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,<=1.10.1', '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(),
+)

src/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, SubgridScaleModel
+from .lbstep import LatticeBoltzmannStep
+from .macroscopic_value_kernels import (
+    pdf_initialization_assignments,
+    macroscopic_values_getter,
+    strain_rate_tensor_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_update_rule",
+    "LBMConfig",
+    "LBMOptimisation",
+    "Stencil",
+    "Method",
+    "ForceModel",
+    "CollisionSpace",
+    "SubgridScaleModel",
+    "LatticeBoltzmannStep",
+    "pdf_initialization_assignments",
+    "macroscopic_values_getter",
+    "strain_rate_tensor_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 . import _version
+__version__ = _version.get_versions()['version']

lbmpy/advanced_streaming/__init__.py → src/lbmpy/advanced_streaming/__init__.py

-from .indexing import BetweenTimestepsIndexing, NeighbourOffsetArrays
+from .indexing import BetweenTimestepsIndexing
 from .communication import get_communication_slices, LBMPeriodicityHandling
 from .utility import Timestep, get_accessor, is_inplace, get_timesteps, \
     numeric_index, numeric_offsets, inverse_dir_index, AccessPdfValues
 
-__all__ = ['BetweenTimestepsIndexing', 'NeighbourOffsetArrays',
+__all__ = ['BetweenTimestepsIndexing',
            'get_communication_slices', 'LBMPeriodicityHandling',
            'Timestep', 'get_accessor', 'is_inplace', 'get_timesteps',
            'numeric_index', 'numeric_offsets', 'inverse_dir_index', 'AccessPdfValues']

lbmpy/advanced_streaming/communication.py → src/lbmpy/advanced_streaming/communication.py

 import itertools
-from pystencils import Field, Assignment
-from pystencils.slicing import shift_slice, get_slice_before_ghost_layer, normalize_slice
-from lbmpy.advanced_streaming.utility import is_inplace, get_accessor, numeric_index, \
-    numeric_offsets, Timestep, get_timesteps
+from pystencils import CreateKernelConfig, Field, Assignment, AssignmentCollection
+from pystencils.slicing import (
+    shift_slice,
+    get_slice_before_ghost_layer,
+    normalize_slice,
+)
+from lbmpy.advanced_streaming.utility import (
+    is_inplace,
+    get_accessor,
+    numeric_index,
+    Timestep,
+    get_timesteps,
+    numeric_offsets,
+)
 from pystencils.datahandling import SerialDataHandling
 from pystencils.enums import Target
 from itertools import chain
 
 
-def _trim_slice_in_direction(slices, direction):
-    assert len(slices) == len(direction)
+class LBMPeriodicityHandling:
 
-    result = []
-    for s, d in zip(slices, direction):
-        if isinstance(s, int):
-            result.append(s)
-            continue
-        start = s.start + 1 if d == -1 else s.start
-        stop = s.stop - 1 if d == 1 else s.stop
-        result.append(slice(start, stop, s.step))
+    def __init__(
+        self,
+        stencil,
+        data_handling,
+        pdf_field_name,
+        streaming_pattern="pull",
+        ghost_layers=1,
+        cupy_direct_copy=True,
+    ):
+        """
+        Periodicity Handling for Lattice Boltzmann Streaming.
+
+        **On the usage with cuda:**
+        - cupy allows the copying of sliced arrays within device memory using the numpy syntax,
+        e.g. `dst[:,0] = src[:,-1]`. In this implementation, this is the default for periodicity
+        handling. Alternatively, if you set `cupy_direct_copy=False`, GPU kernels are generated and
+        compiled. The compiled kernels are almost twice as fast in execution as cupy array copying,
+        but especially for large stencils like D3Q27, their compilation can take up to 20 seconds.
+        Choose your weapon depending on your use case.
+        """
+        if not isinstance(data_handling, SerialDataHandling):
+            raise ValueError("Only serial data handling is supported!")
 
