.flake8

+[flake8]
+max-line-length=120
+exclude=src/pystencils/jupyter.py,
+        src/pystencils/plot.py
+        src/pystencils/session.py
+ignore = W293 W503 W291 C901 E741

.gitattributes

+src/pystencils/_version.py export-subst

.gitignore

+__pycache__
+.ipynb_checkpoints
+.coverage*
+*.pyc
+*.vti
+/build
+/dist
+*.egg-info
+.cache
+_build
+/html_doc
+/.idea
+.vscode
+.cache
+_local_tmp
+RELEASE-VERSION
+test-report
+src/pystencils/boundaries/createindexlistcython.c
+src/pystencils/boundaries/createindexlistcython.*.so
+tests/tmp
+tests/var
+tests/kerncraft_inputs/.2d-5pt.c_kerncraft/
+tests/kerncraft_inputs/.3d-7pt.c_kerncraft/
+report.xml
+coverage_report/
+
+
+# macOS
+**/.DS_Store
+*.uuid

.gitlab-ci.yml

+stages:
+  - pretest
+  - test
+  - nightly
+  - docs
+  - deploy
+
+
+# --------------------------  Templates ------------------------------------------------------------------------------------
+
+# Base configuration for jobs meant to run at every commit
+.every-commit:
+  rules:
+    - if: $CI_PIPELINE_SOURCE != "schedule"
+
+# Configuration for jobs meant to run on each commit to pycodegen/pystencils/master
+.every-commit-master:
+  rules:
+    - if: '$CI_PIPELINE_SOURCE != "schedule" && $CI_PROJECT_PATH == "pycodegen/pystencils" && $CI_COMMIT_BRANCH == "master"'
+
+# Base configuration for jobs meant to run at a schedule
+.scheduled:
+  rules:
+    - if: $CI_PIPELINE_SOURCE == "schedule"
+
+# --------------------------  Tests ------------------------------------------------------------------------------------
+
+# Normal test - runs on every commit all but "long run" tests
+tests-and-coverage:
+  stage: pretest
+  extends: .every-commit
+  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full:cupy12.3
+  before_script:
+    - pip install -e .
+  script:
+    - env
+    - pip list
+    - export NUM_CORES=$(nproc --all)
+    - mkdir -p ~/.config/matplotlib
+    - echo "backend:template" > ~/.config/matplotlib/matplotlibrc
+    - mkdir public
+    - pytest -v -n $NUM_CORES --cov-report html --cov-report xml --cov-report term --cov=. -m "not longrun" --html test-report/index.html --junitxml=report.xml
+    - python -m coverage xml
+  tags:
+    - docker
+    - cuda11
+    - AVX
+  coverage: /Total coverage:\s\d+.\d+\%/
+  artifacts:
+    when: always
+    paths:
+      - coverage_report
+      - test-report
+    reports:
+      coverage_report:
+        coverage_format: cobertura
+        path: coverage.xml
+      junit: report.xml
+
+# Normal test with longruns
+tests-and-coverage-with-longrun:
+  stage: test
+  when: manual
+  allow_failure: true
+  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full:cupy12.3
+  before_script:
+    - pip install sympy --upgrade
+    - pip install -e .
+  script:
+    - env
+    - pip list
+    - export NUM_CORES=$(nproc --all)
+    - mkdir -p ~/.config/matplotlib
+    - echo "backend:template" > ~/.config/matplotlib/matplotlibrc
+    - mkdir public
+    - py.test -v -n $NUM_CORES
+  tags:
+    - docker
+    - cuda11
+    - AVX
+
+# pipeline with latest python version
+latest-python:
+  stage: test
+  extends: .every-commit
+  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/latest_python
+  before_script:
+    - pip install -e .
+  script:
+    - env
+    - pip list
+    - pip install -e .
+    - export NUM_CORES=$(nproc --all)
+    - mkdir -p ~/.config/matplotlib
+    - echo "backend:template" > ~/.config/matplotlib/matplotlibrc
+    - mkdir public
+    - py.test -v -n $NUM_CORES -m "not longrun" --junitxml=report.xml
+  tags:
+    - docker
+    - AVX
+  artifacts:
+    when: always
+    reports:
+      junit: report.xml
+
+
+# Minimal tests in windows environment
+#minimal-windows:
+#  stage: test
+#  tags:
+#    - win
+#  script:
+#    - export NUM_CORES=$(nproc --all)
+#    - source /cygdrive/c/Users/build/Miniconda3/Scripts/activate
+#    - source activate pystencils
+#    - pip install joblib
+#    - pip list
+#    - python -c "import numpy"
+#    - py.test -v -m "not (notebook or longrun)"
+
+ubuntu:
+  stage: test
+  extends: .every-commit
+  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/ubuntu
+  before_script:
+    - ln -s /usr/include/locale.h /usr/include/xlocale.h
+    - pip3 install -e .
+  script:
+    - export NUM_CORES=$(nproc --all)
+    - mkdir -p ~/.config/matplotlib
+    - echo "backend:template" > ~/.config/matplotlib/matplotlibrc
+    - sed -i 's/--doctest-modules //g' pytest.ini
+    - env
+    - pip list
+    - pytest -v -n $NUM_CORES -m "not longrun" --junitxml=report.xml
+  tags:
+    - docker
+    - cuda11
+    - AVX
+  artifacts:
+    when: always
+    reports:
+      junit: report.xml
+
+.multiarch_template:
+  stage: test
+  extends: .every-commit
+  allow_failure: true
+  before_script: &multiarch_before_script
+    # - pip3 install -v .
+    - export PYTHONPATH=src
+    - python3 -c "import pystencils as ps; ps.cpu.cpujit.read_config()"
+    - sed -i '/^fail_under.*/d' pytest.ini
+  script:
+    - export NUM_CORES=$(nproc --all)
+    - mkdir -p ~/.config/matplotlib
+    - echo "backend:template" > ~/.config/matplotlib/matplotlibrc
+    - sed -i 's/--doctest-modules //g' pytest.ini
+    - env
+    - pip3 list
+    - python3 -m pytest -v -n $NUM_CORES --cov-report html --cov-report xml --cov=. --junitxml=report.xml tests/test_*vec*.py tests/test_random.py tests/test_half_precision.py
+    - python3 -m coverage xml
+  tags:
+    - docker
+    - AVX
+  artifacts:
+    when: always
+    paths:
+      - coverage_report
+    reports:
+      coverage_report:
+        coverage_format: cobertura
+        path: coverage.xml
