stage changes

Fix: openfoam: wrong path expressions

.circleci/config.yml

@@ -0,0 +1,28 @@
+version: 2
+
+workflows:
+  version: 2
+  test:
+    jobs:
+      - test-3.10
+
+jobs:
+  test-3.10:
+    docker:
+      - image: cimg/python:3.10
+    steps:
+      - checkout
+      - run:
+          name: install packages
+          command: |
+            pip install poetry
+            poetry config virtualenvs.in-project true
+            poetry install
+      - run:
+          name: run tests
+          command: |
+            mkdir test-reports
+            poetry run pytest --cov=anisotropy --json-report --json-report-file test-reports/pytest.json -v tests
+      - store_artifacts:
+          path: test-reports
+

.gitignore

@@ -4,6 +4,7 @@ logs/
 storage/
 temp/
 env/
+*output/
 *.gz
 *.xz
 *.fls
@@ -18,3 +19,11 @@ env/
 *.toc
 *.out
 *.egg-info
+.ipynb_checkpoints/
+.coverage
+.venv
+.pytest_cache
+dist/
+doc/anisotropy/*
+!doc/anisotropy/.gitkeep
+/.idea

.vscode/launch.json

@@ -0,0 +1,15 @@
+{
+    "version": "0.2.0",
+    "configurations": [
+        {
+            "name": "anisotropy compute",
+            "type": "python",
+            "request": "launch",
+            "program": "${workspaceFolder}/anisotropy/core/cli.py",
+            "args": ["compute", "-v"],
+            "console": "integratedTerminal",
+            "cwd": "/tmp/anisotropy",
+            "preLaunchTask": "prepare"
+        }
+    ]
+}

.vscode/settings.json

@@ -0,0 +1,12 @@
+{
+    "python.pythonPath": "${env:HOME}/.local/share/mambaforge/envs/anisotropy/bin/python",
+    "python.testing.pytestArgs": [
+        "tests"
+    ],
+    "python.testing.unittestEnabled": false,
+    "python.testing.pytestEnabled": true,
+    "python.linting.enabled": true,
+    "python.linting.pylintEnabled": false,
+    "python.linting.flake8Enabled": true,
+    "python.linting.flake8Args": ["--ignore=E402,E251,E501,E201,E202,W293,W291,W504,E203", "--verbose"]
+}

.vscode/tasks.json

@@ -0,0 +1,9 @@
+{
+    "version": "2.0.0",
+    "tasks": [{
+        "label": "prepare",
+        "command": "mkdir",
+        "args": ["-p", "/tmp/anisotropy"],
+        "type": "shell",
+    }]
+}

ISSUES.rst

@@ -0,0 +1,2 @@
+List of known issues
+====================

README.rst

@@ -1,3 +1,6 @@
+.. image:: https://circleci.com/gh/L-Nafaryus/anisotropy/tree/devel.svg?style=shield&circle-token=423bc964a997ded671ebd4ceacc25f9967acdffa
+    :target: https://circleci.com/gh/L-Nafaryus/anisotropy/tree/devel
+
 anisotropy
 ==========
 
@@ -31,7 +34,14 @@ Dependencies
 
 .. Installation
 
-.. include:: INSTALL.rst
+.. code-block:: bash
+
+   $ git clone https://github.com/L-Nafaryus/anisotropy.git
+   $ cd anisotropy
+   $ conda env create
+   $ conda activate anisotropy
+   $ poetry install
+   $ anisotropy --help
 
 Getting Started
 ===============

anisotropy/__init__.py

@@ -1,40 +1,42 @@
 # -*- coding: utf-8 -*-
-# This file is part of anisotropy.
-# License: GNU GPL version 3, see the file "LICENSE" for details.
 
 """anisotropy
 
 *anisotropy* is a ``Python`` package that is the result of science-research work 
 on the anisotropy of permeability in the periodic porous media. 
-A project uses own wrappers around external applications 
-for constructing a shapes and meshes (``Salome``) and computing a flow (``OpenFOAM``).
 """
 
 __license__ = "GPL3"
-__version__ = "1.3.0"
+__version__ = "1.2.0"
 __author__ = __maintainer__ = "George Kusayko"
 __email__ = "gkusayko@gmail.com"
+__repository__ = "https://github.com/L-Nafaryus/anisotropy"
 
 ###
 #   Environment
 ##
-import os
+from os import path, environ
 
-env = dict(
-    ROOT = os.path.abspath(os.path.join(os.path.dirname(__file__), ".."))
-)
-env.update(
-    BUILD = os.path.join(env["ROOT"], "build"),
-    LOG = os.path.join(env["ROOT"], "logs"),
-    CONFIG = os.path.join(env["ROOT"], "anisotropy/config/default.toml"),
-    DOCS = os.path.join(env["ROOT"], "docs")
-)
-env.update(
-    logger_name = "anisotropy",
-    db_name = "anisotropy",
-    db_path = env["BUILD"],
-    salome_timeout = 15 * 60,
-    openfoam_template = os.path.join(env["ROOT"], "anisotropy/openfoam/template")
-)
 
-del os
+PROJECT = path.abspath(path.dirname(__file__))
+TMP = "/tmp/anisotropy"
+
+env = {
+    "PROJECT": path.abspath(path.dirname(__file__)),
+    "TMP": TMP,
+    "CWD": TMP,
+    "BUILD_DIR": "build",
+    "CONF_FILE": "anisotropy.toml",
+    "LOG_FILE": "anisotropy.log",
+    "DB_FILE": "anisotropy.db"
+}
+
+
+def loadEnv():
+    prefix = "AP_"
+
+    for k, v in env.items():
+        environ[f"{ prefix }{ k }"] = v
+
+
+del path, PROJECT, TMP

anisotropy/cli/__init__.py

@@ -0,0 +1,15 @@
+# -*- coding: utf-8 -*-
+
+from . import utils
+
+from .cli import anisotropy_cli
+
+
+__all__ = [
+    "utils",
+    "anisotropy_cli"
+]
+
+
+if __name__ == "__main__":
+    anisotropy_cli()

anisotropy/cli/cli.py

@@ -0,0 +1,181 @@
+# -*- coding: utf-8 -*-
+
+import click
+import pathlib
+import os
+import logging
+
+from . import utils
+
+
+@click.group()
+@click.version_option()
+def anisotropy_cli():
+    pass
+
+
+@anisotropy_cli.command(
+    help = "Initialize new anisotropy project."
+)
+@click.option(
+    "-P", "--path", "path",
+    default = os.getcwd(),
+    help = "Specify directory to use (instead of cwd)"
+)
+@click.option(
+    "-v", "--verbose", "verbose",
+    count = True,
+    help = "Increase verbose level"
+)
+def init(path, verbose):
+    from anisotropy.core import config as core_config
+    from anisotropy.core import utils as core_utils
+    
+    core_utils.setupLogger(utils.verbose_level(verbose))
+    logger = logging.getLogger(__name__)
+    
+    config = core_config.default_config() 
+    filepath = os.path.abspath(os.path.join(path, "anisotropy.toml"))
+    
+    logger.info(f"Saving file at { filepath }")
+    config.dump(filepath)
+    
+    
+@anisotropy_cli.command()
+@click.option(
+    "-P", "--path", "path",
+    default = os.getcwd(),
+    help = "Specify directory to use (instead of cwd)"
+)
+@click.option(
+    "-C", "--conf", "configFile"
+)
+@click.option(
+    "-N", "--nprocs", "nprocs",
+    type = click.INT,
+    # default = 1,
+    help = "Count of parallel processes"
+)
+@click.option(
+    "-s", "--stage", "stage", 
+    type = click.Choice(["all", "shape", "mesh", "flow", "postProcess"]),
+    # default = "all",
+    help = "Current computation stage"
+)
+@click.option(
+    "-f", "--force", "overwrite",
+    is_flag = True,
+    default = None,
+    help = "Overwrite existing entries"
+)
+@click.option(
+    "-p", "--params", "params", 
+    metavar = "key=value", 
+    multiple = True, 
+    cls = utils.KeyValueOption,
+    help = "Overwrite existing parameter (except control variables)"
+)
+@click.option(
+    "-v", "--verbose", "verbose",
+    count = True,
+    help = "Increase verbose level"
+)
+@click.option(
+    "--exec-id", "execution"
+)
+@click.option(
+    "--pid", "pid",
+    help = "Specify pid file path"
+)
+@click.option(
+    "--logfile", "logfile",
+    help = "Specify log file path"
+)
+def compute(path, configFile, nprocs, stage, overwrite, params, verbose, execution, pid, logfile):
+    import anisotropy
+    from anisotropy.core import UltimateRunner
+    from anisotropy.core import config as core_config
+    from anisotropy.core import utils as core_utils
+    
+    anisotropy.loadEnv()
+
+    if path:
+        path = pathlib.Path(path).resolve()
+
+        os.makedirs(path, exist_ok = True)
+        os.chdir(path)
+        os.environ["AP_CWD"] = str(path)
+
+    core_utils.setupLogger(utils.verbose_level(verbose), logfile)
+    logger = logging.getLogger(__name__)
+    
+    config = core_config.default_config() 
+
+    if configFile:
+        configFile = pathlib.Path(configFile).resolve()
+
+        logger.info(f"Loading file from { configFile }")
+
+        try:
+            config.load(configFile)
+
+        except FileNotFoundError:
+            config.dump(configFile)
+
+    else:
+        logger.info("Using default configuration")
+
+    args = {
+        "nprocs": nprocs,
+        "stage": stage,
+        "overwrite": overwrite 
+    }
+    
+    for k, v in args.items():
+        if v is not None:
+            config.update(**{ k: v })
+
+    if pid:
+        pid = pathlib.Path(pid).resolve()
+
+        with open(pid, "w") as io:
+            io.write(str(os.getpid()))
+
+    runner = UltimateRunner(config = config, exec_id = execution)
+    runner.prepare_queue()
+    runner.start()
+
+    if pid:
+        os.remove(pid)
+
+    logger.info("Computation done. Exiting ...")
+
+
+@anisotropy_cli.command()
+@click.option(
+    "-P", "--path", "path",
+    default = os.getcwd(),
+    help = "Specify directory to use (instead of cwd)"
+)
+@click.option(
+    "-v", "--verbose", "verbose",
+    count = True,
+    help = "Increase verbose level"
+)
+def gui(path, verbose):
+    import anisotropy
+    from anisotropy.core import utils as core_utils
+    from anisotropy import gui
+
+    anisotropy.loadEnv()
+
+    path = pathlib.Path(path).resolve()
+    path.mkdir(parents = True, exist_ok = True)
+    
+    os.chdir(path)
+    os.environ["ANISOTROPY_CWD"] = str(path)
+
+    core_utils.setupLogger(utils.verbose_level(verbose))
+    # logger = logging.getLogger(__name__)
+
+    gui.run(debug = True)

anisotropy/cli/utils.py

@@ -0,0 +1,74 @@
+# -*- coding: utf-8 -*-
+
+import click
+import ast
+import logging
+
+
+class LiteralOption(click.Option):
+    def type_cast_value(self, ctx, value):
+        try:
+            return ast.literal_eval(value)
+
+        except Exception:
+            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 Exception:
+            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 verbose_level(level: int):
+    return {
+        0: logging.ERROR,
+        1: logging.INFO,
+        2: logging.DEBUG
+    }.get(level, logging.ERROR)

anisotropy/config/bashrc

@@ -1,3 +0,0 @@
-# Example of anisotropy bashrc entries (modify it)
-export PATH="${HOME}/programs/salome/SALOME-9.7.0-MPI:${PATH}"
-source "${HOME}/programs/OpenFOAM/OpenFOAM-v2012/etc/bashrc"

anisotropy/config/default.toml

@@ -1,281 +0,0 @@
-# -*- coding: utf-8 -*-
-# This file is part of anisotropy.
-# License: GNU GPL version 3, see the file "LICENSE" for details.
-
-[logger]
-name = "anisotropy"
-format = "[ %(levelname)s ] %(message)s"
-
-[base]
-simple = true 
-bodyCentered = true 
-faceCentered = true 
-
-[[structures]]
-    [structures.structure]
-    type = "simple"
-    # auto # from theta: list # theta: float
-    theta = [0.01, 0.28, 0.01]  # [min, max, step]
-    # auto # from directions:list # direction: list
-    directions = [  
-        [1, 0, 0],
-        [0, 0, 1],
-        [1, 1, 1]
-    ]
-
-    # r0 = 
-    # L = 
-    # radius = 
-
-    filletsEnabled = true
-    # auto # fillets: float
-
-    [structures.mesh]
-    maxSize = 0.5
-    minSize = 0.05
-
-    fineness = 5
-    growthRate = 0.5
-    nbSegPerEdge = 2
-    nbSegPerRadius = 1
-    
-    chordalErrorEnabled = true
-    chordalError = 0.25
-    
-    secondOrder = false
-    optimize = true
-    quadAllowed = false
-    useSurfaceCurvature = true
-    fuseEdges = true
-    checkChartBoundary = false
-
-    viscousLayers = true
-    thickness = [0.01, 0.005]   # [min, max] # step is controlled by theta count
-    numberOfLayers = 1
-    stretchFactor = 1
-    isFacesToIgnore = true 
-    facesToIgnore = ["inlet", "outlet"]
-    # auto # faces: list
-    extrusionMethod = "SURF_OFFSET_SMOOTH"
-
-    [[structures.submesh]]
-    name = "strips"
-    maxSize = 0.5
-    minSize = 0.05
-
-    fineness = 5
-    growthRate = 0.2
-    nbSegPerEdge = 2
-    nbSegPerRadius = 3
-    
-    chordalErrorEnabled = true
-    chordalError = 0.25
-    
-    secondOrder = false
-    optimize = true
-    quadAllowed = false
-    useSurfaceCurvature = true
-    fuseEdges = true
-    checkChartBoundary = false
-
-    [structures.flowapproximation]
-    transportProperties.nu = 1e-6
-
-    pressure.boundaryField.inlet = { type = "fixedValue", value = 1e-3 }
-    pressure.boundaryField.outlet = { type = "fixedValue", value = 0.0 }
-
-    # multiplication velocity value with flow direction vector
-    velocity.boundaryField.inlet = { type = "fixedValue", value = 6e-5 }
-    velocity.boundaryField.outlet = { type = "zeroGradient", value = "None" }
-
-    [structures.flow]
-    scale = [ 1e-5, 1e-5, 1e-5 ]
-
-    transportProperties.nu = 1e-6
-
-    pressure.boundaryField.inlet = { type = "fixedValue", value = 1e-3 }
-    pressure.boundaryField.outlet = { type = "fixedValue", value = 0.0 }
-
-    velocity.boundaryField.inlet = { type = "pressureInletVelocity", value = 0.0 }
-    velocity.boundaryField.outlet = { type = "zeroGradient", value = "None" }
-
-
-[[structures]]
-    [structures.structure]
-    type = "bodyCentered"
-    # auto # from theta: list # theta: float
-    theta = [0.01, 0.17, 0.01]  # [min, max, step]
-    # auto # from directions:list # direction: list
-    directions = [  
-        [1, 0, 0],
-        [0, 0, 1],
-        [1, 1, 1]
-    ]
-
-    # r0 = 
-    # L = 
-    # radius = 
-
-    filletsEnabled = true
-    # auto # fillets: float
-
-    [structures.mesh]
-    maxSize = 0.5
-    minSize = 0.05
-
-    fineness = 5
-    growthRate = 0.5
-    nbSegPerEdge = 2
-    nbSegPerRadius = 1
-    
-    chordalErrorEnabled = true
-    chordalError = 0.25
-    
-    secondOrder = false
-    optimize = true
-    quadAllowed = false
-    useSurfaceCurvature = true
-    fuseEdges = true
-    checkChartBoundary = false
-
-    viscousLayers = true
-    thickness = [0.005, 0.0005]   # [min, max] # step is controlled by theta count
-    numberOfLayers = 1
-    stretchFactor = 1
-    isFacesToIgnore = true 
-    facesToIgnore = ["inlet", "outlet"]
-    # auto # faces: list
-    extrusionMethod = "SURF_OFFSET_SMOOTH"
-
-    [[structures.submesh]]
-    name = "strips"
-    maxSize = 0.5
-    minSize = 0.05
-
-    fineness = 5
-    growthRate = 0.2
-    nbSegPerEdge = 2
-    nbSegPerRadius = 3
-    
-    chordalErrorEnabled = true
-    chordalError = 0.25
-    
-    secondOrder = false
-    optimize = true
-    quadAllowed = false
-    useSurfaceCurvature = true
-    fuseEdges = true
-    checkChartBoundary = false
-
-    [structures.flowapproximation]
-    transportProperties.nu = 1e-6
-
-    pressure.boundaryField.inlet = { type = "fixedValue", value = 1e-3 }
-    pressure.boundaryField.outlet = { type = "fixedValue", value = 0.0 }
-
-    # multiplication velocity value with direction vector
-    velocity.boundaryField.inlet = { type = "fixedValue", value = 6e-5 }
-    velocity.boundaryField.outlet = { type = "zeroGradient", value = "None" }
-
-    [structures.flow]
-    scale = [ 1e-5, 1e-5, 1e-5 ]
-
-    transportProperties.nu = 1e-6
-
-    pressure.boundaryField.inlet = { type = "fixedValue", value = 1e-3 }
-    pressure.boundaryField.outlet = { type = "fixedValue", value = 0.0 }
-
-    velocity.boundaryField.inlet = { type = "pressureInletVelocity", value = 0.0 }
-    velocity.boundaryField.outlet = { type = "zeroGradient", value = "None" }
-
-
-[[structures]]
-    [structures.structure]
-    type = "faceCentered"
-    # auto # from theta: list # theta: float
-    theta = [0.01, 0.12, 0.01]  # [min, max, step]
-    # auto # from directions:list # direction: list
-    directions = [  
-        [1, 0, 0],
-        [0, 0, 1],
-        [1, 1, 1]
-    ]
-
-    # r0 = 
-    # L = 
-    # radius = 
-
-    filletsEnabled = true
-    # auto # fillets: float
-
-    [structures.mesh]
-    maxSize = 0.5
-    minSize = 0.05
-
-    fineness = 5
-    growthRate = 0.5
-    nbSegPerEdge = 2
-    nbSegPerRadius = 1
-    
-    chordalErrorEnabled = true
-    chordalError = 0.25
-    
-    secondOrder = false
-    optimize = true
-    quadAllowed = false
-    useSurfaceCurvature = true
-    fuseEdges = true
-    checkChartBoundary = false
-
-    viscousLayers = true
-    thickness = [0.001, 0.0005]   # [min, max] # step is controlled by theta count
-    numberOfLayers = 1
-    stretchFactor = 1
-    isFacesToIgnore = true 
-    facesToIgnore = ["inlet", "outlet"]
-    # auto # faces: list
-    extrusionMethod = "SURF_OFFSET_SMOOTH"
-
-    [[structures.submesh]]
-    name = "strips"
-    maxSize = 0.5
-    minSize = 0.05
-
-    fineness = 5
-    growthRate = 0.2
-    nbSegPerEdge = 2
-    nbSegPerRadius = 3
-    
-    chordalErrorEnabled = true
-    chordalError = 0.25
-    
-    secondOrder = false
-    optimize = true
-    quadAllowed = false
-    useSurfaceCurvature = true
-    fuseEdges = true
-    checkChartBoundary = false
-
-    [structures.flowapproximation]
-    transportProperties.nu = 1e-6
-
-    pressure.boundaryField.inlet = { type = "fixedValue", value = 1e-3 }
-    pressure.boundaryField.outlet = { type = "fixedValue", value = 0.0 }
-
-    # multiplication velocity value with direction vector
-    velocity.boundaryField.inlet = { type = "fixedValue", value = 6e-5 }
-    velocity.boundaryField.outlet = { type = "zeroGradient", value = "None" }
-
-    [structures.flow]
-    scale = [ 1e-5, 1e-5, 1e-5 ]
-
-    transportProperties.nu = 1e-6
-    
-    pressure.boundaryField.inlet = { type = "fixedValue", value = 1e-3 }
-    pressure.boundaryField.outlet = { type = "fixedValue", value = 0.0 }
-
-    velocity.boundaryField.inlet = { type = "pressureInletVelocity", value = 0.0 }
-    velocity.boundaryField.outlet = { type = "zeroGradient", value = "None" }
-
-
-

anisotropy/core/__init__.py

@@ -1,5 +1,17 @@
 # -*- coding: utf-8 -*-
-# This file is part of anisotropy.
-# License: GNU GPL version 3, see the file "LICENSE" for details.
+
+from . import utils
+from . import config
+from . import postprocess
+
+from .parallel import ParallelRunner
+from .runner import UltimateRunner
 
 
+__all__ = [
+    "utils",
+    "config",
+    "postprocess",
+    "ParallelRunner",
+    "UltimateRunner"
+]

anisotropy/core/cli.py

@@ -1,579 +0,0 @@
-# -*- coding: utf-8 -*-
-# This file is part of anisotropy.
-# License: GNU GPL version 3, see the file "LICENSE" for details.
-
-import click
-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)
-
-        
-def version():
-    msg = "Missed package anisotropy"
-
-    try:
-        from anisotropy.core.main import Anisotropy
-        msg = Anisotropy.version()
-
-    except ImportError:
-        pass
-
-    return msg
-
-@click.group()
-@click.version_option(version = "", message = version())
-def anisotropy():
-    pass
-
-
-@anisotropy.command(
-    help = "Initialize new anisotropy project."
-)
-@click.option(
-    "-P", "--path", "path",
-    default = os.getcwd(),
-    help = "Specify directory to use (instead of cwd)"
-)
-def init(path):
-    from anisotropy import env
-    from anisotropy.core.main import Database
-
-    if not os.path.exists(path) or not os.path.isdir(path):
-        click.echo(f"Cannot find directory { path }")
-
-        return
-
-    wds = [ "build", "logs" ]
-
-    for wd in wds:
-        os.makedirs(os.path.join(path, wd), exist_ok = True)
-
-    shutil.copy(env["CONFIG"], os.path.join(path, "anisotropy.toml"), follow_symlinks = True)
-    
-    db = Database(env["db_name"], path)
-    db.setup()
-
-    click.echo(f"Initialized anisotropy project in { path }")
-
-
-@anisotropy.command(
-    help = "Load parameters from configuration file and update database."
-)
-@click.option(
-    "-f", "--force", "force",
-    is_flag = True,
-    default = False,
-    help = "Overwrite existing entries"
-)
-@click.option(
-    "-p", "--params", "params", 
-    metavar = "key=value", 
-    multiple = True, 
-    cls = KeyValueOption,
-    help = "Specify control parameters to update (type, direction, theta)"
-)
-@click.option(
-    "-P", "--path", "path",
-    default = os.getcwd(),
-    help = "Specify directory to use (instead of cwd)"
-)
-def update(force, params, path):
-    from anisotropy import env
-    from anisotropy.core.main import Anisotropy, Database
-
-    env.update(
-        LOG = os.path.join(path, "logs"),
-        BUILD = os.path.join(path, "build"),
-        CONFIG = os.path.join(path, "anisotropy.toml"),
-        db_path = path
-    )
-
-    args = dict()
-
-    for param in params:
-        args.update(param)
-
-
-    model = Anisotropy()
-    database = Database(env["db_name"], env["db_path"]) 
-        
-    click.echo("Configuring database ...")
-    database.setup()
-
-    if database.isempty() or update:
-        paramsAll = model.loadFromScratch(env["CONFIG"])
-
-        if args.get("type"):
-            paramsAll = [ entry for entry in paramsAll if args["type"] == entry["structure"]["type"] ]
-
-        if args.get("direction"):
-            paramsAll = [ entry for entry in paramsAll if args["direction"] == entry["structure"]["direction"] ]
-
-        if args.get("theta"):
-            paramsAll = [ entry for entry in paramsAll if args["theta"] == entry["structure"]["theta"] ]
-
-        for entry in paramsAll:
-            database.update(entry)
-
-        click.echo("{} entries was updated.".format(len(paramsAll)))
-
-    else:
-        click.echo("Database was not modified.")
-
-
-@anisotropy.command(
-    help = """Compute cases by chain (mesh -> flow)
-    
-    Control parameters: type, direction, theta (each parameter affects on a queue)
-    """
-)
-@click.option(
-    "-s", "--stage", "stage", 
-    type = click.Choice(["all", "mesh", "flow", "postProcessing"]), 
-    default = "all",
-    help = "Current computation stage"
-)
-@click.option(
-    "-N", "--nprocs", "nprocs",
-    type = click.INT,
-    default = 1,
-    help = "Count of parallel processes"
-)
-@click.option(
-    "-f", "--force", "force",
-    is_flag = True,
-    default = False,
-    help = "Overwrite existing entries"
-)
-@click.option(
-    "-p", "--params", "params", 
-    metavar = "key=value", 
-    multiple = True, 
-    cls = KeyValueOption,
-    help = "Overwrite existing parameter (except control variables)"
-)
-@click.option(
-    "-P", "--path", "path",
-    default = os.getcwd(),
-    help = "Specify directory to use (instead of cwd)"
-)
-def compute(stage, nprocs, force, params, path):
-    from anisotropy import env
-    from anisotropy.core.main import Anisotropy, Database, logger
-    from anisotropy.core.utils import setupLogger, parallel
-
-    env.update(
-        LOG = os.path.join(path, "logs"),
-        BUILD = os.path.join(path, "build"),
-        CONFIG = os.path.join(path, "anisotropy.toml"),
-        db_path = path
-    )
-
-    setupLogger(logger, logging.INFO, env["LOG"])
-    args = dict()
-
-    for param in params:
-        args.update(param)
-
-    ###
-    logger.info("Writing pid ...")
-    pidpath = os.path.join(path, "anisotropy.pid")
-
-    with open(pidpath, "w") as io:
-        io.write(str(os.getpid()))
-
-    ###
-    #   Preparations
-    ##
-    database = Database(env["db_name"], env["db_path"]) 
-        
-    logger.info("Loading database ...")
-    database.setup()
-
-    params = database.loadGeneral(
-        args.get("type"), 
-        args.get("direction"), 
-        args.get("theta")
-    )
-    queueargs = []
-    
-    for p in params:
-        s = p["structure"]
-
-        queueargs.append((s["type"], s["direction"], s["theta"]))
-    
-    ###
-    #   Wrap function
-    ##
-    def computeCase(type, direction, theta):
-        case = Anisotropy()
-        case.db = database
-        case.load(type, direction, theta)
-        case.evalParams()
-        case.update()
-
-        logger.info(f"Case: type = { type }, direction = { direction }, theta = { theta }")
-        logger.info(f"Stage mode: { stage }")
-
-        if stage in ["mesh", "all"]:
-            case.load(type, direction, theta)
-
-            if not case.params["meshresult"]["meshStatus"] == "Done" or force:
-                logger.info("Current stage: mesh")
-                out, err, returncode = case.computeMesh(path)
-
-                if out: logger.info(out)
-                if err: logger.error(err)
-                if returncode:
-                    logger.error("Mesh computation failed. Skipping flow computation ...")
-
-                    return
-
-            else:
-                logger.info("Mesh exists. Skipping ...")
-
-        if stage in ["flow", "all"]:
-            case.load(type, direction, theta)
-
-            if not case.params["flowresult"]["flowStatus"] == "Done" or force:
-                logger.info("Current stage: flow")
-                out, err, returncode = case.computeFlow(path)
-
-                if out: logger.info(out)
-                if err: logger.error(err)
-                if returncode:
-                    logger.error("Flow computation failed.")
-
-                    return
-
-            else:
-                logger.info("Flow exists. Skipping ...")
-
-        if stage in ["postProcessing", "all"]:
-            case.load(type, direction, theta)
-
-            if case.params["meshresult"]["meshStatus"] == "Done":
-                logger.info("Current stage: mesh postProcessing")
-                case.porosity()
-
-            else:
-                logger.warning("Cannot compute mesh post processing values.")
-            
-            if case.params["flowresult"]["flowStatus"] == "Done":
-                logger.info("Current stage: flow postProcessing")
-                case.flowRate()
-
-            else:
-                logger.warning("Cannot compute flow post processing values.")
-
-
-    ###
-    #   Run
-    ##
-    if nprocs == 1:
-        for pos, qarg in enumerate(queueargs):
-            computeCase(*qarg)
-
-    else:
-        parallel(nprocs, queueargs, computeCase)
-
-    if os.path.exists(pidpath):
-        logger.info("Removing pid ...")
-        os.remove(pidpath)
-
-    logger.info("Computation done.")
-
-
-@anisotropy.command(
-    help = "Kill process by pid file"
-)
-@click.option(
-    "-P", "--path", "path",
-    default = os.getcwd(),
-    help = "Specify directory to use (instead of cwd)"
-)
-@click.argument("pidfile")
-def kill(path, pidfile):
-    from anisotropy.salomepl.utils import SalomeManager
-
-    try:
-        with open(os.path.join(path, pidfile), "r") as io:
-            pid = io.read()
-
-        os.kill(int(pid), 9)
-
-    except FileNotFoundError:
-        click.echo(f"Unknown file { pidfile }")
-
-    except ProcessLookupError:
-        click.echo(f"Cannot find process with pid { pid }")
-
-    # TODO: killall method kills all salome instances. Not a good way
-    SalomeManager().killall()
-
-@anisotropy.command(
-    help = "! Internal command"
-)
-@click.argument("root")
-@click.argument("type")
-@click.argument("direction")
-@click.argument("theta")
-@click.argument("path")
-def computemesh(root, type, direction, theta, path):
-    # ISSUE: can't hide command from help, 'hidden = True' doesn't work
-    # [Salome Environment]
-    
-    ###
-    #   Args
-    ##
-    direction = [ float(num) for num in direction[1:-1].split(" ") if num ]
-    theta = float(theta)
-
-    ###
-    #   Modules
-    ##
-    import os, sys
-    
-    pyversion = "{}.{}".format(3, 9) #(*sys.version_info[:2])
-    sys.path.extend([
-        root,
-        os.path.join(root, "env/lib/python{}/site-packages".format(pyversion)),
-        os.path.abspath(".local/lib/python{}/site-packages".format(pyversion))
-    ])
-    
-    from anisotropy import env
-    from anisotropy.core.main import Anisotropy, Database
-    import salome 
-
-    ###
-    model = Anisotropy()
-    model.db = Database(env["db_name"], path)
-    model.load(type, direction, theta)
-    
-    salome.salome_init()
-    model.genmesh(path)
-    salome.salome_close()
-
-
-
-@anisotropy.command()
-@click.option(
-    "-p", "--params", "params", 
-    metavar = "key=value", 
-    multiple = True, 
-    cls = KeyValueOption,
-    help = "Select by control parameters (type, direction, theta)"
-)
-@click.option(
-    "-P", "--path", "path",
-    metavar = "PATH",
-    default = os.getcwd(),
-    help = "Specify directory to use (instead of cwd)"
-)
-@click.option(
-    "--list", "printlist",
-    is_flag = True,
-    help = "Print a list of avaliable fields."
-)
-@click.option(
-    "--export",
-    metavar = "PATH",
-    help = "Export output."
-)
-@click.option(
-    "--fields", "fields",
-    metavar = "f1,f2,...",
-    multiple = True,
-    cls = CliListOption,
-    help = "Select fields to use."
-)
-@click.argument(
-    "output",
-    required = False,
-    type = click.Choice(["cli", "plot"]),
-    default = "cli"
-)
-def show(params, path, printlist, export, fields, output):
-    from anisotropy import env
-    from anisotropy.core.database import Database, Structure
-    from pandas import DataFrame, Series
-    import matplotlib.pyplot as plt
-
-    env.update(
-        LOG = os.path.join(path, "logs"),
-        BUILD = os.path.join(path, "build"),
-        CONFIG = os.path.join(path, "anisotropy.toml"),
-        db_path = path
-    )
-
-    args = dict()
-
-    for param in params:
-        args.update(param)
-
-
-    ###
-    db = Database(env["db_name"], env["db_path"]) 
-    db.setup()
-
-    searchargs = []
-
-    if args.get("type"):
-        searchargs.append(Structure.type == args["type"])
-
-    if args.get("direction"):
-        searchargs.append(Structure.direction == str(args["direction"]))
-
-    if args.get("theta"):
-        searchargs.append(Structure.theta == args["theta"])
-
-    result = db.search(searchargs)
-    result.sort(key = lambda src: f"{ src['type'] }{ src['direction'] }{ src['theta'] }")
-
-    df = DataFrame(result)
-    df_keys = [ key for key in df.keys() ]
-    
-    if printlist:
-        click.echo("Avaliable fields for query:")
-        click.echo("\t{}".format("\n\t".join(df_keys)))
-
-        return
-
-    if not result:
-        click.echo("Empty result.")
-
-        return
-
-    tables = []
-
-    if fields:
-        for fieldslist in fields:
-            for field in fieldslist:
-                if field not in df_keys:
-                    click.echo(f"Unknown field '{ field }'. Try to use '--list' flag to see all avaliable fields.")
-
-                    return
-        
-            tables.append(df[fieldslist])
-    else:
-        tables.append(df)
-
-    if output == "plot":
-        fig, ax = plt.subplots(nrows = 1, ncols = 1)
-
-        for table in tables:
-            table.plot(table.keys()[0], table.keys()[1], ax = ax, style = "o")
-
-        plt.legend()
-        plt.grid()
-    
-    if export:
-        supported = ["csv", "jpg"]
-        filepath, ext = os.path.splitext(export)
-        ext = ext.replace(".", "")
-
-        if ext not in supported:
-            click.echo(f"Unknown extension '{ ext }'.")
-
-            return
-
-        if ext == "csv":
-            if len(tables) == 1:
-                tables[0].to_csv(export, sep = ";")
-            
-            else:
-                for n, table in enumerate(tables):
-                    table.to_csv("{}.{}.{}".format(filepath, n, ext), sep = ";")
-
-        elif ext == "jpg":
-            plt.savefig(export)
-
-    else:
-
-        if output == "cli":
-            res = "\n\n".join([ table.to_string() for table in tables ])
-            click.echo(res)
-
-        elif output == "plot":
-            plt.show()
-
-    
-###
-#   CLI entry
-##
-if __name__ == "__main__":
-    #try:
-        anisotropy()
-
-    #except KeyboardInterrupt:
-    #    click.echo("Interrupted!")
-
-    #finally:
-    #    from anisotropy.salomepl.utils import SalomeManager
-    #    click.echo("Exiting ...")
-
-    #    if os.path.exists("anisotropy.pid"):
-    #        os.remove("anisotropy.pid")
-
-    #    SalomeManager().killall()
-
-    #    sys.exit(0)