-    return tuple(result)
+        self.stencil = stencil
+        self.dim = stencil.D
+        self.dh = data_handling
 
+        assert data_handling.default_target in [Target.CPU, Target.GPU]
+        self.target = data_handling.default_target
 
-def _extend_dir(direction):
-    if len(direction) == 0:
-        yield tuple()
-    elif direction[0] == 0:
-        for d in [-1, 0, 1]:
-            for rest in _extend_dir(direction[1:]):
-                yield (d, ) + rest
-    else:
-        for rest in _extend_dir(direction[1:]):
-            yield (direction[0], ) + rest
+        self.pdf_field_name = pdf_field_name
+        self.ghost_layers = ghost_layers
+        self.periodicity = data_handling.periodicity
+        self.inplace_pattern = is_inplace(streaming_pattern)
 
+        self.cpu = self.target == Target.CPU
+        self.cupy_direct_copy = self.target == Target.GPU and cupy_direct_copy
 
-def _get_neighbour_transform(direction, ghost_layers):
-    return tuple(d * (ghost_layers + 1) for d in direction)
+        def is_copy_direction(direction):
+            s = 0
+            for d, p in zip(direction, self.periodicity):
+                s += abs(d)
+                if d != 0 and not p:
+                    return False
 
+            return s != 0
 
-def _fix_length_one_slices(slices):
-    """Slices of length one are replaced by their start value for correct periodic shifting"""
-    if isinstance(slices, int):
-        return slices
-    elif isinstance(slices, slice):
-        if slices.stop is not None and abs(slices.start - slices.stop) == 1:
-            return slices.start
-        elif slices.stop is None and slices.start == -1:
-            return -1  # [-1:] also has length one
+        full_stencil = itertools.product(*([-1, 0, 1] for _ in range(self.dim)))
+        copy_directions = tuple(filter(is_copy_direction, full_stencil))
+        self.comm_slices = []
+        timesteps = get_timesteps(streaming_pattern)
+        for timestep in timesteps:
+            slices_per_comm_dir = get_communication_slices(
+                stencil=stencil,
+                comm_stencil=copy_directions,
+                streaming_pattern=streaming_pattern,
+                prev_timestep=timestep,
+                ghost_layers=ghost_layers,
+            )
+            self.comm_slices.append(
+                list(chain.from_iterable(v for k, v in slices_per_comm_dir.items()))
+            )
+
+        if self.target == Target.GPU and not cupy_direct_copy:
+            self.device_copy_kernels = list()
+            for timestep in timesteps:
+                self.device_copy_kernels.append(self._compile_copy_kernels(timestep))
+
+    def __call__(self, prev_timestep=Timestep.BOTH):
+        if self.cpu:
+            self._periodicity_handling_cpu(prev_timestep)
         else:
-            return slices
-    else:
-        return tuple(_fix_length_one_slices(s) for s in slices)
+            self._periodicity_handling_gpu(prev_timestep)
+
+    def _periodicity_handling_cpu(self, prev_timestep):
+        arr = self.dh.cpu_arrays[self.pdf_field_name]
+        comm_slices = self.comm_slices[prev_timestep.idx]
+        for src, dst in comm_slices:
+            arr[dst] = arr[src]
+
+    def _compile_copy_kernels(self, timestep):
+        assert self.target == Target.GPU
+        pdf_field = self.dh.fields[self.pdf_field_name]
+        kernels = []
+        for src, dst in self.comm_slices[timestep.idx]:
+            kernels.append(periodic_pdf_gpu_copy_kernel(pdf_field, src, dst))
+        return kernels
+
+    def _periodicity_handling_gpu(self, prev_timestep):
+        arr = self.dh.gpu_arrays[self.pdf_field_name]
+        if self.cupy_direct_copy:
+            for src, dst in self.comm_slices[prev_timestep.idx]:
+                arr[dst] = arr[src]
+        else:
+            kernel_args = {self.pdf_field_name: arr}
+            for kernel in self.device_copy_kernels[prev_timestep.idx]:
+                kernel(**kernel_args)
 