+      junit: report.xml
+
+arm64v8:
+  extends: .multiarch_template
+  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/arm64
+  variables:
+    QEMU_CPU: "cortex-a76"
+  before_script:
+    - *multiarch_before_script
+    - sed -i s/march=native/march=armv8-a/g ~/.config/pystencils/config.json
+
+ppc64le:
+  extends: .multiarch_template
+  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/ppc64le
+  before_script:
+    - *multiarch_before_script
+    - sed -i s/mcpu=native/mcpu=power8/g ~/.config/pystencils/config.json
+
+arm64v9:
+  # SVE support is still unreliable in GCC 11 (incorrect code for fixed-width vectors, internal compiler errors).
+  # For half precision Clang is necessary
+  extends: .multiarch_template
+  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/arm64
+  before_script:
+    - *multiarch_before_script
+    - sed -i s/march=native/march=armv9-a+sve2+sme/g ~/.config/pystencils/config.json
+    - sed -i s/g\+\+/clang++/g ~/.config/pystencils/config.json
+
+riscv64:
+  # RISC-V vector extension are currently not supported by GCC.
+  extends: .multiarch_template
+  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/riscv64
+  variables:
+    # explicitly set SIMD as detection requires QEMU >= 8.1
+    PYSTENCILS_SIMD: "rvv"
+    QEMU_CPU: "rv64,v=true,zicboz=true"
+  before_script:
+    - *multiarch_before_script
+    - sed -i 's/march=native/march=rv64imfdvzicboz/g' ~/.config/pystencils/config.json
+    - sed -i s/g\+\+/clang++-15/g ~/.config/pystencils/config.json
+
+minimal-conda:
+  stage: pretest
+  extends: .every-commit
+  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/minimal_conda
+  before_script:
+    - pip install -e .
+  script:
+    - python quicktest.py
+  tags:
+    - docker
+    - cuda
+
+
+minimal-sympy-master:
+  stage: test
+  extends: .every-commit
+  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/minimal_conda
+  before_script:
+    - pip install -e .
+  script:
+    - python -m pip install --upgrade git+https://github.com/sympy/sympy.git
+    - python quicktest.py
+  allow_failure: true
+  tags:
+    - docker
+    - cuda
+
+
+pycodegen-integration:
+  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full
+  stage: test
+  when: manual
+  allow_failure: true
+  script:
+    - git clone https://gitlab-ci-token:${CI_JOB_TOKEN}@i10git.cs.fau.de/pycodegen/pycodegen.git
+    - cd pycodegen
+    - git submodule sync --recursive
+    - git submodule update --init --recursive
+    - git submodule foreach git fetch origin   # compare the latest master version!
+    - git submodule foreach git reset --hard origin/master
+    - cd pystencils
+    - git remote add test $CI_REPOSITORY_URL
+    - git fetch test
+    - git reset --hard $CI_COMMIT_SHA
+    - cd ..
+    - pip install -e pystencils/
+    - pip install -e lbmpy/
+    - cmake --version
+    - ./install_walberla.sh
+    - export NUM_CORES=$(nproc --all)
+    - mkdir -p ~/.config/matplotlib
+    - echo "backend:template" > ~/.config/matplotlib/matplotlibrc
+    - cd pystencils
+    - py.test -v -n $NUM_CORES --junitxml=report.xml .
+    - cd ../lbmpy
+    - py.test -v -n $NUM_CORES --junitxml=report.xml .
+    - cd ../walberla/build/
+    - make -j $NUM_CORES CodegenJacobiCPU CodegenJacobiGPU CodegenPoissonCPU CodegenPoissonGPU MicroBenchmarkGpuLbm LbCodeGenerationExample
+    - make -j $NUM_CORES multiphaseCPU multiphaseGPU FluctuatingMRT FlowAroundSphereCodeGen FieldLayoutAndVectorizationTest GeneratedOutflowBC
+    - cd apps/benchmarks/UniformGridGPU
+    - make -j $NUM_CORES
+    - cd ../UniformGridCPU
+    - make -j $NUM_CORES
+  tags:
+    - docker
+    - cuda11
+    - AVX
+  artifacts:
+    when: always
+    reports:
+      junit: pycodegen/*/report.xml
+
+
+# -------------------- Scheduled Tasks --------------------------------------------------------------------------
+
+
+# Nightly test against the latest (pre-release) version of SymPy published on PyPI
+nightly-sympy:
+  stage: nightly
+  needs: []
+  extends: .scheduled
+  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/latest_python
+  before_script:
+    - pip install -e .
+    - pip install --upgrade --pre sympy
+  script:
+    - env
+    - pip list
+    - export NUM_CORES=$(nproc --all)
+    - mkdir -p ~/.config/matplotlib
+    - echo "backend:template" > ~/.config/matplotlib/matplotlibrc
+    - mkdir public
+    - pytest -v -n $NUM_CORES -m "not longrun" --junitxml=report.xml
+  tags:
+    - docker
+    - AVX
+    - cuda
+  artifacts:
+    when: always
+    reports:
+      junit: report.xml
+
+# -------------------- Linter & Documentation --------------------------------------------------------------------------
+
+
+flake8-lint:
+  stage: pretest
+  extends: .every-commit
+  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full
+  script:
+    - flake8 src/pystencils
+  tags:
+    - docker
+
+
+build-documentation:
+  stage: docs
+  extends: .every-commit
+  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/documentation
+  needs: []
+  before_script:
+    - pip install -e .
+  script:
+    - mkdir html_doc
+    - sphinx-build -b html doc  html_doc
+    - sphinx-build -W -b html doc  html_doc
+  tags:
+    - docker
+  artifacts:
+    paths:
+      - html_doc
+
+
+pages:
+  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full
+  extends: .every-commit-master
+  stage: deploy
+  needs: ["tests-and-coverage", "build-documentation"]
+  script:
+    - ls -l
+    - mv coverage_report html_doc
+    - mv html_doc public  # folder has to be named "public" for gitlab to publish it
+  artifacts:
+    paths:
+      - public
+  tags:
+    - docker