anisotropy/core/config.py

@@ -0,0 +1,143 @@
+# -*- coding: utf-8 -*-
+# This file is part of anisotropy.
+# License: GNU GPL version 3, see the file "LICENSE" for details.
+
+import os
+import toml
+import copy
+import numpy as np
+
+
+class Config(object):
+    def __init__(self):
+        self.content = {}
+        self.options = {}
+        self.params = {}
+        self.cases = None
+
+    def __getitem__(self, key):
+        return self.options[key]
+
+    def __setitem__(self, key, value):
+        self.options[key] = value
+
+    def __delitem__(self, key):
+        del self.options[key]
+
+    def update(self, **kwargs):
+        self.options.update(**kwargs)
+
+    def __len__(self):
+        return len(self.options)
+
+    def __iter__(self):
+        for key in self.options:
+            yield key
+
+    def load(self, filename: str):
+        path = os.path.abspath(filename)
+
+        if not os.path.exists(path):
+            raise FileNotFoundError(path)
+
+        self.content = toml.load(path)
+        self.options = copy.deepcopy(self.content["options"])
+        self.content.pop("options")
+
+    def dump(self, filename: str):
+        path = os.path.abspath(filename)
+        ext = os.path.splitext(path)[1]
+
+        if not ext == ".toml":
+            path += ".toml"
+
+        os.makedirs(os.path.split(path)[0], exist_ok = True)
+
+        self.content.update(options = self.options)
+
+        with open(path, "w") as io:
+            toml.dump(self.content, io, encoder = toml.TomlNumpyEncoder())
+
+    def minimize(self):
+        self.content = None
+        self.cases = None
+
+    def purge(self):
+        self.minimize()
+        self.params = None
+
+    def copy(self):
+        return copy.deepcopy(self)
+
+    def expand(self):
+        self.cases = []
+
+        #   Expand structures for each direction and each alpha
+        for structure in self.content["structures"]:
+            structure = copy.deepcopy(structure)
+            alphaA = np.round(np.arange(
+                structure["alpha"][0], 
+                structure["alpha"][1] + structure["alphaStep"], 
+                structure["alphaStep"]
+            ), 9)
+            directionA = np.array(structure["directions"], dtype = float) 
+            structure.pop("alpha")
+            structure.pop("directions")
+
+            for direction in directionA:
+                for alpha in alphaA:
+                    self.cases.append({
+                        "alpha": alpha,
+                        "direction": direction,
+                        **structure
+                    })
+
+    def chooseParams(self, idn: int):
+        if len(self.cases) > 0:
+            self.params = self.cases[idn]
+
+        else:
+            raise IndexError("list index out of range in cause of zero length of 'cases'")
+
+
+def default_config() -> Config:
+    config = Config()
+
+    config.options = {
+        "nprocs": 1,
+        "stage": "all",
+        "overwrite": False,
+        "database": "anisotropy.db",
+        "build": "build",
+        "logs": "logs",
+        "shapefile": "shape.step",
+        "meshfile": "mesh.mesh"
+    }
+
+    config.content = {
+        "structures": []
+    }
+
+    labels = ["simple", "bodyCentered", "faceCentered"]
+    alphas = [[0.01, 0.28], [0.01, 0.17], [0.01, 0.13]]
+
+    for label, alpha in zip(labels, alphas):
+        config.content["structures"].append({
+            "label": label,
+            "alpha": alpha,
+            "alphaStep": 0.01,
+            "directions": [[1., 0., 0.], [0., 0., 1.], [1., 1., 1.]],
+            "r0": 1,
+            "filletsEnabled": True,
+            "pressureInlet": 1,
+            "pressureOutlet": 0,
+            "pressureInternal": 0,
+            "velocityInlet": [0., 0., 0.],
+            "velocityOutlet": None,
+            "velocityInternal": [0., 0., 0.],
+            "density": 1000,
+            "viscosity": 1e-3,
+            "scale": [1e-5, 1e-5, 1e-5]
+        })
+    
+    return config

anisotropy/core/database.py

@@ -1,405 +0,0 @@
-# -*- coding: utf-8 -*-
-# This file is part of anisotropy.
-# License: GNU GPL version 3, see the file "LICENSE" for details.
-
-import os
-import logging
-from copy import deepcopy
-
-from anisotropy import env
-from anisotropy.core.utils import setupLogger
-from anisotropy.core.models import (
-    db, JOIN, 
-    Structure, 
-    Mesh, SubMesh, MeshResult, 
-    Flow, FlowApproximation, FlowResult
-)
-from peewee import OperationalError
-
-logger = logging.getLogger(env["logger_name"])
-#setupLogger(logger, logging.INFO, env["LOG"])
-
-# NOTE: Temporary solution for multiprocessing mode when database is locked
-def tryUntilDone(func):
-    def inner(*args, **kwargs):
-        done = False 
-
-        while not done:
-            try:
-                ret = func(*args, **kwargs)
-                done = True
-
-            except OperationalError as e:
-                logger.error(e)
-
-        return ret
-
-    return inner
-
-
-class Database(object):
-    def __init__(self, name: str, filepath: str):
-        self.name = name
-        self.filepath = filepath
-        self.__db = db
-
-
-    def setup(self):
-        os.makedirs(self.filepath, exist_ok = True)
-
-        fullpath = os.path.join(self.filepath, "{}.db".format(self.name))
-        self.__db.init(fullpath)
-
-        if not os.path.exists(fullpath):
-            self.__db.create_tables([
-                Structure, 
-                Mesh,
-                SubMesh,
-                MeshResult,
-                Flow,
-                FlowApproximation,
-                FlowResult
-            ])
-
-
-    def isempty(self) -> bool:
-        """Checks DB for main table existence (Structure)
-
-        :return: True if exists
-        :rtype: bool
-        """
-        query = Structure.select()
-
-        return not query.exists()
-
-
-    def load(self, structure_type: str, structure_direction: list, structure_theta: float) -> dict:
-        structureQuery = (
-            Structure
-            .select()
-            .where(
-                Structure.type == structure_type,
-                Structure.direction == str(structure_direction),
-                Structure.theta == structure_theta
-            )
-        )
-        
-        params = {}
-
-        with self.__db.atomic():
-            if structureQuery.exists():
-                params["structure"] = structureQuery.dicts().get()
-
-                meshQuery = structureQuery.get().meshes
-
-                if meshQuery.exists():
-                    params["mesh"] = meshQuery.dicts().get()
-
-                    submeshQuery = meshQuery.get().submeshes
-                    
-                    if submeshQuery.exists():
-                        params["submesh"] = [ entry for entry in submeshQuery.dicts() ]
-
-                    meshresultQuery = meshQuery.get().meshresults
-
-                    if meshresultQuery.exists():
-                        params["meshresult"] = meshresultQuery.dicts().get()
-
-                flowQuery = structureQuery.get().flows
-
-                if flowQuery.exists():
-                    params["flow"] = flowQuery.dicts().get()
-
-                    flowapproximationQuery = flowQuery.get().flowapproximations
-
-                    if flowapproximationQuery.exists():
-                        params["flowapproximation"] = flowapproximationQuery.dicts().get()
-
-                    flowresultsQuery = flowQuery.get().flowresults
-
-                    if flowresultsQuery.exists():
-                        params["flowresult"] = flowresultsQuery.dicts().get()
-            else:
-                logger.error("Missed Structure table")
-
-        return params
-
-
-    def loadGeneral(self, type: str = None, direction: list = None, theta: float = None) -> list:
-        query = (
-            Structure
-            .select()
-            .order_by(Structure.type, Structure.direction, Structure.theta)
-        )
-        response = []
-
-        if type:
-            query = query.where(Structure.type == type)
-
-        if direction:
-            query = query.where(Structure.direction == str(direction))
-
-        if theta:
-            query = query.where(Structure.theta == theta)
-
-        for entry in query.dicts():
-            response.append({ "structure": entry })
-
-        return response
-
-
-    def update(self, params: dict):
-        if not params:
-            logger.error("Trying to update db from empty parameters")
-            return
-
-        query = (
-            Structure
-            .select(Structure, Mesh, Flow)
-            .join(
-                Mesh, 
-                JOIN.INNER, 
-                on = (Mesh.structure_id == Structure.structure_id)
-            )
-            .join(
-                Flow,
-                JOIN.INNER,
-                on = (Flow.structure_id == Structure.structure_id)
-            )
-            .where(
-                Structure.type == params["structure"]["type"],
-                Structure.direction == str(params["structure"]["direction"]),
-                Structure.theta == params["structure"]["theta"]
-            )
-        )
-        
-        structureID = tryUntilDone(self._updateStructure)(params.get("structure", {}), query)
-        
-        meshID = tryUntilDone(self._updateMesh)(params.get("mesh", {}), query, structureID)
-
-        for submeshParams in params.get("submesh", []):
-            tryUntilDone(self._updateSubMesh)(submeshParams, query, meshID)
-
-        tryUntilDone(self._updateMeshResult)(params.get("meshresult", {}), query, meshID)
-
-        flowID = tryUntilDone(self._updateFlow)(params.get("flow", {}), query, structureID)
-
-        tryUntilDone(self._updateFlowApproximation)(params.get("flowapproximation", {}), query, flowID)
-
-        tryUntilDone(self._updateFlowResult)(params.get("flowresult", {}), query, flowID)
-
-
-    def search(self, args: list):
-        result = {}
-        query = (
-            Structure
-            .select(Structure, Mesh, SubMesh, MeshResult, Flow, FlowApproximation, FlowResult)
-            .join(
-                Mesh,
-                JOIN.INNER,
-                on = (Mesh.structure_id == Structure.structure_id)
-            )
-            .join(
-                SubMesh,
-                JOIN.INNER,
-                on = (SubMesh.mesh_id == Mesh.mesh_id)
-            )
-            .join(
-                MeshResult,
-                JOIN.INNER,
-                on = (MeshResult.mesh_id == Mesh.mesh_id)
-            )
-            .join(
-                Flow,
-                JOIN.INNER,
-                on = (Flow.structure_id == Structure.structure_id)
-            )
-            .join(
-                FlowApproximation,
-                JOIN.INNER,
-                on = (FlowApproximation.flow_id == Flow.flow_id)
-            )
-            .join(
-                FlowResult,
-                JOIN.INNER,
-                on = (FlowResult.flow_id == Flow.flow_id)
-            )
-        )
-
-        for arg in args:
-            query = query.where(arg)
-
-
-        with self.__db.atomic():
-            if not self.isempty():
-                result = [ entry for entry in query.dicts() ] 
-
-            else:
-                logger.error("Missed Structure table")
-
-        return result
-
-
-    def _updateStructure(self, src: dict, queryMain) -> int:
-        raw = deepcopy(src)
-
-        with self.__db.atomic():
-            if not queryMain.exists():
-                tabID = Structure.create(**raw)
-
-            else:
-                req = queryMain.dicts().get()
-                tabID = req["structure_id"]
-
-                query = (
-                    Structure.update(**raw)
-                    .where(
-                        Structure.type == req["type"],
-                        Structure.direction == str(req["direction"]),
-                        Structure.theta == req["theta"]
-                    )
-                )
-                query.execute()
-
-        return tabID
-
-    def _updateMesh(self, src: dict, queryMain, structureID) -> int:
-        raw = deepcopy(src)
-
-        with self.__db.atomic():
-            if not queryMain.exists():
-                tabID = Mesh.create(
-                    structure_id = structureID,
-                    **raw
-                )
-
-            else:
-                req = queryMain.dicts().get()
-                tabID = req["mesh_id"]
-
-                query = (
-                    Mesh.update(**raw)
-                    .where(
-                        Mesh.structure_id == structureID
-                    )
-                )
-                query.execute()
-
-        return tabID
-
-    def _updateSubMesh(self, src: dict, queryMain, meshID):
-        #if not src:
-        #    return
-
-        raw = deepcopy(src)
-        
-        with self.__db.atomic():
-            if not SubMesh.select().where(SubMesh.mesh_id == meshID).exists():
-                tabID = SubMesh.create(
-                    mesh_id = meshID,
-                    **raw
-                )
-                logger.debug(f"[ DB ] Created SubMesh entry { tabID }")
-
-            else:
-                query = (
-                    SubMesh.update(**raw)
-                    .where(
-                        SubMesh.mesh_id == meshID,
-                        SubMesh.name == src["name"]
-                    )
-                )
-                query.execute()
-
-    def _updateMeshResult(self, src: dict, queryMain, meshID):
-        #if not src:
-        #    return
-
-        raw = deepcopy(src)
-
-        with self.__db.atomic():
-            if not MeshResult.select().where(MeshResult.mesh_id == meshID).exists():
-                tabID = MeshResult.create(
-                    mesh_id = meshID,
-                    **raw
-                )
-                logger.debug(f"[ DB ] Created MeshResult entry { tabID }")
-
-            else:
-                query = (
-                    MeshResult.update(**raw)
-                    .where(
-                        MeshResult.mesh_id == meshID 
-                    )
-                )
-                query.execute()
-
-    def _updateFlow(self, src: dict, queryMain, structureID):
-        raw = deepcopy(src)
-
-        with self.__db.atomic():
-            if not queryMain.exists():
-                tabID = Flow.create(
-                    structure_id = structureID,
-                    **raw
-                )
-
-            else:
-                req = queryMain.dicts().get()
-                tabID = req["flow_id"]
-
-                query = (
-                    Flow.update(**raw)
-                    .where(
-                        Flow.structure_id == structureID
-                    )
-                )
-                query.execute()
-
-        return tabID
-
-    def _updateFlowApproximation(self, src: dict, queryMain, flowID):
-        #if not src:
-        #    return
-
-        raw = deepcopy(src)
-
-        with self.__db.atomic():
-            if not FlowApproximation.select().where(FlowApproximation.flow_id == flowID).exists():
-                tabID = FlowApproximation.create(
-                    flow_id = flowID,
-                    **raw
-                )
-                logger.debug(f"[ DB ] Created FlowApproximation entry { tabID }")
-
-            else:
-                query = (
-                    FlowApproximation.update(**raw)
-                    .where(
-                        FlowApproximation.flow_id == flowID 
-                    )
-                )
-                query.execute()
-
-    def _updateFlowResult(self, src: dict, queryMain, flowID):
-        #if not src:
-        #    return
-
-        raw = deepcopy(src)
-
-        with self.__db.atomic():
-            if not FlowResult.select().where(FlowResult.flow_id == flowID).exists():
-                tabID = FlowResult.create(
-                    flow_id = flowID,
-                    **raw
-                )
-                logger.debug(f"[ DB ] Created FlowResult entry { tabID }")
-
-            else:
-                query = (
-                    FlowResult.update(**raw)
-                    .where(
-                        FlowResult.flow_id == flowID 
-                    )
-                )
-                query.execute()

anisotropy/core/main.py

@@ -1,580 +0,0 @@
-# -*- coding: utf-8 -*-
-# This file is part of anisotropy.
-# License: GNU GPL version 3, see the file "LICENSE" for details.
-
-import os, sys
-import time
-from datetime import timedelta, datetime
-import shutil
-import logging
-from copy import deepcopy
-from math import sqrt
-
-import toml
-
-from anisotropy import (
-    __version__, env,
-    openfoam
-)
-from anisotropy.core.utils import setupLogger, Timer
-from anisotropy.core.database import Database
-from anisotropy import salomepl
-import anisotropy.salomepl.utils
-import anisotropy.salomepl.geometry
-import anisotropy.salomepl.mesh
-from anisotropy.samples import Simple, FaceCentered, BodyCentered
-
-logger = logging.getLogger(env["logger_name"])
-#setupLogger(logger, logging.INFO, env["LOG"])
-
-#peeweeLogger = logging.getLogger("peewee")
-#peeweeLogger.setLevel(logging.INFO)
-
-
-class Anisotropy(object):
-    """Ultimate class that organizes whole working process"""
-
-    def __init__(self):
-        """Constructor method"""
-
-        self.env = env
-        self.db = None #Database(self.env["db_name"], self.env["db_path"])
-        self.params = []
-
-
-    def load(self, structure_type: str, structure_direction: list, structure_theta: float):
-        """Shortcut for `Database.setup` and `Database.load`. 
-
-        See :class:`anisotropy.core.database.Database` for more details.
-        """
-        self.db.setup()
-        self.params = self.db.load(structure_type, structure_direction, structure_theta)
-
-    def update(self, params: dict = None):
-        """Shortcut for `Database.setup` and `Database.update`. 
-
-        See :class:`anisotropy.core.database.Database` for more details.
-        """
-        self.db.setup()
-        self.db.update(self.params if not params else params)
-
-
-    @staticmethod
-    def version():
-        """Returns versions of all used main programs
-
-        :return: 
-            Versions joined by next line symbol
-        """
-        versions = {
-            "anisotropy": __version__,
-            "Python": sys.version.split(" ")[0],
-            "Salome": "[missed]",
-            "OpenFOAM": "[missed]"
-        }
-
-        try:
-            versions["Salome"] = salomepl.utils.SalomeManager().version()
-            versions["OpenFOAM"] = openfoam.version()
-
-        except Exception:
-            pass
-
-        return "\n".join([ f"{ k }: { v }" for k, v in versions.items() ])
-
-    
-    def loadFromScratch(self, configpath: str = None) -> list:
-        """Loads parameters from configuration file and expands special values
-
-        :return: 
-            List of dicts with parameters
-        """
-        config = configpath or self.env["CONFIG"]
-
-        if not os.path.exists(config):
-            logger.error("Missed configuration file")
-            return
-
-        else:
-            logger.info(f"Configuration file: { config }")
-
-        buf = toml.load(config).get("structures")
-        paramsAll = []
-
-
-        for entry in buf:
-            #   Shortcuts
-            _theta = entry["structure"]["theta"]
-            thetaMin = int(_theta[0] / _theta[2])
-            thetaMax = int(_theta[1] / _theta[2]) + 1
-            thetaList = list(
-                map(lambda n: n * _theta[2], range(thetaMin, thetaMax))
-            )
-
-            _thickness = entry["mesh"]["thickness"]
-            count = len(thetaList)
-            thicknessList = list(
-                map(lambda n: _thickness[0] + n * (_thickness[1] - _thickness[0]) / (count - 1), range(0, count))
-            )
-
-            for direction in entry["structure"]["directions"]:
-                for n, theta in enumerate(thetaList):
-                    mesh = deepcopy(entry["mesh"])
-                    mesh["thickness"] = thicknessList[n]
-
-                    entryNew = {
-                        "structure": dict(
-                            type = entry["structure"]["type"],
-                            theta = theta,
-                            direction = [ float(num) for num in direction ],
-                            filletsEnabled = entry["structure"]["filletsEnabled"]
-                        ),
-                        "mesh": mesh,
-                        "submesh": deepcopy(entry["submesh"]),
-                        "meshresult": dict(),
-                        "flow": deepcopy(entry["flow"]),
-                        "flowapproximation": deepcopy(entry["flowapproximation"]),
-                        "flowresult": dict(),
-                    }
-
-                    # For `type = fixedValue` only
-                    _velocity = entryNew["flowapproximation"]["velocity"]["boundaryField"]["inlet"]["value"]
-                    entryNew["flowapproximation"]["velocity"]["boundaryField"]["inlet"]["value"] = [ 
-                        val * _velocity for val in entryNew["structure"]["direction"] 
-                    ]
-
-                    _velocity = entryNew["flow"]["velocity"]["boundaryField"]["inlet"]["value"]
-                    entryNew["flow"]["velocity"]["boundaryField"]["inlet"]["value"] = [ 
-                        val * _velocity for val in entryNew["structure"]["direction"] 
-                    ]
-
-                    
-                    paramsAll.append(entryNew)
-
-        return paramsAll
-
-    
-    def evalParams(self):
-        """Evals specific geometry(structure) parameters"""
-
-        structure = self.params.get("structure")
-
-        if not structure:
-            logger.error("Trying to eval empty parameters")
-            return
-        
-        if structure["type"] == "simple":
-            thetaMin = 0.01
-            thetaMax = 0.28
-
-            r0 = 1
-            L = 2 * r0
-            radius = r0 / (1 - structure["theta"])
-
-            C1, C2 = 0.8, 0.5
-            Cf = C1 + (C2 - C1) / (thetaMax - thetaMin) * (structure["theta"] - thetaMin)
-            delta = 0.2
-            fillets = delta - Cf * (radius - r0)
-
-        elif structure["type"] == "faceCentered":
-            thetaMin = 0.01
-            thetaMax = 0.13
-
-            L = 1.0
-            r0 = L * sqrt(2) / 4
-            radius = r0 / (1 - structure["theta"])
-
-            C1, C2 = 0.3, 0.2
-            Cf = C1 + (C2 - C1) / (thetaMax - thetaMin) * (structure["theta"] - thetaMin)
-            delta = 0.012
-            fillets = delta - Cf * (radius - r0)
-
-        elif structure["type"] == "bodyCentered":
-            thetaMin = 0.01
-            thetaMax = 0.18
-    
-            L = 1.0
-            r0 = L * sqrt(3) / 4
-            radius = r0 / (1 - structure["theta"])
-
-            C1, C2 = 0.3, 0.2
-            Cf = C1 + (C2 - C1) / (thetaMax - thetaMin) * (structure["theta"] - thetaMin)
-            delta = 0.02
-            fillets = delta - Cf * (radius - r0)
-
-        self.params["structure"].update(
-            L = L,
-            r0 = r0,
-            radius = radius,
-            fillets = fillets 
-        )
-
-    def getCasePath(self, path: str = None) -> str:
-        """Constructs case path from control parameters
-        
-        :return: Absolute path to case
-        :rtype: str
-        """
-        structure = self.params.get("structure")
-
-        if not structure:
-            logger.error("Trying to use empty parameters")
-            return
-
-        if path:
-            path = os.path.join(path, "build")
-    
-        else:
-            path = self.env["BUILD"]
-
-        return os.path.join(
-            path, 
-            structure["type"],
-            "direction-{}".format(str(structure['direction']).replace(" ", "")),
-            f"theta-{ structure['theta'] }"
-        )
-
-
-    def computeMesh(self, path):
-        """Computes a mesh on shape via Salome
-
-        :return: Process output, error messages and returncode
-        :rtype: tuple(str, str, int)
-        """
-        p = self.params["structure"]
-        scriptpath = os.path.join(self.env["ROOT"], "anisotropy/core/cli.py")
-        salomeargs = [
-            "computemesh",
-            p["type"], 
-            p["direction"], 
-            p["theta"],
-            path
-        ]
-        manager = salomepl.utils.SalomeManager()
-        casepath = self.getCasePath(path)
-
-        self.params["meshresult"]["meshStatus"] = "Computing"
-        self.update()
-        timer = Timer()
-
-        out, err, returncode = manager.execute(
-            scriptpath, 
-            *salomeargs, 
-            timeout = self.env["salome_timeout"],
-            root = self.env["ROOT"],
-            logpath = casepath
-        )
-        self.load(p["type"], p["direction"], p["theta"])
-
-        if not returncode:
-            self.params["meshresult"].update(
-                meshStatus = "Done",
-                meshCalculationTime = timer.elapsed()
-            )
-
-        else:
-            self.params["meshresult"].update(
-                meshStatus = "Failed"
-            )
-
-        self.update()
-
-        return out, err, returncode
-
-
-    def genmesh(self, path):
-        """Computes a mesh on shape
-
-        Warning: Working only inside Salome Environment
-        """
-
-        setupLogger(logger, logging.INFO, self.env["LOG"])
-        p = self.params
-
-        ###
-        #   Shape
-        ##
-        logger.info("Constructing shape ...")
-
-        geompy = salomepl.geometry.getGeom()
-        structure = dict(
-            simple = Simple,
-            bodyCentered = BodyCentered,
-            faceCentered = FaceCentered
-        )[p["structure"]["type"]]
-        shapeGeometry = structure(**p["structure"])
-        shape, groups = shapeGeometry.build()
-
-        [length, surfaceArea, volume] = geompy.BasicProperties(shape, theTolerance = 1e-06)
-
-
-        ###
-        #   Mesh
-        ##
-        logger.info("Prepairing mesh ...")
-
-        mp = p["mesh"]
-
-        lengths = [
-            geompy.BasicProperties(edge)[0] for edge in geompy.SubShapeAll(shape, geompy.ShapeType["EDGE"]) 
-        ]
-        meanSize = sum(lengths) / len(lengths)
-        mp["maxSize"] = meanSize
-        mp["minSize"] = meanSize * 1e-1
-        mp["chordalError"] = mp["maxSize"] / 2
-
-        faces = []
-        for group in groups:
-            if group.GetName() in mp["facesToIgnore"]:
-                faces.append(group)
-
-
-        mesh = salomepl.mesh.Mesh(shape)
-        mesh.Tetrahedron(**mp)
-
-        if mp["viscousLayers"]:
-            mesh.ViscousLayers(**mp, faces = faces)
-
-        #   Submesh
-        smp = p["submesh"]
-
-        for submesh in smp:
-            for group in groups:
-                if submesh["name"] == group.GetName():
-                    subshape = group
-
-                    submesh["maxSize"] = meanSize * 1e-1
-                    submesh["minSize"] = meanSize * 1e-3
-                    submesh["chordalError"] = submesh["minSize"] * 1e+1
-
-                    mesh.Triangle(subshape, **submesh)
-
-
-        self.update()
-        logger.info("Computing mesh ...")
-        out, err, returncode = mesh.compute()
-
-        ###
-        #   Results
-        ##
-        #p["meshresult"] = dict()
-
-        if not returncode:
-            mesh.removePyramids()
-            mesh.assignGroups()
-
-            casePath = self.getCasePath(path)
-            os.makedirs(casePath, exist_ok = True)
-            logger.info("Exporting mesh ...")
-            returncode, err = mesh.exportUNV(os.path.join(casePath, "mesh.unv"))
-    
-            if returncode:
-                logger.error(err)
-
-            meshStats = mesh.stats()
-            p["meshresult"].update(
-                surfaceArea = surfaceArea,
-                volume = volume,
-                volumeCell = shapeGeometry.volumeCell,
-                **meshStats
-            )
-            self.update()
-
-        else:
-            logger.error(err)
-
-            p["meshresult"].update(
-                surfaceArea = surfaceArea,
-                volume = volume,
-                volumeCell = shapeGeometry.volumeCell
-            )
-            self.update()
-
-
-    def computeFlow(self, path):
-        """Computes a flow on mesh via OpenFOAM
-
-        :return: 
-            Process output, error messages and returncode
-        """
-        ###
-        #   Case preparation
-        ##
-        foamCase = [ "0", "constant", "system" ]
-        #self.params["flowresult"] = dict()
-        self.params["flowresult"]["flowStatus"] = "Computing"
-        self.update()
-        timer = Timer()
-
-        flow = self.params["flow"]
-        flowapproximation = self.params["flowapproximation"]
-
-        # ISSUE: ideasUnvToFoam cannot import mesh with '-case' flag so 'os.chdir' for that
-        casePath = self.getCasePath(path)
-
-        if not os.path.exists(casePath):
-            err = f"Cannot find case path { casePath }"
-            self.params["flowresult"]["flowStatus"] = "Failed"
-            self.update()
-
-            return "", err, 1
-
-        os.chdir(casePath)
-        openfoam.foamClean()
-
-        for d in foamCase:
-            shutil.copytree(
-                os.path.join(self.env["openfoam_template"], d), 
-                os.path.join(casePath, d)
-            )
-        
-        ###
-        #   Mesh manipulations
-        ##
-        if not os.path.exists("mesh.unv"):
-            os.chdir(path or self.env["ROOT"])
-
-            err = f"Missed 'mesh.unv'"
-            self.params["flowresult"]["flowStatus"] = "Failed"
-            self.update()
-
-            return "", err, 1
-
-        out, err, returncode = openfoam.ideasUnvToFoam("mesh.unv")
-
-        if returncode:
-            os.chdir(path or self.env["ROOT"])
-
-            self.params["flowresult"]["flowStatus"] = "Failed"
-            self.update()
-            
-            return out, err, returncode
-        
-        openfoam.createPatch(dictfile = "system/createPatchDict")
-
-        openfoam.foamDictionary(
-            "constant/polyMesh/boundary", 
-            "entry0.defaultFaces.type", 
-            "wall"
-        )
-        openfoam.foamDictionary(
-            "constant/polyMesh/boundary", 
-            "entry0.defaultFaces.inGroups", 
-            "1 (wall)"
-        )
-        
-        out, err, returncode = openfoam.checkMesh()
-        
-        if out: logger.warning(out)
-        
-        openfoam.transformPoints(flow["scale"])
-        
-        ###
-        #   Decomposition and initial approximation
-        #
-        #   NOTE: Temporary without decomposition
-        ##
-        openfoam.foamDictionary(
-            "constant/transportProperties",
-            "nu",
-            str(flow["transportProperties"]["nu"])
-        )
-
-        # openfoam.decomposePar()
-
-        openfoam.renumberMesh()
-
-        pressureBF = flowapproximation["pressure"]["boundaryField"]
-        velocityBF = flowapproximation["velocity"]["boundaryField"]
-
-        openfoam.foamDictionary(
-            "0/p", 
-            "boundaryField.inlet.value", 
-            openfoam.uniform(pressureBF["inlet"]["value"])
-        )
-        openfoam.foamDictionary(
-            "0/p", 
-            "boundaryField.outlet.value", 
-            openfoam.uniform(pressureBF["outlet"]["value"])
-        )
-        
-        openfoam.foamDictionary(
-            "0/U", 
-            "boundaryField.inlet.value", 
-            openfoam.uniform(velocityBF["inlet"]["value"])
-        )
-        
-        openfoam.potentialFoam()
-        
-        ###
-        #   Main computation
-        ##
-        pressureBF = flow["pressure"]["boundaryField"]
-        velocityBF = flow["velocity"]["boundaryField"]
-
-        openfoam.foamDictionary(
-            "0/U",
-            "boundaryField.inlet.type",
-            velocityBF["inlet"]["type"] 
-        )
-        openfoam.foamDictionary(
-            "0/U",
-            "boundaryField.inlet.value",
-            openfoam.uniform(velocityBF["inlet"]["value"])
-        )
-
-        #for n in range(os.cpu_count()):
-        #    openfoam.foamDictionary(
-        #        f"processor{n}/0/U", 
-        #        "boundaryField.inlet.type", 
-        #        velocityBF.inlet.type
-        #    )
-        #    openfoam.foamDictionary(
-        #        f"processor{n}/0/U", 
-        #        "boundaryField.inlet.value", 
-        #        openfoam.uniform(velocityBF.inlet.value[direction])
-        #    )
-        
-        out, err, returncode = openfoam.simpleFoam()
-
-        if not returncode:
-            self.params["flowresult"]["flowCalculationTime"] = timer.elapsed()
-            self.params["flowresult"]["flowStatus"] = "Done"
-
-        else:
-            self.params["flowresult"]["flowStatus"] = "Failed"
-
-        self.update()
-        os.chdir(path or self.env["ROOT"])
-        
-        return out, str(err, "utf-8"), returncode
-
-
-    def flowRate(self):
-        casePath = self.getCasePath()
-        foamPostProcessing = "postProcessing/flowRatePatch(name=outlet)/0/surfaceFieldValue.dat"
-        path = os.path.join(casePath, foamPostProcessing)
-
-        if not os.path.exists(path):
-            logger.warning(f"Unable to compute flow rate. Missed { path }")
-
-            return
-
-        with open(path, "r") as io:
-            lastLine = io.readlines()[-1]
-            flowRate = float(lastLine.replace(" ", "").replace("\n", "").split("\t")[1])
-
-        self.params["flowresult"]["flowRate"] = flowRate
-        self.update()
-
-        return flowRate
-
-
-    def porosity(self):
-        mr = self.params["meshresult"] 
-        fr = self.params["flowresult"]
-
-        fr["porosity"] = mr["volume"] / mr["volumeCell"]
-        self.update()
-
-        return fr["porosity"]

anisotropy/core/models.py

@@ -1,174 +0,0 @@
-# -*- coding: utf-8 -*-
-# This file is part of anisotropy.
-# License: GNU GPL version 3, see the file "LICENSE" for details.
-
-from peewee import (
-    SqliteDatabase, JOIN, 
-    Model, Field, 
-    AutoField, ForeignKeyField, 
-    TextField, FloatField, 
-    IntegerField, BooleanField, 
-    TimeField
-)
-import json
-
-db = SqliteDatabase(
-    None,
-    pragmas = { "foreign_keys": 1 },
-    field_types = { "list": "text" }
-)
-
-class BaseModel(Model):
-    class Meta:
-        database = db
-
-
-class ListField(Field):
-    field_type = "list"
-
-    def db_value(self, value):
-        return str(value)
-
-    def python_value(self, value):
-        pval = []
-
-        for entry in value[1 : -1].split(","):
-            try:
-                pval.append(float(entry))
-
-            except:
-                pval.append(entry.strip().replace("'", ""))
-
-        return pval
-
-
-class JSONField(TextField):
-    def db_value(self, value):
-        return json.dumps(value)
-
-    def python_value(self, value):
-        if value is not None:
-            return json.loads(value)
-
-
-class Structure(BaseModel):
-    structure_id = AutoField()
-
-    type = TextField()
-    direction = ListField()
-    theta = FloatField()
-
-    r0 = FloatField(null = True)
-    L = FloatField(null = True)
-    radius = FloatField(null = True)
-
-    filletsEnabled = BooleanField(null = True)
-    fillets = FloatField(null = True)
-    #path = TextField()
-
-
-class Mesh(BaseModel):
-    mesh_id = AutoField()
-    structure_id = ForeignKeyField(Structure, backref = "meshes")
-
-    maxSize = FloatField(null = True) 
-    minSize = FloatField(null = True) 
-
-    fineness = IntegerField(null = True) 
-    growthRate = FloatField(null = True)
-    nbSegPerEdge = FloatField(null = True)
-    nbSegPerRadius = FloatField(null = True)
-    
-    chordalErrorEnabled = BooleanField(null = True)
-    chordalError = FloatField(null = True)
-    
-    secondOrder = BooleanField(null = True)
-    optimize = BooleanField(null = True)
-    quadAllowed = BooleanField(null = True)
-    useSurfaceCurvature = BooleanField(null = True)
-    fuseEdges = BooleanField(null = True)
-    checkChartBoundary = BooleanField(null = True)
-
-    viscousLayers = BooleanField(null = True)
-    thickness = FloatField(null = True)
-    numberOfLayers = IntegerField(null = True)
-    stretchFactor = FloatField(null = True)
-    isFacesToIgnore = BooleanField(null = True)
-    facesToIgnore = ListField(null = True)
-    #faces = []
-    extrusionMethod = TextField(null = True)
-
-
-class SubMesh(BaseModel):
-    submesh_id = AutoField()
-    mesh_id = ForeignKeyField(Mesh, backref = "submeshes")
-    name = TextField()
-
-    maxSize = FloatField(null = True) 
-    minSize = FloatField(null = True) 
-
-    fineness = IntegerField(null = True) 
-    growthRate = FloatField(null = True)
-    nbSegPerEdge = FloatField(null = True)
-    nbSegPerRadius = FloatField(null = True)
-    
-    chordalErrorEnabled = BooleanField(null = True)
-    chordalError = FloatField(null = True)
-    
-    secondOrder = BooleanField(null = True)
-    optimize = BooleanField(null = True)
-    quadAllowed = BooleanField(null = True)
-    useSurfaceCurvature = BooleanField(null = True)
-    fuseEdges = BooleanField(null = True)
-    checkChartBoundary = BooleanField(null = True)
-
-
-class MeshResult(BaseModel):
-    meshresult_id = AutoField()
-    mesh_id = ForeignKeyField(Mesh, backref = "meshresults")
-    
-    surfaceArea = FloatField(null = True)
-    volume = FloatField(null = True)
-    volumeCell = FloatField(null = True)
-    
-    elements = IntegerField(null = True)
-    edges = IntegerField(null = True)
-    faces = IntegerField(null = True)
-    volumes = IntegerField(null = True)
-    tetrahedrons = IntegerField(null = True)
-    prisms = IntegerField(null = True)
-    pyramids = IntegerField(null = True)
-
-    meshStatus = TextField(null = True, default = "Idle")
-    meshCalculationTime = TimeField(null = True)
-
-
-class Flow(BaseModel):
-    flow_id = AutoField()
-    structure_id = ForeignKeyField(Structure, backref = "flows")
-
-    scale = ListField(null = True)
-    pressure = JSONField(null = True)
-    velocity = JSONField(null = True)
-    transportProperties = JSONField(null = True)
-
-   
-class FlowApproximation(BaseModel):
-    flow_approximation_id = AutoField()
-    flow_id = ForeignKeyField(Flow, backref = "flowapproximations")
-
-    pressure = JSONField(null = True)
-    velocity = JSONField(null = True)
-    transportProperties = JSONField(null = True)
-
-
-class FlowResult(BaseModel):
-    flowresult_id = AutoField()
-    flow_id = ForeignKeyField(Flow, backref = "flowresults")
-
-    flowRate = FloatField(null = True)
-    porosity = FloatField(null = True)
-    permeability = FloatField(null = True)
-
-    flowStatus = TextField(null = True, default = "Idle")
-    flowCalculationTime = TimeField(null = True)

anisotropy/core/parallel.py

@@ -0,0 +1,64 @@
+# -*- coding: utf-8 -*-
+
+import multiprocessing as mlp
+import dill
+
+
+class ParallelRunner(object):
+    def __init__(self, nprocs: int = 1, daemon: bool = True):
+        self.nprocs = nprocs
+        self.daemon = daemon
+        
+        self.processes = []
+        self.queueInput = mlp.Queue(maxsize = 1)
+        self.queueOutput = mlp.Queue()
+        
+        self.__pos = -1
+        self.output = []
+    
+    def append(self, command, args = [], kwargs = {}):
+        self.__pos += 1
+        self.queueInput.put(dill.dumps((self.__pos, command, args, kwargs)))
+        
+    def extend(self, commands: list, args: list = [], kwargs: list = []):
+        for command, cargs, ckwargs in zip(commands, args, kwargs):
+            self.append(command, cargs, ckwargs)
+    
+    @staticmethod
+    def queueRelease(queueInput, queueOutput):
+        while True:
+            pos, command, args, kwargs = dill.loads(queueInput.get())
+            
+            if pos is None or command is None:
+                break
+                
+            output = command(*args, **kwargs)
+            
+            queueOutput.put((pos, output))
+    
+    def start(self):
+        for n in range(self.nprocs):
+            self.processes.append(mlp.Process(
+                target = self.queueRelease, 
+                args = (self.queueInput, self.queueOutput),
+                name = f"worker-{ n + 1 }"
+            ))
+        
+        for proc in self.processes:
+            proc.daemon = self.daemon
+            proc.start()
+        
+    def wait(self):
+        for _ in range(self.nprocs):
+            self.append(None)
+        
+        self.output = [ [] for _ in range(self.queueOutput.qsize()) ]
+        
+        for _ in range(self.queueOutput.qsize()):
+            pos, output = self.queueOutput.get()
+            self.output[pos] = output
+        
+        for proc in self.processes:
+            proc.join()
+        
+        self.__pos = -1

