {Coreixas, Christophe and Chopard, Bastien and Latt, Jonas},
+  journal = {Phys. Rev. E},
+  volume = {100},
+  issue = {3},
+  pages = {033305},
+  numpages = {46},
+  year = {2019},
+  month = {Sep},
+  publisher = {American Physical Society},
+  doi = {10.1103/PhysRevE.100.033305},
+  url = {https://link.aps.org/doi/10.1103/PhysRevE.100.033305}
 }
 
 @PhdThesis{Geier2006,
@@ -104,3 +149,169 @@ doi = {10.1016/j.camwa.2015.05.001}
   title  = {Ab inito derivation of the cascaded lattice Boltzmann automaton},
   year   = {2006},
 }
+
+@article{Fakhari2018,
+title = {A phase-field lattice {Boltzmann} model for simulating multiphase flows in porous media: Application and comparison to experiments of {CO2} sequestration at pore scale},
+journal = {Advances in Water Resources},
+volume = {114},
+pages = {119-134},
+year = {2018},
+issn = {0309-1708},
+doi = {10.1016/j.advwatres.2018.02.005},
+author = {Fakhari, A. and Li, Y. and Bolster, D. and Christensen, K. T.},
+}
+
+@article{silva2010,
+title = {A study on the inclusion of body forces in the lattice Boltzmann BGK equation to recover steady-state hydrodynamics},
+journal = {Physica A: Statistical Mechanics and its Applications},
+volume = {390},
+number = {6},
+pages = {1085-1095},
+year = {2011},
+doi = {10.1016/j.physa.2010.11.037},
+author = {Silva, G. and Semiao, V.},
+keywords = {{Lattice Boltzmann} method, {BGK} collision operator, Steady-state flows, Body force driven flows}
+}
+
+@article{silva2020,
+  title = {Force methods for the two-relaxation-times lattice {Boltzmann}},
+  author = {Postma, B. and Silva, G.},
+  journal = {Phys. Rev. E},
+  volume = {102},
+  issue = {6},
+  year = {2020},
+  month = {12},
+  publisher = {American Physical Society},
+  doi = {10.1103/PhysRevE.102.063307},
+}
+
+@book{lbm_book,
+  doi = {10.1007/978-3-319-44649-3},
+  year = {2017},
+  publisher = {Springer International Publishing},
+  author = {Kr\"{u}ger, T. and Kusumaatmaja, H. and Kuzmin, A. and Shardt, O. and Silva, G. and Viggen, E. M.},
+  title = {The Lattice {Boltzmann} Method}
+}
+
+@article{Ansumali2003,
+	doi = {10.1209/epl/i2003-00496-6},
+	year = 2003,
+	month = {sep},
+	journal = {{IOP} Publishing},
+	volume = {63},
+	number = {6},
+	pages = {798--804},
+	author = {S Ansumali and I. V Karlin and H. C Öttinger},
+	title = {Minimal entropic kinetic models for hydrodynamics},
+	abstract = {We derive minimal discrete models of the Boltzmann equation consistent with equilibrium thermodynamics, and which recover correct hydrodynamics in arbitrary dimensions. A new discrete velocity model is proposed for the simulation of the Navier-Stokes-Fourier equation and is tested in the setup of Taylor vortex flow. A simple analytical procedure for constructing the equilibrium for thermal hydrodynamics is established. For the lattice Boltzmann method of isothermal hydrodynamics, the explicit analytical form of the equilibrium distribution is presented. This results in an entropic version of the isothermal lattice Boltzmann method with the simplicity and computational efficiency of the standard lattice Boltzmann model.}
+}
+
+@Article{raw_moments,
+  author  = {D. D'Humières},
+  journal = {Rarefied gas dynamics},
+  title   = {Generalized lattice-{Boltzmann} equations},
+  year    = {1992},
+}
+
+@article{FAKHARI201722,
+    author = "Abbas Fakhari and Diogo Bolster and Li-Shi Luo",
+    title = "A weighted multiple-relaxation-time lattice {Boltzmann} method for multiphase flows and its application to partial coalescence cascades",
+    journal = "Journal of Computational Physics",
+    year = "2017",
+    doi = "10.1016/j.jcp.2017.03.062"
+}
+
+@article{TRT,
+author = {Ginzburg Irina and Frederik Verhaeghe and D. D'Humières},
+year = {2008},
+month = {01},
+pages = {427-478},
+title = {Two-relaxation-time Lattice Boltzmann scheme: about parametrization, velocity, pressure and mixed boundary conditions},
+volume = {3},
+journal = {Communications in Computational Physics}
+}
+
+@Article{HeIncompressible,
+  author    = {Xiaoyi He and Li-Shi Luo},
+  journal   = {Journal of Statistical Physics},
+  title     = {Lattice Boltzmann Model for the Incompressible Navier{\textendash}Stokes Equation},
+  year      = {1997},
+  month     = {aug},
+  number    = {3/4},
+  pages     = {927--944},
+  volume    = {88},
+  doi       = {10.1023/b:joss.0000015179.12689.e4},
+  publisher = {Springer Science and Business Media {LLC}},
+}
+
+@Article{GruszczynskiCascadedPhaseFieldModel,
+  author    = {G. Gruszczy{\'{n}}ski and T. Mitchell and C. Leonardi and {\L}. {\L}aniewski-Wo{\l}{\l}k and T. Barber},
+  journal   = {Computers {\&} Mathematics with Applications},
+  title     = {A cascaded phase-field lattice Boltzmann model for the simulation of incompressible, immiscible fluids with high density contrast},
+  year      = {2020},
+  month     = {feb},
+  number    = {4},
+  pages     = {1049--1071},
+  volume    = {79},
+  doi       = {10.1016/j.camwa.2019.08.018},
+  publisher = {Elsevier {BV}},
+}
+
+@Article{Casson,
+  author    = {R. Ouared and B. Chopard},
+  journal   = {Journal of Statistical Physics},
+  title     = {Lattice {Boltzmann} Simulations of Blood Flow: {Non-Newtonian} Rheology and Clotting Processes},
+  year      = {2005},
+  doi       = {10.1007/s10955-005-8415-x},
+  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/maxwellian_equilibrium.rst