.isort.cfg

+[settings]
+line_length=100
+balanced_wrapping=True
+multi_line_output=4
+known_third_party=sympy

AUTHORS.txt

+
+Contributors:
+-------------
+
+  - Martin Bauer <martin.bauer@fau.de>
+  - Markus Holzer <markus.holzer@fau.de>
+  - Stephan Seitz <stephan.seitz@fau.de>
+  - Michael Kuron <mkuron@icp.uni-stuttgart.de>
+  - Jan Hönig <jan.hoenig@fau.de>
+  - Julian Hammer <julian.hammer@fau.de>
+  - Nils Kohl <nils.kohl@fau.de>
+  - Frederik Hennig <frederik.hennig@fau.de>
+  - Dominik Ernst <dominik.ernst@fau.de>
+  - Christian Godenschwager <christian.godenschwager@fau.de>
+  - Dominik Thoennes <dominik.thoennes@fau.de>

CHANGELOG.md

+# Change Log
+
+## Unreleased
+
+### Removed
+* LLVM backend because it was not used much and not good integrated in pystencils.
+* OpenCL backend because it was not used much and not good integrated in pystencils.

CONTRIBUTING.md

+# Contributing
+
+Contributions to pystencils are always welcome, and they are greatly appreciated!
+A list of open problems can be found [here]( https://i10git.cs.fau.de/pycodegen/pystencils/-/issues).
+Of course, it is also always appreciated to bring own ideas and problems to the community!
+
+
+Please submit all contributions to the official [GitLab repository](https://i10git.cs.fau.de/pycodegen/pystencils) in the form of a Merge Request. Please do not submit git diffs or files containing the changes.
+There also exists a GitHub repository, which is only a mirror to the GitLab repository. Contributions to the GitHub repository are not considered.
+
+`pystencils` is an open-source python package under the license of  AGPL3. Thus we consider the act of contributing to the code by submitting a Merge Request as the "Sign off" or agreement to the AGPL3 license.
+
+You can contribute in many different ways:
+
+## Types of Contributions
+
+### Report Bugs
+
+Report bugs at [https://i10git.cs.fau.de/pycodegen/pystencils/-/issues](https://i10git.cs.fau.de/pycodegen/pystencils/-/issues).
+
+For pystencils, it is often necessary to provide the python and [SymPy](https://www.sympy.org/en/index.html) versions used and hardware information like the
+processor architecture and the compiler version used to compile the generated kernels.
+
+### Fix Issues
+
+Look through the GitLab issues. Different tags are indicating the status of the issues.
+The "bug" tag indicates problems with pystencils, while the "feature" tag shows ideas that should be added in the future.
+
+### Write Documentation
+
+The documentation of pystencils can be found [here](https://pycodegen.pages.i10git.cs.fau.de/pystencils/). Jupyter notebooks are used to provide an
+interactive start to pystencils. It is always appreciated if new document notebooks are provided
+since this helps others a lot.
+
+## Get Started!
+
+Ready to contribute? Here is how to set up `pystencils` for local development.
+
+1. Fork the `pystencils` repo on GitLab.
+2. Clone your fork locally:
+```bash
+    $ git clone https://i10git.cs.fau.de/your-name/pystencils
+```
+3. Install your local copy into a virtualenv. It is also recommended to use anaconda or miniconda to manage the python environments.
+```bash
+    $ mkvirtualenv pystencils
+    $ cd pystencils/
+    $ pip install -e .
+```
+4. Create a branch for local development:
+```bash
+    $ git checkout -b name-of-your-bugfix-or-feature
+```
+   Now you can make your changes locally.
+
+5. When you're done making changes, check that your changes pass flake8 and the
+   tests
+```bash
+    $ flake8 pystencils
+    $ py.test -v -n $NUM_CORES -m "not longrun" .
+   
+```
+
+   To get all packages needed for development, a requirements list can be found [here](https://i10git.cs.fau.de/pycodegen/pycodegen/-/blob/master/conda_environment_dev.yml). This includes flake8 and pytest.
+
+6. Commit your changes and push your branch to GitHub::
+```bash
+    $ git add .
+    $ git commit -m "Your detailed description of your changes."
+    $ git push origin name-of-your-bugfix-or-feature
+```
+7. Submit a Merge Request on GitLab.
+
+## Merge Request Guidelines
+
+Before you submit a Merge Request, check that it meets these guidelines:
+
+1. All functionality that is implemented through this Merge Request should be covered by unit tests. These are implemented in `pystencil_tests`
+2. If the Merge Request adds functionality, the docs should be updated. Put your new functionality into a function with a docstring.
+3. If you have a maintainer status for `pystencils`, you can merge Merge Requests to the master branch. However, every Merge Request needs to be reviewed by another developer. Thus it is not allowed to merge a Merge Request, which is submitted by oneself.
+
+## Tips
+
+To run a subset of tests:
+```bash
+$ py.test my_test.py
+```
\ No newline at end of file

MANIFEST.in

+include AUTHORS.txt
+include CONTRIBUTING.md
+include CHANGELOG.md

README.md

+pystencils
+==========
+
+[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/mabau/pystencils/master?filepath=doc%2Fnotebooks)
+[![Docs](https://img.shields.io/badge/read-the_docs-brightgreen.svg)](https://pycodegen.pages.i10git.cs.fau.de/pystencils)
+[![pypi-package](https://badge.fury.io/py/pystencils.svg)](https://badge.fury.io/py/pystencils)
+[![pipeline status](https://i10git.cs.fau.de/pycodegen/pystencils/badges/master/pipeline.svg)](https://i10git.cs.fau.de/pycodegen/pystencils/commits/master)
+[![coverage report](https://i10git.cs.fau.de/pycodegen/pystencils/badges/master/coverage.svg)](http://pycodegen.pages.i10git.cs.fau.de/pystencils/coverage_report)
+
+Run blazingly fast stencil codes on numpy arrays.
+
+*pystencils* uses sympy to define stencil operations, that can be executed on numpy arrays.
+Exploiting the stencil structure makes *pystencils* run faster than normal numpy code and even as Cython and numba,
+[as demonstrated in this notebook](https://pycodegen.pages.i10git.cs.fau.de/pystencils/notebooks/demo_benchmark.html).
+
+
+Here is a code snippet that computes the average of neighboring cells:
+```python
+import pystencils as ps
+import numpy as np
+
+f, g = ps.fields("f, g : [2D]")
+stencil = ps.Assignment(g[0, 0],
+                       (f[1, 0] + f[-1, 0] + f[0, 1] + f[0, -1]) / 4)
+kernel = ps.create_kernel(stencil).compile()
+
+f_arr = np.random.rand(1000, 1000)
+g_arr = np.empty_like(f_arr)
+kernel(f=f_arr, g=g_arr)
+```
+
+*pystencils* is mostly used for numerical simulations using finite difference or finite volume methods.
+It comes with automatic finite difference discretization for PDEs:
+
+```python
+import pystencils as ps
+import sympy as sp
+
+c, v = ps.fields("c, v(2): [2D]")
+adv_diff_pde = ps.fd.transient(c) - ps.fd.diffusion(c, sp.symbols("D")) + ps.fd.advection(c, v)
+discretize = ps.fd.Discretization2ndOrder(dx=1, dt=0.01)
+discretization = discretize(adv_diff_pde)
+```
+
+Installation
+------------
+
+```bash
+pip install pystencils[interactive]
+```
+
+Without `[interactive]` you get a minimal version with very little dependencies.
+
+All options:
+- `gpu`: use this if an NVIDIA or AMD GPU is available and CUDA or ROCm is installed
+- `alltrafos`: pulls in additional dependencies for loop simplification e.g. libisl
+- `bench_db`: functionality to store benchmark result in object databases
+- `interactive`: installs dependencies to work in Jupyter including image I/O, plotting etc.
+- `doc`: packages to build documentation
+
+Options can be combined e.g.
+```bash
+pip install pystencils[interactive, gpu, doc]
+```
+
+pystencils is also fully compatible with Windows machines. If working with visual studio and cupy makes sure to run example files first to ensure that cupy can find the compiler's executable.
+
+Documentation
+-------------
+
+Read the docs [here](https://pycodegen.pages.i10git.cs.fau.de/pystencils) and
+check out the Jupyter notebooks in `doc/notebooks`. The **Changelog** of pystencils can be found [here](https://i10git.cs.fau.de/pycodegen/pystencils/-/blob/master/CHANGELOG.md).
+
+Authors
+-------
+
+Many thanks go to the [contributors](https://i10git.cs.fau.de/pycodegen/pystencils/-/blob/master/AUTHORS.txt) of pystencils.
+
+### Please cite us
+
+If you use pystencils in a publication, please cite the following articles:
+
+Overview:
+  - M. Bauer et al, Code Generation for Massively Parallel Phase-Field Simulations. Association for Computing Machinery, 2019. https://doi.org/10.1145/3295500.3356186
+
+Performance Modelling:
+  - D. Ernst et al, Analytical performance estimation during code generation on modern GPUs. Journal of Parallel and Distributed Computing, 2023. https://doi.org/10.1016/j.jpdc.2022.11.003