anisotropy/core/postprocess.py

@@ -0,0 +1,97 @@
+# -*- coding: utf-8 -*-
+
+import pathlib
+import numpy as np
+
+import anisotropy.openfoam as of
+
+
+def flowRate(patch: str, path: str = None):
+    func = f"patchFlowRate(patch={ patch })"
+
+    path = pathlib.Path(path or "").resolve()
+    outfile = path / "postProcessing" / func / "0/surfaceFieldValue.dat"
+
+    of.commands.postProcess(func, cwd = path, logpath = path / "patchFlowRate.log")
+    surfaceFieldValue = of.conversion.read_dat(outfile)["sum(phi)"][-1]
+
+    return surfaceFieldValue
+
+
+def permeability(viscosity = None, flowRate = None, length = None, areaCross = None, pressureInlet = None, pressureOutlet = None, **kwargs):
+    viscosity = kwargs.get("viscosity", viscosity)
+    flowRate = kwargs.get("flowRate", flowRate)
+    length = kwargs.get("length", length)
+    areaCross = kwargs.get("areaCross", areaCross)
+    pressureInlet = kwargs.get("pressureInlet", pressureInlet)
+    pressureOutlet = kwargs.get("pressureOutlet", pressureOutlet)
+
+    return viscosity * length * flowRate / (areaCross * (pressureInlet - pressureOutlet))
+
+
+def mean_nan(arr):
+    temp = arr.copy()
+
+    if np.isnan(temp[0]):
+        temp[0] = temp[1]
+
+    for n, item in enumerate(temp):
+        if np.all(np.isnan(item)):
+            
+            vals = temp[n - 1 : n + 2]
+
+            if np.sum(~np.isnan(vals)) <= 1:
+                vals = temp[n - 2 : n + 3]
+
+            temp[n] = vals[~np.isnan(vals)].mean()
+
+    return temp
+
+
+def filter_group(arr, nan = True, qhigh = True, quantile = 0.97):
+    temp = arr.copy()
+    check = True
+    quan = np.quantile(temp[~np.isnan(temp)], quantile)
+    limit = 1000
+
+    while check:
+        if nan and np.any(np.isnan(temp)):
+            temp = mean_nan(temp)
+            check = True
+        
+        elif qhigh and np.any(quan < temp):
+            temp[quan < temp] = np.nan
+            check = True
+
+        else:
+            check = False 
+        
+        if limit <= 0:
+            break
+
+        else:
+            limit -= 1
+
+    return temp
+
+
+def pad_nan(x, y):
+    return np.pad(y, (0, x.size - y.size), 'constant', constant_values = np.nan)
+
+
+"""
+def multiplot_y(
+    x, 
+    y,
+    labels = [],
+    lines = [],
+    axes_labels = ["", ""],
+    legend = True,
+    grid = True,
+    figsize = (12, 6)
+    ):
+    fig, ax = plt.subplots(nrows = 1, ncols = 1, figsize = figsize)
+
+    for n, y_arr in enumerate(y):
+        ax.plot(x, y_arr, )
+"""

anisotropy/core/runner.py

@@ -0,0 +1,388 @@
+# -*- coding: utf-8 -*-
+
+from os import PathLike
+
+from os import environ
+from datetime import datetime
+import pathlib
+import logging
+import numpy as np
+
+from anisotropy.database import Database, tables
+from anisotropy import shaping
+from anisotropy import meshing
+from anisotropy import solving
+from anisotropy import openfoam
+
+from . import config as core_config
+from . import postprocess
+from . import utils
+from . import ParallelRunner
+
+
+logger = logging.getLogger(__name__)
+
+
+class UltimateRunner(object):
+    def __init__(self, config = None, exec_id: int = None, _type: str = "master"):
+
+        self.type = _type
+
+        # Configuration file
+        self.config = config or core_config.default_config()
+        
+        # Database preparation
+        self.database = Database(self.config["database"])
+        self.exec_id = None
+
+        if exec_id is not None:
+            if self.database.getExecution(int(exec_id)):
+                self.exec_id = int(exec_id)
+            
+            else:
+                logger.warning(f"Execution id '{ exec_id }' not found. Creating new.")
+
+        if self.exec_id is None:
+            with self.database:
+                self.exec_id = tables.Execution.create(date = datetime.now()).exec_id
+
+        if self.type == "master":
+            logger.info(f"Current execution id: { self.exec_id }")
+
+        # Parameters
+        self.queue = []
+
+    def _query_database(self, tableName: str, to_dict: bool = False):
+        tableName = tableName.lower()
+        get_row = {
+            "shape": self.database.getShape,
+            "mesh": self.database.getMesh,
+            "flowonephase": self.database.getFlowOnephase
+        }[tableName]
+        #   query
+        args = (
+            self.config.params["label"],
+            self.config.params["direction"],
+            self.config.params["alpha"],
+            self.exec_id,
+            to_dict
+        )
+
+        return get_row(*args)
+
+    def prepare_database(self):
+        # create a row in each table for the current case
+        #   shape
+        with self.database:
+            shape = self.database.getShape(execution = self.exec_id, **self.config.params)
+
+        if not shape:
+            shape = tables.Shape(exec_id = self.exec_id, **self.config.params)
+            self.database.csave(shape)
+
+        #   mesh
+        with self.database:
+            mesh = self.database.getMesh(execution = self.exec_id, **self.config.params)
+
+        if not mesh:
+            mesh = tables.Mesh(shape_id = shape.shape_id)
+            self.database.csave(mesh)
+
+        # onephase flow
+        with self.database:
+            flow = self.database.getFlowOnephase(execution = self.exec_id, **self.config.params)
+
+        if not flow:
+            flow = tables.FlowOnephase(mesh_id = mesh.mesh_id, **self.config.params)
+            self.database.csave(flow)
+
+    def prepare_queue(self):
+        self.config.expand()
+        logger.info(f"Preparing queue: { len(self.config.cases) }")
+        
+        for idn, case in enumerate(self.config.cases):
+            config = self.config.copy()
+            config.chooseParams(idn)
+            config.minimize()
+
+            kwargs = {
+                "config": config,
+                "exec_id": self.exec_id
+            }
+            self.queue.append(kwargs)
+    
+    def start(self, queue: list = None, nprocs: int = None):
+        nprocs = nprocs or self.config["nprocs"]
+        
+        logger.info(f"Starting subprocesses: { nprocs }")
+        parallel = ParallelRunner(nprocs = nprocs)
+        parallel.start()
+        
+        for kwargs in self.queue:
+            parallel.append(self.subrunner, kwargs = kwargs)
+
+        parallel.wait()
+
+    @property
+    def casepath(self) -> PathLike:
+        params = self.config.params
+
+        path = pathlib.Path(environ["AP_CWD"], environ["AP_BUILD_DIR"])
+        path /= "execution-{}".format(self.exec_id)
+        path /= "{}-[{},{},{}]-{}".format(
+            params["label"], 
+            *[ str(d) for d in params["direction"] ], 
+            params["alpha"]
+        )
+
+        return path.resolve()
+
+    @property
+    def shapefile(self) -> PathLike:
+        return self.casepath / self.config["shapefile"]
+    
+    @property
+    def meshfile(self) -> PathLike:
+        return self.casepath / self.config["meshfile"]
+
+    def compute_shape(self):
+        params = self.config.params
+        shapeParams = self._query_database("shape")
+
+        logger.info("Computing shape for {} with direction = {} and alpha = {}".format(
+            params["label"], params["direction"], params["alpha"]
+        ))
+        timer = utils.Timer()
+        
+        #   check physical existence
+        if self.shapefile.exists() and self.config["overwrite"] is not True:
+            logger.info("Shape exists, skipping ...")
+            return
+        
+        #
+        generate_shape = {
+            "simple": shaping.primitives.simple,
+            "bodyCentered": shaping.primitives.body_centered,
+            "faceCentered": shaping.primitives.face_centered
+        }[shapeParams.label]
+
+        try:
+            #   generate shape
+            shape = generate_shape(
+                shapeParams.alpha,
+                shapeParams.direction,
+                r0 = shapeParams.r0,
+                filletsEnabled = shapeParams.filletsEnabled
+            )
+
+            #   export
+            self.casepath.mkdir(parents = True, exist_ok = True)
+
+            shape.write(self.shapefile)
+        
+        except Exception as e:
+            logger.error(e, exc_info = True)
+
+            shapeParams.shapeStatus = "failed"
+
+        else:
+            shapeParams.shapeStatus = "done"
+            shapeParams.volume = shape.shape.volume * np.prod(params["scale"])
+            shapeParams.volumeCell = shape.cell.volume * np.prod(params["scale"])
+            shapeParams.radius = shape.radius
+            shapeParams.fillets = shape.fillets
+            shapeParams.porosity = shapeParams.volume / shapeParams.volumeCell
+            shapeParams.areaOutlet = np.sum([ 
+                face.mass for face in shape.shape.faces if face.name == "outlet" 
+            ]) * params["scale"][0] ** 2
+            shapeParams.length = shape.length * params["scale"][0]
+            shapeParams.areaCellOutlet = np.sum([ 
+                face.mass for face in shape.cell.faces if face.name == "outlet" 
+            ]) * params["scale"][0] ** 2
+
+        #   commit parameters
+        shapeParams.shapeExecutionTime = timer.elapsed()
+        self.database.csave(shapeParams)
+
+    def compute_mesh(self):
+        params = self.config.params
+        meshParams = self._query_database("mesh")
+
+        logger.info("Computing mesh for {} with direction = {} and alpha = {}".format(
+            params["label"], params["direction"], params["alpha"]
+        ))
+        timer = utils.Timer()
+
+        #   check physical existence
+        if self.meshfile.exists() and self.config["overwrite"] is not True:
+            logger.info("Mesh exists, skipping ...")
+            return
+        
+        elif not self.shapefile.exists():
+            logger.error("Cannot find shape file to build a mesh.")
+            return
+
+        #   Shape
+        shape = None
+
+        try:
+            #   load shape
+            shape = shaping.Shape().read(self.shapefile)
+
+            #   generate mesh
+            parameters = meshing.MeshingParameters()
+            mesh = meshing.Mesh(shape)
+            mesh.generate(parameters)
+
+            #   export
+            self.casepath.mkdir(parents = True, exist_ok = True)
+
+            mesh.write(self.meshfile)
+            mesh.write(self.casepath / "mesh.msh")
+
+        except Exception as e:
+            logger.error(e, exc_info = True)
+
+            meshParams.meshStatus = "failed"
+
+        else:
+            meshParams.meshStatus = "done"
+            meshParams.faces = len(mesh.faces)
+            meshParams.volumes = len(mesh.volumes)
+
+        #   commit parameters
+        meshParams.meshExecutionTime = timer.elapsed()
+        self.database.csave(meshParams)
+
+    def compute_flow(self):
+        params = self.config.params
+        flowParams = self._query_database("flowonephase")
+
+        logger.info("Computing flow for {} with direction = {} and alpha = {}".format(
+            params["label"], params["direction"], params["alpha"]
+        ))
+        timer = utils.Timer()
+        
+        #   check physical existence
+        if openfoam.FoamCase(path = self.casepath).is_converged() and not self.config["overwrite"]:
+            logger.info("Solution exists. Skipping ...")
+            return
+        
+        elif not self.shapefile.exists():
+            logger.error("Cannot find shape file to compute a solution.")
+            return
+        
+        elif not self.meshfile.exists():
+            logger.error("Cannot find mesh file to compute a solution.")
+            return       
+
+        #   precalculate some parameters
+        flowParams.viscosityKinematic = flowParams.viscosity / flowParams.density
+        self.database.csave(flowParams)            
+
+        #
+        flowParamsDict = self._query_database("flowonephase", to_dict = True)
+
+        try:
+            #   load shape
+            shape = shaping.Shape().read(self.shapefile)
+
+            #
+            flow = solving.FlowOnePhase(
+                path = self.casepath,
+                direction = params["direction"], 
+                patches = shape.patches(group = True, shiftIndex = True, prefix = "patch"),
+                scale = params["scale"],
+                **flowParamsDict
+            )
+
+            #   generate solution
+            flow.generate()
+
+        except Exception as e:
+            logger.error(e, exc_info = True)
+
+            flowParams.flowStatus = "failed"
+
+        else:
+            flowParams.flowStatus = "done"
+
+        #   commit parameters
+        flowParams.flowExecutionTime = timer.elapsed()
+        self.database.csave(flowParams)
+
+    def compute_postprocess(self):
+        params = self.config.params
+        flowParams = self._query_database("flowonephase")
+
+        logger.info("Computing post process for {} with direction = {} and alpha = {}".format(
+            params["label"], params["direction"], params["alpha"]
+        ))
+
+        if flowParams.flowStatus == "done":
+            if flowParams.flowRate is None and self.config["overwrite"] is not True:
+                flowParams.flowRate = postprocess.flowRate("outlet", self.casepath)
+
+        self.database.csave(flowParams)
+        
+    def pipeline(self, stage: str = None):
+        stage = stage or self.config["stage"]
+        stages = ["shape", "mesh", "flow", "postProcess", "all"]
+
+        if stage not in stages:
+            logger.error(f"Unknown stage '{ stage }'.")
+            return
+        
+        for current in stages:
+            if current == "shape":
+                params = self._query_database("shape")
+                
+                #   check database entry
+                if params.shapeStatus == "done" and self.config["overwrite"] is not True:
+                    logger.info("Successful shape entry exists, skipping ...")
+                    continue
+
+                self.compute_shape()
+
+            if current == "mesh":
+                params = self._query_database("mesh")
+
+                #   check database entry
+                if params.meshStatus == "done" and self.config["overwrite"] is not True:
+                    logger.info("Successful mesh entry exists, skipping ...")
+                    continue
+
+                self.compute_mesh()
+
+            if current == "flow":
+                params = self._query_database("flowonephase")
+
+                #   check database entry
+                if params.flowStatus == "done" and self.config["overwrite"] is not True:
+                    logger.info("Successful flow entry exists, skipping ...")
+                    continue
+
+                self.compute_flow()
+
+            if current == "postProcess":
+                params = self._query_database("flowonephase")
+
+                #   check database entry
+                # if params.flowStatus == "done" and self.config["overwrite"] is not True:
+                #    logger.info("Successful flow entry exists, skipping ...")
+                #    continue
+
+                self.compute_postprocess()
+            
+            if current == stage or current == "all":
+                break
+
+    @staticmethod
+    def subrunner(*args, **kwargs):
+        runner = UltimateRunner(
+            config = kwargs["config"], 
+            exec_id = kwargs["exec_id"],
+            _type = "worker"
+        )
+        runner.prepare_database()
+        runner.pipeline()

anisotropy/core/utils.py

@@ -1,286 +1,113 @@
 # -*- coding: utf-8 -*-
-# This file is part of anisotropy.
-# License: GNU GPL version 3, see the file "LICENSE" for details.
 
 import logging
-
-from multiprocessing import Queue, Process, cpu_count
-import socket
-import copy
 import time
-from types import FunctionType
-import os
+import contextlib
+
 
 class CustomFormatter(logging.Formatter):
-    def _getFormat(self, level: int):
+    def __init__(self, colors: bool = True):
+        self.colors = colors
+
+    def applyColors(self, level: int, info: str, msg: str):
         grey = "\x1b[38;21m"
         yellow = "\x1b[33;21m"
         red = "\x1b[31;21m"
         bold_red = "\x1b[31;1m"
         reset = "\x1b[0m"
-        format = "[ %(asctime)s ] [ %(processName)s ] [ %(levelname)s ] %(message)s"
-
+        
         formats = {
-            logging.DEBUG: grey + format + reset,
-            logging.INFO: grey + format + reset,
-            logging.WARNING: yellow + format + reset,
-            logging.ERROR: red + format + reset,
-            logging.CRITICAL: bold_red + format + reset
+            logging.DEBUG: grey + info + reset + msg,
+            logging.INFO: grey + info + reset + msg,
+            logging.WARNING: yellow + info + reset + msg,
+            logging.ERROR: red + info + reset + msg,
+            logging.CRITICAL: bold_red + info + reset + msg
         }
 
         return formats.get(level)
 
     def format(self, record):
-        log_fmt = self._getFormat(record.levelno)
-        time_fmt = "%H:%M:%S %d-%m-%y"
+        info = "[%(levelname)s %(processName)s %(asctime)s %(funcName)s]"  # [ %(processName)s ]
+        msg = " %(message)s"
+        
+        if self.colors:
+            log_fmt = self.applyColors(record.levelno, info, msg)
+
+        else:
+            log_fmt = info + msg
+
+        time_fmt = "%d-%m-%y %H:%M:%S"
         formatter = logging.Formatter(log_fmt, time_fmt)
 
         return formatter.format(record)
 
 
-def setupLogger(logger, level: int, filepath: str = None):
-    """Applies settings to logger
+def setupLogger(level: int, filepath: str = None):
+    """Applies settings to root logger
 
-    :param logger: 
-        Instance of :class:`logging.Logger`
-    
     :param level: 
         Logging level (logging.INFO, logging.WARNING, ..)
 
     :param filepath: 
         Path to directory
     """
-    logger.handlers = []
-    logger.setLevel(level)
 
+    logging.addLevelName(logging.INFO, "II")
+    logging.addLevelName(logging.WARNING, "WW")
+    logging.addLevelName(logging.ERROR, "EE")
+    logging.addLevelName(logging.CRITICAL, "CC")
+    
     streamhandler = logging.StreamHandler()
     streamhandler.setLevel(level)
     streamhandler.setFormatter(CustomFormatter())
-    logger.addHandler(streamhandler)
-
-    if filepath:
-        if not os.path.exists(filepath):
-            os.makedirs(filepath, exist_ok = True)
-
-        filehandler = logging.FileHandler(
-            os.path.join(filepath, "{}.log".format(logger.name))
-        )
-        filehandler.setLevel(level)
-        filehandler.setFormatter(CustomFormatter())
-        logger.addHandler(filehandler)
-
-
-class struct:
-    def __init__(self, *args, **kwargs):
-        if len(args) > 0:
-            if type(args[0]) == dict:
-                for (k, v) in args[0].items():
-                    if type(v) == dict:
-                        setattr(self, k, struct(v))
-                    
-                    else:
-                        setattr(self, k, v)
-        else:
-            self.__dict__.update(kwargs)
-
-    def __iter__(self):
-        for k in self.__dict__:
-            if type(getattr(self, k)) == struct:
-                yield k, dict(getattr(self, k))
-
-            else:
-                yield k, getattr(self, k)
-
-    def __str__(self):
-        members = []
-
-        for key in self.__dict__.keys():
-            members.append(f"{ key } = ")
-
-            if type(self.__dict__[key]) == str:
-                members[len(members) - 1] += f"\"{ self.__dict__[key] }\""
-
-            else: 
-                members[len(members) - 1] += f"{ self.__dict__[key] }"
-             
-        return f"struct({', '.join(members)})"
-
-    def __repr__(self):
-        return str(self)
-
-
-def deepupdate(target, src):
-    for k, v in src.items():
-        if isinstance(v, dict):
-            if not k in target:
-                target[k] = copy.deepcopy(v)
-
-            else:
-                deepupdate(target[k], v)
-
-        else:
-            target[k] = copy.copy(v)
-
-def collapse(source, key = None, level = 0, sep = "_"):
-    if isinstance(source, dict) and source:
-        level = level + 1
-        res = {}
-
-        for k, v in source.items():
-            ret, lvl = collapse(v, k, level)
-
-            for kk,vv in ret.items():
-                if level == lvl:
-                    newkey = k
-
-                else:
-                    newkey = "{}{}{}".format(k, sep, kk)
-
-                res.update({ newkey: vv })
-
-        if level == 1:
-            return res
-
-        else:
-            return res, level
-
-    else:
-        return { key: source }, level
-
-def expand(source, sep = "_"):
-    res = {}
-
-    for k, v in source.items():
-        if k.find(sep) == -1:
-            res.update({ k: v })
-
-        else:
-            keys = k.split(sep)
-            cur = res
-
-            for n, kk in enumerate(keys):
-                if not len(keys) == n + 1:
-                    if not cur.get(kk):
-                        cur.update({ kk: {} })
-
-                    cur = cur[kk]
-
-                else:
-                    cur[kk] = v
-    return res
-
-#if os.path.exists(env["CONFIG"]):
-#    config = toml.load(env["CONFIG"])
-
-#    for restricted in ["ROOT", "BUILD", "LOG", "CONFIG"]:
-#        if config.get(restricted):
-#            config.pop(restricted)
-
-    # TODO: not working if custom config empty and etc
-#    for m, structure in enumerate(config["structures"]):
-#        for n, estructure in enumerate(env["structures"]):
-#            if estructure["name"] == structure["name"]:
-#                deepupdate(env["structures"][n], config["structures"][m])
-
-#    config.pop("structures")
-#    deepupdate(env, config)
-
-def timer(func: FunctionType) -> (tuple, float):
-    """(Decorator) Returns output of inner function and execution time
+    logging.root.addHandler(streamhandler)
     
-    :param func: inner function
-    :type func: FunctionType
+    logging.root.setLevel(level)
+    
+    if filepath:
+        filehandler = logging.FileHandler(filepath)
+        filehandler.setLevel(logging.INFO)
+        filehandler.setFormatter(CustomFormatter(colors = False))
 
-    :return: output, elapsed time
-    :rtype: tuple(tuple, float)
-    """
-
-    def inner(*args, **kwargs):
-        start = time.monotonic()
-        ret = func(*args, **kwargs)
-        elapsed = time.monotonic() - start
-
-        return ret, elapsed
-
-    return inner
+        logging.root.addHandler(filehandler)
 
 
 class Timer(object):
     def __init__(self):
-        self.start = time.monotonic()
+        self.update()
 
+    def update(self):
+        self.start = time.monotonic()
+        
     def elapsed(self):
         return time.monotonic() - self.start
 
 
-def queue(cmd, qin, qout, *args):
-    
-    while True:
-        # Get item from the queue
-        pos, var = qin.get()
+class ErrorHandler(contextlib.AbstractContextManager):
+    def __init__(self):
+        self.error = ""
+        self.returncode = 0
+        self.traceback = None
+
+    def __enter__(self):
+        return self, self.handle
+
+    def __exit__(self, exc_type, exc_value, traceback):
+        if exc_type:
+            self.error = exc_value.args
+            self.returncode = 1
+            self.traceback = traceback
+
+    def handle(self, obj):
+        def inner(*args, **kwargs):
+            try:
+                output = obj(*args, **kwargs)
+            
+            except Exception as e:
+                self.error = e.args
+                self.returncode = 1
+            
+            else:
+                return output
         
-        # Exit point 
-        if pos is None:
-            break
-
-        # Execute command
-        res = cmd(*var, *args)
-
-        # Put results to the queue
-        qout.put((pos, res))
-
-    return
-
-
-def parallel(np, var, cmd):
-
-    varcount = len(var)
-
-    processes = []
-    nprocs = np if np <= cpu_count() else cpu_count()
-    
-    qin = Queue(1)
-    qout = Queue()
-    
-    # Create processes
-    for n in range(nprocs):
-        pargs = [cmd, qin, qout]
-
-        p = Process(target = queue, args = tuple(pargs))
-
-        processes.append(p)
-    
-    # Start processes
-    for p in processes:
-        p.daemon = True
-        p.start()
-
-    # Fill queue
-    for n in range(varcount):
-        qin.put((n, var[n]))
-
-    for _ in range(nprocs):
-        qin.put((None, None))
-    
-    # Get results
-    results = [[] for n in range(varcount)]
-
-    for n in range(varcount):
-        index, res = qout.get()
-        
-        results[index] = res
-    
-    # Wait until each processor has finished
-    for p in processes:
-        p.join()
-
-    return results
-
-    
-def portIsFree(address, port):
-
-    with socket.socket(socket.AF_INET, socket.SOCK_STREAM) as s:
-        return s.connect_ex((address, port)) == 0
-
-
-
+        return inner

anisotropy/database/__init__.py

@@ -0,0 +1,13 @@
+# -*- coding: utf-8 -*-
+
+from . import utils
+from . import tables
+
+from .database import Database
+
+
+__all__ = [
+    "utils",
+    "tables",
+    "Database"
+]

anisotropy/database/database.py

@@ -0,0 +1,309 @@
+# -*- coding: utf-8 -*-
+
+from __future__ import annotations
+from numpy import ndarray
+
+import peewee as pw
+import pathlib
+import time
+import pandas as pd
+
+from . import tables 
+
+
+class Database(pw.SqliteDatabase):
+    def __init__(self, filename: str = None, *args, **kwargs):
+        """A Database object contains SQLite database with convient
+        properties and methods
+        """
+        self.path = filename 
+        self.pragmas_ = kwargs.get("pragmas", { "foreign_keys": 1, "journal_mode": "wal" })
+        self.field_types_ = kwargs.get("field_types", { "list": "text" })
+        self.autoconnect_ = kwargs.get("autoconnect", False)
+        
+        pw.SqliteDatabase.__init__(
+            self,
+            None,
+            pragmas = self.pragmas_,
+            field_types = self.field_types_,
+            autoconnect = self.autoconnect_
+        )
+
+        if self.path:
+            self.setup()
+
+    @property
+    def tables(self) -> list:
+        """Return all tables as list.
+        """
+        return [ tables.__dict__[table] for table in tables.__all__ ]
+    
+    def setup(self, filename: str = None):
+        """Initialize database and create tables.
+
+        :param filename:
+            Path to the file.
+        :return:
+            Self.
+        """        
+        self.path = pathlib.Path(filename or self.path).resolve()
+        self.init(
+            self.path,
+            pragmas = self.pragmas_
+        )
+        tables.database_proxy.initialize(self)
+
+        with self:
+            self.create_tables(self.tables)
+
+        return self
+
+    def csave(self, table: pw.Model, tries: int = 5000):
+        """Try to save data from model to the database ignoring
+        peewee.OperationalError. Usefull for concurrent processes.
+
+        :param table:
+            Table to save.
+        :param tries:
+            Number of tries. Falling to sleep for 1 second if database 
+            is locked.
+        """
+        while tries >= 0:
+            if self.is_closed():
+                self.connect()
+            
+            try:
+                table.save()
+            
+            except pw.OperationalError:
+                tries -= 1
+                time.sleep(1)
+            
+            else:
+                self.close()
+                break
+
+    def getExecution(
+        self, 
+        idn: int,
+        to_dict: bool = False,
+        **kwargs
+    ) -> tables.Execution | None:
+        """Get execution entry from database.
+
+        :param idn:
+            Index of the execution.
+        :return:
+            If entry is found returns Model instance else None.
+        """
+        query = tables.Execution.select().where(tables.Execution.exec_id == idn)
+
+        with self:
+            if to_dict:
+                table = query.dicts().get() if query.exists() else None
+            
+            else:
+                table = query.get() if query.exists() else None
+
+        return table
+
+    def getLatest(self) -> tables.Execution | None:
+        """Get latest execution entry from database.
+
+        :return:
+            If entry is found returns Model instance else None.
+        """
+        query = tables.Execution.select()
+
+        with self:
+            table = query[-1] if query.exists() else None
+
+        return table
+
+    def getShape(
+        self, 
+        label: str = None, 
+        direction: list[float] | ndarray = None, 
+        alpha: float = None, 
+        execution: int = None, 
+        to_dict: bool = False,
+        **kwargs
+    ) -> tables.Shape | None:
+        """Get shape entry from database.
+
+        :param label:
+            Label of the shape.
+        :param direction:
+            Array of floats represents direction vector.
+        :param alpha:
+            Spheres overlap parameter.
+        :param execution:
+            Index of the execution. If None, use latest.
+        :return:
+            If entry is found returns Model instance else None.
+        """
+        execution = execution or self.getLatest()
+        query = (
+            tables.Shape
+            .select()
+            .join(tables.Execution, pw.JOIN.LEFT_OUTER)
+            .where(
+                tables.Execution.exec_id == execution,
+                tables.Shape.label == label,
+                tables.Shape.direction == direction,
+                tables.Shape.alpha == alpha
+            )
+        )
+
+        with self:
+            if to_dict:
+                table = query.dicts().get() if query.exists() else None
+            
+            else:
+                table = query.get() if query.exists() else None
+
+        return table
+
+    def getMesh(
+        self, 
+        label: str = None, 
+        direction: list[float] | ndarray = None, 
+        alpha: float = None, 
+        execution: int = None, 
+        to_dict: bool = False,
+        **kwargs
+    ) -> tables.Mesh | None:
+        """Get mesh entry from database.
+
+        :param label:
+            Label of the shape.
+        :param direction:
+            Array of floats represents direction vector.
+        :param alpha:
+            Spheres overlap parameter.
+        :param execution:
+            Index of the execution. If None, use latest.
+        :return:
+            If entry is found returns Model instance else None.
+        """
+        execution = execution or self.getLatest()
+        query = (
+            tables.Mesh
+            .select()
+            .join(tables.Shape, pw.JOIN.LEFT_OUTER)
+            .join(tables.Execution, pw.JOIN.LEFT_OUTER)
+            .where(
+                tables.Execution.exec_id == execution,
+                tables.Shape.label == label,
+                tables.Shape.direction == direction,
+                tables.Shape.alpha == alpha
+            )
+        )
+
+        with self:
+            if to_dict:
+                table = query.dicts().get() if query.exists() else None
+            
+            else:
+                table = query.get() if query.exists() else None
+
+        return table
+
+    def getFlowOnephase(
+        self, 
+        label: str = None, 
+        direction: list[float] | ndarray = None, 
+        alpha: float = None, 
+        execution: int = None, 
+        to_dict: bool = False,
+        **kwargs
+    ) -> tables.Mesh | dict | None:
+        """Get one phase flow entry from database.
+
+        :param label:
+            Label of the shape.
+        :param direction:
+            Array of floats represents direction vector.
+        :param alpha:
+            Spheres overlap parameter.
+        :param execution:
+            Index of the execution. If None, use latest.
+        :param to_dict:
+            If True, convert result to dict.
+        :return:
+            If entry is found returns Model instance or dict else None.
+        """
+        execution = execution or self.getLatest()
+        query = (
+            tables.FlowOnephase
+            .select()
+            .join(tables.Mesh, pw.JOIN.LEFT_OUTER)
+            .join(tables.Shape, pw.JOIN.LEFT_OUTER)
+            .join(tables.Execution, pw.JOIN.LEFT_OUTER)
+            .where(
+                tables.Execution.exec_id == execution,
+                tables.Shape.label == label,
+                tables.Shape.direction == direction,
+                tables.Shape.alpha == alpha
+            )
+        )
+
+        with self:
+            if to_dict:
+                table = query.dicts().get() if query.exists() else None
+            
+            else:
+                table = query.get() if query.exists() else None
+
+        return table
+
+    def load(
+        self, 
+        field: str,
+        execution: int = None,
+        label: str = None, 
+        direction: list[float] | ndarray = None
+    ):
+        execution = execution or self.getLatest()
+
+        for table in self.tables:
+            try:
+                column = getattr(table, field)
+            
+            except AttributeError:
+                pass
+
+            else:
+                break
+
+        query = table.select(tables.Shape.alpha, column, tables.Shape.direction, tables.Shape.label)
+
+        for current in reversed(self.tables[ :self.tables.index(table)]):
+            query = query.join(table, pw.JOIN.LEFT_OUTER)
+            
+        query = (
+            query.switch(tables.Shape)
+            .where(tables.Shape.exec_id == execution)
+            .order_by(tables.Shape.label, tables.Shape.direction, tables.Shape.alpha)
+        )
+        resp = None
+
+        with self:
+            if query.exists():
+                resp = []
+                for row in query.dicts():
+                    for k in row.keys():
+                        if type(row[k]) == list:
+                            row[k] = str(row[k])
+
+                    resp.append(row)
+            
+        resp = pd.DataFrame(resp)
+
+        if label is not None:
+            resp = resp[resp.label == label]
+        
+        if direction is not None:
+            resp = resp[resp.direction == direction]
+        
+        return resp[field]

anisotropy/database/tables.py

@@ -0,0 +1,106 @@
+# -*- coding: utf-8 -*-
+
+import peewee as pw
+
+from . import utils
+
+
+#   proxy, assign database later
+database_proxy = pw.Proxy()
+
+
+class Execution(pw.Model):
+    exec_id = pw.AutoField()
+
+    date = pw.DateTimeField()
+    executionTime = pw.TimeField(null = True)
+
+    class Meta:
+        database = database_proxy
+        table_name = "executions"
+
+
+class Shape(pw.Model):
+    shape_id = pw.AutoField()
+    exec_id = pw.ForeignKeyField(Execution, backref = "executions", on_delete = "CASCADE")
+
+    shapeStatus = pw.TextField(null = True, default = "idle")
+    shapeExecutionTime = pw.TimeField(null = True)   
+    
+    label = pw.TextField(null = True)
+    direction = utils.JSONField(null = True)
+    alpha = pw.FloatField(null = True)
+
+    r0 = pw.FloatField(null = True)
+    L = pw.FloatField(null = True)
+    radius = pw.FloatField(null = True)
+
+    filletsEnabled = pw.BooleanField(null = True)
+    fillets = pw.FloatField(null = True)
+
+    volumeCell = pw.FloatField(null = True)
+    volume = pw.FloatField(null = True)
+    porosity = pw.FloatField(null = True)
+
+    areaOutlet = pw.FloatField(null = True)
+    length = pw.FloatField(null = True)
+    areaCellOutlet = pw.FloatField(null = True)
+
+    class Meta:
+        database = database_proxy
+        table_name = "shapes"
+        # depends_on = Execution
+
+
+class Mesh(pw.Model):
+    mesh_id = pw.AutoField()
+    shape_id = pw.ForeignKeyField(Shape, backref = "shapes", on_delete = "CASCADE")
+ 
+    meshStatus = pw.TextField(null = True, default = "idle")
+    meshExecutionTime = pw.TimeField(null = True)   
+    
+    elements = pw.IntegerField(null = True)
+    edges = pw.IntegerField(null = True)
+    faces = pw.IntegerField(null = True)
+    volumes = pw.IntegerField(null = True)
+    tetrahedrons = pw.IntegerField(null = True)
+    prisms = pw.IntegerField(null = True)
+    pyramids = pw.IntegerField(null = True)
+
+    class Meta:
+        database = database_proxy
+        table_name = "meshes"
+        # depends_on = Execution
+
+
+class FlowOnephase(pw.Model):
+    flow_id = pw.AutoField()
+    mesh_id = pw.ForeignKeyField(Mesh, backref = "meshes", on_delete = "CASCADE")
+
+    flowStatus = pw.TextField(null = True, default = "idle")
+    flowExecutionTime = pw.TimeField(null = True)
+
+    pressureInlet = pw.FloatField(null = True)
+    pressureOutlet = pw.FloatField(null = True)
+    pressureInternal = pw.FloatField(null = True)
+    velocityInlet = utils.JSONField(null = True)
+    velocityOutlet = utils.JSONField(null = True)
+    velocityInternal = utils.JSONField(null = True)
+    viscosity = pw.FloatField(null = True)
+    viscosityKinematic = pw.FloatField(null = True)
+    density = pw.FloatField(null = True)
+    flowRate = pw.FloatField(null = True)
+    permeability = pw.FloatField(null = True)
+
+    class Meta:
+        database = database_proxy
+        table_name = "flows"
+        # depends_on = Execution
+
+
+__all__ = [
+    "Execution",
+    "Shape",
+    "Mesh",
+    "FlowOnephase"
+]

