diff --git a/.gitignore b/.gitignore index 7392a28..605155a 100644 --- a/.gitignore +++ b/.gitignore @@ -20,3 +20,6 @@ env/ *.out *.egg-info .ipynb_checkpoints/ +.coverage +.venv +.pytest_cache diff --git a/anisotropy/core/cli.py b/anisotropy/core/cli.py index 22c0ec4..2aaaf85 100644 --- a/anisotropy/core/cli.py +++ b/anisotropy/core/cli.py @@ -7,6 +7,71 @@ import ast import os, sys, shutil import logging + +class LiteralOption(click.Option): + def type_cast_value(self, ctx, value): + try: + return ast.literal_eval(value) + + except: + raise click.BadParameter(f"{ value } (Type error)") + +class KeyValueOption(click.Option): + def _convert(self, ctx, value): + if not value: + return {} + + if value.find("=") == -1: + raise click.BadParameter(f"{ value } (Missed '=')") + + params = value.split("=") + + if not len(params) == 2: + raise click.BadParameter(f"{ value } (Syntax error)") + + key, val = params[0].strip(), params[1].strip() + + if val[0].isalpha(): + val = f"'{ val }'" + + try: + return { key: ast.literal_eval(val) } + + except: + raise click.BadParameter(f"{ value } (Type error)") + + def type_cast_value(self, ctx, value): + if isinstance(value, list): + return [ self._convert(ctx, val) for val in value ] + + else: + return self._convert(ctx, value) + +class CliListOption(click.Option): + def _convert(self, ctx, value): + if not value: + return [] + + output = [ val for val in value.split(",") ] + + if "" in output: + raise click.BadParameter(f"{ value } (Trying to pass empty item)") + + return output + + + def type_cast_value(self, ctx, value): + if isinstance(value, list): + return [ self._convert(ctx, val) for val in value ] + + else: + return self._convert(ctx, value) + + +@click.group() +def anisotropy(): + pass + @anisotropy.command() @click.option( "-P", "--path", "path", @@ -71,67 +136,8 @@ def compute(path, configFile, nprocs, stage, overwrite): baseRunner.parallel(queue) +############## -class LiteralOption(click.Option): - def type_cast_value(self, ctx, value): - try: - return ast.literal_eval(value) - - except: - raise click.BadParameter(f"{ value } (Type error)") - -class KeyValueOption(click.Option): - def _convert(self, ctx, value): - if not value: - return {} - - if value.find("=") == -1: - raise click.BadParameter(f"{ value } (Missed '=')") - - params = value.split("=") - - if not len(params) == 2: - raise click.BadParameter(f"{ value } (Syntax error)") - - key, val = params[0].strip(), params[1].strip() - - if val[0].isalpha(): - val = f"'{ val }'" - - try: - return { key: ast.literal_eval(val) } - - except: - raise click.BadParameter(f"{ value } (Type error)") - - def type_cast_value(self, ctx, value): - if isinstance(value, list): - return [ self._convert(ctx, val) for val in value ] - - else: - return self._convert(ctx, value) - -class CliListOption(click.Option): - def _convert(self, ctx, value): - if not value: - return [] - - output = [ val for val in value.split(",") ] - - if "" in output: - raise click.BadParameter(f"{ value } (Trying to pass empty item)") - - return output - - - def type_cast_value(self, ctx, value): - if isinstance(value, list): - return [ self._convert(ctx, val) for val in value ] - - else: - return self._convert(ctx, value) - - def version(): msg = "Missed package anisotropy" @@ -237,7 +243,7 @@ def update(force, params, path): paramsAll = [ entry for entry in paramsAll if args["theta"] == entry["structure"]["theta"] ] from anisotropy.core.models import Structure, Mesh - from numpy + #from numpy for entry in paramsAll: database.update(entry) diff --git a/anisotropy/meshing/mesh.py b/anisotropy/meshing/mesh.py index 2caedc2..28c6cda 100644 --- a/anisotropy/meshing/mesh.py +++ b/anisotropy/meshing/mesh.py @@ -11,25 +11,74 @@ class Mesh(object): self.geometry = OCCGeometry(shape) self.mesh = None + # Parameters + self.maxh = 0.2 + self.curvaturesafety = 5 + self.segmentsperedge = 3 + self.grading = 0.1 + self.chartdistfac = 5 + self.linelengthfac = 3 + self.closeedgefac = 5 + self.minedgelen = 2.0 + self.surfmeshcurvfac = 5.0 + self.optsteps2d = 5 + self.optsteps3d = 5 + + @property def parameters(self): return meshing.MeshingParameters( - maxh = 0.2, - curvaturesafety = 5, - segmentsperedge = 3, - grading = 0.1, - chartdistfac = 5, - linelengthfac = 3, - closeedgefac = 5, - minedgelen = 2.0, - surfmeshcurvfac = 5.0, - optsteps2d = 5, - optsteps3d = 5 + maxh = self.maxh, + curvaturesafety = self.curvaturesafety, + segmentsperedge = self.segmentsperedge, + grading = self.grading, + chartdistfac = self.chartdistfac, + linelengthfac = self.linelengthfac, + closeedgefac = self.closeedgefac, + minedgelen = self.minedgelen, + surfmeshcurvfac = self.surfmeshcurvfac, + optsteps2d = self.optsteps2d, + optsteps3d = self.optsteps3d ) def build(self): self.mesh = self.geometry.GenerateMesh(self.parameters) + def export(self, filename: str): + """Export a shape. + + Supported formats: vol, mesh. + + :param filename: + Name of the file to store the given shape in. + + :return: + Output, error messages and returncode + """ + out, err, returncode = "", "", 0 + ext = os.path.splitext(filename)[1][1: ] + + try: + # TODO: write correct boundary names + if ext == "vol": + self.mesh.Save(filename) + + elif ext == "mesh": + self.mesh.Export(filename, "Neutral Format") + + else: + raise NotImplementedError(f"{ ext } is not supported") + + except NotImplementedError as e: + err = e + returncode = 1 + + except Exception as e: + err = e + returncode = 1 + + return out, err, returncode + def doubleExport(self): pass diff --git a/anisotropy/solving/onephase.py b/anisotropy/solving/onephase.py new file mode 100644 index 0000000..1ed00ed --- /dev/null +++ b/anisotropy/solving/onephase.py @@ -0,0 +1,158 @@ +# -*- coding: utf-8 -*- +# This file is part of anisotropy. +# License: GNU GPL version 3, see the file "LICENSE" for details. + +import anisotropy.openfoam as openfoam +from openfoam.presets import ( + ControlDict, FvSchemes, FvSolution, + TransportProperties, TurbulenceProperties, CreatePatchDict, + P, U +) +from openfoam.foamcase import FoamCase + +class OnePhaseFlow(FoamCase): + def __init__(self): + FoamCase.__init__(self) + + controlDict = ControlDict() + controlDict.update( + startFrom = "latestTime", + endTime = 5000, + writeInterval = 100, + runTimeModifiable = "true" + ) + + fvSchemes = FvSchemes() + + fvSolution = FvSolution() + fvSolution["solvers"]["U"].update( + nSweeps = 2, + tolerance = 1e-08 + ) + fvSolution["solvers"]["Phi"] = dict( + solver = "GAMG", + smoother = "DIC", + cacheAgglomeration = "yes", + agglomerator = "faceAreaPair", + nCellsInCoarsestLevel = 10, + mergeLevels = 1, + tolerance = 1e-06, + relTol = 0.01 + ) + fvSolution["potentialFlow"] = dict( + nNonOrthogonalCorrectors = 20, + PhiRefCell = 0, + PhiRefPoint = 0, + PhiRefValue = 0, + Phi = 0 + ) + fvSolution["cache"] = { "grad(U)": None } + fvSolution["SIMPLE"].update( + nNonOrthogonalCorrectors = 10, + residualControl = dict( + p = 1e-05, + U = 1e-05 + ) + ) + fvSolution["relaxationFactors"]["equations"]["U"] = 0.5 + + transportProperties = TransportProperties() + transportProperties.update( + nu = 1e-06 + ) + + turbulenceProperties = TurbulenceProperties() + turbulenceProperties.content = dict( + simulationType = "laminar" + ) + + createPatchDict = CreatePatchDict() + createPatchDict["patches"] = [] + + for patch in ["inlet", "outlet", "wall", "strips", *[ f"symetry{ n }" for n in range(6) ]]: + newPatch = dict( + name = patch, + patchInfo = dict( + type = "patch", + inGroups = [patch] + ), + constructFrom = "patches", + patches = [ f"smesh_{ patch }" ] + ) + + match patch: + case "wall" | "strips": + newPatch["patchInfo"].update( + type = "wall", + inGroups = [ "wall" ] + ) + + case patch if patch.find("symetry") == 0: + newPatch["patchInfo"]["inGroups"] = [ "symetryPlane" ] + + createPatchDict["patches"].append(newPatch) + + + boundaries = [ "inlet", "outlet", "symetryPlane", "wall", "strips" ] + p = P() + p["boundaryField"] = {} + u = U() + u["boundaryField"] = {} + + # ISSUE: add proxy from geometry direction to outlet boundaryField. + for boundary in boundaries: + match boundary: + case "inlet": + p["boundaryField"][boundary] = dict( + type = "fixedValue", + value = "uniform 1e-3" + ) + u["boundaryField"][boundary] = dict( + type = "fixedValue", + value = "uniform (0 0 -6e-5)" # * direction + ) + + case "outlet": + p["boundaryField"][boundary] = dict( + type = "fixedValue", + value = "uniform 0" + ) + u["boundaryField"][boundary] = dict( + type = "zeroGradient", + ) + + case _: + p["boundaryField"][boundary] = dict( + type = "zeroGradient" + ) + u["boundaryField"][boundary] = dict( + type = "fixedValue", + value = "uniform (0 0 0)" + ) + + self.extend([ + controlDict, fvSchemes, fvSolution, createPatchDict, + transportProperties, turbulenceProperties, + p, u + ]) + + def build(self): + # TODO: configure working directory (FoamCase) + self.write() + + openfoam.ideasUnvToFoam("mesh.unv") + openfoam.createPatch() + openfoam.checkMesh() + openfoam.transformPoints((1e-5, 1e-5, 1e-5)) + openfoam.renumberMesh() + openfoam.potentialFoam() + + self.read() + + self.solution.U["boundaryField"]["outlet"] = dict( + type = "pressureInletVelocity", + value = "uniform (0 0 0)" # * direction + ) + self.write() + + openfoam.simpleFoam() diff --git a/poetry.lock b/poetry.lock new file mode 100644 index 0000000..e978491 --- /dev/null +++ b/poetry.lock @@ -0,0 +1,1298 @@ +[[package]] +name = "alabaster" +version = "0.7.12" +description = "A configurable sidebar-enabled Sphinx theme" +category = "dev" +optional = true +python-versions = "*" + +[[package]] +name = "argh" +version = "0.26.2" +description = "An unobtrusive argparse wrapper with natural syntax" +category = "dev" +optional = true +python-versions = "*" + +[[package]] +name = "atomicwrites" +version = "1.4.0" +description = "Atomic file writes." +category = "dev" +optional = false +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" + +[[package]] +name = "attrs" +version = "21.2.0" +description = "Classes Without Boilerplate" +category = "dev" +optional = false +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" + +[package.extras] +dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface", "furo", "sphinx", "sphinx-notfound-page", "pre-commit"] +docs = ["furo", "sphinx", "zope.interface", "sphinx-notfound-page"] +tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface"] +tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins"] + +[[package]] +name = "babel" +version = "2.9.1" +description = "Internationalization utilities" +category = "dev" +optional = true +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" + +[package.dependencies] +pytz = ">=2015.7" + +[[package]] +name = "certifi" +version = "2021.10.8" +description = "Python package for providing Mozilla's CA Bundle." +category = "dev" +optional = true +python-versions = "*" + +[[package]] +name = "charset-normalizer" +version = "2.0.7" +description = "The Real First Universal Charset Detector. 