 
 def get_communication_slices(
-        stencil, comm_stencil=None, streaming_pattern='pull', prev_timestep=Timestep.BOTH, ghost_layers=1):
+    stencil,
+    comm_stencil=None,
+    streaming_pattern="pull",
+    prev_timestep=Timestep.BOTH,
+    ghost_layers=1,
+):
     """
     Return the source and destination slices for periodicity handling or communication between blocks.
 
     :param stencil: The stencil used by the LB method.
-    :param comm_stencil: The stencil defining the communication directions. If None, it will be set to the 
+    :param comm_stencil: The stencil defining the communication directions. If None, it will be set to the
                          full stencil (D2Q9 in 2D, D3Q27 in 3D, etc.).
     :param streaming_pattern: The streaming pattern.
     :param prev_timestep: Timestep after which communication is run.
@@ -71,7 +141,9 @@ def get_communication_slices(
     if comm_stencil is None:
         comm_stencil = itertools.product(*([-1, 0, 1] for _ in range(stencil.D)))
 
-    pdfs = Field.create_generic('pdfs', spatial_dimensions=len(stencil[0]), index_shape=(stencil.Q,))
+    pdfs = Field.create_generic(
+        "pdfs", spatial_dimensions=len(stencil[0]), index_shape=(stencil.Q,)
+    )
     write_accesses = get_accessor(streaming_pattern, prev_timestep).write(pdfs, stencil)
     slices_per_comm_direction = dict()
 
@@ -83,19 +155,27 @@ def get_communication_slices(
 
         for streaming_dir in set(_extend_dir(comm_dir)) & set(stencil):
             d = stencil.index(streaming_dir)
-            write_offsets = numeric_offsets(write_accesses[d])
             write_index = numeric_index(write_accesses[d])[0]
 
+            origin_slice = get_slice_before_ghost_layer(
+                comm_dir, ghost_layers=ghost_layers, thickness=1
+            )
+            src_slice = _fix_length_one_slices(origin_slice)
+
+            write_offsets = numeric_offsets(write_accesses[d])
             tangential_dir = tuple(s - c for s, c in zip(streaming_dir, comm_dir))
-            origin_slice = get_slice_before_ghost_layer(comm_dir, ghost_layers=ghost_layers, thickness=1)
-            origin_slice = _fix_length_one_slices(origin_slice)
-            src_slice = shift_slice(_trim_slice_in_direction(origin_slice, tangential_dir), write_offsets)
+
+            # TODO: this is just a hotfix. _trim_slice_in_direction breaks FreeSlip BC with adjacent periodic side
+            if streaming_pattern != "pull":
+                src_slice = shift_slice(
+                    _trim_slice_in_direction(src_slice, tangential_dir), write_offsets
+                )
 
             neighbour_transform = _get_neighbour_transform(comm_dir, ghost_layers)
             dst_slice = shift_slice(src_slice, neighbour_transform)
 
-            src_slice = src_slice + (write_index, )
-            dst_slice = dst_slice + (write_index, )
+            src_slice = src_slice + (write_index,)
+            dst_slice = dst_slice + (write_index,)
 
             slices_for_dir.append((src_slice, dst_slice))
 
@@ -103,10 +183,10 @@ def get_communication_slices(
     return slices_per_comm_direction
 