anisotropy/database/utils.py

@@ -0,0 +1,160 @@
+# -*- coding: utf-8 -*-
+
+from numpy import ndarray
+
+import peewee as pw
+import json
+
+
+class ListField(pw.TextField):
+    field_type = "list"
+
+    def db_value(self, value):
+        return str(value)
+
+    def python_value(self, value):
+        pval = []
+
+        for entry in value[1 : -1].split(","):
+            try:
+                pval.append(float(entry))
+
+            except Exception:
+                pval.append(entry.strip().replace("'", ""))
+
+        return pval
+
+
+class JSONPath(pw.ColumnBase):
+    def __init__(self, field, path = None):
+        super(JSONPath, self).__init__()
+        
+        self._field = field
+        self._path = path or ()
+
+    @property
+    def path(self):
+        return pw.Value('$%s' % ''.join(self._path))
+
+    def __getitem__(self, idx):
+        if isinstance(idx, int):
+            item = '[%s]' % idx
+
+        else:
+            item = '.%s' % idx
+
+        return JSONPath(self._field, self._path + (item,))
+
+    def set(self, value, as_json = None):
+        if as_json or isinstance(value, (list, dict)):
+            value = pw.fn.json(self._field._json_dumps(value))
+
+        return pw.fn.json_set(self._field, self.path, value)
+
+    def update(self, value):
+        return self.set(pw.fn.json_patch(self, self._field._json_dumps(value)))
+
+    def remove(self):
+        return pw.fn.json_remove(self._field, self.path)
+
+    def json_type(self):
+        return pw.fn.json_type(self._field, self.path)
+
+    def length(self):
+        return pw.fn.json_array_length(self._field, self.path)
+
+    def children(self):
+        return pw.fn.json_each(self._field, self.path)
+
+    def tree(self):
+        return pw.fn.json_tree(self._field, self.path)
+
+    def __sql__(self, ctx):
+        return ctx.sql(
+            pw.fn.json_extract(self._field, self.path)
+            if self._path else self._field
+        )
+
+
+class JSONField(pw.TextField):
+    field_type = 'TEXT'
+    unpack = False
+
+    def __init__(self, json_dumps = None, json_loads = None, **kwargs):
+        super(JSONField, self).__init__(**kwargs)
+
+        self._json_dumps = json_dumps or json.dumps
+        self._json_loads = json_loads or json.loads
+
+    def python_value(self, value):
+        if value is not None:
+            try:
+                return json.loads(value)
+
+            except (TypeError, ValueError):
+                return value
+
+    def db_value(self, value):
+        if value is not None:
+            if isinstance(value, ndarray):
+                value = list(value)
+
+            if not isinstance(value, pw.Node):
+                value = json.dumps(value)
+
+            return value
+
+    def _e(op):
+        def inner(self, rhs):
+            if isinstance(rhs, (list, dict)):
+                rhs = pw.Value(rhs, converter = self.db_value, unpack = False)
+            
+            return pw.Expression(self, op, rhs)
+        
+        return inner
+    
+    __eq__ = _e(pw.OP.EQ)
+    __ne__ = _e(pw.OP.NE)
+    __gt__ = _e(pw.OP.GT)
+    __ge__ = _e(pw.OP.GTE)
+    __lt__ = _e(pw.OP.LT)
+    __le__ = _e(pw.OP.LTE)
+    __hash__ = pw.Field.__hash__
+
+    def __getitem__(self, item):
+        return JSONPath(self)[item]
+
+    def set(self, value, as_json = None):
+        return JSONPath(self).set(value, as_json)
+
+    def update(self, data):
+        return JSONPath(self).update(data)
+
+    def remove(self):
+        return JSONPath(self).remove()
+
+    def json_type(self):
+        return pw.fn.json_type(self)
+
+    def length(self):
+        return pw.fn.json_array_length(self)
+
+    def children(self):
+        """
+        Schema of `json_each` and `json_tree`:
+
+        key,
+        value,
+        type TEXT (object, array, string, etc),
+        atom (value for primitive/scalar types, NULL for array and object)
+        id INTEGER (unique identifier for element)
+        parent INTEGER (unique identifier of parent element or NULL)
+        fullkey TEXT (full path describing element)
+        path TEXT (path to the container of the current element)
+        json JSON hidden (1st input parameter to function)
+        root TEXT hidden (2nd input parameter, path at which to start)
+        """
+        return pw.fn.json_each(self)
+
+    def tree(self):
+        return pw.fn.json_tree(self)

anisotropy/gui/__init__.py

@@ -0,0 +1,15 @@
+# -*- coding: utf-8 -*-
+
+from . import layouts
+from .layouts import app
+
+
+app.layout = layouts.base
+
+
+def run(*args, **kwargs):
+    app.run_server(*args, **kwargs)
+
+
+if __name__ == "__main__":
+    run(debug = True)

anisotropy/gui/app.py

@@ -0,0 +1,8 @@
+# -*- coding: utf-8 -*-
+
+import dash
+import dash_bootstrap_components as dbc
+
+app = dash.Dash(__name__, external_stylesheets = [ dbc.themes.LUX ])
+app.title = "Anisotropy"
+app.config["update_title"] = None 

anisotropy/gui/layouts/__init__.py

@@ -0,0 +1,29 @@
+# -*- coding: utf-8 -*-
+
+from . import (
+    runner,
+    settings,
+    database,
+    visualization,
+    about,
+    base
+)
+from .base import app
+
+
+runner = runner.layout
+settings = settings.layout
+database = database.layout
+visualization = visualization.layout
+about = about.layout
+base = base.layout
+
+__all__ = [
+    "runner",
+    "settings",
+    "database",
+    "visualization",
+    "about",
+    "base",
+    "app"
+]

anisotropy/gui/layouts/about.py

@@ -0,0 +1,21 @@
+# -*- coding: utf-8 -*-
+
+from dash import html
+
+import anisotropy
+
+
+###
+#   Layout
+##
+layout = html.Div([
+    html.H1(anisotropy.__name__),
+    html.Hr(),
+    html.P([
+        "Author: {}".format(anisotropy.__author__),
+        html.Br(),
+        "License: {}".format(anisotropy.__license__),
+        html.Br(),
+        "Version: {}".format(anisotropy.__version__)
+    ])
+]) 

anisotropy/gui/layouts/base.py

@@ -0,0 +1,81 @@
+# -*- coding: utf-8 -*-
+
+from dash import html
+from dash import dcc
+from dash.dependencies import Input, Output
+import dash_bootstrap_components as dbc
+
+from . import (
+    runner,
+    settings,
+    database,
+    visualization,
+    about
+)
+from ..app import app
+from .. import styles
+
+import anisotropy
+
+###
+#   Layout
+##
+layout = html.Div([
+    #   Location
+    dcc.Location(id = "url", refresh = False), 
+
+    #   Sidebar
+    html.Div([
+        #   Sidebar
+        html.H2([html.Img(src = "/assets/simple.png", height = "150px")], style = styles.logo),
+        html.Hr(style = { "color": "#ffffff" }),
+        dbc.Nav([
+            dbc.NavLink("Runner", href = "/", active = "exact", style = styles.white),
+            dbc.NavLink("Settings", href = "/settings", active = "exact", style = styles.white),
+            dbc.NavLink("Database", href = "/database", active = "exact", style = styles.white),
+            dbc.NavLink("Visualization", href = "/visualization", active = "exact", style = styles.white),
+            dbc.NavLink("About", href = "/about", active = "exact", style = styles.white),
+        ], vertical = True, pills = True),
+        
+        #   Misc
+        html.Hr(style = styles.white),
+        dbc.Container([
+            dbc.Row([
+                dbc.Col("v1.2.0"),
+                dbc.Col(
+                    html.A(
+                        html.Img(src = "/assets/gh-light.png", height = "20px"), 
+                        href = anisotropy.__repository__ 
+                    )
+                )
+            ])
+        ], style = styles.misc)
+    ], style = styles.sidebar),
+
+    #   Content
+    html.Div(id = "page-content", style = styles.page),
+], style = styles.content)
+
+
+###
+#   Callbacks
+##
+@app.callback(
+    Output("page-content", "children"),
+    [ Input("url", "pathname") ]
+)
+def displayPage(pathname):
+    if pathname == "/settings":
+        return settings.layout
+
+    elif pathname == "/about":
+        return about.layout
+
+    elif pathname == "/database":
+        return database.layout
+
+    elif pathname == "/visualization":
+        return visualization.layout
+
+    else:
+        return runner.layout 

anisotropy/gui/layouts/database.py

@@ -0,0 +1,101 @@
+# -*- coding: utf-8 -*-
+
+from dash.dash_table import DataTable
+from dash import html
+from dash import dcc
+import dash_bootstrap_components as dbc
+from dash.dependencies import Input, Output, State
+
+import pathlib
+from os import environ
+
+from ..app import app
+from .. import styles
+
+
+###
+#   Layout
+##
+layout = html.Div([
+    #   Messages and timer
+    dbc.Alert(
+        id = "db_status", 
+        duration = 10000, 
+        dismissable = True, 
+        is_open = False, 
+        style = styles.message 
+    ),
+    # dcc.Interval(id = "interval", interval = 1000, n_intervals = 0), 
+
+    #   Query
+    html.H2("Database"),
+    html.Hr(),
+    html.P("Query"),
+    dcc.Textarea(id = "db_input", style = { "min-width": "100%"}),
+    html.Br(),
+    dbc.Button("Query", id = "query", style = styles.minWidth),
+
+    #   Output
+    html.Hr(),
+    html.P("Output"),
+    DataTable(
+        id = "db_output", 
+        columns = [], 
+        data = [], 
+        style_table = { "overflow": "scroll"}, 
+        style_cell = {
+            'textAlign': 'left',
+            'width': '150px',
+            'minWidth': '180px',
+            'maxWidth': '180px',
+            'whiteSpace': 'no-wrap',
+            'overflow': 'hidden',
+            'textOverflow': 'ellipsis',
+        }
+    ),
+])
+
+
+###
+#   Callbacks
+##
+@app.callback(
+    Output("db_output", "columns"),
+    Output("db_output", "data"),
+    Output("db_status", "children"), 
+    Output("db_status", "is_open"), 
+    Output("db_status", "color"),
+    [ Input("query", "n_clicks") ],
+    [ State("db_input", "value") ],
+    prevent_initial_call = True
+)
+def db_query(clicks, db_input):
+    from anisotropy import database
+    import peewee as pw
+
+    path = pathlib.Path(environ["AP_CWD"], environ["AP_DB_FILE"])
+    db = database.Database(path)
+    
+    try:
+        db.connect()
+        cursor = db.execute_sql(db_input)
+    
+    except pw.OperationalError as e:
+        db.close()
+        return None, None, str(e), True, "danger"
+    
+    else:
+        columns = [ { "name": col[0], "id": col[0] } for col in cursor.description ]
+        data = []
+
+        for row in cursor.fetchall():
+            item = {}
+
+            for key, value in zip(columns, row):
+                item[key["name"]] = value
+            
+            data.append(item)
+        
+        db.close()
+
+        return columns, data, "", False, "success"

anisotropy/gui/layouts/runner.py

@@ -0,0 +1,180 @@
+# -*- coding: utf-8 -*-
+
+from dash.dash_table import DataTable
+from dash import html
+from dash import dcc
+import dash_bootstrap_components as dbc
+from dash.dependencies import Input, Output, State
+
+import pathlib
+import os
+from os import environ
+
+from ..app import app
+from .. import styles
+from .. import utils
+
+
+###
+#   Layout
+##
+layout = html.Div([
+    #   Messages and timer
+    dbc.Alert(
+        id = "status", 
+        duration = 10000, 
+        dismissable = True, 
+        is_open = False, 
+        style = styles.message 
+    ),
+    dcc.Interval(id = "interval", interval = 1000, n_intervals = 0), 
+
+    #   Runner
+    html.H2("Runner"),
+    html.Hr(),
+    html.P("Execution (leave zero for the latest)"),
+    dcc.Input(id = "execution", type = "number", value = 0, min = 0, style = styles.minWidth),
+    html.Br(),
+    dbc.Button("Start", id = "start", color = "success", style = styles.minWidth),
+    dbc.Button("Stop", id = "stop", color = "danger", disabled = True, style = styles.minWidth),
+
+    #   Monitor
+    html.H2("Monitor"),
+    html.Hr(),
+    html.P(id = "runner-status"),
+    DataTable(id = "monitor", columns = [], data = [], style_table = styles.table),
+
+    #   Log
+    html.H2("Log"),
+    html.Hr(),
+    dbc.Button("Delete", id = "delete", style = styles.minWidth),
+    dcc.Textarea(id = "logger", disabled = True, style = styles.bigText)
+
+])
+
+
+###
+#   Callbacks
+##
+@app.callback(
+    Output("start", "active"),
+    [ Input("start", "n_clicks") ],
+    [ State("execution", "value") ],
+    prevent_initial_call = True
+)
+def runnerStart(clicks, execution):
+    import subprocess
+
+    command = [
+        "anisotropy",
+        "compute",
+        "-v",
+        "--path", environ["AP_CWD"],
+        "--conf", environ["AP_CONF_FILE"],
+        "--pid", "anisotropy.pid",
+        "--logfile", environ["AP_LOG_FILE"],
+    ]
+
+    if execution > 0:
+        command.extend([ "--exec-id", str(execution) ])
+
+    subprocess.run(
+        command,
+        start_new_session = True,
+    )
+
+    return True
+
+
+@app.callback(
+    Output("stop", "active"),
+    [ Input("stop", "n_clicks") ],
+    prevent_initial_call = True
+)
+def runnerStop(clicks):
+    import psutil
+    import signal
+
+    pidpath = pathlib.Path(environ["AP_CWD"], "anisotropy.pid")
+
+    try:
+        pid = int(open(pidpath, "r").read())
+        master = psutil.Process(pid)
+    
+    except (FileNotFoundError, psutil.NoSuchProcess):
+        return True
+
+    else:
+        os.killpg(master.pid, signal.SIGTERM)
+
+        return True
+
+
+@app.callback(
+    Output("monitor", "columns"),
+    Output("monitor", "data"),
+    Output("runner-status", "children"),
+    Output("start", "disabled"),
+    Output("stop", "disabled"),
+    Output("delete", "disabled"),
+    [ Input("interval", "n_intervals") ],
+)
+def monitorUpdate(intervals):
+    import psutil
+
+    pidpath = pathlib.Path(environ["AP_CWD"], "anisotropy.pid")
+    processes = []
+
+    try:
+        pid = int(open(pidpath, "r").read())
+        master = psutil.Process(pid)
+    
+    except (FileNotFoundError, psutil.NoSuchProcess):
+        return [], [], "Status: not running", False, True, False
+    
+    else:
+        for process in [ master, *master.children() ]:
+            created = psutil.time.localtime(process.create_time())
+            processes.append({
+                "name": process.name(),
+                "pid": process.pid,
+                "status": process.status(),
+                "memory": utils.getSize(process.memory_full_info().uss),
+                "threads": process.num_threads(),
+                "created": "{}:{}:{}".format(created.tm_hour, created.tm_min, created.tm_sec)
+            })
+        
+        columns = [ { "name": col, "id": col } for col in processes[0].keys() ]
+
+        return columns, processes, "Status: running", True, False, True
+
+
+@app.callback(
+    Output("logger", "value"),
+    [ Input("interval", "n_intervals") ]
+)
+def logUpdate(intervals):
+    logpath = pathlib.Path(environ["AP_CWD"], "anisotropy.log")
+
+    if os.path.exists(logpath):
+        with open(logpath, "r") as io:
+            log = io.read()
+        
+        return log
+    
+    else:
+        return "Not found"
+
+
+@app.callback(
+    Output("delete", "active"),
+    [ Input("delete", "n_clicks") ],
+    prevent_initial_call = True
+)
+def logDelete(clicks):
+    logpath = pathlib.Path(environ["AP_CWD"], "anisotropy.log")
+
+    if os.path.exists(logpath):
+        os.remove(logpath)
+    
+    return True

anisotropy/gui/layouts/settings.py

@@ -0,0 +1,141 @@
+# -*- coding: utf-8 -*-
+
+from dash import html
+from dash import dcc
+import dash_bootstrap_components as dbc
+from dash.dependencies import Input, Output, State
+
+import pathlib
+from os import environ
+
+from ..app import app
+from .. import styles
+
+
+###
+#   Layout
+##
+layout = html.Div([
+    #   Messages
+    dbc.Alert(
+        id = "status", 
+        duration = 10000, 
+        dismissable = True, 
+        is_open = False, 
+        style = styles.message 
+    ),
+    dbc.Alert(
+        id = "general-status", 
+        duration = 10000, 
+        dismissable = True, 
+        is_open = False, 
+        style = styles.message 
+    ),
+    #   General
+    html.H2("General"),
+    html.Hr(),
+    html.P("Path"),
+    dcc.Input(id = "cwd", style = { "min-width": "500px" }),
+    html.Br(),
+    dbc.Button("Save general", id = "general-save", style = styles.minWidth),
+    
+    #   Options
+    html.H2("Options"),
+    html.Hr(),
+    html.P("Nprocs"),
+    dcc.Input(id = "nprocs", type = "number", style = styles.minWidth),
+    html.P("Stage"),
+    dcc.Dropdown(
+        id = "stage",
+        options = [ { "label": k, "value": k } for k in ["all", "shape", "mesh", "flow", "postProcess"] ],
+        style = styles.minWidth 
+    ),
+    dbc.Button("Save", id = "submit", style = styles.minWidth),
+
+    #   Cases
+    html.H2("Cases"),
+    html.Hr(),
+    dcc.Textarea(id = "cases", style = styles.bigText),
+])
+
+
+###
+#   Callbacks
+##
+@app.callback(
+    Output("general-status", "children"), 
+    Output("general-status", "is_open"), 
+    Output("general-status", "color"),
+    [ Input("general-save", "n_clicks") ],
+    [ 
+        State("cwd", "value"),
+    ],
+    prevent_initial_call = True
+)
+def generalSave(clicks, cwd):
+    path = pathlib.Path(cwd)
+
+    if not path.is_absolute():
+        return "Cwd path must be absolute", True, "danger"
+    
+    environ["AP_CWD"] = str(path)
+
+    return "General settings saved", True, "success"
+
+
+@app.callback(
+    Output("cwd", "value"),
+    Output("nprocs", "value"),
+    Output("stage", "value"),
+    Output("cases", "value"),
+    [ Input("url", "pathname") ]
+)
+def settingsLoad(pathname):
+    from anisotropy.core import config as core_config
+    import toml
+
+    path = pathlib.Path(environ["AP_CWD"], environ["AP_CONF_FILE"])
+    config = core_config.default_config()
+
+    if path.exists():
+        config.load(path)
+
+    return environ["AP_CWD"], config["nprocs"], config["stage"], toml.dumps(config.content)
+
+
+@app.callback(
+    Output("status", "children"), 
+    Output("status", "is_open"), 
+    Output("status", "color"),
+    [ Input("submit", "n_clicks") ],
+    [ 
+        State("nprocs", "value"),
+        State("stage", "value"),
+        State("cases", "value") 
+    ],
+    prevent_initial_call = True
+)
+def settingsSave(nclick, nprocs, stage, cases):
+    from anisotropy.core import config as core_config
+    import toml
+
+    path = pathlib.Path(environ["AP_CWD"], environ["AP_CONF_FILE"])
+    config = core_config.default_config()
+
+    if path.exists():
+        config.load(path) 
+
+    config.update(
+        nprocs = nprocs,
+        stage = stage
+    )
+    
+    try:
+        config.content = toml.loads(cases)
+        config.dump(path)
+
+    except Exception as e:
+        return str(e), True, "danger"
+    
+    else:
+        return f"Saved to { path }", True, "success"

anisotropy/gui/layouts/visualization.py

@@ -0,0 +1,405 @@
+# -*- coding: utf-8 -*-
+
+from dash import html
+from dash import dcc
+import dash_bootstrap_components as dbc
+from dash.dependencies import Input, Output, State
+import dash_vtk
+import dash_vtk.utils
+import vtk
+
+import pathlib
+from os import environ
+
+from ..app import app
+from .. import styles
+
+
+class MeshRepresentation(object):
+    def __init__(self, path):
+        self.mesh = vtk.vtkXMLUnstructuredGridReader()
+        self.mesh.SetFileName(path)
+        self.mesh.Update()
+
+        self.clip = False
+        self.crinkle = False
+        self.wireframe = True
+        self.planeNormal = [0, 0, -1]
+        self.planeOrigin = [0, 0, 1]
+
+    def getRepresentation(self):
+        if not self.clip:
+            dataset = self.mesh.GetOutput()
+        
+        else:
+            plane = vtk.vtkPlane()
+            plane.SetNormal(self.planeNormal)
+            plane.SetOrigin(self.planeOrigin)
+
+            if self.crinkle:
+                implfunc = vtk.vtkImplicitBoolean()
+                implfunc.AddFunction(plane)
+                implfunc.Modified()
+
+                clipper = vtk.vtkExtractGeometry()
+                clipper.SetInputConnection(self.mesh.GetOutputPort())
+                clipper.SetImplicitFunction(implfunc)
+                clipper.SetExtractInside(1)
+                clipper.SetExtractOnlyBoundaryCells(0)
+                clipper.SetExtractBoundaryCells(1)
+                clipper.ExtractInsideOff()
+
+            else:
+                clipper = vtk.vtkTableBasedClipDataSet()
+                clipper.SetInputData(self.mesh.GetOutput())
+                clipper.SetClipFunction(plane)
+                clipper.SetValue(0.0)
+                clipper.GenerateClippedOutputOn()
+            
+            clipper.Update()
+            dataset = clipper.GetOutput()
+
+        representation = dash_vtk.GeometryRepresentation(
+            id = "mesh-representation",
+            children = [
+                dash_vtk.Mesh(id = "mesh", state = dash_vtk.utils.to_mesh_state(dataset))
+            ],
+            property = { "edgeVisibility": self.wireframe }
+        )
+
+        return representation
+        
+
+def databaseColumns():
+    from anisotropy.database import Database
+    import re
+
+    db = Database()
+    idcol = re.compile(r"\s*_id")
+    columns = []
+
+    for table in db.tables:
+        for column in table._meta.columns.keys():
+            if not idcol.search(column):
+                columns.append(column)
+    
+    return columns
+
+
+###
+#   Layout
+##
+controls = html.Div([
+    html.P("Execution"),
+    dcc.Input(id = "exec_id", type = "number", value = 0, min = 0, style = styles.minWidth),
+    html.Br(),
+
+    html.P("Structure"),
+    dcc.Dropdown(
+        id = "structure",
+        options = [ { "label": v, "value": v } for v in [ "simple", "bodyCentered", "faceCentered" ] ],
+        value = "simple",
+        style = styles.minWidth
+    ),
+    html.Br(),
+    
+    html.P("Direction"),
+    dcc.Dropdown(
+        id = "direction",
+        options = [ { "label": str(v), "value": str(v)} for v in [ [1., 0., 0.], [0., 0., 1.], [1., 1., 1.] ] ],
+        value = str([1., 0., 0.]),
+    ),
+    html.Br(),
+    
+    html.P("Alpha"),
+    dcc.Input(id = "alpha", type = "number", value = 0.01, min = 0.01, step = 0.01, style = styles.minWidth),
+    html.Br(),
+
+    html.P("Clip"),
+    dbc.Checkbox(id = "clip", value = False),
+    html.Br(),
+
+    html.P("Crinkle"),
+    dbc.Checkbox(id = "crinkle", value = False),
+    html.Br(),
+
+    html.P("Plane normal"),
+    dcc.Input(id = "normal-x", type = "number", value = 0, style = { "width": "100px", "margin-bottom": "20px" }), 
+    dcc.Input(id = "normal-y", type = "number", value = 0, style = { "width": "100px", "margin-bottom": "20px" }), 
+    dcc.Input(id = "normal-z", type = "number", value = -1, style = { "width": "100px", "margin-bottom": "20px" }),
+    html.Br(),
+
+    html.P("Plane origin"),
+    dcc.Input(id = "origin-x", type = "number", value = 0, style = { "width": "100px", "margin-bottom": "20px" }), 
+    dcc.Input(id = "origin-y", type = "number", value = 0, style = { "width": "100px", "margin-bottom": "20px" }), 
+    dcc.Input(id = "origin-z", type = "number", value = 1, style = { "width": "100px", "margin-bottom": "20px" }),
+    html.Br(),
+
+    html.P("Wireframe"),
+    dbc.Checkbox(id = "wireframe", value = True),
+    html.Br(),
+
+    dbc.Button("Draw", id = "draw"),
+])
+
+plotcontrols = html.Div([
+    html.P("Execution"),
+    dcc.Input(id = "plot-exec_id", type = "number", value = 0, min = 0, style = styles.minWidth),
+    html.Br(),
+
+    html.P("Structure"),
+    dcc.Dropdown(
+        id = "plot-structure",
+        options = [ 
+            { "label": v, "value": v } 
+            for v in [ "simple", "bodyCentered", "faceCentered" ] 
+        ],
+        value = "simple"
+    ),
+    html.Br(),
+    
+    html.P("Direction"),
+    dcc.Dropdown(
+        id = "plot-direction",
+        options = [ 
+            { "label": str(v), "value": str(v)} 
+            for v in [ [1., 0., 0.], [0., 0., 1.], [1., 1., 1.], "all" ] 
+        ],
+        value = str([1., 0., 0.]),
+    ),
+    html.Br(),
+
+    html.P("Data"),
+    dcc.Dropdown(
+        id = "plot-data",
+        options = [ { "label": v, "value": v } for v in databaseColumns() ], 
+        value = "porosity",
+    ),
+    html.Br(),
+
+    dbc.Button("Draw", id = "plot-draw"),
+])
+
+layout = html.Div([
+    html.H2("Plot"),
+    html.Hr(),
+    dbc.Container(
+        fluid = True,
+        children = [
+            dbc.Row([
+                dbc.Col(width = 4, children = plotcontrols, style = { "min-width": "350px" }),
+                dbc.Col(
+                    width = 8,
+                    children = [
+                        html.Div(id = "plot-output", style = { "width": "100%", "min-width": "800px" })
+                    ],
+                    style = { "min-width": "800px" }
+                ),
+            ], style = { "height": "100%"}),
+        ]),
+    html.Br(),
+
+    html.H2("Mesh"),
+    html.Hr(),
+    dbc.Container(
+        fluid = True,
+        children = [
+            dbc.Row([
+                dbc.Col(width = 4, children = controls, style = { "min-width": "350px" }),
+                dbc.Col(
+                    width = 8,
+                    children = [
+                        html.Div(
+                            id = "vtk-output", 
+                            style = { "height": "800px", "width": "100%", "min-width": "800px" }
+                        )
+                    ],
+                    style = { "min-width": "800px" }),
+            ], style = { "height": "100%"}),
+        ])
+])
+
+
+@app.callback(
+    [ Output("plot-output", "children") ],
+    [ Input("plot-draw", "n_clicks") ],
+    [
+        State("plot-exec_id", "value"),
+        State("plot-structure", "value"),
+        State("plot-direction", "value"),
+        State("plot-data", "value"),
+    ]
+)
+def plotDraw(clicks, execution, structure, direction, data):
+    import peewee as pw
+    from anisotropy.database import Database, tables
+    import json
+    from pandas import DataFrame
+    import plotly.express as px
+
+    path = pathlib.Path(environ["AP_CWD"], environ["AP_DB_FILE"])
+
+    if not path.is_file():
+        return [ "Database not found" ]
+    
+    db = Database(path)
+    
+    if not db.getExecution(execution):
+        return [ "Execution not found" ]
+    
+    for model in db.tables:
+        try:
+            column = getattr(model, data)
+        
+        except AttributeError:
+            pass
+
+        else:
+            break
+
+    if direction == "all":
+        select = (tables.Shape.alpha, column, tables.Shape.direction)
+    
+    else:
+        select = (tables.Shape.alpha, column)
+
+    """query = (
+        tables.Shape
+        .select(*select)
+        .join(tables.Execution, JOIN.LEFT_OUTER)
+        .switch(tables.Shape)
+        .join(tables.Mesh, JOIN.LEFT_OUTER)
+        #.switch(tables.Shape)
+        .join(tables.FlowOnephase, JOIN.LEFT_OUTER)
+        .switch(tables.Shape)
+        .where(
+            tables.Shape.exec_id == execution,
+            tables.Shape.label == structure,
+        )
+    )"""
+    query = model.select(*select)
+    idn = db.tables.index(model)
+
+    for table in reversed(db.tables[ :idn]):
+        query = query.join(table, pw.JOIN.LEFT_OUTER)
+    
+    query = query.switch(tables.Shape)
+    query = query.where(
+        tables.Shape.exec_id == execution,
+        tables.Shape.label == structure,
+    )
+    query = query.order_by(tables.Shape.alpha)
+    
+    if not direction == "all":
+        query = query.where(tables.Shape.direction == json.loads(direction))
+
+    with db:
+        if query.exists():
+            table = []
+            for row in query.dicts():
+                for k in row.keys():
+                    if type(row[k]) == list:
+                        row[k] = str(row[k])
+
+                table.append(row)
+        
+        else:
+            table = None
+    
+    if not table:
+        return [ "Results not found" ]
+
+    import plotly.io as plt_io
+
+    plt_io.templates["custom_dark"] = plt_io.templates["plotly_dark"]
+
+    plt_io.templates["custom_dark"]['layout']['paper_bgcolor'] = '#30404D'
+    plt_io.templates["custom_dark"]['layout']['plot_bgcolor'] = '#30404D'
+
+    plt_io.templates['custom_dark']['layout']['yaxis']['gridcolor'] = '#4f687d'
+    plt_io.templates['custom_dark']['layout']['xaxis']['gridcolor'] = '#4f687d'
+    
+    fig = px.line(
+        DataFrame(table), x = "alpha", y = data, title = structure, markers = True
+    )
+
+    if direction == "all":
+        fig = px.line(
+            DataFrame(table), x = "alpha", y = data, title = structure, markers = True, color = "direction"
+        )
+
+    fig.layout.template = "custom_dark"
+    fig.update_xaxes(showline = True, linewidth = 1, linecolor = '#4f687d', mirror = True)
+    fig.update_yaxes(showline = True, linewidth = 1, linecolor = '#4f687d', mirror = True)
+
+    plot = dcc.Graph(
+        figure = fig
+    )
+
+    return [ plot ]
+        
+
+@app.callback(
+    [ Output("alpha", "min"), Output("alpha", "max") ],
+    [ Input("structure", "value") ]
+)
+def alphaLimits(label):
+    if label == "simple":
+        return 0.01, 0.29
+    
+    elif label == "bodyCentered":
+        return 0.01, 0.18
+
+    elif label == "faceCentered":
+        return 0.01, 0.13
+
+
+@app.callback(
+    [ Output("vtk-output", "children") ],
+    [ Input("draw", "n_clicks") ],
+    [
+        State("exec_id", "value"),
+        State("structure", "value"),
+        State("direction", "value"),
+        State("alpha", "value"),
+        State("clip", "value"),
+        State("crinkle", "value"),
+        State("wireframe", "value"),
+        State("normal-x", "value"),
+        State("normal-y", "value"),
+        State("normal-z", "value"),
+        State("origin-x", "value"),
+        State("origin-y", "value"),
+        State("origin-z", "value"),
+    ],
+    prevent_initial_call = True
+)
+def meshDraw(clicks, execution, structure, direction, alpha, clip, crinkle, wireframe, normal_x, normal_y, normal_z, origin_x, origin_y, origin_z):
+    import meshio
+    
+    path = pathlib.Path(environ["AP_CWD"], environ["AP_BUILD_DIR"])
+    path /= "execution-{}".format(execution)
+    path /= "{}-{}-{}".format(
+        structure, 
+        direction.replace(" ", ""),
+        alpha
+    )
+    basemeshpath = path / "mesh.msh"
+    meshpath = path / "mesh.vtu"
+
+    if not basemeshpath.exists():
+        return [ "Mesh not found" ]
+
+    if not meshpath.exists() or not meshpath.is_file():
+        meshold = meshio.read(basemeshpath)
+        meshold.write(meshpath)
+
+    meshrepr = MeshRepresentation(meshpath)
+    meshrepr.clip = clip 
+    meshrepr.crinkle = crinkle 
+    meshrepr.wireframe = wireframe
+    meshrepr.planeNormal = [ normal_x, normal_y, normal_z ]
+    meshrepr.planeOrigin = [ origin_x, origin_y, origin_z ]
+    view = dash_vtk.View([ meshrepr.getRepresentation() ])
+
+    return [ view ] 

anisotropy/gui/styles.py

@@ -0,0 +1,57 @@
+# -*- coding: utf-8 -*-
+
+minWidth = { 
+    "min-width": "200px", 
+    "max-width": "200px", 
+    "margin-bottom": "15px" 
+}
+
+bigText = { 
+    "min-width": "100%", 
+    "min-height": "500px" 
+}
+
+message = { 
+    "position": "fixed", 
+    "top": "30px", 
+    "right": "30px",
+}
+
+page = { 
+    "padding": "30px 50px 0px 50px" 
+}
+
+table = {
+    "margin-bottom": "15px",
+    "min-width": "100%"
+}
+
+sidebar = {
+    "position": "fixed",
+    "top": 0,
+    "left": 0,
+    "bottom": 0,
+    "width": "16rem",
+    "padding": "2rem 1rem",
+    "background-color": "#363636"
+}
+
+content = {
+    "margin-left": "18rem",
+    "margin-right": "2rem",
+    "padding": "2rem 1rem",
+}
+
+misc = { 
+    "color": "#757575", 
+    "text-align": "center" 
+}
+
+logo = {
+    "color": "#ffffff", 
+    "text-align": "center" 
+}
+
+white = {
+    "color": "#ffffff"
+}

anisotropy/gui/utils.py

@@ -0,0 +1,8 @@
+# -*- coding: utf-8 -*-
+
+def getSize(bytes):
+    for unit in ["", "K", "M", "G", "T", "P"]:
+        if bytes < 1024:
+            return f"{bytes:.2f} {unit}iB"
+
+        bytes /= 1024

anisotropy/meshing/__init__.py

@@ -0,0 +1,16 @@
+# -*- coding: utf-8 -*-
+
+from . import utils
+from . import conversion
+from . import metrics
+
+from .mesh import Mesh, MeshingParameters
+
+
+__all__ = [
+    "utils",
+    "conversion",
+    "metrics",
+    "Mesh",
+    "MeshingParameters"
+]

anisotropy/meshing/conversion.py

@@ -0,0 +1,145 @@
+
+from numpy import ndarray
+from os import PathLike
+
+import numpy as np
+from pathlib import Path
+
+from . import utils
+
+
+def write_neutral(
+    points: ndarray, 
+    cells: list[utils.CellBlock], 
+    dim: int, 
+    filename: PathLike
+):
+    """Write mesh to the netgen file (Neutral format [.mesh]).
+
+    :param points:
+        Array of points.
+    :param cells:
+        List of cell blocks.
+    :param dim:
+        Dimension of the mesh.
+    :param filename:
+        Path of the file.
+    """
+    precision = "6f"
+    floatValue = "{value:>{width}." + precision + "}"
+    intValue = "{value:>{width}}"
+    outfile = open(Path(filename).resolve(), "w")
+
+    #   write points
+    outfile.write(str(len(points)) + "\n")
+
+    for n in range(len(points)):
+        point = points[n]
+
+        outfile.write(floatValue.format(value = point[0], width = 10) + " ")
+        outfile.write(floatValue.format(value = point[1], width = 9) + " ")
+
+        if dim == 3:
+            outfile.write(floatValue.format(value = point[2], width = 9) + " ")
+
+        outfile.write("\n")
+    
+    #   write volume cells
+    if dim == 3:
+        count = sum([ len(cell.data) for cell in cells if cell.dim == 3])
+        outfile.write(str(count) + "\n")
+
+        for cellBlock in cells:
+            if cellBlock.dim == 3:
+                for cell in cellBlock.data:
+                    outfile.write(intValue.format(value = 1, width = 4))
+
+                    for pointId in cell:
+                        outfile.write(" ")
+                        #   shift id up, in netgen it starts from one
+                        outfile.write(intValue.format(value = pointId + 1, width = 8))
+                    
+                    outfile.write("\n")
+    
+    #   write faces
+    count = sum([ len(cell.data) for cell in cells if cell.dim == 2])
+    outfile.write(str(count) + "\n")
+
+    for cellBlock in cells:
+        if cellBlock.dim == 2:
+            for index, cell in zip(cellBlock.indices, cellBlock.data):
+                outfile.write(intValue.format(value = index, width = 4) + "    ")
+
+                for pointId in cell:
+                    outfile.write(" ")
+                    #   shift id up, in netgen it starts from one
+                    outfile.write(intValue.format(value = pointId + 1, width = 8))
+
+                outfile.write("\n")
+
+    #   write segments
+    #   important?
+
+
+def read_neutral(filename: PathLike) -> tuple[list, list]:
+    """Read mesh from netgen file (Neutral format [.mesh]).
+
+    :param filename:
+        Path of the file.
+    :return:
+        List of points and list of cell blocks.
+    """
+    infile = open(Path(filename).resolve(), "r")
+
+    #   read points from file, starts with single integer
+    npoints = int(infile.readline())
+    points = [] 
+
+    for n in range(npoints):
+        points.append(np.fromstring(infile.readline(), dtype = float, sep = " "))
+
+    #   dimension
+    dim = None if len(points) == 0 else points[0].size
+
+    #   read volume cells
+    nvolumes = int(infile.readline())
+    volume_indices = []
+    volumes = []
+
+    for n in range(nvolumes):
+        data = np.fromstring(infile.readline(), dtype = int, sep = " ")
+        volume_indices.append(data[0])
+        #   shift node indices down, in netgen it starts from one, need from zero
+        volumes.append(data[1: ] - 1)
+    
+    #   read surface cells
+    nsurfaces = int(infile.readline())
+    surface_indices = []
+    surfaces = []
+
+    for n in range(nsurfaces):
+        data = np.fromstring(infile.readline(), dtype = int, sep = " ")
+        surface_indices.append(data[0])
+        #   shift node indices down, in netgen it starts from one, need from zero
+        surfaces.append(data[1: ] - 1)
+    
+    #   read segment cells
+    #   important?
+
+    #   write data to object
+    points = np.asarray(points)
+    cells = []
+
+    if len(volumes) > 0:
+        cells += utils.collect_cells(volumes, 3, volume_indices)
+
+    if len(surfaces) > 0:
+        cellBlocks = utils.collect_cells(surfaces, 2, surface_indices)
+
+        if dim == 3:
+            for cellBlock in cellBlocks:
+                cellBlock.is_boundary = True
+        
+        cells += cellBlocks
+
+    return points, cells 