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+[tool.poetry] +name = "anisotropy" +version = "1.2.0" +description = "Anisotropy of permeability in the periodic porous media." +authors = ["George Kusayko "] +license = "GPL-3.0-only" +readme = "README.rst" +repository = "https://github.com/L-Nafaryus/anisotropy" +keywords = ["anisotropy", "console", "CFD"] +classifiers = [ + "Environment :: Console", + "Operating System :: POSIX", + "Operating System :: Unix", + "Intended Audience :: Developers", + "Intended Audience :: Science/Research", + "License :: OSI Approved :: GNU General Public License v3 (GPLv3)", + "Programming Language :: Python :: 3.9" +] +packages = [ + { include = "anisotropy" } +] + +[tool.poetry.scripts] +anisotropy = "anisotropy.core.cli:anisotropy" + +[tool.poetry.dependencies] +python = ">=3.9,<3.11" +toml = "^0.10.2" +peewee = "^3.14.8" +numpy = "^1.21.4" +pandas = "^1.3.4" +matplotlib = "^3.5.0" +pyfoam = "^2021.6" +click = "^8.0.3" +pyqt5 = "^5.15.6" + +[tool.poetry.dev-dependencies] +pytest = "^5.2" +vulture = "^2.3" +pytest-cov = "^3.0.0" +pycodestyle = "^2.8.0" +pydeps = {version = "^1.10.12", optional = true} +peewee-erd = {version = "^0.1.3", optional = true} +Sphinx = {version = "^4.3.0", optional = true} +sphinx-rtd-theme = {version = "^1.0.0", optional = true} + +[tool.poetry.extras] +analyze = ["jupyterlab", "seaborn", "sklearn"] +docs = ["Sphinx", "sphinx-rtd-theme", "pydeps", "peewee-erd"] + +[build-system] +requires = ["poetry-core>=1.0.0"] +build-backend = "poetry.core.masonry.api" + + diff --git a/requirements-jupyter.txt b/requirements-jupyter.txt deleted file mode 100644 index d8c4b14..0000000 --- a/requirements-jupyter.txt +++ /dev/null @@ -1 +0,0 @@ -@arbennett/base16-gruvbox-dark diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index 72945d4..0000000 --- a/requirements.txt +++ /dev/null @@ -1,10 +0,0 @@ -wheel -numpy -pyquaternion -toml -peewee -pandas -Click -matplotlib -pyqt5 -PyFoam diff --git a/setup.py b/setup.py deleted file mode 100644 index 67c95d1..0000000 --- a/setup.py +++ /dev/null @@ -1,89 +0,0 @@ -#!/usr/bin/env python -# -*- coding: utf-8 -*- -# This file is part of anisotropy. -# License: GNU GPL version 3, see the file "LICENSE" for details. - -import os -from setuptools import setup - -import anisotropy - -def read(filename, split = False): - content = "" - - with open(os.path.join(os.path.dirname(__file__), filename), "r") as io: - content = io.read() - - return content.strip().split("\n") if split else content - -def findall(directory): - return [ - os.path.join(directory, f) for f in os.listdir(directory) - if os.path.isfile(os.path.join(directory, f)) - ] - -def main(): - setup( - name = "anisotropy", - description = "Anisotropy", - long_description = read("README.rst"), - long_description_content_type = "text/x-rst", - version = anisotropy.__version__, - author = anisotropy.__author__, - author_email = anisotropy.__email__, - license = anisotropy.__license__, - - url = "https://github.com/L-Nafaryus/anisotropy", - project_urls = { - "Source": "https://github.com/L-Nafaryus/anisotropy" - }, - - keywords = "anisotropy console CFD", - classifiers = [ - "Environment :: Console", - "Operating System :: POSIX", - "Operating System :: Unix", - "Intended Audience :: Developers", - "Intended Audience :: Science/Research", - "License :: OSI Approved :: GNU General Public License v3 (GPLv3)", - "Programming Language :: Python :: 3.9" - ], - - data_files = [ - ("share/doc/anisotropy", findall("docs")), - ("share/doc/anisotropy/source", findall("docs/source")), - ("share/doc/anisotropy/source/static", findall("docs/source/static")), - ("share/doc/anisotropy/source/notes", findall("docs/source/notes")) - ], - - package_data = { - "anisotropy": [ - "config/default.toml", - "config/bashrc" - ] - }, - packages = ( - "anisotropy", - "anisotropy.config", - "anisotropy.core", - "anisotropy.openfoam", - "anisotropy.salomepl", - "anisotropy.samples" - ), - - python_requires = ">=3.6", - install_requires = read("requirements.txt", True), - extras_require = { - "documentation": ["Sphinx", "sphinx-rtd-theme", "pydeps", "peewee-erd" ], - "extra": ["jupyterlab", "seaborn", "sklearn"] - }, - entry_points = { - "console_scripts": [ - "anisotropy=anisotropy.core.cli:anisotropy" - ] - } - ) - - -if __name__ == "__main__": - main() diff --git a/tests/test_anisotropy.py b/tests/test_anisotropy.py deleted file mode 100644 index d7ccefe..0000000 --- a/tests/test_anisotropy.py +++ /dev/null @@ -1,44 +0,0 @@ -import os -import unittest - -unittest.TestLoader.sortTestMethodsUsing = None - -# TODO: update tests -class TestAnisotropy(unittest.TestCase): - def setUp(self): - from anisotropy.core.main import Anisotropy - self.model = Anisotropy() - - def test_01_create_db(self): - self.model.db.setup() - path = os.path.join(self.model.env["db_path"], "anisotropy.db") - - self.assertTrue(os.path.exists(path)) - - def test_02_load_from_scratch(self): - passed = True - - try: - paramsAll = self.model.loadFromScratch() - - for entry in paramsAll: - self.model.update(entry) - - except Exception as e: - passed = False - print(e) - - self.assertTrue(passed) - - def test_03_load_db(self): - self.model.load("simple", [1.0, 0.0, 0.0], 0.01) - - self.assertEqual(self.model.params["structure"]["type"], "simple") - - def tearDown(self): - #os.removedirs(self.model.env["BUILD"]) - #os.removedirs(self.model.env["LOG"]) - pass - -if __name__ == "__main__": - unittest.main() diff --git a/tests/test_faceCentered_lattice.py b/tests/test_faceCentered_lattice.py deleted file mode 100644 index 856ba74..0000000 --- a/tests/test_faceCentered_lattice.py +++ /dev/null @@ -1,22 +0,0 @@ -import os -import unittest - -unittest.TestLoader.sortTestMethodsUsing = None - -class TestFaceCentered(unittest.TestCase): - def setUp(self): - self.outputPath = os.path.join(os.path.abspath("."), "tests/test_shaping_output") - os.makedirs(self.outputPath, exist_ok = True) - - def test_faceCentered_lattice(self): - from anisotropy.shaping import FaceCentered - - fc = FaceCentered([1, 0, 0], alpha = 0.01, filletsEnabled = True) - fc.build() - fc.lattice.WriteStep(os.path.join(self.outputPath, "fc_lattice.step")) - - def tearDown(self): - pass - -if __name__ == "__main__": - unittest.main() diff --git a/tests/test_shaping.py b/tests/test_shaping.py index bc51995..f615c53 100644 --- a/tests/test_shaping.py +++ b/tests/test_shaping.py @@ -38,6 +38,11 @@ class TestShaping(unittest.TestCase): bodyCentered001.export(os.path.join(self.outputPath, "bodyCentered001.step")) bodyCentered111.export(os.path.join(self.outputPath, "bodyCentered111.step")) + def test_faceCentered_lattice(self): + fc = self.shaping.FaceCentered([1, 0, 0], alpha = 0.01, filletsEnabled = True) + fc.build() + fc.lattice.WriteStep(os.path.join(self.outputPath, "fc_lattice.step")) + def test_faceCentered(self): faceCentered100 = self.shaping.FaceCentered(direction = [1, 0, 0], alpha = 0.01) faceCentered001 = self.shaping.FaceCentered(direction = [0, 0, 1], alpha = 0.01) diff --git a/thirdparty/netgen b/thirdparty/netgen new file mode 160000 index 0000000..9477fb0 --- /dev/null +++ b/thirdparty/netgen @@ -0,0 +1 @@ +Subproject commit 9477fb032184d16ff12c50b2e1ee8c868fa1f23a