assignment_collection/nestedscopes.py

-class NestedScopes:
-    """Symbol visibility model using nested scopes
-
-    - every accessed symbol that was not defined before, is added as a "free parameter"
-    - free parameters are global, i.e. they are not in scopes
-    - push/pop adds or removes a scope
-
-    >>> s = NestedScopes()
-    >>> s.access_symbol("a")
-    >>> s.is_defined("a")
-    False
-    >>> s.free_parameters
-    {'a'}
-    >>> s.define_symbol("b")
-    >>> s.is_defined("b")
-    True
-    >>> s.push()
-    >>> s.is_defined_locally("b")
-    False
-    >>> s.define_symbol("c")
-    >>> s.pop()
-    >>> s.is_defined("c")
-    False
-    """
-
-    def __init__(self):
-        self.free_parameters = set()
-        self._defined = [set()]
-
-    def access_symbol(self, symbol):
-        if not self.is_defined(symbol):
-            self.free_parameters.add(symbol)
-
-    def define_symbol(self, symbol):
-        self._defined[-1].add(symbol)
-
-    def is_defined(self, symbol):
-        return any(symbol in scopes for scopes in self._defined)
-
-    def is_defined_locally(self, symbol):
-        return symbol in self._defined[-1]
-
-    def push(self):
-        self._defined.append(set())
-
-    def pop(self):
-        self._defined.pop()
-        assert self.depth >= 1
-
-    @property
-    def depth(self):
-        return len(self._defined)