 
-def periodic_pdf_copy_kernel(pdf_field, src_slice, dst_slice,
-                             domain_size=None, target=Target.GPU):
-    """Copies a rectangular array slice onto another non-overlapping array slice"""
-    from pystencils.gpucuda.kernelcreation import create_cuda_kernel
+def periodic_pdf_gpu_copy_kernel(pdf_field, src_slice, dst_slice, domain_size=None):
+    """Generate a GPU kernel which copies all values from one slice of a field
+    to another non-overlapping slice."""
+    from pystencils import create_kernel
 
     pdf_idx = src_slice[-1]
     assert isinstance(pdf_idx, int), "PDF index needs to be an integer constant"
@@ -114,6 +194,7 @@ def periodic_pdf_copy_kernel(pdf_field, src_slice, dst_slice,
     src_slice = src_slice[:-1]
     dst_slice = dst_slice[:-1]
 
+    # TODO this is the domain_size with GL
     if domain_size is None:
         domain_size = pdf_field.spatial_shape
 
@@ -126,105 +207,71 @@ def periodic_pdf_copy_kernel(pdf_field, src_slice, dst_slice,
     def _stop(s):
         return s.stop if isinstance(s, slice) else s
 
-    offset = [_start(s1) - _start(s2) for s1, s2 in zip(normalized_from_slice, normalized_to_slice)]
-    assert offset == [_stop(s1) - _stop(s2) for s1, s2 in zip(normalized_from_slice, normalized_to_slice)], \
-        "Slices have to have same size"
+    offset = [
+        _start(s1) - _start(s2)
+        for s1, s2 in zip(normalized_from_slice, normalized_to_slice)
+    ]
+    assert offset == [
+        _stop(s1) - _stop(s2)
+        for s1, s2 in zip(normalized_from_slice, normalized_to_slice)
+    ], "Slices have to have same size"
+
+    copy_eq = AssignmentCollection(
+        main_assignments=[
+            Assignment(pdf_field(pdf_idx), pdf_field[tuple(offset)](pdf_idx))
+        ]
+    )
+    config = CreateKernelConfig(
+        iteration_slice=dst_slice,
+        skip_independence_check=True,
+        target=Target.GPU,
+    )
+
+    ast = create_kernel(copy_eq, config=config)
+    return ast.compile()
 
-    copy_eq = Assignment(pdf_field(pdf_idx), pdf_field[tuple(offset)](pdf_idx))
-    ast = create_cuda_kernel([copy_eq], iteration_slice=dst_slice, skip_independence_check=True)
-    if target == Target.GPU:
-        from pystencils.gpucuda import make_python_function
-        return make_python_function(ast)
-    else:
-        raise ValueError('Invalid target:', target)
-
-
-class LBMPeriodicityHandling:
-
-    def __init__(self, stencil, data_handling, pdf_field_name,
-                 streaming_pattern='pull', ghost_layers=1,
-                 pycuda_direct_copy=True):
-        """
-            Periodicity Handling for Lattice Boltzmann Streaming.
-
-            **On the usage with cuda:**
-            - pycuda allows the copying of sliced arrays within device memory using the numpy syntax,
-            e.g. `dst[:,0] = src[:,-1]`. In this implementation, this is the default for periodicity
-            handling. Alternatively, if you set `pycuda_direct_copy=False`, GPU kernels are generated and
-            compiled. The compiled kernels are almost twice as fast in execution as pycuda array copying,
-            but especially for large stencils like D3Q27, their compilation can take up to 20 seconds. 
-            Choose your weapon depending on your use case.
-        """
-        if not isinstance(data_handling, SerialDataHandling):
-            raise ValueError('Only serial data handling is supported!')
-
-        self.stencil = stencil
-        self.dim = stencil.D
-        self.dh = data_handling
-
-        target = data_handling.default_target
-        assert target in [Target.CPU, Target.GPU]
 
-        self.pdf_field_name = pdf_field_name
-        self.ghost_layers = ghost_layers
-        periodicity = data_handling.periodicity
-        self.inplace_pattern = is_inplace(streaming_pattern)
-        self.target = target
-        self.cpu = target == Target.CPU
-        self.pycuda_direct_copy = target == Target.GPU and pycuda_direct_copy
+def _extend_dir(direction):
+    if len(direction) == 0:
+        yield tuple()
+    elif direction[0] == 0:
+        for d in [-1, 0, 1]:
+            for rest in _extend_dir(direction[1:]):
+                yield (d,) + rest
+    else:
+        for rest in _extend_dir(direction[1:]):
+            yield (direction[0],) + rest
 