anisotropy/meshing/mesh.py

@@ -0,0 +1,242 @@
+# -*- coding: utf-8 -*-
+# This file is part of anisotropy.
+# License: GNU GPL version 3, see the file "LICENSE" for details.
+
+from __future__ import annotations
+from numpy import ndarray
+from os import PathLike
+
+import numpy as np
+import netgen.occ as ng_occ
+import netgen.meshing as ng_meshing
+import meshio
+import pathlib
+
+from . import utils
+from . import metrics
+from . import conversion
+
+
+class NoGeometrySpecified(Exception):
+    pass
+
+
+class NotSupportedMeshFormat(Exception):
+    """Exception for not supported mesh format IO operations.
+    """
+    pass
+
+
+class MeshingParameters:
+    def __init__(self, **kwargs):
+        """A MeshingParameters object contains parameters for netgen mesher.
+        """
+        self.preset(2, **kwargs)
+       
+    def preset(self, key: int, **kwargs):
+        """Apply predefined parameters.
+
+        :param key:
+            0: very_coarse
+            1: coarse
+            2: moderate
+            3: fine
+            4: very_fine
+        """
+        self.__dict__.update(kwargs)
+        
+        self.maxh = kwargs.get("maxh", 0.1)
+        self.curvaturesafety = kwargs.get("curvaturesafety", [1, 1.5, 2, 3, 5][key])
+        self.segmentsperedge = kwargs.get("segmentsperedge", [0.3, 0.5, 1, 2, 3][key])
+        self.grading = kwargs.get("grading", [0.7, 0.5, 0.3, 0.2, 0.1][key])
+        self.chartdistfac = kwargs.get("chartdistfac", [0.8, 1, 1.5, 2, 5][key])
+        self.linelengthfac = kwargs.get("linelengthfac", [0.2, 0.35, 0.5, 1.5, 3][key])
+        self.closeedgefac = kwargs.get("closeedgefac", [0.5, 1, 2, 3.5, 5][key])
+        self.minedgelen = kwargs.get("minedgelen", [0.002, 0.02, 0.2, 1.0, 2.0][key])
+        self.surfmeshcurvfac = kwargs.get("surfmeshcurvfac", [1, 1.5, 2, 3, 5.0][key])
+        self.optsteps2d = kwargs.get("optsteps2d", 5)
+        self.optsteps3d = kwargs.get("optsetps3d", 5)
+
+        return self
+
+    def get(self) -> ng_meshing.MeshingParameters:
+        return ng_meshing.MeshingParameters(**self.__dict__)
+    
+    def __repr__(self):
+        items = [ f"{ key }: { val }" for key, val in self.__dict__.items() ]
+
+        return "<MeshingParameters, " + ", ".join(items) + ">"
+
+
+class Mesh:
+    def __init__(self, shape = None):
+        """A Mesh object contains a mesh
+
+        :param shape:
+            OCC shape.
+        """
+        self.shape = shape
+        self.mesh = None
+
+        self.points = []
+        self.cells = []
+
+        self._dim = None
+
+    @property
+    def dim(self) -> float | None:
+        """Mesh dimension.
+
+        :return:
+            float or None if mesh contains no points.
+        """
+        return None if len(self.points) == 0 else self.points[0].size
+
+    @property
+    def geometry(self) -> ng_occ.OCCGeometry | None:
+        """Netgen OCCGeometry object.
+
+        :return:
+            OCCGeometry object that can be used for meshing
+            or None if shape is not defined.
+        """
+        if self.shape is not None:
+            if hasattr(self.shape, "geometry"):
+                return self.shape.geometry
+            
+            else:
+                return ng_occ.OCCGeometry(self.shape)
+
+        return None
+
+    def generate(
+        self, 
+        parameters: ng_meshing.MeshingParameters = None, 
+        refineSteps: int = 0, 
+        refineOptimize: bool = True,
+        scale: float = 0
+    ):
+        """Generate mesh using netgen mesher on occ geometry.
+
+        :param parameters:
+            Meshing parameters object.
+        :param refineSteps:
+            Refine mesh after main meshing.
+        :param refineOptimize:
+            If True, optimize surface and volume mesh after each refine step.
+        :param scale:
+            Scale mesh after all operations.
+        """
+        if not self.geometry:
+            raise NoGeometrySpecified("Cannot build mesh without geometry")
+    
+        parameters = parameters or MeshingParameters()
+        #   generate volume mesh
+        mesh = self.geometry.GenerateMesh(parameters.get())
+
+        if refineSteps > 0:
+            for n in range(refineSteps):
+                mesh.Refine()
+            
+            #   optimize surface and volume mesh
+            if refineOptimize:
+                mesh.OptimizeMesh2d(parameters.get())
+                mesh.OptimizeVolumeMesh(parameters.get())
+        
+        if scale > 0:
+            mesh.Scale(scale)
+        
+        self.points = utils.extract_netgen_points(mesh)
+        self.cells = []
+
+        if mesh.dim == 3:
+            volume_cells, volume_indices = utils.extract_netgen_cells(mesh, 3)
+            self.cells += utils.collect_cells(volume_cells, 3, volume_indices)
+
+            surface_cells, surface_indices = utils.extract_netgen_cells(mesh, 2)
+            cell_blocks = utils.collect_cells(surface_cells, 2, surface_indices)
+
+            for cellBlock in cell_blocks:
+                cellBlock.is_boundary = True
+            
+            self.cells += cell_blocks
+        
+        # TODO: dim == 2
+
+        return self
+
+    def read(self, filename: str):
+        """Import a mesh from the file.
+        
+        :param filename:
+            Path of the file.
+        """        
+        path = pathlib.Path(filename).resolve()
+        ext = path.suffix[1: ]
+
+        #   Force netgen neutral format
+        if ext == "mesh":
+            self.points, self.cells = conversion.read_neutral(path)
+
+        else:
+            mesh = meshio.read(path)
+            self.points = mesh.points
+            self.cells = mesh.cells
+        
+        return self
+
+    def write(self, filename: PathLike):
+        """Export mesh to the file.
+        
+        :param filename:
+            Path of the file to store the given mesh in.
+        """     
+        path = pathlib.Path(filename).resolve()
+        ext = path.suffix[1: ]
+        
+        #   Force netgen neutral format
+        if ext == "mesh":
+            conversion.write_neutral(self.points, self.cells, self.dim, path)
+
+        else:
+            mesh = meshio.Mesh(self.points, self.cells)
+            mesh.write(path)
+
+    @property
+    def volumes(self) -> list[ndarray]: 
+        """Volumes.
+
+        :return:
+            List of points.
+        """
+        points = []
+
+        for cellBlock in self.cells:
+            if cellBlock.dim == 3:
+                points += [ *self.points[cellBlock.data] ]
+
+        return points
+
+    @property
+    def volume(self) -> float:
+        """Volume of whole mesh.
+        
+        :return:
+            Volume.
+        """
+        return np.sum([ metrics.volume(cell) for cell in self.volumes ]) 
+
+    @property
+    def faces(self) -> list[ndarray]: 
+        """Boundary faces.
+
+        :return:
+            List of boundary faces.
+        """
+        points = []
+
+        for cellBlock in self.cells:
+            if cellBlock.dim == 2 and cellBlock.is_boundary:
+                points += [ *self.points[cellBlock.data] ]
+
+        return points 

anisotropy/meshing/metrics.py

@@ -0,0 +1,43 @@
+# -*- coding: utf-8 -*-
+# This file is part of anisotropy.
+# License: GNU GPL version 3, see the file "LICENSE" for details.
+
+import numpy as np
+from numpy import ndarray
+
+from . import utils
+
+
+def volume(points: ndarray) -> ndarray:
+    """Volume of the cell.
+
+    :param points:
+        Array of points that represents volumetric cell.
+    :return:
+        Volume.
+    """
+    cellType = utils.cell_type(3, len(points))
+
+    if cellType == "tetra":
+        return 1 / 6 * np.linalg.det(np.append(points.transpose(), np.array([[1, 1, 1, 1]]), axis = 0))
+    
+    else:
+        raise Exception(f"Not supported cell type '{ cellType }'")
+
+
+def area(points: ndarray) -> ndarray:
+    """Area of the cell.
+
+    :param points:
+        Array of points that represents surface cell.
+    :return:
+        Area.
+    """
+    cellType = utils.cell_type(2, len(points))
+    vecs = np.roll(points, shift = -1, axis = 0) - points
+
+    if cellType == "triangle":
+        return 0.5 * np.abs(np.cross(*vecs[ :-1]))
+
+    else:
+        raise Exception(f"Not supported cell type '{ cellType }'")

anisotropy/meshing/utils.py

@@ -0,0 +1,178 @@
+from __future__ import annotations
+from numpy import ndarray
+
+import numpy as np
+import netgen.meshing as ng_meshing
+import meshio
+
+
+topo_dim = meshio._mesh.topological_dimension
+cell_nodes = meshio._common.num_nodes_per_cell
+
+
+def cell_type(dimension: int, num_nodes: int) -> str | None:
+    """Detect a cell topology type.
+
+    :param dimension:
+        Cell dimension.
+    :param num_nodes:
+        Number of nodes in the cell.
+    :return:
+        Cell type or None if cell type if not supported. 
+    """
+    for dim in topo_dim.keys():
+        for num in cell_nodes.keys():
+            if (
+                topo_dim[dim] == dimension and 
+                cell_nodes[num] == num_nodes and 
+                dim == num
+            ):
+                return dim
+    
+    return None 
+
+
+class CellBlock:
+    def __init__(
+        self, 
+        cellType: str, 
+        data: list | ndarray, 
+        tags: list[str] = [],
+        indices: list | ndarray = [],
+        is_boundary: bool = False,
+        names: list[str] = []
+    ):
+        """A CellBlock object contains cells information of the same type.
+
+        :param cellType:
+            Type of the cell.
+        :param data:
+            Array of cells.
+        :param tags:
+            Some cell tags.
+        :param indices:
+            Array of indices of cells. Must be the same length as data length.
+            Usefull for detecting boundary faces, etc.
+        :param is_boundary:
+            Flag that cells are not internal.
+        :param names:
+            Array of names of cells. Must be the same length as data length.
+            Usefull for detecting boundary faces, etc.
+        """
+        self.type = cellType
+        self.data = data
+
+        if cellType.startswith("polyhedron"):
+            self.dim = 3
+        
+        else:
+            self.data = np.asarray(self.data)
+            self.dim = topo_dim[cellType]
+
+        self.tags = tags
+        self.indices = np.asarray(indices)
+        self.is_boundary = is_boundary 
+        self.names = names
+
+    def __repr__(self):
+        items = [
+            "CellBlock",
+            f"type: { self.type }",
+            f"num cells: { len(self.data) }",
+            f"tags: { self.tags }",
+        ]
+        return "<" + ", ".join(items) + ">"
+
+    def __len__(self):
+        return len(self.data)
+
+
+def collect_cells(cells: list, dim: int, indices: list | ndarray = None, cellType: str = None) -> list[CellBlock]:
+    """Collect cell blocks from a list of cells.
+
+    :param cells:
+        List of cells.
+    :param dim:
+        Cell dimension.
+    :param indices:
+        List of cell indices. Must be the same length as list of cells.
+    :return:
+        List of cell blocks.
+    """ 
+    cellBlocks = []
+
+    if indices is not None:
+        assert len(cells) == len(indices), "cells and indices arrays must be the same length"
+    
+    for n, cell in enumerate(cells):
+        cellType = cellType or cell_type(dim, len(cell))
+        index = indices[n] if indices else None
+        is_added = False
+        
+        #   update cell block
+        for cellBlock in cellBlocks:
+            if cellBlock.type == cellType:
+                cellBlock.data += [ cell ]
+
+                if index:
+                    cellBlock.indices.append(index)
+
+                is_added = True
+
+        #   or create new                
+        if not is_added:
+            cellBlock = CellBlock(cellType, [])
+            cellBlock.data = [ cell ]
+
+            if index:
+                cellBlock.indices = [ index ]
+
+            cellBlocks.append(cellBlock)
+
+    #   convert arrays to numpy    
+    for cellBlock in cellBlocks:
+        cellBlock.data = np.asarray(cellBlock.data)
+        cellBlock.indices = np.asarray(cellBlock.indices)
+
+    return cellBlocks
+
+
+def extract_netgen_points(mesh: ng_meshing.Mesh) -> ndarray:
+    """Extract points from netgen mesh object.
+
+    :param mesh:
+        Netgen mesh object.
+    :return:
+        Array of points.
+    """
+    return np.array([ point.p for point in mesh.Points() ], dtype = float)
+
+
+def extract_netgen_cells(mesh: ng_meshing.Mesh, dim: int) -> tuple[list, list]:
+    """Extract cells from netgen mesh according to cell dimension.
+
+    :param mesh:
+        Netgen mesh object.
+    :param dim:
+        Cell dimension.
+    :return:
+        List of cells and list of indices.
+    """
+    cells = []
+    indices = []
+    elements = {
+        0: mesh.Elements0D(),
+        1: mesh.Elements1D(),
+        2: mesh.Elements2D(),
+        3: mesh.Elements3D()
+    }[dim]
+
+    if len(elements) > 0:
+        for cell in elements:
+            #   shift nodes values, they should start from zero
+            nodes = np.array([ node.nr for node in cell.points ], dtype = int) - 1
+            cells.append(nodes)
+            indices.append(cell.index)        
+    
+    return cells, indices
+ 

anisotropy/newgui/geometry.py

@@ -0,0 +1,137 @@
+import dearpygui.dearpygui as dpg
+
+def create_geometry(parent):
+    with dpg.child_window(
+            tag = "geometry_container", 
+            parent = parent
+        ) as container:
+            dpg.add_button(label = "Add case", callback = Case.create(container))
+            with dpg.group(horizontal = True):
+                dpg.add_text("Cases")
+                dpg.add_separator()
+        
+    return container
+
+class Case:
+    case_list = []
+
+    def __init__(self, parent):
+        self.parent = parent
+        self.uuid = dpg.generate_uuid()
+        self.values = {}
+        Case.case_list.append(self)
+        
+
+    def __str__(self):
+        return f"<Case: { self.uuid }, type: geometry>"
+
+    def __repr__(self):
+        return self.__str__()
+
+    @staticmethod
+    def create(parent):
+        def create_callback():
+            case = Case(parent)
+
+            with dpg.collapsing_header(label = f"g-case-{ case.uuid }", parent = case.parent) as case._case:
+                with dpg.child_window(height = 300) as case.child_window:
+                    with dpg.group(horizontal = True):
+                        case._source = dpg.add_combo(["", "from file", "periodic"], label = "Source")
+                        
+                        dpg.add_button(label = "Remove", callback = case.remove_case)
+                        dpg.add_button(label = "Edit", callback = case.edit_case)
+
+                    case.create_stats()
+
+            case.create_params_file()
+            case.create_params_periodic()
+        
+        return create_callback
+    
+    def remove_case(self):
+        dpg.delete_item(self._case)
+        Case.case_list.remove(self)
+
+    def edit_case(self):
+        source_val = dpg.get_value(self._source)
+
+        if source_val == "from file":
+            dpg.show_item(self._file_params)
+        
+        elif source_val == "periodic":
+            dpg.show_item(self._periodic_params)
+    
+    def create_stats(self):
+        with dpg.table(header_row = True, parent = self.child_window) as self._case_stats:
+            dpg.add_table_column(label = "Parameters")
+            dpg.add_table_column(label = "")
+
+            for k, v in self.values.items():
+                with dpg.table_row():
+                    dpg.add_text(k)
+                    dpg.add_text(v)
+
+    def update_stats(self):
+        dpg.delete_item(self._case_stats)
+        self.create_stats()
+
+    def create_params_file(self):
+        with dpg.window(show = False, modal = True, height = 600, width = 400) as self._file_params:
+            with dpg.group(horizontal = True):
+                self._file_input = dpg.add_input_text(label = "File")
+                dpg.add_button(label = "..", callback = lambda: dpg.show_item(self._file_dialog))
+
+                with dpg.file_dialog(
+                    directory_selector = False, 
+                    show = False, 
+                    modal = True, 
+                    callback = lambda s, d: dpg.set_value(self._file_input, d['file_path_name']), 
+                    height = 400, 
+                    width = 600
+                ) as self._file_dialog:
+                    dpg.add_file_extension(".geo")
+
+            dpg.add_button(label = "Save", width = -1)
+
+    def create_params_periodic(self):
+        def alpha_type_cb(s, d):
+            type_val = dpg.get_value(self._alpha_type)
+
+            if type_val == "float":
+                dpg.show_item(self._alpha_float)
+                dpg.hide_item(self._alpha_range)
+
+            elif type_val == "range":
+                dpg.hide_item(self._alpha_float)
+                dpg.show_item(self._alpha_range)
+
+        with dpg.window(show = False, modal = True, height = 600, width = 400) as self._periodic_params:
+            self._label_str = dpg.add_input_text(label = "label")
+
+            with dpg.group(horizontal = True):
+                self._alpha_type = dpg.add_combo(["float", "range"], default_value = "float", width = 100, callback = alpha_type_cb)
+                self._alpha_float = dpg.add_input_float(label = "alpha")
+                self._alpha_range = dpg.add_input_floatx(label = "alpha", size = 3, show = False)
+
+            self._r0_float = dpg.add_input_float(label = "r_0")
+
+            dpg.add_separator()
+            dpg.add_button(label = "Save", width = -1, callback = self.save_params)
+    
+    def save_params(self):
+        source_val = dpg.get_value(self._source)
+
+        if source_val == "from file":
+            self.values.update(
+                filepath = dpg.get_value(self._file_input)
+            )
+
+        elif source_val == "periodic":
+            self.values.update(
+                label = dpg.get_value(self._label_str),
+                alpha = dpg.get_value(self._alpha_range) if dpg.get_value(self._alpha_type) == "range" else dpg.get_value(self._alpha_float),
+                r0 = dpg.get_value(self._r0_float),
+            )
+        
+        self.update_stats()
+        dpg.hide_item(self._periodic_params)

anisotropy/newgui/newgui.py

@@ -0,0 +1,88 @@
+import dearpygui.dearpygui as dpg
+import pathlib
+
+import geometry
+
+
+gui_path = pathlib.Path(__file__).resolve().parent
+dpg.create_context()
+
+
+with dpg.font_registry():
+    print(gui_path)
+    default_font = dpg.add_font(gui_path / "fonts/NotoSansMono-Regular-Nerd-Font-Complete.ttf", 20)
+
+
+
+with dpg.window(tag = "Primary") as primary:
+    dpg.bind_font(default_font)
+
+    with dpg.menu_bar(tag = "m1"):
+        with dpg.menu(label = "File"):
+            dpg.add_menu_item(label = "Preferences", callback = lambda: dpg.configure_item("preferences", show = True))
+            dpg.add_menu_item(label = "Exit", callback = lambda: dpg.destroy_context())
+
+        with dpg.menu(label = "Tools"):
+            dpg.add_menu_item(label = "Geometry", callback = lambda: dpg.show_item("geometry"))
+            dpg.add_menu_item(label = "Mesh", callback = lambda: dpg.show_item("mesh"))
+            dpg.add_menu_item(label = "Solver", callback = lambda: dpg.show_item("solver"))
+            dpg.add_menu_item(label = "Runner", callback = lambda: dpg.show_item("runner"))
+            dpg.add_separator()
+            dpg.add_menu_item(label = "Database", callback = lambda: dpg.show_item("database"))
+            dpg.add_menu_item(label = "Post-processing", callback = lambda: dpg.show_item("post-processing"))
+
+    with dpg.child_window(tag = "Test22", border = False, height = -40):
+        
+        with dpg.child_window(tag = "Test", border = False):
+            with dpg.tab_bar(label = "tabbar"):
+                with dpg.tab(label = "Geometry", tag = "geometry", closable = True, show = False):
+                    geometry.create_geometry("geometry")
+
+                with dpg.item_handler_registry(tag="widget handler"):
+                    dpg.add_item_edited_handler(callback = lambda: dpg.delete_item("mesh") if not dpg.is_item_shown("mesh") else None)
+
+                with dpg.tab(label = "Mesh", tag = "mesh", closable = True, show = False):
+                    with dpg.child_window(tag = "mesh_container", border = True):
+                        dpg.add_text("")
+                
+                # bind item handler registry to item
+                dpg.bind_item_handler_registry("mesh", "widget handler")
+
+                with dpg.tab(label = "Solver", tag = "solver", closable = True, show = False):
+                    with dpg.child_window(tag = "solver_container", border = True):
+                        dpg.add_text("")
+                
+                with dpg.tab(label = "Runner", tag = "runner", closable = True, show = False):
+                    with dpg.child_window(tag = "runner_container", border = True):
+                        dpg.add_text("")
+                
+                with dpg.tab(label = "Database", tag = "database", closable = True, show = False):
+                    with dpg.child_window(tag = "database_container", border = True):
+                        dpg.add_text("")
+
+                with dpg.tab(label = "Post-processing", tag = "post-processing", closable = True, show = False):
+                    with dpg.child_window(tag = "post-processing_container", border = True):
+                        dpg.add_text("")
+    
+    dpg.add_separator()
+    with dpg.table(tag = "statusbar", header_row = False):
+        dpg.add_table_column(label = "")
+        dpg.add_table_column(label = "")
+
+        with dpg.table_row():
+            dpg.add_button(label = "Debug", callback = lambda: print(dpg.get_value("mesh")))
+            dpg.add_text("status")
+
+with dpg.window(label = "Preferences", tag = "preferences", modal = True, show = False, width = 400, height = 600):
+    with dpg.collapsing_header(label = "General"):
+        with dpg.group(horizontal = True):
+            dpg.add_text("Font")
+            dpg.add_text(dpg.get_item_font("Primary"))
+
+dpg.create_viewport(title = "New GUI", width = 1000, height = 800)
+dpg.setup_dearpygui()
+dpg.show_viewport()
+dpg.set_primary_window("Primary", True)
+dpg.start_dearpygui()
+
+dpg.destroy_context()

anisotropy/openfoam/__init__.py

@@ -1,37 +1,22 @@
 # -*- coding: utf-8 -*-
-# This file is part of anisotropy.
-# License: GNU GPL version 3, see the file "LICENSE" for details.
 
+from . import utils
+from . import conversion
+
+from .file import FoamFile
+from .runner import FoamRunner
+from .case import FoamCase
+
+from . import presets
+from . import commands
 
-from .meshConversion import ideasUnvToFoam
-from .meshManipulation import createPatch, transformPoints, checkMesh, renumberMesh
-from .miscellaneous import foamDictionary
-from .parallelProcessing import decomposePar
-from .solvers import potentialFoam, simpleFoam
-from .utils import version, foamClean, uniform
 
 __all__ = [
-    # meshConversion
-    "ideasUnvToFoam",
-
-    # meshManipulation
-    "createPatch",
-    "transformPoints",
-    "checkMesh",
-    "renumberMesh",
-
-    # miscellaneous
-    "foamDictionary",
-
-    # parallelProcessing
-    "decomposePar",
-
-    # solvers
-    "potentialFoam",
-    "simpleFoam",
-
-    # utils
-    "version",
-    "foamClean",
-    "uniform"
+    "utils",
+    "conversion",
+    "FoamFile",
+    "FoamRunner",
+    "FoamCase",
+    "presets",
+    "commands"
 ]

anisotropy/openfoam/application.py

@@ -1,51 +0,0 @@
-# -*- coding: utf-8 -*-
-# This file is part of anisotropy.
-# License: GNU GPL version 3, see the file "LICENSE" for details.
-
-import os, sys
-import subprocess
-
-import logging
-logger = logging.getLogger()
-
-def application(name: str, *args: str, case: str = None, stderr: bool = True, useMPI: bool = False) -> int:
-    
-    cmd = []
-
-    if useMPI:
-        nprocs = os.cpu_count()
-        cmd.extend(["mpirun", "-np", str(nprocs), "--oversubscribe"])
-    
-    cmd.append(name)
-
-    if case:
-        cmd.extend(["-case", case])
-
-    if args:
-        cmd.extend([*args])
-        
-    logger.info("{}: {}".format(name, [*args]))
-    logpath = os.path.join(case if case else "", "{}.log".format(name))
-   
-    with subprocess.Popen(cmd, 
-        stdout = subprocess.PIPE, 
-        stderr = subprocess.PIPE) as p, \
-        open(logpath, "wb") as logfile:
-        
-        for line in p.stdout:
-            #sys.stdout.buffer.write(line) 
-            logfile.write(line)
-
-        #for line in p.stderr:
-        #    logfile.write(line)
-
-        out, err = p.communicate()
-        logfile.write(err)
-
-        #if err and stderr:
-        #    logger.error("""{}:
-        #    {}""".format(name, str(err, "utf-8")))
-
-    return out, err, p.returncode
-
-

anisotropy/openfoam/case.py

@@ -0,0 +1,174 @@
+# -*- coding: utf-8 -*-
+
+from __future__ import annotations
+
+import os
+import shutil
+import re
+import pathlib
+import io
+from lz.reversal import reverse as lz_reverse
+
+from . import FoamFile
+
+
+class FoamCase(object):
+    def __init__(self, files: FoamFile | list[FoamFile] = None, path: str = None):
+        
+        self.path = path 
+        self._backpath = None
+        self._files = []
+        
+        if files is not None:
+            self.add(files)
+    
+    def __repr__(self) -> str:
+        content = [ file.object for file in self._files ]
+
+        return "<FoamCase: {}>".format(", ".join(content) or None)
+
+    def add(self, files: FoamFile | list[FoamFile]):
+        if type(files) is not list:
+            assert type(files) is FoamFile, "passed object is not a FoamFile"
+
+            files = [ files ]
+
+        for file in files:
+            assert type(file) is FoamFile, "passed object is not a FoamFile"
+            assert file.object is not None, "FoamFile object attribute is None"
+
+            idn = self.contains(file.object)
+
+            if idn is not None:
+                self._files.pop(idn)
+                self._files.append(file)
+                
+                return self
+            
+            self._files.append(file)
+        
+        return self
+            
+    def __add__(self, files: FoamFile | list[FoamFile]):
+        return self.add(files)
+
+    def contains(self, name: str) -> int | None:
+        for n, file in enumerate(self._files):
+            if file.object == name:
+                return n
+
+        return None
+
+    def write(self, path: str = None):
+        path = pathlib.Path(path or self.path or "")
+
+        for file in self._files:
+            path_ = path / (
+                file.location + "/" + file.object 
+                if file.location else file.object
+            )
+
+            file.write(path_.resolve())
+    
+    def read(self, path: str = None):
+        path = pathlib.Path(path or self.path or "")
+
+        for file in self._files:
+            path_ = path / (
+                file.location + "/" + file.object 
+                if file.location else file.object
+            )
+
+            file.read(path_.resolve())
+
+    def remove(self, path: str = None):
+        path = pathlib.Path(path or self.path or "")
+
+        for file in self._files:
+            path_ = path / (
+                file.location + "/" + file.object 
+                if file.location else file.object
+            )
+
+            file.remove(path_.resolve())
+
+    def clean(self, included: list = ["0", "constant", "system"]):
+        regxs = [
+            r"^\d+.\d+$",
+            r"^\d+$",
+            r"^processor\d+$",
+            r"^log..+$",
+            r"^.+.log$",
+            r"^logs$",
+            r"^postProcessing$",
+            r"^polyMesh$"
+        ]
+        excluded = []
+
+        for root, dirs, files in os.walk(os.path.abspath("")):
+            for _dir in dirs:
+                excluded += [ 
+                    os.path.join(root, _dir) 
+                    for regx in regxs if re.match(regx, _dir) 
+                ]
+
+            for file in files:
+                excluded += [ 
+                    os.path.join(root, file) 
+                    for regx in regxs if re.match(regx, file) 
+                ]
+
+        for file in excluded:
+            if os.path.split(file)[1] not in included and os.path.exists(file):
+                if os.path.isdir(file):
+                    shutil.rmtree(file)
+
+                if os.path.isfile(file):
+                    os.remove(file)
+
+    def chdir(self, path: str = None):
+        path = pathlib.Path(path or self.path or "").resolve()
+        self._backpath = os.getcwd()
+        
+        os.chdir(path)
+    
+    def chback(self):
+        path = pathlib.Path(self._backpath or "").resolve()
+
+        os.chdir(path)
+
+    def is_converged(self, path: str = None) -> None | bool:
+        path = pathlib.Path(path or self.path or "").resolve()
+        controlDict = FoamFile()
+
+        if controlDict.exists(path / "system" / "controlDict"):
+            controlDict.read(path / "system" / "controlDict")
+        
+        else:
+            return None
+        
+        application = controlDict.get("application")
+
+        if application is None:
+            return None
+        
+        logfile = (
+            path / f"{ application }.log" 
+            if (path / f"{ application }.log").exists() else (path / f"log.{ application }")
+        )
+        status = False
+        
+        if logfile.exists():
+            with open(logfile, "r") as infile:
+                limit = 30
+
+                for line in lz_reverse(infile, batch_size = io.DEFAULT_BUFFER_SIZE):
+                    if not line.find("End") < 0:
+                        status = True
+                    
+                    if limit <= 0:
+                        status = False
+                    
+                    limit -= 1
+
+        return status

anisotropy/openfoam/commands.py

@@ -0,0 +1,211 @@
+# -*- coding: utf-8 -*-
+
+from . import FoamRunner
+
+
+###
+#   meshConversion
+##
+
+def netgenNeutralToFoam(meshfile: str, run: bool = True, **kwargs) -> FoamRunner:
+    command = "netgenNeutralToFoam"
+    kwargs.update(logpath = kwargs.get("logpath", f"{ command }.log"))
+    kwargs.update(exit = True)
+    args = [ meshfile ]
+
+    runner = FoamRunner(command, args = args, **kwargs)
+
+    if run:
+        runner.run()
+
+    return runner
+
+
+def ideasUnvToFoam(meshfile: str, run: bool = True, **kwargs) -> FoamRunner:
+    command = "ideasUnvToFoam"
+    kwargs.update(logpath = kwargs.get("logpath", f"{ command }.log"))
+    kwargs.update(exit = True)
+    args = [ meshfile ]
+
+    runner = FoamRunner(command, args = args, **kwargs)
+
+    if run:
+        runner.run()
+
+    return runner
+
+
+###
+#   meshManipulation
+##
+
+def createPatch(dictfile: str = None, overwrite: bool = True, run: bool = True, **kwargs) -> FoamRunner:
+    command = "createPatch"
+    kwargs.update(logpath = kwargs.get("logpath", f"{ command }.log"))
+    kwargs.update(exit = True)
+    args = []
+
+    if dictfile:
+        args.extend(["-dict", dictfile])
+
+    if overwrite:
+        args.append("-overwrite")
+
+    runner = FoamRunner(command, args = args, **kwargs)
+
+    if run:
+        runner.run()
+
+    return runner
+
+
+def transformPoints(transformations: dict, run: bool = True, **kwargs) -> FoamRunner:
+    command = "transformPoints"
+    kwargs.update(logpath = kwargs.get("logpath", f"{ command }.log"))
+    kwargs.update(exit = True)
+    args = []
+    arg = []
+
+    for k, v in transformations.items():
+        if type(v) == int or type(v) == float:
+            value = str(v)
+
+        elif type(v) == tuple or type(v) == list:
+            value = "({} {} {})".format(*v)
+
+        arg.append("{}={}".format(k, value))
+
+    args.append(", ".join(arg))
+
+    runner = FoamRunner(command, args = args, **kwargs)
+
+    if run:
+        runner.run()
+
+    return runner
+
+
+def checkMesh(allGeometry: bool = True, allTopology: bool = True, run: bool = True, **kwargs) -> FoamRunner:
+    command = "checkMesh"
+    kwargs.update(logpath = kwargs.get("logpath", f"{ command }.log"))
+    kwargs.update(exit = True)
+    args = []
+
+    if allGeometry:
+        args.append("-allGeometry")
+
+    if allTopology:
+        args.append("-allTopology")
+
+    runner = FoamRunner(command, args = args, **kwargs)
+
+    if run:
+        runner.run()
+
+    return runner
+
+
+def renumberMesh(overwrite: bool = True, run: bool = True, **kwargs) -> FoamRunner:
+    command = "renumberMesh"
+    kwargs.update(logpath = kwargs.get("logpath", f"{ command }.log"))
+    kwargs.update(exit = True)
+    args = []
+
+    if overwrite:
+        args.append("-overwrite")
+
+    runner = FoamRunner(command, args = args, **kwargs)
+
+    if run:
+        runner.run()
+
+    return runner
+
+
+###
+#   miscellaneous
+##
+
+# def foamDictionary()
+
+
+###
+#   parallelProcessing
+##
+
+def decomposePar(run: bool = True, **kwargs) -> FoamRunner:
+    command = "decomposePar"
+    kwargs.update(logpath = kwargs.get("logpath", f"{command}.log"))
+    kwargs.update(exit = True)
+    args = []
+
+    runner = FoamRunner(command, args = args, **kwargs)
+
+    if run:
+        runner.run()
+
+    return runner
+
+
+###
+#   solvers
+##
+
+def potentialFoam(parallel: bool = False, run: bool = True, **kwargs) -> FoamRunner:
+    command = "potentialFoam"
+    kwargs.update(logpath = kwargs.get("logpath", f"{command}.log"))
+    kwargs.update(exit = True)
+    args = []
+
+    if parallel:
+        args.append("-parallel")
+        kwargs.update(mpi = True)
+
+    runner = FoamRunner(command, args = args, **kwargs)
+
+    if run:
+        runner.run()
+
+    return runner
+
+
+def simpleFoam(parallel: bool = False, run: bool = True, **kwargs) -> FoamRunner:
+    command = "simpleFoam"
+    kwargs.update(logpath = kwargs.get("logpath", f"{command}.log"))
+    kwargs.update(exit = True)
+    args = []
+
+    if parallel:
+        args.append("-parallel")
+        kwargs.update(mpi = True)
+
+    runner = FoamRunner(command, args = args, **kwargs)
+
+    if run:
+        runner.run()
+
+    return runner
+
+
+###
+#   postProcessing
+##
+
+def postProcess(func: str = None, latestTime: bool = False, run: bool = True, **kwargs) -> FoamRunner:
+    command = "postProcess"
+    kwargs.update(logpath=kwargs.get("logpath", f"{command}.log"))
+    kwargs.update(exit = True)
+    args = []
+
+    if func:
+        args.extend(["-func", func])
+
+    if latestTime:
+        args.append("-latestTime")
+
+    runner = FoamRunner(command, args = args, **kwargs)
+
+    if run:
+        runner.run()
+
+    return runner