backends/cbackend.py

-import sympy as sp
-from collections import namedtuple
-from sympy.core import S
-from typing import Set
-from sympy.printing.ccode import C89CodePrinter
-try:
-    from sympy.printing.ccode import C99CodePrinter as CCodePrinter
-except ImportError:
-    from sympy.printing.ccode import CCodePrinter  # for sympy versions < 1.1
-
-from pystencils.integer_functions import bitwise_xor, bit_shift_right, bit_shift_left, bitwise_and, \
-    bitwise_or, modulo_ceil
-from pystencils.astnodes import Node, KernelFunction
-from pystencils.data_types import create_type, PointerType, get_type_of_expression, VectorType, cast_func, \
-    vector_memory_access
-
-__all__ = ['generate_c', 'CustomCppCode', 'PrintNode', 'get_headers', 'CustomSympyPrinter']
-
-
-def generate_c(ast_node: Node, signature_only: bool = False) -> str:
-    """Prints an abstract syntax tree node as C or CUDA code.
-
-    This function does not need to distinguish between C, C++ or CUDA code, it just prints 'C-like' code as encoded
-    in the abstract syntax tree (AST). The AST is built differently for C or CUDA by calling different create_kernel
-    functions.
-
-    Args:
-        ast_node:
-        signature_only:
-
-    Returns:
-        C-like code for the ast node and its descendants
-    """
-    printer = CBackend(signature_only=signature_only,
-                       vector_instruction_set=ast_node.instruction_set)
-    return printer(ast_node)
-
-
-def get_headers(ast_node: Node) -> Set[str]:
-    """Return a set of header files, necessary to compile the printed C-like code."""
-    headers = set()
-
-    if isinstance(ast_node, KernelFunction) and ast_node.instruction_set:
-        headers.update(ast_node.instruction_set['headers'])
-
-    if hasattr(ast_node, 'headers'):
-        headers.update(ast_node.headers)
-    for a in ast_node.args:
-        if isinstance(a, Node):
-            headers.update(get_headers(a))
-
-    return headers
-
-
-# --------------------------------------- Backend Specific Nodes -------------------------------------------------------
-
-
-class CustomCppCode(Node):
-    def __init__(self, code, symbols_read, symbols_defined, parent=None):
-        super(CustomCppCode, self).__init__(parent=parent)
-        self._code = "\n" + code
-        self._symbolsRead = set(symbols_read)
-        self._symbolsDefined = set(symbols_defined)
-        self.headers = []
-
-    @property
-    def code(self):
-        return self._code
-
-    @property
-    def args(self):
-        return []
-
-    @property
-    def symbols_defined(self):
-        return self._symbolsDefined
-
-    @property
-    def undefined_symbols(self):
-        return self.symbols_defined - self._symbolsRead
-
-
-class PrintNode(CustomCppCode):
-    # noinspection SpellCheckingInspection
-    def __init__(self, symbol_to_print):
-        code = '\nstd::cout << "%s  =  " << %s << std::endl; \n' % (symbol_to_print.name, symbol_to_print.name)
-        super(PrintNode, self).__init__(code, symbols_read=[symbol_to_print], symbols_defined=set())
-        self.headers.append("<iostream>")
-
-
-# ------------------------------------------- Printer ------------------------------------------------------------------
-
-
-# noinspection PyPep8Naming
-class CBackend:
-
-    def __init__(self, sympy_printer=None,
-                 signature_only=False, vector_instruction_set=None):
-        if sympy_printer is None:
-            if vector_instruction_set is not None:
-                self.sympy_printer = VectorizedCustomSympyPrinter(vector_instruction_set)
-            else:
-                self.sympy_printer = CustomSympyPrinter()
-        else:
-            self.sympy_printer = sympy_printer
-
-        self._vectorInstructionSet = vector_instruction_set
-        self._indent = "   "
-        self._signatureOnly = signature_only
-
-    def __call__(self, node):
-        prev_is = VectorType.instruction_set
-        VectorType.instruction_set = self._vectorInstructionSet
-        result = str(self._print(node))
-        VectorType.instruction_set = prev_is
-        return result
-
-    def _print(self, node):
-        for cls in type(node).__mro__:
-            method_name = "_print_" + cls.__name__
-            if hasattr(self, method_name):
-                return getattr(self, method_name)(node)
-
-        raise NotImplementedError("CBackend does not support node of type " + str(type(node)))
-
-    def _print_KernelFunction(self, node):
-        function_arguments = ["%s %s" % (str(s.symbol.dtype), s.symbol.name) for s in node.get_parameters()]
-        func_declaration = "FUNC_PREFIX void %s(%s)" % (node.function_name, ", ".join(function_arguments))
-        if self._signatureOnly:
-            return func_declaration
-
-        body = self._print(node.body)
-        return func_declaration + "\n" + body
-
-    def _print_Block(self, node):
-        block_contents = "\n".join([self._print(child) for child in node.args])
-        return "{\n%s\n}" % (self._indent + self._indent.join(block_contents.splitlines(True)))
-
-    def _print_PragmaBlock(self, node):
-        return "%s\n%s" % (node.pragma_line, self._print_Block(node))
-
-    def _print_LoopOverCoordinate(self, node):
-        counter_symbol = node.loop_counter_name
-        start = "int %s = %s" % (counter_symbol, self.sympy_printer.doprint(node.start))
-        condition = "%s < %s" % (counter_symbol, self.sympy_printer.doprint(node.stop))
-        update = "%s += %s" % (counter_symbol, self.sympy_printer.doprint(node.step),)
-        loop_str = "for (%s; %s; %s)" % (start, condition, update)
-
-        prefix = "\n".join(node.prefix_lines)
-        if prefix:
-            prefix += "\n"
-        return "%s%s\n%s" % (prefix, loop_str, self._print(node.body))
-
-    def _print_SympyAssignment(self, node):
-        if node.is_declaration:
-            data_type = "const " + str(node.lhs.dtype) + " " if node.is_const else str(node.lhs.dtype) + " "
-            return "%s%s = %s;" % (data_type, self.sympy_printer.doprint(node.lhs),
-                                   self.sympy_printer.doprint(node.rhs))
-        else:
-            lhs_type = get_type_of_expression(node.lhs)
-            if type(lhs_type) is VectorType and isinstance(node.lhs, cast_func):
-                arg, data_type, aligned, nontemporal = node.lhs.args
-                instr = 'storeU'
-                if aligned:
-                    instr = 'stream' if nontemporal else 'storeA'
-
-                return self._vectorInstructionSet[instr].format("&" + self.sympy_printer.doprint(node.lhs.args[0]),
-                                                                self.sympy_printer.doprint(node.rhs)) + ';'
-            else:
-                return "%s = %s;" % (self.sympy_printer.doprint(node.lhs), self.sympy_printer.doprint(node.rhs))
-
-    def _print_TemporaryMemoryAllocation(self, node):
-        align = 64
-        np_dtype = node.symbol.dtype.base_type.numpy_dtype
-        required_size = np_dtype.itemsize * node.size + align
-        size = modulo_ceil(required_size, align)
-        code = "{dtype} {name}=({dtype})aligned_alloc({align}, {size}) + {offset};"
-        return code.format(dtype=node.symbol.dtype,
-                           name=self.sympy_printer.doprint(node.symbol.name),
-                           size=self.sympy_printer.doprint(size),
-                           offset=int(node.offset(align)),
-                           align=align)
-
-    def _print_TemporaryMemoryFree(self, node):
-        align = 64
-        return "free(%s - %d);" % (self.sympy_printer.doprint(node.symbol.name), node.offset(align))
-
-    @staticmethod
-    def _print_CustomCppCode(node):
-        return node.code
-
-    def _print_Conditional(self, node):
-        condition_expr = self.sympy_printer.doprint(node.condition_expr)
-        true_block = self._print_Block(node.true_block)
-        result = "if (%s)\n%s " % (condition_expr, true_block)
-        if node.false_block:
-            false_block = self._print_Block(node.false_block)
-            result += "else " + false_block
-        return result
-
-
-# ------------------------------------------ Helper function & classes -------------------------------------------------
-
-
-# noinspection PyPep8Naming
-class CustomSympyPrinter(CCodePrinter):
-
-    def __init__(self):
-        super(CustomSympyPrinter, self).__init__()
-        self._float_type = create_type("float32")
-        if 'Min' in self.known_functions:
-            del self.known_functions['Min']
-        if 'Max' in self.known_functions:
-            del self.known_functions['Max']
-
-    def _print_Pow(self, expr):
-        """Don't use std::pow function, for small integer exponents, write as multiplication"""
-        if expr.exp.is_integer and expr.exp.is_number and 0 < expr.exp < 8:
-            return "(" + self._print(sp.Mul(*[expr.base] * expr.exp, evaluate=False)) + ")"
-        elif expr.exp.is_integer and expr.exp.is_number and - 8 < expr.exp < 0:
-            return "1 / ({})".format(self._print(sp.Mul(*[expr.base] * (-expr.exp), evaluate=False)))
-        else:
-            return super(CustomSympyPrinter, self)._print_Pow(expr)
-