-        def is_copy_direction(direction):
-            s = 0
-            for d, p in zip(direction, periodicity):
-                s += abs(d)
-                if d != 0 and not p:
-                    return False
 
-            return s != 0
+def _get_neighbour_transform(direction, ghost_layers):
+    return tuple(d * (ghost_layers + 1) for d in direction)
 
-        full_stencil = itertools.product(*([-1, 0, 1] for _ in range(self.dim)))
-        copy_directions = tuple(filter(is_copy_direction, full_stencil))
-        self.comm_slices = []
-        timesteps = get_timesteps(streaming_pattern)
-        for timestep in timesteps:
-            slices_per_comm_dir = get_communication_slices(stencil=stencil,
-                                                           comm_stencil=copy_directions,
-                                                           streaming_pattern=streaming_pattern,
-                                                           prev_timestep=timestep,
-                                                           ghost_layers=ghost_layers)
-            self.comm_slices.append(list(chain.from_iterable(v for k, v in slices_per_comm_dir.items())))
-
-        if target == Target.GPU and not pycuda_direct_copy:
-            self.device_copy_kernels = []
-            for timestep in timesteps:
-                self.device_copy_kernels.append(self._compile_copy_kernels(timestep))
 
-    def __call__(self, prev_timestep=Timestep.BOTH):
-        if self.cpu:
-            self._periodicity_handling_cpu(prev_timestep)
+def _fix_length_one_slices(slices):
+    """Slices of length one are replaced by their start value for correct periodic shifting"""
+    if isinstance(slices, int):
+        return slices
+    elif isinstance(slices, slice):
+        if slices.stop is not None and abs(slices.start - slices.stop) == 1:
+            return slices.start
+        elif slices.stop is None and slices.start == -1:
+            return -1  # [-1:] also has length one
         else:
-            self._periodicity_handling_gpu(prev_timestep)
+            return slices
+    else:
+        return tuple(_fix_length_one_slices(s) for s in slices)
 
-    def _periodicity_handling_cpu(self, prev_timestep):
-        arr = self.dh.cpu_arrays[self.pdf_field_name]
-        comm_slices = self.comm_slices[prev_timestep.idx]
-        for src, dst in comm_slices:
-            arr[dst] = arr[src]
 
-    def _compile_copy_kernels(self, timestep):
-        pdf_field = self.dh.fields[self.pdf_field_name]
-        kernels = []
-        for src, dst in self.comm_slices[timestep.idx]:
-            kernels.append(
-                periodic_pdf_copy_kernel(pdf_field, src, dst, target=self.target))
-        return kernels
+def _trim_slice_in_direction(slices, direction):
+    assert len(slices) == len(direction)
 
-    def _periodicity_handling_gpu(self, prev_timestep):
-        arr = self.dh.gpu_arrays[self.pdf_field_name]
-        if self.pycuda_direct_copy:
-            for src, dst in self.comm_slices[prev_timestep.idx]:
-                arr[dst] = arr[src]
-        else:
-            kernel_args = {self.pdf_field_name: arr}
-            for kernel in self.device_copy_kernels[prev_timestep.idx]:
-                kernel(**kernel_args)
+    result = []
+    for s, d in zip(slices, direction):
+        if isinstance(s, int):
+            result.append(s)
+            continue
+        start = s.start + 1 if d == -1 else s.start
+        stop = s.stop - 1 if d == 1 else s.stop
+        result.append(slice(start, stop, s.step))
+
+    return tuple(result)