anisotropy/openfoam/conversion.py

@@ -0,0 +1,120 @@
+# -*- coding: utf-8 -*-
+
+import pathlib
+from PyFoam.RunDictionary.ParsedParameterFile import ParsedParameterFile
+from PyFoam.Basics.FoamFileGenerator import FoamFileGenerator
+import numpy as np
+
+from . import utils
+
+
+def read_foamfile(filename: str) -> tuple[dict, dict]:
+    """Read a FoamFile.
+
+    :param filename:
+        Path to the file.
+    :return:
+        Two dictionaries that contains header and content information
+        of the FoamFile.
+    """
+    path = pathlib.Path(filename).resolve()
+    ppf = ParsedParameterFile(path)
+    header = ppf.header or {}
+    content = ppf.content or {}
+
+    if type(content) == dict:
+        if content.get("internalField"):
+            content["internalField"] = np.asarray(content["internalField"])
+
+    return header, content
+
+
+def write_foamfile(header: dict, content: dict, filename: str):
+    """Write a FoamFile to the file.
+
+    :param header:
+        Header block with the FoamFile metadata.
+    :param content:
+        Content block of the FoamFile.
+    :param filename:
+        Path to the file.
+    """
+    path = pathlib.Path(filename).resolve()
+
+    #   preformat
+    header = (
+        FoamFileGenerator({}, header = header)
+        .makeString()[ :-2]
+        .replace("\n ", "\n" + 4 * " ")
+    )
+    content = (
+        FoamFileGenerator(content)
+        .makeString()[ :-1]
+        .replace("\n  ", "\n" + 4 * " ")
+        .replace(" \t// " + 73 * "*" + " //", "")
+        .replace(" /* empty */ ", "")
+    )
+
+    with open(path, "w") as outfile:
+        outfile.write(utils.template(header, content) + "\n")
+
+
+def read_dat(filename: str):
+    """Read dat file.
+
+    :param filename:
+        Path to the file.
+    :return:
+        Dictionary with arrays. Keys are created according file header
+        block or numerated with string numbers if header is not found.
+    """
+    path = pathlib.Path(filename).resolve()
+    header = []
+    content = []
+
+    with open(path, "r") as infile:
+        for line in infile.readlines():
+            if line.startswith("#"):
+                header.append(line)
+
+            else:
+                content.append(line)
+
+    columns = []
+
+    if header[-1].find(":") < 0:
+        for column in header[-1].replace("#", "").split("\t"):
+            columns.append(column.strip())
+
+        header.pop(-1)
+
+    else:
+        for column in range(len(content[0].split("\t"))):
+            columns.append(str(column))
+
+    output = {}
+
+    for row in header:
+        key, value = row.replace("#", "").split(":")
+
+        try:
+            value = float(value.strip())
+
+        except Exception:
+            value = value.strip()
+
+        output[key.strip()] = value
+
+    for column in columns:
+        output[column] = []
+
+    for row in content:
+        values = row.split("\t")
+
+        for column, value in zip(columns, values):
+            output[column].append(float(value))
+
+    for key in output.keys():
+        output[key] = np.asarray(output[key])
+
+    return output

anisotropy/openfoam/file.py

@@ -0,0 +1,171 @@
+# -*- coding: utf-8 -*-
+
+import pathlib
+
+from . import conversion
+
+
+class FoamFile(object):
+    def __init__(
+        self, 
+        filename: str = None,
+        _version: float = 2.0,
+        _format: str = "ascii",
+        _class: str = "dictionary",
+        _object: str = None,
+        _location: str = None
+    ):
+        """A FoamFile object.
+
+        :param filename:
+            Can be used as shortcut to set _location and _object,
+            _location and _object parameters will be ignored.
+        :param _version:
+            Version of the file format, current is 2.0.
+        :param _format:
+            ASCII or binary representation, currently ascii only
+            supported.
+        :param _class:
+            Class of the file.
+        :param _object:
+            Usually contains name of the file.
+        :param _location:
+            Path to the parent directory of the file according 
+            to the case root.
+        """
+
+        if filename:
+            splitted = filename.split("/")
+            _object = splitted[-1]
+            _location = "/".join(splitted[ :-1])
+
+        self.header = { 
+            "version": _version,
+            "format": _format,
+            "class": _class,
+            "object": _object
+        }
+        self.content = {}
+
+        if _location:
+            self.header["location"] = f'"{ _location }"'
+
+    @property
+    def version(self) -> str:
+        return self.header.get("version")
+
+    @property
+    def format(self) -> str:
+        return self.header.get("format")
+
+    @property
+    def class_(self) -> str:
+        return self.header.get("class")
+
+    @property
+    def object(self) -> str:
+        return self.header.get("object")
+
+    @property
+    def location(self) -> str:
+        return (
+            self.header.get("location").replace('"', "") 
+            if self.header.get("location") else None
+        )
+
+    def __getitem__(self, key):
+        return self.content[key]
+
+    def get(self, key, default = None):
+        return self.content.get(key, default)
+
+    def __setitem__(self, key, value):
+        self.content[key] = value
+
+    def __delitem__(self, key):
+        del self.content[key]
+
+    def update(self, **kwargs):
+        self.content.update(**kwargs)
+
+    def __len__(self):
+        return len(self.content)
+
+    def __iter__(self):
+        for key in self.content:
+            yield key
+
+    def __repr__(self) -> str:
+        return "<FoamFile: {}>".format(self.header["object"] or None)
+
+    def __add__(self, file):
+        from . import FoamCase
+
+        assert type(file) is FoamFile
+
+        return FoamCase([ self, file ])
+
+    def exists(self, filename: str = None) -> bool:
+        filename = filename or (
+            self.location + "/" + self.object 
+            if self.location else self.object
+        )
+        path = pathlib.Path(filename).resolve()
+
+        return path.exists() and path.is_file()
+
+    def read(self, filename: str = None):
+        """Read a FoamFile.
+
+        :param filename:
+            Path to the file. If None, use location and object from header with
+            the current working directory.
+        :return:
+            Self.
+        """
+        filename = filename or (
+            self.location + "/" + self.object 
+            if self.location else self.object
+        )
+        path = pathlib.Path(filename).resolve()
+        header, content = conversion.read_foamfile(path)
+
+        self.header = header
+        
+        if not header.get("object"):
+            self.header["object"] = path.parts[-1]
+
+        self.content = content
+
+        return self
+
+    def write(self, filename: str = None):
+        """Write a FoamFile to the file.
+
+        :param filename:
+            Path to the file. If None, use location and object from header with
+            the current working directory.
+        """  
+        filename = filename or (
+            self.location + "/" + self.object 
+            if self.location else self.object
+        )
+        path = pathlib.Path(filename).resolve()
+        path.parent.mkdir(parents = True, exist_ok = True)
+        conversion.write_foamfile(self.header, self.content, path)
+
+    def remove(self, filename: str = None):
+        """Remove a FoamFile.
+
+        :param filename:
+            Path to the file. If None, use location and object from header with
+            the current working directory.
+        """  
+        filename = filename or (
+            self.location + "/" + self.object 
+            if self.location else self.object
+        )
+        path = pathlib.Path(filename).resolve()
+
+        if path.exists():
+            pathlib.os.remove(filename)

anisotropy/openfoam/meshConversion.py

@@ -1,9 +0,0 @@
-# -*- coding: utf-8 -*-
-# This file is part of anisotropy.
-# License: GNU GPL version 3, see the file "LICENSE" for details.
-
-from .application import application
-
-def ideasUnvToFoam(mesh: str, case: str = None) -> (str, int):
-    return application("ideasUnvToFoam", mesh, case = case, stderr = True)
-

anisotropy/openfoam/meshManipulation.py

@@ -1,42 +0,0 @@
-# -*- coding: utf-8 -*-
-# This file is part of anisotropy.
-# License: GNU GPL version 3, see the file "LICENSE" for details.
-
-from .application import application
-
-import re
-
-def createPatch(dictfile: str = None, case: str = None):
-    args = ["-overwrite"]
-
-    if dictfile:
-        args.extend(["-dict", dictfile])
-
-    application("createPatch", *args, case = case, stderr = True)
-
-
-def transformPoints(scale, case: str = None):
-    _scale = f"({ scale[0] } { scale[1] } { scale[2] })"
-
-    application("transformPoints", "-scale", _scale, case = case, stderr = True)
-
-
-def checkMesh(case: str = None) -> str:
-    _, err, returncode = application("checkMesh", "-allGeometry", "-allTopology", case = case, stderr = True)
-    out = ""
-
-    with open("checkMesh.log", "r") as io:
-        warnings = []
-        for line in io:
-            if re.search("\*\*\*", line):
-                warnings.append(line.replace("***", "").strip())
-
-        if warnings:
-            out = "checkMesh:\n\t{}".format("\n\t".join(warnings))
-
-    return out, err, returncode
-
-
-def renumberMesh(case: str = None):
-    application("renumberMesh", "-overwrite", useMPI = False, case = case, stderr = True)
-

anisotropy/openfoam/miscellaneous.py

@@ -1,14 +0,0 @@
-# -*- coding: utf-8 -*-
-# This file is part of anisotropy.
-# License: GNU GPL version 3, see the file "LICENSE" for details.
-
-from .application import application
-
-def foamDictionary(filepath: str, entry: str, value: str = None, case: str = None):
-    args = [filepath, "-entry", entry]
-
-    if value:
-        args.extend(["-set", value])
-
-    application("foamDictionary", *args, case = case, stderr = False)
-

anisotropy/openfoam/parallelProcessing.py

@@ -1,9 +0,0 @@
-# -*- coding: utf-8 -*-
-# This file is part of anisotropy.
-# License: GNU GPL version 3, see the file "LICENSE" for details.
-
-from .application import application
-
-def decomposePar(case: str = None):
-    application("decomposePar", case = case, stderr = True)
-

anisotropy/openfoam/presets.py

@@ -0,0 +1,223 @@
+# -*- coding: utf-8 -*-
+
+from . import FoamFile
+
+
+def controlDict() -> FoamFile:
+    ff = FoamFile(filename = "system/controlDict")
+
+    ff.content = {
+        "application": "simpleFoam",
+        "startFrom": "startTime",
+        "startTime": 0,
+        "stopAt": "endTime",
+        "endTime": 2000,
+        "deltaT": 1,
+        "writeControl": "timeStep",
+        "writeInterval": 100,
+        "purgeWrite": 0,
+        "writeFormat": "ascii",
+        "writePrecision": 6,
+        "writeCompression": "off",
+        "timeFormat": "general",
+        "timePrecision": 6,
+        "runTimeModifiable": "true"
+    }
+
+    return ff
+
+
+def fvSolution() -> FoamFile:
+    ff = FoamFile(filename = "system/fvSolution")
+
+    ff.content = {
+        "solvers": {
+            "p": {
+                "solver": "GAMG",
+                "tolerance": 1e-06,
+                "relTol": 0.1,
+                "smoother": "GaussSeidel"
+            },
+            "U": {
+                "solver": "smoothSolver",
+                "smoother": "symGaussSeidel",
+                "tolerance": 1e-05,
+                "relTol": 0.1
+            }
+        },
+        "SIMPLE": {
+            "nNonOrthogonalCorrectors": 0,
+            "consistent": "yes",
+            "residualControl": {
+                "p": 1e-02,
+                "U": 1e-03
+            }
+        },
+        "relaxationFactors": {
+            "fields": {
+                "p": 0.3
+            },
+            "equations": {
+                "U": 0.7
+            }
+        }
+    }
+
+    return ff
+
+
+def fvSchemes() -> FoamFile:
+    ff = FoamFile(filename = "system/fvSchemes")
+
+    ff.content = {
+        "ddtSchemes": {
+            "default": "steadyState"
+        }, 
+        "gradSchemes": {
+            "default": ("Gauss", "linear")
+        }, 
+        "divSchemes": {
+            "default": "none", 
+            "div(phi,U)": ("bounded", "Gauss", "linearUpwind", "grad(U)"), 
+            "div((nuEff*dev2(T(grad(U)))))": ("Gauss", "linear"), 
+            "div(nonlinearStress)": ("Gauss", "linear")
+        }, 
+        "laplacianSchemes": {
+            "default": ("Gauss", "linear", "corrected")
+        }, 
+        "interpolationSchemes": {
+            "default": "linear"
+        }, 
+        "snGradSchemes": {
+            "default": "corrected"
+        } 
+    }
+
+    return ff
+
+
+def transportProperties() -> FoamFile:
+    ff = FoamFile(filename = "constant/transportProperties")
+
+    ff.content = {
+        "transportModel": "Newtonian",
+        "nu": 1e-05
+    }
+
+    return ff
+
+
+def turbulenceProperties() -> FoamFile:
+    ff = FoamFile(filename = "constant/turbulenceProperties")
+
+    ff.content = {
+        "simulationType": "RAS", 
+        "RAS": {
+            "RASModel": "kEpsilon", 
+            "turbulence": "on", 
+            "printCoeffs": "on"
+        }
+    }
+
+    return ff
+
+
+def p() -> FoamFile:
+    ff = FoamFile("0/p", _class = "volScalarField")
+
+    ff.content = {
+        "dimensions": "[0 2 -2 0 0 0 0]",
+        "internalField": "uniform 0",
+        "boundaryField": {
+            "inlet": {
+                "type": "fixedValue",
+                "value": "uniform 0.001"
+            },
+            "outlet": {
+                "type": "fixedValue",
+                "value": "uniform 0"
+            },
+            "wall": {
+                "type": "zeroGradient"
+            }
+        }
+    }
+
+    return ff
+
+
+def U() -> FoamFile:
+    ff = FoamFile("0/U", _class = "volVectorField")
+
+    ff.content = {
+        "dimensions": "[0 1 -1 0 0 0 0]",
+        "internalField": "uniform (0 0 0)",
+        "boundaryField": {
+            "inlet": {
+                "type": "fixedValue",
+                "value": "uniform (0 0 -6e-5)"
+            },
+            "outlet": {
+                "type": "zeroGradient",
+            },
+            "wall": {
+                "type": "fixedValue",
+                "value": "uniform (0 0 0)"
+            }
+        }
+    }
+
+    return ff
+
+
+def createPatchDict() -> FoamFile:
+    ff = FoamFile("system/createPatchDict")
+
+    ff.content = {
+        "pointSync": False,
+        "patches": [
+            {
+                "name": "inlet",
+                "patchInfo": {
+                    "type": "patch",
+                    "inGroups": ["inlet"]
+                },
+                "constructFrom": "patches",
+                "patches": ["some_inlet"]
+            },
+            {
+                "name": "output",
+                "patchInfo": {
+                    "type": "patch",
+                    "inGroups": ["outlet"]
+                },
+                "constructFrom": "patches",
+                "patches": ["some_outlet"]
+            },
+            {
+                "name": "wall",
+                "patchInfo": {
+                    "type": "wall",
+                    "inGroups": ["wall"]
+                },
+                "constructFrom": "patches",
+                "patches": ["some_wall"]
+            }
+        ]
+    }
+
+    return ff
+
+
+def decomposeParDict() -> FoamFile:
+    ff = FoamFile("system/decomposeParDict")
+
+    ff.content = {
+        "numberOfSubdomains": 4,
+        "method": "simple",
+        "coeffs": {
+            "n": [2, 2, 2]
+        }
+    }
+
+    return ff

anisotropy/openfoam/runner.py

@@ -0,0 +1,80 @@
+# -*- coding: utf-8 -*-
+
+import os
+import subprocess
+import logging
+
+logger = logging.getLogger(__name__)
+
+
+class FoamRunner(object):
+    def __init__(self, command: str, args: list[str] = None, mpi: bool = False, cwd: str = None, logpath: str = None, exit: bool = False):
+        self.command = command
+        self.args = args
+        self.mpi = mpi
+        self.cwd = cwd or os.getcwd()
+        self.logpath = logpath
+        self.exit = exit
+        self.output = ""
+        self.error = ""
+        self.returncode = 0
+
+    def fullcommand(self) -> list[str]:
+        command = []
+
+        if self.mpi:
+            nprocs = os.cpu_count()
+            command.extend(["mpirun", "-np", str(nprocs), "--oversubscribe"])
+
+        command.append(self.command)
+
+        if self.args:
+            command.extend([ str(arg) for arg in self.args ])
+
+        return command
+
+    def run(self) -> tuple[str, str, int]:
+        try:
+            proc = subprocess.Popen(
+                self.fullcommand(),
+                stdout = subprocess.PIPE,
+                stderr = subprocess.PIPE,
+                encoding = "utf-8",
+                cwd = self.cwd
+            )
+
+            logger.debug(f"Starting subprocess: { proc.args }")
+
+            if self.logpath:
+                with proc, open(self.logpath, "w") as io:
+                    while True:
+                        output = proc.stdout.read(1)
+
+                        if output == "" and proc.poll() is not None:
+                            break
+
+                        if not output == "":
+                            io.write(output)
+
+                    error = proc.stderr.read()
+
+                    if not error == "":
+                        self.error = error
+                        io.write(error)
+
+            self.returncode = proc.returncode
+
+            if self.logpath and self.error:
+                with open(self.logpath, "a") as io:
+                    io.write(self.error)
+
+        except FileNotFoundError as err:
+            self.error = err.args[1]
+            self.returncode = 2
+
+            logger.error(self.error, exc_info = True)
+
+        if not self.returncode == 0 and self.exit:
+            raise Exception(f"Subprocess failed: { self.error }")
+
+        return self.output, self.error, self.returncode

anisotropy/openfoam/solvers.py

@@ -1,34 +0,0 @@
-# -*- coding: utf-8 -*-
-# This file is part of anisotropy.
-# License: GNU GPL version 3, see the file "LICENSE" for details.
-
-from .application import application
-
-import re 
-
-def potentialFoam(case: str = None, useMPI: bool = False):
-    if useMPI:
-        out, err, returncode = application("potentialFoam", "-parallel", useMPI = True, case = case, stderr = True)
-
-    else:
-        out, err, returncode = application("potentialFoam", case = case, stderr = True)
-
-    return out, err, returncode
-
-
-def simpleFoam(case: str = None, useMPI: bool = False):
-    if useMPI:
-        out, err, returncode = application("simpleFoam", "-parallel", useMPI = True, case = case, stderr = True)
-
-    else:
-        out, err, returncode = application("simpleFoam", case = case, stderr = True)
-
-    out = ""
-
-    with open("simpleFoam.log", "r") as io:
-        for line in io:
-            if re.search("solution converged", line):
-                out = "simpleFoam:\n\t{}".format(line.strip())
-
-    return out, err, returncode 
-

anisotropy/openfoam/template/0/U

@@ -1,58 +0,0 @@
-/*--------------------------------*- C++ -*----------------------------------*\
-| =========                 |                                                 |
-| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  v2012                                 |
-|   \\  /    A nd           | Website:  www.openfoam.com                      |
-|    \\/     M anipulation  |                                                 |
-\*---------------------------------------------------------------------------*/
-FoamFile
-{
-    version     2.0;
-    format      ascii;
-    class       volVectorField;
-    location    "0";
-    object      U;
-}
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-dimensions      [0 1 -1 0 0 0 0];
-
-
-internalField   uniform (0 0 0);
-
-boundaryField
-{
-    inlet
-    {
-        type            fixedValue;
-        value           uniform (0 0 -6e-5);
-    }
-    outlet
-    {
-        type            zeroGradient;
-    }
-    symetryPlane
-    {
-        type            fixedValue;
-        value           uniform (0 0 0);
-    }
-    wall
-    {
-        type            fixedValue;
-        value           uniform (0 0 0);
-    }
-    strips
-    {
-        type            fixedValue;
-        value           uniform (0 0 0);
-    }
-
-    defaultFaces
-    {
-        type fixedValue;
-        value uniform (0 0 0);
-    }
-}
-
-
-// ************************************************************************* //

anisotropy/openfoam/template/0/p

@@ -1,55 +0,0 @@
-/*--------------------------------*- C++ -*----------------------------------*\
-| =========                 |                                                 |
-| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  v2012                                 |
-|   \\  /    A nd           | Website:  www.openfoam.com                      |
-|    \\/     M anipulation  |                                                 |
-\*---------------------------------------------------------------------------*/
-FoamFile
-{
-    version     2.0;
-    format      ascii;
-    class       volScalarField;
-    location    "0";
-    object      p;
-}
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-dimensions      [0 2 -2 0 0 0 0];
-
-
-internalField   uniform 0;
-
-boundaryField
-{
-    inlet
-    {
-        type            fixedValue;
-        value           uniform 0.001;
-    }
-    outlet
-    {
-        type            fixedValue;
-        value           uniform 0;
-    }
-    symetryPlane
-    {
-        type            zeroGradient;
-    }
-    wall
-    {
-        type            zeroGradient;
-    } 
-    strips
-    {
-        type            zeroGradient;
-    } 
-
-    defaultFaces
-    {
-        type zeroGradient;
-    }
-}
-
-
-// ************************************************************************* //

anisotropy/openfoam/template/constant/transportProperties

@@ -1,22 +0,0 @@
-/*--------------------------------*- C++ -*----------------------------------*\
-| =========                 |                                                 |
-| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  v2012                                 |
-|   \\  /    A nd           | Website:  www.openfoam.com                      |
-|    \\/     M anipulation  |                                                 |
-\*---------------------------------------------------------------------------*/
-FoamFile
-{
-    version     2.0;
-    format      ascii;
-    class       dictionary;
-    location    "constant";
-    object      transportProperties;
-}
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-transportModel  Newtonian;
-
-nu              1e-06;
-
-// ************************************************************************* //

anisotropy/openfoam/template/constant/turbulenceProperties

@@ -1,23 +0,0 @@
-/*--------------------------------*- C++ -*----------------------------------*\
-| =========                 |                                                 |
-| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  v2012                                 |
-|   \\  /    A nd           | Website:  www.openfoam.com                      |
-|    \\/     M anipulation  |                                                 |
-\*---------------------------------------------------------------------------*/
-FoamFile
-{
-    version     2.0;
-    format      ascii;
-    class       dictionary;
-    location    "constant";
-    object      turbulenceProperties;
-}
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-simulationType laminar;
-
-
-
-
-// ************************************************************************* //

anisotropy/openfoam/template/system/collapseDict

@@ -1,28 +0,0 @@
-/*--------------------------------*- C++ -*----------------------------------*\
-| =========                 |                                                 |
-| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  v2012                                 |
-|   \\  /    A nd           | Website:  www.openfoam.com                      |
-|    \\/     M anipulation  |                                                 |
-\*---------------------------------------------------------------------------*/
-FoamFile
-{
-    version     2.0;
-    format      ascii;
-    class       dictionary;
-    object      collapseDict;
-}
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-collapseEdgesCoeffs
-{
-    // Edges shorter than this absolute value will be merged
-    minimumEdgeLength   2e-7;
-
-    // The maximum angle between two edges that share a point attached to
-    // no other edges
-    maximumMergeAngle   5;
-}
-
-
-// ************************************************************************* //

anisotropy/openfoam/template/system/controlDict

@@ -1,80 +0,0 @@
-/*--------------------------------*- C++ -*----------------------------------*\
-| =========                 |                                                 |
-| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  v2012                                 |
-|   \\  /    A nd           | Website:  www.openfoam.com                      |
-|    \\/     M anipulation  |                                                 |
-\*---------------------------------------------------------------------------*/
-FoamFile
-{
-    version     2.0;
-    format      ascii;
-    class       dictionary;
-    location    "system";
-    object      controlDict;
-}
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-application     simpleFoam;
-
-startFrom       latestTime; //startTime;
-
-startTime       0;
-
-stopAt          endTime;
-
-endTime         5000;
-
-deltaT          1;
-
-writeControl    timeStep;
-
-writeInterval   50;
-
-purgeWrite      0;
-
-writeFormat     ascii;
-
-writePrecision  6;
-
-writeCompression off;
-
-timeFormat      general;
-
-timePrecision   6;
-
-runTimeModifiable true;
-
-functions
-{
-    flowRatePatch(name=inlet)
-    {
-        name            inlet;
-        type            surfaceFieldValue;
-        libs            ( "libfieldFunctionObjects.so" );
-        writeControl    timeStep;
-        writeInterval   1;
-        writeFields     false;
-        log             false;
-        regionType      patch;
-        fields          ( phi );
-        operation       sum;
-    }
-    
-    flowRatePatch(name=outlet)
-    {
-        name            outlet;
-        type            surfaceFieldValue;
-        libs            ( "libfieldFunctionObjects.so" );
-        writeControl    timeStep;
-        writeInterval   1;
-        writeFields     false;
-        log             false;
-        regionType      patch;
-        fields          ( phi );
-        operation       sum;
-    }
-}
-
-
-// ************************************************************************* //

anisotropy/openfoam/template/system/createPatchDict

@@ -1,168 +0,0 @@
-/*--------------------------------*- C++ -*----------------------------------*\
-| =========                 |                                                 |
-| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  v2012                                 |
-|   \\  /    A nd           | Website:  www.openfoam.com                      |
-|    \\/     M anipulation  |                                                 |
-\*---------------------------------------------------------------------------*/
-FoamFile
-{
-    version     2.0;
-    format      ascii;
-    class       dictionary;
-    object      createPatchDict;
-}
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-pointSync   false;
-
-// Patches to create.
-patches
-(
-    {
-        name defaultFaces;
-        
-        patchInfo
-        {
-            type empty;
-        }
-
-        constructFrom patches;
-        patches (defaultFaces);
-    }
-    
-    {
-        name inlet;
-        
-        patchInfo
-        {
-            type patch;
-            inGroups (inlet);
-        }
-
-        constructFrom patches;
-        patches (smesh_inlet);
-    }
-
-    {
-        name outlet;
-        
-        
-        patchInfo
-        {
-            type patch;
-            inGroups (outlet);
-        }
-
-        constructFrom patches;   
-        patches (smesh_outlet);
-    }
-    
-    {
-        name wall;
-
-        patchInfo
-        {
-            type wall;
-            inGroups (wall);
-        }
-
-        constructFrom patches;
-        patches (smesh_wall);
-    }
-
-    {
-        name symetry0;
-        
-        patchInfo
-        {
-            type symetryPlane;
-            inGroups (symetryPlane);
-        }
-
-        constructFrom patches;
-        patches (smesh_symetry0);
-    }
-
-    {
-        name symetry1;
-        
-        patchInfo
-        {
-            type symetryPlane;
-            inGroups (symetryPlane);
-        }
-
-        constructFrom patches;
-        patches (smesh_symetry1);
-    }
-
-    {
-        name symetry2;
-        
-        patchInfo
-        {
-            type symetryPlane;
-            inGroups (symetryPlane);
-        }
-
-        constructFrom patches;
-        patches (smesh_symetry2);
-    }
-
-    {
-        name symetry3;
-        
-        patchInfo
-        {
-            type symetryPlane;
-            inGroups (symetryPlane);
-        }
-
-        constructFrom patches;
-        patches (smesh_symetry3);
-    }
-
-    {
-        name symetry4;
-        
-        patchInfo
-        {
-            type symetryPlane;
-            inGroups (symetryPlane);
-        }
-
-        constructFrom patches;
-        patches (smesh_symetry4);
-    }
-
-    {
-        name symetry5;
-        
-        patchInfo
-        {
-            type symetryPlane;
-            inGroups (symetryPlane);
-        }
-
-        constructFrom patches;
-        patches (smesh_symetry5);
-    }
-
-    {
-        name strips;
-
-        patchInfo
-        {
-            type wall;
-            inGroups (wall);
-        }
-
-        constructFrom patches;
-        patches (smesh_strips);
-    }
-
-
-);
-
-// ************************************************************************* //

anisotropy/openfoam/template/system/decomposeParDict

@@ -1,26 +0,0 @@
-/*--------------------------------*- C++ -*----------------------------------*\
-| =========                 |                                                 |
-| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  v2012                                 |
-|   \\  /    A nd           | Website:  www.openfoam.com                      |
-|    \\/     M anipulation  |                                                 |
-\*---------------------------------------------------------------------------*/
-FoamFile
-{
-    version     2.0;
-    format      ascii;
-    class       dictionary;
-    object      decomposeParDict;
-}
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-numberOfSubdomains 4;
-
-method          simple;
-
-coeffs
-{
-    n           (2 2 1);
-}
-
-// ************************************************************************* //

anisotropy/openfoam/template/system/fvSchemes

@@ -1,53 +0,0 @@
-/*--------------------------------*- C++ -*----------------------------------*\
-| =========                 |                                                 |
-| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  v2012                                 |
-|   \\  /    A nd           | Website:  www.openfoam.com                      |
-|    \\/     M anipulation  |                                                 |
-\*---------------------------------------------------------------------------*/
-FoamFile
-{
-    version     2.0;
-    format      ascii;
-    class       dictionary;
-    location    "system";
-    object      fvSchemes;
-}
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-ddtSchemes
-{
-    default         steadyState;
-}
-
-gradSchemes
-{
-    default         Gauss linear;
-//    grad(Phi)   Gauss linear;
-}
-
-divSchemes
-{
-    default         none;
-    div(phi,U)      bounded Gauss linearUpwind grad(U);
-    div((nuEff*dev2(T(grad(U))))) Gauss linear;
-    div(nonlinearStress) Gauss linear;
-}
-
-laplacianSchemes
-{
-    default         Gauss linear corrected;
-//    laplacian(1, Phi)   Gauss linear corrected;
-}
-
-interpolationSchemes
-{
-    default         linear;
-}
-
-snGradSchemes
-{
-    default         corrected;
-}
-
-// ************************************************************************* //

anisotropy/openfoam/template/system/fvSolution

@@ -1,96 +0,0 @@
-/*--------------------------------*- C++ -*----------------------------------*\
-| =========                 |                                                 |
-| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  v2012                                 |
-|   \\  /    A nd           | Website:  www.openfoam.com                      |
-|    \\/     M anipulation  |                                                 |
-\*---------------------------------------------------------------------------*/
-FoamFile
-{
-    version     2.0;
-    format      ascii;
-    class       dictionary;
-    location    "system";
-    object      fvSolution;
-}
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-solvers
-{
-    p
-    {
-        solver          GAMG;
-        tolerance       1e-06;
-        relTol          0.1;
-        smoother        GaussSeidel;
-    }
-
-    U
-    {
-        solver          smoothSolver;
-        smoother        GaussSeidel;
-        nSweeps         2;
-        tolerance       1e-08;
-        relTol          0.1;
-    }
-    
-    /*Phi
-    {
-        solver  GAMG;
-        smoother    GaussSeidel;
-        tolerance   1e-08;
-        relTol  0.01;
-    }*/
-    Phi
-    {
-        solver GAMG;
-        smoother DIC;
-        cacheAgglomeration on;
-        agglomerator faceAreaPair;
-        nCellsInCoarsestLevel 10;
-        mergeLevels 1;
-
-        tolerance 1e-06;
-        relTol 0.01;
-    }
-}
-
-potentialFlow
-{
-    nNonOrthogonalCorrectors 20;
-    PhiRefCell  0;
-    PhiRefPoint 0;
-    PhiRefValue 0;
-    Phi 0;
-}
-
-cache
-{
-    grad(U);
-} 
-
-SIMPLE
-{
-    nNonOrthogonalCorrectors 10;
-
-    residualControl
-    {
-        p               1e-5;
-        U               1e-5;
-    }
-}
-
-relaxationFactors
-{
-    fields
-    {
-        p               0.3;
-    }
-    equations
-    {
-        U               0.5;
-    }
-}
-
-
-// ************************************************************************* //

anisotropy/openfoam/utils.py

@@ -1,39 +1,61 @@
 # -*- coding: utf-8 -*-
-# This file is part of anisotropy.
-# License: GNU GPL version 3, see the file "LICENSE" for details.
+
+from __future__ import annotations
+from numpy.typing import ArrayLike
+from numpy import ndarray
 
 import os
-import shutil
-from .application import application
-
-def version() -> str:
-    return os.environ["WM_PROJECT_VERSION"]
 
 
-def foamCleanCustom(case: str = None):
-    rmDirs = ["0", "constant", "system", "postProcessing", "logs"]
-    rmDirs.extend([ "processor{}".format(n) for n in range(os.cpu_count()) ])
-    path = case if case else ""
+def version() -> str | None:
+    """Version of the current OpenFOAM installation.
 
-    for d in rmDirs:
-        if os.path.exists(os.path.join(path, d)):
-            shutil.rmtree(os.path.join(path, d))
+    :return:
+        Version string or None if installation is not found.
+    """
+    return os.environ.get("WM_PROJECT_VERSION")
 
-def foamClean(case: str = None):
-    rmDirs = ["0", "constant", "system"]
-    path = case if case else ""
 
-    for d in rmDirs:
-        if os.path.exists(os.path.join(path, d)):
-            shutil.rmtree(os.path.join(path, d))
+def template(header: dict, content: dict) -> str:
+    """Render FoamFile with current template.
 