-    def _print_Rational(self, expr):
-        """Evaluate all rationals i.e. print 0.25 instead of 1.0/4.0"""
-        res = str(expr.evalf().num)
-        return res
-
-    def _print_Equality(self, expr):
-        """Equality operator is not printable in default printer"""
-        return '((' + self._print(expr.lhs) + ") == (" + self._print(expr.rhs) + '))'
-
-    def _print_Piecewise(self, expr):
-        """Print piecewise in one line (remove newlines)"""
-        result = super(CustomSympyPrinter, self)._print_Piecewise(expr)
-        return result.replace("\n", "")
-
-    def _print_Function(self, expr):
-        infix_functions = {
-            bitwise_xor: '^',
-            bit_shift_right: '>>',
-            bit_shift_left: '<<',
-            bitwise_or: '|',
-            bitwise_and: '&',
-        }
-        if hasattr(expr, 'to_c'):
-            return expr.to_c(self._print)
-        if isinstance(expr, cast_func):
-            arg, data_type = expr.args
-            if isinstance(arg, sp.Number):
-                return self._typed_number(arg, data_type)
-            else:
-                return "*((%s)(& %s))" % (PointerType(data_type, restrict=False), self._print(arg))
-        elif expr.func in infix_functions:
-            return "(%s %s %s)" % (self._print(expr.args[0]), infix_functions[expr.func], self._print(expr.args[1]))
-        else:
-            return super(CustomSympyPrinter, self)._print_Function(expr)
-
-    def _typed_number(self, number, dtype):
-        res = self._print(number)
-        if dtype.is_float():
-            if dtype == self._float_type:
-                if '.' not in res:
-                    res += ".0f"
-                else:
-                    res += "f"
-            return res
-        else:
-            return res
-
-    _print_Max = C89CodePrinter._print_Max
-    _print_Min = C89CodePrinter._print_Min
-
-
-# noinspection PyPep8Naming
-class VectorizedCustomSympyPrinter(CustomSympyPrinter):
-    SummandInfo = namedtuple("SummandInfo", ['sign', 'term'])
-
-    def __init__(self, instruction_set):
-        super(VectorizedCustomSympyPrinter, self).__init__()
-        self.instruction_set = instruction_set
-
-    def _scalarFallback(self, func_name, expr, *args, **kwargs):
-        expr_type = get_type_of_expression(expr)
-        if type(expr_type) is not VectorType:
-            return getattr(super(VectorizedCustomSympyPrinter, self), func_name)(expr, *args, **kwargs)
-        else:
-            assert self.instruction_set['width'] == expr_type.width
-            return None
-
-    def _print_Function(self, expr):
-        if isinstance(expr, vector_memory_access):
-            arg, data_type, aligned, _ = expr.args
-            instruction = self.instruction_set['loadA'] if aligned else self.instruction_set['loadU']
-            return instruction.format("& " + self._print(arg))
-        elif isinstance(expr, cast_func):
-            arg, data_type = expr.args
-            if type(data_type) is VectorType:
-                return self.instruction_set['makeVec'].format(self._print(arg))
-
-        return super(VectorizedCustomSympyPrinter, self)._print_Function(expr)
-
-    def _print_And(self, expr):
-        result = self._scalarFallback('_print_And', expr)
-        if result:
-            return result
-
-        arg_strings = [self._print(a) for a in expr.args]
-        assert len(arg_strings) > 0
-        result = arg_strings[0]
-        for item in arg_strings[1:]:
-            result = self.instruction_set['&'].format(result, item)
-        return result
-
-    def _print_Or(self, expr):
-        result = self._scalarFallback('_print_Or', expr)
-        if result:
-            return result
-
-        arg_strings = [self._print(a) for a in expr.args]
-        assert len(arg_strings) > 0
-        result = arg_strings[0]
-        for item in arg_strings[1:]:
-            result = self.instruction_set['|'].format(result, item)
-        return result
-
-    def _print_Add(self, expr, order=None):
-        result = self._scalarFallback('_print_Add', expr)
-        if result:
-            return result
-
-        summands = []
-        for term in expr.args:
-            if term.func == sp.Mul:
-                sign, t = self._print_Mul(term, inside_add=True)
-            else:
-                t = self._print(term)
-                sign = 1
-            summands.append(self.SummandInfo(sign, t))
-        # Use positive terms first
-        summands.sort(key=lambda e: e.sign, reverse=True)
-        # if no positive term exists, prepend a zero
-        if summands[0].sign == -1:
-            summands.insert(0, self.SummandInfo(1, "0"))
-
-        assert len(summands) >= 2
-        processed = summands[0].term
-        for summand in summands[1:]:
-            func = self.instruction_set['-'] if summand.sign == -1 else self.instruction_set['+']
-            processed = func.format(processed, summand.term)
-        return processed
-
-    def _print_Pow(self, expr):
-        result = self._scalarFallback('_print_Pow', expr)
-        if result:
-            return result
-
-        if expr.exp.is_integer and expr.exp.is_number and 0 < expr.exp < 8:
-            return "(" + self._print(sp.Mul(*[expr.base] * expr.exp, evaluate=False)) + ")"
-        elif expr.exp == -1:
-            one = self.instruction_set['makeVec'].format(1.0)
-            return self.instruction_set['/'].format(one, self._print(expr.base))
-        elif expr.exp == 0.5:
-            return self.instruction_set['sqrt'].format(self._print(expr.base))
-        elif expr.exp.is_integer and expr.exp.is_number and - 8 < expr.exp < 0:
-            one = self.instruction_set['makeVec'].format(1.0)
-            return self.instruction_set['/'].format(one,
-                                                    self._print(sp.Mul(*[expr.base] * (-expr.exp), evaluate=False)))
-        else:
-            raise ValueError("Generic exponential not supported: " + str(expr))
-
-    def _print_Mul(self, expr, inside_add=False):
-        # noinspection PyProtectedMember
-        from sympy.core.mul import _keep_coeff
-
-        result = self._scalarFallback('_print_Mul', expr)
-        if result:
-            return result
-
-        c, e = expr.as_coeff_Mul()
-        if c < 0:
-            expr = _keep_coeff(-c, e)
-            sign = -1
-        else:
-            sign = 1
-
-        a = []  # items in the numerator
-        b = []  # items that are in the denominator (if any)
-
-        # Gather args for numerator/denominator
-        for item in expr.as_ordered_factors():
-            if item.is_commutative and item.is_Pow and item.exp.is_Rational and item.exp.is_negative:
-                if item.exp != -1:
-                    b.append(sp.Pow(item.base, -item.exp, evaluate=False))
-                else:
-                    b.append(sp.Pow(item.base, -item.exp))
-            else:
-                a.append(item)
-
-        a = a or [S.One]
-
-        a_str = [self._print(x) for x in a]
-        b_str = [self._print(x) for x in b]
-
-        result = a_str[0]
-        for item in a_str[1:]:
-            result = self.instruction_set['*'].format(result, item)
-
-        if len(b) > 0:
-            denominator_str = b_str[0]
-            for item in b_str[1:]:
-                denominator_str = self.instruction_set['*'].format(denominator_str, item)
-            result = self.instruction_set['/'].format(result, denominator_str)
-
-        if inside_add:
-            return sign, result
-        else:
-            if sign < 0:
-                return self.instruction_set['*'].format(self._print(S.NegativeOne), result)
-            else:
-                return result
-
-    def _print_Relational(self, expr):
-        result = self._scalarFallback('_print_Relational', expr)
-        if result:
-            return result
-        return self.instruction_set[expr.rel_op].format(self._print(expr.lhs), self._print(expr.rhs))
-
-    def _print_Equality(self, expr):
-        result = self._scalarFallback('_print_Equality', expr)
-        if result:
-            return result
-        return self.instruction_set['=='].format(self._print(expr.lhs), self._print(expr.rhs))
-
-    def _print_Piecewise(self, expr):
-        result = self._scalarFallback('_print_Piecewise', expr)
-        if result:
-            return result
-
-        if expr.args[-1].cond.args[0] is not sp.sympify(True):
-            # We need the last conditional to be a True, otherwise the resulting
-            # function may not return a result.
-            raise ValueError("All Piecewise expressions must contain an "
-                             "(expr, True) statement to be used as a default "
-                             "condition. Without one, the generated "
-                             "expression may not evaluate to anything under "
-                             "some condition.")
-
-        result = self._print(expr.args[-1][0])
-        for true_expr, condition in reversed(expr.args[:-1]):
-            # noinspection SpellCheckingInspection
-            result = self.instruction_set['blendv'].format(result, self._print(true_expr), self._print(condition))
-        return result