lbmpy/advanced_streaming/indexing.py → src/lbmpy/advanced_streaming/indexing.py

@@ -3,17 +3,12 @@ import sympy as sp
 import pystencils as ps
 
 from pystencils.typing import TypedSymbol, create_type
-from pystencils.backends.cbackend import CustomCodeNode
-
 from lbmpy.advanced_streaming.utility import get_accessor, inverse_dir_index, is_inplace, Timestep
+from lbmpy.custom_code_nodes import TranslationArraysNode
 
 from itertools import product
 
 
-def _array_pattern(dtype, name, content):
-    return f"const {str(dtype)} {name} [] = {{ {','.join(str(c) for c in content)} }}; \n"
-
-
 class BetweenTimestepsIndexing:
 
     #   ==============================================
@@ -30,7 +25,7 @@ class BetweenTimestepsIndexing:
 
     @property
     def inverse_dir_symbol(self):
-        """Symbol denoting the inversion of a PDF field index. 
+        """Symbol denoting the inversion of a PDF field index.
         Use only at top-level of index to f_out or f_in, otherwise it can't be correctly replaced."""
         return sp.IndexedBase('invdir')
 
@@ -168,90 +163,21 @@ class BetweenTimestepsIndexing:
         return trivial_index_translations, trivial_offset_translations
 
     def create_code_node(self):
-        return BetweenTimestepsIndexing.TranslationArraysNode(self)
-
-    class TranslationArraysNode(CustomCodeNode):
-
-        def __init__(self, indexing):
-            code = ''
-            symbols_defined = set()
-
-            for f_dir, inv in indexing._required_index_arrays:
-                indices, offsets = indexing._get_translated_indices_and_offsets(f_dir, inv)
-                index_array_symbol = indexing._index_array_symbol(f_dir, inv)
-                symbols_defined.add(index_array_symbol)
-                code += _array_pattern(indexing._index_dtype, index_array_symbol.name, indices)
-
-            for f_dir, inv in indexing._required_offset_arrays:
-                indices, offsets = indexing._get_translated_indices_and_offsets(f_dir, inv)
-                offset_array_symbols = indexing._offset_array_symbols(f_dir, inv)
-                symbols_defined |= set(offset_array_symbols)
-                for d, arrsymb in enumerate(offset_array_symbols):
-                    code += _array_pattern(indexing._offsets_dtype, arrsymb.name, offsets[d])
-
-            super(BetweenTimestepsIndexing.TranslationArraysNode, self).__init__(
-                code, symbols_read=set(), symbols_defined=symbols_defined)
+        array_content = list()
+        symbols_defined = set()
+        for f_dir, inv in self._required_index_arrays:
+            indices, offsets = self._get_translated_indices_and_offsets(f_dir, inv)
+            index_array_symbol = self._index_array_symbol(f_dir, inv)
+            symbols_defined.add(index_array_symbol)
+            array_content.append((self._index_dtype, index_array_symbol.name, indices))
 
-        def __str__(self):
-            return "Variable PDF Access Translation Arrays"
+        for f_dir, inv in self._required_offset_arrays:
+            indices, offsets = self._get_translated_indices_and_offsets(f_dir, inv)
+            offset_array_symbols = self._offset_array_symbols(f_dir, inv)
+            symbols_defined |= set(offset_array_symbols)
+            for d, arrsymb in enumerate(offset_array_symbols):
+                array_content.append((self._offsets_dtype, arrsymb.name, offsets[d]))
 
-        def __repr__(self):
-            return "Variable PDF Access Translation Arrays"
+        return TranslationArraysNode(array_content, symbols_defined)
 