-    application("foamCleanTutorials", useMPI = False, case = case, stderr = True)
+    :param header:
+        Header block with the FoamFile metadata.
+    :param content:
+        Content block of the FoamFile.
+    :return:
+        Generated string of the whole FoamFile.
+    """
+    limit = 78
+    desc = [
+        "/*--------------------------------*- C++ -*----------------------------------*\\",
+        "| =========                 |                                                 |",
+        "| \\\\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |",
+        "|  \\\\    /   O peration     |",
+        "|   \\\\  /    A nd           |                                                 |",
+        "|    \\\\/     M anipulation  |                                                 |",
+        "\\*---------------------------------------------------------------------------*/"
+    ]
+    desc[3] += " Version: {}".format(version() or "missed")
+    desc[3] += " " * (limit - len(desc[3])) + "|"
+    afterheader = "// " + 37 * "* " + "//"
+    endfile = "// " + 73 * "*" + " //"
 
-def uniform(value) -> str:
-    if type(value) == list or type(value) == tuple:
+    return "\n".join([*desc, header, afterheader, content, endfile])
+
+
+def uniform(value: ArrayLike | float | int) -> str:
+    """Convert value to the OpenFOAM uniform representation.
+
+    :param value:
+        Vector or scalar value.
+    :return:
+        Uniform string representation.
+    """
+    if type(value) in [list, tuple, ndarray]:
         return f"uniform ({ value[0] } { value[1] } { value[2] })"
 
-    elif type(value) == int or type(value) == float:
+    elif type(value) in [int, float]:
         return f"uniform { value }"
 
     else:

anisotropy/salomepl/__init__.py

@@ -1,5 +0,0 @@
-# -*- coding: utf-8 -*-
-# This file is part of anisotropy.
-# License: GNU GPL version 3, see the file "LICENSE" for details.
-
-

anisotropy/salomepl/geometry.py

@@ -1,25 +0,0 @@
-# -*- coding: utf-8 -*-
-# This file is part of anisotropy.
-# License: GNU GPL version 3, see the file "LICENSE" for details.
-
-import logging
-
-logger = logging.getLogger("anisotropy")
-
-try:
-    import GEOM
-    from salome.geom import geomBuilder
-
-except ImportError:
-    logger.debug("Trying to get SALOME geometry modules outside SALOME environment. Modules won't be imported.")
-
-if globals().get("geomBuilder"):
-    geompy = geomBuilder.New()
-
-else:
-    geompy = None
-
-def getGeom():
-    return geompy
-
-

anisotropy/salomepl/mesh.py

@@ -1,173 +0,0 @@
-# -*- coding: utf-8 -*-
-# This file is part of anisotropy.
-# License: GNU GPL version 3, see the file "LICENSE" for details.
-
-import logging
-
-logger = logging.getLogger("anisotropy")
-
-try:
-    import SMESH
-    from salome.smesh import smeshBuilder
-
-except ImportError:
-    logger.debug("Trying to get SALOME mesh modules outside SALOME environment. Modules won't be imported.")
-
-if globals().get("smeshBuilder"):
-    smesh = smeshBuilder.New()
-
-else:
-    smesh = None
-
-import enum
-
-class Fineness(enum.Enum):
-    VeryCoarse = 0
-    Coarse = 1
-    Moderate = 2
-    Fine = 3
-    VeryFine = 4
-    Custom = 5
-
-
-def getSmesh():
-    return smesh
-
-
-def updateParams(old, new: dict):
-    old.SetMaxSize(new.get("maxSize", old.GetMaxSize()))
-    old.SetMinSize(new.get("minSize", old.GetMinSize()))
-
-    old.SetFineness(new.get("fineness", old.GetFineness()))
-    old.SetGrowthRate(new.get("growthRate", old.GetGrowthRate()))
-    old.SetNbSegPerEdge(new.get("nbSegPerEdge", old.GetNbSegPerEdge()))
-    old.SetNbSegPerRadius(new.get("nbSegPerRadius", old.GetNbSegPerRadius()))
-
-    old.SetChordalErrorEnabled(new.get("chordalErrorEnabled", old.GetChordalErrorEnabled()))
-    old.SetChordalError(new.get("chordalError", old.GetChordalError()))
-
-    old.SetSecondOrder(new.get("secondOrder", old.GetSecondOrder()))
-    old.SetOptimize(new.get("optimize", old.GetOptimize()))
-    old.SetQuadAllowed(new.get("quadAllowed", old.GetQuadAllowed()))
-    old.SetUseSurfaceCurvature(new.get("useSurfaceCurvature", old.GetUseSurfaceCurvature()))
-    old.SetFuseEdges(new.get("fuseEdges", old.GetFuseEdges()))
-    old.SetCheckChartBoundary(new.get("checkChartBoundary", old.GetCheckChartBoundary()))
-
-
-class Mesh(object):
-    def __init__(self, shape, name = ""):
-        self.name = name if name else shape.GetName()
-        self.mesh = smesh.Mesh(shape, self.name)
-        self.geom = shape
-        self.algo = None
-        self.params = None
-        self.viscousLayers = None
-
-        self.submeshes = []
-    
-    def Tetrahedron(self, **kwargs):
-        self.algo = self.mesh.Tetrahedron(algo = smeshBuilder.NETGEN_1D2D3D)
-        self.params = self.algo.Parameters()
-
-        self.params = updateParams(self.params, kwargs)
-
-    def _extrusionMethod(self, key: str):
-        return dict(
-            SURF_OFFSET_SMOOTH = smeshBuilder.SURF_OFFSET_SMOOTH,
-            FACE_OFFSET = smeshBuilder.FACE_OFFSET,
-            NODE_OFFSET = smeshBuilder.NODE_OFFSET,
-        ).get(key, smeshBuilder.SURF_OFFSET_SMOOTH)
-
-    def ViscousLayers(self,
-            thickness = 1, 
-            numberOfLayers = 1, 
-            stretchFactor = 0,
-            faces = [], 
-            isFacesToIgnore = True, 
-            extrMethod = "SURF_OFFSET_SMOOTH",
-            **kwargs
-        ):
-
-        self.viscousLayers = self.algo.ViscousLayers(
-            thickness,
-            numberOfLayers,
-            stretchFactor,
-            faces,
-            isFacesToIgnore,
-            self._extrusionMethod(extrMethod)
-        )
-
-    def Triangle(self, subshape, **kwargs):
-        submesh = Submesh(self.mesh, subshape)
-        submesh.algo = self.mesh.Triangle(algo = smeshBuilder.NETGEN_1D2D, geom = subshape)
-        submesh.mesh = submesh.algo.subm
-        submesh.params = submesh.algo.Parameters()
-
-        submesh.params = updateParams(submesh.params, kwargs)
-
-        self.submeshes.append(submesh)
-    
-    def assignGroups(self, withPrefix = True):
-        prefix = "smesh_" if withPrefix else ""
-
-        for group in self.mesh.geompyD.GetGroups(self.geom):
-            if group.GetName():
-                self.mesh.GroupOnGeom(group, f"{ prefix }{ group.GetName() }", SMESH.FACE)
-
-    def compute(self):
-        isDone = self.mesh.Compute()
-        returncode = int(not isDone)
-        err = self.mesh.GetComputeErrors()
-
-        return "", err, returncode
-
-    def stats(self):
-        return {
-            "elements":     self.mesh.NbElements(),
-            "edges":        self.mesh.NbEdges(),
-            "faces":        self.mesh.NbFaces(),
-            "volumes":      self.mesh.NbVolumes(),
-            "tetrahedrons": self.mesh.NbTetras(),
-            "prisms":       self.mesh.NbPrisms(),
-            "pyramids":     self.mesh.NbPyramids()
-        }
-
-    def exportUNV(self, path):
-        returncode = 0
-        error = ""
-
-        try:
-            self.mesh.ExportUNV(path)
-
-        except Exception as e:
-            error = e.details.text
-            returncode = 1
-
-        return returncode, error
-
-    def removePyramids(self):
-        if self.mesh.NbPyramids() > 0:
-            pyramidCriterion = smesh.GetCriterion(
-                SMESH.VOLUME,
-                SMESH.FT_ElemGeomType,
-                SMESH.FT_Undefined,
-                SMESH.Geom_PYRAMID
-            )
-            pyramidGroup = self.mesh.MakeGroupByCriterion("pyramids", pyramidCriterion)
-            pyramidVolumes = self.mesh.GetIDSource(pyramidGroup.GetIDs(), SMESH.VOLUME)
-
-            self.mesh.SplitVolumesIntoTetra(pyramidVolumes, smesh.Hex_5Tet)
-            
-            self.mesh.RemoveGroup(pyramidGroup)
-            self.mesh.RenumberElements()
-
-
-
-class Submesh(object):
-    def __init__(self, father, subshape, name = ""):
-        self.name = name if name else subshape.GetName()
-        self.mesh = None
-        self.geom = subshape
-        self.algo = None
-        self.params = None
-

anisotropy/salomepl/utils.py

@@ -1,112 +0,0 @@
-# -*- coding: utf-8 -*-
-# This file is part of anisotropy.
-# License: GNU GPL version 3, see the file "LICENSE" for details.
-
-import subprocess
-import logging
-import sys, os
-import re
-
-
-class SalomeNotFound(Exception):
-    pass
-
-
-class SalomeManager(object):
-    def __init__(self):
-        self.__port = None
-        self.__lastproc = None
-
-
-    def runner(self, cmdargs: list, **kwargs):
-        timeout = kwargs.pop("timeout") if kwargs.get("timeout") else None
-
-        try:
-            with subprocess.Popen(
-                cmdargs,
-                stdout = kwargs.pop("stdout") if kwargs.get("stdout") else subprocess.PIPE,
-                stderr = kwargs.pop("stdout") if kwargs.get("stderr") else subprocess.PIPE,
-                **kwargs
-            ) as proc:
-                self.__lastproc = proc
-                out, err = proc.communicate(timeout = timeout)
-
-        except FileNotFoundError:
-            raise SalomeNotFound()
-
-        return out, err, proc.returncode
-
-
-    def port(self) -> int:
-        out, err, returncode = self.runner(["salome", "start", "--print-port"], text = True)
-        
-        if returncode == 0:
-            reg = re.search("(?!port:)([0-9]+)", out)
-
-            if reg:
-                return int(reg.group())
-
-        return 2810
-
-
-    def version(self) -> int:
-        out, err, returncode = self.runner(["salome", "--version"], text = True)
-
-        return out.strip().split(" ")[-1]
-
-
-    def kill(self, port: int = None):
-        return self.runner(["salome", "kill", str(self.__port or port)])
-
-
-    def killall(self):
-        return self.runner(["salome", "killall"])
-
-
-    def execute(self, scriptpath: str, *args, root: str = None, logpath: str = None, timeout: int = None, **kwargs):
-
-        if not root:
-            root = os.environ["HOME"]
-
-        # ISSUE: salome removes commas from string list
-        args = list(args)
-        args.insert(1, root)
-
-        salomeargs = "args:"
-        salomeargs += ",".join([ '"{}"'.format(str(arg)) for arg in args ])
-
-        if kwargs:
-            salomeargs += "," + ",".join([ '{}="{}"'.format(k, v) for k, v in kwargs.items() ])
-
-        ###
-        self.__port = self.port()
-        cmd = [
-            "salome",
-            "start", 
-            "-t",
-            "--shutdown-servers=1",
-            "--port", str(self.__port),
-            scriptpath,
-            salomeargs
-        ]
-
-        try:
-            out, err, returncode = self.runner(cmd, timeout = timeout)
-
-        except subprocess.TimeoutExpired:
-            lastproc = self.__lastproc
-            self.kill()
-
-            out, err = lastproc.communicate()
-            returncode = lastproc.returncode
-
-        if logpath:
-            os.makedirs(logpath, exist_ok = True)
-
-            with open(os.path.join(logpath, "salome.log"), "wb") as io:
-                io.write(out)
-                io.write(err)
-
-        return str(out, "utf-8"), str(err, "utf-8"), returncode
-
-

anisotropy/samples/__init__.py

@@ -1,7 +0,0 @@
-# -*- coding: utf-8 -*-
-# This file is part of anisotropy.
-# License: GNU GPL version 3, see the file "LICENSE" for details.
-
-from anisotropy.samples.simple import Simple
-from anisotropy.samples.bodyCentered import BodyCentered
-from anisotropy.samples.faceCentered import FaceCentered

anisotropy/samples/bodyCentered.py

@@ -1,230 +0,0 @@
-# -*- coding: utf-8 -*-
-# This file is part of anisotropy.
-# License: GNU GPL version 3, see the file "LICENSE" for details.
-
-from math import pi, sqrt
-from anisotropy.salomepl import geometry
-
-class BodyCentered(object):
-    def __init__(self, **kwargs):
-
-        self.direction = kwargs.get("direction", [1, 0, 0])
-        self.theta = kwargs.get("theta", 0.01)
-        self.L = kwargs.get("L", 1)
-        self.r0 = kwargs.get("r0", self.L * sqrt(3) / 4)
-        self.radius = kwargs.get("radius", self.r0 / (1 - self.theta)) 
-        self.filletsEnabled = kwargs.get("filletsEnabled", False)
-        self.fillets = kwargs.get("fillets", 0)
-        self.volumeCell = None
-
-
-    def build(self):
-
-        geompy = geometry.getGeom()
-
-        ###
-        #   Pore Cell
-        ##
-        if self.direction in [[1, 0, 0], [0, 0, 1]]:
-            ###
-            #   Parameters
-            ##
-            xn, yn, zn = 3, 3, 3 
-            
-            length = 2 * self.r0
-            width = self.L / 2
-            diag = self.L * sqrt(2)
-            height = self.L
-
-            point = []
-            xl = sqrt(diag ** 2 + diag ** 2) * 0.5
-            yw = xl
-            zh = height
-
-            scale = 100
-            oo = geompy.MakeVertex(0, 0, 0)
-            spos1 = (0, 0, 0)
-            spos2 = (0, 0, 0)
-
-            ###
-            #   Bounding box
-            ##
-            if self.direction == [1, 0, 0]:
-                sk = geompy.Sketcher3D()
-                sk.addPointsAbsolute(xl, 0, 0)
-                sk.addPointsAbsolute(0, yw, 0)
-                sk.addPointsAbsolute(0, yw, zh)
-                sk.addPointsAbsolute(xl, 0, zh)
-                sk.addPointsAbsolute(xl, 0, 0)
-
-                inletface = geompy.MakeFaceWires([sk.wire()], True)
-                vecflow = geompy.GetNormal(inletface)
-                poreCell = geompy.MakePrismVecH(inletface, vecflow, diag)
-
-            elif self.direction == [0, 0, 1]:
-                sk = geompy.Sketcher3D()
-                sk.addPointsAbsolute(0, yw, 0)
-                sk.addPointsAbsolute(xl, 0, 0)
-                sk.addPointsAbsolute(2 * xl, yw, 0)
-                sk.addPointsAbsolute(xl, 2 * yw, 0)
-                sk.addPointsAbsolute(0, yw, 0)
-
-                inletface = geompy.MakeFaceWires([sk.wire()], True)
-                vecflow = geompy.GetNormal(inletface)
-                poreCell = geompy.MakePrismVecH(inletface, vecflow, zh)
-
-            [_, _, self.volumeCell] = geompy.BasicProperties(poreCell, theTolerance = 1e-06)
-            
-            inletface = geompy.MakeScaleTransform(inletface, oo, scale)
-            poreCell = geompy.MakeScaleTransform(poreCell, oo, scale)
-
-            faces = geompy.ExtractShapes(poreCell, geompy.ShapeType["FACE"], False)
-            symetryface = []
-
-            for face in faces:
-                norm = geompy.GetNormal(face)
-                angle = round(geompy.GetAngle(norm, vecflow), 0)
-
-                if (angle == 0 or angle == 180) and not face == inletface:
-                    outletface = face
-        
-                else:
-                    symetryface.append(face)
-    
-        elif self.direction == [1, 1, 1]:
-            ###
-            #   Parameters
-            ##
-            xn, yn, zn = 3, 3, 3 
-            
-            length = 2 * self.r0
-            width = self.L / 2
-            diag = self.L * sqrt(2)
-            height = diag / 3
-
-            point = []
-            xl, yw, zh = -self.L / 4, -self.L / 4, -self.L / 4
-            point.append((self.L / 3 + xl, self.L / 3 + yw, 4 * self.L / 3 + zh))
-            point.append((self.L + xl, 0 + yw, self.L + zh))
-            point.append((4 * self.L / 3 + xl, self.L / 3 + yw, self.L / 3 + zh))
-            point.append((self.L + xl, self.L + yw, 0 + zh))
-            point.append((self.L / 3 + xl, 4 * self.L / 3 + yw, self.L / 3 + zh))
-            point.append((0 + xl, self.L + yw, self.L + zh))
-            point.append((self.L / 3 + xl, self.L / 3 + yw, 4 * self.L / 3 + zh))
-
-            scale = 100
-            oo = geompy.MakeVertex(0, 0, 0)
-            spos1 = (0, 0, 0)
-            spos2 = (0, 0, 0)
-
-            ###
-            #   Bounding box
-            ## 
-            sk = geompy.Sketcher3D()
-
-            for p in point:
-                sk.addPointsAbsolute(*p)
-            
-            inletface = geompy.MakeFaceWires([sk.wire()], False)
-            vecflow = geompy.GetNormal(inletface)
-            poreCell = geompy.MakePrismVecH(inletface, vecflow, self.L * sqrt(3))
-
-            [_, _, self.volumeCell] = geompy.BasicProperties(poreCell, theTolerance = 1e-06)
-
-            inletface = geompy.MakeScaleTransform(inletface, oo, scale)
-            poreCell = geompy.MakeScaleTransform(poreCell, oo, scale)
-
-            faces = geompy.ExtractShapes(poreCell, geompy.ShapeType["FACE"], False)
-            symetryface = []
-
-            for face in faces:
-                norm = geompy.GetNormal(face)
-                angle = round(geompy.GetAngle(norm, vecflow), 0)
-
-                if (angle == 0 or angle == 180) and not face == inletface:
-                    outletface = face
-                
-                else:
-                    symetryface.append(face)
-
-        else:
-            raise Exception(f"Direction { self.direction } is not implemented")
-        
-        ###
-        #   Grains
-        ##
-        ox = geompy.MakeVectorDXDYDZ(1, 0, 0)
-        oy = geompy.MakeVectorDXDYDZ(0, 1, 0)
-        oz = geompy.MakeVectorDXDYDZ(0, 0, 1)
-        xy = geompy.MakeVectorDXDYDZ(1, 1, 0)
-        xmy = geompy.MakeVectorDXDYDZ(1, -1, 0)
-
-        grain = geompy.MakeSpherePntR(geompy.MakeVertex(*spos1), self.radius)
-        lattice1 = geompy.MakeMultiTranslation2D(grain, ox, self.L, xn, oy, self.L, yn)
-        lattice1 = geompy.MakeMultiTranslation1D(lattice1, oz, self.L, zn)
-
-        #grain = geompy.MakeSpherePntR(geompy.MakeVertex(*spos2), radius)
-        #lattice2 = geompy.MakeMultiTranslation2D(grain, xy, length, xn + 1, xmy, length, yn + 1)
-        #lattice2 = geompy.MakeMultiTranslation1D(lattice2, oz, L, zn)
-        lattice2 = geompy.MakeTranslation(lattice1, 0.5 * self.L, 0.5 * self.L, 0.5 * self.L)
-        
-        grains = geompy.ExtractShapes(lattice1, geompy.ShapeType["SOLID"], True)
-        grains += geompy.ExtractShapes(lattice2, geompy.ShapeType["SOLID"], True)
-        grains = geompy.MakeFuseList(grains, False, False)
-
-        grains = geompy.MakeScaleTransform(grains, oo, scale)
-        grainsOrigin = None
-
-        if self.filletsEnabled:
-            grainsOrigin =  geompy.MakeScaleTransform(grains, oo, 1 / scale)
-            grains = geompy.MakeFilletAll(grains, self.fillets * scale)
-
-        ###
-        #   Groups
-        ##
-        shape = geompy.MakeCutList(poreCell, [grains])
-        shape = geompy.MakeScaleTransform(shape, oo, 1 / scale, theName = "bodyCentered")
-
-        sall = geompy.CreateGroup(shape, geompy.ShapeType["FACE"])
-        geompy.UnionIDs(sall,
-            geompy.SubShapeAllIDs(shape, geompy.ShapeType["FACE"]))
-
-        inlet = geompy.CreateGroup(shape, geompy.ShapeType["FACE"], theName = "inlet")
-        inletshape = geompy.MakeCutList(inletface, [grains])
-        inletshape = geompy.MakeScaleTransform(inletshape, oo, 1 / scale)
-        geompy.UnionList(inlet, geompy.SubShapeAll(
-            geompy.GetInPlace(shape, inletshape, True), geompy.ShapeType["FACE"]))
-
-        outlet = geompy.CreateGroup(shape, geompy.ShapeType["FACE"], theName = "outlet")
-        outletshape = geompy.MakeCutList(outletface, [grains])
-        outletshape = geompy.MakeScaleTransform(outletshape, oo, 1 / scale)
-        geompy.UnionList(outlet, geompy.SubShapeAll(
-            geompy.GetInPlace(shape, outletshape, True), geompy.ShapeType["FACE"]))
-        
-        symetry = []
-        for (n, face) in enumerate(symetryface):
-            name = "symetry" + str(n)
-            symetry.append(geompy.CreateGroup(shape, geompy.ShapeType["FACE"], theName = name))
-            symetryshape = geompy.MakeCutList(face, [grains])
-            symetryshape = geompy.MakeScaleTransform(symetryshape, oo, 1 / scale)
-            geompy.UnionList(symetry[n], geompy.SubShapeAll(
-                geompy.GetInPlace(shape, symetryshape, True), geompy.ShapeType["FACE"]))
-
-        groups = []
-        groups.append(inlet)
-        groups.append(outlet)
-        groups.extend(symetry)
-
-        if self.filletsEnabled:
-            strips = geompy.CreateGroup(shape, geompy.ShapeType["FACE"], theName = "strips")
-            shapeShell = geompy.ExtractShapes(shape, geompy.ShapeType["SHELL"], True)
-            stripsShape = geompy.MakeCutList(shapeShell[0], groups + [grainsOrigin])
-            geompy.UnionList(strips, geompy.SubShapeAll(
-                geompy.GetInPlace(shape, stripsShape, True), geompy.ShapeType["FACE"]))
-            groups.append(strips)
-        
-        wall = geompy.CutListOfGroups([sall], groups, theName = "wall")
-        groups.append(wall)
-
-        return shape, groups
-

anisotropy/samples/faceCentered.py

@@ -1,230 +0,0 @@
-# -*- coding: utf-8 -*-
-# This file is part of anisotropy.
-# License: GNU GPL version 3, see the file "LICENSE" for details.
-
-from math import pi, sqrt
-from anisotropy.salomepl import geometry
-
-class FaceCentered(object):
-    def __init__(self, **kwargs):
-
-        self.direction = kwargs.get("direction", [1, 0, 0])
-        self.theta = kwargs.get("theta", 0.01)
-        self.L = kwargs.get("L", 1)
-        self.r0 = kwargs.get("r0", self.L * sqrt(2) / 4)
-        self.radius = kwargs.get("radius", self.r0 / (1 - self.theta)) 
-        self.filletsEnabled = kwargs.get("filletsEnabled", False)
-        self.fillets = kwargs.get("fillets", 0)
-        self.volumeCell = None
-
-
-    def build(self):
-
-        geompy = geometry.getGeom()
-
-        ###
-        #   Pore Cell
-        ##
-        if self.direction in [[1, 0, 0], [0, 0, 1]]:
-            ###
-            #   Parameters
-            ##
-            xn, yn, zn = 3, 3, 3 
-            
-            length = 2 * self.r0
-            width = self.L / 2
-            diag = self.L * sqrt(3)
-            height = diag / 3
-
-            point = []
-            xl = sqrt(length ** 2 + length ** 2) * 0.5
-            yw = xl
-            zh = width
-
-            scale = 100
-            oo = geompy.MakeVertex(0, 0, 0)
-            spos1 = (-width * (xn - 1), 0, -width * (zn - 2))
-            spos2 = (-width * xn, 0, -width * (zn - 1))
-
-            ###
-            #   Bounding box
-            ##
-            if self.direction == [1, 0, 0]:
-                sk = geompy.Sketcher3D()
-                sk.addPointsAbsolute(0, 0, -zh)
-                sk.addPointsAbsolute(-xl, yw, -zh)
-                sk.addPointsAbsolute(-xl, yw, zh)
-                sk.addPointsAbsolute(0, 0, zh)
-                sk.addPointsAbsolute(0, 0, -zh)
-
-                inletface = geompy.MakeFaceWires([sk.wire()], True)
-                vecflow = geompy.GetNormal(inletface)
-                poreCell = geompy.MakePrismVecH(inletface, vecflow, length)
-
-            elif self.direction == [0, 0, 1]:
-                sk = geompy.Sketcher3D()
-                sk.addPointsAbsolute(0, 0, -zh)
-                sk.addPointsAbsolute(xl, yw, -zh)
-                sk.addPointsAbsolute(0, 2 * yw, -zh)
-                sk.addPointsAbsolute(-xl, yw, -zh)
-                sk.addPointsAbsolute(0, 0, -zh)
-
-                inletface = geompy.MakeFaceWires([sk.wire()], True)
-                vecflow = geompy.GetNormal(inletface)
-                poreCell = geompy.MakePrismVecH(inletface, vecflow, 2 * zh)
-
-            [_, _, self.volumeCell] = geompy.BasicProperties(poreCell, theTolerance = 1e-06)
-            
-            inletface = geompy.MakeScaleTransform(inletface, oo, scale)
-            poreCell = geompy.MakeScaleTransform(poreCell, oo, scale)
-
-            faces = geompy.ExtractShapes(poreCell, geompy.ShapeType["FACE"], False)
-            symetryface = []
-
-            for face in faces:
-                norm = geompy.GetNormal(face)
-                angle = round(geompy.GetAngle(norm, vecflow), 0)
-
-                if (angle == 0 or angle == 180) and not face == inletface:
-                    outletface = face
-                
-                else:
-                    symetryface.append(face)
-    
-        elif self.direction == [1, 1, 1]:
-            ###
-            #   Parameters
-            ##
-            xn, yn, zn = 3, 3, 3 
-            
-            length = 2 * self.r0
-            width = self.L / 2
-            diag = self.L * sqrt(3)
-            height = diag / 3
-
-            point = []
-            xl, yw, zh = -(xn - 2) * self.L / 3, -(yn - 2) * self.L / 3, -(zn - 2) * self.L / 3
-            point.append((-2 * width / 3 + xl, -2 * width / 3 + yw, width / 3 + zh))
-            point.append((0 + xl, -width + yw, 0 + zh))
-            point.append((width / 3 + xl, -2 * width / 3 + yw, -2 * width / 3 + zh))
-            point.append((0 + xl, 0 + yw, -width + zh))
-            point.append((-2 * width / 3 + xl, width / 3 + yw, -2 * width / 3 + zh))
-            point.append((-width + xl, 0 + yw, 0 + zh))
-            point.append((-2 * width / 3 + xl, -2 * width / 3 + yw, width / 3 + zh))
-
-            scale = 100
-            oo = geompy.MakeVertex(0, 0, 0)
-            spos1 = (-width * (xn - 1), 0, -width * (zn - 2))
-            spos2 = (-width * xn, 0, -width * (zn - 1))
-
-            ###
-            #   Bounding box
-            ## 
-            sk = geompy.Sketcher3D()
-
-            for p in point:
-                sk.addPointsAbsolute(*p)
-            
-            inletface = geompy.MakeFaceWires([sk.wire()], False)
-            vecflow = geompy.GetNormal(inletface)
-            poreCell = geompy.MakePrismVecH(inletface, vecflow, self.L * sqrt(3))
-
-            [_, _, self.volumeCell] = geompy.BasicProperties(poreCell, theTolerance = 1e-06)
-
-            inletface = geompy.MakeScaleTransform(inletface, oo, scale)
-            poreCell = geompy.MakeScaleTransform(poreCell, oo, scale)
-
-            faces = geompy.ExtractShapes(poreCell, geompy.ShapeType["FACE"], False)
-            symetryface = []
-
-            for face in faces:
-                norm = geompy.GetNormal(face)
-                angle = round(geompy.GetAngle(norm, vecflow), 0)
-
-                if (angle == 0 or angle == 180) and not face == inletface:
-                    outletface = face
-                
-                else:
-                    symetryface.append(face)
-
-        else:
-            raise Exception(f"Direction { self.direction } is not implemented")
-        
-        ###
-        #   Grains
-        ##
-        ox = geompy.MakeVectorDXDYDZ(1, 0, 0)
-        oy = geompy.MakeVectorDXDYDZ(0, 1, 0)
-        oz = geompy.MakeVectorDXDYDZ(0, 0, 1)
-        xy = geompy.MakeVectorDXDYDZ(1, 1, 0)
-        xmy = geompy.MakeVectorDXDYDZ(1, -1, 0)
-
-        grain = geompy.MakeSpherePntR(geompy.MakeVertex(*spos1), self.radius)
-        lattice1 = geompy.MakeMultiTranslation2D(grain, xy, length, xn, xmy, length, yn)
-        lattice1 = geompy.MakeMultiTranslation1D(lattice1, oz, self.L, zn - 1)
-
-        grain = geompy.MakeSpherePntR(geompy.MakeVertex(*spos2), self.radius)
-        lattice2 = geompy.MakeMultiTranslation2D(grain, xy, length, xn + 1, xmy, length, yn + 1)
-        lattice2 = geompy.MakeMultiTranslation1D(lattice2, oz, self.L, zn)
-        
-        grains = geompy.ExtractShapes(lattice1, geompy.ShapeType["SOLID"], True)
-        grains += geompy.ExtractShapes(lattice2, geompy.ShapeType["SOLID"], True)
-        grains = geompy.MakeFuseList(grains, False, False)
-
-        grains = geompy.MakeScaleTransform(grains, oo, scale)
-        grainsOrigin = None
-
-        if self.filletsEnabled:
-            grainsOrigin =  geompy.MakeScaleTransform(grains, oo, 1 / scale)
-            grains = geompy.MakeFilletAll(grains, self.fillets * scale)
-
-        ###
-        #   Groups
-        ##
-        shape = geompy.MakeCutList(poreCell, [grains])
-        shape = geompy.MakeScaleTransform(shape, oo, 1 / scale, theName = "faceCentered")
-        
-        sall = geompy.CreateGroup(shape, geompy.ShapeType["FACE"])
-        geompy.UnionIDs(sall,
-            geompy.SubShapeAllIDs(shape, geompy.ShapeType["FACE"]))
-
-        inlet = geompy.CreateGroup(shape, geompy.ShapeType["FACE"], theName = "inlet")
-        inletshape = geompy.MakeCutList(inletface, [grains])
-        inletshape = geompy.MakeScaleTransform(inletshape, oo, 1 / scale)
-        geompy.UnionList(inlet, geompy.SubShapeAll(
-            geompy.GetInPlace(shape, inletshape, True), geompy.ShapeType["FACE"]))
-
-        outlet = geompy.CreateGroup(shape, geompy.ShapeType["FACE"], theName = "outlet")
-        outletshape = geompy.MakeCutList(outletface, [grains])
-        outletshape = geompy.MakeScaleTransform(outletshape, oo, 1 / scale)
-        geompy.UnionList(outlet, geompy.SubShapeAll(
-            geompy.GetInPlace(shape, outletshape, True), geompy.ShapeType["FACE"]))
-        
-        symetry = []
-        for (n, face) in enumerate(symetryface):
-            name = "symetry" + str(n)
-            symetry.append(geompy.CreateGroup(shape, geompy.ShapeType["FACE"], theName = name))
-            symetryshape = geompy.MakeCutList(face, [grains])
-            symetryshape = geompy.MakeScaleTransform(symetryshape, oo, 1 / scale)
-            geompy.UnionList(symetry[n], geompy.SubShapeAll(
-                geompy.GetInPlace(shape, symetryshape, True), geompy.ShapeType["FACE"]))
-
-        groups = []
-        groups.append(inlet)
-        groups.append(outlet)
-        groups.extend(symetry)
-
-        if self.filletsEnabled:
-            strips = geompy.CreateGroup(shape, geompy.ShapeType["FACE"], theName = "strips")
-            shapeShell = geompy.ExtractShapes(shape, geompy.ShapeType["SHELL"], True)
-            stripsShape = geompy.MakeCutList(shapeShell[0], groups + [grainsOrigin])
-            geompy.UnionList(strips, geompy.SubShapeAll(
-                geompy.GetInPlace(shape, stripsShape, True), geompy.ShapeType["FACE"]))
-            groups.append(strips)
-
-        wall = geompy.CutListOfGroups([sall], groups, theName = "wall")
-        groups.append(wall)
-
-        return shape, groups
-
-

anisotropy/samples/simple.py

@@ -1,215 +0,0 @@
-# -*- coding: utf-8 -*-
-# This file is part of anisotropy.
-# License: GNU GPL version 3, see the file "LICENSE" for details.
-
-from math import pi, sqrt
-from anisotropy.salomepl import geometry
-
-class Simple(object):
-    def __init__(self, **kwargs):
-
-        self.direction = kwargs.get("direction", [1, 0, 0])
-        self.theta = kwargs.get("theta", 0.01)
-        self.r0 = kwargs.get("r0", 1)
-        self.L = kwargs.get("L", 2 * self.r0)
-        self.radius = kwargs.get("radius", self.r0 / (1 - self.theta)) 
-        self.filletsEnabled = kwargs.get("filletsEnabled", False)
-        self.fillets = kwargs.get("fillets", 0)
-        self.volumeCell = None
-
-
-    def build(self):
-
-        geompy = geometry.getGeom()
-
-        ###
-        #   Pore Cell
-        ##
-        if self.direction in [[1, 0, 0], [0, 0, 1]]:
-            ###
-            #   Parameters
-            ##
-            xn, yn, zn = 3, 3, 3 
-            
-            length = self.L * sqrt(2)
-            width = self.L * sqrt(2)
-            height = self.L
-
-            xl = sqrt(length ** 2 * 0.5)
-            yw = xl
-            zh = height
-
-            scale = 100
-            oo = geompy.MakeVertex(0, 0, 0)
-
-            ###
-            #   Bounding box
-            ##
-            if self.direction == [1, 0, 0]:
-                sk = geompy.Sketcher3D()
-                sk.addPointsAbsolute(xl, 0, 0)
-                sk.addPointsAbsolute(0, yw, 0)
-                sk.addPointsAbsolute(0, yw, zh)
-                sk.addPointsAbsolute(xl, 0, zh)
-                sk.addPointsAbsolute(xl, 0, 0)
-
-                inletface = geompy.MakeFaceWires([sk.wire()], True)
-                vecflow = geompy.GetNormal(inletface)
-                poreCell = geompy.MakePrismVecH(inletface, vecflow, width)
-
-            elif self.direction == [0, 0, 1]:
-                sk = geompy.Sketcher3D()
-                sk.addPointsAbsolute(0, yw, 0)
-                sk.addPointsAbsolute(xl, 0, 0)
-                sk.addPointsAbsolute(2 * xl, yw, 0)
-                sk.addPointsAbsolute(xl, 2 * yw, 0)
-                sk.addPointsAbsolute(0, yw, 0)
-
-                inletface = geompy.MakeFaceWires([sk.wire()], True)
-                vecflow = geompy.GetNormal(inletface)
-                poreCell = geompy.MakePrismVecH(inletface, vecflow, height)
-
-            [_, _, self.volumeCell] = geompy.BasicProperties(poreCell, theTolerance = 1e-06)
-                
-            inletface = geompy.MakeScaleTransform(inletface, oo, scale)
-            poreCell = geompy.MakeScaleTransform(poreCell, oo, scale)
-
-            faces = geompy.ExtractShapes(poreCell, geompy.ShapeType["FACE"], False)
-            symetryface = []
-
-            for face in faces:
-                norm = geompy.GetNormal(face)
-                angle = round(geompy.GetAngle(norm, vecflow), 0)
-
-                if (angle == 0 or angle == 180) and not face == inletface:
-                    outletface = face
-                
-                else:
-                    symetryface.append(face)
-
-        elif self.direction == [1, 1, 1]:
-            ###
-            #   Parameters
-            ##
-            xn, yn, zn = 3, 3, 3 
-            
-            length = self.L * sqrt(2)
-            width = self.L * sqrt(2)
-            height = self.L
-
-            point = []
-            xl, yw, zh = -self.L - self.L / 6, -self.L - self.L / 6, -self.L / 6
-            point.append((self.L + xl, self.L + yw, self.L + zh))
-            point.append((5 * self.L / 3 + xl, 2 * self.L / 3 + yw, 2 * self.L / 3 + zh))
-            point.append((2 * self.L + xl, self.L + yw, 0 + zh))
-            point.append((5 * self.L / 3 + xl, 5 * self.L / 3 + yw, -self.L / 3 + zh))
-            point.append((self.L + xl, 2 * self.L + yw, 0 + zh))
-            point.append((2 * self.L / 3 + xl, 5 * self.L / 3 + yw, 2 * self.L / 3 + zh))
-            point.append((self.L + xl, self.L + yw, self.L + zh))
-
-            scale = 100
-            oo = geompy.MakeVertex(0, 0, 0)
-
-            ###
-            #   Bounding box
-            ## 
-            sk = geompy.Sketcher3D()
-
-            for p in point:
-                sk.addPointsAbsolute(*p)
-            
-            inletface = geompy.MakeFaceWires([sk.wire()], False)
-            vecflow = geompy.GetNormal(inletface)
-            poreCell = geompy.MakePrismVecH(inletface, vecflow, self.L * sqrt(3))
-
-            [_, _, self.volumeCell] = geompy.BasicProperties(poreCell, theTolerance = 1e-06)
-
-            inletface = geompy.MakeScaleTransform(inletface, oo, scale)
-            poreCell = geompy.MakeScaleTransform(poreCell, oo, scale)
-
-            faces = geompy.ExtractShapes(poreCell, geompy.ShapeType["FACE"], False)
-            symetryface = []
-
-            for face in faces:
-                norm = geompy.GetNormal(face)
-                angle = round(geompy.GetAngle(norm, vecflow), 0)
-
-                if (angle == 0 or angle == 180) and not face == inletface:
-                    outletface = face
-                
-                else:
-                    symetryface.append(face)
-
-        else:
-            raise Exception(f"Direction { self.direction } is not implemented")
-        
-        ###
-        #   Grains
-        ##
-        ox = geompy.MakeVectorDXDYDZ(1, 0, 0)
-        oy = geompy.MakeVectorDXDYDZ(0, 1, 0)
-        oz = geompy.MakeVectorDXDYDZ(0, 0, 1)
-
-        grain = geompy.MakeSphereR(self.radius)
-        lattice = geompy.MakeMultiTranslation2D(grain, ox, self.L, xn, oy, self.L, yn)
-        lattice = geompy.MakeMultiTranslation1D(lattice, oz, self.L, zn)
-        
-        grains = geompy.ExtractShapes(lattice, geompy.ShapeType["SOLID"], True)
-        grains = geompy.MakeFuseList(grains, False, False)
-
-        grains = geompy.MakeScaleTransform(grains, oo, scale)
-        grainsOrigin = None
-
-        if self.filletsEnabled:
-            grainsOrigin =  geompy.MakeScaleTransform(grains, oo, 1 / scale)
-            grains = geompy.MakeFilletAll(grains, self.fillets * scale)
-
-        ###
-        #   Groups
-        ##
-        shape = geompy.MakeCutList(poreCell, [grains])
-        shape = geompy.MakeScaleTransform(shape, oo, 1 / scale, theName = "simple")
-
-        sall = geompy.CreateGroup(shape, geompy.ShapeType["FACE"])
-        geompy.UnionIDs(sall,
-            geompy.SubShapeAllIDs(shape, geompy.ShapeType["FACE"]))
-
-        inlet = geompy.CreateGroup(shape, geompy.ShapeType["FACE"], theName = "inlet")
-        inletshape = geompy.MakeCutList(inletface, [grains])
-        inletshape = geompy.MakeScaleTransform(inletshape, oo, 1 / scale)
-        geompy.UnionList(inlet, geompy.SubShapeAll(
-            geompy.GetInPlace(shape, inletshape, True), geompy.ShapeType["FACE"]))
-
-        outlet = geompy.CreateGroup(shape, geompy.ShapeType["FACE"], theName = "outlet")
-        outletshape = geompy.MakeCutList(outletface, [grains])
-        outletshape = geompy.MakeScaleTransform(outletshape, oo, 1 / scale)
-        geompy.UnionList(outlet, geompy.SubShapeAll(
-            geompy.GetInPlace(shape, outletshape, True), geompy.ShapeType["FACE"]))
-        
-        symetry = []
-        for (n, face) in enumerate(symetryface):
-            name = "symetry" + str(n)
-            symetry.append(geompy.CreateGroup(shape, geompy.ShapeType["FACE"], theName = name))
-            symetryshape = geompy.MakeCutList(face, [grains])
-            symetryshape = geompy.MakeScaleTransform(symetryshape, oo, 1 / scale)
-            geompy.UnionList(symetry[n], geompy.SubShapeAll(
-                geompy.GetInPlace(shape, symetryshape, True), geompy.ShapeType["FACE"]))
-
-        groups = []
-        groups.append(inlet)
-        groups.append(outlet)
-        groups.extend(symetry)
-        
-        if self.filletsEnabled:
-            strips = geompy.CreateGroup(shape, geompy.ShapeType["FACE"], theName = "strips")
-            shapeShell = geompy.ExtractShapes(shape, geompy.ShapeType["SHELL"], True)
-            stripsShape = geompy.MakeCutList(shapeShell[0], groups + [grainsOrigin])
-            geompy.UnionList(strips, geompy.SubShapeAll(
-                geompy.GetInPlace(shape, stripsShape, True), geompy.ShapeType["FACE"]))
-            groups.append(strips)
-
-        wall = geompy.CutListOfGroups([sall], groups, theName = "wall")
-        groups.append(wall)
-
-        return shape, groups
-