backends/simd_instruction_sets.py

-
-
-# noinspection SpellCheckingInspection
-def get_vector_instruction_set(data_type='double', instruction_set='avx'):
-    base_names = {
-        '+': 'add[0, 1]',
-        '-': 'sub[0, 1]',
-        '*': 'mul[0, 1]',
-        '/': 'div[0, 1]',
-
-        '==': 'cmp[0, 1, _CMP_EQ_UQ  ]',
-        '!=': 'cmp[0, 1, _CMP_NEQ_UQ ]',
-        '>=': 'cmp[0, 1, _CMP_GE_OQ  ]',
-        '<=': 'cmp[0, 1, _CMP_LE_OQ  ]',
-        '<': 'cmp[0, 1, _CMP_NGE_UQ ]',
-        '>': 'cmp[0, 1, _CMP_NLE_UQ ]',
-        '&': 'and[0, 1]',
-        '|': 'or[0, 1]',
-        'blendv': 'blendv[0, 1, 2]',
-
-        'sqrt': 'sqrt[0]',
-
-        'makeVec': 'set[]',
-        'makeZero': 'setzero[]',
-
-        'loadU': 'loadu[0]',
-        'loadA': 'load[0]',
-        'storeU': 'storeu[0,1]',
-        'storeA': 'store[0,1]',
-        'stream': 'stream[0,1]',
-    }
-
-    headers = {
-        'avx512': ['<immintrin.h>'],
-        'avx': ['<immintrin.h>'],
-        'sse': ['<xmmintrin.h>', '<emmintrin.h>', '<pmmintrin.h>', '<tmmintrin.h>', '<smmintrin.h>', '<nmmintrin.h>']
-    }
-
-    suffix = {
-        'double': 'pd',
-        'float': 'ps',
-    }
-    prefix = {
-        'sse': '_mm',
-        'avx': '_mm256',
-        'avx512': '_mm512',
-    }
-
-    width = {
-        ("double", "sse"): 2,
-        ("float", "sse"): 4,
-        ("double", "avx"): 4,
-        ("float", "avx"): 8,
-        ("double", "avx512"): 8,
-        ("float", "avx512"): 16,
-    }
-
-    result = {
-        'width': width[(data_type, instruction_set)],
-    }
-    pre = prefix[instruction_set]
-    suf = suffix[data_type]
-    for intrinsic_id, function_shortcut in base_names.items():
-        function_shortcut = function_shortcut.strip()
-        name = function_shortcut[:function_shortcut.index('[')]
-
-        if intrinsic_id == 'makeVec':
-            arg_string = "({})".format(",".join(["{0}"] * result['width']))
-        else:
-            args = function_shortcut[function_shortcut.index('[') + 1: -1]
-            arg_string = "("
-            for arg in args.split(","):
-                arg = arg.strip()
-                if not arg:
-                    continue
-                if arg in ('0', '1', '2', '3', '4', '5'):
-                    arg_string += "{" + arg + "},"
-                else:
-                    arg_string += arg + ","
-            arg_string = arg_string[:-1] + ")"
-        result[intrinsic_id] = pre + "_" + name + "_" + suf + arg_string
-
-    result['dataTypePrefix'] = {
-        'double': "_" + pre + 'd',
-        'float': "_" + pre,
-    }
-
-    bit_width = result['width'] * (64 if data_type == 'double' else 32)
-    result['double'] = "__m%dd" % (bit_width,)
-    result['float'] = "__m%d" % (bit_width,)
-    result['int'] = "__m%di" % (bit_width,)
-    result['bool'] = "__m%dd" % (bit_width,)
-
-    result['headers'] = headers[instruction_set]
-    return result
-
-
-def get_supported_instruction_sets():
-    """List of supported instruction sets on current hardware, or None if query failed."""
-    try:
-        from cpuinfo import get_cpu_info
-    except ImportError:
-        return None
-
-    result = []
-    required_sse_flags = {'sse', 'sse2', 'ssse3', 'sse4_1', 'sse4_2'}
-    required_avx_flags = {'avx'}
-    required_avx512_flags = {'avx512f'}
-    flags = set(get_cpu_info()['flags'])
-    if flags.issuperset(required_sse_flags):
-        result.append("sse")
-    if flags.issuperset(required_avx_flags):
-        result.append("avx")
-    if flags.issuperset(required_avx512_flags):
-        result.append("avx512")
-    return result

binder/apt.txt

+build-essential
+graphviz
+ffmpeg

binder/environment.yml

+
+# ----------------------------------------------------------------------------------------------------------------------
+# Environment with all dependencies to use pystencils
+#
+#
+# Download conda at https://conda.io/miniconda.html and create this environment by running:
+#     conda env create -f conda_environment_user.yml
+#     . activate pystencils
+#
+# If you have CUDA or ROCm installed and want to use your GPU, uncomment the last line to install cupy
+#
+# ----------------------------------------------------------------------------------------------------------------------
+
+name: pystencils
+dependencies:
+  # Basic dependencies:
+  - python >= 3.8
+  - numpy
+  - sympy >= 1.1
+  - appdirs # to find default cache directory on each platform
+  - joblib # caching on hard-disk, this is optional, but if not installed lbmpy is really slow
+  - cython # speed up boundary list computation (optional)
+  - matplotlib
+  - imageio
+  - pandas
+  - scipy
+  - pip
+  - pip:
+      - islpy # used to optimize staggered kernels
+      - py-cpuinfo # get cpu info like cache sizes, supported vector instruction sets, ...
+      - graphviz  # can show abstract syntax trees as formatted graphs
+      - ipy_table  # HTML tables for jupyter notebooks
+      - pyevtk # VTK output for serial simulations
+      - blitzdb # file-based No-SQL database to store simulation results
+      #- cupy # add this if you have CUDA or ROCm installed

binder/start

+#!/bin/bash
+
+python3 setup.py develop
+
+exec "$@"
\ No newline at end of file