 #   end class AdvancedStreamingIndexing
-
-
-class NeighbourOffsetArrays(CustomCodeNode):
-
-    @staticmethod
-    def neighbour_offset(dir_idx, stencil):
-        if isinstance(sp.sympify(dir_idx), sp.Integer):
-            return stencil[dir_idx]
-        else:
-            return tuple([sp.IndexedBase(symbol, shape=(1,))[dir_idx]
-                         for symbol in NeighbourOffsetArrays._offset_symbols(len(stencil[0]))])
-
-    @staticmethod
-    def _offset_symbols(dim):
-        return [TypedSymbol(f"neighbour_offset_{d}", create_type(np.int32)) for d in ['x', 'y', 'z'][:dim]]
-
-    def __init__(self, stencil, offsets_dtype=np.int32):
-        offsets_dtype = create_type(offsets_dtype)
-        dim = len(stencil[0])
-
-        array_symbols = NeighbourOffsetArrays._offset_symbols(dim)
-        code = "\n"
-        for i, arrsymb in enumerate(array_symbols):
-            code += _array_pattern(offsets_dtype, arrsymb.name, (d[i] for d in stencil))
-
-        offset_symbols = NeighbourOffsetArrays._offset_symbols(dim)
-        super(NeighbourOffsetArrays, self).__init__(code, symbols_read=set(),
-                                                    symbols_defined=set(offset_symbols))
-
-
-class MirroredStencilDirections(CustomCodeNode):
-
-    @staticmethod
-    def mirror_stencil(direction, mirror_axis):
-        assert mirror_axis <= len(direction), f"only {len(direction)} axis available for mirage"
-        direction = list(direction)
-        direction[mirror_axis] = -direction[mirror_axis]
-
-        return tuple(direction)
-
-    @staticmethod
-    def _mirrored_symbol(mirror_axis):
-        axis = ['x', 'y', 'z']
-        return TypedSymbol(f"{axis[mirror_axis]}_axis_mirrored_stencil_dir", create_type(np.int32))
-
-    def __init__(self, stencil, mirror_axis, dtype=np.int32):
-        offsets_dtype = create_type(dtype)
-
-        mirrored_stencil_symbol = MirroredStencilDirections._mirrored_symbol(mirror_axis)
-        mirrored_directions = [stencil.index(MirroredStencilDirections.mirror_stencil(direction, mirror_axis))
-                               for direction in stencil]
-        code = "\n"
-        code += _array_pattern(offsets_dtype, mirrored_stencil_symbol.name, mirrored_directions)
-
-        super(MirroredStencilDirections, self).__init__(code, symbols_read=set(),
-                                                        symbols_defined={mirrored_stencil_symbol})

lbmpy/advanced_streaming/utility.py → src/lbmpy/advanced_streaming/utility.py

@@ -58,24 +58,27 @@ odd_accessors = {
 }
 
 
+def is_inplace(streaming_pattern):
+    if streaming_pattern not in streaming_patterns:
+        raise ValueError('Invalid streaming pattern', streaming_pattern)
+
+    return streaming_pattern in ['aa', 'esotwist', 'esopull', 'esopush']
+
+
 def get_accessor(streaming_pattern: str, timestep: Timestep) -> PdfFieldAccessor:
     if streaming_pattern not in streaming_patterns:
         raise ValueError(
             "Invalid value of parameter 'streaming_pattern'.", streaming_pattern)
 
+    if is_inplace(streaming_pattern) and (timestep == Timestep.BOTH):
+        raise ValueError(f"Invalid timestep for streaming pattern {streaming_pattern}: {str(timestep)}")
+
     if timestep == Timestep.EVEN:
         return even_accessors[streaming_pattern]
     else:
         return odd_accessors[streaming_pattern]
 