-**********************
-Maxwellian Equilibrium
-**********************
+*******************************
+Maxwellian Equilibrium (Legacy)
+*******************************
 
 .. automodule:: lbmpy.maxwellian_equilibrium
     :members:
@@ -11,7 +11,7 @@ Maxwellian Equilibrium
 
     .. autofunction:: lbmpy.maxwellian_equilibrium.continuous_maxwellian_equilibrium
 
-    .. autofunction:: lbmpy.maxwellian_equilibrium.get_moments_of_continuous_maxwellian_equilibrium
+    .. autofunction:: lbmpy.maxwellian_equilibrium.get_equilibrium_values_of_maxwell_boltzmann_function
 
     .. autofunction:: lbmpy.maxwellian_equilibrium.get_moments_of_discrete_maxwellian_equilibrium
 

doc/sphinx/methodcreation.rst

-Creating LBM methods
-====================
-
-This module is a lower level API to construct methods.
-When possible use the high level API.
-
-.. automodule:: lbmpy.methods.creationfunctions
-    :members:

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
 
@@ -13,13 +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

doc/sphinx/zbibliography.rst

@@ -2,4 +2,4 @@ Bibliography
 ------------
 
 .. bibliography:: lbmpy.bib
-   :cited:
\ No newline at end of file
+   :all:
\ No newline at end of file

doc/version_from_git.py

-import subprocess
-from distutils.version import StrictVersion
-
-
-def version_number_from_git(tag_prefix='release/', sha_length=10, version_format="{version}.dev{commits}+{sha}"):
-    def get_released_versions():
-        tags = sorted(subprocess.getoutput('git tag').split('\n'))
-        versions = [t[len(tag_prefix):] for t in tags if t.startswith(tag_prefix)]
-        return versions
-
-    def tag_from_version(v):
-        return tag_prefix + v
-
-    def increment_version(v):
-        parsed_version = [int(i) for i in v.split('.')]
-        parsed_version[-1] += 1
-        return '.'.join(str(i) for i in parsed_version)
-
-    version_strings = get_released_versions()
-    version_strings.sort(key=StrictVersion)
-    latest_release = version_strings[-1]
-    commits_since_tag = subprocess.getoutput('git rev-list {}..HEAD --count'.format(tag_from_version(latest_release)))
-    sha = subprocess.getoutput('git rev-parse HEAD')[:sha_length]
-    is_dirty = len(subprocess.getoutput("git status --untracked-files=no -s")) > 0
-
-    if int(commits_since_tag) == 0:
-        version_string = latest_release
-    else:
-        next_version = increment_version(latest_release)
-        version_string = version_format.format(version=next_version, commits=commits_since_tag, sha=sha)
-
-    if is_dirty:
-        version_string += ".dirty"
-    return version_string

lbmpy/__init__.py

-def _get_release_file():
-    import os.path
-    file_path = os.path.abspath(os.path.dirname(__file__))
-    return os.path.join(file_path, '..', 'RELEASE-VERSION')
-
-
-try:
-    __version__ = open(_get_release_file(), 'r').read()
-except IOError:
-    __version__ = 'development'

lbmpy/boundaries/__init__.py

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

lbmpy/methods/__init__.py

-from lbmpy.methods.creationfunctions import (
-    create_mrt_orthogonal, create_mrt_raw, create_srt, create_trt, create_trt_kbc,
-    create_trt_with_magic_number, create_with_continuous_maxwellian_eq_moments,
-    create_with_discrete_maxwellian_eq_moments, mrt_orthogonal_modes_literature,
-    create_centered_cumulant_model, create_with_default_polynomial_cumulants)
-
-from lbmpy.methods.abstractlbmethod import AbstractLbMethod, RelaxationInfo
-from lbmpy.methods.conservedquantitycomputation import AbstractConservedQuantityComputation
-
-from .conservedquantitycomputation import DensityVelocityComputation
-
-__all__ = ['RelaxationInfo', 'AbstractLbMethod',
-           'AbstractConservedQuantityComputation', 'DensityVelocityComputation',
-           'create_srt', 'create_trt', 'create_trt_with_magic_number', 'create_trt_kbc',
-           'create_mrt_orthogonal', 'create_mrt_raw',
-           'create_with_continuous_maxwellian_eq_moments', 'create_with_discrete_maxwellian_eq_moments',
-           'mrt_orthogonal_modes_literature', 'create_centered_cumulant_model',
-           'create_with_default_polynomial_cumulants']