anisotropy/shaping/__init__.py

@@ -0,0 +1,21 @@
+# -*- coding: utf-8 -*-
+"""
+Shaping is a library for using OCC shapes, provides more convient
+functionality with power NumPy and Python OOP and contains interesing
+primitives.
+"""
+
+from . import utils
+
+from .shape import Shape
+from .periodic import Periodic
+
+from . import primitives
+
+
+__all__ = [
+    "utils",
+    "primitives",
+    "Shape",
+    "Periodic"
+]

anisotropy/shaping/periodic.py

@@ -0,0 +1,69 @@
+# -*- coding: utf-8 -*-
+
+import numpy as np
+
+from . import Shape
+
+
+class Periodic(Shape):
+    def __init__(
+        self,
+        alpha: float = None,
+        r0: float = 1,
+        L: float = None,
+        filletsEnabled: bool = True,
+        gamma = None,
+        **kwargs
+    ):
+        """A Periodic object contains periodic structure.
+        
+        :param alpha:
+            Spheres overlap parameter.
+        :param r0:
+            Initial spheres radius.
+        :param L:
+            Side length of periodic cell. Depends on r0.
+        :param gamma:
+            Angle between lines that connect centers of spheres.
+        :param filletsEnabled:
+            If True, calculate fillets beetween spheres.
+        """
+        Shape.__init__(self)
+        
+        #   Parameters
+        self.alpha = alpha
+        self.r0 = r0
+        self.L = L
+
+        #   for lattice
+        # self.theta = 0.5 * pi
+
+        self.gamma = gamma or np.pi - 2 * (0.5 * 0.5 * np.pi)
+        self.filletsEnabled = filletsEnabled
+        self.filletsScale = 0.8
+        
+        #   scale parameters for precision boolean operations
+        self.maximize = 1e+2
+        self.minimize = 1e-2
+
+    @property
+    def radius(self) -> float:
+        """Spheres radius
+
+        :return:
+            Radius.
+        """
+        return self.r0 / (1 - self.alpha)
+
+    @property
+    def fillets(self):
+        """Fillets radius beetween spheres.
+
+        :return:
+            Radius.
+        """
+        analytical = self.r0 * np.sqrt(2) / np.sqrt(1 - np.cos(self.gamma)) - self.radius
+        rTol = 3
+        minRound = np.fix(10 ** rTol * analytical) * 10 ** -rTol
+
+        return minRound * self.filletsScale

anisotropy/shaping/primitives.py

@@ -0,0 +1,510 @@
+# -*- coding: utf-8 -*-
+
+from __future__ import annotations
+from numpy import ndarray
+
+import numpy as np
+import netgen.occ as ng_occ
+
+from . import Periodic
+from . import utils
+
+
+def simple(alpha: float, direction: list | ndarray, **kwargs) -> Periodic:
+    """Simple periodic structure.
+
+    :param alpha:
+        Spheres overlap parameter.
+    :param direction:
+        Flow direction vector. This parameter affects the geometry type
+        and boundary (faces) names.
+    :return:
+        Periodic object.
+    """
+    #   base object
+    pc = Periodic(
+        alpha = alpha,
+        gamma = np.pi - 2 * (0.5 * 0.5 * np.pi)
+    )
+    
+    #   additional parameters
+    pc.__dict__.update(kwargs)
+    pc.L = 2 * pc.r0
+    pc.direction = np.asarray(direction)
+    pc.length = 0.
+
+    #   additional attributes
+    pc.cell: ng_occ.Solid = None
+    pc.lattice: ng_occ.Solid = None
+
+    #   constants
+    zero = ng_occ.Pnt(0, 0, 0)
+
+    #   Lattice
+    spheres = [] 
+
+    for zn in range(3):
+        z = zn * pc.L
+
+        for yn in range(3):
+            y = yn * pc.L
+
+            for xn in range(3):
+                x = xn * pc.L
+
+                spheres.append(ng_occ.Sphere(ng_occ.Pnt(x, y, z), pc.radius))
+
+    pc.lattice = np.sum(spheres)
+
+    if pc.filletsEnabled:
+        pc.lattice = pc.lattice.Scale(zero, pc.maximize)
+        pc.lattice = (
+            pc.lattice
+            .MakeFillet(pc.lattice.edges, pc.fillets * pc.maximize)
+            .Scale(zero, pc.minimize)
+        )
+    
+    #   Inlet face
+    if np.all(pc.direction == [1., 0., 0.]):
+        length = pc.L * np.sqrt(2)
+        width = pc.L * np.sqrt(2)
+        height = pc.L
+
+        xl = np.sqrt(length ** 2 * 0.5)
+        yw = xl
+        zh = height
+
+        vertices = np.array([
+            (xl, 0, 0),
+            (0, yw, 0),
+            (0, yw, zh),
+            (xl, 0, zh)
+        ])
+        extr = width
+
+    elif np.all(pc.direction == [0., 0., 1.]):
+        length = pc.L * np.sqrt(2)
+        width = pc.L * np.sqrt(2)
+        height = pc.L
+
+        xl = np.sqrt(length ** 2 * 0.5)
+        yw = xl
+        zh = height
+
+        vertices = np.array([
+            (0, yw, 0),
+            (xl, 0, 0),
+            (2 * xl, yw, 0),
+            (xl, 2 * yw, 0)
+        ])
+        extr = height
+
+    elif np.all(pc.direction == [1., 1., 1.]):
+        length = pc.L * np.sqrt(2)
+        width = pc.L * np.sqrt(2)
+        height = pc.L
+
+        xl = -pc.L - pc.L / 6 
+        yw = -pc.L - pc.L / 6
+        zh = -pc.L / 6
+
+        vertices = np.array([
+            (pc.L + xl, pc.L + yw, pc.L + zh),
+            (5 * pc.L / 3 + xl, 2 * pc.L / 3 + yw, 2 * pc.L / 3 + zh),
+            (2 * pc.L + xl, pc.L + yw, 0 + zh),
+            (5 * pc.L / 3 + xl, 5 * pc.L / 3 + yw, -pc.L / 3 + zh),
+            (pc.L + xl, 2 * pc.L + yw, 0 + zh),
+            (2 * pc.L / 3 + xl, 5 * pc.L / 3 + yw, 2 * pc.L / 3 + zh)
+        ])
+        extr = pc.L * np.sqrt(3) 
+
+    else:
+        raise Exception(f"Direction { pc.direction } is not implemented")
+    
+    #   Cell
+    circuit = ng_occ.Wire([ 
+        ng_occ.Segment(ng_occ.Pnt(*v1), ng_occ.Pnt(*v2))
+        for v1, v2 in zip(vertices, np.roll(vertices, -1, axis = 0)) 
+    ])
+    inletface = ng_occ.Face(circuit)
+    inletface.name = "inlet"
+
+    vecFlow = utils.normal(inletface)
+    pc.cell = inletface.Extrude(extr, ng_occ.Vec(*vecFlow))
+    pc.length = extr
+    
+    #   Boundary faces
+    symetryId = 0
+
+    for face in pc.cell.faces:
+        fNorm = utils.normal(face)
+        fAngle = utils.angle(vecFlow, fNorm)
+        
+        if fAngle == 0 or fAngle == np.pi:
+            if np.all(utils.pos(face.center) == utils.pos(inletface.center)):
+                face.name = "inlet"
+                
+            else:
+                face.name = "outlet"
+
+        else:
+            face.name = f"symetry{ symetryId }"
+            symetryId += 1
+
+    #   Main shape
+    pc.shape = pc.cell - pc.lattice
+
+    assert len(pc.shape.solids) == 1, "Expected single solid shape"
+
+    pc.shape = pc.shape.solids[0]
+
+    #   Boundary faces (walls)
+    for face in pc.shape.faces:
+        if face.name not in ["inlet", "outlet", *[ f"symetry{ n }" for n in range(6) ]]:
+            face.name = "wall"
+
+    return pc
+
+
+def body_centered(alpha: float, direction: list | ndarray, **kwargs) -> Periodic:
+    """Body centered periodic structure.
+
+    :param alpha:
+        Spheres overlap parameter.
+    :param direction:
+        Flow direction vector. This parameter affects the geometry type
+        and boundary (faces) names.
+    :return:
+        Periodic object.
+    """
+    #   base object 
+    pc = Periodic(
+        alpha = alpha,
+        gamma = np.pi - 2 * np.arccos(np.sqrt(2 / 3))
+    )
+
+    #   additional parameters
+    pc.__dict__.update(kwargs)
+    pc.L = 4 / np.sqrt(3) * pc.r0
+    pc.direction = np.asarray(direction)
+
+    #   additional attributes
+    pc.cell: ng_occ.Solid = None
+    pc.lattice: ng_occ.Solid = None
+    pc.length = 0.
+
+    #   constants   
+    zero = ng_occ.Pnt(0, 0, 0)
+
+    #   Lattice
+    spheres = [] 
+
+    for zn in range(3):
+        z = zn * pc.L
+        z2 = z - 0.5 * pc.L
+
+        for yn in range(3):
+            y = yn * pc.L
+            y2 = y - 0.5 * pc.L
+
+            for xn in range(3):
+                x = xn * pc.L
+                x2 = x - 0.5 * pc.L
+
+                spheres.append(ng_occ.Sphere(ng_occ.Pnt(x, y, z), pc.radius))
+                # shifted
+                spheres.append(ng_occ.Sphere(ng_occ.Pnt(x2, y2, z2), pc.radius))
+
+    pc.lattice = np.sum(spheres)
+
+    if pc.filletsEnabled:
+        pc.lattice = pc.lattice.Scale(zero, pc.maximize)
+        pc.lattice = (
+            pc.lattice
+            .MakeFillet(pc.lattice.edges, pc.fillets * pc.maximize)
+            .Scale(zero, pc.minimize)
+        )
+    
+    #   Inlet face
+    if np.all(pc.direction == [1., 0., 0.]):
+        # length = 2 * pc.r0
+        # width = pc.L / 2
+        diag = pc.L * np.sqrt(2)
+        height = pc.L
+
+        xl = np.sqrt(diag ** 2 + diag ** 2) * 0.5
+        yw = xl
+        zh = height
+
+        vertices = np.array([
+            (xl, 0, 0),
+            (0, yw, 0),
+            (0, yw, zh),
+            (xl, 0, zh)
+        ])
+        extr = diag
+
+    elif np.all(pc.direction == [0., 0., 1.]):
+        # length = 2 * pc.r0
+        # width = pc.L / 2
+        diag = pc.L * np.sqrt(2)
+        height = pc.L
+
+        xl = np.sqrt(diag ** 2 + diag ** 2) * 0.5
+        yw = xl
+        zh = height
+
+        vertices = np.array([
+            (0, yw, 0),
+            (xl, 0, 0),
+            (2 * xl, yw, 0),
+            (xl, 2 * yw, 0)
+        ])
+        extr = height
+
+    elif np.all(pc.direction == [1., 1., 1.]):
+        # length = 2 * pc.r0
+        # width = pc.L / 2
+        diag = pc.L * np.sqrt(2)
+        height = diag / 3
+
+        xl = -pc.L / 4
+        yw = -pc.L / 4
+        zh = -pc.L / 4
+
+        vertices = np.array([
+            (pc.L / 3 + xl, pc.L / 3 + yw, 4 * pc.L / 3 + zh),
+            (pc.L + xl, 0 + yw, pc.L + zh),
+            (4 * pc.L / 3 + xl, pc.L / 3 + yw, pc.L / 3 + zh),
+            (pc.L + xl, pc.L + yw, 0 + zh),
+            (pc.L / 3 + xl, 4 * pc.L / 3 + yw, pc.L / 3 + zh),
+            (0 + xl, pc.L + yw, pc.L + zh)
+        ])
+        extr = pc.L * np.sqrt(3) 
+
+    else:
+        raise Exception(f"Direction { pc.direction } is not implemented")
+
+    #   Cell
+    circuit = ng_occ.Wire([ 
+        ng_occ.Segment(ng_occ.Pnt(*v1), ng_occ.Pnt(*v2)) 
+        for v1, v2 in zip(vertices, np.roll(vertices, -1, axis = 0)) 
+    ])
+    inletface = ng_occ.Face(circuit)
+    inletface.name = "inlet"
+
+    vecFlow = utils.normal(inletface)
+    pc.cell = inletface.Extrude(extr, ng_occ.Vec(*vecFlow))
+    pc.length = extr
+    
+    #   Boundary faces
+    symetryId = 0
+
+    for face in pc.cell.faces:
+        fNorm = utils.normal(face)
+        fAngle = utils.angle(vecFlow, fNorm)
+        
+        if fAngle == 0 or fAngle == np.pi:
+            if np.all(utils.pos(face.center) == utils.pos(inletface.center)):
+                face.name = "inlet"
+
+            else:
+                face.name = "outlet"
+
+        else:
+            face.name = f"symetry{ symetryId }"
+            symetryId += 1
+
+    #   Main shape
+    pc.shape = pc.cell - pc.lattice
+
+    assert len(pc.shape.solids) == 1, "Expected single solid shape"
+
+    pc.shape = pc.shape.solids[0]
+
+    #   Boundary faces (walls)
+    for face in pc.shape.faces:
+        if face.name not in ["inlet", "outlet", *[ f"symetry{ n }" for n in range(6) ]]:
+            face.name = "wall"
+
+    return pc
+
+
+def face_centered(alpha: float, direction: list | ndarray, **kwargs) -> Periodic:
+    """Face centered periodic structure.
+
+    :param alpha:
+        Spheres overlap parameter.
+    :param direction:
+        Flow direction vector. This parameter affects the geometry type
+        and boundary (faces) names.
+    :return:
+        Periodic object.
+    """
+    #   base class
+    pc = Periodic(
+        alpha = alpha,
+        gamma = 2 / 3 * np.pi 
+    )
+
+    #   additional parameters
+    pc.__dict__.update(kwargs)
+    pc.L = pc.r0 * 4 / np.sqrt(2)
+    pc.direction = np.asarray(direction)
+    pc.length = 0.
+
+    #   additional attributes
+    pc.cell: ng_occ.Solid = None
+    pc.lattice: ng_occ.Solid = None
+
+    #   constants   
+    zero = ng_occ.Pnt(0, 0, 0)
+
+    #   Lattice
+    spheres = [] 
+    x0 = 0  
+    x20 = 0  
+    z0 = -0.5 * pc.L * (3 - 2)
+    z20 = -0.5 * pc.L * (3 - 1)
+
+    for zn in range(3):
+        z = z0 + zn * pc.L 
+        z2 = z20 + zn * pc.L 
+
+        for yn in range(3):
+            y = yn * 2 * pc.r0
+            y2 = yn * 2 * pc.r0 + pc.r0
+
+            for xn in range(3):
+                x = x0 + xn * 2 * pc.r0
+                x2 = x20 + xn * 2 * pc.r0 + pc.r0
+
+                spheres.append(
+                    ng_occ.Sphere(ng_occ.Pnt(x, y, z), pc.radius)
+                    .Rotate(ng_occ.Axis(ng_occ.Pnt(x, y, z), ng_occ.X), 45)
+                    .Rotate(ng_occ.Axis(ng_occ.Pnt(x, y, z), ng_occ.Z), 45)
+                )
+                # shifted
+                spheres.append(
+                    ng_occ.Sphere(ng_occ.Pnt(x2, y2, z2), pc.radius)
+                    .Rotate(ng_occ.Axis(ng_occ.Pnt(x2, y2, z2), ng_occ.X), 45)
+                    .Rotate(ng_occ.Axis(ng_occ.Pnt(x2, y2, z2), ng_occ.Z), 45)
+                )
+
+    pc.lattice = (
+        np.sum(spheres)
+        .Move(ng_occ.Vec(-pc.r0 * 2, -pc.r0 * 2, 0))
+        .Rotate(ng_occ.Axis(zero, ng_occ.Z), 45)
+    )
+
+    if pc.filletsEnabled:
+        pc.lattice = pc.lattice.Scale(zero, pc.maximize)
+        pc.lattice = (
+            pc.lattice
+            .MakeFillet(pc.lattice.edges, pc.fillets * pc.maximize)
+            .Scale(zero, pc.minimize)
+        )
+
+    #   Inlet face
+    if np.all(pc.direction == [1., 0., 0.]):
+        length = 2 * pc.r0
+        width = pc.L / 2
+        # diag = pc.L * np.sqrt(3)
+        # height = diag / 3
+
+        xl = np.sqrt(length ** 2 + length ** 2) * 0.5
+        yw = xl
+        zh = width
+
+        vertices = np.array([
+            (0, 0, -zh),
+            (-xl, yw, -zh),
+            (-xl, yw, zh),
+            (0, 0, zh)
+        ])
+        extr = length
+
+    elif np.all(pc.direction == [0., 0., 1.]):
+        length = 2 * pc.r0
+        width = pc.L / 2
+        # diag = pc.L * np.sqrt(3)
+        # height = diag / 3
+
+        xl = np.sqrt(length ** 2 + length ** 2) * 0.5
+        yw = xl
+        zh = width
+
+        vertices = np.array([
+            (0, 0, -zh),
+            (xl, yw, -zh),
+            (0, 2 * yw, -zh),
+            (-xl, yw, -zh)
+        ])
+        extr = 2 * width
+
+    elif np.all(pc.direction == [1., 1., 1.]):
+        length = 2 * pc.r0
+        width = pc.L / 2
+        # diag = pc.L * np.sqrt(3)
+        # height = diag / 3
+
+        xl = -(3 - 2) * pc.L / 3
+        yw = -(3 - 2) * pc.L / 3
+        zh = -(3 - 2) * pc.L / 3
+
+        vertices = np.array([
+            (-2 * width / 3 + xl, -2 * width / 3 + yw, width / 3 + zh),
+            (0 + xl, -width + yw, 0 + zh),
+            (width / 3 + xl, -2 * width / 3 + yw, -2 * width / 3 + zh),
+            (0 + xl, 0 + yw, -width + zh),
+            (-2 * width / 3 + xl, width / 3 + yw, -2 * width / 3 + zh),
+            (-width + xl, 0 + yw, 0 + zh)
+        ])
+        extr = np.sqrt(3) * pc.L
+        
+    else:
+        raise Exception(f"Direction { pc.direction } is not implemented")
+    
+    #   Cell
+    circuit = ng_occ.Wire([ 
+        ng_occ.Segment(ng_occ.Pnt(*v1), ng_occ.Pnt(*v2)) 
+        for v1, v2 in zip(vertices, np.roll(vertices, -1, axis = 0)) 
+    ])
+    inletface = ng_occ.Face(circuit)
+    inletface.name = "inlet"
+
+    vecFlow = utils.normal(inletface)
+    pc.cell = inletface.Extrude(extr, ng_occ.Vec(*vecFlow))
+    pc.length = extr
+    
+    #   Boundary faces
+    symetryId = 0
+
+    for face in pc.cell.faces:
+        fNorm = utils.normal(face)
+        fAngle = utils.angle(vecFlow, fNorm)
+        
+        if fAngle == 0 or fAngle == np.pi:
+            if np.all(utils.pos(face.center) == utils.pos(inletface.center)):
+                face.name = "inlet"
+
+            else:
+                face.name = "outlet"
+
+        else:
+            face.name = f"symetry{ symetryId }"
+            symetryId += 1
+
+    #   Main shape
+    pc.shape = pc.cell - pc.lattice
+
+    assert len(pc.shape.solids) == 1, "Expected single solid shape"
+
+    pc.shape = pc.shape.solids[0]
+
+    #   Boundary faces (walls)
+    for face in pc.shape.faces:
+        if face.name not in ["inlet", "outlet", *[ f"symetry{ n }" for n in range(6) ]]:
+            face.name = "wall"
+
+    return pc

anisotropy/shaping/shape.py

@@ -0,0 +1,121 @@
+# -*- coding: utf-8 -*-
+
+from __future__ import annotations
+from numpy import ndarray
+from os import PathLike
+
+import numpy as np
+import netgen.occ as ng_occ
+import pathlib
+
+from . import utils
+
+
+class Shape(object):
+    def __init__(self):
+        """A Shape object contains OCC shape.
+        """
+        self.shape = None
+
+    @property
+    def geometry(self) -> ng_occ.OCCGeometry:
+        """Shape as OCCGeometry object.
+        """
+        return ng_occ.OCCGeometry(self.shape)
+    
+    @property
+    def type(self) -> ng_occ.TopAbs_ShapeEnum:
+        """Type of the shape. (shortcut)
+        """
+        return self.shape.type
+    
+    @property
+    def volume(self) -> float:
+        """Volume of the shape. (shortcut)
+        """
+        return self.shape.volume
+
+    @property
+    def center(self) -> ndarray:
+        """Center of the shape.
+        """
+        return np.array(utils.pos(self.shape.center))
+
+    def write(self, filename: PathLike):
+        """Export a shape to the file.
+        Supported formats: step.
+        
+        :param filename:
+            Path of the file.
+        """
+        path = pathlib.Path(filename).resolve()
+        ext = path.suffix[1: ]
+        
+        if ext == "step":
+            self.shape.WriteStep(str(path))
+        
+        else:
+            raise NotImplementedError(f"Shape format '{ ext }' is not supported")
+            
+    def read(self, filename: PathLike):
+        """Import a shape from the file.
+        Supported formats: step, iges, brep.
+
+        :param filename:
+            Path of the file.
+        """        
+        path = pathlib.Path(filename).resolve()
+        ext = path.suffix[1: ]
+
+        if ext in ["step", "iges", "brep"]:
+            self.shape = ng_occ.OCCGeometry(str(path)).shape
+
+        else:
+            raise NotImplementedError(f"Shape format '{ext}' is not supported")
+        
+        return self
+
+    def patches(
+        self, 
+        group: bool = False, 
+        shiftIndex: bool = False, 
+        prefix: str = None
+    ) -> list | dict:
+        """Get patches indices with their names.
+
+        :param group:
+            Group indices together with the same patches names.
+        :param shiftIndex:
+            Start numerating with one instead of zero.
+        :param prefix:
+            Add string prefix to the index.
+        :return:
+            List if group = False else dictionary.
+        """
+        if group:
+            patches_ = {}
+
+            for idn, face in enumerate(self.shape.faces):
+                if shiftIndex:
+                    idn += 1
+
+                item = idn if not prefix else prefix + str(idn)
+                
+                if patches_.get(face.name):
+                    patches_[face.name].append(item)
+
+                else:
+                    patches_[face.name] = [ item ]
+
+        else:
+            patches_ = []
+
+            for idn, face in enumerate(self.shape.faces):
+                if shiftIndex:
+                    idn += 1
+                
+                item = idn if not prefix else prefix + str(idn)
+
+                patches_.append((item, face.name))
+
+        return patches_ 

anisotropy/shaping/utils.py

@@ -0,0 +1,47 @@
+# -*- coding: utf-8 -*-
+
+from numpy import ndarray
+
+import numpy as np
+import netgen.occ as ng_occ
+
+
+def pos(point: ng_occ.gp_Pnt) -> ndarray:
+    """Extract coordinates from point.
+
+    :param point:
+        OCC point object
+    :return:
+        Array of coordinates.
+    """
+    return np.array([ point.x, point.y, point.z ])
+
+
+def normal(face: ng_occ.Face) -> ndarray: 
+    """Calculate normal vector from face.
+
+    :param face:
+        OCC face object.
+    :return:
+        Normal vector from face.
+    """
+    _, u, v = face.surf.D1(0, 0)
+
+    return np.cross([u.x, u.y, u.z], [v.x, v.y, v.z]) 
+
+
+def angle(vec1: ndarray, vec2: ndarray) -> float:
+    """Angle between two vectors.
+
+    :param vec1:
+        Array of points that represents first vector.
+    :param vec2:
+        Array of points that represents second vector.
+    :return:
+        Angle between two vectors in radians.
+    """
+    inner = np.inner(vec1, vec2)
+    norms = np.linalg.norm(vec1) * np.linalg.norm(vec2)
+    cos = inner / norms
+
+    return np.arccos(np.clip(cos, -1.0, 1.0))

anisotropy/solving/__init__.py

@@ -0,0 +1,8 @@
+# -*- coding: utf-8 -*-
+
+from .onephase import FlowOnePhase
+
+
+__all__ = [
+    "FlowOnePhase"
+]

anisotropy/solving/onephase.py

@@ -0,0 +1,268 @@
+# -*- coding: utf-8 -*-
+
+import numpy as np
+
+import anisotropy.openfoam as of
+from anisotropy.openfoam import presets
+from anisotropy.openfoam import commands
+
+
+class FlowOnePhase:
+    def __init__(
+        self,
+        path: str = None,
+        direction: list[float] = None,
+        patches: dict = None,
+        pressureInlet: float = None,
+        pressureOutlet: float = None,
+        pressureInternal: float = None,
+        velocityInlet: float = None,
+        velocityOutlet: float = None,
+        velocityInternal: float = None,
+        density: float = None,
+        viscosityKinematic: float = None,
+        scale: list[float] = None,
+        **kwargs
+    ):
+        
+        self.direction = direction 
+        self.patches = patches
+        self.path = path
+        self.case = None
+        self.boundaryNames = ["inlet", "outlet", "symetry", "wall"]
+
+        self.pressureInlet = pressureInlet 
+        self.pressureOutlet = pressureOutlet 
+        self.pressureInternal = pressureInternal 
+        self.velocityInlet = velocityInlet 
+        self.velocityOutlet = velocityOutlet 
+        self.velocityInternal = velocityInternal 
+        self.density = density 
+        self.viscosityKinematic = viscosityKinematic
+        self.scale = scale
+
+    def controlDict(self) -> of.FoamFile:
+        ff = presets.controlDict()
+        ff.update(
+            startFrom = "latestTime",
+            endTime = 5000,
+            writeInterval = 100,
+            runTimeModifiable = "true"
+        )
+
+        return ff
+
+    def fvSchemes(self) -> of.FoamFile:
+        ff = presets.fvSchemes()
+
+        return ff
+    
+    def fvSolution(self) -> of.FoamFile:    
+        ff = presets.fvSolution()
+        ff["solvers"]["U"].update(
+            nSweeps = 2,
+            tolerance = 1e-08,
+            smoother = "GaussSeidel"
+        )
+        ff["solvers"]["Phi"] = dict(
+            solver = "GAMG",
+            smoother = "DIC",
+            cacheAgglomeration = "yes",
+            agglomerator = "faceAreaPair",
+            nCellsInCoarsestLevel = 10,
+            mergeLevels = 1,
+            tolerance = 1e-06,
+            relTol = 0.01
+        )
+        ff["potentialFlow"] = dict(
+            nNonOrthogonalCorrectors = 13,
+            PhiRefCell = 0,
+            PhiRefPoint = 0,
+            PhiRefValue = 0,
+            Phi = 0
+        )
+        ff["cache"] = { "grad(U)": None }
+        ff["SIMPLE"].update(
+            nNonOrthogonalCorrectors = 6,
+            residualControl = dict(
+                p = 1e-05,
+                U = 1e-05
+            )
+        )
+        ff["relaxationFactors"]["equations"]["U"] = 0.5
+
+        return ff
+
+    def transportProperties(self) -> of.FoamFile:
+        ff = presets.transportProperties()
+        ff.update(
+            nu = self.viscosityKinematic
+        )
+
+        return ff
+        
+    def turbulenceProperties(self) -> of.FoamFile:
+        ff = presets.turbulenceProperties()
+        ff.content = dict(
+            simulationType = "laminar"
+        )
+
+        return ff
+
+    def p(self) -> of.FoamFile:
+        ff = presets.p()
+        ff["boundaryField"] = {}
+
+        for boundary in self.boundaryNames:
+            if boundary == "inlet":
+                ff["boundaryField"][boundary] = dict(
+                    type = "fixedValue",
+                    value = of.utils.uniform(self.pressureInlet / self.density)
+                )
+
+            elif boundary == "outlet":
+                ff["boundaryField"][boundary] = dict(
+                    type = "fixedValue",
+                    value = of.utils.uniform(self.pressureOutlet / self.density)
+                )
+
+            else:
+                ff["boundaryField"][boundary] = dict(
+                    type = "zeroGradient"
+                )
+ 
+        return ff
+
+    def U_approx(self) -> of.FoamFile:
+        ff = presets.U()
+        ff["boundaryField"] = {}
+
+        for boundary in self.boundaryNames:
+            if boundary == "inlet":
+                ff["boundaryField"][boundary] = dict(
+                    type = "fixedValue",
+                    value = of.utils.uniform(np.array(self.direction) * -6e-5)
+                )
+
+            elif boundary == "outlet":
+                ff["boundaryField"][boundary] = dict(
+                    type = "zeroGradient",
+                )
+
+            else:
+                ff["boundaryField"][boundary] = dict(
+                    type = "fixedValue",
+                    value = of.utils.uniform([0., 0., 0.])
+                ) 
+
+        return ff
+
+    def U(self) -> of.FoamFile:
+        ff = presets.U()
+        ff["boundaryField"] = {}
+
+        for boundary in self.boundaryNames:
+            if boundary == "inlet":
+                ff["boundaryField"][boundary] = dict(
+                    type = "pressureInletVelocity",
+                    value = of.utils.uniform(self.velocityInlet)
+                )
+
+            elif boundary == "outlet":
+                ff["boundaryField"][boundary] = dict(
+                    type = "zeroGradient",
+                )
+
+            else:
+                ff["boundaryField"][boundary] = dict(
+                    type = "fixedValue",
+                    value = of.utils.uniform([0., 0., 0.])
+                ) 
+
+        return ff
+
+    def createPatchDict(self) -> of.FoamFile:
+        # initial 43 unnamed patches ->
+        # 6 named patches (inlet, outlet, wall, symetry 0 to 3 or 5) ->
+        # 4 inGroups (inlet, outlet, wall, symetry)
+
+        ff = presets.createPatchDict()
+        ff["patches"] = []
+
+        for name in self.patches.keys():
+            if name == "inlet":
+                patchGroup = "inlet"
+                patchType = "patch"
+
+            elif name == "outlet":
+                patchGroup = "outlet"
+                patchType = "patch"
+
+            elif name == "wall":
+                patchGroup = "wall"
+                patchType = "wall"
+
+            else:
+                patchGroup = "symetry"
+                patchType = "symetryPlane"
+
+            ff["patches"].append({
+                "name": name,
+                "patchInfo": {
+                    "type": patchType,
+                    "inGroups": [patchGroup]
+                },
+                "constructFrom": "patches",
+                "patches": self.patches[name]
+            })
+
+        return ff
+
+    def generate(self, approximation: bool = False, meshfile: str = "mesh.mesh"):
+
+        self.case = of.FoamCase(
+            path = self.path,
+            files = [
+                self.controlDict(),
+                self.fvSchemes(),
+                self.fvSolution(),
+                self.transportProperties(), 
+                self.turbulenceProperties(),
+                self.p()
+            ]
+        )
+
+        if self.patches is not None:
+            self.case += self.createPatchDict()
+        
+        self.case += self.U_approx() if approximation else self.U()
+        
+        self.case.write(self.path)
+
+        self.case.chdir()
+
+        commands.netgenNeutralToFoam(meshfile)
+
+        # TODO: contain
+        if self.case.contains("createPatchDict"):
+            commands.createPatch()
+
+        commands.checkMesh()
+
+        if self.scale is not None:
+            commands.transformPoints({
+                "scale": self.scale
+            })
+
+        commands.renumberMesh()
+
+        if approximation:
+            commands.potentialFoam()
+
+            #   replace velocity for the main simulation
+            self.case += self.U()
+            self.case.write(self.path)
+        
+        commands.simpleFoam()
+
+        self.case.chback()

data/.gitignore

@@ -0,0 +1,3 @@
+*.png
+*.tiff
+*.sql

data/anisotropy.toml

@@ -0,0 +1,57 @@
+[[structures]]
+label = "simple"
+alpha = [ 0.01, 0.27,]
+alphaStep = 0.005
+directions = [ [ 1.0, 0.0, 0.0,], [ 0.0, 0.0, 1.0,], [ 1.0, 1.0, 1.0,],]
+r0 = 1
+filletsEnabled = true
+pressureInlet = 1
+pressureOutlet = 0
+pressureInternal = 0
+velocityInlet = [ 0.0, 0.0, 0.0,]
+velocityInternal = [ 0.0, 0.0, 0.0,]
+density = 1000
+viscosity = 0.001
+scale = [ 1e-5, 1e-5, 1e-5,]
+
+[[structures]]
+label = "bodyCentered"
+alpha = [ 0.01, 0.16,]
+alphaStep = 0.005
+directions = [ [ 1.0, 0.0, 0.0,], [ 0.0, 0.0, 1.0,], [ 1.0, 1.0, 1.0,],]
+r0 = 1
+filletsEnabled = true
+pressureInlet = 1
+pressureOutlet = 0
+pressureInternal = 0
+velocityInlet = [ 0.0, 0.0, 0.0,]
+velocityInternal = [ 0.0, 0.0, 0.0,]
+density = 1000
+viscosity = 0.001
+scale = [ 1e-5, 1e-5, 1e-5,]
+
+[[structures]]
+label = "faceCentered"
+alpha = [ 0.01, 0.12,]
+alphaStep = 0.005
+directions = [ [ 1.0, 0.0, 0.0,], [ 0.0, 0.0, 1.0,], [ 1.0, 1.0, 1.0,],]
+r0 = 1
+filletsEnabled = true
+pressureInlet = 1
+pressureOutlet = 0
+pressureInternal = 0
+velocityInlet = [ 0.0, 0.0, 0.0,]
+velocityInternal = [ 0.0, 0.0, 0.0,]
+density = 1000
+viscosity = 0.001
+scale = [ 1e-5, 1e-5, 1e-5,]
+
+[options]
+nprocs = 4
+stage = "shape"
+overwrite = false
+database = "anisotropy.db"
+build = "build"
+logs = "logs"
+shapefile = "shape.step"
+meshfile = "mesh.mesh"

doc/Makefile

@@ -20,6 +20,7 @@ help:
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile
 	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+	[ -d "$(BUILDDIR)/html" ] && cp -vf "$(BUILDDIR)/html" anisotropy/
 
 update:
 	@$(SPHINXAPIDOC) -f -o "$(SOURCEDIR)" "$(PROJECTDIR)"