 
-def is_inplace(streaming_pattern):
-    if streaming_pattern not in streaming_patterns:
-        raise ValueError('Invalid streaming pattern', streaming_pattern)
-
-    return streaming_pattern in ['aa', 'esotwist', 'esopull', 'esopush']
-
-
 def get_timesteps(streaming_pattern):
     return (Timestep.EVEN, Timestep.ODD) if is_inplace(streaming_pattern) else (Timestep.BOTH, )
 

src/lbmpy/analytical_solutions.py

+from typing import Union
+from numpy.typing import NDArray
+
+
+def poiseuille_flow(middle_distance: Union[float, NDArray], height,
+                    ext_force_density: float, dyn_visc: float) -> Union[float, NDArray]:
+    """
+    Analytical solution for plane Poiseuille flow.
+
+    Args:
+        middle_distance: Distance to the middle plane of the channel.
+        height: Distance between the boundaries.
+        ext_force_density: Force density on the fluid normal to the boundaries.
+        dyn_visc: dyn_visc
+
+    Returns:
+        A numpy array of the poiseuille profile if middle_distance is given as array otherwise of velocity of
+        the position given with middle_distance
+    """
+    return ext_force_density * 1. / (2 * dyn_visc) * (height**2.0 / 4.0 - middle_distance**2.0)

src/lbmpy/boundaries/__init__.py

+from lbmpy.boundaries.boundaryconditions import (
+    UBB, FixedDensity, DiffusionDirichlet, SimpleExtrapolationOutflow, WallFunctionBounce,
+    ExtrapolationOutflow, NeumannByCopy, NoSlip, NoSlipLinearBouzidi, QuadraticBounceBack, StreamInConstant, FreeSlip)
+from lbmpy.boundaries.boundaryhandling import LatticeBoltzmannBoundaryHandling
+from lbmpy.boundaries.wall_function_models import MoninObukhovSimilarityTheory, LogLaw, MuskerLaw, SpaldingsLaw
+
+__all__ = ['NoSlip', 'NoSlipLinearBouzidi', 'QuadraticBounceBack', 'FreeSlip', 'WallFunctionBounce',
+           'UBB', 'FixedDensity',
+           'SimpleExtrapolationOutflow', 'ExtrapolationOutflow',
+           'DiffusionDirichlet', 'NeumannByCopy', 'StreamInConstant',
+           'LatticeBoltzmannBoundaryHandling',
+           'MoninObukhovSimilarityTheory', 'LogLaw', 'MuskerLaw', 'SpaldingsLaw']

lbmpy/boundaries/boundaries_in_kernel.py → src/lbmpy/boundaries/boundaries_in_kernel.py

 import sympy as sp
 
-from lbmpy.boundaries.boundaryhandling import LbmWeightInfo
 from lbmpy.advanced_streaming.indexing import BetweenTimestepsIndexing
 from lbmpy.advanced_streaming.utility import Timestep, get_accessor
+from lbmpy.custom_code_nodes import LbmWeightInfo
 from pystencils.boundaries.boundaryhandling import BoundaryOffsetInfo
 from pystencils.assignment import Assignment
 from pystencils.astnodes import Block, Conditional, LoopOverCoordinate, SympyAssignment
@@ -67,7 +67,7 @@ def boundary_conditional(boundary, direction, streaming_pattern, prev_timestep,
 
     assignments = []
     for direction_idx in dir_indices:
-        rule = boundary(f_out, f_in, direction_idx, inv_dir, lb_method, index_field=None)
+        rule = boundary(f_out, f_in, direction_idx, inv_dir, lb_method, index_field=None, force_vector=None)
 
         #   rhs: replace f_out by post collision symbols.
         rhs_substitutions = {f_out(i): sym for i, sym in enumerate(lb_method.post_collision_pdf_symbols)}

lbmpy/chapman_enskog/chapman_enskog.py → src/lbmpy/chapman_enskog/chapman_enskog.py

@@ -370,7 +370,7 @@ def take_moments(eqn, pdf_to_moment_name=(('f', '\\Pi'), ('\\Omega f', '\\Upsilo
                 if new_f_index is None:
                     rest *= factor
                 else:
-                    assert not(new_f_index and f_index)
+                    assert not (new_f_index and f_index)
                     f_index = new_f_index
 
         moment_tuple = [0] * len(velocity_terms)