boundaries/createindexlist.py

-import numpy as np
-import itertools
-import warnings
-
-try:
-    import pyximport
-
-    pyximport.install(language_level=3)
-    from pystencils.boundaries.createindexlistcython import create_boundary_index_list_2d, create_boundary_index_list_3d
-
-    cython_funcs_available = True
-except Exception:
-    cython_funcs_available = False
-    create_boundary_index_list_2d = None
-    create_boundary_index_list_3d = None
-
-boundary_index_array_coordinate_names = ["x", "y", "z"]
-direction_member_name = "dir"
-
-
-def numpy_data_type_for_boundary_object(boundary_object, dim):
-    coordinate_names = boundary_index_array_coordinate_names[:dim]
-    return np.dtype([(name, np.int32) for name in coordinate_names] +
-                    [(direction_member_name, np.int32)] +
-                    [(i[0], i[1].numpy_dtype) for i in boundary_object.additional_data], align=True)
-
-
-def _create_boundary_index_list_python(flag_field_arr, nr_of_ghost_layers, boundary_mask, fluid_mask, stencil):
-    coordinate_names = boundary_index_array_coordinate_names[:len(flag_field_arr.shape)]
-    index_arr_dtype = np.dtype([(name, np.int32) for name in coordinate_names] + [(direction_member_name, np.int32)])
-
-    result = []
-    gl = nr_of_ghost_layers
-    for cell in itertools.product(*reversed([range(gl, i - gl) for i in flag_field_arr.shape])):
-        cell = cell[::-1]
-        if not flag_field_arr[cell] & fluid_mask:
-            continue
-        for dir_idx, direction in enumerate(stencil):
-            neighbor_cell = tuple([cell_i + dir_i for cell_i, dir_i in zip(cell, direction)])
-            if flag_field_arr[neighbor_cell] & boundary_mask:
-                result.append(cell + (dir_idx,))
-
-    return np.array(result, dtype=index_arr_dtype)
-
-
-def create_boundary_index_list(flag_field, stencil, boundary_mask, fluid_mask, nr_of_ghost_layers=1):
-    dim = len(flag_field.shape)
-    coordinate_names = boundary_index_array_coordinate_names[:dim]
-    index_arr_dtype = np.dtype([(name, np.int32) for name in coordinate_names] + [(direction_member_name, np.int32)])
-
-    if cython_funcs_available:
-        stencil = np.array(stencil, dtype=np.int32)
-        if dim == 2:
-            idx_list = create_boundary_index_list_2d(flag_field, nr_of_ghost_layers, boundary_mask, fluid_mask, stencil)
-        elif dim == 3:
-            idx_list = create_boundary_index_list_3d(flag_field, nr_of_ghost_layers, boundary_mask, fluid_mask, stencil)
-        else:
-            raise ValueError("Flag field has to be a 2 or 3 dimensional numpy array")
-        return np.array(idx_list, dtype=index_arr_dtype)
-    else:
-        if flag_field.size > 1e6:
-            warnings.warn("Boundary setup may take very long! Consider installing cython to speed it up")
-        return _create_boundary_index_list_python(flag_field, nr_of_ghost_layers, boundary_mask, fluid_mask, stencil)
-
-
-def create_boundary_index_array(flag_field, stencil, boundary_mask, fluid_mask, boundary_object, nr_of_ghost_layers=1):
-    idx_array = create_boundary_index_list(flag_field, stencil, boundary_mask, fluid_mask, nr_of_ghost_layers)
-    dim = len(flag_field.shape)
-
-    if boundary_object.additional_data:
-        coordinate_names = boundary_index_array_coordinate_names[:dim]
-        index_arr_dtype = numpy_data_type_for_boundary_object(boundary_object, dim)
-        extended_idx_field = np.empty(len(idx_array), dtype=index_arr_dtype)
-        for prop in coordinate_names + ['dir']:
-            extended_idx_field[prop] = idx_array[prop]
-
-        idx_array = extended_idx_field
-
-    return idx_array

boundaries/createindexlistcython.pyx

-# Workaround for cython bug
-# see https://stackoverflow.com/questions/8024805/cython-compiled-c-extension-importerror-dynamic-module-does-not-define-init-fu
-WORKAROUND = "Something"
-
-import cython
-
-ctypedef fused IntegerType:
-    short
-    int
-    long
-    long long
-    unsigned short
-    unsigned int
-    unsigned long
-
-@cython.boundscheck(False) # turn off bounds-checking for entire function
-@cython.wraparound(False)  # turn off negative index wrapping for entire function
-def create_boundary_index_list_2d(object[IntegerType, ndim=2] flag_field,
-                                  int nr_of_ghost_layers, IntegerType boundary_mask, IntegerType fluid_mask,
-                                  object[int, ndim=2] stencil):
-    cdef int xs, ys, x, y
-    cdef int dirIdx, num_directions, dx, dy
-
-    xs, ys = flag_field.shape
-    boundary_index_list = []
-    num_directions = stencil.shape[0]
-
-    for y in range(nr_of_ghost_layers, ys - nr_of_ghost_layers):
-        for x in range(nr_of_ghost_layers, xs - nr_of_ghost_layers):
-            if flag_field[x, y] & fluid_mask:
-                for dirIdx in range(num_directions):
-                    dx = stencil[dirIdx,0]
-                    dy = stencil[dirIdx,1]
-                    if flag_field[x + dx, y + dy] & boundary_mask:
-                        boundary_index_list.append((x,y, dirIdx))
-    return boundary_index_list
-
-
-@cython.boundscheck(False) # turn off bounds-checking for entire function
-@cython.wraparound(False)  # turn off negative index wrapping for entire function
-def create_boundary_index_list_3d(object[IntegerType, ndim=3] flag_field,
-                                  int nr_of_ghost_layers, IntegerType boundary_mask, IntegerType fluid_mask,
-                                  object[int, ndim=2] stencil):
-    cdef int xs, ys, zs, x, y, z
-    cdef int dirIdx, num_directions, dx, dy, dz
-
-    xs, ys, zs = flag_field.shape
-    boundary_index_list = []
-    num_directions = stencil.shape[0]
-
-    for z in range(nr_of_ghost_layers, zs - nr_of_ghost_layers):
-        for y in range(nr_of_ghost_layers, ys - nr_of_ghost_layers):
-            for x in range(nr_of_ghost_layers, xs - nr_of_ghost_layers):
-                if flag_field[x, y, z] & fluid_mask:
-                    for dirIdx in range(num_directions):
-                        dx = stencil[dirIdx,0]
-                        dy = stencil[dirIdx,1]
-                        dz = stencil[dirIdx,2]
-                        if flag_field[x + dx, y + dy, z + dz] & boundary_mask:
-                            boundary_index_list.append((x,y,z, dirIdx))
-    return boundary_index_list
-
-

cache.py

-import os
-
-try:
-    from functools import lru_cache as memorycache
-except ImportError:
-    from backports.functools_lru_cache import lru_cache as memorycache
-
-try:
-    from joblib import Memory
-    from appdirs import user_cache_dir
-    if 'PYSTENCILS_CACHE_DIR' in os.environ:
-        cache_dir = os.environ['PYSTENCILS_CACHE_DIR']
-    else:
-        cache_dir = user_cache_dir('pystencils')
-    disk_cache = Memory(cachedir=cache_dir, verbose=False).cache
-    disk_cache_no_fallback = disk_cache
-except ImportError:
-    # fallback to in-memory caching if joblib is not available
-    disk_cache = memorycache(maxsize=64)
-
-    def disk_cache_no_fallback(o):
-        return o
-
-
-# Disable memory cache:
-# disk_cache = lambda o: o
-# disk_cache_no_fallback = lambda o: o